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Buahom J, Siripornadulsil S, Sukon P, Sooksawat T, Siripornadulsil W. Survivability of freeze- and spray-dried probiotics and their effects on the growth and health performance of broilers. Vet World 2023; 16:1849-1865. [PMID: 37859958 PMCID: PMC10583877 DOI: 10.14202/vetworld.2023.1849-1865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/09/2023] [Indexed: 10/21/2023] Open
Abstract
Background and Aim Many strains of probiotics have been exploited and used as animal dietary supplements for broiler production. The efficacy and survival of probiotics during production may reflect better activities of the probiotics in the host. This study investigated the effects of freeze- and spray-drying on the survivability and properties of probiotics and their ability to improve the growth and health performance of broilers. Materials and Methods Probiotic powders of four strains of lactic acid bacteria, Enterococcus faecium CA4, Enterococcus durans CH33, Ligilactobacillus salivarius CH24, Pediococcus acidilactici SH8, and Bacillus subtilis KKU213, were prepared using rice bran/chitosan/carboxy methyl cellulose as the carrier. The survival of each probiotic strain was investigated under stress conditions, including freeze-drying, spray-drying, and simulated gastrointestinal conditions. The body weight gain (BWG) and intestinal histomorphology were determined to assess broiler growth performance. Results All dried probiotics yielded a high survival rate during freeze-drying (95.8-98.6%) and spray-drying (94.4-98.2%). In addition, an analysis of the main effect revealed that the effectiveness of freeze-drying was higher than that of spray-drying in minimizing the loss of cell viability. The antimicrobial activity of all immobilized dried probiotic strains against Salmonella was maintained. The immobilized probiotics tolerated a low pH value of 2.0 and 0.5% (w/v) bile salt. Probiotic administration of a mixture of the five dried probiotics to 1-day-old hatched male broilers at early and late ages resulted in potential colonization in the broiler intestine, and enhancements in the BWG, lipid metabolism, and gut health (villus height and cryptal depth) were observed in the probiotic-treated groups. Conclusion The administration of three doses of the spray-dried probiotic mixture at days 15, 17, and 19 after hatching was sufficient to achieve long-term growth and health benefits in broilers. This finding might provide a cost-effective alternative to the administration of commonly used antibiotics in broiler production.
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Affiliation(s)
- Juthamas Buahom
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen 40002 Thailand
| | - Surasak Siripornadulsil
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen 40002 Thailand
- Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Peerapol Sukon
- Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Treerat Sooksawat
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen 40002 Thailand
| | - Wilailak Siripornadulsil
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen 40002 Thailand
- Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen 40002, Thailand
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Morales-Ruíz LM, Rodríguez-Cisneros M, Kerber-Díaz JC, Rojas-Rojas FU, Ibarra JA, Estrada-de Los Santos P. Burkholderia orbicola sp. nov., a novel species within the Burkholderia cepacia complex. Arch Microbiol 2022; 204:178. [PMID: 35174425 DOI: 10.1007/s00203-022-02778-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Genome analysis of strains placed in the NCBI genome database as Burkholderia cenocepacia defined nine genomic species groups. The largest group (259 strains) corresponds to B. cenocepacia and the second largest group (58 strains) was identified as "Burkholderia servocepacia", a Burkholderia species classification which has not been validly published. The publication of "B. servocepacia" did not comply with Rule 27 and Recommendation 30 from the International Code of Nomenclature of Prokaryotes (ICNP) and have errors in the type strain name and the protologue describing the novel species. Here, we correct the position of this species by showing essential information that meets the criteria defined by ICNP. After additional analysis complying with taxonomic criteria, we propose that the invalid "B. servocepacia" be renamed as Burkholderia orbicola sp. nov. The original study proposing "B. servocepacia" was misleading, because this name derives from the Latin "servo" meaning "to protect/watch over", and the authors proposed this based on the beneficial biocontrol properties of several strains within the group. However, it is clear that "B. servocepacia" isolates are capable of opportunistic infection, and the proposed name Burkholderia orbicola sp. nov. takes into account these diverse phenotypic traits. The type strain is TAtl-371 T (= LMG 30279 T = CM-CNRG 715 T).
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Affiliation(s)
- Leslie-Mariana Morales-Ruíz
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Mariana Rodríguez-Cisneros
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Jeniffer-Chris Kerber-Díaz
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Fernando-Uriel Rojas-Rojas
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México.,Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León), Blvd. UNAM 2011, 37684, León, Guanajuato, México
| | - J Antonio Ibarra
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Paulina Estrada-de Los Santos
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México.
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3
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Ghequire MGK, Öztürk B, De Mot R. Lectin-Like Bacteriocins. Front Microbiol 2018; 9:2706. [PMID: 30483232 PMCID: PMC6240691 DOI: 10.3389/fmicb.2018.02706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/23/2018] [Indexed: 12/22/2022] Open
Abstract
Bacteria produce a diverse array of antagonistic compounds to restrict growth of microbial rivals. Contributing to this warfare are bacteriocins: secreted antibacterial peptides, proteins and multi-protein complexes. These compounds typically eliminate competitors closely related to the producer. Lectin-like bacteriocins (LlpAs) constitute a distinct class of such proteins, produced by Pseudomonas as well as some other proteobacterial genera. LlpAs share a common architecture consisting of two B-lectin domains, followed by a short carboxy-terminal extension. Two surface-exposed moieties on susceptible Pseudomonas cells are targeted by the respective lectin modules. The carboxy-terminal domain binds D-rhamnose residues present in the lipopolysaccharide layer, whereas the amino-terminal domain interacts with a polymorphic external loop of the outer-membrane protein insertase BamA, hence determining selectivity. The absence of a toxin-immunity module as found in modular bacteriocins and other polymorphic toxin systems, hints toward a novel mode of killing initiated at the cellular surface, not requiring bacteriocin import. Despite significant progress in understanding the function of LlpAs, outstanding questions include the secretion machinery recruited by lectin-like bacteriocins for their release, as well as a better understanding of the environmental signals initiating their expression.
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Affiliation(s)
| | - Başak Öztürk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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4
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Rojas-Rojas FU, Salazar-Gómez A, Vargas-Díaz ME, Vásquez-Murrieta MS, Hirsch AM, De Mot R, Ghequire MGK, Ibarra JA, Estrada-de los Santos P. Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere. Microbiology (Reading) 2018; 164:1072-1086. [DOI: 10.1099/mic.0.000675] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Fernando Uriel Rojas-Rojas
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - Anuar Salazar-Gómez
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - María Elena Vargas-Díaz
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - María Soledad Vásquez-Murrieta
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - Ann M. Hirsch
- 2Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- 3Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - René De Mot
- 4Centre of Microbial and Plant Genetics, University of Leuven, Kasteelpark Arenberg 20 box 2460, 3001, Heverlee-Leuven, Belgium
| | - Maarten G. K. Ghequire
- 4Centre of Microbial and Plant Genetics, University of Leuven, Kasteelpark Arenberg 20 box 2460, 3001, Heverlee-Leuven, Belgium
| | - J. Antonio Ibarra
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
| | - Paulina Estrada-de los Santos
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, Del. Miguel Hidalgo. México, Cd. de, México
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Godino A, Príncipe A, Fischer S. A ptsP deficiency in PGPR Pseudomonas fluorescens SF39a affects bacteriocin production and bacterial fitness in the wheat rhizosphere. Res Microbiol 2015; 167:178-89. [PMID: 26708985 DOI: 10.1016/j.resmic.2015.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 11/26/2022]
Abstract
Pseudomonas fluorescens SF39a is a plant-growth-promoting bacterium isolated from wheat rhizosphere. In this report, we demonstrate that this native strain secretes bacteriocins that inhibit growth of phytopathogenic strains of the genera Pseudomonas and Xanthomonas. An S-type pyocin gene was detected in the genome of strain SF39a and named pys. A non-polar pys::Km mutant was constructed. The bacteriocin production was impaired in this mutant. To identify genes involved in bacteriocin regulation, random transposon mutagenesis was carried out. A miniTn5Km1 mutant, called P. fluorescens SF39a-451, showed strongly reduced bacteriocin production. This phenotype was caused by inactivation of the ptsP gene which encodes a phosphoenolpyruvate phosphotransferase (EI(Ntr)) of the nitrogen-related phosphotransferase system (PTS(Ntr)). In addition, this mutant showed a decrease in biofilm formation and protease production, and an increase in surface motility and pyoverdine production compared with the wild-type strain. Moreover, we investigated the ability of strain SF39a-451 to colonize the wheat rhizosphere under greenhouse conditions. Interestingly, the mutant was less competitive than the wild-type strain in the rhizosphere. To our knowledge, this study provides the first evidence of both the relevance of the ptsP gene in bacteriocin production and functional characterization of a pyocin S in P. fluorescens.
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Affiliation(s)
- Agustina Godino
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
| | - Analía Príncipe
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
| | - Sonia Fischer
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
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Ghequire MGK, Dillen Y, Lambrichts I, Proost P, Wattiez R, De Mot R. Different Ancestries of R Tailocins in Rhizospheric Pseudomonas Isolates. Genome Biol Evol 2015; 7:2810-28. [PMID: 26412856 PMCID: PMC4684702 DOI: 10.1093/gbe/evv184] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacterial genomes accommodate a variety of mobile genetic elements, including bacteriophage-related clusters that encode phage tail-like protein complexes playing a role in interactions with eukaryotic or prokaryotic cells. Such tailocins are unable to replicate inside target cells due to the lack of a phage head with associated DNA. A subset of tailocins mediate antagonistic activities with bacteriocin-like specificity. Functional characterization of bactericidal tailocins of two Pseudomonas putida rhizosphere isolates revealed not only extensive similarity with the tail assembly module of the Pseudomonas aeruginosa R-type pyocins but also differences in genomic integration site, regulatory genes, and lytic release modules. Conversely, these three features are quite similar between strains of the P. putida and Pseudomonas fluorescens clades, although phylogenetic analysis of tail genes suggests them to have evolved separately. Unlike P. aeruginosa R pyocin elements, the tailocin gene clusters of other pseudomonads frequently carry cargo genes, including bacteriocins. Compared with P. aeruginosa, the tailocin tail fiber sequences that act as specificity determinants have diverged much more extensively among the other pseudomonad species, mostly isolates from soil and plant environments. Activity of the P. putida antibacterial particles requires a functional lipopolysaccharide layer on target cells, but contrary to R pyocins from P. aeruginosa, strain susceptibilities surpass species boundaries.
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Affiliation(s)
- Maarten G K Ghequire
- Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Heverlee, Belgium
| | - Yörg Dillen
- Group of Morphology, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Leuven, Belgium
| | - Ivo Lambrichts
- Group of Morphology, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology and Immunology, Rega Institute, University of Leuven, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics (CMPG), University of Leuven, Heverlee, Belgium
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7
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Dawoud TM, Jiang T, Mandal RK, Ricke SC, Kwon YM. Improving the efficiency of transposon mutagenesis in Salmonella enteritidis by overcoming host-restriction barriers. Mol Biotechnol 2015; 56:1004-10. [PMID: 24973023 DOI: 10.1007/s12033-014-9779-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Transposon mutagenesis using transposome complex is a powerful method for functional genomics analysis in diverse bacteria by creating a large number of random mutants to prepare a genome-saturating mutant library. However, strong host restriction barriers can lead to limitations with species- or strain-specific restriction-modification systems. The purpose of this study was to enhance the transposon mutagenesis efficiency of Salmonella Enteritidis to generate a larger number of random insertion mutants. Host-adapted Tn5 DNA was used to form a transposome complex, and this simple approach significantly and consistently improved the efficiency of transposon mutagenesis, resulting in a 46-fold increase in the efficiency as compared to non-adapted transposon DNA fragments. Random nature of Tn5 insertions was confirmed by high-throughput sequencing of the Tn5-junction sequences. The result based on S. Enteritidis in this study should find broad applications in preparing a comprehensive mutant library of other species using transposome complex.
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Affiliation(s)
- Turki M Dawoud
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA,
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8
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Ghequire MGK, De Mot R. Ribosomally encoded antibacterial proteins and peptides from Pseudomonas. FEMS Microbiol Rev 2014; 38:523-68. [PMID: 24923764 DOI: 10.1111/1574-6976.12079] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/05/2014] [Accepted: 05/16/2014] [Indexed: 12/26/2022] Open
Abstract
Members of the Pseudomonas genus produce diverse secondary metabolites affecting other bacteria, fungi or predating nematodes and protozoa but are also equipped with the capacity to secrete different types of ribosomally encoded toxic peptides and proteins, ranging from small microcins to large tailocins. Studies with the human pathogen Pseudomonas aeruginosa have revealed that effector proteins of type VI secretion systems are part of the antibacterial armamentarium deployed by pseudomonads. A novel class of antibacterial proteins with structural similarity to plant lectins was discovered by studying antagonism among plant-associated Pseudomonas strains. A genomic perspective on pseudomonad bacteriocinogeny shows that the modular architecture of S pyocins of P. aeruginosa is retained in a large diversified group of bacteriocins, most of which target DNA or RNA. Similar modularity is present in as yet poorly characterized Rhs (recombination hot spot) proteins and CDI (contact-dependent inhibition) proteins. Well-delimited domains for receptor recognition or cytotoxicity enable the design of chimeric toxins with novel functionalities, which has been applied successfully for S and R pyocins. Little is known regarding how these antibacterials are released and ultimately reach their targets. Other remaining issues concern the identification of environmental triggers activating these systems and assessment of their ecological impact in niches populated by pseudomonads.
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Abstract
Gram-negative phytopathogens cause significant losses in a diverse range of economically important crop plants. The effectiveness of traditional countermeasures, such as the breeding and introduction of resistant cultivars, is often limited by the dearth of available sources of genetic resistance. An alternative strategy to reduce loss to specific bacterial phytopathogens is to use narrow-spectrum protein antibiotics such as colicin-like bacteriocins as biocontrol agents. A number of colicin-like bacteriocins active against phytopathogenic bacteria have been described previously as have strategies for their application to biocontrol. In the present paper, we discuss these strategies and our own recent work on the identification and characterization of candidate bacteriocins and how these potent and selective antimicrobial agents can be effectively applied to the control of economically important plant disease.
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Palmer ME, Wiedmann M, Boor KJ. sigma(B) and sigma(L) contribute to Listeria monocytogenes 10403S response to the antimicrobial peptides SdpC and nisin. Foodborne Pathog Dis 2010; 6:1057-65. [PMID: 19642919 DOI: 10.1089/fpd.2009.0292] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The ability of the foodborne pathogen Listeria monocytogenes to survive antimicrobial treatments is a public health concern; therefore, this study was designed to investigate genetic mechanisms contributing to antimicrobial response in L. monocytogenes. In previous studies, the putative bacteriocin immunity gene lmo2570 was predicted to be regulated by the stress responsive alternative sigma factor, sigma(B). As the alternative sigma factor sigma(L) controls expression of genes important for resistance to some antimicrobial peptides, we hypothesized roles for lmo2570, sigma(B), and sigma(L) in L. monocytogenes antimicrobial response. Results from phenotypic characterization of a L. monocytogenes lmo2570 null mutant suggested that this gene does not contribute to resistance to nisin or to SdpC, an antimicrobial peptide produced by some strains of Bacillus subtilis. While lmo2570 transcript levels were confirmed to be sigma(B) dependent, they were sigma(L) independent and were not affected by the presence of nisin under the conditions used in this study. In spot-on-lawn assays with the SdpC-producing B. subtilis EG351, the L. monocytogenes DeltasigB, DeltasigL, and DeltasigB/DeltasigL strains all showed increased sensitivity to SdpC, indicating that both sigma(B) and sigma(L) regulate genes contributing to SdpC resistance. Nisin survival assays showed that sigma(B) and sigma(L) both affect L. monocytogenes sensitivity to nisin in broth survival assays; that is, a sigB null mutant is more resistant than the parent strain to nisin, while a sigB null mutation in DeltasigL background leads to reduced nisin resistance. In summary, while the sigma(B)-dependent lmo2570 does not contribute to resistance of L. monocytogenes to nisin or SdpC, both sigma(B) and sigma(L) contribute to the L. monocytogenes antimicrobial response.
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Mavrodi DV, Loper JE, Paulsen IT, Thomashow LS. Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5. BMC Microbiol 2009; 9:8. [PMID: 19144133 PMCID: PMC2647930 DOI: 10.1186/1471-2180-9-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 01/13/2009] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Pseudomonas fluorescens Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and and produces secondary metabolites suppressive of fungal and oomycete plant pathogens. The Pf-5 genome is rich in features consistent with its commensal lifestyle, and its sequence has revealed attributes associated with the strain's ability to compete and survive in the dynamic and microbiologically complex rhizosphere habitat. In this study, we analyzed mobile genetic elements of the Pf-5 genome in an effort to identify determinants that might contribute to Pf-5's ability to adapt to changing environmental conditions and/or colonize new ecological niches. RESULTS Sequence analyses revealed that the genome of Pf-5 is devoid of transposons and IS elements and that mobile genetic elements (MGEs) are represented by prophages and genomic islands that collectively span over 260 kb. The prophages include an F-pyocin-like prophage 01, a chimeric prophage 03, a lambdoid prophage 06, and decaying prophages 02, 04 and 05 with reduced size and/or complexity. The genomic islands are represented by a 115-kb integrative conjugative element (ICE) PFGI-1, which shares plasmid replication, recombination, and conjugative transfer genes with those from ICEs found in other Pseudomonas spp., and PFGI-2, which resembles a portion of pathogenicity islands in the genomes of the plant pathogens Pseudomonas syringae and P. viridiflava. Almost all of the MGEs in the Pf-5 genome are associated with phage-like integrase genes and are integrated into tRNA genes. CONCLUSION Comparative analyses reveal that MGEs found in Pf-5 are subject to extensive recombination and have evolved in part via exchange of genetic material with other Pseudomonas spp. having commensal or pathogenic relationships with plants and animals. Although prophages and genomic islands from Pf-5 exhibit similarity to MGEs found in other Pseudomonas spp., they also carry a number of putative niche-specific genes that could affect the survival of P. fluorescens Pf-5 in natural habitats. Most notable are an approximately 35-kb segment of "cargo" genes in genomic island PFGI-1 and bacteriocin genes associated with prophages 1 and 4.
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Affiliation(s)
- Dmitri V Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Joyce E Loper
- USDA-ARS Horticultural Crops Research Laboratory, 3420 N. W. Orchard Ave, Corvallis, OR 97330, USA
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Linda S Thomashow
- USDA-ARS Root Disease and Biocontrol Research Unit, Washington State University, Pullman, WA 99164-6430, USA
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12
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Tsang P, Merritt J, Nguyen T, Shi W, Qi F. Identification of genes associated with mutacin I production in Streptococcus mutans using random insertional mutagenesis. MICROBIOLOGY-SGM 2006; 151:3947-3955. [PMID: 16339939 DOI: 10.1099/mic.0.28221-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptococcus mutans is a major pathogen implicated in dental caries. Its virulence is enhanced by its ability to produce bacteriocins, called mutacins, which inhibit the growth of other Gram-positive bacteria. The goal of this study is to use a random insertional mutagenesis approach to search for genes that are associated with mutacin I production in the virulent strain UA140. A random insertional mutagenesis library consisting of 11,000 clones was constructed and screened for a mutacin-defective phenotype. Mutacin-defective clones were isolated, and their insertion sites were determined by PCR amplification or plasmid rescue followed by sequencing. A total of twenty-five unique genes were identified. These genes can be categorized into the following functional classes: two-component sensory systems, stress responses, energy metabolism and central cellular processes. Several conserved hypothetical proteins with unknown functions were also identified. These results suggest that mutacin I production is stringently controlled by diverse and complex regulatory pathways.
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Affiliation(s)
- Phoebe Tsang
- UCLA School of Dentistry, Los Angeles, CA 90025, USA
| | - Justin Merritt
- UCLA Molecular Biology Institute, Los Angeles, CA 90025, USA
| | - Trang Nguyen
- UCLA School of Dentistry, Los Angeles, CA 90025, USA
| | - Wenyuan Shi
- UCLA Molecular Biology Institute, Los Angeles, CA 90025, USA
- UCLA School of Dentistry, Los Angeles, CA 90025, USA
| | - Fengxia Qi
- UCLA School of Dentistry, Los Angeles, CA 90025, USA
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13
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Leveau JHJ, Gerards S, Fritsche K, Zondag G, van Veen JA. Genomic flank-sequencing of plasposon insertion sites for rapid identification of functional genes. J Microbiol Methods 2006; 66:276-85. [PMID: 16457898 DOI: 10.1016/j.mimet.2005.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Revised: 12/02/2005] [Accepted: 12/13/2005] [Indexed: 10/25/2022]
Abstract
Plasposons are modified mini-Tn5 transposons for random mutagenesis of Gram-negative bacteria. Their unique design allows for the rescue cloning and sequencing of DNA that flanks insertion sites in plasposon mutants. However, this process can be laborious and time-consuming, as it involves genomic DNA isolation, restriction endonuclease treatment, subsequent religation, transformation of religated DNA into an Escherichia coli host, and re-isolation as a plasmid, which is then used as a template in sequencing reactions with primers that read from the plasposon ends into the flanking DNA regions. We describe here a method that produces flanking DNA sequences directly from genomic DNA that is isolated from plasposon mutants. By eliminating the need for rescue cloning, our protocol dramatically reduces time and effort, typically by 2 to 3 working days, as well as costs associated with digestion, ligation, transformation, and plasmid isolation. Furthermore, it allows for a high-throughput automated approach to analysis of the plasposome, i.e. the collective set of plasposon insertion sites in a plasposon mutant library. We have tested the utility of genomic flank-sequencing on three plasposon mutants of the soil bacterium Collimonas fungivorans with abolished ability to degrade chitin.
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Affiliation(s)
- Johan H J Leveau
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Microbial Ecology, Boterhoeksestraat 48, 6666 GA Heteren, The Netherlands.
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Parret AHA, Temmerman K, De Mot R. Novel lectin-like bacteriocins of biocontrol strain Pseudomonas fluorescens Pf-5. Appl Environ Microbiol 2005; 71:5197-207. [PMID: 16151105 PMCID: PMC1214683 DOI: 10.1128/aem.71.9.5197-5207.2005] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriocin LlpA, produced by Pseudomonas sp. strain BW11M1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (A. H. A. Parret, G. Schoofs, P. Proost, and R. De Mot, J. Bacteriol. 185:897-908, 2003). Biocontrol strain Pseudomonas fluorescens Pf-5 contains two llpA-like genes, named llpA1(Pf-5) and llpA2(Pf-5). Recombinant Escherichia coli cells expressing llpA1(Pf-5) or llpA2(Pf-5) acquired bacteriocin activity and secreted a 31-kDa protein cross-reacting with LlpA(BW11M1) antibodies. Antibacterial activity of the recombinant proteins was evidenced by gel overlay assays. Analysis of the antimicrobial spectrum indicated that LlpA1(Pf-5) and LlpA2(Pf-5) are able to inhibit P. fluorescens strains, as well as the related mushroom pathogen Pseudomonas tolaasii. LlpA-type bacteriocins are characterized by a domain structure consisting of tandem monocot mannose-binding lectin (MMBL) domains. Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired from different ancestral sources. Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.
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Affiliation(s)
- Annabel H A Parret
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
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