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Miklós Müller - One of the best experts on this subject based on the ideXlab platform.
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Primary structure and Eubacterial relationships of the pyruvate:Ferredoxin oxidoreductase of the amitochondriate eukaryoteTrichomonas vaginalis
Journal of Molecular Evolution, 1995Co-Authors: Ivan Hrdý, Miklós MüllerAbstract:In the eukaryotic unicellular organism Trichomonas vaginalis a key step of energy metabolism, the oxidative decarboxylation of pyruvate with the formation of acetyl-CoA, is catalyzed by the iron-sulfur protein pyruvate:ferredoxin oxidoreductase (PFO) and not by the almost-ubiquitous pyruvate dehydrogenase multienzyme complex. This enzyme is localized in the hydrogenosome, an organelle bounded by a double membrane. PFO and its closely related homolog, pyruvate: flavodoxin oxidoreductase, are enzymes found in a number of archaebacteria and Eubacteria. The presence of these enzymes in eukaryotes is restricted, however, to a few amitochondriate groups. To gain more insight into the evolutionary relationships of T. vaginalis PFO we determined the primary structure of its two genes ( pfoA and pfoB ). The deduced amino acid sequences showed 95% positional identity. Motifs implicated in related enzymes in liganding the Fe-S centers and thiamine pyrophosphate were well conserved. The T. vaginalis PFOs were found to be homologous to Eubacterial pyruvate: flavodoxin oxidoreductases and showed about 40% amino acid identity to these enzymes over their entire length. Lack of Eubacterial PFO sequences precluded a comparison. pfoA and pfoB revealed a greater distance from related enzymes of Archaebacteria. The conceptual translation of the nucleotide sequences predicted an amino-terminal pentapeptide not present in the mature protein. This processed leader sequence was similar to but shorter than leader sequences noted in other hydrogenosomal proteins. These sequences are assumed to be involved in organellar targeting and import. The results underscore the unusual characteristics of T. vaginalis metabolism and of their hydrogenosomes. They also suggest that in its energy metabolism T. vaginalis is closer to Eubacteria than archaebacteria.
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Primary structure and Eubacterial relationships of the pyruvate:Ferredoxin oxidoreductase of the amitochondriate eukaryote Trichomonas vaginalis
Journal of Molecular Evolution, 1995Co-Authors: Ivan Hrdý, Miklós MüllerAbstract:In the eukaryotic unicellular organism Trichomonas vaginalis a key step of energy metabolism, the oxidative decarboxylation of pyruvate with the formation of acetyl-CoA, is catalyzed by the iron-sulfur protein pyruvate:ferredoxin oxidoreductase (PFO) and not by the almost-ubiquitous pyruvate dehydrogenase multienzyme complex. This enzyme is localized in the hydrogenosome, an organelle bounded by a double membrane. PFO and its closely related homolog, pyruvate: flavodoxin oxidoreductase, are enzymes found in a number of archaebacteria and Eubacteria. The presence of these enzymes in eukaryotes is restricted, however, to a few amitochondriate groups. To gain more insight into the evolutionary relationships of T. vaginalis PFO we determined the primary structure of its two genes ( pfoA and pfoB ). The deduced amino acid sequences showed 95% positional identity. Motifs implicated in related enzymes in liganding the Fe-S centers and thiamine pyrophosphate were well conserved. The T. vaginalis PFOs were found to be homologous to Eubacterial pyruvate: flavodoxin oxidoreductases and showed about 40% amino acid identity to these enzymes over their entire length. Lack of Eubacterial PFO sequences precluded a comparison. pfoA and pfoB revealed a greater distance from related enzymes of Archaebacteria. The conceptual translation of the nucleotide sequences predicted an amino-terminal pentapeptide not present in the mature protein. This processed leader sequence was similar to but shorter than leader sequences noted in other hydrogenosomal proteins. These sequences are assumed to be involved in organellar targeting and import. The results underscore the unusual characteristics of T. vaginalis metabolism and of their hydrogenosomes. They also suggest that in its energy metabolism T. vaginalis is closer to Eubacteria than archaebacteria.
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A glyceraldehyde-3-phosphate dehydrogenase with Eubacterial features in the amitochondriate eukaryote, Trichomonas vaginalis
Journal of Molecular Evolution, 1993Co-Authors: Anton Markoš, Anya Miretsky, Miklós MüllerAbstract:Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), localized in the cytosol of Trichomonas vaginalis , was partially purified. The enzyme is specific for NAD^+ and is similar in most of its catalytic properties to glycolytic GAPDHs from other organisms. Its sensitivity to koningic acid is similar to levels observed in GAPDHs from Eubacteria and two orders of magnitude lower than those observed for eukaryotic GAPDHs. The complete amino acid sequence of T. vaginalis GAPDH was derived from the N-terminal sequence of the purified protein and the deduced sequence of a cDNA clone. It showed great similarity to other Eubacterial and eukaryotic GAPDH sequences. The sequence of the S-loop displayed a Eubacterial signature. The overall sequence was more similar to Eubacterial sequences than to cytosolic and glycosomal eukaryotic sequences. In phylogenetic trees obtained with distance matrix and parsimony methods T. vaginalis GAPDH clustered with its Eubacterial homologs. GAPDHs of other amitochondriate protists, belonging to early branches of the eukaryotic lineage ( Giardia lamblia and Entamoeba histolytica —Smith M.W. and Doolittle R.F., unpublished data in GenBank), showed typical eukaryotic signatures and clustered with other eukaryotic sequences, indicating that T. vaginalis GAPDH occupies an anomalous position, possibly due to horizontal gene transfer from a eubacterium.
Yogesh S. Shouche - One of the best experts on this subject based on the ideXlab platform.
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functional Eubacteria species along with trans domain gut inhabitants favour dysgenic diversity in oxalate stone disease
Scientific Reports, 2018Co-Authors: Mangesh V. Suryavanshi, Shrikant S. Bhute, Rahul P. Gune, Yogesh S. ShoucheAbstract:Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (Eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to Eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy Eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing Eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to Eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.
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Functional Eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease
Scientific reports, 2018Co-Authors: Mangesh V. Suryavanshi, Shrikant S. Bhute, Rahul P. Gune, Yogesh S. ShoucheAbstract:Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (Eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to Eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy Eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p
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Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes.
Frontiers in microbiology, 2017Co-Authors: Shrikant S. Bhute, Mangesh V. Suryavanshi, Suyog M. Joshi, Chittaranjan S. Yajnik, Yogesh S. Shouche, Saroj S. GhaskadbiAbstract:Diabetes in India has distinct genetic, nutritional, developmental and socio-economic aspects; owing to the fact that changes in gut microbiota are associated with diabetes, we employed semiconductor-based sequencing to characterize gut microbiota of diabetic subjects from this region. We suggest consolidated dysbiosis of Eubacterial, archaeal and eukaryotic components in the gut microbiota of newly diagnosed (New-DMs) and long-standing diabetic subjects (Known-DMs) compared to healthy subjects (NGTs). Increased abundance of phylum Firmicutes (p = 0.010) and Operational Taxonomic Units (OTUs) of Lactobacillus (p < 0.01) were observed in Known-DMs subjects along with the concomitant graded decrease in butyrate-producing bacterial families like Ruminococcaceae and Lachnospiraceae. Eukaryotes and fungi were the least affected components in these subjects but archaea, except Methanobrevibacter were significantly decreased in them. The two dominant archaea viz. Methanobrevibacater and Methanosphaera followed opposite trends in abundance from NGTs to Known-DMs subjects. There was a substantial reduction in Eubacteria, with a noticeable decrease in Bacteroidetes phylum (p = 0.098) and an increased abundance of fungi in New-DMs subjects. Likewise, opportunistic fungal pathogens such as Aspergillus, Candida were found to be enriched in New-DMs subjects. Analysis of Eubacterial interaction network revealed disease-state specific patterns of ecological interactions, suggesting the distinct behavior of individual components of Eubacteria in response to the disease. PERMANOVA test indicated that the Eubacterial component was associated with diabetes-related risk factors like high triglyceride (p = 0.05), low HDL (p = 0.03), and waist-to-hip ratio (p = 0.02). Metagenomic imputation of Eubacteria depict deficiencies of various essential functions such as carbohydrate metabolism, amino acid metabolism etc. in New-DMs subjects. Results presented here shows that in diabetes, microbial dysbiosis may not be just limited to Eubacteria. Due to the inter-linked metabolic interactions among the Eubacteria, archaea and eukarya in the gut, it may extend into other two domains leading to trans-domain dysbiosis in microbiota. Our results thus contribute to and expand the identification of biomarkers in diabetes.
Aymen S Yassin - One of the best experts on this subject based on the ideXlab platform.
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insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of Eubacterial initiation factor 1
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Md Emdadul Haque, Partha P Datta, Nilesh K Banavali, Kimberly Elmore, Aymen S Yassin, Linda L Spremulli, Rajendra K AgrawalAbstract:Mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or ATP generation). Translation initiation in mammalian mitochondria requires two initiation factors, IF2mt and IF3mt, instead of the three that are present in Eubacteria. The mammalian IF2mt possesses a unique 37 amino acid insertion domain, which is known to be important for the formation of the translation initiation complex. We have obtained a three-dimensional cryoelectron microscopic map of the mammalian IF2mt in complex with initiator and the Eubacterial ribosome. We find that the 37 amino acid insertion domain interacts with the same binding site on the ribosome that would be occupied by the Eubacterial initiation factor IF1, which is absent in mitochondria. Our finding suggests that the insertion domain of IF2mt mimics the function of Eubacterial IF1, by blocking the ribosomal aminoacyl-tRNA binding site (A site) at the initiation step.
Adelbert Bacher - One of the best experts on this subject based on the ideXlab platform.
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evolution of vitamin b2 biosynthesis structural and functional similarity between pyrimidine deaminases of Eubacterial and plant origin
Journal of Biological Chemistry, 2004Co-Authors: Markus Fischer, Werner Romisch, Sabine Saller, Boris Illarionov, Gerald Richter, Felix Rohdich, Wolfgang Eisenreich, Adelbert BacherAbstract:Abstract The Arabidopsis thaliana open reading frame At4g20960 predicts a protein whose N-terminal part is similar to the Eubacterial 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5′-phosphate deaminase domain. A synthetic open reading frame specifying a pseudomature form of the plant enzyme directed the synthesis of a recombinant protein which was purified to apparent homogeneity and was shown by NMR spectroscopy to convert 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5′-phosphate into 5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5′-phosphate at a rate of 0.9 μmol mg–1 min–1. The substrate and product of the enzyme are both subject to spontaneous anomerization of the ribosyl side chain as shown by 13C NMR spectroscopy. The protein contains 1 eq of Zn2+/subunit. The deaminase activity could be assigned to the N-terminal section of the plant protein. The deaminase domains of plants and Eubacteria share a high degree of similarity, in contrast to deaminases from fungi. These data show that the riboflavin biosynthesis in plants proceeds by the same reaction steps as in Eubacteria, whereas fungi use a different pathway.
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biosynthesis of riboflavin an unusual riboflavin synthase of methanobacterium thermoautotrophicum
Journal of Bacteriology, 1997Co-Authors: Sabine Eberhardt, Susanne Korn, Friedrich Lottspeich, Adelbert BacherAbstract:Riboflavin synthase was purified by a factor of about 1,500 from cell extract of Methanobacterium thermoautotrophicum. The enzyme had a specific activity of about 2,700 nmol mg(-1) h(-1) at 65 degrees C, which is relatively low compared to those of riboflavin synthases of Eubacteria and yeast. Amino acid sequences obtained after proteolytic cleavage had no similarity with known riboflavin synthases. The gene coding for riboflavin synthase (designated ribC) was subsequently cloned by marker rescue with a ribC mutant of Escherichia coli. The ribC gene of M. thermoautotrophicum specifies a protein of 153 amino acid residues. The predicted amino acid sequence agrees with the information gleaned from Edman degradation of the isolated protein and shows 67% identity with the sequence predicted for the unannotated reading frame MJ1184 of Methanococcus jannaschii. The ribC gene is adjacent to a cluster of four genes with similarity to the genes cbiMNQO of Salmonella typhimurium, which form part of the cob operon (this operon contains most of the genes involved in the biosynthesis of vitamin B12). The amino acid sequence predicted by the ribC gene of M. thermoautotrophicum shows no similarity whatsoever to the sequences of riboflavin synthases of Eubacteria and yeast. Most notably, the M. thermoautotrophicum protein does not show the internal sequence homology characteristic of Eubacterial and yeast riboflavin synthases. The protein of M. thermoautotrophicum can be expressed efficiently in a recombinant E. coli strain. The specific activity of the purified, recombinant protein is 1,900 nmol mg(-1) h(-1) at 65 degrees C. In contrast to riboflavin synthases from Eubacteria and fungi, the methanobacterial enzyme has an absolute requirement for magnesium ions. The 5' phosphate of 6,7-dimethyl-8-ribityllumazine does not act as a substrate. The findings suggest that riboflavin synthase has evolved independently in Eubacteria and methanobacteria.
Mangesh V. Suryavanshi - One of the best experts on this subject based on the ideXlab platform.
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functional Eubacteria species along with trans domain gut inhabitants favour dysgenic diversity in oxalate stone disease
Scientific Reports, 2018Co-Authors: Mangesh V. Suryavanshi, Shrikant S. Bhute, Rahul P. Gune, Yogesh S. ShoucheAbstract:Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (Eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to Eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy Eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p < 0.001 & FDR = 0.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing Eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to Eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.
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Functional Eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease
Scientific reports, 2018Co-Authors: Mangesh V. Suryavanshi, Shrikant S. Bhute, Rahul P. Gune, Yogesh S. ShoucheAbstract:Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (Eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to Eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy Eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p
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Gut Microbial Diversity Assessment of Indian Type-2-Diabetics Reveals Alterations in Eubacteria, Archaea, and Eukaryotes.
Frontiers in microbiology, 2017Co-Authors: Shrikant S. Bhute, Mangesh V. Suryavanshi, Suyog M. Joshi, Chittaranjan S. Yajnik, Yogesh S. Shouche, Saroj S. GhaskadbiAbstract:Diabetes in India has distinct genetic, nutritional, developmental and socio-economic aspects; owing to the fact that changes in gut microbiota are associated with diabetes, we employed semiconductor-based sequencing to characterize gut microbiota of diabetic subjects from this region. We suggest consolidated dysbiosis of Eubacterial, archaeal and eukaryotic components in the gut microbiota of newly diagnosed (New-DMs) and long-standing diabetic subjects (Known-DMs) compared to healthy subjects (NGTs). Increased abundance of phylum Firmicutes (p = 0.010) and Operational Taxonomic Units (OTUs) of Lactobacillus (p < 0.01) were observed in Known-DMs subjects along with the concomitant graded decrease in butyrate-producing bacterial families like Ruminococcaceae and Lachnospiraceae. Eukaryotes and fungi were the least affected components in these subjects but archaea, except Methanobrevibacter were significantly decreased in them. The two dominant archaea viz. Methanobrevibacater and Methanosphaera followed opposite trends in abundance from NGTs to Known-DMs subjects. There was a substantial reduction in Eubacteria, with a noticeable decrease in Bacteroidetes phylum (p = 0.098) and an increased abundance of fungi in New-DMs subjects. Likewise, opportunistic fungal pathogens such as Aspergillus, Candida were found to be enriched in New-DMs subjects. Analysis of Eubacterial interaction network revealed disease-state specific patterns of ecological interactions, suggesting the distinct behavior of individual components of Eubacteria in response to the disease. PERMANOVA test indicated that the Eubacterial component was associated with diabetes-related risk factors like high triglyceride (p = 0.05), low HDL (p = 0.03), and waist-to-hip ratio (p = 0.02). Metagenomic imputation of Eubacteria depict deficiencies of various essential functions such as carbohydrate metabolism, amino acid metabolism etc. in New-DMs subjects. Results presented here shows that in diabetes, microbial dysbiosis may not be just limited to Eubacteria. Due to the inter-linked metabolic interactions among the Eubacteria, archaea and eukarya in the gut, it may extend into other two domains leading to trans-domain dysbiosis in microbiota. Our results thus contribute to and expand the identification of biomarkers in diabetes.