Comparative Analysis of Mycoplasma gallisepticum vlhA Promoters.

Mikhail Orlov,Gleb Y Fisunov,Anatoly Sorokin,Irina Garanina

doi:10.3389/fgene.2018.00569

Mikhail Orlov, Gleb Y Fisunov + Show 2 more

Open Access

https://doi.org/10.3389/fgene.2018.00569

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Abstract

Mycoplasma gallisepticum is an intracellular parasite affecting respiratory tract of poultry that belongs to class Mollicutes. M. gallisepticum features numerous variable lipoprotein hemagglutinin genes (vlhA) that play a role in immune escape. The vlhA promoters have a set of distinct properties in comparison to promoters of the other genes. The vlhA promoters carry a variable GAA repeats region at approximately 40 nts upstream of transcription start site. The promoters have been considered active only in the presence of exactly 12 GAA repeats. The mechanisms of vlhA expression regulation and GAA number variation are not described. Here we tried to understand these mechanisms using different computational methods. We conducted a comparative analysis among several M. gallisepticum strains. Nucleotide sequences analysis showed the presence of highly conserved regions flanking repeated trinucleotides that are not linked to GAA number variation. VlhA genes with 12 GAA repeats and their orthologs in 12 M. gallisepticum strains are more conserved than other vlhA genes and have narrower GAA number distribution. We conducted comparative analysis of physicochemical profiles of M. gallisepticum vlhA and sigma-70 promoters. Stress-induced duplex destabilization (SIDD) profiles showed that sigma-70 group is characterized by the common to prokaryotic promoters sharp maxima while vlhA promoters are hardly destabilized with the region between GAA repeats and transcription start site having zero opening probability. Electrostatic potential profiles of vlhA promoters indicate the presence of the distinct patterns that appear to govern initial stages of specific DNA-protein recognition. Open state dynamics profiles of vlhA demonstrate the pattern that might facilitate transcription bubble formation. Obtained data could be the basis for experimental identification of mechanisms of phase variation in M. gallisepticum.

Highlights

Mycoplasmas are genome-reduced bacteria without a cell wall and with a parasitic lifestyle
Previous studies revealed that activation of variable lipoprotein hemagglutinin genes (vlhA) transcription occurs if 12 gene sequences upstream and downstream of (GAA) repeats are present within the promoter
We analyzed conservation of GAA flanks among different M. gallisepticum strains and vlhA orthologous groups to identify the mechanism of vlhA expression activation

Summary

Introduction

Mycoplasmas are genome-reduced bacteria without a cell wall and with a parasitic lifestyle. One of main mechanisms Mycoplasmas employ is changing the repertoire of surface lipoproteins (phase variation) (Rosengarten and Wise, 1990). Other pathogenic bacteria, including Haemophilus, Chlamydia, and Streptococcus species, Mycoplasma VlhA Promoters use phase variation to escape of host defense mechanisms (Noormohammadi, 2007). Numerous mechanisms of phase variation are described for Mycoplasmas (Citti et al, 2010). The mechanisms of variation are species-specific and occur in one species or closely related Mycoplasmas. They include DNA slippage, site-specific recombination, reciprocal recombination, and gene conversion (Citti et al, 2010). The phase variation system of Mycoplasma gallisepticum is unique, and has not been described so far. Studying phase variation genes can reveal novel mechanisms of gene expression regulation in bacteria

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