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Candidate attenuators were identified that regulate operons responsible for biosynthesis of branched amino acids, histidine, threonine, tryptophan, and phenylalanine in gamma- and alpha-proteobacteria, and in some cases in low-GC Gram-positive bacteria, Thermotogales and Bacteroidetes/Chlorobi. This allowed us not only to describe the evolutionary dynamics(More)
T-box antitermination is one of the main mechanisms of regulation of genes involved in amino acid metabolism in Gram-positive bacteria. T-box regulatory sites consist of conserved sequence and RNA secondary structure elements. Using a set of known T-box sites, we constructed the common pattern and used it to scan available bacterial genomes. New T-boxes(More)
Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria.(More)
A model is proposed primarily for the classical RNA attenuation regulation of gene expression through premature transcription termination. The model is based on the concept of the RNA secondary structure macrostate within the regulatory region between the ribosome and RNA-polymerase, on hypothetical equation describing deceleration of RNA-polymerase by a(More)
We demonstrate the scarcity of conserved bacterial-type promoters in plastids of Streptophyta and report widely conserved promoters only for genes psaA, psbA, psbB, psbE, rbcL. Among the reasonable explanations are: evolutionary changes of sigma subunit paralogs and phage-type RNA polymerases possibly entailing the loss of corresponding nuclear genes, de(More)
A long recognized problem is the inference of the supertree S that amalgamates a given set {G j } of trees G j , with leaves in each G j being assigned homologous elements. We ground on an approach to find the tree S by minimizing the total cost of mappings α j of individual gene trees G j into S. Traditionally, this cost is defined basically as a sum of(More)
Expression of many bacterial genes is regulated by formation of alternative secondary RNA structure within the leader mRNA sequence. Our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and gamma-proteobacteria. The attenuators of these(More)
Plastome is thought to be a very conservative part of plant genome but little is known about the evolution of plastome promoters. It was previously shown that one light-regulated promoter (LRPpsbD) is highly conserved in different flowering plant species and in black pine. We have undertaken search and demonstrated that gene ndhF is located in a plastome(More)
The paper provides a short description of the originally developed algorithm for searching of the conservative protein-RNA binding sites. The algorithm is applied to analyze chloroplast genes. The candidate protein-RNA binding sites were detected upstream of atpF, petB, clpP, psaA, psbA, and psbB genes in many chloroplasts of algae and plants. We suggest(More)
We suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. The search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. Numeric values are introduced to measure the discrepancy between the trees. This(More)