Abstract
BackgroundIn bacteria, small non-coding RNAs (sRNAs) have been recognized as important regulators of various cellular processes. Approximately 200 bacterial sRNAs in total have been reported. However, very few sRNAs have been identified from phytopathogenic bacteria.ResultsXanthomons campestris pathovar campestris (Xcc) is the causal agent of black rot disease of cruciferous crops. In this study, a cDNA library was constructed from the low-molecular weight RNA isolated from the Xcc strain 8004 grown to exponential phase in the minimal medium XVM2. Seven sRNA candidates were obtained by sequencing screen of 2,500 clones from the library and four of them were confirmed to be sRNAs by Northern hybridization, which were named sRNA-Xcc1, sRNA-Xcc2, sRNA-Xcc3, and sRNA-Xcc4. The transcription start and stop sites of these sRNAs were further determined. BLAST analysis revealed that the four sRNAs are novel. Bioinformatics prediction showed that a large number of genes with various known or unknown functions in Xcc 8004 are potential targets of sRNA-Xcc1, sRNA-Xcc3 and sRNA-Xcc4. In contrast, only a few genes were predicted to be potential targets of sRNA-Xcc2.ConclusionWe have identified four novel sRNAs from Xcc by a large-scale screen. Bioinformatics analysis suggests that they may perform various functions. This work provides the first step toward understanding the role of sRNAs in the molecular mechanisms of Xanthomonas campestris pathogenesis.
Highlights
In bacteria, small non-coding RNAs have been recognized as important regulators of various cellular processes
Among the identified bacterial small non-coding RNAs (sRNAs), almost half were from Escherichia coli [12,13], and the other half were mainly from Bacillus subtilis [14], Caulobacter crescentus [15], Listeria monocytogenes [16], Mycobacterium tuberculosis [17], Pseudomonas aeruginosa [18], Salmonella typhimurium [19], Sinorhizobium meliloti [20,21], Staphylococcus aureus [22], and Vibrio cholerae [23]
This strategy, known as small RNA shotgun cloning, allows detection of sRNAs that are expressed in the bacterial cells grown at given conditions but does not require prior knowledge of sRNA characteristics [12,25]
Summary
Small non-coding RNAs (sRNAs) have been recognized as important regulators of various cellular processes. 200 bacterial sRNAs in total have been reported. Very few sRNAs have been identified from phytopathogenic bacteria. Numerous evidences show that small non-coding RNAs (sRNAs) exist in all three domains of life, i.e. Eukarya, Bacteria and Archaea. It has been demonstrated that many bacterial sRNAs act as regulators of gene expression, the function of the majority of identified bacterial sRNAs is still unknown. Most bacterial sRNAs characterized to date regulate gene expression either by pairing to their mRNA targets and affecting their stability and/or transla-. There are still a large number of unknown sRNAs in bacteria including the standard model bacterium E. coli. Very few sRNAs have been reported from plant pathogenic bacteria
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