Signaling specificity in the c-di-GMP-dependent network regulating antibiotic synthesis in Lysobacter

Xu, Gaoge; Han, Sen; Huo, Cuimei; Chin, Ko‐Hsin; Chou, Shan‐Ho; Gomelsky, Mark; Qian, Guoliang; Liu, Fengquan

doi:10.1093/nar/gky803

Cited by 57 publications

(148 citation statements)

References 60 publications

(88 reference statements)

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“…Clp has been well studied as a cyclic di-GMP-responsive transcriptional regulator that plays essential roles in virulence factor production and in the DSF signaling network (30,31). Previous findings have demonstrated that Clp is the major regulator of HSAF biosynthesis gene expression in L. enzymogenes (20,32). The present study revealed that Clp acts as a transcriptional activator to directly positively regulate RpfB1 and RpfB2 expression ( Fig.…”

Section: Lenzymogenessupporting

confidence: 61%

Two Functional Fatty Acyl Coenzyme A Ligases Affect Free Fatty Acid Metabolism To Block Biosynthesis of an Antifungal Antibiotic in Lysobacter enzymogenes

Hou

et al. 2020

Appl Environ Microbiol

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In Lysobacter enzymogenes OH11, RpfB1 and RpfB2 were predicted to encode acyl coenzyme A (CoA) ligases. RpfB1 is located in the Rpf gene cluster. Interestingly, we found an RpfB1 homolog (RpfB2) outside this canonical gene cluster, and nothing is known about its functionality or mechanism. Here, we report that rpfB1 and rpfB2 can functionally replace EcFadD in the Escherichia coli fadD mutant JW1794. RpfB activates long-chain fatty acids (n-C16:0 and n-C18:0) for the corresponding fatty acyl-CoA ligase (FCL) activity in vitro, and Glu-361 plays critical roles in the catalytic mechanism of RpfB1 and RpfB2. Deletion of rpfB1 and rpfB2 resulted in significantly increased heat-stable antifungal factor (HSAF) production, and overexpression of rpfB1 or rpfB2 completely suppressed HSAF production. Deletion of rpfB1 and rpfB2 resulted in increased L. enzymogenes diffusible signaling factor 3 (LeDSF3) synthesis in L. enzymogenes. Overall, our results showed that changes in intracellular free fatty acid levels significantly altered HSAF production. Our report shows that intracellular free fatty acids are required for HSAF production and that RpfB affects HSAF production via FCL activity. The global transcriptional regulator Clp directly regulated the expression of rpfB1 and rpfB2. In conclusion, these findings reveal new roles of RpfB in antibiotic biosynthesis in L. enzymogenes. IMPORTANCE Understanding the biosynthetic and regulatory mechanisms of heat-stable antifungal factor (HSAF) could improve the yield in Lysobacter enzymogenes. Here, we report that RpfB1 and RpfB2 encode acyl coenzyme A (CoA) ligases. Our research shows that RpfB1 and RpfB2 affect free fatty acid metabolism via fatty acyl-CoA ligase (FCL) activity to reduce the substrate for HSAF synthesis and, thereby, block HSAF production in L. enzymogenes. Furthermore, these findings reveal new roles for the fatty acyl-CoA ligases RpfB1 and RpfB2 in antibiotic biosynthesis in L. enzymogenes. Importantly, the novelty of this work is the finding that RpfB2 lies outside the Rpf gene cluster and plays a key role in HSAF production, which has not been reported in other diffusible signaling factor (DSF)/Rpf-producing bacteria.

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Section: Lenzymogenessupporting

confidence: 61%

Two Functional Fatty Acyl Coenzyme A Ligases Affect Free Fatty Acid Metabolism To Block Biosynthesis of an Antifungal Antibiotic in Lysobacter enzymogenes

Hou

et al. 2020

Appl Environ Microbiol

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“…C). Since we already knew that expression of this operon is sensitive to c‐di‐GMP concentrations (Xu et al , ) and CdgL binding to c‐di‐GMP (Fig. A), we decided to investigate the mechanism through which CdgL operates.…”

Section: Resultsmentioning

confidence: 99%

“…Since CdgL protein lacks a distinct DNA‐binding domain, it is unlikely to control transcription of HSAF operon directly. We thus hypothesized that CdgL affects HSAF operon transcription by acting upstream of one of the previously identified transcription regulators of this operon, Clp, MarR or LysR (Su et al , , ; Xu et al , ). To test this hypothesis, we assessed the ability of CdgL to bind to each of these activators.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, cyclic di‐GMP (c‐di‐GMP), a ubiquitous bacterial second messenger (Ross et al , ) that controls cellular processes through binding to intracellular receptor (or effectors) proteins and riboswitches, also controls HSAF biosynthesis according to our earlier studies, where we found that elevated levels of c‐di‐GMP inhibited antibiotic production at the level of HSAF biosynthesis operon transcription (Chen et al , ). We have identified a signal transduction pathway involving the c‐di‐GMP‐binding transcription activator, Clp, as the major target of c‐di‐GMP‐dependent inhibition (Xu et al , ). Cyclic di‐GMP decreases the affinity of Clp binding to the promoter region upstream of the HSAF biosynthesis operon, which lowers operon expression.…”

Section: Introductionmentioning

confidence: 99%

“…Cyclic di‐GMP decreases the affinity of Clp binding to the promoter region upstream of the HSAF biosynthesis operon, which lowers operon expression. Interestingly, Clp is sequestered by a membrane‐bound c‐di‐GMP phosphodiesterase, PDE (LchP), and is released to function in response to an as yet unidentified environmental factor (Xu et al , ).…”

Section: Introductionmentioning

confidence: 99%

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A YajQ‐LysR‐like, cyclic di‐GMP‐dependent system regulating biosynthesis of an antifungal antibiotic in a crop‐protecting bacterium, Lysobacter enzymogenes

Han

Shen

Wang

et al. 2019

Molecular Plant Pathology

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YajQ, a binding protein of the universal bacterial second messenger cyclic di-GMP (c-di-GMP), affects virulence in several bacterial pathogens, including Xanthomonas campestris. In this bacterium, YajQ interacts with the transcription factor LysR. Upon c-di-GMP binding, the whole c-di-GMP-YajQ-LysR complex is found to dissociate from DNA, resulting in virulence gene regulation. Here, we identify a YajQ-LysR-like system in the bacterial biocontrol agent Lysobacter enzymogenes OH11 that secretes an antifungal antibiotic, heat-stable antifungal factor (HSAF) against crop fungal pathogens. We show that the YajQ homologue, CdgL (c-di-GMP receptor interacting with LysR) affects expression of the HSAF biosynthesis operon by interacting with the transcription activator LysR. The CdgL-LysR interaction enhances the apparent affinity of LysR to the promoter region upstream of the HSAF biosynthesis operon, which increases operon expression. Unlike the homologues CdgL (YajQ)-LysR system in X. campestris, we show that c-di-GMP binding to CdgL seems to weaken CdgL-LysR interactions and promote the release of CdgL from the LysR-DNA complex, which leads to decreased expression. Together, this study takes the YajQ-LysR-like system from bacterial pathogens to a crop-protecting bacterium that is able to regulate antifungal HSAF biosynthesis via disassembly of the c-di-GMP receptortranscription activator complex.

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Identification of atypical T4SS effector proteins mediating bacterial defense

Shen,

Yang,

et al. 2023

mLife

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To remain competitive, proteobacteria use various contact‐dependent weapon systems to defend against microbial competitors. The bacterial‐killing type IV secretion system (T4SS) is one such powerful weapon. It commonly controls the killing/competition between species by secreting the lethal T4SS effector (T4E) proteins carrying conserved XVIPCD domains into competing cells. In this study, we sought knowledge to understand whether the bacterial‐killing T4SS‐producing bacteria encode T4E‐like proteins and further explore their biological functions. To achieve this, we designed a T4E‐guided approach to discover T4E‐like proteins that are designated as atypical T4Es. Initially, this approach required scientists to perform simple BlastP search to identify T4E homologs that lack the XVIPCD domain in the genomes of T4SS‐producing bacteria. These homologous genes were then screened in Escherichia coli to identify antibacterial candidates (atypical T4Es) and their neighboring detoxification proteins, followed by testing their gene cotranscription and validating their physical interactions. Using this approach, we did discover two atypical T4E proteins from the plant‐beneficial Lysobacter enzymogenes and the phytopathogen Xanthomonas citri. We also provided substantial evidence to show that the atypical T4E protein Le1637‐mediated bacterial defense in interspecies interactions between L. enzymogenes and its competitors. Therefore, the newly designed T4E‐guided approach holds promise for detecting functional atypical T4E proteins in bacterial cells.

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Signaling specificity in the c-di-GMP-dependent network regulating antibiotic synthesis in Lysobacter

Cited by 57 publications

References 60 publications

Two Functional Fatty Acyl Coenzyme A Ligases Affect Free Fatty Acid Metabolism To Block Biosynthesis of an Antifungal Antibiotic in Lysobacter enzymogenes

Two Functional Fatty Acyl Coenzyme A Ligases Affect Free Fatty Acid Metabolism To Block Biosynthesis of an Antifungal Antibiotic in Lysobacter enzymogenes

A YajQ‐LysR‐like, cyclic di‐GMP‐dependent system regulating biosynthesis of an antifungal antibiotic in a crop‐protecting bacterium, Lysobacter enzymogenes

Identification of atypical T4SS effector proteins mediating bacterial defense

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