Journal articles: 'Choanoflagellida'

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THOMSEN, HELGE A., KURT R. BUCK, SUSAN L. COALE, DAVID L. GARRISON, and MARCIA M. GOWING. "Loricate choanoflagellates (Acanthoecidae, Choanoflagellida) from the Weddell Sea, Antarctica." Zoologica Scripta 19, no. 4 (October 1990): 367–87. http://dx.doi.org/10.1111/j.1463-6409.1990.tb00264.x.

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Espeland, Gyrid, and Jahn Throndsen. "Flagellates from Kilsfjorden, southern Norway, with description of two new species of Choanoflagellida." Sarsia 71, no. 3-4 (October 15, 1986): 209–26. http://dx.doi.org/10.1080/00364827.1986.10419691.

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BUCK, KURT R., HARVEY J. MARCHANT, HELGE A. THOMSEN, and DAVID L. GARRISON. "Kakoeca antarctica gen. et sp.n., a loricate choanoflagellate (Acanthoecidae, Choanoflagellida) from Antarctic sea ice with a unique protoplast suspensory membrane." Zoologica Scripta 19, no. 4 (October 1990): 389–94. http://dx.doi.org/10.1111/j.1463-6409.1990.tb00265.x.

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Lefranc, Marie, Aurélie Thénot, Cécile Lepère, and Didier Debroas. "Genetic Diversity of Small Eukaryotes in Lakes Differing by Their Trophic Status." Applied and Environmental Microbiology 71, no. 10 (October 2005): 5935–42. http://dx.doi.org/10.1128/aem.71.10.5935-5942.2005.

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ABSTRACT Small eukaryotes, cells with a diameter of less than 5 μm, are fundamental components of lacustrine planktonic systems. In this study, small-eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem.

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Zheng, Bao-Hai, Zhao-Jin Chen, Yu-Ying Li, Nicola Fohrer, Yun Zhang, Dong-Yu Wu, Xue-Yan Yan, and Bai-Lian Li. "Structural Characteristics and Driving Factors of the Planktonic Eukaryotic Community in the Danjiangkou Reservoir, China." Water 12, no. 12 (December 12, 2020): 3499. http://dx.doi.org/10.3390/w12123499.

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Planktonic eukaryotes are widespread in aquatic ecosystems, and the study of their community composition and driving factors is of great significance to protecting and maintaining the balance of these ecosystems. This study evaluates five typical ecological sites in the Danjiangkou Reservoir—the water source for the project. This was done to comprehensively understand the composition of Danjiangkou Reservoir planktonic eukaryotes, and ensure the ecological balance of the water source for the South-to-North Water Diversion Project. The diversity of the planktonic eukaryotes in surface water and the factors driving changes in their abundance are analyzed with an 18S ribosomal DNA sequencing approach. Monitoring shows that the Danjiangkou Reservoir has good water quality. The Danjiangkou Reservoir planktonic eukaryote community is mainly composed of 11 phyla, of which Cryptomonadales is dominant, accounting for an average percentage of 65.19% of the community (47.2–84.90%). LEFSe analysis shows significant differences among samples in the abundances of 13 phyla, 20 classes, 23 orders, 26 families, and 27 genera, and there are also significant differences in the diversity of planktonic eukaryotes at different temporal and spatial scales. Redundancy analysis (RDA) show that water temperature, DO, SD, TN, and Chla are significant factors that affect the composition of the planktonic eukaryote community. Spearman rank correlation analysis combined with taxonomic difference analysis shows that Kathablepharidae and Choanoflagellida are not sensitive to environmental or physicochemical factors and that the interannual variations in their abundance are not significant. Network analysis shows that Protalveolata, Basidiomycota, P1-31, Bicosoecida, and Ochrophyta represent important nodes in the single-factor network, while Chytridiomycota, P1-31, Cryptomycota, Ochrophyta, Ichthyosporea, Bicosoecida, Protalveolata, and physicochemical factors (ORP, TN, WT, DO, SD, NH3-N, and NO3-N) represent important nodes in the two-factor network.

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Zhang, Dapeng, Yanwei Xi, Maria L. Coccimiglio, Jan A. Mennigen, Michael G. Jonz, Marc Ekker, and Vance L. Trudeau. "Functional prediction and physiological characterization of a novel short trans-membrane protein 1 as a subunit of mitochondrial respiratory complexes." Physiological Genomics 44, no. 23 (December 1, 2012): 1133–40. http://dx.doi.org/10.1152/physiolgenomics.00079.2012.

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Mitochondrial respiration is mediated by a set of multisubunit assemblies of proteins that are embedded in the mitochondrial inner membranes. Respiratory complexes do not only contain central catalytic subunits essential for the bioenergetic transformation, but also many short trans-membrane subunits (sTMs) that are implicated in the proper assembly of complexes. Defects in sTMs have been discovered in some human neurodegenerative diseases. Here we identify a new subunit that we named Stmp1 and have characterized its function using both computational and experimental approaches. Stmp1 is a short trans-membrane protein, and sequence/structure analysis revealed that it shares common features like the small size, presence of a single or two TM region, and a COOH-terminal charged region, as many typical sTMs of respiratory complexes. In situ hybridization and RT-PCR assays showed that the Stmp1 expression is ubiquitous throughout zebrafish embryogenesis. In adults, Stmp1 expression was highest in the brain compared with muscle and liver. In zebrafish larvae (3–5 days postfertilization), antisense morpholino oligonucleotide-mediated knockdown of the Stmp1 gene (Stmp1-MO) resulted in a series of mild morphological defects, including abnormal shape of head and jaw and cardiac edema. Larvae injected with the Stmp1-MO had negligible responses to touch stimuli. By ventilation frequency analysis we found that Stmp1-MO-injected zebrafish displayed a severe dysfunction of ventilatory activities when exposed to hypoxic conditions, suggesting a defective mitochondrial activity induced by the loss of Stmp1. Phylogenetic profiling of known respiratory sTMs compared with Stmp1 revealed that all defined sTMs from four respiratory complexes have restricted or variable phyletic distribution, indicating that they are products of evolutionary innovations to fulfill lineage-related functional requirements for respiratory complexes. Thus, being present in animals, filasterea, choanoflagellida, amoebozoa, and plants, Stmp1 may have evolved to confer a new or complementary regulation of respiratory activities.

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Thomsen, Helge Abildhauge, David L. Garrison, and Carol Kosman. "Choanoflagellates (acanthoecidae, choanoflagellida) from the Weddell Sea, Antarctica, Taxonomy and community structure with particular emphasis on the ice biota; with preliminary remarks on choanoflagellates from Arctic sea ice (Northeast Water Polynya, Greenland)." Archiv für Protistenkunde 148, no. 1-2 (June 1997): 77–114. http://dx.doi.org/10.1016/s0003-9365(97)80038-3.

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IkÄvalko, Johanna, Helge Abildhauge Thomsen, and Marina Carstens. "A Preliminary Study of NE Greenland Shallow Meltwater Ponds with Particular Emphasis on Loricate and Scale-covered Forms (Choanoflagellida, Chrysophyceae sensu lato, Synurophyceae, Heliozoea), Including the Descriptions of Epipyxis thamnoides spnovand Pseudokephyrion poculiforme spnov(Chrysophyceae)." Archiv für Protistenkunde 147, no. 1 (May 1996): 29–42. http://dx.doi.org/10.1016/s0003-9365(96)80006-6.

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9

Lipps, Jere H., and James W. Valentine. "Late Neoproterozoic Metazoa: Weird, Wonderful and Ghostly." Paleontological Society Papers 10 (November 2004): 51–66. http://dx.doi.org/10.1017/s1089332600002333.

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The Late Neoproterozoic or Ediacaran biota contains a variety of enigmatic fossils of uncertain, but likely metazoan, affinities. The protistan group Choanoflagellata and Metazoa share a common ancestor predating the first fossils by perhaps 100's of millions of years. Sponge choanocytes closely resemble choanoflagellates, establishing a morphologic similarity as well. Fossils in the late Neoproterozoic may represent stem or early groups of cnidarians, while others resemble eumetazoans and bilaterians. These organisms occurred on all continents except Antarctica, and occupied four major habitats from prodeltaic to deep slope environments in each area. Their paleoecology was complex but similar to modern soft-bodied slope organisms. Ediacaran trophic structures were complex as well and included a wide variety of feeding types from detritovores, herbivores on microbial mats, filter-feeders, and predators. Ediacaran assemblages thus constitute the evolutionary and ecological precursors of later Phanerozoic and modern biotas.

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Thai Tran, Bai, and Binh Tran Thi Thanh. "The limits of subkingdom Protozoa in unicellular Eukarya." Journal of Science Natural Science 66, no. 4F (November 2021): 161–69. http://dx.doi.org/10.18173/2354-1059.2021-0079.

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According to the five-kingdom system, all unicellular eukaryotes are classified under the kingdom Protista, and multicellular eukaryotes contain only Animals, Plants, and Fungi. This classification is generally not accepted by zoologists. Many zoological textbooks still classify Animals into two large groups: Protozoa and Metazoa. However, the criterion for selecting Protozoa is the specific digestive system of heterotrophic nutrition for animals, thus, the range of Protozoa is often wide, includes many different, far related groups in unicellular eukaryotes. The entire eukaryotic phylogenetic tree (both unicellular and multicellular) built on molecular sequence comparisons of recent genetics indicates that only a few single-celled eukaryotic groups have phylogenetic relationship with the ancestor of multicellular eukaryotes in the animal kingdom. This situation forces a narrowing of the range of protozoan groups. According to principle (1) Kingdom taxa must include all groups of organisms that are monophyletic, i.e. have the same root in the phylogenetic tree of eukaryotes. This principle holds for all taxa above species. (2) Inheriting the traditional perception of considering Animals, Fungi and Plants (including unicellular and multicellular) as kingdom taxons. Protozoa includes 3 groups Choanoflagellata, Filasterea and Ichthyosporea. The article also updates the morphological, biological and taxonomic characteristics of these three groups.

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Alzugaray, María Eugenia, María Victoria Gavazzi, and Jorge Rafael Ronderos. "Calcium signalling in early divergence of Metazoa: mechanisms involved in the control of muscle-like cell contraction in Hydra plagiodesmica." Canadian Journal of Zoology 97, no. 9 (September 2019): 812–24. http://dx.doi.org/10.1139/cjz-2018-0295.

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Our laboratory has previously examined the effect of neuropeptides on the activity of the hypostome of the hydra Hydra plagiodesmica Dioni, 1968 (Cnidaria: Hydrozoa). These results showed that the hypostome, a structure extruded during feeding, responds to myoregulatory peptides and that this mechanism might be regulated by changes in the cytosolic levels of calcium (Ca2+). We analyse now the ways in which Ca2+ modulates hypostome activity during feeding. The use of calcium chelators confirms that Ca2+ is relevant in inducing hypostome extrusion. The assay of compounds that modulate the activity of Ca2+ channels in the endoplasmic reticulum suggests that, beyond the extracellular influx of calcium, intracellular sources of the ion are involved and might include both ryanodine receptors (RyR) and the inositol 1,4,5-trisphosphate receptor (IP3R). Bioinformatic searches based on sequences of RyR and IP3R of humans (Homo sapiens Linnaeus, 1758) show that IP3Rs are present in all groups analysed, including Fungi and Choanoflagellata. Although H. plagiodesmica responds to caffeine and ryanodine, which are known to modulate RyRs, this family of receptors seems not to be predicted in Cnidaria, suggesting that this phylum either lacks these kinds of channels or that they possess a different structure compared with those possessed by other Metazoa.

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Käse, Laura, Alexandra C. Kraberg, Katja Metfies, Stefan Neuhaus, Pim A. A. Sprong, Bernhard M. Fuchs, Maarten Boersma, and Karen H. Wiltshire. "Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea." Journal of Plankton Research 42, no. 3 (May 2020): 305–19. http://dx.doi.org/10.1093/plankt/fbaa017.

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Abstract The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations.

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Mylnikov, Alexander P., Denis V. Tikhonenkov, Sergey A. Karpov, and Claudia Wylezich. "Microscopical Studies on Ministeria vibrans Tong, 1997 (Filasterea) Highlight the Cytoskeletal Structure of the Common Ancestor of Filasterea, Metazoa and Choanoflagellata." Protist 170, no. 4 (August 2019): 385–96. http://dx.doi.org/10.1016/j.protis.2019.07.001.

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Huang, Weihong, Shuantong Li, Saisai Li, Hendrikus J. Laanbroek, and Qiufang Zhang. "Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian." Frontiers in Microbiology 14 (April 26, 2023). http://dx.doi.org/10.3389/fmicb.2023.1151768.

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The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.

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Akter, Salma, M. Shaminur Rahman, Hazrat Ali, Benjamin Minch, Kaniz Mehzabin, Md Moradul Siddique, Syed Md Galib, et al. "Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast." Scientific Reports 13, no. 1 (September 25, 2023). http://dx.doi.org/10.1038/s41598-023-43306-4.

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AbstractThe Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB’s eastern coast, viz., Saint Martin and Cox’s Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox’s Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox’s Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox’s Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.

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Ramond, Pierre, Raffaele Siano, Marc Sourisseau, and Ramiro Logares. "Assembly processes and functional diversity of marine protists and their rare biosphere." Environmental Microbiome 18, no. 1 (July 13, 2023). http://dx.doi.org/10.1186/s40793-023-00513-w.

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Abstract Background The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny and morpho-trophic traits of these protists, we also explore their functional potential. Results Taxonomic community composition remained stable along rank abundance curves. Conditionally rare taxa, driven by selection processes, and transiently rare taxa, with stochastic distributions, were evidenced along the rank abundance curves of all size-fractions. Specific taxa within the divisions Sagenista, Picozoa, Telonemia, and Choanoflagellida were rare across time and space. The distribution of traits along rank abundance curves outlined a high functional redundancy between rare and abundant protists. Nevertheless, trophic traits illustrated an interplay between the trophic groups of different size-fractions. Conclusions Our results suggest that rare and abundant protists are evolutionary closely related, most notably due to the high microdiversity found in the rare biosphere. We evidenced a succession of assembly processes and strategies of rarity along rank abundance curves that we hypothesize to be common to most microbiomes at the regional scale. Despite high functional redundancy in the rare protistan biosphere, permanently rare protists were evidenced, and they could play critical functions as bacterivores and decomposers from within the rare biosphere. Finally, changes in the composition of the rare protistan biosphere could be influenced by the trophic regime of aquatic ecosystems. Our work contributes to understanding the role of rare protists in microbiomes.

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Sheikh, Shaghayegh, Tomáš Pánek, Ondřej Gahura, Jiří Týč, Kristína Záhonová, Julius Lukeš, Marek Eliáš, and Hassan Hashimi. "A novel group of dynamin-related proteins shared by eukaryotes and giant viruses is able to remodel mitochondria from within the matrix." Molecular Biology and Evolution, June 6, 2023. http://dx.doi.org/10.1093/molbev/msad134.

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Abstract The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted, but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action is contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX’s unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.

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Junqueira Alves, Chrystian, Júlia Silva Ladeira, Theodore Hannah, Roberto J. Pedroso Dias, Priscila V. Zabala Capriles, Karla Yotoko, Hongyan Zou, and Roland H. Friedel. "Evolution and Diversity of Semaphorins and Plexins in Choanoflagellates." Genome Biology and Evolution 13, no. 3 (February 24, 2021). http://dx.doi.org/10.1093/gbe/evab035.

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Abstract Semaphorins and plexins are cell surface ligand/receptor proteins that affect cytoskeletal dynamics in metazoan cells. Interestingly, they are also present in Choanoflagellata, a class of unicellular heterotrophic flagellates that forms the phylogenetic sister group to Metazoa. Several members of choanoflagellates are capable of forming transient colonies, whereas others reside solitary inside exoskeletons; their molecular diversity is only beginning to emerge. Here, we surveyed genomics data from 22 choanoflagellate species and detected semaphorin/plexin pairs in 16 species. Choanoflagellate semaphorins (Sema-FN1) contain several domain features distinct from metazoan semaphorins, including an N-terminal Reeler domain that may facilitate dimer stabilization, an array of fibronectin type III domains, a variable serine/threonine-rich domain that is a potential site for O-linked glycosylation, and a SEA domain that can undergo autoproteolysis. In contrast, choanoflagellate plexins (Plexin-1) harbor a domain arrangement that is largely identical to metazoan plexins. Both Sema-FN1 and Plexin-1 also contain a short homologous motif near the C-terminus, likely associated with a shared function. Three-dimensional molecular models revealed a highly conserved structural architecture of choanoflagellate Plexin-1 as compared to metazoan plexins, including similar predicted conformational changes in a segment that is involved in the activation of the intracellular Ras-GAP domain. The absence of semaphorins and plexins in several choanoflagellate species did not appear to correlate with unicellular versus colonial lifestyle or ecological factors such as fresh versus salt water environment. Together, our findings support a conserved mechanism of semaphorin/plexin proteins in regulating cytoskeletal dynamics in unicellular and multicellular organisms.

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Petit, Daniel, Roxana Elin Teppa, and Anne Harduin-Lepers. "A phylogenetic view and functional annotation of the animal β1,3-glycosyltransferases of the GT31 CAZy family." Glycobiology, September 3, 2020. http://dx.doi.org/10.1093/glycob/cwaa086.

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Abstract The formation of β1,3-linkages on animal glycoconjugates is catalyzed by a subset of β1,3-glycosyltransferases grouped in the Carbohydrate-Active enZYmes family glycosyltransferase-31 (GT31). This family represents an extremely diverse set of β1,3-N-acetylglucosaminyltransferases [B3GNTs and Fringe β1,3-N-acetylglucosaminyltransferases], β1,3-N-acetylgalactosaminyltransferases (B3GALNTs), β1,3-galactosyltransferases [B3GALTs and core 1 β1,3-galactosyltransferases (C1GALTs)], β1,3-glucosyltransferase (B3GLCT) and β1,3-glucuronyl acid transferases (B3GLCATs or CHs). The mammalian enzymes were particularly well studied and shown to use a large variety of sugar donors and acceptor substrates leading to the formation of β1,3-linkages in various glycosylation pathways. In contrast, there are only a few studies related to other metazoan and lower vertebrates GT31 enzymes and the evolutionary relationships of these divergent sequences remain obscure. In this study, we used bioinformatics approaches to identify more than 920 of putative GT31 sequences in Metazoa, Fungi and Choanoflagellata revealing their deep ancestry. Sequence-based analysis shed light on conserved motifs and structural features that are signatures of all the GT31. We leverage pieces of evidence from gene structure, phylogenetic and sequence-based analyses to identify two major subgroups of GT31 named Fringe-related and B3GALT-related and demonstrate the existence of 10 orthologue groups in the Urmetazoa, the hypothetical last common ancestor of all animals. Finally, synteny and paralogy analysis unveiled the existence of 30 subfamilies in vertebrates, among which 5 are new and were named C1GALT2, C1GALT3, B3GALT8, B3GNT10 and B3GNT11. Altogether, these various approaches enabled us to propose the first comprehensive analysis of the metazoan GT31 disentangling their evolutionary relationships.

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Gomis-Rüth, F. Xavier, and Walter Stöcker. "Structural and evolutionary insights into astacin metallopeptidases." Frontiers in Molecular Biosciences 9 (January 4, 2023). http://dx.doi.org/10.3389/fmolb.2022.1080836.

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The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a “Met-turn” methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.

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Journal articles on the topic 'Choanoflagellida'

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