Genome organization in Mycoplasma hyopneumoniae: identification of promoter-like sequences

Abstract

Information related to open reading frame (ORF) organization, transcription regulation and promoter sequence has been available for the Mycoplasma hyopneumoniae 7448 genome, demonstrating that the ORFs are continuously transcribed (cotranscription) in large clusters. A species-specific position-specific scoring matrix was applied to scan for putative promoters upstream of all coding sequences on a genome scale in M. hyopneumoniae. This study consisted of a detailed in silico promoter localization analysis by scanning the position-specific promoters upstream of predicted ORF clusters (OCs) and mCs (monocistronic genes) in the M. hyopneumoniae whole genome; this was combined with experimental data for the promoterless ORFs. Promoter-like sequences were found in 86% of the OCs (from the OC first gene) and in 85% of the mCs. A transcription analysis of the promoterless ORF was performed by RT-PCR. This strategy allowed the definition of a specific promoter sequence for all OCs and mCs indicating that all the transcriptional units are preceded by putative promoter sequences (matrix and manually located) and providing evidence for functional gene organization in the M. hyopneumoniae genome. These results shown that the species-specific, position-specific scoring matrix for promoter prediction is effective, further increasing the knowledge of gene organization and transcription initiation in mycoplasmas.

Unravelling the Transcriptome Profile of the Swine Respiratory Tract Mycoplasmas

“…Mycoplasmas are characterized by the presence of long TUs containing genes that encode highly functionally variable products. Moreover, all the M. hyopneumoniae TUs are preceded by putative promoter sequences [20] , providing evidence of gene organization as an important factor in the regulation of transcription. A subset of genes within TUs that are able to be transcribed by alternative internal promoters have been demonstrated and associated with possible complex transcriptional organization in M. hyopneumoniae genomes [18] – [20] .…”

“…Moreover, all the M. hyopneumoniae TUs are preceded by putative promoter sequences [20] , providing evidence of gene organization as an important factor in the regulation of transcription. A subset of genes within TUs that are able to be transcribed by alternative internal promoters have been demonstrated and associated with possible complex transcriptional organization in M. hyopneumoniae genomes [18] – [20] . According to previous predictions [20] , 70% of M. hyopneumoniae TUs possess internal promoter sites, which is in agreement with the high variations in expression levels that were observed within the TUs.…”

“…A subset of genes within TUs that are able to be transcribed by alternative internal promoters have been demonstrated and associated with possible complex transcriptional organization in M. hyopneumoniae genomes [18] – [20] . According to previous predictions [20] , 70% of M. hyopneumoniae TUs possess internal promoter sites, which is in agreement with the high variations in expression levels that were observed within the TUs. These findings are also similar to others that have been described in many bacterial species, including those in the M. pneumoniae transcriptome, which has been characterized by the frequent occurrence of polycistronic operons with alternative transcripts [21] , and the Bacillus subtilis transcriptome, in which 20% of the genes in polycistronic operons are transcribed from more than one promoter [67] ; additionally, approximately 6% of the polycistronic operons contain internal read-through terminators, at which partial continuation of transcription occurs [68] .…”

“…Analyses related to transcriptional unit (TU) organization, transcriptional regulation and promoter sequence composition have been performed on the M. hyopneumoniae 7448 genome [18] – [20] . Global assessments of the TU organization of the M. hyopneumoniae genome by both in silico and in vitro approaches have suggested that the ORFs are continuously transcribed (cotranscribed) in large clusters (TUs).…”

Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation

“…hyopneumoniae . The occurrence of transcription units [4, 9, 10], promoters [11, 12] and terminators [13] has already been described in this species, but the existence of other regulatory sequences remains to be elucidated.…”