Second Messenger Signaling in Bacillus subtilis: Accumulation of Cyclic di-AMP Inhibits Biofilm Formation

AbstractThe guanosine-based second messengers (p)ppGpp and c-di-GMP are key players of the physiological regulation of the Gram-positive model organism Bacillus subtilis. Their regulatory spectrum ranges from key metabolic processes over motility to biofilm formation. Here we review our mechanistic knowledge on their synthesis and degradation in response to environmental and stress signals as well as what is known on their cellular effectors and targets. Moreover, we discuss open questions and our gaps in knowledge on these two important second messengers.

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Yin and Yang of Biofilm Formation and Cyclic di-GMP Signaling of the Gastrointestinal Pathogen Salmonella enterica Serovar Typhimurium

Journal of Innate Immunity ◽

10.1159/000519573 ◽

2021 ◽

pp. 1-18

Author(s):

Agaristi Lamprokostopoulou ◽

Ute Römling

Keyword(s):

Biofilm Formation ◽

Second Messenger ◽

Bacterial Biofilm ◽

Chronic Infections ◽

Nutrient Sources ◽

Microbial Biofilms ◽

Extracellular Signaling ◽

Serovar Typhimurium ◽

Yin And Yang ◽

Second Messenger Signaling

Within the last 60 years, microbiological research has challenged many dogmas such as bacteria being unicellular microorganisms directed by nutrient sources; these investigations produced new dogmas such as cyclic diguanylate monophosphate (cyclic di-GMP) second messenger signaling as a ubiquitous regulator of the fundamental sessility/motility lifestyle switch on the single-cell level. Successive investigations have not yet challenged this view; however, the complexity of cyclic di-GMP as an intracellular bacterial signal, and, less explored, as an extracellular signaling molecule in combination with the conformational flexibility of the molecule, provides endless opportunities for cross-kingdom interactions. Cyclic di-GMP-directed microbial biofilms commonly stimulate the immune system on a lower level, whereas host-sensed cyclic di-GMP broadly stimulates the innate and adaptive immune responses. Furthermore, while the intracellular second messenger cyclic di-GMP signaling promotes bacterial biofilm formation and chronic infections, oppositely, <i>Salmonella</i> Typhimurium cellulose biofilm inside immune cells is not endorsed. These observations only touch on the complexity of the interaction of biofilm microbial cells with its host. In this review, we describe the Yin and Yang interactive concepts of biofilm formation and cyclic di-GMP signaling using <i>S</i>. Typhimurium as an example.

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Evidence for Cyclic Di-GMP-Mediated Signaling in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.01092-12 ◽

2012 ◽

Vol 194 (18) ◽

pp. 5080-5090 ◽

Cited By ~ 69

Author(s):

Yun Chen ◽

Yunrong Chai ◽

Jian-hua Guo ◽

Richard Losick

Keyword(s):

Bacillus Subtilis ◽

Biofilm Formation ◽

Second Messenger ◽

Negative Control ◽

Gram Negative Bacteria ◽

Flagellar Motor ◽

Positive Bacterium ◽

Content Type ◽

Deletion Mutations ◽

Cellular Processes

ABSTRACTCyclic di-GMP (c-di-GMP) is a second messenger that regulates diverse cellular processes in bacteria, including motility, biofilm formation, cell-cell signaling, and host colonization. Studies of c-di-GMP signaling have chiefly focused on Gram-negative bacteria. Here, we investigated c-di-GMP signaling in the Gram-positive bacteriumBacillus subtilisby constructing deletion mutations in genes predicted to be involved in the synthesis, breakdown, or response to the second messenger. We found that a putative c-di-GMP-degrading phosphodiesterase, YuxH, and a putative c-di-GMP receptor, YpfA, had strong influences on motility and that these effects depended on sequences similar to canonical EAL and RxxxR—D/NxSxxG motifs, respectively. Evidence indicates that YpfA inhibits motility by interacting with the flagellar motor protein MotA and thatyuxHis under the negative control of the master regulator Spo0A∼P. Based on these findings, we propose that YpfA inhibits motility in response to rising levels of c-di-GMP during entry into stationary phase due to the downregulation ofyuxHby Spo0A∼P. We also present evidence that YpfA has a mild influence on biofilm formation.In toto, our results demonstrate the existence of a functional c-di-GMP signaling system inB. subtilisthat directly inhibits motility and directly or indirectly influences biofilm formation.

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Cyclic di-AMP Acts as an Extracellular Signal That ImpactsBacillus subtilisBiofilm Formation and Plant Attachment

mBio ◽

10.1128/mbio.00341-18 ◽

2018 ◽

Vol 9 (2) ◽

Cited By ~ 26

Author(s):

Loni Townsley ◽

Sarah M. Yannarell ◽

Tuanh Ngoc Huynh ◽

Joshua J. Woodward ◽

Elizabeth A. Shank

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Intracellular Signaling ◽

Biofilm Formation ◽

Plant Root ◽

Second Messenger ◽

Pathogen Resistance ◽

Plant Roots ◽

Extracellular Signal ◽

The Impact

ABSTRACTThere is a growing appreciation for the impact that bacteria have on higher organisms. Plant roots often harbor beneficial microbes, such as the Gram-positive rhizobacteriumBacillus subtilis, that influence their growth and susceptibility to disease. The ability to form surface-attached microbial communities called biofilms is crucial for the ability ofB. subtilisto adhere to and protect plant roots. In this study, strains harboring deletions of theB. subtilisgenes known to synthesize and degrade the second messenger cyclic di-adenylate monophosphate (c-di-AMP) were examined for their involvement in biofilm formation and plant attachment. We found that intracellular production of c-di-AMP impacts colony biofilm architecture, biofilm gene expression, and plant attachment inB. subtilis. We also show thatB. subtilissecretes c-di-AMP and that putative c-di-AMP transporters impact biofilm formation and plant root colonization. Taken together, our data describe a new role for c-di-AMP as a chemical signal that affects important cellular processes in the environmentally and agriculturally important soil bacteriumB. subtilis. These results suggest that the “intracellular” signaling molecule c-di-AMP may also play a previously unappreciated role in interbacterial cell-cell communication within plant microbiomes.IMPORTANCEPlants harbor bacterial communities on their roots that can significantly impact their growth and pathogen resistance. In most cases, however, the signals that mediate host-microbe and microbe-microbe interactions within these communities are unknown. A detailed understanding of these interaction mechanisms could facilitate the manipulation of these communities for agricultural or environmental purposes.Bacillus subtilisis a plant-growth-promoting bacterium that adheres to roots by forming biofilms. We therefore began by exploring signals that might impact its biofilm formation. We found thatB. subtilissecretes c-di-AMP and that the ability to produce, degrade, or transport cyclic di-adenylate monophosphate (c-di-AMP; a common bacterial second messenger) affectsB. subtilisbiofilm gene expression and plant attachment. To our knowledge, this is the first demonstration of c-di-AMP impacting a mutualist host-microbe association and suggests that c-di-AMP may function as a previously unappreciated extracellular signal able to mediate interactions within plant microbiomes.

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Intercepting second-messenger signaling by rationally designed peptides sequestering c-di-GMP

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2001232117 ◽

2020 ◽

Vol 117 (29) ◽

pp. 17211-17220 ◽

Cited By ~ 2

Author(s):

Chee-Seng Hee ◽

Judith Habazettl ◽

Christoph Schmutz ◽

Tilman Schirmer ◽

Urs Jenal ◽

...

Keyword(s):

Biofilm Formation ◽

Complex Structure ◽

Second Messenger ◽

Effector Protein ◽

Binding Motif ◽

Stacking Interactions ◽

Cellular Functions ◽

Growth And Survival ◽

Wide Range ◽

Second Messenger Signaling

The bacterial second messenger cyclic diguanylate (c-di-GMP) regulates a wide range of cellular functions from biofilm formation to growth and survival. Targeting a second-messenger network is challenging because the system involves a multitude of components with often overlapping functions. Here, we present a strategy to intercept c-di-GMP signaling pathways by directly targeting the second messenger. For this, we developed a c-di-GMP–sequestering peptide (CSP) that was derived from a CheY-like c-di-GMP effector protein. CSP binds c-di-GMP with submicromolar affinity. The elucidation of the CSP⋅c-di-GMP complex structure by NMR identified a linear c-di-GMP–binding motif, in which a self-intercalated c-di-GMP dimer is tightly bound by a network of H bonds and π-stacking interactions involving arginine and aromatic residues. Structure-based mutagenesis yielded a variant with considerably higher, low-nanomolar affinity, which subsequently was shortened to 19 residues with almost uncompromised affinity. We demonstrate that endogenously expressed CSP intercepts c-di-GMP signaling and effectively inhibits biofilm formation inPseudomonas aeruginosa, the most widely used model for serious biofilm-associated medical implications.

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Nucleotide Second Messenger Signaling as a Target for the Control of Bacterial Biofilm Formation

Current Topics in Medicinal Chemistry ◽

10.2174/1568026617666170105144424 ◽

2017 ◽

Vol 17 (17) ◽

pp. 1928-1944 ◽

Cited By ~ 6

Author(s):

Alberto J. Martin-Rodriguez ◽

Ute Romling

Keyword(s):

Biofilm Formation ◽

Second Messenger ◽

Bacterial Biofilm ◽

Second Messenger Signaling

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Regulation of Second Messenger Signaling in Hypoxic Neonatal Rats: Effect of Glucose, Oxygen and Epinephrine Resuscitation

International Conference on Earth, Environment and Life sciences (EELS-2014) Dec. 23-24, 2014 Dubai (UAE) ◽

10.15242/iicbe.c1214035 ◽

2014 ◽

Keyword(s):

Second Messenger ◽

Neonatal Rats ◽

Second Messenger Signaling ◽

Effect Of Glucose

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Spatial organization enhances versatility and specificity in cyclic di-GMP signaling

Biological Chemistry ◽

10.1515/hsz-2020-0202 ◽

2020 ◽

Vol 401 (12) ◽

pp. 1323-1334

Author(s):

Sandra Kunz ◽

Peter L. Graumann

Keyword(s):

Protein Interactions ◽

Cell Cycle Progression ◽

Spatial Organization ◽

Caulobacter Crescentus ◽

Second Messenger ◽

Protein Protein Interactions ◽

Spatial Cues ◽

Signaling Specificity ◽

Regulatory Circuits ◽

Second Messenger Signaling

AbstractThe second messenger cyclic di-GMP regulates a variety of processes in bacteria, many of which are centered around the decision whether to adopt a sessile or a motile life style. Regulatory circuits include pathogenicity, biofilm formation, and motility in a wide variety of bacteria, and play a key role in cell cycle progression in Caulobacter crescentus. Interestingly, multiple, seemingly independent c-di-GMP pathways have been found in several species, where deletions of individual c-di-GMP synthetases (DGCs) or hydrolases (PDEs) have resulted in distinct phenotypes that would not be expected based on a freely diffusible second messenger. Several recent studies have shown that individual signaling nodes exist, and additionally, that protein/protein interactions between DGCs, PDEs and c-di-GMP receptors play an important role in signaling specificity. Additionally, subcellular clustering has been shown to be employed by bacteria to likely generate local signaling of second messenger, and/or to increase signaling specificity. This review highlights recent findings that reveal how bacteria employ spatial cues to increase the versatility of second messenger signaling.

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