Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria

Background  

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.     

Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees

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 approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. This resulted in a list of the candidate genes for which the hypothesis of horizontal transfer in evolution looks true.     

Reconstructing the evolution of genes along the species tree

A model and algorithm are proposed to infer the evolution of a gene family described by the corresponding gene tree, with respect to the species evolution described by the corresponding species tree. The model describes the evolution using the new concept of a nested tree. The algorithm performance is illustrated by the example of several orthologous protein groups. The considered evolutionary events are speciation, gene duplication and loss, and horizontal gene transfer retaining the original gene copy. The transfer event with the loss of the original gene copy is considered as a combination of gene transfer and loss. The model maps each evolutionary event onto the species phylogeny.     

Attenuation regulation of the amino acid and aminoacyl-tRNA biosynthesis operons in bacteria: A comparative genomic analysis

A large-scale search for attenuation regulation in bacteria was performed using two original computer programs, which modeled the attenuation regulation and multiple alignment along a phylogenetic tree. The programs are available at http://lab6.iitp.ru. Candidate attenuations were predicted for many organisms belonging to α-, ß-, γ-, and δ-proteobacteria, Actinobacteria, Bact eroidetes/Chlorobi, Firmicutes, and Thermotoga; in Cloroflexi, the corresponding sites were found upstream of hisG, hisZ, hisS, pheA, pheST, trpEG, trpA, trpB, trpE, trpS, thrA, thrS, leuA, leuS, ilvB, ilvI, ilvA, ilvC, ilvD, and ilvG. Searches were conducted across all bacterial genomes contained in GenBank, NCBI. Other bacterial taxa were not predicted to have attenuation. It was possible to assume, in some cases, that RNA triplexes play a substantial role in the formation of an active antiterminator and terminator or pseudoknots during termination. The attenuation regulation of Lactobacillus lactis lysQ was assumed to depend on the histidyl-tRNA concentration. Several types of attenuation regulation and the evolution of attenuation are discussed.