Unveiling Mycoplasma hyopneumoniae Promoters: Sequence Definition and Genomic Distribution

• Published in: DNA research Vol. 19; no. 2; pp. 103 - 115
• Main Authors: Weber, Shana de Souto, Sant'Anna, Fernando Hayashi, Schrank, Irene Silveira
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01-04-2012
• Subjects: Base Sequence; Biological and medical sciences; codons; Diverse techniques; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Fundamental and applied biological sciences. Psychology; genes; Genes. Genome; Genetics of eukaryotes. Biological and molecular evolution; Genome, Bacterial; Gram-positive bacteria; Molecular and cellular biology; Molecular genetics; Molecular Sequence Data; Mycoplasma hyopneumoniae; Mycoplasma hyopneumoniae - genetics; Mycoplasma hyopneumoniae - isolation & purification; nucleotides; Open Reading Frames; pathogens; Position-Specific Scoring Matrices; promoter regions; Promoter Regions, Genetic; RNA, Bacterial - genetics; RNA, Bacterial - isolation & purification; Sequence Analysis, DNA; Species Specificity; swine; transcription (genetics); Transcription Initiation Site; sigma; Transcription; Genomics; Definition; Mycoplasma; matrix; Mycoplasmataceae; Mollicutes; Promoter; Mycoplasmatales; Mycoplasma hyopneumoniae; Distribution; Bacteria; Genome
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/dsr045

Several Mycoplasma species have had their genome completely sequenced, including four strains of the swine pathogen Mycoplasma hyopneumoniae. Nevertheless, little is known about the nucleotide sequences that control transcriptional initiation in these microorganisms. Therefore, with the objective of investigating the promoter sequences of M. hyopneumoniae, 23 transcriptional start sites (TSSs) of distinct genes were mapped. A pattern that resembles the σ70 promoter –10 element was found upstream of the TSSs. However, no –35 element was distinguished. Instead, an AT-rich periodic signal was identified. About half of the experimentally defined promoters contained the motif 5'-TRTGn-3', which was identical to the –16 element usually found in Gram-positive bacteria. The defined promoters were utilized to build position-specific scoring matrices in order to scan putative promoters upstream of all coding sequences (CDSs) in the M. hyopneumoniae genome. Two hundred and one signals were found associated with 169 CDSs. Most of these sequences were located within 100 nucleotides of the start codons. This study has shown that the number of promoter-like sequences in the M. hyopneumoniae genome is more frequent than expected by chance, indicating that most of the sequences detected are probably biologically functional.