Mwita Liberata, Chan Wai Yin, Pretorius Theresa, Lyantagaye Sylvester L, Lapa Svitlana V, Avdeeva Lilia V, Reva Oleg N
Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
Gene. 2016 Sep 15;590(1):18-28. doi: 10.1016/j.gene.2016.05.045. Epub 2016 Jun 1.
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.
尽管植物促生根际细菌（PGPR）在农业中得到了成功应用，但对于在植物定殖过程中促进细菌与植物有效交流的基因调控具体机制，人们了解甚少。本研究对活性PGPR菌株萎缩芽孢杆菌UCMB - 5137进行了研究。在利用根系分泌物刺激模拟细菌与植物相互作用的实验中，生成了RNA测序图谱。研究发现，萎缩芽孢杆菌UCMB - 5137对根系分泌物刺激的基因调控与在类似条件下解淀粉芽孢杆菌FZB42（被视为典型PGPR）所报道的基因调控不同。这种差异可通过UCMB - 5137对根系分泌物刺激的超敏反应来解释，该超敏反应促使其通过CcpA - CodY - AbrB调控进入固着性根系定殖行为。研究发现转录因子DegU在植物定殖过程中的基因调控中也可能发挥重要作用。注意到并讨论了根系分泌物对体外培养的萎缩芽孢杆菌UCMB - 5137造成的显著应激。多个相互冲突的基因调控案例表明我们对芽孢杆菌调控网络的了解不足。其中一些相互冲突的调控可通过非编码RNA（ncRNA）的干扰来解释。通过差异表达基因间区域搜索，发现了49个受根系分泌物刺激调控的ncRNA推定位点。预测了可能的靶标mRNA，并设计了萎缩芽孢杆菌UCMB - 5137基因组的一般调控网络。
