ArticleBMC genomics2016
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.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 64 citations in OpenAlex.
- Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights.Microorganisms · 2026Review
- Role of Tad pili during the transition from planktonic to biofilm state inJournal of bacteriology · 2026Article
- TSSpredator-Web: A web-application for transcription start site prediction and exploration.PloS one · 2026Article
- Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene.RNA biology · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression.Scientific reports · 2023Article
- Unraveling the small proteome of the plant symbiontmicroLife · 2023Article
- Identification of sigma factor 54-regulated small non-coding RNAs by employing genome-wide and transcriptome-based methods in rhizobium strains.3 Biotech · 2022Article
- Genome-Wide Transcription Start Sites Mapping inMicroorganisms · 2022Article
- Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15).BMC microbiology · 2022Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Incoherent dual regulation by a SAM-II riboswitch controlling translation at a distance.RNA biology · 2022Article
- Computationally Reconstructed Interactome ofInternational journal of molecular sciences · 2021Article
- Identification of the Important Genes ofFrontiers in microbiology · 2021Article
- A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems.Frontiers in microbiology · 2021Article
- Structure of a Core Promoter in Bifidobacterium longum NCC2705.Journal of bacteriology · 2020Article
- Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria.Microorganisms · 2020Review
- Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human EnteropathogenFrontiers in microbiology · 2020Article
- Transcription attenuation-derived small RNA rnTrpL regulates tryptophan biosynthesis gene expression in trans.Nucleic acids research · 2019Article
- Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow.BMC evolutionary biology · 2019Article
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Authors and funding
12 authors at 8 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDifferential 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.
resultsA 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.
conclusionsThe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.