Editorial: LuxR Solos are Becoming Major Players in Cell–Cell Communication in Bacteria

Venturi, Vittorio; Ahmer, Brian M. M.

doi:10.3389/fcimb.2015.00089

Cited by 24 publications

(17 citation statements)

References 26 publications

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“…41,42 In fact, several genomic studies across different species have found many QS-related luxR type genes that are unpaired to a cognate luxI to synthesize the signaling molecule and thus encode “orphan” LuxR receptors or “solos”. 43,44 This supports our hypothesis that an “orphan” LuxR in Micromonospora sp. may be involved in interspecies communication by interacting with the small molecule signal from Rhodococcus sp.…”

Section: Resultssupporting

confidence: 86%

Omics Technologies to Understand Activation of a Biosynthetic Gene Cluster in Micromonospora sp. WMMB235: Deciphering Keyicin Biosynthesis

et al. 2019

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DNA sequencing of a large collection of bacterial genomes reveals a wealth of orphan biosynthetic gene clusters (BGCs) with no identifiable products. BGC silencing, for those orphan clusters that are truly silent, rather than those whose products have simply evaded detection and cluster correlation, is postulated to result from transcriptional inactivation of these clusters under standard laboratory conditions. Here, we employ a multi-omics approach to demonstrate how interspecies interactions modulate the keyicin producing kyc cluster at the transcriptome level in cocultures of kyc-bearing Micromonospora sp. and a Rhodococcus sp. We further correlate coculture dependent changes in keyicin production to changes in transcriptomic and proteomic profiles and show that these changes are attributable to small molecule signaling consistent with a quorum sensing pathway. In piecing together the various elements underlying keyicin production in coculture, this study highlights how omics technologies can expedite future efforts to understand and exploit silent BGCs.

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Section: Resultssupporting

confidence: 86%

Omics Technologies to Understand Activation of a Biosynthetic Gene Cluster in Micromonospora sp. WMMB235: Deciphering Keyicin Biosynthesis

et al. 2019

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“…Completely sequenced genomes of F. psychrophilum indicate the presence of quorum-sensing-related genes encoding LuxR-like proteins, but not LuxI homologs 2 . Nonetheless, it is well-known that LuxR “Solos” (i.e., LuxR-like receptors that lack a cognate LuxI-like synthase) can also respond to ligands other than AHLs (Venturi and Ahmer, 2015 ). We identified two luxR “Solos” in our transcriptomes, one of them being classified as non-DEG (FP0715) and another significantly downregulated in the biofilm state (FP2071, Table 1 ).…”

Section: Discussionmentioning

confidence: 99%

Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State

Levipan

Avendaño‐Herrera²

2017

Front. Cell. Infect. Microbiol.

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Flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease and the rainbow trout fry syndrome in salmonid aquaculture worldwide. However, there have been few studies into the capacity of F. psychrophilum to form biofilms and how these cellular accretions differ from planktonic cells or how they affect potential virulence. We evaluated the biofilm formation by three Chilean isolates of F. psychrophilum (LM-02-Fp, LM-06-Fp, and LM-13-Fp) and two non-Chilean strains (JIP02/86 and NCMB1947T), and compared biofilm and planktonic states to obtain insights into expression differences of virulence- and biofilm-related genes (VBRGs). Our findings are based on scanning confocal laser microscopy (SCLM) and LIVE/DEAD staining, enzymatic reactions, reverse transcription-quantitative PCR (RT-qPCR) of genes encoding putative virulence factors, and transcriptomes (RNA-Seq). The LM-02-Fp and NCMB1947T strains were the strongest and weakest biofilm producers, respectively. The strong-biofilm producer showed different physiological cell states distributed in different layers of mature biofilms, whereas the NCMB1947T biofilms consisted of cells arranged in a monolayer. WGA-binding exopolysaccharides would be the main components of their corresponding extracellular matrices. Transcriptomes of F. psychrophilum NCMB1947T and LM-02-Fp were clustered by state (biofilm vs. planktonic) rather than by strain, indicating important state-dependent differences in gene expression. Analysis of differentially expressed genes between states identified putative VBRGs involved in polysaccharide biosynthesis, lateral gene transfer, membrane transport (e.g., for drugs and Fe3+), sensory mechanisms, and adhesion, and indicated that about 60–100% of VBRGs involved in these processes was significantly upregulated in the biofilm state. Conversely, upregulated motility-related genes in the biofilm state were not identified, whereas a lower fraction of proteolysis-related genes (33%) was upregulated in biofilms. In summary, F. psychrophilum strains that produce different biofilm phenotypes show global transcriptional activity in the mature biofilm state that differs significantly from their planktonic counterparts. Also, different biofilm phenotypes share a genetic potential for virulence that is transcriptionally enhanced with respect to free-living cells. Our results suggest that the F. psychrophilum biofilm lifestyle acts as a reservoir for a given set of putative virulence factors, and recommend a deeper understanding of which could help prevent recurring infections in salmonid farms.

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“…However, SdiA is an orphan HSL receptor in E. coli and closely related species, which cannot synthesize HSLs. While SdiA maintains weak activity in the absence of HSL, binding to cognate HSLs of other species improves its function and permits sensing of the microbial environment (Smith and Ahmer, 2003;Dyszel et al, 2010;Venturi and Ahmer, 2015). The finding that HSLs produced by other species act as a signal to E. coli via SdiA, with important effects on physiology (Hughes et al, 2010;Sperandio, 2010;Lu et al, 2017), suggests that the Csr system may participate in the regulation of bacterial interspecies communications, in addition to its well-studied roles in virulence and host-microbe interactions (Vakulskas et al, 2015).…”

Section: Reciprocal Interactions With Transcriptional Regulatory Systemsmentioning

confidence: 99%

Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA

et al. 2020

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The carbon storage regulator (Csr) or repressor of stationary phase metabolites (Rsm) system of Gammaproteobacteria is among the most complex and best-studied posttranscriptional regulatory systems. Based on a small RNA-binding protein, CsrA and homologs, it controls metabolism, physiology, and bacterial lifestyle decisions by regulating gene expression on a vast scale. Binding of CsrA to sequences containing conserved GGA motifs in mRNAs can regulate translation, RNA stability, riboswitch function, and transcript elongation. CsrA governs the expression of dozens of transcription factors and other regulators, further expanding its influence on cellular physiology, and these factors can participate in feedback to the Csr system. Expression of csrA itself is subject to autoregulation via translational inhibition and indirect transcriptional activation. CsrA activity is controlled by small noncoding RNAs (sRNAs), CsrB and CsrC in Escherichia coli, which contain multiple high affinity CsrA binding sites that compete with those of mRNA targets. Transcription of CsrB/C is induced by certain nutrient limitations, cellular stresses, and metabolites, while these RNAs are targeted for degradation by the presence of a preferred carbon source. Consistent with these findings, CsrA tends to activate pathways and processes that are associated with robust growth and repress stationary phase metabolism and stress responses. Regulatory loops between Csr components affect the signaling dynamics of the Csr system. Recently, systems-based approaches have greatly expanded our understanding of the roles played by CsrA, while reinforcing the notion that much remains to be learned about the Csr system.

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Editorial: LuxR Solos are Becoming Major Players in Cell–Cell Communication in Bacteria

Cited by 24 publications

References 26 publications

Omics Technologies to Understand Activation of a Biosynthetic Gene Cluster in Micromonospora sp. WMMB235: Deciphering Keyicin Biosynthesis

Omics Technologies to Understand Activation of a Biosynthetic Gene Cluster in Micromonospora sp. WMMB235: Deciphering Keyicin Biosynthesis

Different Phenotypes of Mature Biofilm in Flavobacterium psychrophilum Share a Potential for Virulence That Differs from Planktonic State

Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA

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