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Przytulska, A., J. Comte, S. Crevecoeur, C. Lovejoy, I. Laurion, and W. F. Vincent. "Phototrophic pigment diversity and picophytoplankton in permafrost thaw lakes." Biogeosciences 13, no. 1 (January 14, 2016): 13–26. http://dx.doi.org/10.5194/bg-13-13-2016.
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Abstract. Permafrost thaw lakes (thermokarst lakes) are widely distributed across the northern landscape, and are known to be biogeochemically active sites that emit large amounts of carbon to the atmosphere as CH4 and CO2. However, the abundance and composition of the photosynthetic communities that fix CO2 have been little explored in this ecosystem type. In order to identify the major groups of phototrophic organisms and their controlling variables, we sampled 12 permafrost thaw lakes along a permafrost degradation gradient in northern Québec, Canada. Additional samples were taken from five rock-basin reference lakes in the region to determine if the thaw lakes differed in limnological properties and phototrophs. Phytoplankton community structure was determined by high-performance liquid chromatography analysis of their photoprotective and photosynthetic pigments, and autotrophic picoplankton concentrations were assessed by flow cytometry. One of the black-colored lakes located in a landscape of rapidly degrading palsas (permafrost mounds) was selected for high-throughput 18S rRNA sequencing to complement conclusions based on the pigment and cytometry analyses. The results showed that the limnological properties of the thaw lakes differed significantly from the reference lakes, and were more highly stratified. However, both waterbody types contained similarly diverse phytoplankton groups, with dominance of the pigment assemblages by fucoxanthin-containing taxa, as well as chlorophytes, cryptophytes and cyanobacteria. Chlorophyll a concentrations (Chl a) were correlated with total phosphorus (TP), and both were significantly higher in the thaw lakes (overall means of 3.3 µg Chl a L−1 and 34 µg TP L−1) relative to the reference lakes (2.0 µg Chl a L−1 and 8.2 µg TP L−1). Stepwise multiple regression of Chl a against the other algal pigments showed that it was largely a function of alloxanthin, fucoxanthin and Chl b (R2 = 0.85). The bottom waters of two of the thaw lakes also contained high concentrations of bacteriochlorophyll d, showing the presence of green photosynthetic sulphur bacteria. The molecular analyses indicated a relatively minor contribution of diatoms, while chrysophytes, dinoflagellates and chlorophytes were well represented; the heterotrophic eukaryote fraction was dominated by numerous ciliate taxa, and also included Heliozoa, Rhizaria, chytrids and flagellates. Autotrophic picoplankton occurred in biovolume concentrations up to 3.1 × 105 µm3 picocyanobacteria mL−1 and 1.9 × 106 µm3 picoeukaryotes mL−1, with large variations among lakes. Both groups of picophytoplankton were positively correlated with total phytoplankton abundance, as measured by Chl a; picocyanobacteria were inversely correlated with dissolved organic carbon, while picoeukaryotes were inversely correlated with conductivity. Despite their net heterotrophic character, subarctic thaw lakes are rich habitats for diverse phototrophic communities.
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Przytulska, A., J. Comte, S. Crevecoeur, C. Lovejoy, I. Laurion, and W. F. Vincent. "Phototrophic pigment diversity and picophytoplankton abundance in permafrost thaw lakes." Biogeosciences Discussions 12, no. 15 (August 4, 2015): 12121–56. http://dx.doi.org/10.5194/bgd-12-12121-2015.
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Abstract. Permafrost thaw lakes (thermokarst lakes) are widely distributed across the northern landscape, and are known to be biogeochemically active sites that emit large amounts of carbon to the atmosphere as CH4 and CO2. However, the abundance and composition of the photosynthetic communities that consume CO2 have been little explored in this ecosystem type. In order to identify the major groups of phototrophic organisms and their controlling variables, we sampled 12 permafrost thaw lakes along a permafrost degradation gradient in northern Québec, Canada. Additional samples were taken from 5 rock-basin reference lakes in the region to determine if the thaw waters differed in limnological properties and phototrophs. Phytoplankton community structure was determined by high performance liquid chromatography analysis of their photoprotective and photosynthetic pigments, and autotrophic picoplankton concentrations were assessed by flow cytometry. One of the black colored lakes located in a andscape of rapidly degrading palsas (permafrost mounds) was selected for high-throughput 18S rRNA sequencing to help interpret the pigment and cytometry data. The results showed that the limnological properties of the thaw lakes differed significantly from the reference lakes, and were more highly stratified. However, both waterbody types contained similarly diverse phytoplankton groups, with dominance of the pigment assemblages by fucoxanthin-containing taxa, as well as chlorophytes, cryptophytes and cyanobacteria. Chlorophyll a concentrations (Chl a) were correlated with total phosphorus (TP), and both were significantly higher in the thaw lakes (overall means of 3.3 μg Chl a L−1 and 34 μg TP L−1) relative to the reference lakes (2.0 μg Chl a L−1 and 8.2 μg TP L−1). Stepwise multiple regression of Chl a against the other algal pigments showed that it was largely a function of lutein, fucoxanthin and peridinin (R2 = 0.78). The bottom waters of two of the thaw lakes also contained high concentrations of bacteriochlorophyll d, showing the presence of green photosynthetic sulphur bacteria. The molecular analyses indicated a relatively minor contribution of diatoms, while chrysophytes, dinoflagellates and chlorophytes were well represented; the heterotrophic eukaryote fraction was dominated by numerous ciliate taxa, and also included Heliozoa, Rhizaria, chytrids and flagellates. Autotrophic picoplankton occurred in cell concentrations up to 8.8 × 105 mL−1 (picocyanobacteria) and 4.6 × 105 mL−1 (picoeukaryotes). Both groups of picophytoplankton were positively correlated with total phytoplankton abundance, as measured by Chl a; picocyanobacteria were inversely correlated with dissolved organic carbon, while picoeukaryotes were correlated with conductivity. Despite their net heterotrophic character, subarctic thaw lakes are rich habitats for diverse phototrophic communities.
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Couturier, Jérémy, Jean-Pierre Jacquot, and Nicolas Rouhier. "Evolution and diversity of glutaredoxins in photosynthetic organisms." Cellular and Molecular Life Sciences 66, no. 15 (June 9, 2009): 2539–57. http://dx.doi.org/10.1007/s00018-009-0054-y.
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Wardley, William P., Johannes W. Goessling, and Martin Lopez-Garcia. "Measuring Photonics in Photosynthesis: Combined Micro-Fourier Image Spectroscopy and Pulse Amplitude Modulated Chlorophyll Fluorimetry at the Micrometre-Scale." Biomimetics 7, no. 3 (August 7, 2022): 107. http://dx.doi.org/10.3390/biomimetics7030107.
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Natural photonic structures are common across the biological kingdoms, serving a diversity of functionalities. The study of implications of photonic structures in plants and other phototrophic organisms is still hampered by missing methodologies for determining in situ photonic properties, particularly in the context of constantly adapting photosynthetic systems controlled by acclimation mechanisms on the cellular scale. We describe an innovative approach to determining spatial and spectral photonic properties and photosynthesis activity, employing micro-Fourier Image Spectroscopy and Pulse Amplitude Modulated Chlorophyll Fluorimetry in a combined microscope setup. Using two examples from the photosynthetic realm, the dynamic Bragg-stack-like thylakoid structures of Begonia sp. and complex 2.5 D photonic crystal slabs from the diatom Coscinodiscus granii, we demonstrate how the setup can be used for measuring self-adapting photonic-photosynthetic systems and photonic properties on single-cell scales. We suggest that the setup is well-suited for the determination of photonic–photosynthetic systems in a diversity of organisms, facilitating the cellular, temporal, spectral and angular resolution of both light distribution and combined chlorophyll fluorescence determination. As the catalogue of photonic structure from photosynthetic organisms is rich and diverse in examples, a deepened study could inspire the design of novel optical- and light-harvesting technologies.
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Bag, Pushan. "Light Harvesting in Fluctuating Environments: Evolution and Function of Antenna Proteins across Photosynthetic Lineage." Plants 10, no. 6 (June 10, 2021): 1184. http://dx.doi.org/10.3390/plants10061184.
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Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.
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Gabaldón, Toni. "Peroxisome diversity and evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1541 (March 12, 2010): 765–73. http://dx.doi.org/10.1098/rstb.2009.0240.
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Peroxisomes are organelles bounded by a single membrane that can be found in all major groups of eukaryotes. A single evolutionary origin of this cellular compartment is supported by the presence, in diverse organisms, of a common set of proteins implicated in peroxisome biogenesis and maintenance. Their enzymatic content, however, can vary substantially across species, indicating a high level of evolutionary plasticity. Proteomic analyses have greatly expanded our knowledge on peroxisomes in some model organisms, including plants, mammals and yeasts. However, we still have a limited knowledge about the distribution and functionalities of peroxisomes in the vast majority of groups of microbial eukaryotes. Here, I review recent advances in our understanding of peroxisome diversity and evolution, with a special emphasis on peroxisomes in microbial eukaryotes.
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Ward, Lewis M., and Patrick M. Shih. "Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer." PLOS ONE 16, no. 1 (January 28, 2021): e0239248. http://dx.doi.org/10.1371/journal.pone.0239248.
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Photosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.
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Sjöqvist, Conny. "Evolution of Phytoplankton as Estimated from Genetic Diversity." Journal of Marine Science and Engineering 10, no. 4 (March 24, 2022): 456. http://dx.doi.org/10.3390/jmse10040456.
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Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.
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Vöcking, Oliver, Aide Macias-Muñoz, Stuart J. Jaeger, and Todd H. Oakley. "Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals." Cells 11, no. 24 (December 8, 2022): 3966. http://dx.doi.org/10.3390/cells11243966.
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Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a “deep diversity” of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.
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Hernández, Greco, Christopher G. Proud, Thomas Preiss, and Armen Parsyan. "On the Diversification of the Translation Apparatus across Eukaryotes." Comparative and Functional Genomics 2012 (2012): 1–14. http://dx.doi.org/10.1155/2012/256848.
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Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.
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Richardson, Elisabeth, Kelly Zerr, Anastasios Tsaousis, Richard G. Dorrell, and Joel B. Dacks. "Evolutionary cell biology: functional insight from “endless forms most beautiful”." Molecular Biology of the Cell 26, no. 25 (December 15, 2015): 4532–38. http://dx.doi.org/10.1091/mbc.e14-10-1433.
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In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking.
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Schiesari, Luis, Jansen Zuanon, Claudia Azevedo-Ramos, Marcelo Garcia, Marcelo Gordo, Mariluce Messias, and Emerson Monteiro Vieira. "Macrophyte rafts as dispersal vectors for fishes and amphibians in the Lower Solimões River, Central Amazon." Journal of Tropical Ecology 19, no. 3 (April 28, 2003): 333–36. http://dx.doi.org/10.1017/s0266467403003365.
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Large rivers have played a prominent role in biogeographic theory for their potential to act as barriers for the dispersal of terrestrial organisms,and therefore be involved in the generation of species diversity (Brown & Lomolino 1998). In this paper, we document the potential role of macrophyte rafts as a mechanism by which Amazonian rivers could act as dispersal agents rather than barriers, transferring organisms across banks and possibly across very large distances. These vectors could therefore act against speciation and towards homogenization of the local biota.
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Olivé, I., E. Varela-Álvarez, J. Silva, EA Serrão, and R. Santos. "Physiological potential of the chlorophyte Caulerpa prolifera for proliferation across the Mediterranean-Atlantic basins in a warmer ocean." Marine Ecology Progress Series 668 (June 24, 2021): 73–84. http://dx.doi.org/10.3354/meps13719.
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Ocean warming is altering the metabolic balances of organisms, favouring the expansion of thermo-tolerant individuals. The fast-growing macroalga Caulerpa prolifera is rapidly expanding in the Ria Formosa lagoon (Portugal), a connection area between Mediterranean and Atlantic basins. We investigated the metabolic capacity of C. prolifera to cope with ocean warming, to elucidate its expansion potential. The photosynthetic and respiratory plasticity of 4 populations of C. prolifera spread along the Mediterranean-Atlantic basins was assessed under a temperature range of 20 to 30°C. In addition, molecular markers were used to investigate the genetic identity of the strain found in Ria Formosa, which confirmed its Mediterranean origin. All examined populations showed large physiological thermo-tolerance and metabolic plasticity to warming. The photosynthetic efficiency of C. prolifera improved by 50% with temperature, and the maximum photosynthetic production doubled along the temperature range tested. Respiration did not vary with temperature, whereas the metabolic quotient increased by more than 70%when temperature increased from 20 to 25-30°C. Minor differences in the photosynthetic descriptors were detected among populations, reflecting light- and dark-adapted physiology of Mediterranean and Atlantic populations, respectively. Our results show that all tested populations of C. prolifera have the physiological potential to cope with temperature increases up to 30°C, which indicates that ocean warming may contribute to the expansion of C. prolifera in the Mediterranean-Atlantic basins.
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Molozzi, Joseline, Luiz U. Hepp, and Marcos Callisto. "The additive partitioning of macroinvertebrate diversity in tropical reservoirs." Marine and Freshwater Research 64, no. 7 (2013): 609. http://dx.doi.org/10.1071/mf12354.
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Understanding the ways in which diversity changes across spatial scales is important for the conservation of biodiversity. The objectives of the present study were (1) to characterise the diversity of aquatic macroinvertebrates in three Brazilian tropical reservoirs and (2) to determine how the organisms were distributed at different spatial scales, by using a diversity partitioning approach. We compared the diversity-partition results with the null hypothesis that the macroinvertebrate community was uniform across all spatial scales in the study. We expected that differences in environmental variability (sediment characteristics) among the reservoirs and limitations on the dispersal of organisms among reservoirs result in higher biological variability (β diversity). The results of the spatial partitioning analysis of species richness in the reservoirs showed that each Ekman–Birge dredge-sampling unit (α) represented 43.7% of the total variation. β1 diversity (diversity among Ekman–Birge dredge-sampling units) represented 47.2% of the total variation. A partial Mantel test indicated a correlation between the particle-size matrix and the biological matrix. However, the biological matrix was not correlated with the geographical matrix. The partitioning of overall spatial diversity indicated that the distribution of species in the reservoirs was driven by local factors and that diversity was more pronounced at lower hierarchical levels.
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Koenig, Kristen M., and Jeffrey M. Gross. "Evolution and development of complex eyes: a celebration of diversity." Development 147, no. 19 (October 1, 2020): dev182923. http://dx.doi.org/10.1242/dev.182923.
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ABSTRACTFor centuries, the eye has fascinated scientists and philosophers alike, and as a result the visual system has always been at the forefront of integrating cutting-edge technology in research. We are again at a turning point at which technical advances have expanded the range of organisms we can study developmentally and deepened what we can learn. In this new era, we are finally able to understand eye development in animals across the phylogenetic tree. In this Review, we highlight six areas in comparative visual system development that address questions that are important for understanding the developmental basis of evolutionary change. We focus on the opportunities now available to biologists to study the developmental genetics, cell biology and morphogenesis that underlie the incredible variation of visual organs found across the Metazoa. Although decades of important work focused on gene expression has suggested homologies and potential evolutionary relationships between the eyes of diverse animals, it is time for developmental biologists to move away from this reductive approach. We now have the opportunity to celebrate the differences and diversity in visual organs found across animal development, and to learn what it can teach us about the fundamental principles of biological systems and how they are built.
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Nevo, Eviatar. "Evolution of wild barley at Evolution Canyon: adaptation, speciation, pre-agricultural collection, and barley improvement." Israel Journal of Plant Sciences 62, no. 1-2 (May 18, 2015): 22–32. http://dx.doi.org/10.1080/07929978.2014.940783.
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The present paper reviews the state of cultivated barley,Hordeum vulgare, in Old World agriculture and its domestication through its progenitor, wild barley,Hordeum spontaneum. It focuses on the adaptation, incipient sympatric speciation, and domestication ofH. spontaneumin the “Evolution Canyon” model. The “Evolution Canyon,” at lower Nahal Oren, Mount Carmel, Israel, revealsevolution in actionat a microsite caused by interslope microclimatic divergence across life from viruses and bacteria through fungi, plants, and animals including mammals. The interslope adaptive complexes ofH. spontaneumat “Evolution Canyon” include genetic diversity, drought resistance bydehydrin I, rhizosphere bacteria, andEibi Igene promoter.Isadefense locus and vitamin E components also diverge between the opposite tropical and temperate abutting slopes. A highly likely pre-agricultural collection site ofH. spontaneumis described on the Natufian cemetery of the Oren and Um Usba caves in “Evolution Canyon”. Finally, the paper briefly reviews the remarkable interslope incipient sympatric speciation ofH. spontaneumat “Evolution Canyon”, as is true for other organisms such as bacteria,Drosophila, and spiny mice,Acomys. Sympatric ecological speciation is still controversial and “Evolution Canyon” provides an appropriate site to explore it inH. spontaneumand other organisms across life.
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Sibbald, Shannon J., and John M. Archibald. "Genomic Insights into Plastid Evolution." Genome Biology and Evolution 12, no. 7 (May 13, 2020): 978–90. http://dx.doi.org/10.1093/gbe/evaa096.
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Abstract The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host eukaryote approximately a billion years ago paved the way for the evolution of diverse algal groups in a wide range of aquatic and, eventually, terrestrial environments. Plastids have on multiple occasions also moved horizontally from eukaryote to eukaryote by secondary and tertiary endosymbiotic events. The overall picture of extant photosynthetic diversity can best be described as “patchy”: Plastid-bearing lineages are spread far and wide across the eukaryotic tree of life, nested within heterotrophic groups. The algae do not constitute a monophyletic entity, and understanding how, and how often, plastids have moved from branch to branch on the eukaryotic tree remains one of the most fundamental unsolved problems in the field of cell evolution. In this review, we provide an overview of recent advances in our understanding of the origin and spread of plastids from the perspective of comparative genomics. Recent years have seen significant improvements in genomic sampling from photosynthetic and nonphotosynthetic lineages, both of which have added important pieces to the puzzle of plastid evolution. Comparative genomics has also allowed us to better understand how endosymbionts become organelles.
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Grosse, Maël, Anna Zhadan, Joachim Langeneck, Dieter Fiege, and Alejandro Martínez. "Still Digging: Advances and Perspectives in the Study of the Diversity of Several Sedentarian Annelid Families." Diversity 13, no. 3 (March 18, 2021): 132. http://dx.doi.org/10.3390/d13030132.
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Sedentarian annelids are a diverse and heterogeneous group of marine worms representing more than 8600 species gathered in ca. 43 families. The attention brought to these organisms is unevenly distributed among these families, and the knowledge about them sometimes scarce. We review here the current knowledge about the families Acrocirridae, Cirratulidae (including Ctenodrilidae), Cossuridae, Longosomatidae, Paraonidae, and Sternaspidae in terms of biodiversity as well as the evolution of the taxonomy and systematics of each group. We present the challenges faced when studying these organisms and compare methodologies across groups and perspectives in future research.
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Rezende, Enrico L., and Francisco Bozinovic. "Thermal performance across levels of biological organization." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1778 (June 17, 2019): 20180549. http://dx.doi.org/10.1098/rstb.2018.0549.
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Thermal performance curves are widely used to describe how ambient temperature impacts different attributes of ectothermic organisms, from protein function to life-history traits, and to predict the potential effects of global warming on ecological systems. Nonetheless, from an analytical standpoint, they remain primarily heuristic and few attempts have been made to develop a formal framework to characterize these curves and disentangle which factors contribute to their variation. Here we employ a nonlinear regression approach to assess if they vary systematically in shape depending on the performance proxy of choice. We compare curves at contrasting levels of organization, namely photosynthetic rates in plants ( n = 43), running speeds in lizards ( n = 51) and intrinsic rates of population increase in insects ( n = 47), and show with discriminant analyses that differences lie in a single dimension accounting for 99.1% of the variation, resulting in 75.8% of classification accuracy. Differences revolve primarily around the thermal range for elevated performance (greater than or equal to 50% of maximum performance), which is broader for photosynthetic rates (median of 26.4°C), intermediate for running speeds (19.5°C) and narrower for intrinsic rates of increase (12.5°C). We contend, confounding taxonomic factors aside, that these differences reflect contrasting levels of biological organization, and hypothesize that the thermal range for elevated performance should decrease at higher organization levels. In this scenario, instantaneous or short-term measures of performance may grossly overestimate the thermal safety margins for population growth and reproduction. Taken together, our analyses suggest that descriptors of the curve are highly correlated and respond in tandem, potentially resulting in systematic variation in shape across organization levels. Future studies should take into consideration this potential bias, address if it constitutes a general pattern and, if so, explain why and how it emerges. This article is part of the theme issue ‘Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen’.
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Aoki-Gonçalves, Felipe, Marcos Vinicius Dantas De Queiroz, Thais De Beauclair Guimarães, Viviana Solís Neffa, and Clarisse Palma-Silva. "High gene flow maintains wide-range species cohesion in a Neotropical epiphyte (Tillandsia aeranthos, Bromeliaceae)." Botanical Journal of the Linnean Society 194, no. 2 (July 30, 2020): 239–52. http://dx.doi.org/10.1093/botlinnean/boaa040.
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Abstract Studies of patterns of genetic diversity, genetic structure and ecological data across geographical ranges of species allow us to test hypotheses about the evolutionary responses of organisms to fluctuations in habitat connectivity and availability. Here we present a study aiming to assess genetic diversity, population structure and breeding system across the geographical distribution of a subtropical epiphyte, Tillandsia aeranthos (Bromeliaceae), endemic to the Plata River basin (Pampa biome). Seven nuclear microsatellite markers were genotyped in 203 individuals from 13 localities across Brazil and Argentina and 14 plastid regions were sequenced for a subset of the individuals. Additionally, we performed controlled pollination experiments to discuss correlations between breeding system, genetic diversity and structure in the species. Nuclear diversity levels were high (HE = 0.806, HO = 0.745, allelic richness = 5.860) with no haplotype differentiation detected (c. 9 kpb sequenced). Bayesian assignment analysis, supported by principal coordinate analysis and analysis of molecular variance, show low genetic structure across the studied area (FST = 0.031, P < 0.001). Controlled pollination experiments indicated complete self-incompatibility in all localities analysed. Our results show effective gene flow maintaining low genetic structure between localities for T. aeranthos across an extensive area in the Pampa.
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De Deyn, G. B., H. Quirk, S. Oakley, N. Ostle, and R. D. Bardgett. "Rapid transfer of photosynthetic carbon through the plant-soil system in differently managed species-rich grasslands." Biogeosciences 8, no. 5 (May 13, 2011): 1131–39. http://dx.doi.org/10.5194/bg-8-1131-2011.
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Abstract. Plant-soil interactions are central to short-term carbon (C) cycling through the rapid transfer of recently assimilated C from plant roots to soil biota. In grassland ecosystems, changes in C cycling are likely to be influenced by land use and management that changes vegetation and the associated soil microbial communities. Here we tested whether changes in grassland vegetation composition resulting from management for plant diversity influences short-term rates of C assimilation and transfer from plants to soil microbes. To do this, we used an in situ 13C-CO2 pulse-labelling approach to measure differential C uptake among different plant species and the transfer of the plant-derived 13C to key groups of soil microbiota across selected treatments of a long-term plant diversity grassland restoration experiment. Results showed that plant taxa differed markedly in the rate of 13C assimilation and concentration: uptake was greatest and 13C concentration declined fastest in Ranunculus repens, and assimilation was least and 13C signature remained longest in mosses. Incorporation of recent plant-derived 13C was maximal in all microbial phosopholipid fatty acid (PLFA) markers at 24 h after labelling. The greatest incorporation of 13C was in the PLFA 16:1ω5, a marker for arbuscular mycorrhizal fungi (AMF), while after 1 week most 13C was retained in the PLFA18:2ω6,9 which is indicative of assimilation of plant-derived 13C by saprophytic fungi. Our results of 13C assimilation and transfer within plant species and soil microbes were consistent across management treatments. Overall, our findings suggest that plant diversity restoration management may not directly affect the C assimilation or retention of C by individual plant taxa or groups of soil microbes, it can impact on the fate of recent C by changing their relative abundances in the plant-soil system. Moreover, across all treatments we found that plant-derived C is rapidly transferred specifically to AMF and decomposer fungi, indicating their consistent key role in the cycling of recent plant derived C.
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R. Marcelino, Vanessa, Ma Chiela M. Cremen, Chistopher J. Jackson, Anthony A. W. Larkum, and Heroen Verbruggen. "Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii." Genome Biology and Evolution 8, no. 9 (August 25, 2016): 2939–51. http://dx.doi.org/10.1093/gbe/evw206.
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Abstract Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.
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Badger, Murray R., David Hanson, and G. Dean Price. "Evolution and diversity of CO2 concentrating mechanisms in cyanobacteria." Functional Plant Biology 29, no. 3 (2002): 161. http://dx.doi.org/10.1071/pp01213.
Full textAbstract:
Cyanobacteria have developed an effective photosynthetic CO2 concentrating mechanism (CCM) for improving the efficiency of carboxylation by a relatively inefficient Rubisco. The development of this CCM was presumably in response to the decline in atmospheric CO2 levels and rising O2, both of which were triggered by the development of oxygenic photosynthesis by cyanobacteria themselves. In the past few years there has been a rapid expansion in our understanding of the mechanism and genes responsible for the CCM. In addition, there has been a recent expansion in the availability of complete cyanobacterial genomes, thus increasing our potential to examine questions regarding both the evolution and diversity of components of the CCM across cyanobacteria. This paper considers various CCM and photosynthesis gene components across eight cyanobacteria where significant genomic information is available. Significant conclusions from our analysis of the distribution of various genes indicated the following. Firstly, cyanobacteria have developed with two types of carboxysomes, and this is correlated with the form of Rubisco present. We have coined the terms α-cyanobacteria to refer to cyanobacteria containing Form 1A Rubisco and α-carboxysomes, and β-cyanobacteria having Form 1B Rubisco and β-carboxysomes. Secondly, there are two NDH-1 CO2 uptake systems distributed variably, withProchlorococcus marinus species appearing to lack this CO2 uptake system. There are at least two HCO3– transport systems distributed variably, with some α-cyanobacteria having an absence of systems identified in β-cyanobacteria. Finally, there are multiple forms of carbonic anhydrases (CAs), but with only β-carboxysomal CA having a clearly shown role at present. The α-cyanobacteria appear to lack a clearly identifiable carboxysomal CA. A pathway for the evolution of cyanobacterial CCMs is proposed. The acquisition of carboxysomes triggered by the rapid decline of atmospheric CO2 in the Phanerozoic is argued to be the initial step. This would then be followed by the development of NDH-1 CO2-uptake systems, followed by the development of low-and high-affinity HCO3– transporters. An intriguing question is, were carboxysomes developed first in cyanobacteria, or did they originate by the lateral transfer of pre-existing proteobacterial bacterial microcompartment genes? The potentially late evolution of the CCM genes in cyanobacteria argues for a polyphyletic and separate evolution of CCMs in cyanobacteria, algae, and higher plants.
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Juhmani, Abdul-Salam, Alessandro Vezzi, Mohammad Wahsha, Alessandro Buosi, Fabio De Pascale, Riccardo Schiavon, and Adriano Sfriso. "Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice." Microorganisms 8, no. 11 (October 26, 2020): 1657. http://dx.doi.org/10.3390/microorganisms8111657.
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Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.
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Zhong, Jia, Shaokui Yi, Laiyan Ma, and Weimin Wang. "Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China." Proceedings of the Royal Society B: Biological Sciences 286, no. 1901 (April 24, 2019): 20190076. http://dx.doi.org/10.1098/rspb.2019.0076.
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The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used Misgurnus anguillicaudatus , a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow cytometry. Two mitochondrial markers ( cytochrome b and control region) were then used for phylogeographic analyses to unravel the possible origins of diploids and tetraploids in China. The results showed that diploids have wider geographical distribution than tetraploids and triploids. There was no clear allopatric geographical range or boundary to divide diploid and polyploid populations. Rather, the analysis of mitochondrial DNA sequences indicated that tetraploids were autopolyploids, with lower genetic diversity than diploids. This suggests that tetraploids originated from sympatric diploids via multiple independent polyploidization events. Genetic structure patterns were similar between diploids and tetraploids, whereas complex genetic differentiation was found among different regions. The potential origin of M. anguillicaudatus was deduced to be in the Pearl River basin, which exhibited the highest nucleotide diversity and genetic differentiation. These findings provide insights into the evolution of polyploidy in vertebrates.
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De Deyn, G. B., H. Quirk, S. Oakley, N. Ostle, and R. D. Bardgett. "Rapid transfer of photosynthetic carbon through the plant-soil system in differently managed grasslands." Biogeosciences Discussions 8, no. 1 (February 2, 2011): 921–40. http://dx.doi.org/10.5194/bgd-8-921-2011.
Full textAbstract:
Abstract. Plant-soil interactions are central to short-term carbon (C) cycling through the rapid transfer of recently assimilated C from plant roots to soil biota. In grassland ecosystems, changes in C cycling are likely to be influenced by land use and management that changes vegetation and the associated soil microbial communities. Here we tested whether changes in grassland vegetation composition resulting from management for plant diversity influences short-term rates of C assimilation, retention and transfer from plants to soil microbes. To do this, we used an in situ 13C-CO2 pulse-labeling approach to measure differential C uptake among different plant species and the transfer of the plant-derived 13C to key groups of soil microbiota across selected treatments of a long-term plant diversity grassland restoration experiment. Results showed that plant taxa differed markedly in the rate of 13C assimilation and retention: uptake was greatest and retention lowest in Ranunculus repens, and assimilation was least and retained longest in mosses. Incorporation of recent plant-derived 13C was maximal in all microbial phosopholipid fatty acid (PLFA) markers at 24 h after labeling. The greatest incorporation of 13C was in the PLFA 16:1ω5, a marker for arbuscular mycorrhizal fungi (AMF), while after one week most 13C was retained in the PLFA 18:2ω6,9 which is indicative of assimilation of plant-derived 13C by saprophytic fungi. Our results of 13C assimilation, transfer and retention within plant species and soil microbes were consistent across management treatments. Overall, our findings suggest that changes in vegetation and soil microbial composition resulting from differences in long-term grassland management will affect short-term cycling of photosynthetic C, but that restoration management does not alter the short-term C uptake and transfer within plant species and within key groups of soil microbes. Moreover, across all treatments we found that plant-derived C is rapidly transferred specifically to AMF and decomposer fungi, indicating their consistent key role in the cycling of recent plant derived C.
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Norris, Richard D. "Pelagic species diversity, biogeography, and evolution." Paleobiology 26, S4 (2000): 236–58. http://dx.doi.org/10.1017/s0094837300026956.
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Pelagic (open-ocean) species have enormous population sizes and broad, even global, distributions. These characteristics should damp rates of speciation in allopatric and vicariant evolutionary models since dispersal should swamp diverging populations and prevent divergence. Yet the fossil record suggests that rates of evolutionary turnover in pelagic organisms are often quite rapid, comparable to rates observed in much more highly fragmented terrestrial and shallow-marine environments. Furthermore, genetic and ecological studies increasingly suggest that species diversity is considerably higher in the pelagic realm than inferred from many morphological taxonomies.Zoogeographic evidence suggests that ranges of many pelagic groups are much more limited by their ability to maintain viable populations than by any inability to disperse past tectonic and hydrographic barriers to population exchange. Freely dispersing pelagic taxa resemble airborne spores or wind-dispersed seeds that can drift almost anywhere but complete the entire life cycle only in favorable habitats. It seems likely that vicariant and allopatric models for speciation are far less important in pelagic evolution than sympatric or parapatric speciation in which dispersal is not limiting. Nevertheless, speciation can be quite rapid and involve cladogenesis even in cases where morphological data suggest gradual species transitions. Indeed, recent paleoecological and molecular studies increasingly suggest that classic examples of “phyletic gradualism” involve multiple, cryptic speciation events.Paleoceanographic and climatic change seem to influence rates of turnover by modifying surface water masses and environmental gradients between them to create new habitats rather than by preventing dispersal. Changes in the vertical structure and seasonality of water masses may be particularly important since these can lead to changes in the depth and timing of reproduction. Long-distance dispersal may actually promote evolution by regularly carrying variants of a species across major oceanic fronts and exposing them to very different selection pressures than occur in their home range. High dispersal in pelagic taxa also implies that extinction should be difficult to achieve except though global perturbations that prevent populations from reestablishing themselves following local extinction. High rates of extinction in some pelagic groups suggests either that global perturbations are common, or that the species are much more narrowly adapted than we would infer from current taxonomies.
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Conceição, Eltamara Souza da, Terezinha Maria Castro Della Lucia, Antonio De Oliveira Costa Neto, Érica Dos Santos Araújo, Elmo Borges de A. Koch, and Jacques Hubert Charles Delabie. "Ant Community Evolution According to Aging in Brazilian Cocoa Tree Plantations." Sociobiology 66, no. 1 (April 25, 2019): 33. http://dx.doi.org/10.13102/sociobiology.v66i1.2705.
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Agriculture is frequently held accountable for the depletion of biotic diversity, although a few agroforestry systems support the conservation of a number of organisms. Cocoa farming is noteworthy as an example of an agricultural activity that benefits or maintains species richness. However, the mechanism by which the biodiversity persists throughout the entire process of plant development remains obscure. In Southeastern Bahia, Brazil, cacao tree plantations support the conservation of a large amount of organisms native to the Atlantic Forest, between them the ants. This study aims at recording the relationship between cocoa tree development and ant community structure. The experiment was carried out in a series of six cocoa tree plantations aged one, three, four, eight, fifteen and 33 years, distributed across the experimental grounds of the Cocoa Research Center at Ilhéus. 1,500 ant samples were collected using the sampling techniques: hand collection, honey and sardine baits, entomological blanket and “pitfall”. Highest values for diversity and richness were reported in the 15-years-old cocoa plantation. No significant correlations between diversity, richness or plant age were reported. Considering the faunistic composition, a statistical similarity was observed between the plantations close in age to one another. Plant aging did not exert any influence on the diversity gradient and richness in the succession process of the ant community. In young plantations, there are low differences between the ants found on the ground and the ones found on the young cocoa trees. In older plantations, the ant community divides in two distinct assemblages on the ground and on the trees. The variations observed in the ant community along the plant development were likely caused by the structural organization of the dominant species mosaic.
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Gluck-Thaler, Emile, Sajeet Haridas, Manfred Binder, Igor V. Grigoriev, Pedro W. Crous, Joseph W. Spatafora, Kathryn Bushley, and Jason C. Slot. "The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi." Molecular Biology and Evolution 37, no. 10 (May 18, 2020): 2838–56. http://dx.doi.org/10.1093/molbev/msaa122.
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Abstract Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.
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ÖZtürk, Sevi̇lay. "Cyanobacterial Diversity and Physicochemical Characteristics of Thermal Springs in The Kütahya Province of Turkey." Bangladesh Journal of Plant Taxonomy 28, no. 2 (December 26, 2021): 413–28. http://dx.doi.org/10.3329/bjpt.v28i2.57137.
Full textAbstract:
Thermal springs are very difficult environments for organisms due to the high temperature, and physicochemical parameters. Cyanobacteria, which are photosynthetic prokaryotes, are best adapted to these environments. Kütahya is an important thermal area in Turkey. The aim of the study was to determine the cyanobacterial flora with a morphologic and ecologic approach in the 11 thermal. The physicochemical properties of the thermal springs in Kütahya province were measured. The thermal springs are alkaline (pH6) with an average temperature of 52°C. As a result, 54 cyanobacteria taxa were identified. Oscillatoriales were the predominant order in terms of taxa diversity (24 taxa) and biomass size. Statistical analyses were conducted to reveal the physicochemical properties of the thermal springs and the distribution of cyanobacteria in detail. According to these analyses, the thermal springs were classified into two main groups with a Piper. As a result of the RDA analysis under CANOCO 5.0, the total variation was 55.45455, and the first two axes explained a total of 57.43% of the variance. There was a significant difference (P0.001) in the comparison of the physicochemical parameters including pH, EC, TDS, and temperature values of the thermal springs in the Kruskal Wallis tests. Bangladesh J. Plant Taxon. 28(2): 413-428, 2021 (December)
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Eliason, Chad M., Michael J. Andersen, and Shannon J. Hackett. "Using Historical Biogeography Models to Study Color Pattern Evolution." Systematic Biology 68, no. 5 (February 20, 2019): 755–66. http://dx.doi.org/10.1093/sysbio/syz012.
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Abstract Color is among the most striking features of organisms, varying not only in spectral properties like hue and brightness, but also in where and how it is produced on the body. Different combinations of colors on a bird’s body are important in both environmental and social contexts. Previous comparative studies have treated plumage patches individually or derived plumage complexity scores from color measurements across a bird’s body. However, these approaches do not consider the multivariate nature of plumages (allowing for plumage to evolve as a whole) or account for interpatch distances. Here, we leverage a rich toolkit used in historical biogeography to assess color pattern evolution in a cosmopolitan radiation of birds, kingfishers (Aves: Alcedinidae). We demonstrate the utility of this approach and test hypotheses about the tempo and mode of color evolution in kingfishers. Our results highlight the importance of considering interpatch distances in understanding macroevolutionary trends in color diversity and demonstrate how historical biogeography models are a useful way to model plumage color pattern evolution. Furthermore, they show that distinct color mechanisms (pigments or structural colors) spread across the body in different ways and at different rates. Specifically, net rates are higher for structural colors than pigment-based colors. Together, our study suggests a role for both development and selection in driving extraordinary color pattern diversity in kingfishers. We anticipate this approach will be useful for modeling other complex phenotypes besides color, such as parasite evolution across the body.
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Sou, Ieng Fong, Rebecca M. Pryce, Wee-Wei Tee, and Urszula Lucja McClurg. "Meiosis initiation: a story of two sexes in all creatures great and small." Biochemical Journal 478, no. 20 (October 28, 2021): 3791–805. http://dx.doi.org/10.1042/bcj20210412.
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Meiosis facilitates diversity across individuals and serves as a major driver of evolution. However, understanding how meiosis begins is complicated by fundamental differences that exist between sexes and species. Fundamental meiotic research is further hampered by a current lack of human meiotic cells lines. Consequently, much of what we know relies on data from model organisms. However, contextualising findings from yeast, worms, flies and mice can be challenging, due to marked differences in both nomenclature and the relative timing of meiosis. In this review, we set out to combine current knowledge of signalling and transcriptional pathways that control meiosis initiation across the sexes in a variety of organisms. Furthermore, we highlight the emerging links between meiosis initiation and oncogenesis, which might explain the frequent re-expression of normally silent meiotic genes in a variety of human cancers.
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Sukhova, Ekaterina, Ekaterina Gromova, Lyubov Yudina, Anastasiia Kior, Yana Vetrova, Nikolay Ilin, Evgeny Mareev, Vladimir Vodeneev, and Vladimir Sukhov. "Change in H+ Transport across Thylakoid Membrane as Potential Mechanism of 14.3 Hz Magnetic Field Impact on Photosynthetic Light Reactions in Seedlings of Wheat (Triticum aestivum L.)." Plants 10, no. 10 (October 18, 2021): 2207. http://dx.doi.org/10.3390/plants10102207.
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Natural and artificial extremely low-frequency magnetic fields (ELFMFs) are important factors influencing physiological processes in living organisms including terrestrial plants. Earlier, it was experimentally shown that short-term and long-term treatments by ELFMFs with Schumann resonance frequencies (7.8, 14.3, and 20.8 Hz) influenced parameters of photosynthetic light reactions in wheat leaves. The current work is devoted to an analysis of potential ways of this ELFMF influence on the light reactions. Only a short-term wheat treatment by 14.3 Hz ELFMF was used in the analysis. First, it was experimentally shown that ELFMF-induced changes (an increase in the effective quantum yield of photosystem II, a decrease in the non-photochemical quenching of chlorophyll fluorescence, a decrease in time of changes in these parameters, etc.) were observed under the action of ELFMF with widely ranging magnitudes (from 3 to 180 µT). In contrast, the potential quantum yield of photosystem II and time of relaxation of the energy-dependent component of the non-photochemical quenching were not significantly influenced by ELFMF. Second, it was shown that the ELFMF treatment decreased the proton gradient across the thylakoid membrane. In contrast, the H+ conductivity increased under this treatment. Third, an analysis of the simplest mathematical model of an H+ transport across the thylakoid membrane, which was developed in this work, showed that changes in H+ fluxes related to activities of the photosynthetic electron transport chain and the H+-ATP synthase were not likely a mechanism of the ELFMF influence. In contrast, changes induced by an increase in an additional H+ flux (probably, through the proton leakage and/or through the H+/Ca2+ antiporter activity in the thylakoid membrane) were in good accordance with experimental results. Thus, we hypothesized that this increase is the mechanism of the 14.3 Hz ELFMF influence (and, maybe, influences of other low frequencies) on photosynthetic light reactions in wheat.
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Wang, Xi, Carolina Bernhardsson, and Pär K. Ingvarsson. "Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)." Genome Biology and Evolution 12, no. 2 (January 20, 2020): 3803–17. http://dx.doi.org/10.1093/gbe/evaa005.
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Abstract Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
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Dunning, Luke T., Jose J. Moreno-Villena, Marjorie R. Lundgren, Jacqueline Dionora, Paolo Salazar, Claire Adams, Florence Nyirenda, et al. "Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata." Journal of Experimental Botany 70, no. 12 (April 5, 2019): 3255–68. http://dx.doi.org/10.1093/jxb/erz149.
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Abstract C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: aspartate aminotransferase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxylase. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme pyruvate orthophosphate dikinase. These changes probably created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4 accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous step. These create short bridges across adaptive landscapes that probably facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution.
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VanKuren, Nicholas W., Darli Massardo, Sumitha Nallu, and Marcus R. Kronforst. "Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations." Molecular Biology and Evolution 36, no. 12 (August 28, 2019): 2842–53. http://dx.doi.org/10.1093/molbev/msz194.
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Abstract Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptation. However, the causes of gene reuse remain unclear. A small number of large-effect Mendelian loci control a huge diversity of mimetic butterfly wing color patterns, but reasons for their reuse are difficult to identify because the genetic basis of mimicry has primarily been studied in two systems with correlated factors: female-limited Batesian mimicry in Papilio swallowtails (Papilionidae) and non-sex-limited Müllerian mimicry in Heliconius longwings (Nymphalidae). Here, we break the correlation between phylogenetic relationship and sex-limited mimicry by identifying loci controlling female-limited mimicry polymorphism Hypolimnas misippus (Nymphalidae) and non-sex-limited mimicry polymorphism in Papilio clytia (Papilionidae). The Papilio clytia polymorphism is controlled by the genome region containing the gene cortex, the classic P supergene in Heliconius numata, and loci controlling color pattern variation across Lepidoptera. In contrast, female-limited mimicry polymorphism in Hypolimnas misippus is associated with a locus not previously implicated in color patterning. Thus, although many species repeatedly converged on cortex and its neighboring genes over 120 My of evolution of diverse color patterns, female-limited mimicry polymorphisms each evolved using a different gene. Our results support conclusions that gene reuse occurs mainly within ∼10 My and highlight the puzzling diversity of genes controlling seemingly complex female-limited mimicry polymorphisms.
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Heino, Jani, Timo Muotka, Riku Paavola, and Lauri Paasivirta. "Among-taxon congruence in biodiversity patterns: can stream insect diversity be predicted using single taxonomic groups?" Canadian Journal of Fisheries and Aquatic Sciences 60, no. 9 (September 1, 2003): 1039–49. http://dx.doi.org/10.1139/f03-081.
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The utility of single taxonomic groups as indicators of biodiversity variation in other taxa has recently gained increasing attention, but such studies on stream organisms are lacking. We studied the diversity patterns of mayflies, stoneflies, caddisflies, and chironomid midges across 110 headwater streams in Finland. Specifically, we examined if species richness and assemblage composition showed similar variation among the taxonomic groups across environmental gradients and if a single taxon could be used as a predictor of diversity in the other groups. Species richness and composition in different taxa exhibited slightly different relationships to environmental gradients, leading to low degrees of concordance. The diversity of mayflies and chironomids showed strongest relationships with stream acidity and water colour, whereas stoneflies and caddisflies exhibited more complex correlations with geographical location and local environmental variables. The overall assemblage composition, however, exhibited significant among-taxon congruence, as shown by Mantel tests. However, even these correlations remained rather low, thus limiting their potential for conservation purposes. Overall, our results do not support the use of single taxonomic groups as indicators of insect biodiversity in headwater stream ecosystems. Alternative approaches for lotic biodiversity assessment (e.g., morphospecies, higher-taxon richness, and environmental diversity) should thus be examined in future studies.
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Steury, Currey, Cresko, and Bohannan. "Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback." Genes 10, no. 7 (June 26, 2019): 484. http://dx.doi.org/10.3390/genes10070484.
Full textAbstract:
Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information. Here we integrate population genomic and microbiome analyses in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.
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Grégoire Taillefer, Amélie, and Terry A. Wheeler. "Latitudinal patterns in phylogenetic and functional diversity of Diptera in temperate bogs." Canadian Entomologist 151, no. 02 (March 15, 2019): 187–208. http://dx.doi.org/10.4039/tce.2019.5.
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AbstractConservation of biodiversity is growing in interest, and wetlands are disappearing at an alarming rate, so understanding how communities are assembled and how interactions among species and ecosystems influence evolution is critical to the management of threatened habitats. We compared diversity and assemblages of peatland Diptera within and between ecoregions in Québec, Canada. We then determined the phylogenetic structure of peatland Diptera communities and how the structure differed with spatial scale (trap, site, ecoregion). Finally, we tested alpha and beta diversity along environmental and spatial gradients to determine which processes influence Diptera communities and diversity. Bogs across the three ecoregions support similar abundance, species richness, and functional diversity. We found that the major forces structuring Diptera assemblages in bogs across Québec are stochastic processes such as dispersal limitations. However, those random patterns change to clustering when anthropogenic disturbances modify the landscape. Assembly rules are mostly dictated by patch and landscape parameters specific to each ecoregion affecting dispersal and establishment between sites. Conservation of mobile organisms in habitats such as bogs will depend on conservation plans focusing on both patch quality and surrounding landscape, and that different conservation strategies need to be applied in different ecoregions.
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Santos-Zavaleta, Alberto, Socorro Gama-Castro, and Ernesto Pérez-Rueda. "A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins." Microbiology 157, no. 5 (May 1, 2011): 1393–401. http://dx.doi.org/10.1099/mic.0.042937-0.
Full textAbstract:
The stationary-phase response mediated by the RpoS sigma factor (σS, σ38) has been widely studied as a general mechanism of activation of highly diverse genes that maintain cell viability. In bacteria, genes for diverse functions have been associated with this response, showing that bacteria use a large number of functions to contend with adverse conditions in their environment. However, little is known about how the genes have been functionally recruited in diverse organisms. In this work, we address the analysis of genes regulated by σS, based on a comparative genomic-scale analysis considering four versatile bacterial species that represent different lifestyles and taxonomic groups, Escherichia coli K-12, Geobacter sulfurreducens, Borrelia burgdorferi and Bacillus subtilis, as well as the extent of conservation in bacterial genomes, as a means of assessing the evolution of this sigmulon across all organisms completely sequenced. The analysis presented here shows that genes associated with the σS response have been recruited from diverse regulons to achieve a global response. In addition, and based on the distribution of orthologues, we show a group of genes that is highly conserved among all organisms, mainly associated with glycerol metabolism, as well as diverse functional genes recruited in a lineage-specific manner.
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Musgrave, William B., Hankuil Yi, Dustin Kline, Jeffrey C. Cameron, Jonathan Wignes, Sanghamitra Dey, Himadri B. Pakrasi, and Joseph M. Jez. "Probing the origins of glutathione biosynthesis through biochemical analysis of glutamate-cysteine ligase and glutathione synthetase from a model photosynthetic prokaryote." Biochemical Journal 450, no. 1 (January 24, 2013): 63–72. http://dx.doi.org/10.1042/bj20121332.
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Glutathione biosynthesis catalysed by GCL (glutamate-cysteine ligase) and GS (glutathione synthetase) is essential for maintaining redox homoeostasis and protection against oxidative damage in diverse eukaroytes and bacteria. This biosynthetic pathway probably evolved in cyanobacteria with the advent of oxygenic photosynthesis, but the biochemical characteristics of progenitor GCLs and GSs in these organisms are largely unexplored. In the present study we examined SynGCL and SynGS from Synechocystis sp. PCC 6803 using steady-state kinetics. Although SynGCL shares ~15% sequence identity with the enzyme from plants and α-proteobacteria, sequence comparison suggests that these enzymes share similar active site residues. Biochemically, SynGCL lacks the redox regulation associated with the plant enzymes and functions as a monomeric protein, indicating that evolution of redox regulation occurred later in the green lineage. Site-directed mutagenesis of SynGCL establishes this enzyme as part of the plant-like GCL family and identifies a catalytically essential arginine residue, which is structurally conserved across all forms of GCLs, including those from non-plant eukaryotes and γ-proteobacteria. A reaction mechanism for the synthesis of γ-glutamylcysteine by GCLs is proposed. Biochemical and kinetic analysis of SynGS reveals that this enzyme shares properties with other prokaryotic GSs. Initial velocity and product inhibition studies used to examine the kinetic mechanism of SynGS suggest that it and other prokaryotic GSs uses a random ter-reactant mechanism for the synthesis of glutathione. The present study provides new insight on the molecular mechanisms and evolution of glutathione biosynthesis; a key process required for enhancing bioenergy production in photosynthetic organisms.
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Ng, Jonathan Wei Xiong, Qiao Wen Tan, Camilla Ferrari, and Marek Mutwil. "Diurnal.plant.tools: Comparative Transcriptomic and Co-expression Analyses of Diurnal Gene Expression of the Archaeplastida Kingdom." Plant and Cell Physiology 61, no. 1 (September 10, 2019): 212–20. http://dx.doi.org/10.1093/pcp/pcz176.
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Abstract Almost all organisms coordinate some aspects of their biology through the diurnal cycle. Photosynthetic organisms, and plants especially, have established complex programs that coordinate physiological, metabolic and developmental processes with the changing light. The diurnal regulation of the underlying transcriptional processes is observed when groups of functionally related genes (gene modules) are expressed at a specific time of the day. However, studying the diurnal regulation of these gene modules in the plant kingdom was hampered by the large amount of data required for the analyses. To meet this need, we used gene expression data from 17 diurnal studies spanning the whole Archaeplastida kingdom (Plantae kingdom in the broad sense) to make an online diurnal database. We have equipped the database with tools that allow user-friendly cross-species comparisons of gene expression profiles, entire co-expression networks, co-expressed clusters (involved in specific biological processes), time-specific gene expression and others. We exemplify how these tools can be used by studying three important biological questions: (i) the evolution of cell division, (ii) the diurnal control of gene modules in algae and (iii) the conservation of diurnally controlled modules across species. The database is freely available at http://diurnal.plant.tools.
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Lyall, Rafe, Zoran Nikoloski, and Tsanko Gechev. "Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes." International Journal of Molecular Sciences 21, no. 23 (November 30, 2020): 9131. http://dx.doi.org/10.3390/ijms21239131.
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The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, plants and animals. We included the genomes of 16 extremotolerant Eukaryotes to gain insight into ROS gene evolution in organisms that experience extreme stress conditions. Our analysis focused on ROS genes found in all Eukaryotes (such as catalases, superoxide dismutases, glutathione reductases, peroxidases and glutathione peroxidase/peroxiredoxins) as well as those specific to certain groups, such as ascorbate peroxidases, dehydroascorbate/monodehydroascorbate reductases in plants and other photosynthetic organisms. ROS-producing NADPH oxidases (NOX) were found in most multicellular organisms, although several NOX-like genes were identified in unicellular or filamentous species. However, despite the extreme conditions experienced by extremophile species, we found no evidence for expansion of ROS-related gene families in these species compared to other Eukaryotes. Tardigrades and rotifers do show ROS gene expansions that could be related to their extreme lifestyles, although a high rate of lineage-specific horizontal gene transfer events, coupled with recent tetraploidy in rotifers, could explain this observation. This suggests that the basal Eukaryotic ROS scavenging systems are sufficient to maintain ROS homeostasis even under the most extreme conditions.
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Iwai, Masakazu, Dhruv Patel-Tupper, and Krishna K. Niyogi. "Structural Diversity in Eukaryotic Photosynthetic Light Harvesting." Annual Review of Plant Biology 75, no. 1 (February 15, 2024). http://dx.doi.org/10.1146/annurev-arplant-070623-015519.
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Photosynthesis has been using energy from sunlight to assimilate atmospheric CO2 for at least 3.5 billion years. Through evolution and natural selection, photosynthetic organisms have flourished in almost all aquatic and terrestrial environments. This is partly due to the diversity of light-harvesting complex (LHC) proteins, which facilitate photosystem assembly, efficient excitation energy transfer, and photoprotection. Structural advances have provided Ångström-level structures of many of these proteins and have expanded our understanding of the pigments, lipids, and residues that drive LHC function. In this review, we compare and contrast recently observed cryo-electron microscopy structures across photosynthetic eukaryotes to identify structural motifs that underlie various light-harvesting strategies. We discuss subtle monomer changes that result in macroscale reorganization of LHC oligomers. Additionally, we find recurring patterns across diverse LHCs that may serve as evolutionary stepping stones for functional diversification. Advancing our understanding of LHC protein–environment interactions will improve our capacity to engineer more productive crops. Expected final online publication date for the Annual Review of Plant Biology, Volume 75 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Capó‐Bauçà, Sebastià, Concepción Iñiguez, and Jeroni Galmés. "The diversity and coevolution of Rubisco and CO2 concentrating mechanisms in marine macrophytes." New Phytologist, January 10, 2024. http://dx.doi.org/10.1111/nph.19528.
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SummaryThe kinetic properties of Rubisco, the most important carbon‐fixing enzyme, have been assessed in a small fraction of the estimated existing biodiversity of photosynthetic organisms. Until recently, one of the most significant gaps of knowledge in Rubisco kinetics was marine macrophytes, an ecologically relevant group including brown (Ochrophyta), red (Rhodophyta) and green (Chlorophyta) macroalgae and seagrasses (Streptophyta). These organisms express various Rubisco types and predominantly possess CO2‐concentrating mechanisms (CCMs), which facilitate the use of bicarbonate for photosynthesis. Since bicarbonate is the most abundant form of dissolved inorganic carbon in seawater, CCMs allow marine macrophytes to overcome the slow gas diffusion and low CO2 availability in this environment. The present review aims to compile and integrate recent findings on the biochemical diversity of Rubisco and CCMs in the main groups of marine macrophytes. The Rubisco kinetic data provided demonstrate a more relaxed relationship among catalytic parameters than previously reported, uncovering a variability in Rubisco catalysis that has been hidden by a bias in the literature towards terrestrial vascular plants. The compiled data indicate the existence of convergent evolution between Rubisco and biophysical CCMs across the polyphyletic groups of marine macrophytes and suggest a potential role for oxygen in shaping such relationship.
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Canini, Fabiana, Luigimaria Borruso, Kevin K. Newsham, Federica D'Alò, Luigi P. D'Acqui, and Laura Zucconi. "Wide divergence of fungal communities inhabiting rocks and soils in a hyper‐arid Antarctic desert." Environmental Microbiology, November 14, 2023. http://dx.doi.org/10.1111/1462-2920.16534.
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AbstractHighly simplified microbial communities colonise rocks and soils of continental Antarctica ice‐free deserts. These two habitats impose different selection pressures on organisms, yet the possible filtering effects on the diversity and composition of microbial communities have not hitherto been fully characterised. We hence compared fungal communities in rocks and soils in three localities of inner Victoria Land. We found low fungal diversity in both substrates, with a mean species richness of 28 across all samples, and significantly lower diversity in rocks than in soils. Rock and soil communities were strongly differentiated, with a multinomial species classification method identifying just three out of 328 taxa as generalists with no affinity for either substrate. Rocks were characterised by a higher abundance of lichen‐forming fungi (typically Buellia, Carbonea, Pleopsidium, Lecanora, and Lecidea), possibly owing to the more protected environment and the porosity of rocks permitting photosynthetic activity. In contrast, soils were dominated by obligate yeasts (typically Naganishia and Meyerozyma), the abundances of which were correlated with edaphic factors, and the black yeast Cryomyces. Our study suggests that strong differences in selection pressures may account for the wide divergences of fungal communities in rocks and soils of inner Victoria Land.
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LaSarre, Breah, David T. Kysela, Barry D. Stein, Adrien Ducret, Yves V. Brun, and James B. McKinlay. "Restricted Localization of Photosynthetic Intracytoplasmic Membranes (ICMs) in Multiple Genera of Purple Nonsulfur Bacteria." mBio 9, no. 4 (July 3, 2018). http://dx.doi.org/10.1128/mbio.00780-18.
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ABSTRACTIn bacteria and eukaryotes alike, proper cellular physiology relies on robust subcellular organization. For the phototrophic purple nonsulfur bacteria (PNSB), this organization entails the use of a light-harvesting, membrane-bound compartment known as the intracytoplasmic membrane (ICM). Here we show that ICMs are spatially and temporally localized in diverse patterns among PNSB. We visualized ICMs in live cells of 14 PNSB species across nine genera by exploiting the natural autofluorescence of the photosynthetic pigment bacteriochlorophyll (BChl). We then quantitatively characterized ICM localization using automated computational analysis of BChl fluorescence patterns within single cells across the population. We revealed that while many PNSB elaborate ICMs along the entirety of the cell, species across as least two genera restrict ICMs to discrete, nonrandom sites near cell poles in a manner coordinated with cell growth and division. Phylogenetic and phenotypic comparisons established that ICM localization and ICM architecture are not strictly interdependent and that neither trait fully correlates with the evolutionary relatedness of the species. The natural diversity of ICM localization revealed herein has implications for both the evolution of phototrophic organisms and their light-harvesting compartments and the mechanisms underpinning spatial organization of bacterial compartments.IMPORTANCEMany bacteria organize their cellular space by constructing subcellular compartments that are arranged in specific, physiologically relevant patterns. The purple nonsulfur bacteria (PNSB) utilize a membrane-bound compartment known as the intracytoplasmic membrane (ICM) to harvest light for photosynthesis. It was previously unknown whether ICM localization within cells is systematic or irregular and if ICM localization is conserved among PNSB. Here we surveyed ICM localization in diverse PNSB and show that ICMs are spatially organized in species-specific patterns. Most strikingly, several PNSB resolutely restrict ICMs to regions near the cell poles, leaving much of the cell devoid of light-harvesting machinery. Our results demonstrate that bacteria of a common lifestyle utilize unequal portions of their intracellular space to harvest light, despite light harvesting being a process that is intuitively influenced by surface area. Our findings therefore raise fundamental questions about ICM biology and evolution.
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Badger, Murray R., and Robert E. Sharwood. "Rubisco, the imperfect winner: “it's all about the base”." Journal of Experimental Botany, November 22, 2022. http://dx.doi.org/10.1093/jxb/erac458.
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Abstract Since the discovery of Rubisco as the Fraction 1 protein initially named by Sam Wildman, Rubisco has attracted significant efforts to examine the nature of catalysis and whether diversity exists among photosynthetic organisms. Early studies demonstrate the influence of Rubisco on carbon assimilation and its control over the flux of carbon through the Calvin-Benson-Bassham cycle, which is closely linked to the catalytic properties of the enzyme. Understanding Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth’s multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily has identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubiscos’ catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base which functions both as an activator and a proton abstractor to create the enediol, as a key to understanding how Rubisco may change its kinetic properties. This review discusses the ways in which Rubisco and its partners have overcome catalytic imperfections and thrived in a world of high O2, low CO2 and variable climatic regimes.
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Shen, Jiejie, Wenping Wu, Kangle Wang, Jingyi Wu, Bing Liu, Chunyang Li, Zijun Gong, et al. "Chloroflexus aurantiacus acetyl-CoA carboxylase evolves fused biotin carboxylase and biotin carboxyl carrier protein to complete carboxylation activity." mBio, April 4, 2024. http://dx.doi.org/10.1128/mbio.03414-23.
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ABSTRACT Acetyl-CoA carboxylases (ACCs) convert acetyl-CoA to malonyl-CoA, a key step in fatty acid biosynthesis and autotrophic carbon fixation pathways. Three functionally distinct components, biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and carboxyltransferase (CT), are either separated or partially fused in different combinations, forming heteromeric ACCs. However, an ACC with fused BC-BCCP and separate CT has not been identified, leaving its catalytic mechanism unclear. Here, we identify two BC isoforms (BC1 and BC2) from Chloroflexus aurantiacus , a filamentous anoxygenic phototroph that employs 3-hydroxypropionate (3-HP) bi-cycle rather than Calvin cycle for autotrophic carbon fixation. We reveal that BC1 possesses fused BC and BCCP domains, where BCCP could be biotinylated by E. coli or C. aurantiacus BirA on Lys553 residue. Crystal structures of BC1 and BC2 at 3.2 Å and 3.0 Å resolutions, respectively, further reveal a tetramer of two BC1-BC homodimers, and a BC2 homodimer, all exhibiting similar BC architectures. The two BC1-BC homodimers are connected by an eight-stranded β-barrel of the partially resolved BCCP domain. Disruption of β-barrel results in dissociation of the tetramer into dimers in solution and decreased biotin carboxylase activity. Biotinylation of the BCCP domain further promotes BC1 and CTβ-CTα interactions to form an enzymatically active ACC, which converts acetyl-CoA to malonyl-CoA in vitro and produces 3-HP via co-expression with a recombinant malonyl-CoA reductase in E. coli cells. This study revealed a heteromeric ACC that evolves fused BC-BCCP but separate CTα and CTβ to complete ACC activity. IMPORTANCE Acetyl-CoA carboxylase (ACC) catalyzes the rate-limiting step in fatty acid biosynthesis and autotrophic carbon fixation pathways across a wide range of organisms, making them attractive targets for drug discovery against various infections and diseases. Although structural studies on homomeric ACCs, which consist of a single protein with three subunits, have revealed the “swing domain model” where the biotin carboxyl carrier protein (BCCP) domain translocates between biotin carboxylase (BC) and carboxyltransferase (CT) active sites to facilitate the reaction, our understanding of the subunit composition and catalytic mechanism in heteromeric ACCs remains limited. Here, we identify a novel ACC from an ancient anoxygenic photosynthetic bacterium Chloroflexus aurantiacus , it evolves fused BC and BCCP domain, but separate CT components to form an enzymatically active ACC, which converts acetyl-CoA to malonyl-CoA in vitro and produces 3-hydroxypropionate (3-HP) via co-expression with recombinant malonyl-CoA reductase in E. coli cells. These findings expand the diversity and molecular evolution of heteromeric ACCs and provide a structural basis for potential applications in 3-HP biosynthesis.
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Bai, Tianyu, Lin Guo, Mingyu Xu, and Lirong Tian. "Structural Diversity of Photosystem I and Its Light-Harvesting System in Eukaryotic Algae and Plants." Frontiers in Plant Science 12 (November 30, 2021). http://dx.doi.org/10.3389/fpls.2021.781035.
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Photosystem I (PSI) is one of the most efficient photoelectric apparatus in nature, converting solar energy into condensed chemical energy with almost 100% quantum efficiency. The ability of PSI to attain such high conversion efficiency depends on the precise spatial arrangement of its protein subunits and binding cofactors. The PSI structures of oxygenic photosynthetic organisms, namely cyanobacteria, eukaryotic algae, and plants, have undergone great variation during their evolution, especially in eukaryotic algae and vascular plants for which light-harvesting complexes (LHCI) developed that surround the PSI core complex. A detailed understanding of the functional and structural properties of this PSI-LHCI is not only an important foundation for understanding the evolution of photosynthetic organisms but is also useful for designing future artificial photochemical devices. Recently, the structures of such PSI-LHCI supercomplexes from red alga, green alga, diatoms, and plants were determined by X-ray crystallography and single-particle cryo-electron microscopy (cryo-EM). These findings provide new insights into the various structural adjustments of PSI, especially with respect to the diversity of peripheral antenna systems arising via evolutionary processes. Here, we review the structural details of the PSI tetramer in cyanobacteria and the PSI-LHCI and PSI-LHCI-LHCII supercomplexes from different algae and plants, and then discuss the diversity of PSI-LHCI in oxygenic photosynthesis organisms.