1
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Tezuka T, Mitsuyama K, Date R, Ohnishi Y. A unique sigma/anti-sigma system in the actinomycete Actinoplanes missouriensis. Nat Commun 2023; 14:8483. [PMID: 38123564 PMCID: PMC10733313 DOI: 10.1038/s41467-023-44291-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Bacteria of the genus Actinoplanes form sporangia that contain dormant sporangiospores which, upon contact with water, release motile spores (zoospores) through a process called sporangium dehiscence. Here, we set out to study the molecular mechanisms behind sporangium dehiscence in Actinoplanes missouriensis and discover a sigma/anti-sigma system with unique features. Protein σSsdA contains a functional sigma factor domain and an anti-sigma factor antagonist domain, while protein SipA contains an anti-sigma factor domain and an anti-sigma factor antagonist domain. Remarkably, the two proteins interact with each other via the anti-sigma factor antagonist domain of σSsdA and the anti-sigma factor domain of SipA. Although it remains unclear whether the SipA/σSsdA system plays direct roles in sporangium dehiscence, the system seems to modulate oxidative stress responses in zoospores. In addition, we identify a two-component regulatory system (RsdK-RsdR) that represses initiation of sporangium dehiscence.
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Affiliation(s)
- Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo, Japan.
| | - Kyota Mitsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Risa Date
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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2
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Varponi I, Ferro S, Menilli L, Grapputo A, Moret F, Mastrotto F, Marin O, Sandrelli F. Fighting Pseudomonas aeruginosa Infections: Antibacterial and Antibiofilm Activity of D-Q53 CecB, a Synthetic Analog of a Silkworm Natural Cecropin B Variant. Int J Mol Sci 2023; 24:12496. [PMID: 37569868 PMCID: PMC10419416 DOI: 10.3390/ijms241512496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium responsible for severe nosocomial infections and is considered a critical pulmonary pathogen for both immunocompromised and cystic fibrosis patients. Planktonic cells of P. aeruginosa possess intrinsic and acquired resistances, inactivating several classes of conventional antibiotics. Additionally, this bacterium can grow, forming biofilms, and complex structures, further hampering the action of multiple antibiotics. Here, we report the biological properties of D-Q53 CecB, an all-D enantiomer of the silkworm natural peptide Q53 CecB. Compared to the L-variant, D-Q53 CecB was resistant to in vitro degradation by humans and P. aeruginosa elastases and showed an enhanced bactericidal activity against P. aeruginosa planktonic bacteria. D-Q53 CecB was thermostable and maintained its antimicrobial activity at high salt concentrations and in the presence of divalent cations or fetal-bovine serum, although at reduced levels. Against different types of human cells, D-Q53 CecB showed cytotoxic phenomena at concentrations several folds higher compared to those active against P. aeruginosa. When L- and D-Q53 CecB were compared for their antibiofilm properties, both peptides were active in inhibiting biofilm formation. However, the D-enantiomer was extremely effective in inducing biofilm degradation, suggesting this peptide as a favorable candidate in an anti-Pseudomonas therapy.
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Affiliation(s)
- Irene Varponi
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy; (I.V.); (L.M.); (A.G.); (F.M.)
| | - Stefania Ferro
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy; (S.F.); (O.M.)
| | - Luca Menilli
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy; (I.V.); (L.M.); (A.G.); (F.M.)
| | - Alessandro Grapputo
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy; (I.V.); (L.M.); (A.G.); (F.M.)
- National Biodiversity Future Centre, Piazza Marina 61, 90133 Palermo, Italy
| | - Francesca Moret
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy; (I.V.); (L.M.); (A.G.); (F.M.)
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy;
| | - Oriano Marin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy; (S.F.); (O.M.)
| | - Federica Sandrelli
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy; (I.V.); (L.M.); (A.G.); (F.M.)
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3
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Sánchez-Jiménez A, Llamas MA, Marcos-Torres FJ. Transcriptional Regulators Controlling Virulence in Pseudomonas aeruginosa. Int J Mol Sci 2023; 24:11895. [PMID: 37569271 PMCID: PMC10418997 DOI: 10.3390/ijms241511895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
Pseudomonas aeruginosa is a pathogen capable of colonizing virtually every human tissue. The host colonization competence and versatility of this pathogen are powered by a wide array of virulence factors necessary in different steps of the infection process. This includes factors involved in bacterial motility and attachment, biofilm formation, the production and secretion of extracellular invasive enzymes and exotoxins, the production of toxic secondary metabolites, and the acquisition of iron. Expression of these virulence factors during infection is tightly regulated, which allows their production only when they are needed. This process optimizes host colonization and virulence. In this work, we review the intricate network of transcriptional regulators that control the expression of virulence factors in P. aeruginosa, including one- and two-component systems and σ factors. Because inhibition of virulence holds promise as a target for new antimicrobials, blocking the regulators that trigger the production of virulence determinants in P. aeruginosa is a promising strategy to fight this clinically relevant pathogen.
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Affiliation(s)
| | - María A. Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Francisco Javier Marcos-Torres
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
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4
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Caliskan M, Poschmann G, Gudzuhn M, Waldera-Lupa D, Molitor R, Strunk CH, Streit WR, Jaeger KE, Stühler K, Kovacic F. Pseudomonas aeruginosa responds to altered membrane phospholipid composition by adjusting the production of two-component systems, proteases and iron uptake proteins. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159317. [PMID: 37054907 DOI: 10.1016/j.bbalip.2023.159317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/15/2023]
Abstract
Membrane protein and phospholipid (PL) composition changes in response to environmental cues and during infections. To achieve these, bacteria use adaptation mechanisms involving covalent modification and remodelling of the acyl chain length of PLs. However, little is known about bacterial pathways regulated by PLs. Here, we investigated proteomic changes in the biofilm of P. aeruginosa phospholipase mutant (∆plaF) with altered membrane PL composition. The results revealed profound alterations in the abundance of many biofilm-related two-component systems (TCSs), including accumulation of PprAB, a key regulator of the transition to biofilm. Furthermore, a unique phosphorylation pattern of transcriptional regulators, transporters and metabolic enzymes, as well as differential production of several proteases, in ∆plaF, indicate that PlaF-mediated virulence adaptation involves complex transcriptional and posttranscriptional response. Moreover, proteomics and biochemical assays revealed the depletion of pyoverdine-mediated iron uptake pathway proteins in ∆plaF, while proteins from alternative iron-uptake systems were accumulated. These suggest that PlaF may function as a switch between different iron-acquisition pathways. The observation that PL-acyl chain modifying and PL synthesis enzymes were overproduced in ∆plaF reveals the interconnection of degradation, synthesis and modification of PLs for proper membrane homeostasis. Although the precise mechanism by which PlaF simultaneously affects multiple pathways remains to be elucidated, we suggest that alteration of PL composition in ∆plaF plays a role for the global adaptive response in P. aeruginosa mediated by TCSs and proteases. Our study revealed the global regulation of virulence and biofilm by PlaF and suggests that targeting this enzyme may have therapeutic potential.
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Affiliation(s)
- Muttalip Caliskan
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirja Gudzuhn
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Daniel Waldera-Lupa
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Rebecka Molitor
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany
| | | | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Molecular Proteomics Laboratory, Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-University, Düsseldorf, Düsseldorf, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany.
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5
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He X, Ding H, Gao Z, Zhang X, Wu R, Li K. Variations in the motility and biofilm formation abilities of Escherichia coli O157:H7 during noodle processing. Food Res Int 2023; 168:112670. [PMID: 37120241 DOI: 10.1016/j.foodres.2023.112670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/23/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Motility and biofilm formation help to protect bacteria from host immune responses and facilitate tolerance of environmental stimuli to improve their adaptability. However, few reports have investigated the adaptability of bacteria that live in food substrates undergoing food processing-induced stress. In this study, variations in the surface morphology, bacterial count, motility, and biofilm formation abilities of Escherichia coli O157:H7 NCTC12900 were investigated during noodle processing, including the kneading, squeezing, resting, and sheeting phases. The results showed that bacterial surface morphology, count, and motility were impaired in the squeezing phase, whereas biofilm biomass continuously increased across all processing phases. Twenty-one genes and sRNAs were measured using RT-qPCR to reveal the mechanisms underlying these changes. Of these, the genes adrA, csrA, flgM, flhD, fliM, ydaM, and the sRNA McaS were significantly upregulated, whereas the genes fliA, fliG, and the sRNAs CsrC, DsrA, GcvB, and OxyS were evidently repressed. According to the correlation matrix results based on the reference gene adrA, we found that csrA, GcvB, McaS, and OxyS were the most relevant genes and sRNAs for biofilm formation and motility. For each of them, their overexpressions was found to inhibit bacterial motility and biofilm formation to varying degrees during noodle processing. Among these, 12900/pcsrA had the highest inhibitory potential against motility, yielding a minimum of 11.2 mm motility diameter in the resting phase. Furthermore, 12900/pOxyS showed the most significant inhibitory effect against biofilm formation, yielding a minimum biofilm formation value of 5% of that exhibited the wild strain in the sheeting phase. Therefore, we prospect to find an effective and feasible novel approach to weaken bacterial survival during food processing by regulating the genes or sRNAs related to motility and biofilm formation.
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6
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Alviz-Gazitua P, González A, Lee MR, Aranda CP. Molecular Relationships in Biofilm Formation and the Biosynthesis of Exoproducts in Pseudoalteromonas spp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:431-447. [PMID: 35486299 DOI: 10.1007/s10126-022-10097-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Most members of the Pseudoalteromonas genus have been isolated from living surfaces as members of epiphytic and epizooic microbiomes on marine macroorganisms. Commonly Pseudoalteromonas isolates are reported as a source of bioactive exoproducts, i.e., secondary metabolites, such as exopolymeric substances and extracellular enzymes. The experimental conditions for the production of these agents are commonly associated with sessile metabolic states such as biofilms or liquid cultures in the stationary growth phase. Despite this, the molecular mechanisms that connect biofilm formation and the biosynthesis of exoproducts in Pseudoalteromonas isolates have rarely been mentioned in the literature. This review compiles empirical evidence about exoproduct biosynthesis conditions and molecular mechanisms that regulate sessile metabolic states in Pseudoalteromonas species, to provide a comprehensive perspective on the regulatory convergences that generate the recurrent coexistence of both phenomena in this bacterial genus. This synthesis aims to provide perspectives on the extent of this phenomenon for the optimization of bioprospection studies and biotechnology processes based on these bacteria.
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Affiliation(s)
- P Alviz-Gazitua
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - A González
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - M R Lee
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue km 6, P. Box 5480000, Puerto Montt, Chile
| | - C P Aranda
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile.
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7
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Tuon FF, Dantas LR, Suss PH, Tasca Ribeiro VS. Pathogenesis of the Pseudomonas aeruginosa Biofilm: A Review. Pathogens 2022; 11:pathogens11030300. [PMID: 35335624 PMCID: PMC8950561 DOI: 10.3390/pathogens11030300] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/08/2022] [Accepted: 02/24/2022] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is associated with several human infections, mainly related to healthcare services. In the hospital, it is associated with resistance to several antibiotics, which poses a great challenge to therapy. However, one of the biggest challenges in treating P. aeruginosa infections is that related to biofilms. The complex structure of the P. aeruginosa biofilm contributes an additional factor to the pathogenicity of this microorganism, leading to therapeutic failure, in addition to escape from the immune system, and generating chronic infections that are difficult to eradicate. In this review, we address several molecular aspects of the pathogenicity of P. aeruginosa biofilms.
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8
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Gong C, He Y, Tang Y, Hu R, Lv Y, Zhang Q, Tardy BL, Richardson JJ, He Q, Guo J, Chi Y. Biofilms in plant-based fermented foods: Formation mechanisms, benefits and drawbacks on quality and safety, and functionalization strategies. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.08.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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9
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Ryan Kaler KM, Nix JC, Schubot FD. RetS inhibits Pseudomonas aeruginosa biofilm formation by disrupting the canonical histidine kinase dimerization interface of GacS. J Biol Chem 2021; 297:101193. [PMID: 34529974 PMCID: PMC8498467 DOI: 10.1016/j.jbc.2021.101193] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/30/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
Bacterial signaling histidine kinases (HKs) have long been postulated to function exclusively through linear signal transduction chains. However, several HKs have recently been shown to form complex multikinase networks (MKNs). The most prominent MKN, involving the enzymes RetS and GacS, controls the switch between the motile and biofilm lifestyles in the pathogenic bacterium Pseudomonas aeruginosa. While GacS promotes biofilm formation, RetS counteracts GacS using three distinct mechanisms. Two are dephosphorylating mechanisms. The third, a direct binding between the RetS and GacS HK regions, blocks GacS autophosphorylation. Focusing on the third mechanism, we determined the crystal structure of a cocomplex between the HK region of RetS and the dimerization and histidine phosphotransfer (DHp) domain of GacS. This is the first reported structure of a complex between two distinct bacterial signaling HKs. In the complex, the canonical HK homodimerization interface is replaced by a strikingly similar heterodimeric interface between RetS and GacS. We further demonstrate that GacS autophosphorylates in trans, thus explaining why the formation of a RetS-GacS complex inhibits GacS autophosphorylation. Using mutational analysis in conjunction with bacterial two-hybrid and biofilm assays, we not only corroborate the biological role of the observed RetS-GacS interactions, but also identify a residue critical for the equilibrium between the RetS-GacS complex and the respective RetS and GacS homodimers. Collectively, our findings suggest that RetS and GacS form a domain-swapped hetero-oligomer during the planktonic growth phase of P. aeruginosa before unknown signals cause its dissociation and a relief of GacS inhibition to promote biofilm formation.
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Affiliation(s)
- Kylie M Ryan Kaler
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Jay C Nix
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Florian D Schubot
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA.
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10
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Fernández-Gómez P, Figueredo A, López M, González-Raurich M, Prieto M, Alvarez-Ordóñez A. Heterogeneity in biofilm formation and identification of biomarkers of strong biofilm formation among field isolates of Pseudomonas spp. Food Res Int 2021; 148:110618. [PMID: 34507762 DOI: 10.1016/j.foodres.2021.110618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
The biofilm formation ability of a collection of thirty-three Pseudomonas spp. isolates from food processing facilities was investigated in order to find biomarkers of strong biofilm production, a characteristic that can determine persistence in food processing environments. The strains were classified according to the colony pigmentation on solid media as green, brown or not pigmented. The biofilm production on stainless steel and polystyrene was assessed by spectrometric determination of the fixed crystal violet, and the biofilm formed on glass, through confocal laser scanning microscopy. Besides, pyoverdine production, catalase activity, RpoS status and cellular hydrophobicity were also monitored. A significantly higher biofilm production level on stainless steel and polystyrene was observed for green-pigmented strains as compared to brown or not pigmented strains. The influence of iron availability on biofilm formation on stainless steel was studied through the addition of the iron scavenger 2,2-bipyridine resulting in a decrease of 40 % in biofilm formation for the not pigmented strains. For most of the potential biomarkers studied (i.e., pyoverdine production, catalase activity, cellular hydrophobicity), the phenotypic heterogeneity observed among strains was mainly dependent on the Pseudomonas species and no strong associations with the biofilm formation capacity were detected. However, the green colony pigmentation on solid media showed good potential as a biomarker of strong biofilm formation on stainless steel and polystyrene both in P. aeruginosa and Pseudomonas spp.
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Affiliation(s)
| | | | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Montserrat González-Raurich
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain.
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11
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Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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12
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Ferreiro MD, Gallegos MT. Distinctive features of the Gac-Rsm pathway in plant-associated Pseudomonas. Environ Microbiol 2021; 23:5670-5689. [PMID: 33939255 DOI: 10.1111/1462-2920.15558] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 02/04/2023]
Abstract
Productive plant-bacteria interactions, either beneficial or pathogenic, require that bacteria successfully sense, integrate and respond to continuously changing environmental and plant stimuli. They use complex signal transduction systems that control a vast array of genes and functions. The Gac-Rsm global regulatory pathway plays a key role in controlling fundamental aspects of the apparently different lifestyles of plant beneficial and phytopathogenic Pseudomonas as it coordinates adaptation and survival while either promoting plant health (biocontrol strains) or causing disease (pathogenic strains). Plant-interacting Pseudomonas stand out for possessing multiple Rsm proteins and Rsm RNAs, but the physiological significance of this redundancy is not yet clear. Strikingly, the components of the Gac-Rsm pathway and the controlled genes/pathways are similar, but the outcome of its regulation may be opposite. Therefore, identifying the target mRNAs bound by the Rsm proteins and their mode of action (repression or activation) is essential to explain the resulting phenotype. Some technical considerations to approach the study of this system are also given. Overall, several important features of the Gac-Rsm cascade are now understood in molecular detail, particularly in Pseudomonas protegens CHA0, but further questions remain to be solved in other plant-interacting Pseudomonas.
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Affiliation(s)
- María-Dolores Ferreiro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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13
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Chihara K, Barquist L, Takasugi K, Noda N, Tsuneda S. Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq. RNA Biol 2021; 18:2401-2416. [PMID: 33866926 DOI: 10.1080/15476286.2021.1917184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Pseudomonas aeruginosa harbours two redundant RNA-binding proteins RsmA/RsmN (RsmA/N), which play a critical role in balancing acute and chronic infections. However, in vivo binding sites on target transcripts and the overall impact on the physiology remains unclear. In this study, we applied in vivo UV crosslinking immunoprecipitation followed by RNA-sequencing (UV CLIP-seq) to detect RsmA/N-binding sites at single-nucleotide resolution and mapped more than 500 binding sites to approximately 400 genes directly bound by RsmA/N in P. aeruginosa. This also verified the ANGGA sequence in apical loops skewed towards 5'UTRs as a consensus motif for RsmA/N binding. Genetic analysis combined with CLIP-seq results suggested previously unrecognized RsmA/N targets involved in LPS modification. Moreover, the RsmA/N-titrating RNAs RsmY/RsmZ may be positively regulated by the RsmA/N-mediated translational repression of their upstream regulators, thus providing a possible mechanistic explanation for homoeostasis of the Rsm system. Thus, our study provides a detailed view of RsmA/N-RNA interactions and a resource for further investigation of the pleiotropic effects of RsmA/N on gene expression in P. aeruginosa.
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Affiliation(s)
- Kotaro Chihara
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany.,Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Kenichi Takasugi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
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14
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Bouteiller M, Dupont C, Bourigault Y, Latour X, Barbey C, Konto-Ghiorghi Y, Merieau A. Pseudomonas Flagella: Generalities and Specificities. Int J Mol Sci 2021; 22:ijms22073337. [PMID: 33805191 PMCID: PMC8036289 DOI: 10.3390/ijms22073337] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
Flagella-driven motility is an important trait for bacterial colonization and virulence. Flagella rotate and propel bacteria in liquid or semi-liquid media to ensure such bacterial fitness. Bacterial flagella are composed of three parts: a membrane complex, a flexible-hook, and a flagellin filament. The most widely studied models in terms of the flagellar apparatus are E. coli and Salmonella. However, there are many differences between these enteric bacteria and the bacteria of the Pseudomonas genus. Enteric bacteria possess peritrichous flagella, in contrast to Pseudomonads, which possess polar flagella. In addition, flagellar gene expression in Pseudomonas is under a four-tiered regulatory circuit, whereas enteric bacteria express flagellar genes in a three-step manner. Here, we use knowledge of E. coli and Salmonella flagella to describe the general properties of flagella and then focus on the specificities of Pseudomonas flagella. After a description of flagellar structure, which is highly conserved among Gram-negative bacteria, we focus on the steps of flagellar assembly that differ between enteric and polar-flagellated bacteria. In addition, we summarize generalities concerning the fuel used for the production and rotation of the flagellar macromolecular complex. The last part summarizes known regulatory pathways and potential links with the type-six secretion system (T6SS).
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Affiliation(s)
- Mathilde Bouteiller
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Charly Dupont
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yvann Bourigault
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Corinne Barbey
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
| | - Annabelle Merieau
- LMSM, Laboratoire de Microbiologie Signaux et Microenvironnement, EA 4312, Normandy University, Université de Rouen, 27000 Evreux, France; (M.B.); (C.D.); (Y.B.); (X.L.); (C.B.); (Y.K.-G.)
- SFR NORVEGE, Structure Fédérative de Recherche Normandie Végétale, FED 4277, 76821 Mont-Saint-Aignan, France
- Correspondence:
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15
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Zhang C, Wang C, Jatt AN, Liu H, Liu Y. Role of RpoS in stress resistance, biofilm formation and quorum sensing of Shewanella baltica. Lett Appl Microbiol 2020; 72:307-315. [PMID: 33125713 DOI: 10.1111/lam.13424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
Shewanella baltica is one of the most important bacterial species contributing to spoilage of seafood. Principally, RpoS has been recognized as the central regulator of stress resistance in many bacterial species. However, little is known about the role of RpoS in S. baltica. In this study, an rpoS mutant of S. baltica was constructed and analysed for its functions. The results showed that the survival rate of rpoS mutant decreased when treated with heat, ethanol and H2 O2, while increased the resistance to NaCl. Moreover RpoS promoted the biofilm formation of S. baltica at 30°C, while declined at 4°C. Interestingly, the rpoS-deficient mutant showed increased swimming motility. Furthermore, the results revealed that the production of quorum-sensing (QS) signals such as cyclo-(l-Pro-l-Leu) and cyclo-(l-Pro-l-Phe) reduced in rpoS mutant. Mainly, rpoS positively regulated QS response regulators, as the expression of all luxR genes in rpoS mutant significantly decreased relative to wild type. This study reveals that RpoS is a major regulator involved in stress responses, biofilm formation and quorum sensing system in S. baltica. The present work provides significant information for the control of microbiological spoilage of seafood.
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Affiliation(s)
- C Zhang
- School of Food Engineering, Ludong University, Shandong, China
| | - C Wang
- School of Food Engineering, Ludong University, Shandong, China
| | - A-N Jatt
- Institute of Microbiology, University of Sindh Jamshoro, Jamshoro, Pakistan
| | - H Liu
- School of Food Engineering, Ludong University, Shandong, China
| | - Y Liu
- School of Food Engineering, Ludong University, Shandong, China
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16
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Yu Z, Zhang J, Ding M, Wu S, Shuangjia Li, Zhang M, Yin J, Meng Q. SspA positively controls exopolysaccharides production and biofilm formation by up-regulating the algU expression in Pseudoalteromonas sp. R3. Biochem Biophys Res Commun 2020; 533:988-994. [PMID: 33010891 DOI: 10.1016/j.bbrc.2020.09.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/25/2020] [Indexed: 10/23/2022]
Abstract
Biofilm formation enhances the survival and persistence of microorganisms in response to environmental stresses. It has been revealed that stringent starvation protein A (SspA) can function as an important regulator dealing with environmental stresses for bacterial survival. However, the connection between SspA and biofilm formation is essentially unclear yet. In this study, we presented evidence showing SspA positively controls biofilm formation by up-regulating exopolysaccharides (EPS) production in marine bacterium Pseudoalteromonas sp. R3. Both qPCR and lacZ reporter system congruously revealed that SspA positively controls the expression of EPS biosynthesis gene cluster. Unlike generally accepted thought that SspA regulates bacterial physiology by inhibiting the expression of histone-like nucleotide structuring protein (H-NS) gene, the function of SspA on EPS production and biofilm formation in Pseudoalteromonas sp. R3 is H-NS-independent. Instead, SspA positively regulates the expression of sigma factor AlgU-encoding gene, thus affecting EPS biosynthesis and biofilm formation. In view of the important role of SspA in biofilm formation, we believe that the improvement of tolerance to marine environmental stresses could be related to tuning of SspA-involved biofilm formation.
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Affiliation(s)
- Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China.
| | - Jiadi Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China
| | - Mengdan Ding
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China
| | - Shijun Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China
| | - Shuangjia Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China
| | - Mengting Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China
| | - Jianhua Yin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China
| | - Qiu Meng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang Province, China.
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