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Vol 44(2010) N 1 p. 128-139;
K.V. Lopatovskaya*, A.V. Seliverstov, V.A. Lyubetsky

Attenuation Regulation of the Amino Acid and Aminoacyl-tRNA Biosynthesis Operons in Bacteria: A Comparative Genomic Analysis

Kharkevich Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia

*kristina@iitp.ru
Received - 2009-02-13; Accepted - 2009-06-05

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-, β-, γ-, and δ-proteobacteria, Actinobacteria, Bacteroidetes/Chlorobi, Firmicutes, and Thermotogaе; in Cloroflexi, the corresponding sites were found upstream of hisG, hisZ, hisS, pheA, pheST, trpEG, trpA, trpB, trpE, trpS, thrA, thrS, leuА, leuS, ilvВ, 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.

gene expression in bacteria, attenuation regulation, large-scale searches, attenuation prediction algorithms, tree-based multiple alignment algorithms



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