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Velmourougane K, Prasanna R, Supriya P, Ramakrishnan B, Thapa S, Saxena AK. Transcriptome profiling provides insights into regulatory factors involved in Trichoderma viride-Azotobacter chroococcum biofilm formation. Microbiol Res 2019; 227:126292. [PMID: 31421719 DOI: 10.1016/j.micres.2019.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 06/15/2019] [Indexed: 12/14/2022]
Abstract
Azotobacter chroococcum (Az) and Trichoderma viride (Tv) represent agriculturally important and beneficial plant growth promoting options which contribute towards nutrient management and biocontrol, respectively. When Az and Tv are co-cultured, they form a biofilm, which has proved promising as an inoculant in several crops; however, the basic aspects related to regulation of biofilm formation were not investigated. Therefore, whole transcriptome sequencing (Illumina NextSeq500) and gene expression analyses were undertaken, related to biofilm formation vis a vis Tv and Az growing individually. Significant changes in the transcriptome profiles of biofilm were recorded and validated through qPCR analyses. In-depth evaluation also identified several genes (phoA, phoB, glgP, alg8, sipW, purB, pssA, fadD) specifically involved in biofilm formation in Az, Tv and Tv-Az. Genes coding for RNA-dependent RNA polymerase, ABC transporters, translation elongation factor EF-1, molecular chaperones and double homeobox 4 were either up-regulated or down-regulated during biofilm formation. To our knowledge, this is the first report on the modulation of gene expression in an agriculturally beneficial association, as a biofilm. Our results provide insights into the regulatory factors involved during biofilm formation, which can help to improve the beneficial effects and develop more effective and promising plant- microbe associations.
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Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Puram Supriya
- Centre for Agricultural Bioinformatics, ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Shobit Thapa
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kusmaur, PO Kaitholi, Mau Nath Bhanjan, Uttar Pradesh 275101, India
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Li W, Hu L, Xie Z, Xu H, Li M, Cui T, He ZG. Cyclic di-GMP integrates functionally divergent transcription factors into a regulation pathway for antioxidant defense. Nucleic Acids Res 2019; 46:7270-7283. [PMID: 29982829 PMCID: PMC6101608 DOI: 10.1093/nar/gky611] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/27/2018] [Indexed: 11/14/2022] Open
Abstract
Cyclic diguanylate monophosphate (c-di-GMP) is a global signaling molecule that modulates diverse cellular processes through its downstream receptors. However, no study has fully clarified the mechanisms by which c-di-GMP organizes functionally divergent regulators to drive the gene expression for coping with environmental stress. Here, we reported that c-di-GMP can integrate two functionally opposite receptor transcription factors, namely, LtmA and HpoR, into a pathway to regulate the antioxidant processes in Mycobacterium smegmatis. In contrast to HpoR, LtmA is an activator that positively regulates the expression of redox gene clusters and the mycobacterial H2O2 resistance. LtmA can physically interact with HpoR. A high level of c-di-GMP stimulates the positive regulation of LtmA and boosts the physical interaction between the two regulators, further enhancing the DNA-binding ability of LtmA and reducing the inhibitory activity of HpoR. Therefore, upon exposure to oxidative stress, c-di-GMP can orchestrate functionally divergent transcription factors to trigger antioxidant defense in mycobacteria. This finding presents a noteworthy example of how a bacterium remodels its transcriptional network via c-di-GMP in response to environmental stress.
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Affiliation(s)
- Weihui Li
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihua Hu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiwei Xie
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Xu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Li
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Cui
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng-Guo He
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Regulatory rewiring through global gene regulations by PhoB and alarmone (p)ppGpp under various stress conditions. Microbiol Res 2019; 227:126309. [PMID: 31421713 DOI: 10.1016/j.micres.2019.126309] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022]
Abstract
The phosphorus availability in soil ranged from <0.01 to 1 ppm and found limiting for the utilization by plants. Hence, phosphate solubilizing bacteria (PSB) proficiently fulfill the phosphorus requirement of plants in an eco-friendly manner. The PSB encounter dynamic and challenging environmental conditions viz., high temperature, osmotic, acid, and climatic changes often hamper their activity and proficiency. The modern trend is shifting from isolation of the PSB to their genetic potentials and genome annotation not only for their better performance in the field trials but also to study their ability to cope up with stresses. In order to withstand environmental stress, bacteria need to restructure its metabolic network to ensure its survival. Pi starving condition response regulator (PhoB) and the mediator of stringent stress response alarmone (p)ppGpp known to regulate the global regulatory network of bacteria to provide balanced physiology under various stress condition. The current review discusses the global regulation and crosstalk of genes involved in phosphorus homeostasis, solubilization, and various stress response to fine tune the bacterial physiology. The knowledge of these network crosstalk help bacteria to respond efficiently to the challenging environmental parameters, and their physiological plasticity lead us to develop proficient long-lasting consortia for plant growth promotion.
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Hu Q, Zhang J, Chen Y, Hu L, Li W, He ZG. Cyclic di-GMP co-activates the two-component transcriptional regulator DevR in Mycobacterium smegmatis in response to oxidative stress. J Biol Chem 2019; 294:12729-12742. [PMID: 31270210 DOI: 10.1074/jbc.ra119.008252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/20/2019] [Indexed: 12/27/2022] Open
Abstract
Cyclic di-GMP (c-di-GMP) is an important second messenger in bacteria, and its regulatory network has been extensively studied. However, information regarding the activation mechanisms of its receptors remains limited. In this study, we characterized the two-component regulator DevR as a new c-di-GMP receptor and further uncovered a novel co-activation mechanism for effective regulation of DevR in mycobacteria. We show that high c-di-GMP levels induce the expression of the devR operon in Mycobacterium smegmatis and increase mycobacterial survival under oxidative stress. The deletion of either DevR or its two-component kinase DevS significantly weakened the stimulating effect of c-di-GMP on oxidative-stress tolerance of mycobacteria. We also found that DevR senses the c-di-GMP signal through its C-terminal structure and that c-di-GMP alone does not directly affect the DNA-binding activity of DevR. Strikingly, c-di-GMP stimulated DevR phosphorylation by the kinase DevS, thereby activating DevR's DNA-binding affinity. In summary, our results indicated that c-di-GMP triggers a phosphorylation-dependent mechanism that co-activates DevR's transcriptional activity. Our findings suggest a novel paradigm for the cross-talk between c-di-GMP signaling and two-component regulatory systems that activates transcription of stress-response genes in bacteria.
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Affiliation(s)
- Qingbin Hu
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaxun Zhang
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Chen
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihua Hu
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zheng-Guo He
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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López-Baena FJ, Vinardell JM, Medina C. Regulation of Protein Secretion Systems Mediated by Cyclic Diguanylate in Plant-Interacting Bacteria. Front Microbiol 2019; 10:1289. [PMID: 31263457 PMCID: PMC6584795 DOI: 10.3389/fmicb.2019.01289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
The ubiquitous second messenger cyclic diguanylate (c-di-GMP) is involved in the regulation of different processes in bacteria. In phytopathogens, intracellular fluctuations in the concentration of this molecule contribute to the lifestyle switching from a motile and virulent stage to a sessile and biofilm-forming phase. Among the virulence mechanisms used by bacterial pathogens, different specific type secretion systems (TSSs) and the effector proteins that they translocate are included. Some of these TSS are conceived to suppress host immune responses during bacterial colonization. The modulation of the expression of secretion systems components and/or effector proteins can be influenced by c-di-GMP levels at transcriptional, translational, or post-translational levels and can take place directly by binding to specific or global regulators, or via transducer proteins. Different genera of plant-interacting bacteria have been analyzed to shed some light in the implications of c-di-GMP in the regulation of host plant colonization through protein secretion systems. Expression of (1) adhesins secreted by Type 1 secretion systems to bind the host plant in Pectobacterium (formerly Erwinia) and some beneficial Pseudomonas strains; (2) catalytic exoproteins delivered by Type 2 secretion systems to break plant cell wall in Dickeya; (3) effectors secreted by Type 3 secretion systems to suppress plant immunity in Xanthomonas; or (4) the activity of Type 6 secretion systems to export an ATPase in Pseudomonas, are finely tuned by c-di-GMP levels. In this minireview, we summarize the knowledge available about the implications of c-di-GMP in the regulation of protein secretion in different plant-interacting bacteria. Topic: Secretion systems and effector proteins of phytopathogenic and beneficial bacteria regulated by NSM.
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Affiliation(s)
| | - Jose María Vinardell
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Carlos Medina
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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56
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Abstract
Type I secretion systems (T1SS) are widespread in Gram-negative bacteria, especially in pathogenic bacteria, and they secrete adhesins, iron-scavenger proteins, lipases, proteases, or pore-forming toxins in the unfolded state in one step across two membranes without any periplasmic intermediate into the extracellular space. The substrates of T1SS are in general characterized by a C-terminal secretion sequence and nonapeptide repeats, so-called GG repeats, located N terminal to the secretion sequence. These GG repeats bind Ca2+ ions in the extracellular space, which triggers folding of the entire protein. Here we summarize our current knowledge of how Gram-negative bacteria secrete these substrates, which can possess a molecular mass of up to 1,500 kDa. We also describe recent findings that demonstrate that the absence of periplasmic intermediates, the "classic" mode of action, does not hold true for all T1SS and that we are beginning to realize modifications of a common theme.
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Fontaine BM, Duggal Y, Weinert EE. Exploring the Links between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial Virulence. ACS Infect Dis 2018; 4:1645-1655. [PMID: 30381948 DOI: 10.1021/acsinfecdis.8b00255] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The survival of all organisms depends on implementation of appropriate phenotypic responses upon perception of relevant environmental stimuli. Sensory inputs are propagated via interconnected biochemical and/or electrical cascades mediated by diverse signaling molecules, including gases, metal cations, lipids, peptides, and nucleotides. These networks often comprise second messenger signaling systems in which a ligand (the primary messenger) binds to an extracellular receptor, thereby altering the intracellular concentration of a second messenger molecule which ultimately modulates gene expression through interaction with various effectors. The identification of intersections of these signaling pathways, such as nucleotide second messengers and quorum sensing, provides new insights into the mechanisms by which bacteria use multiple inputs to regulate cellular metabolism and phenotypes. Further investigations of the overlap between bacterial signaling pathways may yield new targets and methods to control bacterial behavior, such as biofilm formation and virulence.
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Affiliation(s)
- Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Yashasvika Duggal
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive NE, Atlanta, Georgia 30322, United States
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Smith TJ, Sondermann H, O’Toole GA. Co-opting the Lap System of Pseudomonas fluorescens To Reversibly Customize Bacterial Cell Surfaces. ACS Synth Biol 2018; 7:2612-2617. [PMID: 30278125 DOI: 10.1021/acssynbio.8b00278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Initial attachment to a surface is a key and highly regulated step in biofilm formation. In this study, we present a platform for reversibly functionalizing bacterial cell surfaces with an emphasis on designing biofilms. We engineered the Lap system of Pseudomonas fluorescens Pf0-1, which is normally used to regulate initial cell surface attachment, to display various protein cargo at the bacterial cell surface and control extracellular release of the cargo in response to changing levels of the second messenger c-di-GMP. To accomplish this goal, we fused the protein cargo between the N-terminal retention module and C-terminal secretion signal of LapA and controlled surface localization of the cargo with natural signals known to stimulate or deplete c-di-GMP levels in P. fluorescens Pf0-1. We show this system can tolerate large cargo in excess of 500 amino acids, direct P. fluorescens Pf0-1 to surfaces it does not typically colonize, and program this microbe to sequester the toxic medal cadmium.
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Affiliation(s)
- T. Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Room 202 Remsen
Building, Hanover, New Hampshire 03755, United States
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, United States
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Room 202 Remsen
Building, Hanover, New Hampshire 03755, United States
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59
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Stritzler M, Soto G, Ayub N. Plant Growth-Promoting Genes can Switch to be Virulence Factors via Horizontal Gene Transfer. MICROBIAL ECOLOGY 2018; 76:579-583. [PMID: 29476343 DOI: 10.1007/s00248-018-1163-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
There are increasing evidences that horizontal gene transfer (HGT) is a critical mechanism of bacterial evolution, while its complete impact remains unclear. A main constraint of HGT effects on microbial evolution seems to be the conservation of the function of the horizontally transferred genes. From this perspective, inflexible nomenclature and functionality criteria have been established for some mobile genetic elements such as pathogenic and symbiotic islands. Adhesion is a universal prerequisite for both beneficial and pathogenic plant-microbe interactions, and thus, adhesion systems (e.g., the Lap cluster) are candidates to have a dual function depending on the genomic background. In this study, we showed that the virulent factor Lap of the phytopathogen Erwinia carotovora SCRI1043, which is located within a genomic island, was acquired by HGT and probably derived from Pseudomonas. The transformation of the phytopathogen Erwinia pyrifoliae Ep1/96 with the beneficial factor Lap from the plant growth-promoting bacterium Pseudomonas fluorescens Pf-5 significantly increased its natural virulence, experimentally recapitulating the beneficial-to-virulence functional switch of the Lap cluster via HGT. To our knowledge, this is the first report of a functional switch of an individual gene or a cluster of genes mediated by HGT.
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Affiliation(s)
- Margarita Stritzler
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), De los Reseros S/N, C25(1712), Castelar, Buenos Aires, Argentina
| | - Gabriela Soto
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), De los Reseros S/N, C25(1712), Castelar, Buenos Aires, Argentina
| | - Nicolás Ayub
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina.
- Instituto Nacional de Tecnología Agropecuaria (INTA), De los Reseros S/N, C25(1712), Castelar, Buenos Aires, Argentina.
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Roy R, Tiwari M, Donelli G, Tiwari V. Strategies for combating bacterial biofilms: A focus on anti-biofilm agents and their mechanisms of action. Virulence 2018; 9:522-554. [PMID: 28362216 PMCID: PMC5955472 DOI: 10.1080/21505594.2017.1313372] [Citation(s) in RCA: 698] [Impact Index Per Article: 116.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Biofilm refers to the complex, sessile communities of microbes found either attached to a surface or buried firmly in an extracellular matrix as aggregates. The biofilm matrix surrounding bacteria makes them tolerant to harsh conditions and resistant to antibacterial treatments. Moreover, the biofilms are responsible for causing a broad range of chronic diseases and due to the emergence of antibiotic resistance in bacteria it has really become difficult to treat them with efficacy. Furthermore, the antibiotics available till date are ineffective for treating these biofilm related infections due to their higher values of minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC), which may result in in-vivo toxicity. Hence, it is critically important to design or screen anti-biofilm molecules that can effectively minimize and eradicate biofilm related infections. In the present article, we have highlighted the mechanism of biofilm formation with reference to different models and various methods used for biofilm detection. A major focus has been put on various anti-biofilm molecules discovered or tested till date which may include herbal active compounds, chelating agents, peptide antibiotics, lantibiotics and synthetic chemical compounds along with their structures, mechanism of action and their respective MICs, MBCs, minimum biofilm inhibitory concentrations (MBICs) as well as the half maximal inhibitory concentration (IC50) values available in the literature so far. Different mode of action of anti biofilm molecules addressed here are inhibition via interference in the quorum sensing pathways, adhesion mechanism, disruption of extracellular DNA, protein, lipopolysaccharides, exopolysaccharides and secondary messengers involved in various signaling pathways. From this study, we conclude that the molecules considered here might be used to treat biofilm-associated infections after significant structural modifications, thereby investigating its effective delivery in the host. It should also be ensured that minimum effective concentration of these molecules must be capable of eradicating biofilm infections with maximum potency without posing any adverse side effects on the host.
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Affiliation(s)
- Ranita Roy
- a Department of Biochemistry , Central University of Rajasthan , Ajmer , India
| | - Monalisa Tiwari
- a Department of Biochemistry , Central University of Rajasthan , Ajmer , India
| | - Gianfranco Donelli
- b Microbial Biofilm Laboratory, IRCCS Fondazione Santa Lucia , Rome , Italy
| | - Vishvanath Tiwari
- a Department of Biochemistry , Central University of Rajasthan , Ajmer , India
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Type 1 Does the Two-Step: Type 1 Secretion Substrates with a Functional Periplasmic Intermediate. J Bacteriol 2018; 200:JB.00168-18. [PMID: 29866808 DOI: 10.1128/jb.00168-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bacteria have evolved several secretion strategies for polling and responding to environmental flux and insult. Of these, the type 1 secretion system (T1SS) is known to secrete an array of biologically diverse proteins-from small, <10-kDa bacteriocins to gigantic adhesins with a mass >1 MDa. For the last several decades, T1SSs have been characterized as a one-step translocation strategy whereby the secreted substrate is transported directly into the extracellular environment from the cytoplasm with no periplasmic intermediate. Recent phylogenetic, biochemical, and genetic evidences point to a distinct subgroup of T1SS machinery linked with a bacterial transglutaminase-like cysteine proteinase (BTLCP), which uses a two-step secretion mechanism. BTLCP-linked T1SSs transport a class of repeats-in-toxin (RTX) adhesins that are critical for biofilm formation. The prototype of this RTX adhesin group, LapA of Pseudomonas fluorescens Pf0-1, uses a novel N-terminal retention module to anchor the adhesin at the cell surface as a secretion intermediate threaded through the outer membrane-localized TolC-like protein LapE. This secretion intermediate is posttranslationally cleaved by the BTLCP family LapG protein to release LapA from its cognate T1SS pore. Thus, the secretion of LapA and related RTX adhesins into the extracellular environment appears to be a T1SS-mediated two-step process that involves a periplasmic intermediate. In this review, we contrast the T1SS machinery and substrates of the BLTCP-linked two-step secretion process with those of the classical one-step T1SS to better understand the newly recognized and expanded role of this secretion machinery.
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62
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Giacalone D, Smith TJ, Collins AJ, Sondermann H, Koziol LJ, O'Toole GA. Ligand-Mediated Biofilm Formation via Enhanced Physical Interaction between a Diguanylate Cyclase and Its Receptor. mBio 2018; 9:e01254-18. [PMID: 29991582 PMCID: PMC6050961 DOI: 10.1128/mbio.01254-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 06/18/2018] [Indexed: 12/21/2022] Open
Abstract
The bacterial intracellular second messenger, cyclic dimeric GMP (c-di-GMP), regulates biofilm formation for many bacteria. The binding of c-di-GMP by the inner membrane protein LapD controls biofilm formation, and the LapD receptor is central to a complex network of c-di-GMP-mediated biofilm formation. In this study, we examine how c-di-GMP signaling specificity by a diguanylate cyclase (DGC), GcbC, is achieved via interactions with the LapD receptor and by small ligand sensing via GcbC's calcium channel chemotaxis (CACHE) domain. We provide evidence that biofilm formation is stimulated by the environmentally relevant organic acid citrate (and a related compound, isocitrate) in a GcbC-dependent manner through enhanced GcbC-LapD interaction, which results in increased LapA localization to the cell surface. Furthermore, GcbC shows little ability to synthesize c-di-GMP in isolation. However, when LapD is present, GcbC activity is significantly enhanced (~8-fold), indicating that engaging the LapD receptor stimulates the activity of this DGC; citrate-enhanced GcbC-LapD interaction further stimulates c-di-GMP synthesis. We propose that the I-site of GcbC serves two roles beyond allosteric control of this enzyme: promoting GcbC-LapD interaction and stabilizing the active conformation of GcbC in the GcbC-LapD complex. Finally, given that LapD can interact with a dozen different DGCs of Pseudomonas fluorescens, many of which have ligand-binding domains, the ligand-mediated enhanced signaling via LapD-GcbC interaction described here is likely a conserved mechanism of signaling in this network. Consistent with this idea, we identify a second example of ligand-mediated enhancement of DGC-LapD interaction that promotes biofilm formation.IMPORTANCE In many bacteria, dozens of enzymes produce the dinucleotide signal c-di-GMP; however, it is unclear how undesired cross talk is mitigated in the context of this soluble signal and how c-di-GMP signaling is regulated by environmental inputs. We demonstrate that GcbC, a DGC, shows little ability to synthesize c-di-GMP in the absence of its cognate receptor LapD; GcbC-LapD interaction enhances c-di-GMP synthesis by GcbC, likely mediated by the I-site of GcbC. We further show evidence for a ligand-mediated mechanism of signaling specificity via increased physical interaction of a DGC with its cognate receptor. We envision a scenario wherein a "cloud" of weakly active DGCs can increase their activity by specific interaction with their receptor in response to appropriate environmental signals, concomitantly boosting c-di-GMP production, ligand-specific signaling, and biofilm formation.
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Affiliation(s)
- David Giacalone
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - T Jarrod Smith
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Alan J Collins
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Lori J Koziol
- Department of Biology, New England College, Henniker, New Hampshire, USA
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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63
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Sanders AJ, Taylor BW. Using ecological stoichiometry to understand and predict infectious diseases. OIKOS 2018. [DOI: 10.1111/oik.05418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Andrew J. Sanders
- Dept of Applied Ecology; North Carolina State Univ.; Raleigh NC 27695 USA
- Rocky Mountain Biological Laboratory; Crested Butte CO 81224 USA
| | - Brad W. Taylor
- Dept of Applied Ecology; North Carolina State Univ.; Raleigh NC 27695 USA
- Rocky Mountain Biological Laboratory; Crested Butte CO 81224 USA
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64
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Opoku-Temeng C, Sintim HO. Targeting c-di-GMP Signaling, Biofilm Formation, and Bacterial Motility with Small Molecules. Methods Mol Biol 2018; 1657:419-430. [PMID: 28889311 DOI: 10.1007/978-1-4939-7240-1_31] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria possess several signaling molecules that regulate distinct phenotypes. Cyclic di-GMP (c-di-GMP) has emerged as a ubiquitous second messenger that regulates bacterial virulence, cell cycle, motility, and biofilm formation. The link between c-di-GMP signaling and biofilm formation affords novel strategies for treatment of biofilm-associated infections, which is a major public health problem. The complex c-di-GMP signaling pathway creates a hurdle in the development of small molecule modulators. Nonetheless, some progress has been made in this regard and inhibitors of c-di-GMP metabolizing enzymes that affect biofilm formation and motility have been documented. Herein we discuss the components of c-di-GMP signaling, their correlation with biofilm formation as well as motility and reported small molecule inhibitors of c-di-GMP signaling.
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Affiliation(s)
- Clement Opoku-Temeng
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Biochemistry Graduate Program, University of Maryland, College Park, MD, 20742, USA.,Department of Chemistry, Center for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA. .,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, 47907, USA.
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Li W, Li M, Hu L, Zhu J, Xie Z, Chen J, He ZG. HpoR, a novel c-di-GMP effective transcription factor, links the second messenger's regulatory function to the mycobacterial antioxidant defense. Nucleic Acids Res 2018; 46:3595-3611. [PMID: 29490073 PMCID: PMC5909442 DOI: 10.1093/nar/gky146] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 01/06/2023] Open
Abstract
Cyclic di-GMP (c-di-GMP) is a global signaling molecule that widely modulates diverse cellular processes. However, whether or not the c-di-GMP signal participates in regulation of bacterial antioxidant defense is unclear, and the involved regulators remain to be explored. In this study, we characterized HpoR as a novel c-di-GMP effective transcription factor and found a link between the c-di-GMP signal and the antioxidant regulation in Mycobacterium smegmatis. H2O2 stress induces c-di-GMP accumulation in M. smegmatis. High level of c-di-GMP triggers expression of a redox gene cluster, designated as hpoR operon, which is required for the mycobacterial H2O2 resistance. HpoR acts as an inhibitor of the hpoR operon and recognizes a 12-bp motif sequence within the upstream regulatory region of the operon. c-di-GMP specifically binds with HpoR at a ratio of 1:1. Low concentrations of c-di-GMP stimulate the DNA-binding activity of HpoR, whereas high concentrations of the signal molecule inhibit the activity. Strikingly, high level of c-di-GMP de-represses the intracellular association of HpoR with the regulatory region of the hpoR operon in M. smegmatis and enhances the mycobacterial H2O2 resistance. Therefore, we report a novel c-di-GMP effective regulator in mycobacteria, which extends the second messenger's function to bacterial antioxidant defense.
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Affiliation(s)
- Weihui Li
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng Li
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihua Hu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingpeng Zhu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiwei Xie
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiarui Chen
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng-Guo He
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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66
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Biofilm formation, pigment production and motility in Pseudomonas spp. isolated from the dairy industry. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.11.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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67
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An N-Terminal Retention Module Anchors the Giant Adhesin LapA of Pseudomonas fluorescens at the Cell Surface: a Novel Subfamily of Type I Secretion Systems. J Bacteriol 2018; 200:JB.00734-17. [PMID: 29437852 DOI: 10.1128/jb.00734-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/31/2018] [Indexed: 11/20/2022] Open
Abstract
LapA of Pseudomonas fluorescens Pf0-1 belongs to a diverse family of cell surface-associated bacterial adhesins that are secreted via the type I secretion system (T1SS). We previously reported that the periplasmic protease LapG cleaves the N terminus of LapA at a canonical dialanine motif to release the adhesin from the cell surface under conditions unfavorable to biofilm formation, thus decreasing biofilm formation. Here, we characterize LapA as the first type I secreted substrate that does not follow the "one-step" rule of T1SS. Rather, a novel N-terminal element, called the retention module (RM), localizes LapA at the cell surface as a secretion intermediate. Our genetic, biochemical, and molecular modeling analyses support a model wherein LapA is tethered to the cell surface through its T1SS outer membrane TolC-like pore, LapE, until LapG cleaves LapA in the periplasm. We further demonstrate that this unusual retention strategy is likely conserved among LapA-like proteins, and it reveals a new subclass of T1SS ABC transporters involved in transporting this group of surface-associated LapA-like adhesins. These studies demonstrate a novel cell surface retention strategy used throughout the Proteobacteria and highlight a previously unappreciated flexibility of function for T1SS.IMPORTANCE Bacteria have evolved multiple secretion strategies to interact with their environment. For many bacteria, the secretion of cell surface-associated adhesins is key for initiating contact with a preferred substratum to facilitate biofilm formation. Our work demonstrates that P. fluorescens uses a previously unrecognized secretion strategy to retain the giant adhesin LapA at its cell surface. Further, we identify likely LapA-like adhesins in various pathogenic and commensal proteobacteria and provide phylogenetic evidence that these adhesins are secreted by a new subclass of T1SS ABC transporters.
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68
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A Multimodal Strategy Used by a Large c-di-GMP Network. J Bacteriol 2018; 200:JB.00703-17. [PMID: 29311282 DOI: 10.1128/jb.00703-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/31/2017] [Indexed: 01/05/2023] Open
Abstract
The Pseudomonas fluorescens genome encodes more than 50 proteins predicted to be involved in c-di-GMP signaling. Here, we demonstrated that, tested across 188 nutrients, these enzymes and effectors appeared capable of impacting biofilm formation. Transcriptional analysis of network members across ∼50 nutrient conditions indicates that altered gene expression can explain a subset of but not all biofilm formation responses to the nutrients. Additional organization of the network is likely achieved through physical interaction, as determined via probing ∼2,000 interactions by bacterial two-hybrid assays. Our analysis revealed a multimodal regulatory strategy using combinations of ligand-mediated signals, protein-protein interaction, and/or transcriptional regulation to fine-tune c-di-GMP-mediated responses. These results create a profile of a large c-di-GMP network that is used to make important cellular decisions, opening the door to future model building and the ability to engineer this complex circuitry in other bacteria.IMPORTANCE Cyclic diguanylate (c-di-GMP) is a key signaling molecule regulating bacterial biofilm formation, and many microbes have up to dozens of proteins that make, break, or bind this dinucleotide. A major open issue in the field is how signaling specificity is conferred in the unpartitioned space of a bacterial cell. Here, we took a systems approach, using mutational analysis, transcriptional studies, and bacterial two-hybrid analysis to interrogate this network. We found that a majority of enzymes are capable of impacting biofilm formation in a context-dependent manner, and we revealed examples of two or more modes of regulation (i.e., transcriptional control with protein-protein interaction) being utilized to generate an observable impact on biofilm formation.
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Rossi C, Chaves‐López C, Serio A, Anniballi F, Valbonetti L, Paparella A. Effect of
Origanum vulgare
essential oil on biofilm formation and motility capacity of
Pseudomonas fluorescens
strains isolated from discoloured Mozzarella cheese. J Appl Microbiol 2018; 124:1220-1231. [DOI: 10.1111/jam.13707] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/20/2017] [Accepted: 01/11/2018] [Indexed: 01/24/2023]
Affiliation(s)
- C. Rossi
- Faculty of Bioscience and Technology for Food, Agriculture and Environment University of Teramo Teramo TE Italy
| | - C. Chaves‐López
- Faculty of Bioscience and Technology for Food, Agriculture and Environment University of Teramo Teramo TE Italy
| | - A. Serio
- Faculty of Bioscience and Technology for Food, Agriculture and Environment University of Teramo Teramo TE Italy
| | - F. Anniballi
- Department of Veterinary Public Health and Food Safety National Reference Centre for Botulism Istituto Superiore di Sanità Rome RM Italy
| | - L. Valbonetti
- Faculty of Bioscience and Technology for Food, Agriculture and Environment University of Teramo Teramo TE Italy
| | - A. Paparella
- Faculty of Bioscience and Technology for Food, Agriculture and Environment University of Teramo Teramo TE Italy
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70
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The stringent response promotes biofilm dispersal in Pseudomonas putida. Sci Rep 2017; 7:18055. [PMID: 29273811 PMCID: PMC5741744 DOI: 10.1038/s41598-017-18518-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 12/12/2017] [Indexed: 01/08/2023] Open
Abstract
Biofilm dispersal is a genetically programmed response enabling bacterial cells to exit the biofilm in response to particular physiological or environmental conditions. In Pseudomonas putida biofilms, nutrient starvation triggers c-di-GMP hydrolysis by phosphodiesterase BifA, releasing inhibition of protease LapG by the c-di-GMP effector protein LapD, and resulting in proteolysis of the adhesin LapA and the subsequent release of biofilm cells. Here we demonstrate that the stringent response, a ubiquitous bacterial stress response, is accountable for relaying the nutrient stress signal to the biofilm dispersal machinery. Mutants lacking elements of the stringent response - (p)ppGpp sythetases [RelA and SpoT] and/or DksA - were defective in biofilm dispersal. Ectopic (p)ppGpp synthesis restored biofilm dispersal in a ∆relA ∆spoT mutant. In vivo gene expression analysis showed that (p)ppGpp positively regulates transcription of bifA, and negatively regulates transcription of lapA and the lapBC, and lapE operons, encoding a LapA-specific secretion system. Further in vivo and in vitro characterization revealed that the PbifA promoter is dependent on the flagellar σ factor FliA, and positively regulated by ppGpp and DksA. Our results indicate that the stringent response stimulates biofilm dispersal under nutrient limitation by coordinately promoting LapA proteolysis and preventing de novo LapA synthesis and secretion.
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71
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Padelli M, Leven C, Sakka M, Plée-Gautier E, Carré JL. [Causes, consequences and treatment of hypophosphatemia: A systematic review]. Presse Med 2017; 46:987-999. [PMID: 29089216 DOI: 10.1016/j.lpm.2017.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/24/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
CONTEXT Although hypophosphatemia is usually very seldom, it can reach two to 3% of hospitalized patients and until 28% of intensive care unit patients. Due to the lack of knowledge, clinical practice regarding seeking or treatment of hypophosphatemia is very heterogenous. However its clinical consequences might be heavy. A better knowledge of its causes, physiopathological effects and treatment should lead to a documented and homogenous care of these patients in clinics. OBJECTIVE The aim of our study was a systematic review of littérature, seeking for publications about causes, consequences and treatment of hypophosphatemia. DOCUMENTARY SOURCES (KEYWORDS AND LANGUAGE) A research has been conducted on the Medline database by using the following keywords "phosphorus supplementation", "hypophosphatemia" and ("physiopathology" or "complications"). RESULTS Three mains mechanisms might be responsible for hypophosphatemia: a decrease in digestive absorption, a rise in kidney excretion and a transfer of phosphorus to the intracellular compartment. Denutrition, acid base balance troubles, parenteral nutrition or several drugs are capable of provoking or favouring hypophosphatemia. All these situations are frequently encountered in intensive care unit. Consequences of hypophosphatemia might be serious. Best studied and documented are cardiac and respiratory muscle contractility decrease, sometimes leading to acute cardiac and respiratory failure, cardiac rhythm troubles and cardiac arrest. Hypophosphatemia is frequent during sepsis. It could be responsible for leucocyte dysfunction that might favour or increase sepsis. The treatment of hypophosphatemia is usually simple through a supplementation that quickly restores a regular concentration, with few adverse effects when regularly used. CONCLUSION During at-risk situations, the systematic search for hypophosphatemia and its treatment may limit the occurrence of serious consequences.
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Affiliation(s)
- Maël Padelli
- University hospital of Brest, department of biochemistry and pharmaco-toxicology, 29200 Brest, France.
| | - Cyril Leven
- University hospital of Brest, department of biochemistry and pharmaco-toxicology, 29200 Brest, France
| | - Mehdi Sakka
- University hospital of Brest, department of biochemistry and pharmaco-toxicology, 29200 Brest, France
| | - Emmanuelle Plée-Gautier
- University hospital of Brest, department of biochemistry and pharmaco-toxicology, 29200 Brest, France
| | - Jean-Luc Carré
- University hospital of Brest, department of biochemistry and pharmaco-toxicology, 29200 Brest, France
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72
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Corver J, Cordo' V, van Leeuwen HC, Klychnikov OI, Hensbergen PJ. Covalent attachment and Pro-Pro endopeptidase (PPEP-1)-mediated release of Clostridium difficile cell surface proteins involved in adhesion. Mol Microbiol 2017. [PMID: 28636257 DOI: 10.1111/mmi.13736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the past decade, Clostridium difficile has emerged as an important gut pathogen. This anaerobic, Gram-positive bacterium is the main cause of infectious nosocomial diarrhea. Whereas much is known about the mechanism through which the C. difficile toxins cause diarrhea, relatively little is known about the dynamics of adhesion and motility, which is mediated by cell surface proteins. This review will discuss the recent advances in our understanding of the sortase-mediated covalent attachment of cell surface (adhesion) proteins to the peptidoglycan layer of C. difficile and their release through the action of a highly specific secreted metalloprotease (Pro-Pro endopeptidase 1, PPEP-1). Specific emphasis will be on a model in which PPEP-1 and its substrates control the switch from a sessile to motile phenotype in C. difficile, and how this is regulated by the cyclic dinucleotide c-di-GMP (3'-5' cyclic dimeric guanosine monophosphate).
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Affiliation(s)
- Jeroen Corver
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Valentina Cordo'
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Hans C van Leeuwen
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Oleg I Klychnikov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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73
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Abstract
Cyclic diguanylate (c-di-GMP) is a near universal signaling molecule produced by diguanylate cyclases that can direct a variety of bacterial behaviors. A major area of research over the last several years has been aimed at understanding how a cell with dozens of diguanylate cyclases can deploy a given subset of them to produce a desired phenotypic outcome without undesired cross talk between c-di-GMP-dependent systems. Several models have been put forward to address this question, including specificity of cyclase activation, tuned binding constants of effector proteins, and physical interaction between cyclases and effectors. Additionally, recent evidence has suggested that there may be a link between the catalytic state of a cyclase and its physical contact with an effector. This review highlights several key studies, examines the proposed global and local models of c-di-GMP signaling specificity in bacteria, and attempts to identify the most fruitful steps that can be taken to better understand how dynamic networks of sibling cyclases and effector proteins result in sensible outputs that govern cellular behavior.
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Affiliation(s)
- Kurt M Dahlstrom
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755;
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755;
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74
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Velmourougane K, Prasanna R, Saxena AK. Agriculturally important microbial biofilms: Present status and future prospects. J Basic Microbiol 2017; 57:548-573. [PMID: 28407275 DOI: 10.1002/jobm.201700046] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/17/2017] [Accepted: 03/19/2017] [Indexed: 11/07/2022]
Abstract
Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms.
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Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau Nath Bhanjan, Uttar Pradesh, India
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75
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Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein. mBio 2017; 8:mBio.00294-17. [PMID: 28325767 PMCID: PMC5362036 DOI: 10.1128/mbio.00294-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When encountering surfaces, many bacteria produce adhesins to facilitate their initial attachment and to irreversibly glue themselves to the solid substrate. A central molecule regulating the processes of this motile-sessile transition is the second messenger c-di-GMP, which stimulates the production of a variety of exopolysaccharide adhesins in different bacterial model organisms. In Caulobacter crescentus, c-di-GMP regulates the synthesis of the polar holdfast adhesin during the cell cycle, yet the molecular and cellular details of this control are currently unknown. Here we identify HfsK, a member of a versatile N-acetyltransferase family, as a novel c-di-GMP effector involved in holdfast biogenesis. Cells lacking HfsK form highly malleable holdfast structures with reduced adhesive strength that cannot support surface colonization. We present indirect evidence that HfsK modifies the polysaccharide component of holdfast to buttress its cohesive properties. HfsK is a soluble protein but associates with the cell membrane during most of the cell cycle. Coincident with peak c-di-GMP levels during the C. crescentus cell cycle, HfsK relocalizes to the cytosol in a c-di-GMP-dependent manner. Our results indicate that this c-di-GMP-mediated dynamic positioning controls HfsK activity, leading to its inactivation at high c-di-GMP levels. A short C-terminal extension is essential for the membrane association, c-di-GMP binding, and activity of HfsK. We propose a model in which c-di-GMP binding leads to the dispersal and inactivation of HfsK as part of holdfast biogenesis progression. Exopolysaccharide (EPS) adhesins are important determinants of bacterial surface colonization and biofilm formation. Biofilms are a major cause of chronic infections and are responsible for biofouling on water-exposed surfaces. To tackle these problems, it is essential to dissect the processes leading to surface colonization at the molecular and cellular levels. Here we describe a novel c-di-GMP effector, HfsK, that contributes to the cohesive properties and stability of the holdfast adhesin in C. crescentus. We demonstrate for the first time that c-di-GMP, in addition to its role in the regulation of the rate of EPS production, also modulates the physicochemical properties of bacterial adhesins. By demonstrating how c-di-GMP coordinates the activity and subcellular localization of HfsK, we provide a novel understanding of the cellular processes involved in adhesin biogenesis control. Homologs of HfsK are found in representatives of different bacterial phyla, suggesting that they play important roles in various EPS synthesis systems.
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76
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Cooley RB, O’Donnell JP, Sondermann H. Coincidence detection and bi-directional transmembrane signaling control a bacterial second messenger receptor. eLife 2016; 5:e21848. [PMID: 28001128 PMCID: PMC5231407 DOI: 10.7554/elife.21848] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/20/2016] [Indexed: 12/15/2022] Open
Abstract
The second messenger c-di-GMP (or cyclic diguanylate) regulates biofilm formation, a physiological adaptation process in bacteria, via a widely conserved signaling node comprising a prototypical transmembrane receptor for c-di-GMP, LapD, and a cognate periplasmic protease, LapG. Previously, we reported a structure-function study of a soluble LapD•LapG complex, which established conformational changes in the receptor that lead to c-di-GMP-dependent protease recruitment (Chatterjee et al., 2014). This work also revealed a basal affinity of c-di-GMP-unbound receptor for LapG, the relevance of which remained enigmatic. Here, we elucidate the structural basis of coincidence detection that relies on both c-di-GMP and LapG binding to LapD for receptor activation. The data indicate that high-affinity for LapG relies on the formation of a receptor dimer-of-dimers, rather than a simple conformational change within dimeric LapD. The proposed mechanism provides a rationale of how external proteins can regulate receptor function and may also apply to c-di-GMP-metabolizing enzymes that are akin to LapD.
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Affiliation(s)
- Richard B Cooley
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States
| | - John P O’Donnell
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States
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Santos-Beneit F, Ordóñez-Robles M, Martín JF. Glycopeptide resistance: Links with inorganic phosphate metabolism and cell envelope stress. Biochem Pharmacol 2016; 133:74-85. [PMID: 27894856 DOI: 10.1016/j.bcp.2016.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/15/2016] [Indexed: 10/20/2022]
Abstract
Antimicrobial resistance is a critical health issue today. Many pathogens have become resistant to many or all available antibiotics and limited new antibiotics are in the pipeline. Glycopeptides are used as a 'last resort' antibiotic treatment for many bacterial infections, but worryingly, glycopeptide resistance has spread to very important pathogens such as Enterococcus faecium and Staphylococcus aureus. Bacteria confront multiple stresses in their natural environments, including nutritional starvation and the action of cell-wall stressing agents. These stresses impact bacterial susceptibility to different antimicrobials. This article aims to review the links between glycopeptide resistance and different stresses, especially those related with cell-wall biosynthesis and inorganic phosphate metabolism, and to discuss promising alternatives to classical antibiotics to avoid the problem of antimicrobial resistance.
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Affiliation(s)
- Fernando Santos-Beneit
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, NE2 4AX Newcastle upon Tyne, UK
| | - María Ordóñez-Robles
- Department of Biotechnology, Faculty of Natural Sciences and Technology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Juan F Martín
- Microbiology Area, Department of Molecular Biology, University of León, 24071 León, Spain.
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78
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Gutiérrez D, Rodríguez-Rubio L, Martínez B, Rodríguez A, García P. Bacteriophages as Weapons Against Bacterial Biofilms in the Food Industry. Front Microbiol 2016; 7:825. [PMID: 27375566 PMCID: PMC4897796 DOI: 10.3389/fmicb.2016.00825] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/16/2016] [Indexed: 12/23/2022] Open
Abstract
Microbiological contamination in the food industry is often attributed to the presence of biofilms in processing plants. Bacterial biofilms are complex communities of bacteria attached to a surface and surrounded by an extracellular polymeric material. Their extreme resistance to cleaning and disinfecting processes is related to a unique organization, which implies a differential bacterial growth and gene expression inside the biofilm. The impact of biofilms on health, and the economic consequences, has promoted the development of different approaches to control or remove biofilm formation. Recently, successful results in phage therapy have boosted new research in bacteriophages and phage lytic proteins for biofilm eradication. In this regard, this review examines the environmental factors that determine biofilm development in food-processing equipment. In addition, future perspectives for the use of bacteriophage-derived tools as disinfectants are discussed.
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Affiliation(s)
- Diana Gutiérrez
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Lorena Rodríguez-Rubio
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
- Laboratory of Gene Technology, Katholieke Universiteit LeuvenLeuven, Belgium
| | - Beatriz Martínez
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Ana Rodríguez
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
| | - Pilar García
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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79
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Zhu L, Chen X, Kong X, Cai YD. Investigation of the roles of trace elements during hepatitis C virus infection using protein-protein interactions and a shortest path algorithm. Biochim Biophys Acta Gen Subj 2016; 1860:2756-68. [PMID: 27208424 DOI: 10.1016/j.bbagen.2016.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/05/2016] [Accepted: 05/13/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hepatitis is a type of infectious disease that induces inflammation of the liver without pinpointing a particular pathogen or pathogenesis. Type C hepatitis, as a type of hepatitis, has been reported to induce cirrhosis and hepatocellular carcinoma within a very short amount of time. It is a great threat to human health. Some studies have revealed that trace elements are associated with infection with and immune rejection against hepatitis C virus (HCV). However, the mechanism underlying this phenomenon is still unclear. METHODS In this study, we aimed to expand our knowledge of this phenomenon by designing a computational method to identify genes that may be related to both HCV and trace element metabolic processes. The searching procedure included three stages. First, a shortest path algorithm was applied to a large network, constructed by protein-protein interactions, to identify potential genes of interest. Second, a permutation test was executed to exclude false discoveries. Finally, some rules based on the betweenness and associations between candidate genes and HCV and trace elements were built to select core genes among the remaining genes. RESULTS 12 lists of genes, corresponding to 12 types of trace elements, were obtained. These genes are deemed to be associated with HCV infection and trace elements metabolism. CONCLUSIONS The analyses indicate that some genes may be related to both HCV and trace element metabolic processes, further confirming the associations between HCV and trace elements. The method was further tested on another set of HCV genes, the results indicate that this method is quite robustness. GENERAL SIGNIFICANCE The newly found genes may partially reveal unknown mechanisms between HCV infection and trace element metabolism. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- LiuCun Zhu
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China
| | - XiJia Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China
| | - Xiangyin Kong
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200025, People's Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, People's Republic of China.
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The Inhibitory Site of a Diguanylate Cyclase Is a Necessary Element for Interaction and Signaling with an Effector Protein. J Bacteriol 2016; 198:1595-603. [PMID: 27002135 DOI: 10.1128/jb.00090-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/14/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many bacteria contain large cyclic diguanylate (c-di-GMP) signaling networks made of diguanylate cyclases (DGCs) and phosphodiesterases that can direct cellular activities sensitive to c-di-GMP levels. While DGCs synthesize c-di-GMP, many DGCs also contain an autoinhibitory site (I-site) that binds c-di-GMP to halt excess production of this small molecule, thus controlling the amount of c-di-GMP available to bind to target proteins in the cell. Many DGCs studied to date have also been found to signal for a specific c-di-GMP-related process, and although recent studies have suggested that physical interaction between DGCs and target proteins may provide this signaling fidelity, the importance of the I-site has not yet been incorporated into this model. Our results from Pseudomonas fluorescens indicate that mutation of residues at the I-site of a DGC disrupts the interaction with its target receptor. By creating various substitutions to a DGC's I-site, we show that signaling between a DGC (GcbC) and its target protein (LapD) is a combined function of the I-site-dependent protein-protein interaction and the level of c-di-GMP production. The dual role of the I-site in modulating DGC activity as well as participating in protein-protein interactions suggests caution in interpreting the function of the I-site as only a means to negatively regulate a cyclase. These results implicate the I-site as an important positive and negative regulatory element of DGCs that may contribute to signaling specificity. IMPORTANCE Some bacteria contain several dozen diguanylate cyclases (DGCs), nearly all of which signal to specific receptors using the same small molecule, c-di-GMP. Signaling specificity in these networks may be partially driven by physical interactions between DGCs and their receptors, in addition to the autoinhibitory site of DGCs preventing the overproduction of c-di-GMP. In this study, we show that disruption of the autoinhibitory site of a DGC in Pseudomonas fluorescens can result in the loss of interactions with its target receptor and reduced biofilm formation, despite increased production of c-di-GMP. Our findings implicate the autoinhibitory site as both an important feature for signaling specificity through the regulation of c-di-GMP production and a necessary element for the physical interaction between a diguanylate cyclase and its receptor.
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81
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Grillo-Puertas M, Rintoul MR, Rapisarda VA. PhoB activation in non-limiting phosphate condition by the maintenance of high polyphosphate levels in the stationary phase inhibits biofilm formation in Escherichia coli. MICROBIOLOGY-SGM 2016; 162:1000-1008. [PMID: 27023099 DOI: 10.1099/mic.0.000281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Polyphosphate (polyP) degradation in Escherichia coli stationary phase triggers biofilm formation via the LuxS quorum sensing system. In media containing excess of phosphate (Pi), high polyP levels are maintained in the stationary phase with the consequent inhibition of biofilm formation. The transcriptional-response regulator PhoB, which is activated under Pi limitation, is involved in the inhibition of biofilm formation in several bacterial species. In the current study, we report, for the first time, we believe that E. coli PhoB can be activated in non-limiting Pi conditions, leading to inhibition of biofilm formation. In fact, PhoB was activated when high polyP levels were maintained in the stationary phase, whereas it remained inactive when the polymer was degraded or absent. PhoB activation was mediated by acetyl phosphate with the consequent repression of biofilm formation owing to the downregulation of c-di-GMP synthesis and the inhibition of autoinducer-2 production. These results allowed us to propose a model showing that PhoB is a component in the signal cascade regulating biofilm formation triggered by fluctuations of polyP levels in E. coli cells during stationary phase.
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Affiliation(s)
- M Grillo-Puertas
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina.,Instituto de Química Biológica, 'Dr Bernabe Bloj', Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina
| | - M R Rintoul
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina.,Instituto de Química Biológica, 'Dr Bernabe Bloj', Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina
| | - V A Rapisarda
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina.,Instituto de Química Biológica, 'Dr Bernabe Bloj', Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina
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82
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Abstract
During the past decade we have gained much knowledge about the molecular mechanisms that are involved in initiation and termination of biofilm formation. In many bacteria, these processes appear to occur in response to specific environmental cues and result in, respectively, induction or termination of biofilm matrix production via the second messenger molecule c-di-GMP. In between initiation and termination of biofilm formation we have defined specific biofilm stages, but the currently available evidence suggests that these transitions are mainly governed by adaptive responses, and not by specific genetic programs. It appears that biofilm formation can occur through multiple pathways and that the spatial structure of the biofilms is species dependent as well as dependent on environmental conditions. Bacterial subpopulations, e.g., motile and nonmotile subpopulations, can develop and interact during biofilm formation, and these interactions can affect the structure of the biofilm. The available evidence suggests that biofilm formation is programmed in the sense that regulated synthesis of extracellular matrix components is involved. Furthermore, our current knowledge suggests that biofilm formation mainly is governed by adaptive responses of individual bacteria, although group-level activities are also involved.
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83
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Sensational biofilms: surface sensing in bacteria. Curr Opin Microbiol 2016; 30:139-146. [PMID: 26968016 DOI: 10.1016/j.mib.2016.02.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/04/2016] [Accepted: 02/08/2016] [Indexed: 12/22/2022]
Abstract
The first step in the development of a bacterial biofilm is contact with the surface on which the microbe will form this community. We review recent progress on 'surface sensing', and engage the question of 'how does a microbe know it is on a surface?'
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84
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Petrova OE, Sauer K. Escaping the biofilm in more than one way: desorption, detachment or dispersion. Curr Opin Microbiol 2016; 30:67-78. [PMID: 26826978 DOI: 10.1016/j.mib.2016.01.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 12/15/2022]
Abstract
Biofilm bacteria have developed escape strategies to avoid stresses associated with biofilm growth, respond to changing environmental conditions, and disseminate to new locations. An ever-expanding body of research suggests that cellular release from biofilms is distinct from a simple reversal of attachment and reversion to a planktonic mode of growth, with biofilm dispersion involving sensing of specific cues, regulatory signal transduction, and consequent physiological alterations. However, dispersion is only one of many ways to escape the biofilm mode of growth. The present review is aimed at distinguishing this active and regulated process of dispersion from the passive processes of desorption and detachment by highlighting the regulatory processes and distinct phenotypes specific to dispersed cells.
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Affiliation(s)
- Olga E Petrova
- Department of Biological Sciences, Binghamton Biofilm Research Center, Binghamton University, Binghamton, NY 13902, United States
| | - Karin Sauer
- Department of Biological Sciences, Binghamton Biofilm Research Center, Binghamton University, Binghamton, NY 13902, United States.
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85
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Biofilm formation mechanisms and targets for developing antibiofilm agents. Future Med Chem 2016; 7:493-512. [PMID: 25875875 DOI: 10.4155/fmc.15.6] [Citation(s) in RCA: 367] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Biofilms are communities of microorganisms that are attached to a surface and play a significant role in the persistence of bacterial infections. Bacteria within a biofilm are several orders of magnitude more resistant to antibiotics, compared with planktonic bacteria. Thus far, no drugs are in clinical use that specifically target bacterial biofilms. This is probably because until recently the molecular details of biofilm formation were poorly understood. Bacteria integrate information from the environment, such as quorum-sensing autoinducers and nutrients, into appropriate biofilm-related gene expression, and the identity of the key players, such as cyclic dinucleotide second messengers and regulatory RNAs are beginning to be uncovered. Herein, we highlight the current understanding of the processes that lead to biofilm formation in many bacteria.
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86
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Yoshioka S, Newell PD. Disruption of de novo purine biosynthesis in Pseudomonas fluorescens Pf0-1 leads to reduced biofilm formation and a reduction in cell size of surface-attached but not planktonic cells. PeerJ 2016; 4:e1543. [PMID: 26788425 PMCID: PMC4715448 DOI: 10.7717/peerj.1543] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/07/2015] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas fluorescens Pf0-1 is one of the model organisms for biofilm research. Our previous transposon mutagenesis study suggested a requirement for the de novo purine nucleotide biosynthesis pathway for biofilm formation by this organism. This study was performed to verify that observation and investigate the basis for the defects in biofilm formation shown by purine biosynthesis mutants. Constructing deletion mutations in 8 genes in this pathway, we found that they all showed reductions in biofilm formation that could be partly or completely restored by nucleotide supplementation or genetic complementation. We demonstrated that, despite a reduction in biofilm formation, more viable mutant cells were recovered from the surface-attached population than from the planktonic phase under conditions of purine deprivation. Analyses using scanning electron microscopy revealed that the surface-attached mutant cells were 25 ∼ 30% shorter in length than WT, which partly explains the reduced biomass in the mutant biofilms. The laser diffraction particle analyses confirmed this finding, and further indicated that the WT biofilm cells were smaller than their planktonic counterparts. The defects in biofilm formation and reductions in cell size shown by the mutants were fully recovered upon adenine or hypoxanthine supplementation, indicating that the purine shortages caused reductions in cell size. Our results are consistent with surface attachment serving as a survival strategy during nutrient deprivation, and indicate that changes in the cell size may be a natural response of P. fluorescens to growth on a surface. Finally, cell sizes in WT biofilms became slightly smaller in the presence of exogenous adenine than in its absence. Our findings suggest that purine nucleotides or related metabolites may influence the regulation of cell size in this bacterium.
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Affiliation(s)
- Shiro Yoshioka
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences , Okazaki, Aichi , Japan
| | - Peter D Newell
- Department of Biological Sciences, Oswego State University of New York , Oswego, NY , USA
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87
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Jiangyu DAI, Guang GAO, Shiqiang WU, Xiufeng WU, Jie ZHOU, Wanyun XUE, Qianqian YANG, Dan CHEN. Bacterial alkaline phosphatases and affiliated encoding genes in natural waters: A review. ACTA ACUST UNITED AC 2016. [DOI: 10.18307/2016.0601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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88
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Aragon IM, Pérez-Mendoza D, Moscoso JA, Faure E, Guery B, Gallegos MT, Filloux A, Ramos C. Diguanylate cyclase DgcP is involved in plant and human Pseudomonas spp. infections. Environ Microbiol 2015; 17:4332-51. [PMID: 25809128 DOI: 10.1111/1462-2920.12856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 03/06/2015] [Indexed: 12/22/2022]
Abstract
The second messenger cyclic di-GMP (c-di-GMP) controls the transition between different lifestyles in bacterial pathogens. Here, we report the identification of DgcP (diguanylate cyclase conserved in Pseudomonads), whose activity in the olive tree pathogen Pseudomonas savastanoi pv. savastanoi is dependent on the integrity of its GGDEF domain. Furthermore, deletion of the dgcP gene revealed that DgcP negatively regulates motility and positively controls biofilm formation in both the olive tree pathogen P. savastanoi pv. savastanoi and the human opportunistic pathogen Pseudomonas aeruginosa. Overexpression of the dgcP gene in P. aeruginosa PAK led to increased exopolysaccharide production and upregulation of the type VI secretion system; in turn, it repressed the type III secretion system, which is a hallmark of chronic infections and persistence for P. aeruginosa. Deletion of the dgcP gene in P. savastanoi pv. savastanoi NCPPB 3335 and P. aeruginosa PAK reduced their virulence in olive plants and in a mouse acute lung injury model respectively. Our results show that diguanylate cyclase DgcP is a conserved Pseudomonas protein with a role in virulence, and confirm the existence of common c-di-GMP signalling pathways that are capable of regulating plant and human Pseudomonas spp. infections.
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Affiliation(s)
- Isabel M Aragon
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Facultad de Ciencias, Universidad de Málaga-CSIC (IHSM-UMA-CSIC), Área de Genética, Campus de Teatinos, Málaga, E-29010, Spain
- Dpto. Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, Flowers Building, London, SW7 2AZ, UK
| | - Daniel Pérez-Mendoza
- Dpto. Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Joana A Moscoso
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, Flowers Building, London, SW7 2AZ, UK
| | - Emmanuel Faure
- Pseudomonas aeruginosa host-pathogen translational research group, Lille School of Medicine, UDSL, Lille North of France University, Lille, France
| | - Benoit Guery
- Pseudomonas aeruginosa host-pathogen translational research group, Lille School of Medicine, UDSL, Lille North of France University, Lille, France
| | - María-Trinidad Gallegos
- Dpto. Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, Flowers Building, London, SW7 2AZ, UK
| | - Cayo Ramos
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Facultad de Ciencias, Universidad de Málaga-CSIC (IHSM-UMA-CSIC), Área de Genética, Campus de Teatinos, Málaga, E-29010, Spain
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89
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Borland S, Oudart A, Prigent-Combaret C, Brochier-Armanet C, Wisniewski-Dyé F. Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum. BMC Genomics 2015; 16:833. [PMID: 26489830 PMCID: PMC4618731 DOI: 10.1186/s12864-015-1962-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/29/2015] [Indexed: 01/05/2023] Open
Abstract
Background Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium senses and responds to its rhizospheric environment. The availability of complete genome sequenced from four Azospirillum strains (A. brasilense Sp245 and CBG 497, A. lipoferum 4B and Azospirillum sp. B510) offers the opportunity to conduct a comprehensive comparative analysis of the TCS gene family. Results Azospirillum genomes harbour a very large number of genes encoding TCS, and are especially enriched in hybrid histidine kinases (HyHK) genes compared to other plant-associated bacteria of similar genome sizes. We gained further insight into HyHK structure and architecture, revealing an intriguing complexity of these systems. An unusual proportion of TCS genes were orphaned or in complex clusters, and a high proportion of predicted soluble HKs compared to other plant-associated bacteria are reported. Phylogenetic analyses of the transmitter and receiver domains of A. lipoferum 4B HyHK indicate that expansion of this family mainly arose through horizontal gene transfer but also through gene duplications all along the diversification of the Azospirillum genus. By performing a genome-wide comparison of TCS, we unraveled important ‘genus-defining’ and ‘plant-specifying’ TCS. Conclusions This study shed light on Azospirillum TCS which may confer important regulatory flexibility. Collectively, these findings highlight that Azospirillum genomes have broad potential for adaptation to fluctuating environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1962-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stéphanie Borland
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Anne Oudart
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Claire Prigent-Combaret
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
| | - Florence Wisniewski-Dyé
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Laboratoire d'Ecologie Microbienne, 43 7 boulevard du 11 novembre 1918, F-69622, Villeurbanne, France.
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90
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Rybtke M, Berthelsen J, Yang L, Høiby N, Givskov M, Tolker-Nielsen T. The LapG protein plays a role in Pseudomonas aeruginosa biofilm formation by controlling the presence of the CdrA adhesin on the cell surface. Microbiologyopen 2015; 4:917-30. [PMID: 26458733 PMCID: PMC4694147 DOI: 10.1002/mbo3.301] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas aeruginosa is a clinically relevant species involved in biofilm-based chronic infections. We provide evidence that the P. aeruginosa LapG protein functions as a periplasmic protease that can cleave the protein adhesin CdrA off the cell surface, and thereby plays a role in biofilm formation and biofilm dispersal. The P. aeruginosa LapG protein is shown to be a functional homolog of the Pseudomonas putida LapG protein which has previously been shown to function as a periplasmic protease that targets the surface adhesin LapA. Transposon mutagenesis and characterization of defined knockout mutants provided evidence that the CdrA adhesin is a target of LapG in P. aeruginosa. A wspF lapG double mutant was hyper-aggregating and hyper biofilm forming, whereas a wspF lapG cdrA triple mutant lost these phenotypes. In addition, western blot detection of CdrA in culture supernatants and whole-cell protein fractions showed that CdrA was retained in the whole-cell protein fraction when LapG was absent, whereas it was found in the culture supernatant when LapG was present. The finding that CdrA is a target of LapG in P. aeruginosa is surprising because CdrA has no homology to LapA.
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Affiliation(s)
- Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Jens Berthelsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Liang Yang
- Singapore Center on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Niels Høiby
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Michael Givskov
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.,Singapore Center on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
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91
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Romero-Jiménez L, Rodríguez-Carbonell D, Gallegos MT, Sanjuán J, Pérez-Mendoza D. Mini-Tn7 vectors for stable expression of diguanylate cyclase PleD* in Gram-negative bacteria. BMC Microbiol 2015; 15:190. [PMID: 26415513 PMCID: PMC4587759 DOI: 10.1186/s12866-015-0521-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/18/2015] [Indexed: 11/18/2022] Open
Abstract
Background The cyclic diguanylate (c-di-GMP) is currently considered an ubiquitous second messenger in bacteria that influences a wide range of cellular processes. One of the methodological approaches to unravel c-di-GMP regulatory networks involves raising the c-di-GMP intracellular levels, e.g. by expressing a diguanylate cyclase (DGC), to provoke phenotypic changes. Results We have constructed mini-Tn7 delivery vectors for the integration and stable expression of the pleD* gene encoding a highly active DGC, which can be used to artificially increase the intracellular levels of c-di-GMP in Gram negative bacteria. The functionality of these new vectors has been validated in several plant-interacting α- and γ-proteobacteria. Similarly to vector plasmid-borne pleD*, the genome-borne mini-Tn7pleD* constructs provide significant increases in intracellular c-di-GMP, provoking expected phenotypic changes such as enhanced polysaccharide production, biofilm formation and reduced motility. However, the mini-Tn7pleD* constructs resulted far more stable in the absence of antibiotics than the plasmid-based pleD* constructs. Furthermore, we have also implemented an inducible system to modulate pleD* expression and intracellular c-di-GMP rises “on demand”. Conclusions mini-Tn7pleD* constructs are very stable and are maintained during bacterial free-living growth as well as during interaction with eukaryotic hosts, in the absence of selective pressure. This high stability ensures experimental homogeneity in time and space with regard to enhancing c-di-GMP intracellular levels in bacteria of interest. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0521-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lorena Romero-Jiménez
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - David Rodríguez-Carbonell
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - María Trinidad Gallegos
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - Juan Sanjuán
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | - Daniel Pérez-Mendoza
- Departamento Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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92
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Santos-Beneit F. The Pho regulon: a huge regulatory network in bacteria. Front Microbiol 2015; 6:402. [PMID: 25983732 PMCID: PMC4415409 DOI: 10.3389/fmicb.2015.00402] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/17/2015] [Indexed: 12/15/2022] Open
Abstract
One of the most important achievements of bacteria is its capability to adapt to the changing conditions of the environment. The competition for nutrients with other microorganisms, especially in the soil, where nutritional conditions are more variable, has led bacteria to evolve a plethora of mechanisms to rapidly fine-tune the requirements of the cell. One of the essential nutrients that are normally found in low concentrations in nature is inorganic phosphate (Pi). Bacteria, as well as other organisms, have developed several systems to cope for the scarcity of this nutrient. To date, the unique mechanism responding to Pi starvation known in detail is the Pho regulon, which is normally controlled by a two component system and constitutes one of the most sensible and efficient regulatory mechanisms in bacteria. Many new members of the Pho regulon have emerged in the last years in several bacteria; however, there are still many unknown questions regarding the activation and function of the whole system. This review describes the most important findings of the last three decades in relation to Pi regulation in bacteria, including: the PHO box, the Pi signaling pathway and the Pi starvation response. The role of the Pho regulon in nutritional regulation cross-talk, secondary metabolite production, and pathogenesis is discussed in detail.
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Affiliation(s)
- Fernando Santos-Beneit
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne UK
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93
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An Integrated Modeling and Experimental Approach to Study the Influence of Environmental Nutrients on Biofilm Formation of Pseudomonas aeruginosa. BIOMED RESEARCH INTERNATIONAL 2015; 2015:506782. [PMID: 25954752 PMCID: PMC4411446 DOI: 10.1155/2015/506782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/09/2015] [Indexed: 12/18/2022]
Abstract
The availability of nutrient components in the environment was identified as a critical regulator of virulence and biofilm formation in Pseudomonas aeruginosa. This work proposes the first systems-biology approach to quantify microbial biofilm formation upon the change of nutrient availability in the environment. Specifically, the change of fluxes of metabolic reactions that were positively associated with P. aeruginosa biofilm formation was used to monitor the trend for P. aeruginosa to form a biofilm. The uptake rates of nutrient components were changed according to the change of the nutrient availability. We found that adding each of the eleven amino acids (Arg, Tyr, Phe, His, Iso, Orn, Pro, Glu, Leu, Val, and Asp) to minimal medium promoted P. aeruginosa biofilm formation. Both modeling and experimental approaches were further developed to quantify P. aeruginosa biofilm formation for four different availability levels for each of the three ions that include ferrous ions, sulfate, and phosphate. The developed modeling approach correctly predicted the amount of biofilm formation. By comparing reaction flux change upon the change of nutrient concentrations, metabolic reactions used by P. aeruginosa to regulate its biofilm formation are mainly involved in arginine metabolism, glutamate production, magnesium transport, acetate metabolism, and the TCA cycle.
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94
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Ueda A, Saneoka H. Characterization of the ability to form biofilms by plant-associated Pseudomonas species. Curr Microbiol 2014; 70:506-13. [PMID: 25487118 DOI: 10.1007/s00284-014-0749-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 10/29/2014] [Indexed: 11/26/2022]
Abstract
Successful colonization is the initial step for plant-bacteria interactions; therefore, the development of strategies to improve adherence to plant surfaces is critically important for environmental bacteria. Biofilm formation is thought to be one such strategy for bacteria to establish stable colonization on inert and living surfaces. Although biofilms play potential roles in enabling persistent bacterial colonization, little attention has been paid to biofilms formed by plant-associated bacteria. In this study, we characterized the biofilm-forming ability of 6 species of bacteria from the family Pseudomonadaceae: Pseudomonas protegens, Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas stutzeri, Pseudomonas mendocina, and Pseudomonas syringae. These strains exhibit different degrees of biofilm formation depending on incubation time and nutrient availability. Distinct preferences for growth media were observed, as biofilms were formed by P. protegens with rich nutrients and by P. fluorescens and P. putida with poor nutrients. Likewise, P. stutzeri did not form biofilms with rich nutrients but did form biofilms under nutrient-poor conditions. These observations indicate that particular components in media may influence biofilm formation. P. putida, one of the strains with high biofilm-forming ability, showed the highest ability for initial attachment, which may be mediated by the hydrophobicity of its cell surface. P. mendocina also has high ability for initial attachment, and this strain produces cell surface-attached extracellular polysaccharides that promote cell aggregation. Thus, each strain possesses different properties that facilitate biofilm formation. Shedding light on bacterial strategies for colonization via biofilm formation would enable a better understanding of plant-bacteria interactions.
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Affiliation(s)
- Akihiro Ueda
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan,
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95
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Ayub ND, Fox AR, García AN, Mozzicafreddo M, Cuccioloni M, Angeletti M, Pagano E, Soto G. Pseudomonas fluorescens Pf-5 genome-wide mutant screen for resistance to the antimicrobial peptide alfalfa snakin-1. FEMS Microbiol Lett 2014; 362:1-6. [PMID: 25670697 DOI: 10.1093/femsle/fnu006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Snakin-1, a peptide produced by higher plants, has broad-spectrum antibiotic activity, inhibiting organisms ranging from Bacteria to Eukaryotes. However, the mode of action against target organisms is poorly understood. As a first step to elucidate the mechanism, we screened a mutation library of Pseudomonas fluorescens Pf-5 in LB and agar medium supplemented with alfalfa snakin-1 (MsSN1). We identified three biofilm formation-related Pseudomonas mutants that showed increased resistance to MsSN1. Genetic, physiological and bioinformatics analysis validated the results of the mutant screens, indicating that bacterial adhesion protein lapA is probably the target of MsSN1. Collectively, these findings suggest that snakin-1 acts on microbial adhesion properties.
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Affiliation(s)
- Nicolás D Ayub
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917, C1033AAJ, Cuidad Autónoma de Buenos Aires, Argentina
| | - Ana R Fox
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917, C1033AAJ, Cuidad Autónoma de Buenos Aires, Argentina
| | - Araceli N García
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina
| | - Matteo Mozzicafreddo
- School of Biosciences and Biotechnology, University of Camerino, 62032 Camerino (MC), Italy
| | | | - Mauro Angeletti
- School of Biosciences and Biotechnology, University of Camerino, 62032 Camerino (MC), Italy
| | - Elba Pagano
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina
| | - Gabriela Soto
- Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los reseros S/N, Castelar C25 (1712), Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avda. Rivadavia 1917, C1033AAJ, Cuidad Autónoma de Buenos Aires, Argentina
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96
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Chekabab SM, Harel J, Dozois CM. Interplay between genetic regulation of phosphate homeostasis and bacterial virulence. Virulence 2014; 5:786-93. [PMID: 25483775 DOI: 10.4161/viru.29307] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacterial pathogens, including those of humans, animals, and plants, encounter phosphate (Pi)-limiting or Pi-rich environments in the host, depending on the site of infection. The environmental Pi-concentration results in modulation of expression of the Pho regulon that allows bacteria to regulate phosphate assimilation pathways accordingly. In many cases, modulation of Pho regulon expression also results in concomitant changes in virulence phenotypes. Under Pi-limiting conditions, bacteria use the transcriptional-response regulator PhoB to translate the Pi starvation signal sensed by the bacterium into gene activation or repression. This regulator is employed not only for the maintenance of bacterial Pi homeostasis but also to differentially regulate virulence. The Pho regulon is therefore not only a regulatory circuit of phosphate homeostasis but also plays an important adaptive role in stress response and bacterial virulence. Here we focus on recent findings regarding the mechanisms of gene regulation that underlie the virulence responses to Pi stress in Vibrio cholerae, Pseudomonas spp., and pathogenic E. coli.
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Affiliation(s)
- Samuel Mohammed Chekabab
- a Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA); Université de Montréal; Faculté de Médecine Vétérinaire ; Saint-Hyacinthe , QC Canada
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97
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Basu Roy A, Sauer K. Diguanylate cyclase NicD-based signalling mechanism of nutrient-induced dispersion by Pseudomonas aeruginosa. Mol Microbiol 2014; 94:771-93. [PMID: 25243483 DOI: 10.1111/mmi.12802] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2014] [Indexed: 01/15/2023]
Abstract
Dispersion enables the transition from the biofilm to the planktonic growth state in response to various cues. While several Pseudomonas aeruginosa proteins, including BdlA and the c-di-GMP phosphodiesterases DipA, RbdA, and NbdA, have been shown to be required for dispersion to occur, little is known about dispersion cue sensing and the signalling translating these cues into the modulation c-di-GMP levels to enable dispersion. Using glutamate-induced dispersion as a model, we report that dispersion-inducing nutrient cues are sensed via an outside-in signalling mechanism by the diguanylate cyclase NicD belonging to a family of seven transmembrane (7TM) receptors. NicD directly interacts with BdlA and the phosphodiesterase DipA, with NicD, BdlA, and DipA being part of the same pathway required for dispersion. Glutamate sensing by NicD results in NicD dephosphorylation and increased cyclase activity. Active NicD contributes to the non-processive proteolysis and activation of BdlA via phosphorylation and temporarily elevated c-di-GMP levels. BdlA, in turn, activates DipA, resulting in the overall reduction of c-di-GMP levels. Our results provide a basis for understanding the signalling mechanism based on NicD to induce biofilm dispersion that may be applicable to various biofilm-forming species and may have implications for the control of biofilm-related infections.
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Affiliation(s)
- Ankita Basu Roy
- Department of Biological Sciences, Binghamton University, 85 Murray Hill Road, Binghamton, NY, 13902, USA
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98
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Neznansky A, Blus-Kadosh I, Yerushalmi G, Banin E, Opatowsky Y. The Pseudomonas aeruginosa phosphate transport protein PstS plays a phosphate-independent role in biofilm formation. FASEB J 2014; 28:5223-33. [PMID: 25223609 DOI: 10.1096/fj.14-258293] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pseudomonas aeruginosa (PA) is a primary cause of nosocomial infections. A key element in PA pathogenicity is its ability to form biofilms that withstand eradication by antibiotics and the immune system. Biofilm formation is controlled by phosphate signaling and here we provide evidence that PstS, a subunit of the PA Pst phosphate transporter, has a surprising role in this process. Using X-ray crystallography, we characterized the unique underpinnings of PstS phosphate binding and identified an unusual 15-residue N' loop extension. Structure-based experiments showed that PstS-mediated phosphate uptake and biofilm formation are in fact two distinct functions. Specifically, a point mutation that abrogated phosphate binding did not eliminate biofilm formation; conversely, truncation of the N' loop diminished the ability of PA to form biofilms but had no effect on phosphate binding and uptake. This places PstS at a junction that separately controls phosphate sensing and uptake and the ultrastructure organization of bacteria.
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Affiliation(s)
- Avi Neznansky
- Mina and Everard Goodman Faculty of Life Sciences and
| | - Inna Blus-Kadosh
- Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Gal Yerushalmi
- Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Ehud Banin
- Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
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99
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Chatterjee D, Cooley RB, Boyd CD, Mehl RA, O'Toole GA, Sondermann H. Mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-GMP. eLife 2014; 3:e03650. [PMID: 25182848 PMCID: PMC4359373 DOI: 10.7554/elife.03650] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Stable surface adhesion of cells is one of the early pivotal steps in bacterial biofilm formation, a prevalent adaptation strategy in response to changing environments. In Pseudomonas fluorescens, this process is regulated by the Lap system and the second messenger cyclic-di-GMP. High cytoplasmic levels of cyclic-di-GMP activate the transmembrane receptor LapD that in turn recruits the periplasmic protease LapG, preventing it from cleaving a cell surface-bound adhesin, thereby promoting cell adhesion. In this study, we elucidate the molecular basis of LapG regulation by LapD and reveal a remarkably sensitive switching mechanism that is controlled by LapD's HAMP domain. LapD appears to act as a coincidence detector, whereby a weak interaction of LapG with LapD transmits a transient outside-in signal that is reinforced only when cyclic-di-GMP levels increase. Given the conservation of key elements of this receptor system in many bacterial species, the results are broadly relevant for cyclic-di-GMP- and HAMP domain-regulated transmembrane signaling. DOI:http://dx.doi.org/10.7554/eLife.03650.001 While bacteria often live as unicellular microorganisms, many bacteria are capable of sticking together on a surface and forming a multicellular structure called a biofilm. Bacterial biofilms occur frequently in nature; for example, on the roots of plants and submerged rocks. While these biofilms are generally innocuous, others pose significant health threats to humans, causing tooth decay, gum disease, and—when they occur on implanted devices such as prosthetic heart valves—potentially serious infections. When in biofilms, many bacteria are tolerant to antibiotics; therefore, working out how to disrupt these films is crucial for developing new treatments. The microorganism Pseudomonas fluorescens is an example of a bacterium that can be found living in a complex biofilm. In response to certain environmental cues, free-swimming P. fluorescens cells adhere to a surface and produce a slime that encases them in a robust biofilm. The decision to shift between a free-swimming and a biofilm life-style is orchestrated by a signaling molecule found inside the bacteria called cyclic-di-GMP. In P. fluorescens, the availability of nutrients—in particular, phosphate—controls how much cyclic-di-GMP is produced inside the cell. If not enough phosphate is available, the level of cyclic-di-GMP falls and the biofilm disperses. Cyclic-di-GMP affects the stability of the biofilm via a group of proteins called the Lap system. When levels of cyclic-di-GMP are high, cyclic-di-GMP binds to a protein called LapD, which can then in turn bind to an enzyme known as LapG. When bound to LapD, LapG is unable to break apart the molecules that help P. fluorescens cells bind to a surface, and so a biofilm can form. If cyclic-di-GMP levels drop, fewer LapD molecules can bind to cyclic-di-GMP. As cyclic-di-GMP-unbound LapD proteins interact poorly with LapG, this leaves some LapG molecules able to destabilize the attachments between the cells and the surface, which disperses the biofilm. Here, Chatterjee et al. reveal the molecular mechanism by which LapD and LapG interact in P. fluorescens. When cyclic-di-GMP is bound to LapD, the shape of LapD changes to produce features that fit into the surface of LapG. It is this shape compatibility, more so than an increase in the number or quality of interactions between the chemical groups that make up the proteins, that enables LapD to bind to LapG. Chatterjee et al. also provide evidence that the LapD–LapG interaction can be disrupted, thereby raising the possibility that biofilm formation could be manipulated by targeting this system. Given that systems similar to the P. fluorescens Lap system exist in numerous other bacterial species, including important pathogens, the findings of Chatterjee et al. could assist efforts to develop medicines and products that eradicate bacterial biofilms. LapD also shares many structural elements with a large number of other signaling proteins; therefore, these findings could also improve the understanding of how other cell signaling systems work. DOI:http://dx.doi.org/10.7554/eLife.03650.002
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Affiliation(s)
- Debashree Chatterjee
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States
| | - Richard B Cooley
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States
| | - Chelsea D Boyd
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States
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100
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Nagar E, Schwarz R. To be or not to be planktonic? Self-inhibition of biofilm development. Environ Microbiol 2014; 17:1477-86. [DOI: 10.1111/1462-2920.12583] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 07/23/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat-Gan 5290002 Israel
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat-Gan 5290002 Israel
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