Reconstruction of Transcription Control Networks in Mollicutes by High-Throughput Identification of Promoters

Abstract

Bacteria of the class Mollicutes have significantly reduced genomes and gene expression control systems. They are also efficient pathogens that can colonize a broad range of hosts including plants and animals. Despite their simplicity, Mollicutes demonstrate complex transcriptional responses to various conditions, which contradicts their reduction in gene expression regulation mechanisms. We analyzed the conservation and distribution of transcription regulators across the 50 Mollicutes species. The majority of the transcription factors regulate transport and metabolism, and there are four transcription factors that demonstrate significant conservation across the analyzed bacteria. These factors include repressors of chaperone HrcA, cell cycle regulator MraZ and two regulators with unclear function from the WhiA and YebC/PmpR families. We then used three representative species of the major clades of Mollicutes (Acholeplasma laidlawii, Spiroplasma melliferum, and Mycoplasma gallisepticum) to perform promoter mapping and activity quantitation. We revealed that Mollicutes evolved towards a promoter architecture simplification that correlates with a diminishing role of transcription regulation and an increase in transcriptional noise. Using the identified operons structure and a comparative genomics approach, we reconstructed the transcription control networks for these three species. The organization of the networks reflects the adaptation of bacteria to specific conditions and hosts.

BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes

“…The second type of coverage we recommend to use for 5′ enriched RNA-seq ( Sharma et al, 2010 ; Creecy and Conway, 2015 ). This type of RNA-seq library preparation used for exact TSSs mapping and quantitate transcript analysis ( Mazin et al, 2014 ; Fisunov et al, 2016 ). The program also can load other quantitate or qualitative data in simple and universal BAC-BROWSER format.…”

“…Regulation by transcription factors is considered as well described for bacteria, but even for model bacteria Escherichia coli and Bacillus subtilis new TFs and targets are still being identified ( Keseler et al, 2013 ; Gama-Castro et al, 2016 ; Fang et al, 2017 ; Belliveau et al, 2018 ; Gao et al, 2018 ). Since the low conservation of regulatory networks, regulation of other bacteria, including important pathogens, remains obscure ( Lozada-Chávez et al, 2006 ; Rodionov, 2007 ; Fisunov et al, 2016 ; Eckweiler et al, 2018 ). Operon structure is one of the interesting and poorly studied features of prokaryotes.…”

“…BAC-BROWSER includes free modules for primer design, vector representation, and analysis. Based on BAC-BROWSER prediction we identified TSSs and gene promoters that helped to reveal a new mechanism of transcriptional regulation and reconstruct transcriptional control network for three bacteria species ( Mazin et al, 2014 ; Fisunov et al, 2016 ).…”

Global analysis of sRNA target genes in Mycoplasma hyopneumoniae

“…Mycoplasmas lack the majority of known transcription factors and regulatory pathways compared with other bacteria. The transcription factors (TFs) represent approximately 2.5% of the total number of genes in mycoplasma species, representing proportionally half of those found in bacterial models like Escherichia coli [ 10 ]. However, mycoplasmas maintain the ability to respond to a variety of environmental and metabolic stresses [ 11 – 13 ], suggesting the presence of alternative transcriptional regulatory mechanisms.…”

Comparative Analysis of Mycoplasma gallisepticum vlhA Promoters

“…VlhA genes lack conserved sigma-70 promoter sequence and often have GTG start codon ( Markham et al, 1994 ). They are proposed to employ an alternative sigma factor binding GCGAAAAT sequence ( Fisunov et al, 2016 ). Long regions of GAA repeats are located upstream of vlhA genes ( Markham et al, 1994 ).…”