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186 results on '"Silberman, Jeffrey D."'

12. Between a Pod and a Hard Test: The Deep Evolution of Amoebae

Author

Kang, Seungho, Tice, Alexander K., Spiegel, Frederick W., Silberman, Jeffrey D., Pánek, Tomáš, Čepička, Ivan, Kostka, Martin, Kosakyan, Anush, Alcântara, Daniel M.C., Roger, Andrew J., Shadwick, Lora L., Smirnov, Alexey, Kudryavtsev, Alexander, Lahr, Daniel J.G., and Brown, Matthew W.

Published
2017
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31. The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic

Author

Silberman Jeffrey D, Baumgartner Manuela, Stechmann Alexandra, and Roger Andrew J

Subjects
Evolution, QH359-425
Abstract

Abstract Background Glycolysis and subsequent fermentation is the main energy source for many anaerobic organisms. The glycolytic pathway consists of ten enzymatic steps which appear to be universal amongst eukaryotes. However, it has been shown that the origins of these enzymes in specific eukaryote lineages can differ, and sometimes involve lateral gene transfer events. We have conducted an expressed sequence tag (EST) survey of the anaerobic flagellate Trimastix pyriformis to investigate the nature of the evolutionary origins of the glycolytic enzymes in this relatively unstudied organism. Results We have found genes in the Trimastix EST data that encode enzymes potentially catalyzing nine of the ten steps of the glycolytic conversion of glucose to pyruvate. Furthermore, we have found two different enzymes that in principle could catalyze the conversion of phosphoenol pyruvate (PEP) to pyruvate (or the reverse reaction) as part of the last step in glycolysis. Our phylogenetic analyses of all of these enzymes revealed at least four cases where the relationship of the Trimastix genes to homologs from other species is at odds with accepted organismal relationships. Although lateral gene transfer events likely account for these anomalies, with the data at hand we were not able to establish with confidence the bacterial donor lineage that gave rise to the respective Trimastix enzymes. Conclusion A number of the glycolytic enzymes of Trimastix have been transferred laterally from bacteria instead of being inherited from the last common eukaryotic ancestor. Thus, despite widespread conservation of the glycolytic biochemical pathway across eukaryote diversity, in a number of protist lineages the enzymatic components of the pathway have been replaced by lateral gene transfer from disparate evolutionary sources. It remains unclear if these replacements result from selectively advantageous properties of the introduced enzymes or if they are neutral outcomes of a gene transfer 'ratchet' from food or endosymbiotic organisms or a combination of both processes.

Published
2006
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35. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

Author

Leger, Michelle M., primary, Kolisko, Martin, additional, Kamikawa, Ryoma, additional, Stairs, Courtney W., additional, Kume, Keitaro, additional, Čepička, Ivan, additional, Silberman, Jeffrey D., additional, Andersson, Jan O., additional, Xu, Feifei, additional, Yabuki, Akinori, additional, Eme, Laura, additional, Zhang, Qianqian, additional, Takishita, Kiyotaka, additional, Inagaki, Yuji, additional, Simpson, Alastair G. B., additional, Hashimoto, Tetsuo, additional, and Roger, Andrew J., additional

Published
2017
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36. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

Author

Leger, Michelle M., Kolisko, Martin, Kamikawa, Ryoma, Stairs, Courtney W., Kume, Keitaro, Cepicka, Ivan, Silberman, Jeffrey D., Andersson, Jan O., Xu, Feifei, Yabuki, Akinori, Eme, Laura, Zhang, Qianqian, Takishita, Kiyotaka, Inagaki, Yuji, Simpson, Alastair G. B., Hashimoto, Tetsuo, Roger, Andrew J., Leger, Michelle M., Kolisko, Martin, Kamikawa, Ryoma, Stairs, Courtney W., Kume, Keitaro, Cepicka, Ivan, Silberman, Jeffrey D., Andersson, Jan O., Xu, Feifei, Yabuki, Akinori, Eme, Laura, Zhang, Qianqian, Takishita, Kiyotaka, Inagaki, Yuji, Simpson, Alastair G. B., Hashimoto, Tetsuo, and Roger, Andrew J.

Abstract

Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. Howewer, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed. Here, we present a large-scale comparative transcriptomic study of MROs across a major eukaryotic group, Metamonada, examining lineage-specific gain and loss of metabolic functions in the MROs of Trichomonas, Giardia, Spironucleus and their free-living relatives. Our analyses uncover a complex history of ATP production machinery in diplomonads such as Giardia, and their closest relative, Dysnectes; and a correlation between the glycine cleavage machinery and lifestyles. Our data further suggest the existence of a previously undescribed biochemical class of MRO that generates hydrogen but is incapable of ATP synthesis.

Published
2017
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39. Between a Pod and a Hard Test: The Deep Evolution of Amoebae.

Author

Seungho Kang, Tice, Alexander K., Spiegel, Frederick W., Silberman, Jeffrey D., Pánek, Tomáš, Čepička, Ivan, Kostka, Martin, Kosakyan, Anush, Alcântara, Daniel M. C., Roger, Andrew J., Shadwick, Lora L., Smirnov, Alexey, Kudryavtsev, Alexander, Lahr, Daniel J. G., and Brown, Matthew W.

Abstract

Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals and Fungi, as well as their protistan relatives, and the breviate and apusomonad flagellates. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. We present a robust phylogeny of Amoebozoa based on broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea, and Tevosa. This phylogeny refutes previous studies in major respects. Our results support the hypothesis that the last common ancestor of Amoebozoa was sexual and flagellated, it also may have had the ability to disperse propagules from a sporocarp-type fruiting body. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features. [ABSTRACT FROM AUTHOR]

Published
2017
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40. Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences

Author

Sergey Karpov, Sogin, Mitchell L., and Silberman, Jeffrey D.

Abstract

The cytoskeleton of Pseudobodo tremulans was investigated by transmission electron microscopy to resolve homologies among flagellar rootlets within the bicosoecids. The rootlet arrangement in P. tremulans is typical for bicosoecids. The basal body of anterior flagellum (bb2) has 2 rootlets: a dorsal rootlet of 2 microtubules and broad ventral rootlet (8+3 microtubules); the basal body of posterior flagellum (bb1) has two rootlets of 1 and of 2 microtubules respectively. There is a fibrillar rootlet that descends to the nucleus, and a set of fibrillar connectives around and between the basal bodies. The ventral rootlet is shown to originate from basal body 2, revealing that it is a homologue of rootlet 2 (not rootlet 3 as was accepted earlier for bicosoecids) of heteroconts. The fibrillar rootlets are not necessarily homologous in this order, as they may originate from either or both basal bodies. In general, all the flagellar microtubular rootlets of bicosoecids are homologues of those described from other stramenopiles. The bicosoecid rootlet 2 is much more developed than in colourless chrysophyceans. Rootlet 3 is often absent in bicosoecids while it is prominent in chrysophyceans as the ventral rootlet associated with feeding. Nuclear small subunit rRNA gene sequence (ssu rDNA) for 6 species of bicosoecids belonging to 2 families (Cafeteriidae and Siluaniidae) are partly congruent with the morphological characterstate data. In agreement with morphological data, the molecular trees robustly support a clade that includes Cafeteria and Symbiomonas (Cafeteriidae) and a clade composed of Adriamonas plus Siluania (Siluaniidae). The ssu rDNA trees also depict a paraphyletic Cafeteriidae (Pseudobodo and Cafeteria are not sister taxa) and a paraphyletic Siluaniidae (Adriamonas and Caecitellus are not sister taxa). The further investigation of the representatives of 2 other families (Pseudodendromonadidae and Bicosoecidae) by electron microscopy and molecular methods is required to clarify the phylogeny of bicosoecids.

Published
2001

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