TY  - JOUR
A1  - Čuklina, Jelena
A1  - Hahn, Julia
A1  - Imakaev, Maxim
A1  - Omasits, Ulrich
A1  - Förstner, Konrad U.
A1  - Ljubimov, Nikolay
A1  - Goebel, Melanie
A1  - Pessi, Gabriella
A1  - Fischer, Hans-Martin
A1  - Ahrens, Christian H.
A1  - Gelfand, Mikhail S.
A1  - Evguenieva-Hackenberg, Elena
T1  - 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
JF  - BMC Genomics
N2  - 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.
KW  - Bradyrhizobium
KW  - RNA-seq
KW  - Promoter prediction
KW  - Genome re-annotation
KW  - Internal transcription start site
KW  - Nodule
KW  - Transcription start site
KW  - Proteogenomics
KW  - Antisense RNA
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-164565
VL  - 17
ER  -