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Comput Biol Chem. 2014 Apr;49:7-13. doi: 10.1016/j.compbiolchem.2014.01.001. Epub 2014 Jan 22.

Gene expression regulation of the PF00480 or PF14340 domain proteins suggests their involvement in sulfur metabolism.

Author information

1
Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Russia. Electronic address: lyubetsk@iitp.ru.
2
Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Russia.

Abstract

The paper studies proteins with domains PF00480 or PF14340, as well as some other poorly characterized proteins, encoded by genes associated with leader peptide genes containing a tract of cysteine codons. Such proteins are hypothetically regulated with cysteine-dependent transcription attenuation, namely the Rho-dependent or classic transcription attenuation. Cysteine is an important structural amino acid in various proteins and is required for synthesis of many sulfur-containing compounds, such as methionine, thiamine, glutathione, taurine and the lipoic acid. Earlier a few species of mycobacteria were predicted by the authors to have cysteine-dependent regulation of operons containing the cysK gene. In Escherichia coli this regulation is absent, and the same operon is regulated by the CysB transcription activator. The paper also studies Rho-dependent and classic transcription regulations in all annotated genes of mycobacteria available in GenBank and their orthologs in Actinomycetales. We predict regulations for many genes involved in sulfur metabolism and transport of sulfur-containing compounds; these regulations differ considerably among species. On the basis of predictions, we assign a putative role to proteins encoded by the regulated genes with unknown function, and also describe the structure of corresponding regulons, predict the lack of such regulations for many genes. Thus, all proteins with the uncharacterized Pfam domains PF14340 and PF00480, as well as some others, are predicted to be involved in sulfur metabolism. We also surmise the affinity of some transporters to sulfur-containing compounds. The obtained results considerably extend earlier large-scale studies of Rho-dependent and classic transcription attenuations.

KEYWORDS:

Classic transcription attenuation; Cysteine; Mycobacteria; Rho-dependent transcription attenuation; Sulfur metabolism; Sulfur-containing compounds transport

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