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σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough
2015
BMC Genomics
Preserved Fulltext
The σ 54 subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown. Results: To characterize the σ 54 -dependent regulome of D. vulgaris Hildenborough, we identified EBP
doi:10.1186/s12864-015-2176-y
pmid:26555820
pmcid:PMC4641369
fatcat:ymsugevel5h43knwetqdcbiine
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... ng motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ 54 -dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ 54 regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ 54 -dependent regulators. Conclusions: The σ 54 -dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ 54 -dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.
PHOG: a database of supergenomes built from proteome complements
2006
BMC Evolutionary Biology
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Orthologs and paralogs are widely used terms in modern comparative genomics. Existing procedures for resolving orthologous/paralogous relationships are often based on manual revision of clusters of orthologous groups and/or lack any rigorous evolutionary base. We developed a completely automated procedure that creates clusters of orthologous groups at each node of the taxonomy tree (PHOGs--Phylogenetic Orthologous Groups). As a result of this procedure, a tree of orthologous groups was
doi:10.1186/1471-2148-6-52
pmid:16792803
pmcid:PMC1523204
fatcat:hmam2wqyxbbohe24vapwnmdx5i
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... Each cluster is a "supergene" and it is represented by an "ancestral" sequence obtained from the multiple alignment of orthologous and paralogous genes. The procedure has been applied to the taxonomy tree of organisms from all three domains of life. Protein complements from 50 bacterial, archaeal and eukaryotic species were used to create PHOGs at all tree nodes. 51367 PHOGs were obtained at the root node. The PHOG database demonstrates that it is possible to automatically process any number of sequenced genomes and to reconstruct orthologous and paralogous relationships between genomes using a rigorous evolutionary approach. This database can become a very useful tool in various areas of comparative genomics.
A dual functioning small RNA/Riboswitch controls the expression of the methionine biosynthesis regulator SahR in Desulfovibrio vulgaris Hildenborough
[article]
2019
bioRxiv
pre-print
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Riboswitches are cis-acting RNA regulatory elements that control expression of a downstream gene(s) by directly binding to a specific metabolite. ...
Here we report a S-adenosylmethionine (SAM)-I riboswitch in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) that plays an additional regulatory role as a trans small noncoding ...
Tomsic, J., McDaniel, B.A., Grundy, F.J. and Henkin, T.M. (2008) Natural 688 variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box 689 elements in Bacillus subtilis exhibit differential ...
doi:10.1101/803072
fatcat:csbp66bicjhpdgttab4zj2xmxm
Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria
2014
PLoS ONE
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Alternatively, SAH is first converted into S-ribosylhomocysteine by SAH nucleosidase Mtn and then utilized to homocysteine and 4,5-dihydroxypentan-2,3-dione by S-ribosylhomocysteine lyase LuxS. ...
Less abundant riboswitches responding to SAM and/or SAH molecules include SAM-III (or S MK -box) that controls metK in Lactobacillus spp. ...
doi:10.1371/journal.pone.0113714
pmid:25411846
pmcid:PMC4239095
fatcat:duknaddhujgcjfpl7kqfi7dqr4
Comparative genomics and evolution of transcriptional regulons in Proteobacteria
2016
Microbial Genomics
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In S. meliloti, hydroxyproline is imported into the cell via the ABC-family transporter HypMNPQ, which is predicted to be a part of HypR regulons only in three other genomes and thus was classified as ...
doi:10.1099/mgen.0.000061
pmid:28348857
pmcid:PMC5343134
fatcat:udolpyslqjesha6inmb5a4mlte
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria
2013
BMC Genomics
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GAS
40
319
150
180
S. gallolyticus UCN34
41
328
167
199
S. mutans UA159
41
317
147
173
S. suis 05ZYH33
43
366
145
173
S. mitis B6
35
305
148
174
S. pneumoniae TIGR4
42 ...
30
263
125
141
S. agalactiae 2603 V/R
38
340
159
186
S. uberis 0140 J
42
330
156
183
S. equi MGCS10565
42
334
143
167
S. dysgalactiae GGS_124
43
356
160
189
S. pyogenes M1 ...
doi:10.1186/1471-2164-14-94
pmid:23398941
pmcid:PMC3616900
fatcat:oppqiq4be5fr5pbotwayuv4uvm
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea
2007
Biology Direct
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Forterre P. and Gribaldo S. ...
i >20s j /(10-s j ) where s i and s j stand for the species-coverage of the species-rich and species-poor descendant nodes, respectively). 4 . ...
doi:10.1186/1745-6150-2-33
pmid:18042280
pmcid:PMC2222616
fatcat:axyzyqfj5fgo3k4juio5ex2eni
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome
2019
Frontiers in Microbiology
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or biochemical route(s) for β-alanine synthesis in these bacteria. ...
Transcriptional regulons for transcription factors (TFs) (BirA, BioQ, NrtR, NiaR, PdxR) and riboswicthes (TPP, FMN, THF, B12) as captured in the RegPrecise database (Novichkov et al., 2013) were used ...
doi:10.3389/fmicb.2019.01316
pmid:31275260
pmcid:PMC6593275
fatcat:kl7wvnot6bebhhbfpb5vxt4eti
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
2009
Nucleic Acids Research
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The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of highquality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed regulons include transcription factors, their cognate DNA
doi:10.1093/nar/gkp894
pmid:19884135
pmcid:PMC2808921
fatcat:yl7n7xaznbgzbodgkyf6j46ozu
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... fs and regulated genes/ operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular regulon across diverse taxonomic lineages; (ii) sets of regulons for a family of transcription factors; (iii) repertoire of regulons in a particular taxonomic group of species; (iv) regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes 11 500 candidate binding sites for 400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genomewide regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate regulon propagation to the closely related genomes.
Comparative genomics and evolution of regulons of the LacI-family transcription factors
2014
Frontiers in Microbiology
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Rodionov, Pavel S. Novichkov, and Mikhail S. Gelfand conceived and designed the research project. Dmitry A. Ravcheev, Dmitry A. Rodionov, and Mikhail S. Gelfand wrote the manuscript. Dmitry A. ...
Matvei S. Khoroshkin analyzed statistical properties of TF regulons. All authors read and approved the final manuscript. ...
doi:10.3389/fmicb.2014.00294
pmid:24966856
pmcid:PMC4052901
fatcat:2n4ngs7yh5elxerpccxdvabn3y
Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases
2021
Frontiers in Molecular Biosciences
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This motivates the strict choice of S and D parameters, which leads to compact MTA descriptions. ...
Alignment hits with value of F in the range between M and M-(1-M)/S and greater than a threshold value D were selected for MTA. ...
doi:10.3389/fmolb.2020.603740
pmid:33537340
pmcid:PMC7848230
fatcat:kcrro6owhfhnbbgz427q6adame
Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits
[article]
2018
bioRxiv
pre-print
Preserved Fulltext
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Positive scores indicate that the gene(s) 263 contained on that fragment lead to an increase in relative fitness, while negative values 264 mean the gene(s) on the fragment reduced relative fitness. ...
Scores near zero indicate no 265 fitness reduction or benefit for the gene(s) under the assayed condition. ...
doi:10.1101/387399
fatcat:fxiklifvj5c4fgczltbirwk4ge
High-throughput mapping of the phage resistance landscape in E. coli
[article]
2020
biorxiv/medrxiv
pre-print
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Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, et al. Systematic discovery of antiphage defense systems in the microbial pangenome. ...
Shin H, Lee J-H, Kim H, Choi Y, Heu S, Ryu S. Receptor diversity and host interaction of bacteriophages infecting Salmonella enterica serovar Typhimurium. ...
doi:10.1101/2020.02.15.951020
fatcat:btcaplvrwvgoxb5aztn2cpov4q
Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes
2010
Molecular biology and evolution
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Comparison of expression levels and breadth and evolutionary rates of intronless and intron-containing mammalian genes shows that intronless genes are expressed at lower levels, tend to be tissue specific, and evolve significantly faster than spliced genes. By contrast, monomorphic spliced genes that are not subject to detectable alternative splicing and polymorphic alternatively spliced genes show similar statistically indistinguishable patterns of expression and evolution. Alternative
doi:10.1093/molbev/msq086
pmid:20360214
pmcid:PMC2908711
fatcat:xqvus3laizdfjelcnuangkhh6u
more »
... is most common in ancient genes, whereas intronless genes appear to have relatively recent origins. These results imply tight coupling between different stages of gene expression, in particular, transcription, splicing, and nucleocytosolic transport of transcripts, and suggest that formation of intronless genes is an important route of evolution of novel tissue-specific functions in animals.
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria
2013
BMC Genomics
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14
predicted
RF01070
C
glnA
glutamine
13
known
RF01739
C
SAM-IV
S-adenosylmethionine
13
known
RF00634
C
SAM-SAH
S-adenosylmethionine,
S-adenosylhomocysteine
13
known
RF01727 ...
C
Smk-box
S-adenosylmethionine
13
known
RF01767
C
speF
? ...
doi:10.1186/1471-2164-14-597
pmid:24060102
pmcid:PMC3766115
fatcat:zrcmb4nshbczjeegaotfsrrocq
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