title: Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium.
abstract: The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq and MS-based proteomics to accurately map coding sequences, transcription start sites (TSSs) and transcript 3'-ends (T3Es). We used obtained data to investigate roles of TSSs and T3Es in stress-induced transcriptional responses. We identified 1061 TSSs at a false discovery rate of 10% and showed that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters surrounded by A/T-rich sequences. Our analysis revealed the pronounced operon structure complexity: on average, each coding operon has one internal TSS and T3Es in addition to the primary ones. Our transcriptomic approach based on the intervals between the two nearest transcript ends allowed us to identify two classes of T3Es: strong, unregulated, hairpin-containing T3Es and weak, heat shock-regulated, hairpinless T3Es. Comparing gene expression levels under different conditions revealed widespread and divergent transcription regulation in M. gallisepticum. Modeling suggested that the core promoter structure plays an important role in gene expression regulation. We have shown that the heat stress activation of cryptic promoters combined with the hairpinless T3Es suppression leads to widespread, seemingly non-functional transcription.
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny 19, Moscow 127994, Russian Federation.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Mazin
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation herr.romanoff@gmail.com.
authors.forename: Gleb Y
authors.initials: GY
authors.lastname: Fisunov
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation.
authors.forename: Alexey Y
authors.initials: AY
authors.lastname: Gorbachev
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation Moscow Institute of Physics and Technology, Institutsky 9, Dolgoprudny 141700, Russian Federation.
authors.forename: Kristina Y
authors.initials: KY
authors.lastname: Kapitskaya
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation Moscow Institute of Physics and Technology, Institutsky 9, Dolgoprudny 141700, Russian Federation.
authors.forename: Ilya A
authors.initials: IA
authors.lastname: Altukhov
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation.
authors.forename: Tatiana A
authors.initials: TA
authors.lastname: Semashko
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation Moscow Institute of Physics and Technology, Institutsky 9, Dolgoprudny 141700, Russian Federation Kazan Federal University, Kremlyovskaya 18, Kazan 420008, Russian Federation.
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Alexeev
authors.affiliation: Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation Moscow Institute of Physics and Technology, Institutsky 9, Dolgoprudny 141700, Russian Federation Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation.
authors.forename: Vadim M
authors.initials: VM
authors.lastname: Govorun
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D006358:Hot Temperature; D045686:Mycoplasma gallisepticum / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D016372:RNA, Antisense / Q000096:biosynthesis; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D014169:Transformation, Bacterial
chemical_list: D001426:Bacterial Proteins; D016372:RNA, Antisense; D012329:RNA, Bacterial