scholarly journals Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 305
Author(s):  
Dominika Houserova ◽  
Donovan J. Dahmer ◽  
Shivam V. Amin ◽  
Valeria M. King ◽  
Emmaline C. Barnhill ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Northern Blotting ◽  
Protein Coding ◽  
Mrna Targets ◽  
Stress Survival ◽  
Serovar Typhimurium ◽  
Intergenic Regions

An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50–500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement in the Salmonella CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the Salmonella enterica sRNAs described to date.

scholarly journals Characterization of 475 novel, putative small RNAs (sRNAs) in Carbon-starved Salmonella enterica serovar typhimurium

2021 ◽  
Author(s):  
Dominika M Houserova ◽  
Donavon J Dahmer ◽  
Shivam V Amin ◽  
Valeria M King ◽  
Emmaline C Barnhill ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Foodborne Pathogen ◽  
Northern Blotting ◽  
Protein Coding ◽  
Mrna Targets ◽  
Stress Survival ◽  
Serovar Typhimurium

An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression when bacteria faces various environmental stressors. Salmonella enterica, a well-studied foodborne pathogen, is known for its ability to survive in and adapt to various environmental challenges, making it a difficult pathogen to eliminate, as well as an important model for examining ncRNA contributions to cellular stress survival. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress response. Generally thought to be 50-500 nucleotides in length and to occur mainly in intergenic regions, sRNAs regulate protein expression through base pairing with mRNA targets. Through employing a refined definition of sRNAs that allows for shorter sequences and for sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during Carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs. Additionally, our computational analyses find the majority to be highly conserved and structurally-related to known sRNAs. Importantly, we show that deletion of one of the dynamic sRNAs, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement (and suggesting the involvements of many other sRNAs identified in this work) in the Salmonella CSR. Strikingly, the 475 novel sRNAs identified in this study more than double the number of Salmonella enterica serovar Typhimurium SL1344 sRNAs described to date, increasing the total number of annotated Salmonella sRNAs from 396 to 871. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and strongly suggests that sRNA loci likely outnumber those of protein-coding genes in Salmonella.

scholarly journals Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium

RNA Biology ◽  
2019 ◽  
Vol 16 (11) ◽  
pp. 1643-1657 ◽  
Author(s):  
Emmaline C. Barnhill ◽  
Aline Crucello ◽  
Dominika Houserova ◽  
Valeria M. King ◽  
Shivam V. Amin ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Small Rnas ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Serovar Typhimurium

scholarly journals Structural and Functional Characterization of ScsC, a Periplasmic Thioredoxin-Like Protein from Salmonella enterica Serovar Typhimurium

2013 ◽  
Vol 19 (13) ◽  
pp. 1494-1506 ◽  
Author(s):  
Mark Shepherd ◽  
Begoña Heras ◽  
Maud E. S. Achard ◽  
Gordon J. King ◽  
M. Pilar Argente ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Functional Characterization ◽  
Serovar Typhimurium

scholarly journals σE Regulates and Is Regulated by a Small RNA in Escherichia coli

2007 ◽  
Vol 189 (11) ◽  
pp. 4243-4256 ◽  
Author(s):  
Karl M. Thompson ◽  
Virgil A. Rhodius ◽  
Susan Gottesman
Keyword(s):  
Escherichia Coli ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Response Regulator ◽  
Heterologous Promoter ◽  
Genomic Libraries ◽  
Multicopy Suppressors ◽  
Intergenic Regions ◽  
Transposon Mutants

ABSTRACT RybB is a small, Hfq-binding noncoding RNA originally identified in a screen of conserved intergenic regions in Escherichia coli. Fusions of the rybB promoter to lacZ were used to screen plasmid genomic libraries and genomic transposon mutants for regulators of rybB expression. A number of plasmids, including some carrying rybB, negatively regulated the fusion. An insertion in the rep helicase and one upstream of dnaK decreased expression of the fusion. Multicopy suppressors of these insertions led to identification of two plasmids that stimulated the fusion. One contained the gene for the response regulator OmpR; the second contained mipA, encoding a murein hydrolase. The involvement of MipA and OmpR in cell surface synthesis suggested that the rybB promoter might be dependent on σE. The sequence upstream of the +1 of rybB contains a consensus σE promoter. The activity of rybB-lacZ was increased in cells lacking the RseA anti-sigma factor and when σE was overproduced from a heterologous promoter. The activity of rybB-lacZ and the detection of RybB were totally abolished in an rpoE-null strain. In vitro, σE efficiently transcribes from this promoter. Both a rybB mutation and an hfq mutation significantly increased expression of both rybB-lacZ and rpoE-lacZ fusions, consistent with negative regulation of the σE response by RybB and other small RNAs. Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate σE-dependent promoters in an RseA-independent fashion.

scholarly journals Characterization of a Laboratory-Derived, High-Level Ampicillin-Resistant Salmonella enterica Serovar Typhimurium Strain That Caused Meningitis in an Infant

2002 ◽  
Vol 46 (5) ◽  
pp. 1604-1606 ◽  
Author(s):  
Cheng-Hsun Chiu ◽  
Chishih Chu ◽  
Lin-Hui Su ◽  
Wan-Yu Wu ◽  
Tsu-Lan Wu
Keyword(s):  
Cerebrospinal Fluid ◽  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Cloning Vector ◽  
Typhimurium Strain ◽  
Serovar Typhimurium ◽  
High Level ◽  
Lactamase Gene

ABSTRACT A Salmonella enterica serovar Typhimurium strain that harbored a plasmid carrying a TEM-1-type β-lactamase gene was isolated from the blood and cerebrospinal fluid of an infant with meningitis. This 3.2-kb plasmid was further characterized to be a nonconjugative pGEM series cloning vector containing a foreign insert. The strain was likely laboratory derived and contaminated the environment before it caused the infection.

scholarly journals Characterization of the Genomes of a Diverse Collection of Salmonella enterica Serovar Typhimurium Definitive Phage Type 104

2008 ◽  
Vol 190 (24) ◽  
pp. 8155-8162 ◽  
Author(s):  
Fiona J. Cooke ◽  
Derek J. Brown ◽  
Maria Fookes ◽  
Derek Pickard ◽  
Alasdair Ivens ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Fragment Size ◽  
Phage Type ◽  
Antibiotic Resistance Genes ◽  
Serovar Typhimurium ◽  
Mlst Type ◽  
Plasmid Profiling ◽  
Type Sequence

ABSTRACT Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We completed the full DNA sequence of one DT104 strain, NCTC13348, and showed that significant differences between the genome of this isolate and the genome of the previously sequenced strain Salmonella serovar Typhimurium LT2 are due to integrated prophage elements and Salmonella genomic island 1 encoding antibiotic resistance genes. Thirteen isolates of Salmonella serovar Typhimurium DT104 with different pulsed-field gel electrophoresis (PFGE) profiles were analyzed by using multilocus sequence typing (MLST), plasmid profiling, hybridization to a pan-Salmonella DNA microarray, and prophage-based multiplex PCR. All the isolates belonged to a single MLST type, sequence type ST19. Microarray data demonstrated that the gene contents of the 13 DT104 isolates were remarkably conserved. The PFGE DNA fragment size differences in these isolates could be explained to a great extent by differences in the prophage and plasmid contents. Thus, here the nature of variation in different Salmonella serovar Typhimurium DT104 isolates is further defined at the gene and whole-genome levels, illustrating how this phage type evolves over time.

scholarly journals First Report of a Foodborne Salmonella enterica Serovar Gloucester (4:i:l,w) ST34 Strain Harboring blaCTX–M–55 and qnrS Genes Located in IS26-Mediated Composite Transposon

2021 ◽  
Vol 12 ◽  
Author(s):  
Lili Li ◽  
Rikke Heidemann Olsen ◽  
Anhua Song ◽  
Jian Xiao ◽  
Chong Wang ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Structural Unit ◽  
Bacterial Species ◽  
Meat Products ◽  
Sequence Type ◽  
E Coli ◽  
Serovar Typhimurium ◽  
Long Read ◽  
Phenotypic And Genotypic Characterization

Extended-spectrum β-lactamases (ESBLs) production and (fluoro)quinolone (FQ) resistance among Salmonella pose a public health threat. The objective of this study was the phenotypic and genotypic characterization of an ESBL-producing and nalidixic acid-resistant Salmonella enterica serovar Gloucester isolate (serotype 4:i:l,w) of sequence type 34 (ST34) from ready-to-eat (RTE) meat products in China. Whole-genome short and long read sequencing (HiSeq and MinION) results showed that it contained blaCTX–M–55, qnrS1, and tetB genes, with blaCTX–M–55 and qnrS1 located in chromosomal IS26-mediated composite transposon (IS26–qnrS1–IS3–Tn3–orf–blaCTX–M–55–ISEcp1–IS26). The same genetic structure was found in the chromosome of S. enterica subsp. enterica serovar Typhimurium strain and in several plasmids of Escherichia coli, indicating that the IS26-mediated composite transposon in the chromosome of S. Gloucester may originate from plasmids of E. coli and possess the ability to disseminate to Salmonella and other bacterial species. Besides, the structural unit qnrS1–IS3–Tn3–orf–blaCTX–M–55 was also observed to be linked with ISKpn19 in both the chromosomes and plasmids of various bacteria species, highlighting the contribution of the insertion sequences (IS26 and ISKpn19) to the co-dissemination of blaCTX–M–55 and qnrS1. To our knowledge, this is the first description of chromosomal blaCTX–M–55 and qnrS in S. Gloucester from RTE meat products. Our work expands the host range and provides additional evidence of the co-transfer of blaCTX–M–55 and qnrS1 among different species of Salmonella through the food chain.

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