Unravelling the Transcriptome Profile of the Swine Respiratory Tract Mycoplasmas

Abstract

The swine respiratory ciliary epithelium is mainly colonized by Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis. While colonization by M. flocculare is virtually asymptomatic, M. hyopneumoniae and M. hyorhinis infections may cause respiratory disease. Information regarding transcript structure and gene abundance provides valuable insight into gene function and regulation, which has not yet been analyzed on a genome-wide scale in these Mycoplasma species. In this study, we report the construction of transcriptome maps for M. hyopneumoniae, M. flocculare and M. hyorhinis, which represent data for conducting comparative studies on the transcriptional repertory. For each species, three cDNA libraries were generated, yielding averages of 415,265, 695,313 and 93,578 reads for M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively, with an average read length of 274 bp. The reads mapping showed that 92%, 98% and 96% of the predicted genes were transcribed in the M. hyopneumoniae, M. flocculare and M. hyorhinis genomes, respectively. Moreover, we showed that the majority of the genes are co-expressed, confirming the previously predicted transcription units. Finally, our data defined the RNA populations in detail, with the map transcript boundaries and transcription unit structures on a genome-wide scale.

Mycoplasma non-coding RNA: identification of small RNAs and targets

“…Previous analyses described the presence of differential transcription in the M. hyopneumoniae transcriptome [35, 49–52]. Therefore, the genes up or down-regulated in the above studies were correlated with the genes predicted as interacting with sRNAs.…”

“…The average length of these putative sRNAs in the genomes of the three mycoplasma species ranged from 85 to 167 bp. Previously, the availability of transcriptome maps of M. hyopneumoniae , M. flocculare and M. hyorhinis allowed the in silico identification of 78, 130 and 72 putative novel ncRNAs, respectively, with lengths ranging from 30 to 600 nucleotides [35]. However, this approach was unable to identify the sRNAs among the ncRNAs [35].…”

“…Previously, the availability of transcriptome maps of M. hyopneumoniae , M. flocculare and M. hyorhinis allowed the in silico identification of 78, 130 and 72 putative novel ncRNAs, respectively, with lengths ranging from 30 to 600 nucleotides [35]. However, this approach was unable to identify the sRNAs among the ncRNAs [35]. Although in Escherichia coli the majority of the new sRNAs, varying in length from 50 to 400 nucleotides, have been identified through an in silico prediction [36, 37], the application of this proposed methodology to other bacterial species has had only limited success as it requires reliable species-specific consensus promoter and terminator sequences.…”

“…It was previously shown that most genes from the genomes of M. hyopneumoniae , M. flocculare and M. hyorhinis are expressed at some basal level and that the majority of the genes are co-transcribed [34, 35]. Therefore, a global determination of the genomic functional elements is a prerequisite to expand our knowledge regarding transcriptional small RNA regulation in swine respiratory mycoplasmas.In the current study, we have analyzed and predicted trans-encoded small RNAs from M. hyopneumoniae , M. flocculare and M. hyorhinis genomes.…”

Comparative proteomics of twoMycoplasma hyopneumoniaestrains andMycoplasma flocculareidentified potential porcine enzootic pneumonia determinants

“…However, previous comparative transcriptomic studies between M. hyopneumoniae and M. flocculare [14] failed to find differences in the relative transcription levels for most genes. On the other hand, pioneer proteomic studies, have provided evidences of differential protein abundance and post-translational processing between M. hyopneumoniae pathogenic (7448 and 7422) and non-pathogenic (J) strains [15].…”