Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates.
Despite successful use of Plant Growth Promoting Rhizobacteria (PGPR) in agriculture, little is known about specific mechanisms of gene regulation facilitating the effective communication between bacteria and plants during plant colonization. Active PGPR strain Bacillus atrophaeus UCMB-5137 was studied in this research. RNA sequencing profiles were generated in experiments where root exudate stimulations were used to mimic interactions between bacteria and plants. It was found that the gene regulation in B. atrophaeus UCMB-5137 in response to the root exudate stimuli differed from the reported gene regulation at similar conditions in B. amyloliquefaciens FZB42, which was considered as a paradigm PGPR. This difference was explained by hypersensitivity of UCMB-5137 to the root exudate stimuli impelling it to a sessile root colonization behavior through the CcpA-CodY-AbrB regulation. It was found that the transcriptional factor DegU also could play an important role in gene regulations during plant colonization. A significant stress caused by the root exudates on in vitro cultivated B. atrophaeus UCMB-5137 was noticed and discussed. Multiple cases of conflicted gene regulations showed scantiness of our knowledge on the regulatory network in Bacillus. Some of these conflicted regulations could be explained by interference of non-coding RNA (ncRNA). Search through differential expressed intergenic regions revealed 49 putative loci of ncRNA regulated by the root exudate stimuli. Possible target mRNA were predicted and a general regulatory network of B. atrophaeus UCMB-5137 genome was designed.
Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
Liberata
L
Mwita
Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
Wai Yin
WY
Chan
Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
Theresa
T
Pretorius
Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania.
Sylvester L
SL
Lyantagaye
Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine.
Svitlana V
SV
Lapa
Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine.
Lilia V
LV
Avdeeva
Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa. Electronic address: oleg.reva@up.ac.za.
Oleg N
ON
Reva
D001407:Bacillus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D000069977:Bacillus amyloliquefaciens / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D018441:Biofilms / Q000254:growth & development; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D056426:Genetic Loci; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D022661:RNA, Untranslated / Q000235:genetics* / Q000378:metabolism; D012230:Rhizobiaceae / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D058441:Rhizosphere; D017423:Sequence Analysis, RNA; D013559:Symbiosis; D003313:Zea mays / Q000382:microbiology
D001426:Bacterial Proteins; D022661:RNA, Untranslated
Non-coding RNA; Plant Growth Promoting Rhizobacteria; RNA sequencing; Transcriptional regulatory network; Transcriptomics