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BMC Genomics. 2016 Apr 23;17:302. doi: 10.1186/s12864-016-2602-9.

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation.

Author information

  • 1AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051, Russia.
  • 2Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudnyy, Moscow region, 141700, Russia.
  • 3Present Address: Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard Hof 1, CH-8093, Zürich, Switzerland.
  • 4Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany.
  • 5Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
  • 6Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), Schloss 1, CH-8820, Wädenswil, Switzerland.
  • 7Core Unit Systems Medicine, University of Würzburg, Josef-Schneider-Str. 2 Bau D15, D-97080, Würzburg, Germany.
  • 8Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Leninskie Gory, 2-nd educational building, Moscow, 119991, Russia.
  • 9ETH, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.
  • 10Present Address: Department of Plant and Microbial Biology University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland.
  • 11Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), Schloss 1, CH-8820, Wädenswil, Switzerland. christian.ahrens@agroscope.admin.ch.
  • 12AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051, Russia. gelfand@iitp.ru.
  • 13Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Vorobievy Gory 73-1, Moscow, 119991, Russia. gelfand@iitp.ru.
  • 14Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany. Elena.Evguenieva-Hackenberg@mikro.bio.uni-giessen.de.

Abstract

BACKGROUND:

Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters.

RESULTS:

A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file.

CONCLUSIONS:

The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.

KEYWORDS:

Antisense RNA; Bradyrhizobium; Genome re-annotation; Internal transcription start site; Nodule; Promoter prediction; Proteogenomics; RNA-seq; Transcription start site

PMID:
27107716
PMCID:
PMC4842269
DOI:
10.1186/s12864-016-2602-9
[PubMed - indexed for MEDLINE]
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