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1
Pandey, Sona. "Plant receptor-like kinase signaling through heterotrimeric G-proteins." Journal of Experimental Botany 71, no. 5 (January 13, 2020): 1742–51. http://dx.doi.org/10.1093/jxb/eraa016.
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Abstract Heterotrimeric G-proteins regulate multiple aspects of plant growth, development, and response to biotic and abiotic stresses. While the core components of heterotrimeric G-proteins and their basic biochemistry are similar in plants and metazoans, key differences exist in their regulatory mechanisms. In particular, the activation mechanisms of plant G-proteins appear diverse and may include both canonical and novel modes. Classical G-protein-coupled receptor-like proteins exist in plants and interact with Gα proteins, but their ability to activate Gα by facilitating GDP to GTP exchange has not been demonstrated. Conversely, there is genetic and functional evidence that plant G-proteins interact with the highly prevalent receptor-like kinases (RLKs) and are phosphorylated by them. This suggests the exciting scenario that in plants the G-proteins integrate RLK-dependent signal perception at the plasma membrane with downstream effectors. Because RLKs are active kinases, it is also likely that the activity of plant G-proteins is regulated via phosphorylation/dephosphorylation rather than GTP–GDP exchange as in metazoans. This review discusses our current knowledge of the possible RLK-dependent regulatory mechanisms of plant G-protein signaling in the context of several biological systems and outlines the diversity that might exist in such regulation.
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Tichá, Tereza, Despina Samakovli, Anna Kuchařová, Tereza Vavrdová, and Jozef Šamaj. "Multifaceted roles of HEAT SHOCK PROTEIN 90 molecular chaperones in plant development." Journal of Experimental Botany 71, no. 14 (April 7, 2020): 3966–85. http://dx.doi.org/10.1093/jxb/eraa177.
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Abstract HEAT SHOCK PROTEINS 90 (HSP90s) are molecular chaperones that mediate correct folding and stability of many client proteins. These chaperones act as master molecular hubs involved in multiple aspects of cellular and developmental signalling in diverse organisms. Moreover, environmental and genetic perturbations affect both HSP90s and their clients, leading to alterations of molecular networks determining respectively plant phenotypes and genotypes and contributing to a broad phenotypic plasticity. Although HSP90 interaction networks affecting the genetic basis of phenotypic variation and diversity have been thoroughly studied in animals, such studies are just starting to emerge in plants. Here, we summarize current knowledge and discuss HSP90 network functions in plant development and cellular homeostasis.
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Soyano, Takashi, Masaki Ishikawa, Ryuichi Nishihama, Satoshi Araki, Mayumi Ito, Masaki Ito, and Yasunori Machida. "Control of plant cytokinesis by an NPK1–mediated mitogen–activated protein kinase cascade." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 357, no. 1422 (June 29, 2002): 767–75. http://dx.doi.org/10.1098/rstb.2002.1094.
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Cytokinesis is the last essential step in the distribution of genetic information to daughter cells and partition of the cytoplasm. In plant cells, various proteins have been found in the phragmoplast, which corresponds to the cytokinetic apparatus, and in the cell plate, which corresponds to a new cross wall, but our understanding of the functions of these proteins in cytokinesis remains incomplete. Reverse genetic analysis of NPK1 MAPKKK (nucleus– and phragmoplast–localized protein kinase 1 mitogen–activated protein kinase kinase kinase) and investigations of factors that might be functionally related to NPK1 have helped to clarify new aspects of the mechanisms of cytokinesis in plant cells. In this review, we summarize the evidence for the involvement of NPK1 in cytokinesis. We also describe the characteristics of a kinesin–like protein and the homologue of a mitogen–activated protein kinase that we identified recently, and we discuss possible relationships among these proteins in cytokinesis.
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Li, Lei, and Detlef Weigel. "One Hundred Years of Hybrid Necrosis: Hybrid Autoimmunity as a Window into the Mechanisms and Evolution of Plant–Pathogen Interactions." Annual Review of Phytopathology 59, no. 1 (August 25, 2021): 213–37. http://dx.doi.org/10.1146/annurev-phyto-020620-114826.
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Hybrid necrosis in plants refers to a genetic autoimmunity syndrome in the progeny of interspecific or intraspecific crosses. Although the phenomenon was first documented in 1920, it has been unequivocally linked to autoimmunity only recently, with the discovery of the underlying genetic and biochemical mechanisms. The most common causal loci encode immune receptors, which are known to differ within and between species. One mechanism can be explained by the guard hypothesis, in which a guard protein, often a nucleotide-binding site–leucine-rich repeat protein, is activated by interaction with a plant protein that mimics standard guardees modified by pathogen effector proteins. Another surprising mechanism is the formation of inappropriately active immune receptor complexes. In this review, we summarize our current knowledge of hybrid necrosis and discuss how its study is not only informing the understanding of immune gene evolution but also revealing new aspects of plant immune signaling.
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Frolova, T. S., V. A. Cherenko, O. I. Sinitsyna, and A. V. Kochetov. "Genetic aspects of potato resistance to phytophthorosis." Vavilov Journal of Genetics and Breeding 25, no. 2 (April 29, 2021): 164–70. http://dx.doi.org/10.18699/vj21.020.
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Phytophthora infestans Mont. de Bary is the main oomycete pathogen of cultivated crops in the family Solanaceae, especially potato (Solanum tuberosum). Because potato is the fourth most cultivated crop worldwide, its annual losses from late blight are tremendous. Studies of the basic mechanisms of interaction between potato and the late blight pathogen not only expand the fundamental knowledge in this area, but also open up new possibilities for regulating these interactions in order to increase resistance to the pathogen. The interaction of potato and the late blight pathogen can be considered from a genetic point of view, and it is interesting to consider both the response of the potato to the colonization process by P. infestans and the change in gene activity in late blight during plant infection. We can also investigate this process by changing the profile of secondary metabolites of the host and the pathogen. In addition to fundamental work in this area, applied work in the form of the development of new preparations for protecting potatoes is of no less importance. This review briefly describes the main stages of studies of potato resistance to late blight, starting almost from the first works. Much attention is paid to key works on changing the profile of secondary metabolites phytoalexins. A separate section is devoted to the description of both qualitative and quantitative characteristics of potato resistance to the late blight pathogen: their contribution to overall resistance, gene mapping, and regulation capabilities. Both types of traits are important for potato breeding: quantitative resistance due to R-genes is quickly overcome by the pathogen, while quantitative trait loci make it possible to create varieties with almost absolute resistance due to the pyramid of effective genes. The latest approaches in molecular biology make it possible to study translatomic profiles, which makes it possible to look at the interaction of potatoes and the late blight pathogen at a different angle. It has been shown that the process of potato colonization affects not only the activity of various genes and the profile of secondary metabolites: proteinsmarkers of the response to infection from potatoes have also been identified: they are pathogen-bound proteins and plastid carbonic anhydrase. On the part of P. infestans, fungal cellulose synthase proteins and haustorium-specific membrane protein were markers of infection. Thus, the review contains information on the most relevant complex studies of the genetic mechanisms of potato resistance to late blight.
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Hadi, Joshua, and Gale Brightwell. "Safety of Alternative Proteins: Technological, Environmental and Regulatory Aspects of Cultured Meat, Plant-Based Meat, Insect Protein and Single-Cell Protein." Foods 10, no. 6 (May 28, 2021): 1226. http://dx.doi.org/10.3390/foods10061226.
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Food security and environmental issues have become global crises that need transformative solutions. As livestock production is becoming less sustainable, alternative sources of proteins are urgently required. These include cultured meat, plant-based meat, insect protein and single-cell protein. Here, we describe the food safety aspects of these novel protein sources, in terms of their technological backgrounds, environmental impacts and the necessary regulatory framework for future mass-scale production. Briefly, cultured meat grown in fetal bovine serum-based media can be exposed to viruses or infectious prion, in addition to other safety risks associated with the use of genetic engineering. Plant-based meat may contain allergens, anti-nutrients and thermally induced carcinogens. Microbiological risks and allergens are the primary concerns associated with insect protein. Single-cell protein sources are divided into microalgae, fungi and bacteria, all of which have specific food safety risks that include toxins, allergens and high ribonucleic acid (RNA) contents. The environmental impacts of these alternative proteins can mainly be attributed to the production of growth substrates or during cultivation. Legislations related to novel food or genetic modification are the relevant regulatory framework to ensure the safety of alternative proteins. Lastly, additional studies on the food safety aspects of alternative proteins are urgently needed for providing relevant food governing authorities with sufficient data to oversee that the technological progress in this area is balanced with robust safety standards.
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Dziechciarková, M., A. Lebeda, I. Doležalová, and D. Astley. "Characterization of Lactuca spp. germplasm by protein and molecular markers – a review." Plant, Soil and Environment 50, No. 2 (November 21, 2011): 47–58. http://dx.doi.org/10.17221/3680-pse.
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The genus Lactuca L. belongs to one of the largest plant families, Asteraceae. Lactuca L. is represented by ca 100 species distributed in different geographical areas and ecological conditions. This is one of the reasons why this genus is characterised by very broad variation of different characters. Electrophoretic detection of some proteins (isozymes) has been applied to the study of genetic variability of Lactuca spp. individuals and populations. The development of molecular genetic methods (RFLP, Restriction Fragment Length Polymorphism; PCR methods: RAPD, Random Amplified Polymorphic DNA; AFLP, Amplified Fragment Length Polymorphism; minisatellites and microsatellites fingerprinting or SSR, Simple Sequence Repeats) and their application has contributed to the elucidation of various aspects related to the taxonomy, variability, biodiversity, genetics and breeding within the genus Lactuca L. Further potential application of these methods is discussed.
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Kayser, Oliver. "Ethnobotany and Medicinal Plant Biotechnology: From Tradition to Modern Aspects of Drug Development." Planta Medica 84, no. 12/13 (May 24, 2018): 834–38. http://dx.doi.org/10.1055/a-0631-3876.
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AbstractSecondary natural products from plants are important drug leads for the development of new drug candidates for rational clinical therapy and exhibit a variety of biological activities in experimental pharmacology and serve as structural template in medicinal chemistry. The exploration of plants and discovery of natural compounds based on ethnopharmacology in combination with high sophisticated analytics is still today an important drug discovery to characterize and validate potential leads. Due to structural complexity, low abundance in biological material, and high costs in chemical synthesis, alternative ways in production like plant cell cultures, heterologous biosynthesis, and synthetic biotechnology are applied. The basis for any biotechnological process is deep knowledge in genetic regulation of pathways and protein expression with regard to todays “omics” technologies. The high number genetic techniques allowed the implementation of combinatorial biosynthesis and wide genome sequencing. Consequently, genetics allowed functional expression of biosynthetic cascades from plants and to reconstitute low-performing pathways in more productive heterologous microorganisms. Thus, de novo biosynthesis in heterologous hosts requires fundamental understanding of pathway reconstruction and multitude of genes in a foreign organism. Here, actual concepts and strategies are discussed for pathway reconstruction and genome sequencing techniques cloning tools to bridge the gap between ethnopharmaceutical drug discovery to industrial biotechnology.
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Sluse, Francis E., and Wieslawa Jarmuszkiewicz. "Uncoupling proteins outside the animal and plant kingdoms: functional and evolutionary aspects." FEBS Letters 510, no. 3 (December 6, 2001): 117–20. http://dx.doi.org/10.1016/s0014-5793(01)03229-x.
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Tripathy, Manas K., Renu Deswal, and Sudhir K. Sopory. "Plant RABs: Role in Development and in Abiotic and Biotic Stress Responses." Current Genomics 22, no. 1 (April 12, 2021): 26–40. http://dx.doi.org/10.2174/1389202922666210114102743.
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Endosomal trafficking plays an integral role in various eukaryotic cellular activities and is vital for higher-order functions in multicellular organisms. RAB GTPases are important proteins that influence various aspects of membrane traffic, which consequently influence many cellular functions and responses. Compared to yeast and mammals, plants have evolved a unique set of plant-specific RABs that play a significant role in their development. RABs form the largest family of small guanosine triphosphate (GTP)-binding proteins, and are divided into eight sub-families named RAB1, RAB2, RAB5, RAB6, RAB7, RAB8, RAB11 and RAB18. Recent studies on different species suggest that RAB proteins play crucial roles in intracellular trafficking and cytokinesis, in autophagy, plant microbe interactions and in biotic and abiotic stress responses. This review recaptures and summarizes the roles of RABs in plant cell functions and in enhancing plant survival under stress conditions.
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Bassi, Roberto, Dorianna Sandona, and Roberta Croce. "Novel aspects of chlorophyll a/b-binding proteins." Physiologia Plantarum 100, no. 4 (August 1997): 769–79. http://dx.doi.org/10.1111/j.1399-3054.1997.tb00004.x.
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Ning, He, Su Yang, Baofang Fan, Cheng Zhu, and Zhixiang Chen. "Expansion and Functional Diversification of TFIIB-Like Factors in Plants." International Journal of Molecular Sciences 22, no. 3 (January 23, 2021): 1078. http://dx.doi.org/10.3390/ijms22031078.
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As sessile organisms, plants have evolved unique patterns of growth and development, elaborate metabolism and special perception and signaling mechanisms to environmental cues. Likewise, plants have complex and highly special programs for transcriptional control of gene expression. A case study for the special transcription control in plants is the expansion of general transcription factors, particularly the family of Transcription Factor IIB (TFIIB)-like factors with 15 members in Arabidopsis. For more than a decade, molecular and genetic analysis has revealed important functions of these TFIIB-like factors in specific biological processes including gametogenesis, pollen tube growth guidance, embryogenesis, endosperm development, and plant-microbe interactions. The redundant, specialized, and diversified roles of these TFIIB-like factors challenge the traditional definition of general transcription factors established in other eukaryotes. In this review, we discuss general transcription factors in plants with a focus on the expansion and functional analysis of plant TFIIB-like proteins to highlight unique aspects of plant transcription programs that can be highly valuable for understanding the molecular basis of plant growth, development and responses to stress conditions.
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Pérez-Clemente, Rosa M., Vicente Vives, Sara I. Zandalinas, María F. López-Climent, Valeria Muñoz, and Aurelio Gómez-Cadenas. "Biotechnological Approaches to Study Plant Responses to Stress." BioMed Research International 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/654120.
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Multiple biotic and abiotic environmental stress factors affect negatively various aspects of plant growth, development, and crop productivity. Plants, as sessile organisms, have developed, in the course of their evolution, efficient strategies of response to avoid, tolerate, or adapt to different types of stress situations. The diverse stress factors that plants have to face often activate similar cell signaling pathways and cellular responses, such as the production of stress proteins, upregulation of the antioxidant machinery, and accumulation of compatible solutes. Over the last few decades advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to abiotic stress conditions. In this paper, recent progresses on systematic analyses of plant responses to stress including genomics, proteomics, metabolomics, and transgenic-based approaches are summarized.
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Kumar, Sivakumar Prasanth, Saumya K. Patel, Ravi G. Kapopara, Yogesh T. Jasrai, and Himanshu A. Pandya. "Evolutionary and Molecular Aspects of Indian Tomato Leaf Curl Virus Coat Protein." International Journal of Plant Genomics 2012 (December 11, 2012): 1–12. http://dx.doi.org/10.1155/2012/417935.
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Tomato leaf curl disease (ToLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface, and stunted plant growth caused by tomato leaf curl virus (ToLCV). In the present study, using computational methods we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, Gujarat (ToLCGV-[Vad]), India. We found that the amino acids in coat protein required for systemic infection, viral particle formation, and insect transmission to host cells were conserved amongst Indian strains. Phylogenetic studies on Indian ToLCV coat proteins showed evolutionary compatibility with other viral taxa. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the viral DNA required for encapsidation and nuclear shuttling was investigated through sequence- and structure-based approaches. We further emphasized the role of loops in coat protein structure as molecular recognition interface.
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Genre, Andrea, and Paola Bonfante. "Check-In Procedures for Plant Cell Entry by Biotrophic Microbes." Molecular Plant-Microbe Interactions® 20, no. 9 (September 2007): 1023–30. http://dx.doi.org/10.1094/mpmi-20-9-1023.
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Significant advances in the cell biology of plant-microbe interactions have been achieved recently, to a large extent based on new technical approaches such as the use of fluorescent protein tags in model plants exploited in conjunction with available genetic resources. They have highlighted the pivotal role played by epidermal cells as the first site at which direct cell-to-cell contact takes place between the plant and microbes it may host. Here, we compare the cellular aspects of early biotrophic interactions with symbiotic and pathogenic microbes and evaluate the hypothesis that their hosting by plant cells share common traits related to the necessity of preserving host-cell integrity. The cellular events that accompany cell entry by the different biotrophs are divided into three categories, depending on whether the cellular changes are triggered by diffusible molecules, direct contact, or cell lumen penetration. Similarities and differences mirror the nutritional and developmental strategies of each plant-interacting organism, underlining the fact that plant cell entry represents a key aspect in the establishment of biotrophy.
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Khosa, Jiffinvir, Francesca Bellinazzo, Rina Kamenetsky Goldstein, Richard Macknight, and Richard G. H. Immink. "PHOSPHATIDYLETHANOLAMINE-BINDING PROTEINS: the conductors of dual reproduction in plants with vegetative storage organs." Journal of Experimental Botany 72, no. 8 (February 19, 2021): 2845–56. http://dx.doi.org/10.1093/jxb/erab064.
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Abstract Geophytes, the plants that form vegetative storage organs, are characterized by a dual reproduction system, in which vegetative and sexual propagation are tightly regulated to ensure fitness in harsh climatic conditions. Recent findings highlight the role of the PEBP (PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN) gene family in geophytes as major players in the molecular cascades underlying both types of reproduction. In this review, we briefly explain the life cycle and reproduction strategies of different geophytes and what is known about the physiological aspects related to these processes. Subsequently, an in-depth overview is provided of the molecular and genetic pathways driving these processes. In the evolution of plants, the PEBP gene family has expanded, followed by neo- and subfunctionalization. Careful characterization revealed that differential expression and differential protein complex formation provide the members of this gene family with unique functions, enabling them to mediate the crosstalk between the two reproductive events in geophytes in response to environmental and endogenous cues. Taking all these studies into account, we propose to regard the PEBPs as conductors of geophyte reproductive development.
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Fusaro, Adriana, Amanda Mangeon, Ricardo Magrani Junqueira, Carla Andréa Benício Rocha, Tatiana Cardoso Coutinho, Rogério Margis, and Gilberto Sachetto-Martins. "Classification, expression pattern and comparative analysis of sugarcane expressed sequences tags (ESTs) encoding glycine-rich proteins (GRPs)." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 263–73. http://dx.doi.org/10.1590/s1415-47572001000100035.
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Since the isolation of the first glycine-rich proteins (GRPs) in plants a wealth of new GRPs have been identified. The highly specific but diverse expression pattern of grp genes, taken together with the distinct sub-cellular localization of some GRP groups, clearly indicate that these proteins are involved in several independent physiological processes. Notwithstanding the absence of a clear definition of the role of GRPs in plant cells, studies conducted with these proteins have provided new and interesting insights into the molecular biology and cell biology of plants. Complexly regulated promoters and distinct mechanisms for the regulation of gene expression have been demonstrated and new protein targeting pathways, as well as the exportation of GRPs from different cell types have been discovered. These data show that GRPs can be useful as markers and/or models to understand distinct aspects of plant biology. In this paper, the structural and functional features of these proteins in sugarcane (Saccharum officinarum L.) are summarized. Since this is the first description of GRPs in sugarcane, special emphasis has been given to the expression pattern of these GRP genes by studying their abundance and prevalence in the different cDNA-libraries of the Sugarcane Expressed Sequence Tag (SUCEST) project . The comparison of sugarcane GRPs with GRPs from other species is also discussed.
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Jing, Ju-Li, Ting Zhang, Ya-Zhong Wang, and Yan He. "Advances Towards How Meiotic Recombination Is Initiated: A Comparative View and Perspectives for Plant Meiosis Research." International Journal of Molecular Sciences 20, no. 19 (September 23, 2019): 4718. http://dx.doi.org/10.3390/ijms20194718.
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Meiosis is an essential cell-division process for ensuring genetic diversity across generations. Meiotic recombination ensures the accuracy of genetic interchange between homolous chromosomes and segregation of parental alleles. Programmed DNA double-strand breaks (DSBs), catalyzed by the evolutionarily conserved topoisomerase VIA (a subunit of the archaeal type II DNA topoisomerase)-like enzyme Spo11 and several other factors, is a distinctive feature of meiotic recombination initiation. The meiotic DSB formation and its regulatory mechanisms are similar among species, but certain aspects are distinct. In this review, we introduced the cumulative knowledge of the plant proteins crucial for meiotic DSB formation and technical advances in DSB detection. We also summarized the genome-wide DSB hotspot profiles for different model organisms. Moreover, we highlighted the classical views and recent advances in our knowledge of the regulatory mechanisms that ensure the fidelity of DSB formation, such as multifaceted kinase-mediated phosphorylation and the consequent high-dimensional changes in chromosome structure. We provided an overview of recent findings concerning DSB formation, distribution and regulation, all of which will help us to determine whether meiotic DSB formation is evolutionarily conserved or varies between plants and other organisms.
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Ahmar, Sunny, Rafaqat Ali Gill, Ki-Hong Jung, Aroosha Faheem, Muhammad Uzair Qasim, Mustansar Mubeen, and Weijun Zhou. "Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook." International Journal of Molecular Sciences 21, no. 7 (April 8, 2020): 2590. http://dx.doi.org/10.3390/ijms21072590.
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In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.
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Yeh, Kuo-Chen, Melicent C. Peck, and Sharon R. Long. "Luteolin and GroESL Modulate In Vitro Activity of NodD." Journal of Bacteriology 184, no. 2 (January 15, 2002): 525–30. http://dx.doi.org/10.1128/jb.184.2.525-530.2002.
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ABSTRACT In the early stages of symbiosis between the soil bacterium Sinorhizobium meliloti and its leguminous host plant, alfalfa, bacterial nodulation (nod) genes are controlled by NodD1, NodD2, and NodD3, members of the LysR family of transcriptional regulators, in response to flavonoid and other inducers released by alfalfa. To gain an understanding of the biochemical aspects of this action, epitope-tagged recombinant NodD1 and NodD3 were overexpressed in Escherichia coli. The DNA binding properties of the purified recombinant NodD proteins were indistinguishable from those of NodD isolated from S. meliloti. In addition, the E. coli GroEL chaperonin copurified with the recombinant NodD proteins. In this study, we showed that NodD proteins are in vitro substrates of the GroESL chaperonin system and that their DNA binding activity is modulated by GroESL. This confirmed the earlier genetic implication that the GroESL chaperonin system is essential for the function of these regulators. Increased DNA binding activity by NodD1 in the presence of luteolin confirmed that NodD1 is involved in recognizing the plant signal during the early stages of symbiosis.
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D’Amelia, Vincenzo, Teresa Docimo, Christoph Crocoll, and Maria Manuela Rigano. "Specialized Metabolites and Valuable Molecules in Crop and Medicinal Plants: The Evolution of Their Use and Strategies for Their Production." Genes 12, no. 6 (June 18, 2021): 936. http://dx.doi.org/10.3390/genes12060936.
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Plants naturally produce a terrific diversity of molecules, which we exploit for promoting our overall well-being. Plants are also green factories. Indeed, they may be exploited to biosynthesize bioactive molecules, proteins, carbohydrates and biopolymers for sustainable and large-scale production. These molecules are easily converted into commodities such as pharmaceuticals, antioxidants, food, feed and biofuels for multiple industrial processes. Novel plant biotechnological, genetics and metabolic insights ensure and increase the applicability of plant-derived compounds in several industrial sectors. In particular, synergy between disciplines, including apparently distant ones such as plant physiology, pharmacology, ‘omics sciences, bioinformatics and nanotechnology paves the path to novel applications of the so-called molecular farming. We present an overview of the novel studies recently published regarding these issues in the hope to have brought out all the interesting aspects of these published studies.
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McDermott, Mark, Michael J. O. Wakelam, and Andrew J. Morris. "Phospholipase D." Biochemistry and Cell Biology 82, no. 1 (February 1, 2004): 225–53. http://dx.doi.org/10.1139/o03-079.
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Phospholipase D catalyses the hydrolysis of the phosphodiester bond of glycerophospholipids to generate phosphatidic acid and a free headgroup. Phospholipase D activities have been detected in simple to complex organisms from viruses and bacteria to yeast, plants, and mammals. Although enzymes with broader selectivity are found in some of the lower organisms, the plant, yeast, and mammalian enzymes are selective for phosphatidylcholine. The two mammalian phospholipase D isoforms are regulated by protein kinases and GTP binding proteins of the ADP-ribosylation and Rho families. Mammalian and yeast phospholipases D are also potently stimulated by phosphatidylinositol 4,5-bisphosphate. This review discusses the identification, characterization, structure, and regulation of phospholipase D. Genetic and pharmacological approaches implicate phospholipase D in a diverse range of cellular processes that include receptor signaling, control of intracellular membrane transport, and reorganization of the actin cytoskeleton. Most ideas about phospholipase D function consider that the phosphatidic acid product is an intracellular lipid messenger. Candidate targets for phospholipase-D-generated phosphatidic acid include phosphatidylinositol 4-phosphate 5-kinases and the raf protein kinase. Phosphatidic acid can also be converted to two other lipid mediators, diacylglycerol and lyso phosphatidic acid. Coordinated activation of these phospholipase-D-dependent pathways likely accounts for the pleitropic roles for these enzymes in many aspects of cell regulation.Key words: phospholipase D, phosphatidic acid, GTP-binding proteins, membrane transport, cytoskeletal regulation.
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Demidchik, Vadim, Frans Maathuis, and Olga Voitsekhovskaja. "Unravelling the plant signalling machinery: an update on the cellular and genetic basis of plant signal transduction." Functional Plant Biology 45, no. 2 (2018): 1. http://dx.doi.org/10.1071/fp17085.
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Plant signalling is a set of phenomena that serves the transduction of external and internal signals into physiological responses such as modification of enzyme activity, cytoskeleton structure or gene expression. It operates at the level of cell compartments, whole cells, tissues, organs or even plant communities. To achieve this, plants have evolved a network of signalling proteins including plasma membrane receptors and ion transporters, cascades of kinases and other enzymes as well as several second messengers such as cytosolic calcium (Ca2+), reactive oxygen/nitrogen species (ROS/RNS), cyclic nucleotides (cAMP and cGMP) and others. Overall, these systems recognise and decode environmental signals and co-ordinate ontogeny programs. This paper summarises recent progress in the field of plant signalling, which was a major theme of the 4th International Symposium on Plant Signalling and Behaviour, 2016, in Saint Petersburg, Russia. Several novel hypotheses and concepts were proposed during this meeting. First, the concept of ROS-Ca2+ hubs has found further evidence and acceptance. This concept is based on reciprocal activation of NADPH oxidases by cytosolic Ca2+ on the one hand, and Ca2+-permeable channels that are activated by NADPH-produced ROS. ROS-Ca2+ hubs enhance the intensity and duration of originally weak Ca2+ and ROS signals. Hubs are directly involved in ROS- and Ca2+-mediated physiological reactions, such as stress response, growth, programmed cell death, autophagy and long-distance signalling. Second, recent findings have widened the list of cyclic nucleotide-regulated processes and strengthened the biochemical basis of cyclic nucleotide biochemistry by exploring cyclase activities of new receptors such as the Phytosulfokine Receptor 1, the pathogen peptide 1 receptor (atPepR1), the brassinosteroid BRI1 receptor and the cell wall-associated kinase like 10. cGMP and cAMP signalling has demonstrated strong link to Ca2+ signalling, via cyclic nucleotide-gated Ca2+-permeable ion channels (CNGCs), and to ROS and RNS via their nitrosylated forms. Third, a novel role for cytosolic K+ as a regulator of plant autophagy and programmed cell death has emerged. The cell death-associated proteases and endonucleases were demonstrated to be activated by a decrease of cytosolic K+ via ROS-induced stimulation of the plasma membrane K+ efflux channel GORK. Importantly, the origin of ROS for induction of autophagy and cell death varies in different tissues and comprises several pools, including NADPH oxidases, peroxidases, photosynthetic and respiratory electron-transporting chains and peroxisomal enzymes. The peroxisome pool is the ‘latest’ addition to established cellular ROS-producing machineries and is dependent on the state and abundance of catalase in this compartment. Finally, new aspects of phytohormone signalling, such as regulation of root hydraulic pressure by abscisic acid and rate of mitosis by cytokinins, as well as localising cytokinin receptors in endoplasmic reticulum, are reported. Other observations suggest that melatonin is a hormone-like substance in plants, because it targets Ca2+, ROS and RNS.
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Srivastava, Rajat, and Rahul Kumar. "The expanding roles of APETALA2/Ethylene Responsive Factors and their potential applications in crop improvement." Briefings in Functional Genomics 18, no. 4 (February 20, 2019): 240–54. http://dx.doi.org/10.1093/bfgp/elz001.
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AbstractUnderstanding the molecular basis of the gene-regulatory networks underlying agronomic traits or plant responses to abiotic/biotic stresses is very important for crop improvement. In this context, transcription factors, which either singularly or in conjugation directly control the expression of many target genes, are suitable candidates for improving agronomic traits via genetic engineering. In this regard, members of one of the largest class of plant-specific APETALA2/Ethylene Response Factor (AP2/ERF) superfamily, which is implicated in various aspects of development and plant stress adaptation responses, are considered high-value targets for crop improvement. Besides their long-known regulatory roles in mediating plant responses to abiotic stresses such as drought and submergence, the novel roles of AP2/ERFs during fruit ripening or secondary metabolites production have also recently emerged. The astounding functional plasticity of AP2/ERF members is considered to be achieved by their interplay with other regulatory networks and signalling pathways. In this review, we have integrated the recently accumulated evidence from functional genomics studies and described their newly emerged functions in plants. The key structural features of AP2/ERF proteins and the modes of their action are briefly summarized. The importance of AP2/ERFs in plant development and stress responses and a summary of the event of their successful applications in crop improvement programs are also provided. Altogether, we envisage that the synthesized information presented in this review will be useful to design effective strategies for improving agronomic traits in crop plants.
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Rafinska, Katarzyna, Krzysztof Zienkiewicz, and Elzbieta Bednarska. "Pollen Transcriptome and Proteome: Molecular and Functional Analysis." Advances in Cell Biology 2, no. 1 (January 1, 2010): 29–57. http://dx.doi.org/10.2478/v10052-010-0003-9.
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SummaryThe pollen grain, because of its unique structural organization, is an extremely useful experimental model in cytological, molecular as well as in genetic studies. Due to the ease of pollen grain isolation, their sorting as well as simple extraction of their DNA, RNA and proteins, male gametophyte cells of angiosperms are presently one of the most intensively studied plant cells. Important and rapid progress in the development of experimental tools for genome exploration caused a significant increase in the number of reports concerning different aspects of gene expression during microsporogenesis and microgametogenesis in angiosperm plants. In this review we present the current knowledge of the pollen transcriptome and proteome during different stages of male gametophyte development, especially in Arabidopsis thaliana. Most of the results presented here were obtained in experiments carried out using microarrays, which were designed on the basis of the known sequence of the Arabidopsis genome.
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Bassal, Hussein, Othmane Merah, Aqeel M. Ali, Akram Hijazi, and Fawaz El Omar. "Psophocarpus tetragonolobus: An Underused Species with Multiple Potential Uses." Plants 9, no. 12 (December 8, 2020): 1730. http://dx.doi.org/10.3390/plants9121730.
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Natural products, particularly those extracted from plants, have been used as therapy for different diseases for thousands of years. The first written records on the plants used in natural medicine, referred to as “medicinal plants”, go back to about 2600 BC. A thorough and complete understanding of medicinal plants encompasses a multiplex of overlapping and integrated sciences such as botany, pharmacognosy, chemistry, enzymology and genetics. Psophocarpus tetragonolobus, a member of Fabaceae family also called winged bean, is a perennial herbaceous plant characterized by its tuberous roots and its winged pod twinning and a perennial legume rich in proteins, oils, vitamins and carbohydrates. Besides nutrients, winged bean also contains bioactive compounds that have therapeutic activities like anti-oxidant, anti-inflammatory, antinociceptive, antibacterial, antifungal, antiproliferative and cytotoxic activity, a few of which already been reported. This plant can also be used as a medicinal plant for future benefits. With this concept in mind, the present review is designed to shed the light on the interests in the various phytochemicals and pharmacological pharmacognostical aspects of Psophocarpus tetragonolobus.
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Vain, Thomas, Sara Raggi, Noel Ferro, Deepak Kumar Barange, Martin Kieffer, Qian Ma, Siamsa M. Doyle, et al. "Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development." Proceedings of the National Academy of Sciences 116, no. 13 (March 8, 2019): 6463–72. http://dx.doi.org/10.1073/pnas.1809037116.
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Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCFTIR1/AFBfunctionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.
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Bertrand, Annick, and Yves Castonguay. "Plant adaptations to overwintering stresses and implications of climate change." Canadian Journal of Botany 81, no. 12 (December 1, 2003): 1145–52. http://dx.doi.org/10.1139/b03-129.
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Winter survival is a complex trait that does not solely rely on the plant's ability to withstand the direct effects of extreme cold temperatures. During long overwintering periods, plants are exposed to multiple abiotic (ice encasement, frost heave, desiccation, anoxia) and biotic (snow mould and other psychrophylic pathogens) stresses. Tolerance to these various stresses is based in part on shared adaptive traits and, consequently, cross-adaptation to environmental stresses is a key aspect of plant adaptation to cold. Increasing evidence of multiple functions for stress-induced proteins in overwintering plants confirms the need for a global approach in the analysis of adaptive mechanisms. From that perspective, the valorization of rapidly increasing knowledge on the molecular and genetic basis of plant and microbe adaptations to cold will demand multidisciplinary collaborations. Climate change will also need to be taken into account to identify the adaptive traits that will be required for agricultural and forest plants to survive winter in the future. More studies at the global and regional scales will be needed to assess the potential impact of climate warming on plant adaptation to winter and their interactions with low-temperature pathogens.Key words: cold adaptation, psychrophylic microorganisms, climate change, fall dormancy, low-temperature plantmicrobe interactions, cold-adaptation genomics.
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Feng, Mingfeng, Ruixiang Cheng, Minglong Chen, Rong Guo, Luyao Li, Zhike Feng, Jianyan Wu, et al. "Rescue of tomato spotted wilt virus entirely from complementary DNA clones." Proceedings of the National Academy of Sciences 117, no. 2 (December 26, 2019): 1181–90. http://dx.doi.org/10.1073/pnas.1910787117.
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Negative-stranded/ambisense RNA viruses (NSVs) include not only dangerous pathogens of medical importance but also serious plant pathogens of agronomic importance. Tomato spotted wilt virus (TSWV) is one of the most important plant NSVs, infecting more than 1,000 plant species, and poses major threats to global food security. The segmented negative-stranded/ambisense RNA genomes of TSWV, however, have been a major obstacle to molecular genetic manipulation. In this study, we report the complete recovery of infectious TSWV entirely from complementary DNA (cDNA) clones. First, a replication- and transcription-competent minigenome replication system was established based on 35S-driven constructs of the S(−)-genomic (g) or S(+)-antigenomic (ag) RNA template, flanked by the 5′ hammerhead and 3′ ribozyme sequence of hepatitis delta virus, a nucleocapsid (N) protein gene and codon-optimized viral RNA-dependent RNA polymerase (RdRp) gene. Next, a movement-competent minigenome replication system was developed based on M(−)-gRNA, which was able to complement cell-to-cell and systemic movement of reconstituted ribonucleoprotein complexes (RNPs) of S RNA replicon. Finally, infectious TSWV and derivatives carrying eGFP reporters were rescued in planta via simultaneous expression of full-length cDNA constructs coding for S(+)-agRNA, M(−)-gRNA, and L(+)-agRNA in which the glycoprotein gene sequence of M(−)-gRNA was optimized. Viral rescue occurred with the addition of various RNAi suppressors including P19, HcPro, and γb, but TSWV NSs interfered with the rescue of genomic RNA. This reverse genetics system for TSWV now allows detailed molecular genetic analysis of all aspects of viral infection cycle and pathogenicity.
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Dong, Chen, Huigang Hu, and Jianghui Xie. "Genome-wide analysis of the DNA-binding with one zinc finger (Dof) transcription factor family in bananas." Genome 59, no. 12 (December 2016): 1085–100. http://dx.doi.org/10.1139/gen-2016-0081.
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DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. In this study, we report a genome-wide search for Musa acuminata Dof (MaDof) genes and their expression profiles at different developmental stages and in response to various abiotic stresses. In addition, a complete overview of the Dof gene family in bananas is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences. Based on the genome-wide analysis, we identified 74 full-length protein-coding MaDof genes unevenly distributed on 11 chromosomes. Phylogenetic analysis with Dof members from diverse plant species showed that MaDof genes can be classified into four subgroups (StDof I, II, III, and IV). The detailed genomic information of the MaDof gene homologs in the present study provides opportunities for functional analyses to unravel the exact role of the genes in plant growth and development.
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Yao, Ting Shan, Xiao Feng Zhu, Jin Hee Jung, and Yuan Hu Xuan. "Qa-SNARE Protein SYP22 Negatively Regulates Brassinosteroid Signaling in the Dark." Acta Biologica Cracoviensia s. Botanica 57, no. 2 (December 1, 2015): 79–88. http://dx.doi.org/10.1515/abcsb-2015-0021.
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Abstract Soluble N-ethyl-maleimide sensitive factor attachment adaptor protein receptor (SNARE) domain-containing proteins were mainly involved in vesicle-associated membrane fusion. Genetic screening has revealed the function of SNARE in different aspects of plant biology. Among them, Synthaxin-22 (SYP22) a Qa-SNARE has been reported to have a pleiotropic function in plant development including regulation of leaf waving, shoot gravitropism and flowering time. In this study, we identified a new role of SYP22 in regulation of brassinosteroid (BR) signaling, especially in the dark. SYP22 interacts with BR receptor, brassinosteroid insensitive 1 (BRI1), and overexpression of SYP22 enhanced a weak BRI1 mutant bri1-5 phenotype. syp22 mutant exhibits short hypocotyl and it is sensitive to exogenously treated BR while slightly insensitive to BR-biosynthesis inhibitor propiconazole (PCZ) in the dark. Expression levels of BR signaling maker genes ACS5, SAUR15 and IAA19 were slightly higher, while BR6OX2, a BR biosynthesis marker gene, was lower in syp22 compared to the wild-type. In addition, syp22 was sensitive to 2,4-D, a synthetic auxin, in the dark. In conclusion, SYP22 is involved in BR- and auxin-mediated hypocotyl growth inhibition in the dark, which might be via interaction with BR and auxin key regulators to alter their internalization in Arabidopsis.
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Paul, Jinny A., Michelle T. Barati, Michael Cooper, and Michael H. Perlin. "Physical and Genetic Interaction between Ammonium Transporters and the Signaling Protein Rho1 in the Plant Pathogen Ustilago maydis." Eukaryotic Cell 13, no. 10 (August 15, 2014): 1328–36. http://dx.doi.org/10.1128/ec.00150-14.
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ABSTRACTDimorphic transitions between yeast-like and filamentous forms occur in many fungi and are often associated with pathogenesis. One of the cues for such a dimorphic switch is the availability of nutrients. Under conditions of nitrogen limitation, fungal cells (such as those ofSaccharomyces cerevisiaeandUstilago maydis) switch from budding to pseudohyphal or filamentous growth. Ammonium transporters (AMTs) are responsible for uptake and, in some cases, for sensing the availability of ammonium, a preferred nitrogen source. Homodimer and/or heterodimer formation may be required for regulating the activity of the AMTs. To investigate the potential interactions of Ump1 and Ump2, the AMTs of the maize pathogenU. maydis, we first used the split-ubiquitin system, followed by a modified split-YFP (yellow fluorescent protein) system, to validate the interactionsin vivo. This analysis showed the formation of homo- and hetero-oligomers by Ump1 and Ump2. We also demonstrated the interaction of the high-affinity ammonium transporter, Ump2, with the Rho1 GTPase, a central protein in signaling, with roles in controlling polarized growth. This is the first demonstration in eukaryotes of the physical interactionin vivoof an ammonium transporter with the signaling protein Rho1. Moreover, the Ump proteins interact with Rho1 during the growth of cells in low ammonium concentrations, a condition required for the expression of the Umps. Based on these results and the genetic evidence for the interaction of Ump2 with both Rho1 and Rac1, another small GTPase, we propose a model for the role of these interactions in controlling filamentation, a fundamental aspect of development and pathogenesis inU. maydis.
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Collings, David A., and Geoffrey O. Wasteneys. "Actin microfilament and microtubule distribution patterns in the expanding root of Arabidopsis thaliana." Canadian Journal of Botany 83, no. 6 (June 1, 2005): 579–90. http://dx.doi.org/10.1139/b05-032.
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Determination of the precise role(s) of actin microfilaments in the control of cell shape and elongation in the root tips of the model genetic system Arabidopsis thaliana (L.) Heynh is frustrated by inadequate microscopy imaging techniques. In this paper, we documented both microfilaments and microtubules in the root tips of Arabidopsis by double immunofluorescence labelling and computer-generated reconstruction of confocal image series. Our procedure, which complements the use of recently developed fluorescent reporter proteins, revealed hitherto undescribed aspects of the Arabidopsis microfilament cytoskeleton that may provide important clues about mechanisms behind cell elongation. We found that preservation of extensive arrays of transverse cortical microfilaments depends on unperturbed microtubule organization. Compared with ordinary epidermal cells, cells situated in the trichoblast or hair-forming cell files were comparatively devoid of endoplasmic microfilaments when in the distal elongation zone, well before hair formation begins. Computer-aided reconstructions also revealed that the nonexpanding end walls of cells in the distal elongation zone have radially oriented microtubules and randomly arranged microfilaments. In dividing cells, microfilaments became more prominent in the cell cortex, and subtle differences between microtubule and microfilament organization were seen within the phragmoplast. These observations will form the basis of understanding the roles of the cytoskeleton in controlling elongation in root tissues. In light of the many Arabidopsis mutants with altered root morphology, our methods offer a reliable approach to assess the function of cytoskeletal proteins and signalling systems in root morphogenesis.Key words: actin microfilaments, Arabidopsis thaliana, distal elongation zone, microtubules, phragmoplast, roots.
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Gianinazzi-Pearson, Vivienne, and Silvio Gianinazzi. "Cellular and genetical aspects of interactions between hosts and fungal symbionts in mycorrhizae." Genome 31, no. 1 (January 1, 1989): 336–41. http://dx.doi.org/10.1139/g89-051.
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Contact between appropriate mycorrhizal symbionts initiates a cascade of events that leads to modifications in the behaviour of both organisms at cell and tissue levels and the establishment of a functionally compatible relationship. Mechanisms that regulate the outcome of the symbiosis must involve a complex interchange of signals that triggers changes in genome expression in either symbiont. Analysis of symbiosis-specific proteins, interspecific grafting experiments, and the obtention of fungal and plant variants with phenotypes deficient for mycorrhiza formation provide information to help unravel the molecular and genetical puzzles of fungus–host interactions in mycorrhizal associations.Key words: mycorrhiza, cellular relations, host mutants, fungal strains, interspecific grafting.
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Glasner, J. D., M. Marquez-Villavicencio, H. S. Kim, C. E. Jahn, B. Ma, B. S. Biehl, A. I. Rissman, et al. "Niche-Specificity and the Variable Fraction of the Pectobacterium Pan-Genome." Molecular Plant-Microbe Interactions® 21, no. 12 (December 2008): 1549–60. http://dx.doi.org/10.1094/mpmi-21-12-1549.
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We compare genome sequences of three closely related soft-rot pathogens that vary in host range and geographical distribution to identify genetic differences that could account for lifestyle differences. The isolates compared, Pectobacterium atrosepticum SCRI1043, P. carotovorum WPP14, and P. brasiliensis 1692, represent diverse lineages of the genus. P. carotovorum and P. brasiliensis genome contigs, generated by 454 pyrosequencing ordered by reference to the previously published complete circular chromosome of P. atrosepticum genome and each other, account for 96% of the predicted genome size. Orthologous proteins encoded by P. carotovorum and P. brasiliensis are approximately 95% identical to each other and 92% identical to P. atrosepticum. Multiple alignment using Mauve identified a core genome of 3.9 Mb conserved among these Pectobacterium spp. Each core genome is interrupted at many points by species-specific insertions or deletions (indels) that account for approximately 0.9 to 1.1 Mb. We demonstrate that the presence of a hrpK-like type III secretion system-dependent effector protein in P. carotovorum and P. brasiliensis and its absence from P. atrosepticum is insufficient to explain variability in their response to infection in a plant. Additional genes that vary among these species include those encoding peptide toxin production, enzyme production, secretion proteins, and antibiotic production, as well as differences in more general aspects of gene regulation and metabolism that may be relevant to pathogenicity.
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Rusnak, Frank, and Pamela Mertz. "Calcineurin: Form and Function." Physiological Reviews 80, no. 4 (January 10, 2000): 1483–521. http://dx.doi.org/10.1152/physrev.2000.80.4.1483.
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Calcineurin is a eukaryotic Ca2+- and calmodulin-dependent serine/threonine protein phosphatase. It is a heterodimeric protein consisting of a catalytic subunit calcineurin A, which contains an active site dinuclear metal center, and a tightly associated, myristoylated, Ca2+-binding subunit, calcineurin B. The primary sequence of both subunits and heterodimeric quaternary structure is highly conserved from yeast to mammals. As a serine/threonine protein phosphatase, calcineurin participates in a number of cellular processes and Ca2+-dependent signal transduction pathways. Calcineurin is potently inhibited by immunosuppressant drugs, cyclosporin A and FK506, in the presence of their respective cytoplasmic immunophilin proteins, cyclophilin and FK506-binding protein. Many studies have used these immunosuppressant drugs and/or modern genetic techniques to disrupt calcineurin in model organisms such as yeast, filamentous fungi, plants, vertebrates, and mammals to explore its biological function. Recent advances regarding calcineurin structure include the determination of its three-dimensional structure. In addition, biochemical and spectroscopic studies are beginning to unravel aspects of the mechanism of phosphate ester hydrolysis including the importance of the dinuclear metal ion cofactor and metal ion redox chemistry, studies which may lead to new calcineurin inhibitors. This review provides a comprehensive examination of the biological roles of calcineurin and reviews aspects related to its structure and catalytic mechanism.
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Tiika, Richard John, Jia Wei, Rui Ma, Hongshan Yang, Guangxin Cui, Huirong Duan, and Yanjun Ma. "Identification and expression analysis of the WRKY gene family during different developmental stages in Lycium ruthenicum Murr. fruit." PeerJ 8 (October 28, 2020): e10207. http://dx.doi.org/10.7717/peerj.10207.
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Background The WRKY gene family, one of the major transcription factor families in plants, plays crucial regulatory roles in physiological and biological developmental processes, and the adaptation of plants to the environment. However, the systematic study of WRKY structure, expression profiling, and regulatory functions has not been extensively reported in Lycium ruthenicum, although these aspects have been comprehensively studied in most plant species. Methods In this study, the WRKY genes were identified from a L. ruthenicum transcriptome database by using bioinformatics. The identification, phylogenetic analysis, zinc-finger structures, and conserved motif prediction were extensively explored. Moreover, the expression levels of 23 selected genes with fragments per kilobase of exons per million mapped reads (FPKM) >5 were assayed during different fruit developmental stages with real-time quantitative polymerase chain reaction (RT-qPCR). Results A total of 73 putative WRKY proteins in the L. ruthenicum transcriptome database were identified and examined. Forty-four proteins with the WRKY domain were identified and divided into three major groups with several subgroups, in accordance with those in other plant species. All 44 LrWRKY proteins contained one or two conserved WRKY domains and a zinc-finger structure. Conserved motif prediction revealed conservation of the WRKY DNA-binding domain in L. ruthenicum proteins. The selected LrWRKY genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five LrWRKYs (-20, -21, -28, -30, and -31) were expressed remarkably throughout the fruit developmental stages. Discussion Our results reveal the characteristics of the LrWRKY gene family, thus laying a foundation for further functional analysis of the WRKY family in L. ruthenicum.
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Theodoulou, Frederica L., and Ian D. Kerr. "ABC transporter research: going strong 40 years on." Biochemical Society Transactions 43, no. 5 (October 1, 2015): 1033–40. http://dx.doi.org/10.1042/bst20150139.
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In most organisms, ABC transporters constitute one of the largest families of membrane proteins. In humans, their functions are diverse and underpin numerous key physiological processes, as well as being causative factors in a number of clinically relevant pathologies. Advances in our understanding of these diseases have come about through combinations of genetic and protein biochemical investigations of these transporters and the power of in vitro and in vivo investigations is helping to develop genotype–phenotype understanding. However, the importance of ABC transporter research goes far beyond human biology; microbial ABC transporters are of great interest in terms of understanding virulence and drug resistance and industrial biotechnology researchers are exploring the potential of prokaryotic ABC exporters to increase the capacity of synthetic biology systems. Plant ABC transporters play important roles in transport of hormones, xenobiotics, metals and secondary metabolites, pathogen responses and numerous aspects of development, all of which are important in the global food security area. For 3 days in Chester, this Biochemical Society Focused Meeting brought together researchers with diverse experimental approaches and with different fundamental questions, all of which are linked by the commonality of ABC transporters.
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Shi, Hui, Mohan Lyu, Yiwen Luo, Shoucheng Liu, Yue Li, Hang He, Ning Wei, Xing Wang Deng, and Shangwei Zhong. "Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors." Proceedings of the National Academy of Sciences 115, no. 25 (May 29, 2018): 6482–87. http://dx.doi.org/10.1073/pnas.1803861115.
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Three families of transcription factors have been reported to play key roles in light control of Arabidopsis seedling morphogenesis. Among them, bHLH protein PIFs and plant-specific protein EIN3/EIN3-LIKE 1 (EIN3/EIL1) accumulate in the dark to maintain skotomorphogenesis. On the other hand, HY5 and HY5 HOMOLOG (HYH), two related bZIP proteins, are stabilized in light and promote photomorphogenic development. To systemically investigate the transcriptional regulation of light-controlled seedling morphogenesis, we generated HY5ox/pifQein3eil1, which contained mutations of EIN3/EIL1 and four PIF genes (pifQein3eil1) and overexpression of HY5. Our results show that dark-grown HY5ox/pifQein3eil1 seedlings display a photomorphogenesis highly similar to that of wild-type seedlings grown in continuous light, with remarkably enhanced photomorphogenic phenotypes compared with the pifQ mutants. Consistent with the genetic evidence, transcriptome analysis indicated that PIFs, EIN3/EIL1, and HY5 are dominant transcription factors in collectively mediating a wide range of light-caused genome-wide transcriptional changes. Moreover, PIFs and EIN3/EIL1 independently control the expression of light-regulated genes such as HLS1 to cooperatively regulate apical hook formation, hypocotyl elongation, and cotyledon opening and expansion. This study illustrates a comprehensive regulatory network of transcription activities that correspond to specific morphological aspects in seedling skotomorphogenesis and photomorphogenesis.
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González-Grandío, Eduardo, Alice Pajoro, José M. Franco-Zorrilla, Carlos Tarancón, Richard G. H. Immink, and Pilar Cubas. "Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds." Proceedings of the National Academy of Sciences 114, no. 2 (December 27, 2016): E245—E254. http://dx.doi.org/10.1073/pnas.1613199114.
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Shoot-branching patterns determine key aspects of plant life and are important targets for crop breeding. However, we are still largely ignorant of the genetic networks controlling locally the most important decision during branch development: whether the axillary bud, or branch primordium, grows out to give a lateral shoot or remains dormant. Here we show that, inside the buds, the TEOSINTE BRANCHED1, CYCLOIDEA, PCF (TCP) transcription factor BRANCHED1 (BRC1) binds to and positively regulates the transcription of three related Homeodomain leucine zipper protein (HD-ZIP)-encoding genes: HOMEOBOX PROTEIN 21 (HB21), HOMEOBOX PROTEIN 40 (HB40), and HOMEOBOX PROTEIN 53 (HB53). These three genes, together with BRC1, enhance 9-CIS-EPOXICAROTENOID DIOXIGENASE 3 (NCED3) expression, lead to abscisic acid accumulation, and trigger hormone response, thus causing suppression of bud development. This TCP/HD-ZIP genetic module seems to be conserved in dicot and monocotyledonous species to prevent branching under light-limiting conditions.
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Zhang, Aidong, Yihua Liu, Chunyan Yu, Linli Huang, Minjie Wu, Junyu Wu, and Yinbo Gan. "Zinc Finger Protein 1 (ZFP1) Is Involved in Trichome Initiation in Arabidopsis thaliana." Agriculture 10, no. 12 (December 18, 2020): 645. http://dx.doi.org/10.3390/agriculture10120645.
Full textAbstract:
Arabidopsis trichome is specialized structure that develops from epidermal cells, and is an excellent model system for studying various aspects of plant cell development and cell differentiation. Our previous studies have shown that C2H2 zinc finger protein family genes, including GIS, GIS2, GIS3, ZFP5, ZFP6 and ZFP8, play an important role in controlling trichome initiation in Arabidopsis. Here, our novel results showed a C2H2 zinc finger protein, ZFP1, which also plays an important role in trichome initiation in Arabidopsis. ZFP1 over-expression lines display significantly increased trichome number on cauline leaves, lateral branches and main stems in comparison with wild type plants. ZFP1 RNAi lines and loss-of-function mutants showed the opposite phenotype. Furthermore, our study also found that ZFP1 mediates the regulation of trichome initiation by cytokinin signaling. The molecular and genetic analyses reveal that ZFP1 acts upstream of key trichome initiation factors, GL3 and TRY.
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Schmidt, Anja. "Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation." Genes 11, no. 3 (March 20, 2020): 329. http://dx.doi.org/10.3390/genes11030329.
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In higher plants, sexual and asexual reproduction through seeds (apomixis) have evolved as alternative strategies. As apomixis leads to the formation of clonal offspring, its great potential for agricultural applications has long been recognized. However, the genetic basis and the molecular control underlying apomixis and its evolutionary origin are to date not fully understood. Both in sexual and apomictic plants, reproduction is tightly controlled by versatile mechanisms regulating gene expression, translation, and protein abundance and activity. Increasing evidence suggests that interrelated pathways including epigenetic regulation, cell-cycle control, hormonal pathways, and signal transduction processes are relevant for apomixis. Additional molecular mechanisms are being identified that involve the activity of DNA- and RNA-binding proteins, such as RNA helicases which are increasingly recognized as important regulators of reproduction. Together with other factors including non-coding RNAs, their association with ribosomes is likely to be relevant for the formation and specification of the apomictic reproductive lineage. Subsequent seed formation appears to involve an interplay of transcriptional activation and repression of developmental programs by epigenetic regulatory mechanisms. In this review, insights into the genetic basis and molecular control of apomixis are presented, also taking into account potential relations to environmental stress, and considering aspects of evolution.
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Price, G. Dean, Dieter Sültemeyer, Barbara Klughammer, Martha Ludwig, and Murray R. Badger. "The functioning of the CO2 concentrating mechanism in several cyanobacterial strains: a review of general physiological characteristics, genes, proteins, and recent advances." Canadian Journal of Botany 76, no. 6 (June 1, 1998): 973–1002. http://dx.doi.org/10.1139/b98-081.
Full textAbstract:
Cyanobacteria (blue-green algae) possess an environmental adaptation for survival at low CO2 concentrations. The adaptation is known as a CO2 concentrating mechanism (CCM), and it functions to actively transport and accumulate inorganic carbon ( and CO2; Ci) within the cell and then uses this Ci pool to provide elevated CO2 concentrations around the primary CO2-fixing enzyme, ribulose bisphosphate carboxylase-oxygenase (Rubisco). It appears that the site of CO2 elevation is within a unique microcompartment known as the carboxysome, which is a proteinaceous polyhedral body that contains most, if not all, of the Rubisco within the cell. This review covers comparative aspects of physiology, genetics, and proteins involved in the cyanobacterial CCM with particular focus on recent advances. This review highlights information on three strains of unicellular cyanobacteria, namely Synechocystis PCC6803 (freshwater strain; for which a full genome database is now available), Synechococcus PCC7002 (coastal marine strain) and Synechococcus PCC7942 (freshwater strain). Genes that may be involved in the CCM, directly or indirectly, are summarized in tabular form. For Synechocystis PCC6803, the number of genes related to CCM activity is now in excess of 50; however, 19 of these components have the potential to code for several distinct type-1, NADH dehydrogenase complexes.Key words: cyanobacteria, CO2 concentrating mechanism, carboxysomes, genes, photosynthesis, transporters.
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Alejska, M., A. Kurzyńska-Kokorniak, M. Broda, R. Kierzek, and M. Figlerowicz. "How RNA viruses exchange their genetic material." Acta Biochimica Polonica 48, no. 2 (June 30, 2001): 391–407. http://dx.doi.org/10.18388/abp.2001_3924.
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One of the most unusual features of RNA viruses is their enormous genetic variability. Among the different processes contributing to the continuous generation of new viral variants RNA recombination is of special importance. This process has been observed for human, animal, plant and bacterial viruses. The collected data reveal a great susceptibility of RNA viruses to recombination. They also indicate that genetic RNA recombination (especially the nonhomologous one) is a major factor responsible for the emergence of new viral strains or species. Although the formation and accumulation of viral recombinants was observed in numerous RNA viruses, the molecular basis of this phenomenon was studied in only a few viral species. Among them, brome mosaic virus (BMV), a model (+)RNA virus offers the best opportunities to investigate various aspects of genetic RNA recombination in vivo. Unlike any other, the BMV-based system enables homologous and nonhomologous recombination studies at both the protein and RNA levels. As a consequence, BMV is the virus for which the structural requirements for genetic RNA recombination have been most precisely established. Nevertheless, the previously proposed model of genetic recombination in BMV still had one weakness: it could not really explain the role of RNA structure in nonhomologous recombination. Recent discoveries concerning the latter problem give us a chance to fill this gap. That is why in this review we present and thoroughly discuss all results concerning nonhomologous recombination in BMV that have been obtained until now.
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Bleecker, Anthony B., Jeffrey J. Esch, Anne E. Hall, Fernando I. Rodríguez, and Brad M. Binder. "The ethylene–receptor family from Arabidopsis : structure and function." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 353, no. 1374 (September 29, 1998): 1405–12. http://dx.doi.org/10.1098/rstb.1998.0295.
Full textAbstract:
The gaseous hormone ethylene regulates many aspects of plant growth and development. Ethylene is perceived by a family of high–affinity receptors typified by the ETR1 protein from Arabidopsis . The ETR1 gene codes for a protein, which contains a hydrophobic N–terminal domain that binds ethylene and a C–terminal domain that is related in sequence to histidine kinase–response regulator two–component signal transducers found in bacteria. A structural model for the ethylene binding domain is presented in which a Cu(I) ion is coordinated within membrane–spanning α–helices of the hydrophobic domain. It is proposed that binding of ethylene to the transition metal would induce a conformational change in the sensor domain that would be propagated to the cytoplasmic transmitter domain of the protein. A total of four additional genes that are related in sequence to ETR1 have been identified in Arabidopsis . Specific missense mutations in any one of the five genes leads to ethylene insensitivity in planta . Models for signal transduction that can account for the genetic dominance of these mutations are discussed.
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Fernandes, Ticiana, Flávia Silva-Sousa, Fábio Pereira, Teresa Rito, Pedro Soares, Ricardo Franco-Duarte, and Maria João Sousa. "Biotechnological Importance of Torulaspora delbrueckii: From the Obscurity to the Spotlight." Journal of Fungi 7, no. 9 (August 30, 2021): 712. http://dx.doi.org/10.3390/jof7090712.
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Torulaspora delbrueckii has attracted interest in recent years, especially due to its biotechnological potential, arising from its flavor- and aroma-enhancing properties when used in wine, beer or bread dough fermentation, as well as from its remarkable resistance to osmotic and freezing stresses. In the present review, genomic, biochemical, and phenotypic features of T. delbrueckii are described, comparing them with other species, particularly with the biotechnologically well-established yeast, Saccharomyces cerevisiae. We conclude about the aspects that make this yeast a promising biotechnological model to be exploited in a wide range of industries, particularly in wine and bakery. A phylogenetic analysis was also performed, using the core proteome of T. delbrueckii, to compare the number of homologous proteins relative to the most closely related species, understanding the phylogenetic placement of this species with robust support. Lastly, the genetic tools available for T. delbrueckii improvement are discussed, focusing on adaptive laboratorial evolution and its potential.
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Onishi, Masayuki, and John R. Pringle. "Robust Transgene Expression from Bicistronic mRNA in the Green Alga Chlamydomonas reinhardtii." G3 Genes|Genomes|Genetics 6, no. 12 (December 1, 2016): 4115–25. http://dx.doi.org/10.1534/g3.116.033035.
Full textAbstract:
Abstract The unicellular green alga Chlamydomonas reinhardtii is a model organism that provides an opportunity to understand the evolution and functional biology of the lineage that includes the land plants, as well as aspects of the fundamental core biology conserved throughout the eukaryotic phylogeny. Although many tools are available to facilitate genetic, molecular biological, biochemical, and cell biological studies in Chlamydomonas, expression of unselected transgenes of interest (GOIs) has been challenging. In most methods used previously, the GOI and a selectable marker are expressed from two separate mRNAs, so that their concomitant expression is not guaranteed. In this study, we developed constructs that allow expression of an upstream GOI and downstream selectable marker from a single bicistronic mRNA. Although this approach in other systems has typically required a translation-enhancing element such as an internal ribosome entry site for the downstream marker, we found that a short stretch of unstructured junction sequence was sufficient to obtain adequate expression of the downstream gene, presumably through post-termination reinitiation. With this system, we obtained robust expression of both endogenous and heterologous GOIs, including fluorescent proteins and tagged fusion proteins, in the vast majority of transformants, thus eliminating the need for tedious secondary screening for GOI-expressing transformants. This improved efficiency should greatly facilitate a variety of genetic and cell-biological studies in Chlamydomonas and also enable new applications such as expression-based screens and large-scale production of foreign proteins.
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Trevaskis, Ben, Gillian Colebatch, Guilhem Desbrosses, Maren Wandrey, Stefanie Wienkoop, Gerhard Saalbach, and Michael Udvardi. "Differentiation of Plant Cells During Symbiotic Nitrogen Fixation." Comparative and Functional Genomics 3, no. 2 (2002): 151–57. http://dx.doi.org/10.1002/cfg.155.
Full textAbstract:
Nitrogen-fixing symbioses between legumes and bacteria of the family Rhizobiaceae involve differentiation of both plant and bacterial cells. Differentiation of plant root cells is required to build an organ, the nodule, which can feed and accommodate a large population of bacteria under conditions conducive to nitrogen fixation. An efficient vascular system is built to connect the nodule to the root, which delivers sugars and other nutrients to the nodule and removes the products of nitrogen fixation for use in the rest of the plant. Cells in the outer cortex differentiate to form a barrier to oxygen diffusion into nodules, which helps to produce the micro-aerobic environment necessary for bacterial nitrogenase activity. Cells of the central, infected zone of nodules undergo multiple rounds of endoreduplication, which may be necessary for colonisation by rhizobia and may enable enlargement and greater metabolic activity of these cells. Infected cells of the nodule contain rhizobia within a unique plant membrane called the peribacteroid or symbiosome membrane, which separates the bacteria from the host cell cytoplasm and mediates nutrient and signal exchanges between the partners. Rhizobia also undergo differentiation during nodule development. Not surprisingly, perhaps, differentiation of each partner is dependent upon interactions with the other. High-throughput methods to assay gene transcripts, proteins, and metabolites are now being used to explore further the different aspects of plant and bacterial differentiation. In this review, we highlight recent advances in our understanding of plant cell differentiation during nodulation that have been made, at least in part, using high-throughput methods.
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Pereira-Netto, Adaucto Bellarmino. "Genes involved in brassinosteroids's metabolism and signal transduction pathways." Brazilian Archives of Biology and Technology 50, no. 4 (July 2007): 605–18. http://dx.doi.org/10.1590/s1516-89132007000400006.
Full textAbstract:
Brassinosteroids (BRs) are plant steroids essential for the normal growth and development, which carry an oxygen moiety at C-3 and additional ones at one or more of the C-2, C-6, C-22 and C-23 carbon atoms. In the past few years, application of molecular genetics allowed significant progress on the understanding of the BRs biosynthetic pathway regulation and on the identification of several components of their signal transduction pathway, as well. Search in eletronic databases show dozens of records for brassinosteroid-related genes for the last twelve months, demonstrating the big efforts being carried out in this field. This review highlights the recent advances on the characterization of genes and mutations that are helping to unravel the molecular mechanisms involved in the BRs synthesis/metabolism, perception and response, with especial emphasis on their role in plant cell elongation. Aspects of the involvement of BRs on the regulation of cell cycle-controlling proteins are discussed as well.
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Zhang, Wei, Jun Huang, and David E. Cook. "Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae." PLOS Genetics 17, no. 2 (February 3, 2021): e1009376. http://dx.doi.org/10.1371/journal.pgen.1009376.
Full textAbstract:
Transcriptional dynamic in response to environmental and developmental cues are fundamental to biology, yet many mechanistic aspects are poorly understood. One such example is fungal plant pathogens, which use secreted proteins and small molecules, termed effectors, to suppress host immunity and promote colonization. Effectors are highly expressedin plantabut remain transcriptionally repressedex planta, but our mechanistic understanding of these transcriptional dynamics remains limited. We tested the hypothesis that repressive histone modification at H3-Lys27 underlies transcriptional silencingex planta, and that exchange for an active chemical modification contributes to transcription ofin plantainduced genes. Using genetics, chromatin immunoprecipitation and sequencing and RNA-sequencing, we determined that H3K27me3 provides significant local transcriptional repression. We detail how regions that lose H3K27me3 gain H3K27ac, and these changes are associated with increased transcription. Importantly, we observed that manyin plantainduced genes were marked by H3K27me3 during axenic growth, and detail how altered H3K27 modification influences transcription. ChIP-qPCR duringin plantagrowth suggests that H3K27 modifications are generally stable, but can undergo dynamics at specific genomic locations. Our results support the hypothesis that dynamic histone modifications at H3K27 contributes to fungal genome regulation and specifically contributes to regulation of genes important during host infection.