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Xanthomonas campestris is a gram-negative, obligate aerobic bacterium that is a member of the Xanthomonas genus, which is a group of bacteria that are commonly known for their association with plant disease. The species is considered to be dominant amongst its genus, as it originally had over 140 identified pathovars and has been found to infect both monocotyledonous and dicotyledonous plants of economical value with various plant diseases. This includes "black rot" in cruciferous vegetables, bacterial wilt of turfgrass, bacterial blight, and leaf spot, for example.
Xanthomonas is a genus of bacteria, many of which cause plant diseases. There are at least 27 plant associated Xanthomonas spp., that all together infect at least 400 plant species. Different species typically have specific host and/or tissue range and colonization strategies.
The OmrA-B RNA gene family is a pair of homologous OmpR-regulated small non-coding RNA that was discovered in E. coli during two large-scale screens. OmrA-B is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well. RygB is adjacent to RygA a closely related RNA. These RNAs bind to the Hfq protein and regulate gene expression by antisense binding. They negatively regulate the expression of several genes encoding outer membrane proteins, including cirA, CsgD, fecA, fepA and ompT by binding in the vicinity of the Shine-Dalgarno sequence, suggesting the control of these targets is dependent on Hfq protein and RNase E. Taken together, these data suggest that OmrA-B participates in the regulation of outer membrane composition, responding to environmental conditions.
In molecular biology the ArcZ RNA is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein. ArcZ is an Hfq binding RNA that functions as an antisense regulator of a number of protein coding genes.
The yybP-ykoY leader RNA element was originally discovered in E. coli during a large scale screen and was named SraF. This family was later found to exist upstream of related families of protein genes in many bacteria, including the yybP and ykoY genes in B. subtilis. The specific functions of these proteins are unknown, but this structured RNA element may be involved in their genetic regulation as a riboswitch. The yybP-ykoY element was later proposed to be manganese-responsive after another associated family of genes, YebN/MntP, was shown to encode Mn2+ efflux pumps in several bacteria. Genetic data and a crystal structure confirmed that yybp-ykoY is a manganese riboswitch that directly binds Mn2+
Pseudomonas sRNA P16 is a ncRNA that was predicted using bioinformatic tools in the genome of the opportunistic pathogen Pseudomonas aeruginosa and its expression verified by northern blot analysis. P16 sRNA appears to be conserved across several Pseudomonas species and is consistently located downstream of a predicted TatD deoxyribonuclease gene. P16 has a predicted Rho independent terminator at the 3′ end but the function of P16 is unknown.
An Hfq binding sRNA is an sRNA that binds the bacterial RNA binding protein called Hfq. A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised . Many of these RNAs share a similar structure composed of three stem-loops. Several studies have expanded this list, and experimentally validated a total of 64 Hfq binding sRNA in Salmonella Typhimurium. A transcriptome wide study on Hfq binding sites in Salmonella mapped 126 Hfq binding sites within sRNAs. Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif 5′-AAYAAYAA-3′. Genome-wide study identified 40 candidate Hfq-dependent sRNAs in plant pathogen Erwinia amylovora. 12 of them were confirmed by Northern blot.
Plant disease resistance protects plants from pathogens in two ways: by pre-formed structures and chemicals, and by infection-induced responses of the immune system. Relative to a susceptible plant, disease resistance is the reduction of pathogen growth on or in the plant, while the term disease tolerance describes plants that exhibit little disease damage despite substantial pathogen levels. Disease outcome is determined by the three-way interaction of the pathogen, the plant and the environmental conditions.
PtaRNA1 is a family of non-coding RNAs. Homologs of PtaRNA1 can be found in the bacterial families, Betaproteobacteria and Gammaproteobacteria. In all cases the PtaRNA1 is located anti-sense to a short protein-coding gene. In Xanthomonas campestris pv. vesicatoria, this gene is annotated as XCV2162 and is included in the plasmid toxin family of proteins.
Bacterial small RNAs (bsRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.
Black rot, caused by the bacterium Xanthomonas campestris pv. campestris (Xcc), is considered the most important and most destructive disease of crucifers, infecting all cultivated varieties of brassicas worldwide. This disease was first described by botanist and entomologist Harrison Garman in Lexington, Kentucky, US in 1889. Since then, it has been found in nearly every country in which vegetable brassicas are commercially cultivated.
sRNA-Xcc1 is a family of trans-acting non-coding RNA. Homologs of sRNA-Xcc1 are found in a few bacterial strains belonging to alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria, and delta-proteobacteria. In Xanthomonascampestris pv. campestris, sRNA-Xcc1 is encoded by an integron gene cassette and is under the positive control of the virulence regulators HrpG and HrpX.
In molecular biology, Streptococcus sRNAs are small RNAs produced by species of Streptococcus bacteria. Several screens have identified numerous sRNAs in different species and strains of Streptococcus including S. pneumoniae, S. pyogenes, S. agalactiae and S.mutans. The function of most of these is currently unknown, however a few have been characterised including FasX small RNA. Many sRNAs have roles in pathogenesis.
D-Man-alpha-(1->3) -D-Glc-beta-(1->4) -D-Glc-alpha-1-diphosphoundecaprenol 2-beta-glucuronyltransferase is an enzyme with the systematic name UDP-glucuronate: D-Man-alpha-(1->3) -D-Glc-beta-(1->4)-D-Glc-alpha-1-diphospho-ditrans,octacis-undecaprenol beta-1,2-glucuronyltransferase. This enzyme catalyses the following chemical reaction:
In molecular biology, the regulator of motility and amylovoran A (RmaA) gene is a bacterial non-coding RNA. It was discovered in genome-wide identification of Hfq binding sRNAs in plant pathogen Erwinia amylovora. Together with Hfq it positively controls motility and negatively controls the production of acidic exopolysaccharide amylovoran in E. amylovora.
Several small RNAs have been identified in Francisella tularensis, pathogenic bacterium that causes the disease tularaemia. Very little is known about Francisella's regulatory networks that allow this bacterium to survive in many environments.
AsponA is a small asRNA transcribed antisense to the penicillin-binding protein 1A gene called ponA. It was identified by RNAseq and the expression was validated by 5' and 3' RACE experiments in Pseudomanas aeruginosa. AsponA expression was up or down regulated under different antibiotic stress. Owing to its location it may be able to prevent the transcription or translation of the opposite gene. Study by Wurtzel et al. and Ferrara et al. also detected its expression.
Subhadeep Chatterjee is an Indian molecular biologist and a scientist at the Centre for DNA Fingerprinting and Diagnostics (CDFD). A member of Guha Research Conference, he is known for his studies on plant-microbe interactions and heads the Lab of Plant-Microbe Interactions at CDFD where he hosts several researchers.
Xanthoferrin is an α-hydroxycarboxylate-type of siderophore produced by xanthomonads. Xanthomonas spp. secrete xanthoferrin to chelate iron under low-iron conditions. The xanthoferrin siderophore mediated iron uptake supports bacterial growth under iron-restricted environment.
Diffusible signal factor (DSF) is found in several gram-negative bacteria and play a role in the formation of biofilms, motility, virulence, and antibiotic resistance. Xanthomonas campestris was the first bacteria known to have DSF. The synthesis of the DSF can be seen in rpfF and rpfB enzymes. An understanding of the DSF signaling mechanism could lead to further disease control.
References
- 1 2 Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J, Hoffmann S, Vogel J, et al. (2011). "Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions". Nucleic Acids Res. 40 (5): 2020–31. doi:10.1093/nar/gkr904. PMC 3300014 . PMID 22080557.
- ↑ Jiang RP, Tang DJ, Chen XL, He YQ, Feng JX, Jiang BL, et al. (2010). "Identification of four novel small non-coding RNAs from Xanthomonas campestris pathovar campestris". BMC Genomics. 11: 316. doi: 10.1186/1471-2164-11-316 . PMC 2996969 . PMID 20482898.
- ↑ Chen XL, Tang DJ, Jiang RP, He YQ, Jiang BL, Lu GT, et al. (2011). "sRNA-Xcc1, an integron-encoded transposon- and plasmid-transferred trans-acting sRNA, is under the positive control of the key virulence regulators HrpG and HrpX of Xanthomonas campestris pathovar campestris". RNA Biol. 8 (6): 947–953. doi:10.4161/rna.8.6.16690. PMC 3256417 . PMID 21941121.
- ↑ Schmidtke, C; Abendroth, U; Brock, J; Serrania, J; Becker, A; Bonas, U (Sep 2013). "Small RNA sX13: A Multifaceted Regulator of Virulence in the Plant Pathogen Xanthomonas". PLOS Pathogens. 9 (9): e1003626. doi: 10.1371/journal.ppat.1003626 . PMC 3771888 . PMID 24068933.
- ↑ Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT (2011). "Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae". BMC Genomics. 12: 87. doi: 10.1186/1471-2164-12-87 . PMC 3039613 . PMID 21276262.