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Lyapina I, Ivanov V, Fesenko I. Peptidome: Chaos or Inevitability. Int J Mol Sci 2021; 22:13128. [PMID: 34884929 PMCID: PMC8658490 DOI: 10.3390/ijms222313128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups-functional protein "degradome", small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the "degradome" in promoting defense signaling, are also considered.
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Affiliation(s)
| | | | - Igor Fesenko
- Department of Functional Genomics and Proteomics of Plants, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, 117997 Moscow, Russia; (I.L.); (V.I.)
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2
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Box-Wilson Design for Optimization of in vitro Levan Production and Levan Application as Antioxidant and Antibacterial Agents. IRANIAN BIOMEDICAL JOURNAL 2021. [PMID: 33486911 PMCID: PMC8183386 DOI: 10.52547/ibj.25.3.202] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background: Methods: Results: Conclusion:
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Hertadi R, Permatasari NU, Ratnaningsih E. Box-Wilson Design for Optimization of in vitro Levan Production and Levan Application as Antioxidant and Antibacterial Agents. IRANIAN BIOMEDICAL JOURNAL 2021; 25:202-12. [PMID: 33486911 PMCID: PMC8183386 DOI: 10.29252/ibj.25.3.202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/07/2020] [Indexed: 01/02/2023]
Abstract
Background Levan or fructan, a polysaccharide of fructose, is widely used in various commercial industries. Levan could be produced by many organisms, including plants and bacteria. The cloning of the gene from Bacillus licheniformis, which expressed levansucrase in Escherichia coli host, was carried out successfully. In the present study, we performed the in vitro production of levan and analyzed its potential application as antibacterial and antioxidant agents. Methods In vitro levan production catalyzed by heterologous-expressed levansucrase Lsbl-bk1 and Lsbl-bk2 was optimized with Box-Wilson design. The antibacterial activity of the produced levan was carried out using agar well diffusion method, while its antioxidant activity was tested by free radical scavenging assays. Results The optimum conditions for levan production were observed at 36 °C and pH 7 in 12% (w/v) sucrose for levansucrase Lsbl-bk1, while the optimum catalysis of levansucrase Lsbl-bk2 was obtained at 32 oC and pH 8 in the same sucrose concentration. The in vitro synthesized levan showed an antibacterial activity within a concentration range of 10-20% (w/v) against Staphylococcus aureus, E. coli, and Pseudomonas aeruginosa. The same levan was also able to inhibit the 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity with the antioxidant strength of 75% compared to ascorbic acid inhibition. Conclusion Our study, therefore, shows that the optimized heterologous expression of levansucrases encoded by Lsbl-bk1 and Lsbl-bk2 could open the way for industrial levan production as an antibacterial and antioxidant agent.
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Affiliation(s)
- Rukman Hertadi
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Indonesia
| | - Nur Umriani Permatasari
- Chemistry Department, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Indonesia
| | - Enny Ratnaningsih
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Indonesia
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Voichek M, Maaß S, Kroniger T, Becher D, Sorek R. Peptide-based quorum sensing systems in Paenibacillus polymyxa. Life Sci Alliance 2020; 3:3/10/e202000847. [PMID: 32764104 PMCID: PMC7425212 DOI: 10.26508/lsa.202000847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022] Open
Abstract
Discovery of conserved communication systems in the agriculturally important Paenibacillus bacteria. These systems are widespread, and some species encode more than 25 different peptide-receptor pairs. Paenibacillus polymyxa is an agriculturally important plant growth–promoting rhizobacterium. Many Paenibacillus species are known to be engaged in complex bacteria–bacteria and bacteria–host interactions, which in other species were shown to necessitate quorum sensing communication. However, to date, no quorum sensing systems have been described in Paenibacillus. Here, we show that the type strain P. polymyxa ATCC 842 encodes at least 16 peptide-based communication systems. Each of these systems is comprised of a pro-peptide that is secreted to the growth medium and processed to generate a mature short peptide. Each peptide has a cognate intracellular receptor of the RRNPP family, and we show that external addition of P. polymyxa communication peptides leads to reprogramming of the transcriptional response. We found that these quorum sensing systems are conserved across hundreds of species belonging to the Paenibacillaceae family, with some species encoding more than 25 different peptide-receptor pairs, representing a record number of quorum sensing systems encoded in a single genome.
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Affiliation(s)
- Maya Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Tobias Kroniger
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Neiditch MB, Capodagli GC, Prehna G, Federle MJ. Genetic and Structural Analyses of RRNPP Intercellular Peptide Signaling of Gram-Positive Bacteria. Annu Rev Genet 2017; 51:311-333. [PMID: 28876981 PMCID: PMC6588834 DOI: 10.1146/annurev-genet-120116-023507] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bacteria use diffusible chemical messengers, termed pheromones, to coordinate gene expression and behavior among cells in a community by a process known as quorum sensing. Pheromones of many gram-positive bacteria, such as Bacillus and Streptococcus, are small, linear peptides secreted from cells and subsequently detected by sensory receptors such as those belonging to the large family of RRNPP proteins. These proteins are cytoplasmic pheromone receptors sharing a structurally similar pheromone-binding domain that functions allosterically to regulate receptor activity. X-ray crystal structures of prototypical RRNPP members have provided atomic-level insights into their mechanism and regulation by pheromones. This review provides an overview of RRNPP prototype signaling; describes the structure-function of this protein family, which is spread widely among gram-positive bacteria; and suggests approaches to target RRNPP systems in order to manipulate beneficial and harmful bacterial behaviors.
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Affiliation(s)
- Matthew B Neiditch
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, USA; ,
| | - Glenn C Capodagli
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, USA; ,
| | - Gerd Prehna
- Center for Structural Biology, Research Resources Center and Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
| | - Michael J Federle
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
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Di Luccia B, D'Apuzzo E, Varriale F, Baccigalupi L, Ricca E, Pollice A. Bacillus megaterium SF185 induces stress pathways and affects the cell cycle distribution of human intestinal epithelial cells. Benef Microbes 2016; 7:609-20. [PMID: 27291405 DOI: 10.3920/bm2016.0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The interaction between the enteric microbiota and intestinal cells often involves signal molecules that affect both microbial behaviour and host responses. Examples of such signal molecules are the molecules secreted by bacteria that induce quorum sensing mechanisms in the producing microorganism and signal transduction pathways in the host cells. The pentapeptide competence and sporulation factor (CSF) of Bacillus subtilis is a well characterized quorum sensing factor that controls competence and spore formation in the producing bacterium and induces cytoprotective heat shock proteins in intestinal epithelial cells. We analysed several Bacillus strains isolated from human ileal biopsies of healthy volunteers and observed that some of them were unable to produce CSF but still able to act in a CSF-like fashion on model intestinal epithelial cells. One of those strains belonging to the Bacillus megaterium species secreted at least two factors with effects on intestinal HT29 cells: a peptide smaller than 3 kDa able to induce heat shock protein 27 (hsp27) and p38-MAPK, and a larger molecule able to induce protein kinase B (PKB/Akt) with a pro-proliferative effect.
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Affiliation(s)
- B Di Luccia
- 1 Department of Biology, Complesso Universitario di Monte Sant'Angelo Federico II University, via Cinthia, 80126 Napoli, Italy
| | - E D'Apuzzo
- 1 Department of Biology, Complesso Universitario di Monte Sant'Angelo Federico II University, via Cinthia, 80126 Napoli, Italy
| | - F Varriale
- 1 Department of Biology, Complesso Universitario di Monte Sant'Angelo Federico II University, via Cinthia, 80126 Napoli, Italy
| | - L Baccigalupi
- 1 Department of Biology, Complesso Universitario di Monte Sant'Angelo Federico II University, via Cinthia, 80126 Napoli, Italy
| | - E Ricca
- 1 Department of Biology, Complesso Universitario di Monte Sant'Angelo Federico II University, via Cinthia, 80126 Napoli, Italy
| | - A Pollice
- 1 Department of Biology, Complesso Universitario di Monte Sant'Angelo Federico II University, via Cinthia, 80126 Napoli, Italy
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Hoover SE, Perez AJ, Tsui HCT, Sinha D, Smiley DL, DiMarchi RD, Winkler ME, Lazazzera BA. A new quorum-sensing system (TprA/PhrA) for Streptococcus pneumoniae D39 that regulates a lantibiotic biosynthesis gene cluster. Mol Microbiol 2015; 97:229-43. [PMID: 25869931 DOI: 10.1111/mmi.13029] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2015] [Indexed: 12/20/2022]
Abstract
The Phr peptides of the Bacillus species mediate quorum sensing, but their identification and function in other species of bacteria have not been determined. We have identified a Phr peptide quorum-sensing system (TprA/PhrA) that controls the expression of a lantibiotic gene cluster in the Gram-positive human pathogen, Streptococcus pneumoniae. Lantibiotics are highly modified peptides that are part of the bacteriocin family of antimicrobial peptides. We have characterized the basic mechanism for a Phr-peptide signaling system in S. pneumoniae and found that it induces the expression of the lantibiotic genes when pneumococcal cells are at high density in the presence of galactose, a main sugar of the human nasopharynx, a highly competitive microbial environment. Activity of the Phr peptide system is not seen when pneumococcal cells are grown with glucose, the preferred carbon source and the most prevalent sugar encountered by S. pneumoniae during invasive disease. Thus, the lantibiotic genes are expressed under the control of both cell density signals via the Phr peptide system and nutritional signals from the carbon source present, suggesting that quorum sensing and the lantibiotic machinery may help pneumococcal cells compete for space and resources during colonization of the nasopharynx.
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Affiliation(s)
- Sharon E Hoover
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 609 Charles E. Young Dr. East, 1602 Molecular Science Building, Los Angeles, California, 90095, USA
| | - Amilcar J Perez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 609 Charles E. Young Dr. East, 1602 Molecular Science Building, Los Angeles, California, 90095, USA
| | - Ho-Ching T Tsui
- Department of Biology, Indiana University Bloomington, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - Dhriti Sinha
- Department of Biology, Indiana University Bloomington, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - David L Smiley
- Department of Chemistry, Indiana University Bloomington, 800 E. Kirkwood Avenue, Bloomington, Indiana, 47405, USA
| | - Richard D DiMarchi
- Department of Chemistry, Indiana University Bloomington, 800 E. Kirkwood Avenue, Bloomington, Indiana, 47405, USA
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 609 Charles E. Young Dr. East, 1602 Molecular Science Building, Los Angeles, California, 90095, USA
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Johnston C, Martin B, Fichant G, Polard P, Claverys JP. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat Rev Microbiol 2014; 12:181-96. [DOI: 10.1038/nrmicro3199] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Corrales-Guerrero L, Mariscal V, Flores E, Herrero A. Functional dissection and evidence for intercellular transfer of the heterocyst-differentiation PatS morphogen. Mol Microbiol 2013; 88:1093-105. [DOI: 10.1111/mmi.12244] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Laura Corrales-Guerrero
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas and Universidad de Sevilla; Américo Vespucio 49; E-41092; Seville; Spain
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas and Universidad de Sevilla; Américo Vespucio 49; E-41092; Seville; Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas and Universidad de Sevilla; Américo Vespucio 49; E-41092; Seville; Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas and Universidad de Sevilla; Américo Vespucio 49; E-41092; Seville; Spain
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Wynendaele E, Bronselaer A, Nielandt J, D'Hondt M, Stalmans S, Bracke N, Verbeke F, Van De Wiele C, De Tré G, De Spiegeleer B. Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides. Nucleic Acids Res 2012. [PMID: 23180797 DOI: 10.1093/nar/gks1137+[doi+link]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Quorum-sensing (QS) peptides are biologically attractive molecules, with a wide diversity of structures and prone to modifications altering or presenting new functionalities. Therefore, the Quorumpeps database (http://quorumpeps.ugent.be) is developed to give a structured overview of the QS oligopeptides, describing their microbial origin (species), functionality (method, result and receptor), peptide links and chemical characteristics (3D-structure-derived physicochemical properties). The chemical diversity observed within this group of QS signalling molecules can be used to develop new synthetic bio-active compounds.
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Affiliation(s)
- Evelien Wynendaele
- Drug Quality and Registration (DruQuaR) group, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent Hospital University, Ghent B-9000, Belgium
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11
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Wynendaele E, Bronselaer A, Nielandt J, D'Hondt M, Stalmans S, Bracke N, Verbeke F, Van De Wiele C, De Tré G, De Spiegeleer B. Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides. Nucleic Acids Res 2012. [PMID: 23180797 PMCID: PMC3531179 DOI: 10.1093/nar/gks1137] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Quorum-sensing (QS) peptides are biologically attractive molecules, with a wide diversity of structures and prone to modifications altering or presenting new functionalities. Therefore, the Quorumpeps database (http://quorumpeps.ugent.be) is developed to give a structured overview of the QS oligopeptides, describing their microbial origin (species), functionality (method, result and receptor), peptide links and chemical characteristics (3D-structure-derived physicochemical properties). The chemical diversity observed within this group of QS signalling molecules can be used to develop new synthetic bio-active compounds.
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Affiliation(s)
- Evelien Wynendaele
- Drug Quality and Registration (DruQuaR) group, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent Hospital University, Ghent B-9000, Belgium
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12
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Wynendaele E, Bronselaer A, Nielandt J, D’Hondt M, Stalmans S, Bracke N, Verbeke F, Van De Wiele C, De Tré G, De Spiegeleer B. Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides. Nucleic Acids Res 2012. [DOI: 10.1093/nar/gks1137 [doi link]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Osmoprotection of Bacillus subtilis through import and proteolysis of proline-containing peptides. Appl Environ Microbiol 2012; 79:576-87. [PMID: 23144141 DOI: 10.1128/aem.01934-12] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bacillus subtilis can attain cellular protection against the detrimental effects of high osmolarity through osmotically induced de novo synthesis and uptake of the compatible solute l-proline. We have now found that B. subtilis can also exploit exogenously provided proline-containing peptides of various lengths and compositions as osmoprotectants. Osmoprotection by these types of peptides is generally dependent on their import via the peptide transport systems (Dpp, Opp, App, and DtpT) operating in B. subtilis and relies on their hydrolysis to liberate proline. The effectiveness with which proline-containing peptides confer osmoprotection varies considerably, and this can be correlated with the amount of the liberated and subsequently accumulated free proline by the osmotically stressed cell. Through gene disruption experiments, growth studies, and the quantification of the intracellular proline pool, we have identified the PapA (YqhT) and PapB (YkvY) peptidases as responsible for the hydrolysis of various types of Xaa-Pro dipeptides and Xaa-Pro-Xaa tripeptides. The PapA and PapB peptidases possess overlapping substrate specificities. In contrast, osmoprotection by peptides of various lengths and compositions with a proline residue positioned at their N terminus was not affected by defects in the PapA and PapB peptidases. Taken together, our data provide new insight into the physiology of the osmotic stress response of B. subtilis. They illustrate the flexibility of this ubiquitously distributed microorganism to effectively exploit environmental resources in its acclimatization to sustained high-osmolarity surroundings through the accumulation of compatible solutes.
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Abstract
Under conditions of nutrient limitation and high population density, the bacterium Bacillus subtilis can initiate a variety of developmental pathways. The signaling systems regulating B. subtilis differentiation are tightly controlled by switch proteins called Raps, named after the founding members of the family, which were shown to be response regulator aspartate phosphatases. A phr gene encoding a secreted pentapeptide that regulates the activity of its associated Rap protein was previously identified downstream of 8 of the chromosomally encoded rap genes. We identify and validate here the sequence of an atypical Phr peptide, PhrH, by in vivo and in vitro analyses. Using a luciferase reporter bioassay combined with in vitro experiments, we found that PhrH is a hexapeptide (TDRNTT), in contrast to the other characterized Phr pentapeptides. We also determined that phrH expression is driven by a promoter lying within rapH. Unlike the previously identified dedicated σ(H)-driven phr promoters, it appears that phrH expression most likely requires σ(A). Furthermore, we show that PhrH can antagonize both of the known activities of RapH: the dephosphorylation of Spo0F and the sequestration of ComA, thus promoting the development of spores and the competent state. Finally, we propose that PhrH is the prototype of a newly identified class of Phr signaling molecules consisting of six amino acids. This class likely includes PhrI, which regulates RapI and the expression, excision, and transfer of the mobile genetic element ICEBs1.
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Anderson TD, Robson SA, Jiang XW, Malmirchegini GR, Fierobe HP, Lazazzera BA, Clubb RT. Assembly of minicellulosomes on the surface of Bacillus subtilis. Appl Environ Microbiol 2011; 77:4849-58. [PMID: 21622797 PMCID: PMC3147385 DOI: 10.1128/aem.02599-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 05/13/2011] [Indexed: 11/20/2022] Open
Abstract
To cost-efficiently produce biofuels, new methods are needed to convert lignocellulosic biomass into fermentable sugars. One promising approach is to degrade biomass using cellulosomes, which are surface-displayed multicellulase-containing complexes present in cellulolytic Clostridium and Ruminococcus species. In this study we created cellulolytic strains of Bacillus subtilis that display one or more cellulase enzymes. Proteins containing the appropriate cell wall sorting signal are covalently anchored to the peptidoglycan by coexpressing them with the Bacillus anthracis sortase A (SrtA) transpeptidase. This approach was used to covalently attach the Cel8A endoglucanase from Clostridium thermocellum to the cell wall. In addition, a Cel8A-dockerin fusion protein was anchored on the surface of B. subtilis via noncovalent interactions with a cell wall-attached cohesin module. We also demonstrate that it is possible to assemble multienzyme complexes on the cell surface. A three-enzyme-containing minicellulosome was displayed on the cell surface; it consisted of a cell wall-attached scaffoldin protein noncovalently bound to three cellulase-dockerin fusion proteins that were produced in Escherichia coli. B. subtilis has a robust genetic system and is currently used in a wide range of industrial processes. Thus, grafting larger, more elaborate minicellulosomes onto the surface of B. subtilis may yield cellulolytic bacteria with increased potency that can be used to degrade biomass.
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Affiliation(s)
| | | | | | | | | | - Beth A. Lazazzera
- Molecular Biology Institute
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, 611 Charles E. Young Drive, Los Angeles, California 90095-1570
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
- Molecular Biology Institute
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Mashburn-Warren L, Morrison DA, Federle MJ. A novel double-tryptophan peptide pheromone controls competence in Streptococcus spp. via an Rgg regulator. Mol Microbiol 2010; 78:589-606. [PMID: 20969646 DOI: 10.1111/j.1365-2958.2010.07361.x] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All streptococcal genomes encode the alternative sigma factor SigX and 21 SigX-dependent proteins required for genetic transformation, yet no pyogenic streptococci are known to develop competence. Resolving this paradox may depend on understanding the regulation of sigX. We report the identification of a regulatory circuit linked to the sigX genes of mutans, pyogenic, and bovis streptococci that uses a novel small, double-tryptophan-containing sigX-inducing peptide (XIP) pheromone. In all three groups, the XIP gene (comS), and sigX have identical, non-canonical promoters consisting of 9 bp inverted repeats separated from a -10 hexamer by 19 bp. comS is adjacent to a gene encoding a putative transcription factor of the Rgg family and is regulated by its product, which we designate ComR. Deletion of comR or comS in Streptococcus mutans abolished transformability, as did deletion of the oligopeptide permease subunit oppD, suggesting that XIP is imported. Providing S. mutans with synthetic fragments of ComS revealed that seven C-terminal residues, including the WW motif, cause robust induction of both sigX and the competent state. We propose that this circuit is the proximal regulator of sigX in S. mutans, and we infer that it controls competence in a parallel way in all pyogenic and bovis streptococci.
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Affiliation(s)
- Lauren Mashburn-Warren
- Center for Pharmaceutical Biotechnology, College of Pharmacy, The University of Illinois at Chicago, Chicago, IL 60607, USA
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Thoendel M, Horswill AR. Biosynthesis of peptide signals in gram-positive bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2010; 71:91-112. [PMID: 20378052 DOI: 10.1016/s0065-2164(10)71004-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gram-positive bacteria coordinate social behavior by sensing the extracellular level of peptide signals. These signals are biosynthesized through divergent pathways and some possess unusual functional chemistry as a result of posttranslational modifications. In this chapter, the biosynthetic pathways of Bacillus intracellular signaling peptides, Enterococcus pheromones, Bacillus subtilis competence pheromones, and cyclic peptide signals from Staphylococcus and other bacteria are covered. With the increasing prevalence of the cyclic peptide signals in diverse Gram-positive bacteria, a focus on this biosynthetic mechanism and variations on the theme are discussed. Due to the importance of peptide systems in pathogenesis, there is emerging interest in quorum-quenching approaches for therapeutic intervention. The quenching strategies that have successfully blocked signal biosynthesis are also covered. As peptide signaling systems continue to be discovered, there is a growing need to understand the details of these communication mechanisms. This information will provide insight on how Gram-positives coordinate cellular events and aid strategies to target these pathways for infection treatments.
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Affiliation(s)
- Matthew Thoendel
- Department of Microbiology, Roy J. and Lucille A. Carver College of Meddicine, University of Iowa, Iowa City, Iowa, USA
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18
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López D, Kolter R. Extracellular signals that define distinct and coexisting cell fates in Bacillus subtilis. FEMS Microbiol Rev 2009; 34:134-49. [PMID: 20030732 DOI: 10.1111/j.1574-6976.2009.00199.x] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The soil-dwelling bacterium Bacillus subtilis differentiates into distinct subpopulations of specialized cells that coexist within highly structured communities. The coordination and interplay between these cell types requires extensive extracellular communication driven mostly by sensing self-generated secreted signals. These extracellular signals activate a set of sensor kinases, which respond by phosphorylating three major regulatory proteins, Spo0A, DegU and ComA. Each phosphorylated regulator triggers a specific differentiation program while at the same time repressing other differentiation programs. This allows a cell to differentiate in response to a specific cue, even in the presence of other, possibly conflicting, signals. The sensor kinases involved respond to an eclectic group of extracellular signals, such as quorum-sensing molecules, natural products, temperature, pH or scarcity of nutrients. This article reviews the cascades of cell differentiation pathways that are triggered by sensing extracellular signals. We also present a tentative developmental model in which the diverse cell types sequentially differentiate to achieve the proper development of the bacterial community.
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Affiliation(s)
- Daniel López
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.
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