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

Abstract

sRNA-Xcc1 is a trans-acting sRNA recently identified from the plant pathogenic bacterium Xanthomonas campestris pathovar campestris (Xcc). Here, the phylogenetic distribution, predicted secondary structure and regulation of expression of sRNA-Xcc1 were analyzed. The analysis showed (1) a total 81 sRNA-Xcc1 homologs that are found in some bacterial strains that are taxonomically unrelated, belonging to the a-, b-, g-, and d-proteobacteria (2) that some sRNA-Xcc1 homologs are located in a plasmid-borne transposon or near a transposase coding gene, (3) that sRNA-Xcc1 is encoded by a integron gene cassette in Xcc and sRNA-Xcc1 homologs occur in integron gene cassettes of some uncultured bacteria and (4) that sRNA-Xcc1 homologs have a highly conserved sequence motif and a stable consensus secondary structure. These findings strongly support the idea that sRNA-Xcc1 represents a novel family of sRNAs which may be originally captured by integrons from natural environments and then spread among different bacterial species via horizontal gene transfer, possibly by means of transposons and plasmids. The expression analysis results demonstrated that the transcription of sRNA-Xcc1 is under the positive control of the key virulence regulators HrpG and HrpX, indicating that sRNA-Xcc1 may be involved in the virulence regulation of Xcc.

Acknowledgments

We are grateful to P.P. Gardner for helpful suggestions, critical reading of the manuscript, and proving useful information. We are grateful to J.M. Dow for critical reading of the manuscript. This work was supported by the National Natural Science Foundation of China (31071141 and 30730004).

Figures and Tables

Figure 1 Schematic presentation of the genomic locations/flanking genes of the sRNA-Xcc1 homologues associated with integrons (A) and transposons/plasmids (B). The black arrow represents sRNA-Xcc1 homologue, the gray arrow represents open reading frame (ORF) and the ORF number and/or the predicted coding product was shown inside or under the arrow. The number on the top of a vertical line indicates the genomic position, and the number above a horizontal line indicates the length of the spacer between the sRNA-Xcc1 homologue and the upstream or downstream genes (or genetic element). The corresponding bacterial strains were shown on the right hand side of the figure. The genomic data were obtained from the NCBI nucleotide database.

Figure 2 The phylogenetic tree of sRNA-Xcc1 homologs based on multiple alignments. Symbols on the right hand side of the name of the bacterial strain indicate the class of the bacterial species, and the location of the sRNA-Xcc1 homolog.

Figure 3 (A) Schematic presentation of the genetic organization of the integron of Xcc and the detailed composition of sRNA-Xcc1 cassette. The blue letters indicates the sRNA-Xcc1 coding sequence and the red letters indicate the 59-be sequence. (B) Detection of the sRNA-Xcc1 level in the wild type strain 8004, the hrpG mutant 8004ΔhrpG and the hrpX mutant 8004ΔhrpX, by using northern Blot.

Figure 4 Multiple alignments and a consensus secondary structure model of the sRNA-Xcc1 homologs. Multiple alignments were done using the ClustalW program and the consensus secondary structure was predicted based on the multiple alignment using RNAalifold program. The conserved sequence motif ‘AUACAAnACCC’ was boxed.