Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1

ABSTRACT Dickeya zeae is an important and aggressive bacterial phytopathogen that can cause substantial economic losses in banana and rice plantations. We previously showed that c-di-GMP signaling proteins (cyclases/phosphodiesterases) in D. zeae strain EC1 play a significant role in the bacterial s...

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Main Authors: Yufan Chen, Jianuan Zhou, Mingfa Lv, Zhibin Liang, Matthew R. Parsek, Lian-hui Zhang
Format: Article
Language:English
Published: American Society for Microbiology 2020-12-01
Series:mBio
Subjects:
Online Access:https://journals.asm.org/doi/10.1128/mBio.02993-20
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author Yufan Chen
Jianuan Zhou
Mingfa Lv
Zhibin Liang
Matthew R. Parsek
Lian-hui Zhang
author_facet Yufan Chen
Jianuan Zhou
Mingfa Lv
Zhibin Liang
Matthew R. Parsek
Lian-hui Zhang
author_sort Yufan Chen
collection DOAJ
description ABSTRACT Dickeya zeae is an important and aggressive bacterial phytopathogen that can cause substantial economic losses in banana and rice plantations. We previously showed that c-di-GMP signaling proteins (cyclases/phosphodiesterases) in D. zeae strain EC1 play a significant role in the bacterial sessile-to-motile transition. To determine whether there is any synergistic effect among these c-di-GMP signaling proteins, we prepared a series of mutant strains by generating consecutive in-frame deletions of the genes encoding diguanylate cyclases (which make c-di-GMP) and phosphodiesterases (which break down c-di-GMP), respectively, using EC1 as a parental strain. The results showed that the complete deletion of all the putative diguanylate cyclases resulted in significantly increased bacterial motility and abrogated biofilm formation but did not appear to affect pathogenicity and virulence factor production. In contrast, the deletion of all the c-di-GMP phosphodiesterase genes disabled motility and prevented the invasion of EC1 into rice seeds. By measuring the c-di-GMP concentrations and swimming motility of all the mutants, we propose that c-di-GMP controlled swimming behavior through a multitiered program in a c-di-GMP concentration-dependent manner, which could be described as an L-shaped regression curve. These features are quite different from those that have been shown for other bacterial species such as Salmonella and Caulobacter crescentus. Further analysis identified three c-di-GMP signaling proteins, i.e., PDE10355, DGC14945, and PDE14950, that play dominant roles in influencing the global c-di-GMP pool of strain EC1. The findings from this study highlight the complexity and plasticity of c-di-GMP regulatory circuits in different bacterial species. IMPORTANCE Dickeya zeae is the etiological agent of bacterial foot rot disease, which can cause massive economic losses in banana and rice plantations. Genome sequence analysis showed that D. zeae strain EC1 contains multiple c-di-GMP turnover genes, but their roles and regulatory mechanisms in bacterial physiology and virulence remain vague. By generating consecutive in-frame deletion mutants of the genes encoding c-di-GMP biosynthesis and degradation, respectively, we analyzed the individual and collective impacts of these c-di-GMP metabolic genes on the c-di-GMP global pool, bacterial physiology, and virulence. The significance of our study is in identifying the mechanism of c-di-GMP signaling in strain EC1 more clearly, which expands the c-di-GMP regulating patterns in Gram-negative species. The methods and experimental designs in this research will provide a valuable reference for the exploration of the complex c-di-GMP regulation mechanisms in other bacteria.
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spelling doaj.art-b3876d496b424711825e290ee4cfcdde2022-12-21T19:08:54ZengAmerican Society for MicrobiologymBio2150-75112020-12-0111610.1128/mBio.02993-20Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1Yufan Chen0Jianuan Zhou1Mingfa Lv2Zhibin Liang3Matthew R. Parsek4Lian-hui Zhang5Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People’s Republic of ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People’s Republic of ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People’s Republic of ChinaGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People’s Republic of ChinaDepartment of Microbiology, University of Washington, Seattle, Washington, USAGuangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People’s Republic of ChinaABSTRACT Dickeya zeae is an important and aggressive bacterial phytopathogen that can cause substantial economic losses in banana and rice plantations. We previously showed that c-di-GMP signaling proteins (cyclases/phosphodiesterases) in D. zeae strain EC1 play a significant role in the bacterial sessile-to-motile transition. To determine whether there is any synergistic effect among these c-di-GMP signaling proteins, we prepared a series of mutant strains by generating consecutive in-frame deletions of the genes encoding diguanylate cyclases (which make c-di-GMP) and phosphodiesterases (which break down c-di-GMP), respectively, using EC1 as a parental strain. The results showed that the complete deletion of all the putative diguanylate cyclases resulted in significantly increased bacterial motility and abrogated biofilm formation but did not appear to affect pathogenicity and virulence factor production. In contrast, the deletion of all the c-di-GMP phosphodiesterase genes disabled motility and prevented the invasion of EC1 into rice seeds. By measuring the c-di-GMP concentrations and swimming motility of all the mutants, we propose that c-di-GMP controlled swimming behavior through a multitiered program in a c-di-GMP concentration-dependent manner, which could be described as an L-shaped regression curve. These features are quite different from those that have been shown for other bacterial species such as Salmonella and Caulobacter crescentus. Further analysis identified three c-di-GMP signaling proteins, i.e., PDE10355, DGC14945, and PDE14950, that play dominant roles in influencing the global c-di-GMP pool of strain EC1. The findings from this study highlight the complexity and plasticity of c-di-GMP regulatory circuits in different bacterial species. IMPORTANCE Dickeya zeae is the etiological agent of bacterial foot rot disease, which can cause massive economic losses in banana and rice plantations. Genome sequence analysis showed that D. zeae strain EC1 contains multiple c-di-GMP turnover genes, but their roles and regulatory mechanisms in bacterial physiology and virulence remain vague. By generating consecutive in-frame deletion mutants of the genes encoding c-di-GMP biosynthesis and degradation, respectively, we analyzed the individual and collective impacts of these c-di-GMP metabolic genes on the c-di-GMP global pool, bacterial physiology, and virulence. The significance of our study is in identifying the mechanism of c-di-GMP signaling in strain EC1 more clearly, which expands the c-di-GMP regulating patterns in Gram-negative species. The methods and experimental designs in this research will provide a valuable reference for the exploration of the complex c-di-GMP regulation mechanisms in other bacteria.https://journals.asm.org/doi/10.1128/mBio.02993-20Dickeya zeaec-di-GMPbiofilm formationswimming motilityconsecutive in-frame deletionsessile-to-motile transition
spellingShingle Yufan Chen
Jianuan Zhou
Mingfa Lv
Zhibin Liang
Matthew R. Parsek
Lian-hui Zhang
Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1
mBio
Dickeya zeae
c-di-GMP
biofilm formation
swimming motility
consecutive in-frame deletion
sessile-to-motile transition
title Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1
title_full Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1
title_fullStr Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1
title_full_unstemmed Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1
title_short Systematic Analysis of c-di-GMP Signaling Mechanisms and Biological Functions in <named-content content-type="genus-species">Dickeya zeae</named-content> EC1
title_sort systematic analysis of c di gmp signaling mechanisms and biological functions in named content content type genus species dickeya zeae named content ec1
topic Dickeya zeae
c-di-GMP
biofilm formation
swimming motility
consecutive in-frame deletion
sessile-to-motile transition
url https://journals.asm.org/doi/10.1128/mBio.02993-20
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