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.
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.
AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051, Russia.|Moscow Institute of Physics and Technology, Institutskiy pereulok 9, Dolgoprudnyy, Moscow region, 141700, Russia.|Present Address: Institute of Molecular Systems Biology, ETH Zürich, Auguste-Piccard Hof 1, CH-8093, Zürich, Switzerland.
Jelena
J
Čuklina
Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany.
Julia
J
Hahn
Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
Maxim
M
Imakaev
Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), Schloss 1, CH-8820, Wädenswil, Switzerland.
Ulrich
U
Omasits
Core Unit Systems Medicine, University of Würzburg, Josef-Schneider-Str. 2 Bau D15, D-97080, Würzburg, Germany.
Konrad U
KU
Förstner
Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Leninskie Gory, 2-nd educational building, Moscow, 119991, Russia.
Nikolay
N
Ljubimov
Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany.
Melanie
M
Goebel
ETH, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.|Present Address: Department of Plant and Microbial Biology University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland.
Gabriella
G
Pessi
ETH, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.
Hans-Martin
HM
Fischer
Agroscope, 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.
Christian H
CH
Ahrens
AA Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow, 127051, Russia. gelfand@iitp.ru.|Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Vorobievy Gory 73-1, Moscow, 119991, Russia. gelfand@iitp.ru.
Mikhail S
MS
Gelfand
Institute 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.
Elena
E
Evguenieva-Hackenberg
D000465:Algorithms; D020369:Bradyrhizobium / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology; D000069550:Machine Learning; D011401:Promoter Regions, Genetic; D020543:Proteome; D012329:RNA, Bacterial / Q000235:genetics; D017423:Sequence Analysis, RNA; D013025:Glycine max / Q000382:microbiology; D013559:Symbiosis; D024363:Transcription Initiation Site
D020543:Proteome; D012329:RNA, Bacterial
Antisense RNA; Bradyrhizobium; Genome re-annotation; Internal transcription start site; Nodule; Promoter prediction; Proteogenomics; RNA-seq; Transcription start site