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A small RNA controlled AND-gate regulates extrachromosomal DNA transfer in Salmonella

ABSTRACT: Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution. Transfer of conjugative plasmids is a complex process that needs to be synchronized with the physiological state of the bacterial host. While several host transcription factors are known to control the plasmid-borne transfer control genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. Here, we describe a post-transcriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two different seed pairing domains to recognize and activate the mRNAs of both the sigma-factor S and RicI, a cytoplasmic membrane protein. The latter is a hitherto unknown conjugation inhibitor whose transcription requires S. Together, RprA and S constitute a feed-forward loop with AND-gate logic which tightly controls RicI synthesis for selective suppression of plasmid conjugation under membrane stress. This study reports the first sRNA-controlled feed-forward loop based on double target activation and an unexpected function for a core-genome encoded small RNA in controlling extrachromosomal DNA transfer.

ORGANISM(S): Salmonella enterica Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

PROVIDER: GSE67187 | GEO | 2015/03/24

SECONDARY ACCESSION(S): PRJNA279204

REPOSITORIES: GEO

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RcgA and RcgR, two novel proteins involved in conjugative transfer of rhizobial plasmids

Project description:Rhizobia are gram-negative bacteria able to establish a symbiotic interaction with leguminous plants. Due to their nitrogen fixing capacity, the study of these microorganisms has acquired great relevance for the agriculture. Rhizobia usually harbor many plasmids in their genome which can be transferred to other organisms by conjugation. Two main mechanisms of regulation of rhizobial plasmid transfer have been described: Quorum sensing (QS) and rctA/rctB system. Nevertheless, new genes and molecules that modulate conjugative transfer have been recently described, demonstrating that new actors can tightly regulate the process. In this work, by means of bioinformatics tools and molecular biology approaches, two hypothetical genes are identified as playing key roles in conjugative transfer. These genes are located between conjugative genes of plasmid pLPU83a from Rhizobium favelukesii LPU83, a plasmid that showed a conjugative transfer behavior depending on the genomic background. One of the two mentioned genes, rcgA, is essential for conjugation, while the other, rcgR, acts as an inhibitor of the process. In addition to introducing this new regulatory mechanism, we show evidence of the functions of these genes in different genomic backgrounds, and confirmed that homologous proteins from non-closely related organisms play the same function. These findings set up a cornerstone for a new molecular circuit of conjugative transfer of plasmids.

2022-08-29 | PXD033583 | Pride

Vertical and horizontal gene transfer tradeoffs direct plasmid fitness

Project description:Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical E. coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.

2022-12-23 | GSE219270 | GEO

Transcriptome of Pseudomonas putida KT2440 harboring plasmid RP4 during conjugative transfer

Project description:We analyzed gene expression during conjugative transfer of plasmid RP4. Pairs of rifampicin-susceptible (RifS) and -resistance (RifR) strains of Pseudomonas putida KT2440 were conjugated for 10 minute on filter membrane in the presence of rifampicin to discriminate the expression changes in the donor and recipient cells.

2020-03-13 | GSE146879 | GEO

Impact of a conjugative plasmid on plant growth-promoting Bacillus velezensis

Project description:Bacillus velezensis strain GH1-13 with a native conjugative plasmid (pBV71) is thought to be beneficial to the bacterium, although no information on its effects exists. Here we show that strain GH1-13 frequently lost the plasmid during normal growth conditions in a rich medium and changed the morphology and sensitivity to selenite and tellurite. Compared to the plasmid-cured cells, the wild-type and complemented cells exhibited multicellular behavior with the expression of conjugative type IV pili and regulatory Rap homologous genes that regulate the interconnection between conjugation and biofilm formation. Further omics-based analyses of morphogenesis, biofilm formation, and antibiotic synthesis suggest that the conjugative plasmid activates envelope stress responses in association with increased biosynthesis of extracellular polysaccharide and antibiotics for protective functions of the host during exponential phase.

2021-05-17 | PXD017305 | Pride

RNASeq libraries of quorum-sensing induced and wild-type M. ciceri bv. biserrulae WSM1271

Project description:M. ciceri WSM1271 carries a novel integrative and conjugative element (ICE) termed a tripartite ICE (ICE3) that exists as thee separated DNA regions in the chromosome. Three site-specific recombinases acting on three distinct pairs of attachment sites catalyse recombination between the three ICE3 DNA regions leading to their excision from the chromosome to form a single plasmid-like entity for horizontal conjugative transfer. RNASeq was used to probe for differentially expressed ICE3-encoded genes in WSM1271 wild-type cells, and engineered WSM1271 cells carrying cloned copies of two quorum-sensing loci that induce ICE3 excision and transfer. Overall, 187 significantly differentially expressed genes (adjusted P-value < 0.05) were identified and although ICEMcSym1271 comprised only ~7.6% of the chromosome, 15.5% (29) of the differentially expressed genes were located on ICEMcSym1271. Genes likely involved in activation of excision and conjugation including rdfS, rlxS, msi172-msi171 and the type-IV conjugative pilus gene cluster msi031-trbBCDEJLFGI-msi021 were all significantly induced. The RNA-Seq libraries generated in this study have strongly aided the development of our model detailing the regulation of excision and transfer of ICE3s.

2018-03-01 | GSE108732 | GEO

SNP analysis of J2530

Project description:To search potential point mutation in J2530 strain which could suppress uvrD252 effect on conjugative plasmid transfer

2023-02-13 | E-MTAB-11748 | biostudies-arrayexpress

Conjugation, genetic reprogamming and horizontal transfer of pathogenicity between Roseobacters

Project description:Horizontal transfer of plasmids is one of the main drivers of bacterial adaptation, resulting e.g. in the spread of antibiotic resistance. We investigated the marine Roseobacter group and studied how conjugation affects the gene expression and biology of the new host. We showed that the two syntenic 126 kb and 191 kb plasmids of Dinoroseobacter shibae can be conjugated into representatives of all major lineages of Rhodobacteraceae. In the model organism Phaeobacter inhibens their acquisition resulted in differential expression of genes related to motility, transport and the synthesis of vitamins. Moreover, the decrease of the potent antibiotic tropodithietic acid reduced the energetic burden of Phaeobacter and resulted in an enhanced growth. While the T4SS systems of both plasmids were silenced in the new host, the ability to kill the dinoflagellate was exclusively transferred via the 191 kb plasmid from D. shibae to P. inhibens. Our findings showed drastic consequences of plasmid conjugation; genetic reprogramming of the novel host resulted in considerable fitness changes leading to the prediction that horizontal gene transfer triggers bacterial speciation.

2019-05-01 | GSE126149 | GEO

An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element

Project description:Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC can represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently-coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.

2021-11-26 | GSE189468 | GEO

Real-time visualization of drug resistance acquisition by horizontal gene transfer reveals a new role for AcrAB-TolC multidrug efflux pump

Project description:In our study, we obtained evidence showing that, in the presence of tetracycline, AcrAB-TolC multidrug efflux pump was required for production of protein encoded by a conjugative plasmid acquired by bacterial conjugation. We then address the role of AcrAB-TolC multidrug efflux pump on the level of protein synthesis activity in the presence of tetracycline, which inhibits protein translation by targeting ribosomal 16S rRNA and competing with binding of the anticodon-stem loop of an A-site tRNA. We used a quantitative TMT-nanoLC-mass spectrometry approach to obtained the protein relative abundance ratio before and after incubation with tetracycline, and so in wild-type(MG1655, K12) and AcrAB-TolC mutant strains (ΔacrA, ΔacrB and ΔtolC).

2019-07-16 | PXD011286 | Pride

High-resolution mapping of the pCAR1 plasmid transcriptomes in Pseudomonas

Project description:High-resolution mapping of the pCAR1 plasmid transcriptomes in the original host Pseudomonas resinovorans CA10 and the transconjugant Pseudomonas putida KT2440(pCAR1) While plasmids are replicated autonomously in their hosts, the transcription of plasmid genes can be switched through horizontal transfer by the change in the transcriptional networks. To examine whether and how the plasmid genome is differentially expressed, we analyzed the transcriptomes of the 199,035-bp IncP-7 carbazole catabolic and conjugative plasmid pCAR1 in the original host Pseudomonas resinovorans CA10 and the transconjugant Pseudomonas putida KT2440(pCAR1) during growth on carbazole or succinate using the high-resolution tiling array. The tiling array successfully detected the relatively large catabolic operons, for which transcription was induced during growth on carbazole regardless of the host. Compared between the hosts, nearly identical regions of pCAR1 were transcribed, but two hypothetical operons, i.e., ORF100-108 and ORF145-146, were transcribed at higher levels in KT2440(pCAR1) than in CA10. We verified the differential expression in heterologous hosts using quantitative RT-PCR. The tiling array analysis clearly revealed the transcription start sites, for which the positions and extents agreed with the primer extension experiments. Our data demonstrate that the transcriptome of the transmissible plasmid is altered through horizontal transfer, and we identified probable genes that are involved in plasmid functions in various hosts. This approach can be used to visualize flexible prokaryotic transcriptomes comprehensively. Keywords: high-resolution RNA mapping

2008-10-18 | GSE10862 | GEO

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