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Molecular Biology

, Volume 44, Issue 1, pp 128–139 | Cite as

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

  • K. V. Lopatovskaya
  • A. V. Seliverstov
  • V. A. Lyubetsky
Bioinformatics

Abstract

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.

Key words

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

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Copyright information

© Pleiades Publishing, Ltd. 2010

Authors and Affiliations

  • K. V. Lopatovskaya
    • 1
  • A. V. Seliverstov
    • 1
  • V. A. Lyubetsky
    • 1
  1. 1.Kharkevich Institute of Information Transmission ProblemsRussian Academy of SciencesMoscowRussia

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