References of "Gelfand, M.S"
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See detailRegulation and evolution of malonate and propionate catabolism in proteobacteria
Suvorova, I.A.; Ravcheev, Dmitry UL; Gelfand, M.S.

in Journal of Bacteriology (2012), 194(12), 3234-3240

Bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. In various bacteria, transcription of these genes is controlled by the GntR family transcription factors (TFs) MatR/MdcY ... [more ▼]

Bacteria catabolize malonate via two pathways, encoded by the mdc and mat genes. In various bacteria, transcription of these genes is controlled by the GntR family transcription factors (TFs) MatR/MdcY and/or the LysR family transcription factor MdcR. Propionate is metabolized via the methylcitrate pathway, comprising enzymes encoded by the prp and acn genes. PrpR, the Fis family sigma 54-dependent transcription factor, is known to be a transcriptional activator of the prp genes. Here, we report a detailed comparative genomic analysis of malonate and propionate metabolism and its regulation in proteobacteria. We characterize genomic loci and gene regulation and identify binding motifs for four new TFs and also new regulon members, in particular, tripartite ATP-independent periplasmic (TRAP) transporters. We describe restructuring of the genomic loci and regulatory interactions during the evolution of proteobacteria. [less ▲]

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See detailA Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
Favorov, A.A.; Gelfand, M.S.; Gerasimova, A.V. et al

in Bioinformatics (2005), 21(10), 2240-2245

Motivation: Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured DNA motifs that are inverted or direct repeats or spaced motif pairs ... [more ▼]

Motivation: Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured DNA motifs that are inverted or direct repeats or spaced motif pairs. However, these motifs are often difficult to identify owing to their high divergence. The motif structure included explicitly into the motif recognition algorithm improves recognition efficiency for highly divergent motifs as well as estimation of motif geometric parameters. Result: We present a modification of the Gibbs sampling motif extraction algorithm, SeSiMCMC (Sequence Similarities by Markov Chain Monte Carlo), which finds structured motifs of these types, as well as non-structured motifs, in a set of unaligned DNA sequences. It employs improved estimators of motif and spacer lengths. The probability that a sequence does not contain any motif is accounted for in a rigorous Bayesian manner. We have applied the algorithm to a set of upstream regions of genes from two Escherichia coli regulons involved in respiration. We have demonstrated that accounting for a symmetric motif structure allows the algorithm to identify weak motifs more accurately. In the examples studied, ArcA binding sites were demonstrated to have the structure of a direct spaced repeat, whereas NarP binding sites exhibited the palindromic structure. Availability: The WWW interface of the program, its FreeBSD (4.0) and Windows 32 console executables are available at http://bioinform.genetika.ru/SeSiMCMC [less ▲]

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See detailRegulation of nitrate and nitrite respiration in γ-proteobacteria: a comparative genomics study
Ravcheev, Dmitry UL; Rakhmaninova, A.B.; Mironov, A.A. et al

in Molecular Biology (2005), 39(5), 727-740

Nitrate and nitrite are the most preferable electron acceptors in the absence of molecular oxygen. In the γ-proteobacterium Escherichia coli, nitrate and nitrite respiration is regulated by two homologous ... [more ▼]

Nitrate and nitrite are the most preferable electron acceptors in the absence of molecular oxygen. In the γ-proteobacterium Escherichia coli, nitrate and nitrite respiration is regulated by two homologous tran- scription factors, NarL and NarP. Although this regulatory system was a subject of intensive research for more than 20 years, many key issues, including the structure of the NarL-binding site, are still unclear. Comparative genomics analysis showed that only NarP is responsible for regulation in most γ-proteobacteria. The NarP reg- ulon was studied in ten genomes. Although its structure considerably differs among some genomes, the mech- anism regulating the nitrate and nitrite reduction genes is highly conserved. A correlation was observed between the evolutionary changes in the nitrate and nitrite respiration system and the relevant regulatory system. Poten- tial NarP-binding sites were found upstream of the gene for the global regulator FNR and the sydAB, mdh, and sucAB aerobic metabolism genes. It was assumed on the basis of this evidence that the role of NarP in regulat- ing respiration changed during evolution. In total, 35 new operons were assigned to the generalized NarP reg- ulon. Autoregulation of the narQP operon was suggested for bacteria of the family Vibrionaceae. [less ▲]

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See detailPurine regulon of gamma-proteobacteria: a detailed description
Ravcheev, Dmitry UL; Gelfand, M.S.; Mironov, A.A. et al

in Russian Journal of Genetics (2002), 38(9), 1015-1025

The structure of the purine regulon was studied by a comparative genomic approach in seven genomes of gamma-proteobacteria: Escherichia coli, Salmonella typhimurium, Yersinia pestis, Haemophilus ... [more ▼]

The structure of the purine regulon was studied by a comparative genomic approach in seven genomes of gamma-proteobacteria: Escherichia coli, Salmonella typhimurium, Yersinia pestis, Haemophilus influenzae, Pasteurella multocida, Actinobacillus actinomycetemcomitans, and Vibrio cholerae. The palindromic binding site of the purine repressor (consensus ACGCAAACGTTTGCGT) is fairly well conserved upstream genes encoding enzymes that participate in the synthesis of inosine monophosphate from phosphoribozylpyrophosphate and in transfer of one-carbon units, and also upstream of some transport protein genes. These genes may be regarded as the main part of the purine regulon. In terms of physiology, the regulation of the purC and gcvTHP/folD genes seems to be especially important, because the PurR site was found upstream nonorthologous but functionally replaceable genes. However, the PurR site is poorly conserved upstream orthologs of some genes belonging to the E. coli purine regulon, such as genes involved in general nitrogen metabolism, biosynthesis of pyrimidines, and synthesis of AMP and GMP from IMP, and also upstream of the purine repressor gene. It is predicted that purine regulons of the examined bacteria include the following genes: upp participating in synthesis of pyrimidines; uraA encoding an uracil transporter gene; serA involved in serine biosynthesis; folD responsible for the conversion of N5,N10-methenyl tetrahydrofolate into N10-formyltetrahydrofolate; rpiA involved in ribose metabolism; and genes with an unknown function (yhhQ and ydiK). The PurR site was shown to have different structure in different genomes. Thus, the tendency for a decline of the conservatism of site positions 2 and 15 was observed in genomes of bacteria belonging to the Pasteurellaceae and Vibrionaceae groups. [less ▲]

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