Alexandra B. Rakhmaninova

Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria

The comparative approach is a powerful tool for the analysis of gene regulation in bacterial genomes. It can be applied to the analysis of regulons that have been studied experimentally as well as that of regulons for which no known regulatory sites are available. It is assumed that the set of co‐regulated genes and the regulatory signal itself are conserved in related genomes. Here, we use genomic comparisons to study the regulation of transport and utilization systems for sugar acids in gamma purple bacteria Escherichia coli, Salmonella typhi, Klebsiella pneumoniae, Yersinia pestis, Erwinia chrysanthemi, Haemophilus influenzae and Vibrio cholerae. The variability of the operon structure and the location of the operator sites for the main transcription factors are demonstrated. The common metabolic map is combined with known and predicted regulatory interactions. It includes all known and predicted members of the GntR, UxuR/ExuR, KdgR, UidR and IdnR regulons. Moreover, most members of these regulons seem to be under catabolite repression mediated by CRP. The candidate UxuR/ExuR signal is proposed, the KdgR consensus is extended, and new operators for all transcription factors are identified in all studied genomes. Two new members of the KdgR regulon, a hypothetical ATP‐dependent transport system OgtABCD and YjgK protein with unknown function, are detected. The former is likely to be the transport system for the products of pectin degradation, oligogalacturonides.

Purine regulon of gamma-proteobacteria: A detailed description

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.

Interhelical contacts determining the architecture of alpha-helical globular proteins.

An approach based on a presentation of alpha-helical protein topology as a graph is presented. The approach allows to estimate a role of each interhelical contact in the whole protein topology and to classify the contacts. It is shown that a consideration of only about a half of the whole pool of interhelical contacts exposed in the protein is enough for a determination of protein architecture. Such contacts are called as major and their quantitative characteristics are obtained. Moreover, providing a clear and simple presentation of the protein topology, the approach can be applied for a description of structural domain/subdomain arrangement of alpha-helical proteins and illustration of their folding/denaturation paths.

Entropy Change for Free Polypeptide Chain upon Hydrogen Bonding

Formation probabilities of different hydrogen bonds between carbonyl oxygen and amide hydrogen were determined by Monte Carlo simulations using a computer model in the space of sterically allowable conformations of alanine and glycine oligopeptides, and the corresponding entropy losses for the peptide backbone, TΔS, were calculated. The model was studied at different criteria of steric interactions. Comparison with the data of other authors showed the values of TΔSto be mainly determined by overall extent and type of the state space and to be only slightly dependent on its energy profile. Both short-range and long-range steric interactions were shown to prevent hydrogen bonding, especially in alanine peptides. In the model studied, the initiation of α(R)-helices is associated with TΔS= 8–10 kT, and prior formation of a 3/10-turn or one three-center H-bond does not appreciably decrease this entropy barrier. Elongation of the α(R)-helix by one residue leads to TΔS= 3.0–3.7 kT, the helices begin to stabilize after at least three sequential H-bonds are formed. The difference in the probability of insertion of Ala and Gly into the helix is lower than it follows from comparison of their mobility. The results could be explained assuming that factors different from helical H-bonds take part in the stabilization of the helices. One may suppose upon modeling of folding that even three sequential H-bonds are unable to fix the structure of a flexible peptide loop, while the elongation of α(R)-helices in the supersecondary helix-loop-helix structure is favorable as long as the loop conformation remains nearly optimal.