Identification and characterization of a cis antisense RNA of the parC gene encoding DNA topoisomerase IV of Salmonella enterica serovar Typhi

A novel cis antisense RNA AsfD promotes Salmonella enterica serovar Typhi motility and biofilm formation

Bacterial non-coding RNAs (ncRNAs) can participate in multiple biological processes, including motility, biofilm formation, and virulence. Using high-throughput sequencing and transcriptome analysis of Salmonella enterica serovar Typhi (S. Typhi), we identified a novel antisense RNA located at the opposite strand of the flhDC operon. In this study, a northern blot and qRT-PCR were used to confirm the expression of this newfound antisense RNA in S. Typhi. Moreover, 5' RACE and 3' RT-PCR were performed to reveal the molecular characteristics of the antisense RNA, which was 2079 nt - 2179 nt in length, covered the entire flhDC operon sequence, and termed AsfD. The level of AsfD expression was higher during the stationary phase of S. Typhi and activated by the regulators, OmpR and Fis. When AsfD was overexpressed, the level of flagellar gene flhDC transcription increased; moreover, the level of fliA and fljB expression, as well as the motility and biofilm formation of S. Typhi were also enhanced. The results of this study suggest that AsfD is likely to enhance the motility and biofilm formation of S. Typhi by up-regulating flhDC expression.

The world of asRNAs in Gram-negative and Gram-positive bacteria

Bacteria exhibit an amazing diversity of mechanisms controlling gene expression to both maintain essential functions and modulate accessory functions in response to environmental cues. Over the years, it has become clear that bacterial regulation of gene expression is still far from fully understood. This review focuses on antisense RNAs (asRNAs), a class of RNA regulators defined by their location in cis and their perfect complementarity with their targets, as opposed to small RNAs (sRNAs) which act in trans with only short regions of complementarity. For a long time, only few functional asRNAs in bacteria were known and were almost exclusively found on mobile genetic elements (MGEs), thus, their importance among the other regulators was underestimated. However, the extensive application of transcriptomic approaches has revealed the ubiquity of asRNAs in bacteria. This review aims to present the landscape of studied asRNAs in bacteria by comparing 67 characterized asRNAs from both Gram-positive and Gram-negative bacteria. First we describe the inherent ambiguity in the existence of asRNAs in bacteria, second, we highlight their diversity and their involvement in all aspects of bacterial life. Finally we compare their location and potential mode of action toward their target between Gram-negative and Gram-positive bacteria and present tendencies and exceptions that could lead to a better understanding of asRNA functions.

Identification and Characterization of a Cis Antisense RNA of the rpoH Gene of Salmonella enterica Serovar Typhi

Antisense RNAs from complementary strands of protein coding genes regulate the expression of genes involved in many cellular processes. Using deep sequencing analysis of the Salmonella enterica serovar Typhi (S. Typhi) transcriptome, a novel antisense RNA encoded on the strand complementary to the rpoH gene was revealed. In this study, the molecular features of this antisense RNA were assessed using northern blotting and rapid amplification of cDNA ends. The 3,508 nt sequence of RNA was identified as the antisense RNA of the rpoH gene and was named ArpH. ArpH was found to attenuate the invasion of HeLa cells by S. Typhi by regulating the expression of SPI-1 genes. In an rpoH mutant strain, the invasive capacity of S. Typhi was increased, whereas overexpression of ArpH positively regulates rpoH mRNA levels. Results of this study suggest that the cis-encoded antisense RNA ArpH is likely to affect the invasive capacity of S. Typhi by regulating the expression of rpoH.

A 3' UTR-derived non-coding RNA RibS increases expression of cfa and promotes biofilm formation of Salmonella enterica serovar Typhi

Bacterial non-coding RNAs (ncRNAs) are widely studied and found to play important roles in regulating various cellular processes. Recently, many ncRNAs have been discovered to be transcribed or processed from 3' untranslated regions (3' UTRs). Here we reported a novel 3' UTR-derived ncRNA, RibS, which could influence biofilm formation of Salmonella enterica serovar Typhi (S. Typhi). RibS was confirmed to be a ∼700 nt processed product produced by RNase III-catalyzed cleavage from the 3' UTR of riboflavin synthase subunit alpha mRNA, RibE. Overexpression of RibS increased the expression of the cyclopropane fatty acid synthase gene, cfa, which was located at the antisense strand. Biofilm formation of S. Typhi was enhanced by overexpressing RibS both in the wild type strain and cfa deletion mutant. Deletion of cfa attenuated biofilm formation of S. Typhi, while complementation of cfa partly restored the phenotype. Moreover, overexpressing cfa enhanced the biofilm formation of S. Typhi. In summary, RibS has been identified as a novel ncRNA derived from the 3' UTR of RibE that promotes biofilm formation of S. Typhi, and it appears to do so, at least in part, by increasing the expression of cfa.

The malS-5′UTR regulates hisG, a key gene in the histidine biosynthetic pathway in Salmonella enterica serovar Typhi

Bacterial noncoding RNAs (ncRNA) regulate diverse cellular processes, including virulence and environmental fitness. The malS 5′ untranslated region (named malS-5′UTR) was identified as a regulatory ncRNA that increases the invasive capacity of Salmonella enterica serovar Typhi. An IntaRNA search suggested base pairing between malS-5′UTR and hisG mRNA, a key gene in the histidine biosynthetic pathway. Overexpression of malS-5′UTR markedly reduced bacterial growth in minimal medium without histidine. Overexpression of malS-5′UTR increased mRNA from his operon genes, independently of the bax gene, and decreased HisG protein in Salmonella Typhi. RNA structure analysis showed base pairing of the malS-5′UTR RNA with the hisG mRNA across the ribosome binding site. Thus, we propose that malS-5′UTR inhibited hisG translation, probably by base pairing to the Shine–Dalgarno sequence.

The novel cis-encoded antisense RNA AsrC positively regulates the expression of rpoE-rseABC operon and thus enhances the motility of Salmonella enterica serovar typhi

Bacterial non-coding RNAs are essential in many cellular processes, including response to environmental stress, and virulence. Deep sequencing analysis of the Salmonella enterica serovar typhi (S. typhi) transcriptome revealed a novel antisense RNA transcribed in cis on the strand complementary to rseC, an activator gene of sigma factor RpoE. In this study, expression of this antisense RNA was confirmed in S. typhi by Northern hybridization. Rapid amplification of cDNA ends and sequence analysis identified an 893 bp sequence from the antisense RNA coding region that covered all of the rseC coding region in the reverse direction of transcription. This sequence of RNA was named as AsrC. After overexpression of AsrC with recombinantant plasmid in S. typhi, the bacterial motility was increased obviously. To explore the mechanism of AsrC function, regulation of rseC and rpoE expression by AsrC was investigated. We found that AsrC increased the levels of rseC mRNA and protein. The expression of rpoE was also increased in S. typhi after overexpression of AsrC, which was dependent on rseC. Thus, we propose that AsrC increased RseC level and indirectly activating RpoE which can initiate fliA expression and promote the motility of S. typhi.

5′-UTR of malS increases the invasive capacity of Salmonella enterica serovar Typhi by influencing the expression of bax

ABSTRACT 

Aim: An RNA-seq analysis recently identified a 236-nucleotide transcript upstream from malS in Salmonella enterica serovar Typhi. Here, we investigated its molecular characteristics and function. Materials & methods: RACE and northern blotting were used to determine the molecular characteristics of the sequence, and mutagenesis, microarray, immunoblotting and an invasion assay were used to investigate the functions of the transcript. Results: The transcript was identified as the malS 5′-untranslated region (UTR), which could influence the expression of the flagellar and SPI-1 genes and the invasion of HeLa cells by S. Typhi. Deletion of bax increased the expression of the invasion genes and the invasive capacity of S. Typhi, whereas the expression of the malS 5′-UTR reduced the expression of bax. Conclusion: The malS 5′-UTR reduces the expression of bax and increases the invasive capacity of S. Typhi.