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Jones I, Vermillion D, Tracy C, Denton R, Davis R, Geszvain K. Isolation, characterization, and genetic manipulation of cold-tolerant, manganese-oxidizing Pseudomonas sp. strains. Appl Environ Microbiol 2024; 90:e0051024. [PMID: 39212379 PMCID: PMC11409713 DOI: 10.1128/aem.00510-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Manganese-oxidizing bacteria (MnOB) produce Mn oxide minerals that can be used by humans for bioremediation, but the purpose for the bacterium is less clear. This study describes the isolation and characterization of cold-tolerant MnOB strains isolated from a compost pile in Morris, Minnesota, USA: Pseudomonas sp. MS-1 and DSV-1. The strains were preliminarily identified as members of species Pseudomonas psychrophila by 16S rRNA analysis and a multi-locus phylogenetic study using a database of 88 genomes from the Pseudomonas genus. However, the average nucleotide identity between these strains and the P. psychrophila sp. CF149 type strain was less than 93%. Thus, the two strains are members of a novel species that diverged from P. psychrophila. DSV-1 and MS-1 are cold tolerant; both grow at 4°C but faster at 24°C. Unlike the mesophilic MnOB P. putida GB-1, both strains are capable of robustly oxidizing Mn at low temperatures. Both DSV-1 and MS-1 genomes contain homologs of several Mn oxidation genes found in P. putida GB-1 (mnxG, mcoA, mnxS1, mnxS2, and mnxR). Random mutagenesis by transposon insertion was successfully performed in both strains and identified genes involved in Mn oxidation that were similar to those found in P. putida GB-1. Our results show that MnOB can be isolated from compost, supporting a role for Mn oxidation in plant waste degradation. The novel isolates Pseudomonas spp. DSV-1 and MS-1 both can oxidize Mn at low temperature and likely employ similar mechanisms and regulation as P. putida GB-1.IMPORTANCEBiogenic Mn oxides have high sorptive capacity and are strong oxidants. These two characteristics make these oxides and the microbes that make them attractive tools for the bioremediation of wastewater and contaminated environments. Identifying MnOB that can be used for bioremediation is an active area of research. As cold-tolerant MnOB, Pseudomonas sp. DSV-1 and MS-1 have the potential to expand the environmental conditions in which biogenic Mn oxide bioremediation can be performed. The similarity of these organisms to the well-characterized MnOB P. putida GB-1 and the ability to manipulate their genomes raise the possibility of modifying them to improve their bioremediation ability.
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Affiliation(s)
- Ian Jones
- Department of Biological Sciences, California State University, Chico, California, USA
| | - Duncan Vermillion
- Division of Science and Math, University of Minnesota, Morris, Minnesota, USA
| | - Chase Tracy
- Department of Biological Sciences, California State University, Chico, California, USA
| | - Robert Denton
- Department of Biology, Marian University, Indianapolis, Indiana, USA
| | - Rick Davis
- Texas State University, NASA Johnson Space Center, Houston, Texas, USA
| | - Kati Geszvain
- Department of Biological Sciences, California State University, Chico, California, USA
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2
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Yurgel SN, Johnson SA, Rice J, Sa N, Bailes C, Baumgartner J, Pitzer JE, Roop RM, Roje S. A novel formamidase is required for riboflavin biosynthesis in invasive bacteria. J Biol Chem 2022; 298:102377. [PMID: 35970388 PMCID: PMC9478397 DOI: 10.1016/j.jbc.2022.102377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/03/2022] Open
Abstract
Biosynthesis of riboflavin, the precursor of the redox cofactors FMN and FAD, was thought to be well understood in bacteria, with all the pathway enzymes presumed to be known and essential. Our previous research has challenged this view by showing that, in the bacterium Sinorhizobium meliloti, deletion of the ribBA gene encoding the enzyme that catalyzes the initial steps on the riboflavin biosynthesis pathway only causes a reduction in flavin secretion rather than riboflavin auxotrophy. This finding led us to hypothesize that RibBA participates in the biosynthesis of flavins destined for secretion, while S. meliloti has another enzyme that performs this function for internal cellular metabolism. Here, we identify and biochemically characterize a novel formamidase (SMc02977) involved in the production of riboflavin for intracellular functions in S. meliloti. This catalyst, which we named Sm-BrbF, releases formate from the early riboflavin precursor 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (AFRPP) to yield 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARoPP). We show that homologs of this enzyme are present in many bacteria, are highly abundant in the Rhizobiales order, and that sequence homologs from Brucella abortus and Liberobacter solanacearum complement the riboflavin auxotrophy of the Sm1021ΔSMc02977 mutant. Furthermore, we show that the B. abortus enzyme (Bab2_0247, Ba-BrbF) is also an AFRPP formamidase, and that the bab2_0247 mutant is a riboflavin auxotroph exhibiting a lower level of intracellular infection than the wild-type strain. Finally, we show that Sm-BrbF and Ba-BrbF directly interact with other riboflavin biosynthesis pathway enzymes. Together, our results provide novel insight into the intricacies of riboflavin biosynthesis in bacteria.
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Affiliation(s)
- Svetlana N Yurgel
- Grain Legume Genetics and Physiology Research Unit, USDA, ARS, Prosser, WA, USA.
| | - Skylar A Johnson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Jennifer Rice
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Na Sa
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Clayton Bailes
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - John Baumgartner
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Josh E Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
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3
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Ramos Y, Rocha J, Hael AL, van Gestel J, Vlamakis H, Cywes-Bentley C, Cubillos-Ruiz JR, Pier GB, Gilmore MS, Kolter R, Morales DK. PolyGlcNAc-containing exopolymers enable surface penetration by non-motile Enterococcus faecalis. PLoS Pathog 2019; 15:e1007571. [PMID: 30742693 PMCID: PMC6386517 DOI: 10.1371/journal.ppat.1007571] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/22/2019] [Accepted: 01/08/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial pathogens have evolved strategies that enable them to invade tissues and spread within the host. Enterococcus faecalis is a leading cause of local and disseminated multidrug-resistant hospital infections, but the molecular mechanisms used by this non-motile bacterium to penetrate surfaces and translocate through tissues remain largely unexplored. Here we present experimental evidence indicating that E. faecalis generates exopolysaccharides containing β-1,6-linked poly-N-acetylglucosamine (polyGlcNAc) as a mechanism to successfully penetrate semisolid surfaces and translocate through human epithelial cell monolayers. Genetic screening and molecular analyses of mutant strains identified glnA, rpiA and epaX as genes critically required for optimal E. faecalis penetration and translocation. Mechanistically, GlnA and RpiA cooperated to generate uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) that was utilized by EpaX to synthesize polyGlcNAc-containing polymers. Notably, exogenous supplementation with polymeric N-acetylglucosamine (PNAG) restored surface penetration by E. faecalis mutants devoid of EpaX. Our study uncovers an unexpected mechanism whereby the RpiA-GlnA-EpaX metabolic axis enables production of polyGlcNAc-containing polysaccharides that endow E. faecalis with the ability to penetrate surfaces. Hence, targeting carbohydrate metabolism or inhibiting biosynthesis of polyGlcNAc-containing exopolymers may represent a new strategy to more effectively confront enterococcal infections in the clinic. Enterococcus faecalis is a microbial inhabitant of the human gastrointestinal tract that can cause lethal infections. Typically classified as a non-motile bacterium, E. faecalis can readily migrate and translocate across epithelial barriers to invade distant organs. Nevertheless, the molecular pathways driving enterococcal invasive attributes remain poorly understood. In this study, we uncover that E. faecalis produces a polyGlcNAc-containing extracellular glycopolymer to efficiently migrate into semisolid surfaces and translocate through human epithelial cell monolayers. Our work provides evidence that non-motile bacterial pathogens can exploit endogenous carbohydrate metabolic pathways to penetrate surfaces. Thus, targeting glycopolymer biosynthetic programs might be useful to control infections by Gram-positive cocci in the clinic.
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Affiliation(s)
- Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
| | - Jorge Rocha
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Ana L. Hael
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Hera Vlamakis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
| | - Gerald B. Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Michael S. Gilmore
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
- Department of Ophthalmology, Harvard Medical School, Boston, MA, United States of America
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
- * E-mail:
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4
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Gao T, Ding M, Yang CH, Fan H, Chai Y, Li Y. The phosphotransferase system gene ptsH plays an important role in MnSOD production, biofilm formation, swarming motility, and root colonization in Bacillus cereus 905. Res Microbiol 2018; 170:86-96. [PMID: 30395927 DOI: 10.1016/j.resmic.2018.10.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/24/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022]
Abstract
The rhizosphere bacterium Bacillus cereus 905 is capable of promoting plant growth through effective colonization on plant roots. The sodA2-encoding manganese-containing superoxide dismutase (MnSOD2) is important for survival of B. cereus 905 in the wheat rhizosphere. However, the genes involved in regulating sodA2 expression and the mechanisms of rhizosphere colonization of B. cereus 905 are not well elucidated. In this study, we found that the deletion of the ptsH gene, which encodes the histidine-phosphorylatable protein (HPr), a component of the phosphotransferase system (PTS), causes a decrease of about 60% in the MnSOD2 expression. Evidences indicate that the ptsH dramatically influences resistance to oxidative stress, glucose uptake, as well as biofilm formation and swarming motility of B. cereus 905. Root colonization assay demonstrated that ΔptsH is defective in colonizing wheat roots, while complementation of the sodA2 gene could partially restore the ability in utilization of arabinose, a non-PTS sugar, and root colonization caused by the loss of the ptsH gene. In toto, based on the current findings, we propose that PtsH contributes to root colonization of B. cereus 905 through multiple indistinct mechanisms, involving PTS and uptake of PTS-sugars, up-regulation of MnSOD2 production, and promotion of biofilm formation and swarming motility.
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Affiliation(s)
- Tantan Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China; Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02215, USA.
| | - Mingzheng Ding
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA.
| | - Haiyan Fan
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Yunrong Chai
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02215, USA.
| | - Yan Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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5
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More than Rotating Flagella: Lipopolysaccharide as a Secondary Receptor for Flagellotropic Phage 7-7-1. J Bacteriol 2018; 200:JB.00363-18. [PMID: 30012730 DOI: 10.1128/jb.00363-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/10/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteriophage 7-7-1, a member of the family Myoviridae, infects the soil bacterium Agrobacterium sp. strain H13-3. Infection requires attachment to actively rotating bacterial flagellar filaments, with flagellar number, length, and rotation speed being important determinants for infection efficiency. To identify the secondary receptor(s) on the cell surface, we isolated motile, phage-resistant Agrobacterium sp. H13-3 transposon mutants. Transposon insertion sites were pinpointed using arbitrary primed PCR and bioinformatics analyses. Three genes were recognized, whose corresponding proteins had the following computationally predicted functions: AGROH133_07337, a glycosyltransferase; AGROH133_13050, a UDP-glucose 4-epimerase; and AGROH133_08824, an integral cytoplasmic membrane protein. The first two gene products are part of the lipopolysaccharide (LPS) synthesis pathway, while the last is predicted to be a relatively small (13.4-kDa) cytosolic membrane protein with up to four transmembrane helices. The phenotypes of the transposon mutants were verified by complementation and site-directed mutagenesis. Additional characterization of motile, phage-resistant mutants is also described. Given these findings, we propose a model for Agrobacterium sp. H13-3 infection by bacteriophage 7-7-1 where the phage initially attaches to the flagellar filament and is propelled down toward the cell surface by clockwise flagellar rotation. The phage then attaches to and degrades the LPS to reach the outer membrane and ejects its DNA into the host using its syringe-like contractile tail. We hypothesize that the integral membrane protein plays an important role in events following viral DNA ejection or in LPS processing and/or deployment. The proposed two-step attachment mechanism may be conserved among other flagellotropic phages infecting Gram-negative bacteria.IMPORTANCE Flagellotropic bacteriophages belong to the tailed-phage order Caudovirales, the most abundant phages in the virome. While it is known that these viruses adhere to the bacterial flagellum and use flagellar rotation to reach the cell surface, their infection mechanisms are poorly understood. Characterizing flagellotropic-phage-host interactions is crucial to understanding how microbial communities are shaped. Using a transposon mutagenesis approach combined with a screen for motile, phage-resistant mutants, we identified lipopolysaccharides as the secondary cell surface receptor for phage 7-7-1. This is the first cell surface receptor identified for flagellotropic phages. One hypothetical membrane protein was also recognized as essential for infection. These new findings, together with previous results, culminated in an infection model for phage 7-7-1.
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6
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Knobloch KM, Von Osten H, Horstkotte MA, Rohde H, Mack D. Biofilm Formation is not Necessary for Development of Quinolone-Resistant “Persister” cells in an Attached Staphylococcus Epidermidis Population. Int J Artif Organs 2018; 31:752-60. [DOI: 10.1177/039139880803100902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Staphylococcus epidermidis is a common pathogen in device-associated infections which is able to attach onto polymeric surfaces and develop multilayered biofilms. Attached S. epidermidis displays reduced susceptibility to antimicrobial agents. In this study we investigated the influence of ciprofloxacin and the group IV quinolones gatifloxacin, gemifloxacin, and moxifloxacin with the minimal attachment killing (MAK) assay. MAK concentrations were determined for three biofilm-positive wild-type strains and their isogenic biofilm-negative mutants Depending on strain and investigated quinolone, it was possible to distinguish between a heterogeneous MAK (MAKhetero), and a homogeneous resistance (MAKhomo) which corresponds to the model of a few persisting cells under antibiotic treatment. A lower MAKhomo was detected for the biofilm-negative mutants as well as for the corresponding wild-types for some of the tested quinolones, which seems to be a result of higher bacterial inocula, whereas the MAKhetero concentrations were comparable for mutants and wild-types for nearly all of the tested antibiotics and strains. These data indicate that biofilm formation is not necessary for persistence of attached S. epidermidis cells under treatment with quinolones and could explain therapeutic failure in foreign body-associated infections due to biofilm-negative S. epidermidis isolates. The individual resistance phenotypes of investigated strains indicate that the determination of MAK concentrations might help to predict the therapy outcome of foreign body-associated infections with both biofilm-positive and biofilm-negative S. epidermidis. Thus, the relatively high activity displayed by group IV quinolones against individual attached staphylococcal isolates indicates a possible treatment option with the respective quinolones for foreign body-associated infections due to these isolates. (Int J Artif Organs 2008; 31: 752–60)
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Affiliation(s)
- K.-M. Knobloch
- Institute for Medical Microbiology and Hygiene, University of Lübeck, Lübeck - Germany
| | - H. Von Osten
- Institute for Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg - Germany
| | - M. A. Horstkotte
- Bioscientia Institut für Medizinische Diagnostik GmbH, Labor Hamburg, Hamburg, Germany
| | - H. Rohde
- Institute for Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg - Germany
| | - D. Mack
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
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7
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Saavedra JT, Schwartzman JA, Gilmore MS. Mapping Transposon Insertions in Bacterial Genomes by Arbitrarily Primed PCR. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2017; 118:15.15.1-15.15.15. [PMID: 28369678 PMCID: PMC5679462 DOI: 10.1002/cpmb.38] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transposons can be used to easily generate and label the location of mutations throughout bacterial and other genomes. Transposon insertion mutants may be screened for a phenotype as individual isolates, or by selection applied to a pool of thousands of mutants. Identifying the location of a transposon insertion is critical for connecting phenotype to the genetic lesion. In this unit, we present an easy and detailed approach for mapping transposon insertion sites using arbitrarily-primed PCR (AP-PCR). Two rounds of PCR are used to (1) amplify DNA spanning the transposon insertion junction, and (2) increase the specific yield of transposon insertion junction fragments for sequence analysis. The resulting sequence is mapped to a bacterial genome to identify the site of transposon insertion. In this protocol, AP-PCR as it is routinely used to map sites of transposon insertion within Staphylococcus aureus, is used to illustrate the principle. Guidelines are provided for adapting this protocol for mapping insertions in other bacterial genomes. Mapping transposon insertions using this method is typically achieved in 2 to 3 days if starting from a culture of the transposon insertion mutant. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- José T Saavedra
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Julia A Schwartzman
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
- Department of Ophthalmology, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
- The Broad Institute, Cambridge, Massachusetts
| | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
- Department of Ophthalmology, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
- The Broad Institute, Cambridge, Massachusetts
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8
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Ethica SN, Semiarti E, Widada J, Oedjijono O, Joko Raharjo T. Characterization of moaC
and a nontarget gene fragments of food-borne pathogen Alcaligenes
sp. JG3 using degenerate colony and arbitrary PCRs. J Food Saf 2017. [DOI: 10.1111/jfs.12345] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | - Jaka Widada
- Agriculture Faculty; Universitas Gadjah Mada
| | | | - Tri Joko Raharjo
- Chemistry Department; Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada
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9
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Sauer C, Syvertsson S, Bohorquez LC, Cruz R, Harwood CR, van Rij T, Hamoen LW. Effect of Genome Position on Heterologous Gene Expression in Bacillus subtilis: An Unbiased Analysis. ACS Synth Biol 2016; 5:942-7. [PMID: 27197833 DOI: 10.1021/acssynbio.6b00065] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fixed gene copy number is important for the in silico construction of engineered synthetic networks. However, the copy number of integrated genes depends on their genomic location. This gene dosage effect is rarely addressed in synthetic biology. Two studies in Escherichia coli presented conflicting data on the impact of gene dosage. Here, we investigate how genome location and gene orientation influences expression in Bacillus subtilis. An important difference with the E. coli studies is that we used an unbiased genome integration approach mediated by random transposon insertion. We found that there is a strong gene dosage effect in fast growing B. subtilis cells, which can amount to a 5-fold difference in gene expression. In contrast, gene orientation with respect to DNA replication direction does not influence gene expression. Our study shows that gene dosage should be taken into account when designing synthetic circuits in B. subtilis and presumably other bacteria.
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Affiliation(s)
- Christopher Sauer
- Centre
for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, NE2 4AX Newcastle, United Kingdom
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Simon Syvertsson
- Centre
for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, NE2 4AX Newcastle, United Kingdom
| | - Laura C. Bohorquez
- Bacterial
Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan, 1081 HZ Amsterdam, The Netherlands
| | - Rita Cruz
- Centre
for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, NE2 4AX Newcastle, United Kingdom
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Colin R. Harwood
- Centre
for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, NE2 4AX Newcastle, United Kingdom
| | - Tjeerd van Rij
- DSM Biotechnology Center, P.O. Box 1, 2600 MA Delft, The Netherlands
| | - Leendert W. Hamoen
- Centre
for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, NE2 4AX Newcastle, United Kingdom
- Bacterial
Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan, 1081 HZ Amsterdam, The Netherlands
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Disruption of the Reductive 1,3-Propanediol Pathway Triggers Production of 1,2-Propanediol for Sustained Glycerol Fermentation by Clostridium pasteurianum. Appl Environ Microbiol 2016; 82:5375-88. [PMID: 27342556 DOI: 10.1128/aem.01354-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/19/2016] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED Crude glycerol, the major by-product of biodiesel production, is an attractive bioprocessing feedstock owing to its abundance, low cost, and high degree of reduction. In line with the advent of the biodiesel industry, Clostridium pasteurianum has gained prominence as a result of its unique capacity to convert waste glycerol into n-butanol, a high-energy biofuel. However, no efforts have been directed at abolishing the production of 1,3-propanediol (1,3-PDO), the chief competing product of C. pasteurianum glycerol fermentation. Here, we report rational metabolic engineering of C. pasteurianum for enhanced n-butanol production through inactivation of the gene encoding 1,3-PDO dehydrogenase (dhaT). In spite of current models of anaerobic glycerol dissimilation, culture growth and glycerol utilization were unaffected in the dhaT disruption mutant (dhaT::Ll.LtrB). Metabolite characterization of the dhaT::Ll.LtrB mutant revealed an 83% decrease in 1,3-PDO production, encompassing the lowest C. pasteurianum 1,3-PDO titer reported to date (0.58 g liter(-1)). With 1,3-PDO formation nearly abolished, glycerol was converted almost exclusively to n-butanol (8.6 g liter(-1)), yielding a high n-butanol selectivity of 0.83 g n-butanol g(-1) of solvents compared to 0.51 g n-butanol g(-1) of solvents for the wild-type strain. Unexpectedly, high-performance liquid chromatography (HPLC) analysis of dhaT::Ll.LtrB mutant culture supernatants identified a metabolite peak consistent with 1,2-propanediol (1,2-PDO), which was confirmed by nuclear magnetic resonance (NMR). Based on these findings, we propose a new model for glycerol dissimilation by C. pasteurianum, whereby the production of 1,3-PDO by the wild-type strain and low levels of both 1,3-PDO and 1,2-PDO by the engineered mutant balance the reducing equivalents generated during cell mass synthesis from glycerol. IMPORTANCE Organisms from the genus Clostridium are perhaps the most notable native cellular factories, owing to their vast substrate utilization range and equally diverse variety of metabolites produced. The ability of C. pasteurianum to sustain redox balance and glycerol fermentation despite inactivation of the 1,3-PDO pathway is a testament to the exceptional metabolic flexibility exhibited by clostridia. Moreover, identification of a previously unknown 1,2-PDO-formation pathway, as detailed herein, provides a deeper understanding of fermentative glycerol utilization in clostridia and will inform future metabolic engineering endeavors involving C. pasteurianum To our knowledge, the C. pasteurianum dhaT disruption mutant derived in this study is the only organism that produces both 1,2- and 1,3-PDOs. Most importantly, the engineered strain provides an excellent platform for highly selective production of n-butanol from waste glycerol.
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11
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Suezawa C, Yasuda M, Negayama K, Kameyama T, Hirauchi M, Nakai T, Okuda J. Identification of genes associated with the penetration activity of the human type of Edwardsiella tarda EdwGII through human colon epithelial cell monolayers. Microb Pathog 2016; 95:148-156. [DOI: 10.1016/j.micpath.2016.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 11/27/2022]
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12
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Rajendran NB, Eikmeier J, Becker K, Hussain M, Peters G, Heilmann C. Important contribution of the novel locus comEB to extracellular DNA-dependent Staphylococcus lugdunensis biofilm formation. Infect Immun 2015; 83:4682-92. [PMID: 26416910 PMCID: PMC4645410 DOI: 10.1128/iai.00775-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/14/2015] [Indexed: 01/15/2023] Open
Abstract
The coagulase-negative species Staphylococcus lugdunensis is an emerging cause of serious and potentially life-threatening infections, such as infective endocarditis. The pathogenesis of these infections is characterized by the ability of S. lugdunensis to form biofilms on either biotic or abiotic surfaces. To elucidate the genetic basis of biofilm formation in S. lugdunensis, we performed transposon (Tn917) mutagenesis. One mutant had a significantly reduced biofilm-forming capacity and carried a Tn917 insertion within the competence gene comEB. Site-directed mutagenesis and subsequent complementation with a functional copy of comEB verified the importance of comEB in biofilm formation. In several bacterial species, natural competence stimulates DNA release via lysis-dependent or -independent mechanisms. Extracellular DNA (eDNA) has been demonstrated to be an important structural component of many bacterial biofilms. Therefore, we quantified the eDNA in the biofilms and found diminished eDNA amounts in the comEB mutant biofilm. High-resolution images and three-dimensional data obtained via confocal laser scanning microscopy (CSLM) visualized the impact of the comEB mutation on biofilm integrity. The comEB mutant did not show reduced expression of autolysin genes, decreased autolytic activities, or increased cell viability, suggesting a cell lysis-independent mechanism of DNA release. Furthermore, reduced amounts of eDNA in the comEB mutant biofilms did not result from elevated levels or activity of the S. lugdunensis thermonuclease NucI. In conclusion, we defined here, for the first time, a role for the competence gene comEB in staphylococcal biofilm formation. Our findings indicate that comEB stimulates biofilm formation via a lysis-independent mechanism of DNA release.
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Affiliation(s)
| | - Julian Eikmeier
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany Interdisciplinary Center for Clinical Research (IZKF), University Hospital of Münster, Münster, Germany
| | - Muzaffar Hussain
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany Interdisciplinary Center for Clinical Research (IZKF), University Hospital of Münster, Münster, Germany
| | - Christine Heilmann
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany Interdisciplinary Center for Clinical Research (IZKF), University Hospital of Münster, Münster, Germany
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13
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Dulermo R, Onodera T, Coste G, Passot F, Dutertre M, Porteron M, Confalonieri F, Sommer S, Pasternak C. Identification of new genes contributing to the extreme radioresistance of Deinococcus radiodurans using a Tn5-based transposon mutant library. PLoS One 2015; 10:e0124358. [PMID: 25884619 PMCID: PMC4401554 DOI: 10.1371/journal.pone.0124358] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/02/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we have developed an extremely efficient in vivo Tn5-based mutagenesis procedure to construct a Deinococcus radiodurans insertion mutant library subsequently screened for sensitivity to genotoxic agents such as γ and UV radiations or mitomycin C. The genes inactivated in radiosensitive mutants belong to various functional categories, including DNA repair functions, stress responses, signal transduction, membrane transport, several metabolic pathways, and genes of unknown function. Interestingly, preliminary characterization of previously undescribed radiosensitive mutants suggests the contribution of cyclic di-AMP signaling in the recovery of D. radiodurans cells from genotoxic stresses, probably by modulating several pathways involved in the overall cell response. Our analyses also point out a new transcriptional regulator belonging to the GntR family, encoded by DR0265, and a predicted RNase belonging to the newly described Y family, both contributing to the extreme radioresistance of D. radiodurans. Altogether, this work has revealed new cell responses involved either directly or indirectly in repair of various cell damage and confirmed that D. radiodurans extreme radiation resistance is determined by a multiplicity of pathways acting as a complex network.
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Affiliation(s)
- Rémi Dulermo
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Takefumi Onodera
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Geneviève Coste
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fanny Passot
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Martine Porteron
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Fabrice Confalonieri
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Suzanne Sommer
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Cécile Pasternak
- Univ. Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
- * E-mail:
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14
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Tran KT, Maeda T, Sanchez-Torres V, Wood TK. Beneficial knockouts in Escherichia coli for producing hydrogen from glycerol. Appl Microbiol Biotechnol 2015; 99:2573-81. [DOI: 10.1007/s00253-014-6338-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/12/2014] [Accepted: 12/14/2014] [Indexed: 12/28/2022]
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15
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Hoogewerf AJ, Dyk LAV, Buit TS, Roukema D, Resseguie E, Plaisier C, Le N, Heeringa L, Griend DAV. Functional characterization of a cadmium resistance operon inStaphylococcus aureusATCC12600: CadC does not function as a repressor. J Basic Microbiol 2014; 55:148-59. [DOI: 10.1002/jobm.201400498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/30/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Arlene J. Hoogewerf
- Calvin College Departments of Biology; Knollcrest Circle SE; Grand Rapids MI USA
| | - Lisa A. Van Dyk
- Calvin College Departments of Biology; Knollcrest Circle SE; Grand Rapids MI USA
| | - Tyler S. Buit
- Calvin College Departments of Biology; Knollcrest Circle SE; Grand Rapids MI USA
| | - David Roukema
- Calvin College Departments of Biology; Knollcrest Circle SE; Grand Rapids MI USA
| | - Emily Resseguie
- Calvin College Departments of Biology; Knollcrest Circle SE; Grand Rapids MI USA
| | | | - Nga Le
- Chemistry & Biochemistry; Knollcrest Circle SE; Grand Rapids MI USA
| | - Lee Heeringa
- Chemistry & Biochemistry; Knollcrest Circle SE; Grand Rapids MI USA
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16
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Widhelm TJ, Yajjala VK, Endres JL, Fey PD, Bayles KW. Methods to generate a sequence-defined transposon mutant library in Staphylococcus epidermidis strain 1457. Methods Mol Biol 2014; 1106:135-42. [PMID: 24222462 DOI: 10.1007/978-1-62703-736-5_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transposon mutant libraries are valuable resources to investigators studying bacterial species, including Staphylococcus epidermidis, which are difficult to genetically manipulate. Although sequence-defined transposon mutant libraries have been constructed in Staphylococcus aureus, no such library exists for S. epidermidis. Nevertheless, the study of Tn917-mediated mutations has been paramount in discovering unique aspects of S. epidermidis biology including initial adherence and accumulation during biofilm formation. Herein, we describe modifications to the methodology first described by Bae et al. to utilize the mariner-based transposon bursa aurealis to generate mutants in S. epidermidis strain 1457.
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Affiliation(s)
- Todd J Widhelm
- Department of Pathology and Microbiology, Center for Staphylococcal Research, University of Nebraska Medical Center, Omaha, NE, USA
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17
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Kim J, Park HD, Chung S. Microfluidic approaches to bacterial biofilm formation. Molecules 2012; 17:9818-34. [PMID: 22895027 PMCID: PMC6268732 DOI: 10.3390/molecules17089818] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/27/2012] [Accepted: 08/09/2012] [Indexed: 12/17/2022] Open
Abstract
Bacterial biofilms-aggregations of bacterial cells and extracellular polymeric substrates (EPS)-are an important subject of research in the fields of biology and medical science. Under aquatic conditions, bacterial cells form biofilms as a mechanism for improving survival and dispersion. In this review, we discuss bacterial biofilm development as a structurally and dynamically complex biological system and propose microfluidic approaches for the study of bacterial biofilms. Biofilms develop through a series of steps as bacteria interact with their environment. Gene expression and environmental conditions, including surface properties, hydrodynamic conditions, quorum sensing signals, and the characteristics of the medium, can have positive or negative influences on bacterial biofilm formation. The influences of each factor and the combined effects of multiple factors may be addressed using microfluidic approaches, which provide a promising means for controlling the hydrodynamic conditions, establishing stable chemical gradients, performing measurement in a high-throughput manner, providing real-time monitoring, and providing in vivo-like in vitro culture devices. An increased understanding of biofilms derived from microfluidic approaches may be relevant to improving our understanding of the contributions of determinants to bacterial biofilm development.
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Affiliation(s)
- Junghyun Kim
- School of Mechanical Engineering, Korea University, Seoul 136-713, Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 136-713, Korea
- Authors to whom correspondence should be addressed; (H.-D.P.)(S.C.); Tel.: +82-2-3290-3352 (S.C.); Fax: +82-2-926-9290 (S.C.)
| | - Seok Chung
- School of Mechanical Engineering, Korea University, Seoul 136-713, Korea
- Authors to whom correspondence should be addressed; (H.-D.P.)(S.C.); Tel.: +82-2-3290-3352 (S.C.); Fax: +82-2-926-9290 (S.C.)
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18
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Inokoshi J, Matsuhama M, Miyake M, Ikeda H, Tomoda H. Molecular cloning of the gene cluster for lariatin biosynthesis of Rhodococcus jostii K01-B0171. Appl Microbiol Biotechnol 2012; 95:451-60. [PMID: 22388571 DOI: 10.1007/s00253-012-3973-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 12/13/2022]
Abstract
The biosynthetic gene cluster for lariatins A and B, anti-mycobacterial peptide antibiotics with a unique "lasso" structure, was cloned from Gram-positive bacterium Rhodococcus jostii K01-B0171. Random transposition mutagenesis using IS1415 derivative was carried out to identify a chromosomal locus involved in lariatin biosynthesis and six independent lariatin non-producing variants were obtained. Arbitrary PCR revealed that one insertion was located near the region involved in lariatin biosynthesis. Using the lariatin gene as a probe, a genomic library of R. jostii K01-B0171 was screened by colony hybridization, and two clones were obtained. Sequence analysis of these clones revealed that the gene cluster for lariatin biosynthesis spanning about 4.5 kb consisted of five open reading frames (larA to larE). We proposed that the linear precursor LarA is processed by LarB, LarC, and LarD, and the mature lariatin is exported by LarE.
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Affiliation(s)
- Junji Inokoshi
- Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, Japan
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19
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Liu Q, Fan J, Niu C, Wang D, Wang J, Wang X, Villaruz AE, Li M, Otto M, Gao Q. The eukaryotic-type serine/threonine protein kinase Stk is required for biofilm formation and virulence in Staphylococcus epidermidis. PLoS One 2011; 6:e25380. [PMID: 21966513 PMCID: PMC3179523 DOI: 10.1371/journal.pone.0025380] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 09/02/2011] [Indexed: 01/15/2023] Open
Abstract
Background Serine/threonine kinases are involved in gene regulation and signal transduction in prokaryotes and eukaryotes. Here, we investigated the role of the serine/threonine kinase Stk in the opportunistic pathogen Staphylococcus epidermidis. Methodology/Principal Findings We constructed an isogenic stk mutant of a biofilm-forming clinical S. epidermidis isolate. Presence of stk was important for biofilm formation in vitro and virulence in a murine subcutaneous foreign body infection model. Furthermore, the stk mutant exhibited phenotypes indicating an impact of stk on metabolic pathways. Using different constructs for the genetic complementation of the stk mutant strain with full-length Stk or specific Stk domains, we determined that the Stk intracellular kinase domain is important for biofilm formation and regulation of purine metabolism. Site-specific inactivation of the Stk kinase domain led to defective biofilm formation, in further support of the notion that the kinase activity of Stk regulates biofilm formation of S. epidermidis. According to immunological detection of the biofilm exopolysaccharide PIA and real-time PCR of the PIA biosynthesis genes, the impact of stk on biofilm formation is mediated, at least in part, by a strong influence on PIA expression. Conclusions Our study identifies Stk as an important regulator of biofilm formation and virulence of S. epidermidis, with additional involvement in purine metabolism and the bacterial stress response.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences, and Institute of Medical Microbiology, Fudan University, Shanghai, People's Republic of China
| | - Jiajia Fan
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences, and Institute of Medical Microbiology, Fudan University, Shanghai, People's Republic of China
| | - Chen Niu
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences, and Institute of Medical Microbiology, Fudan University, Shanghai, People's Republic of China
| | - Decheng Wang
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences, and Institute of Medical Microbiology, Fudan University, Shanghai, People's Republic of China
| | - Jianping Wang
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences, and Institute of Medical Microbiology, Fudan University, Shanghai, People's Republic of China
| | - Xing Wang
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences, and Institute of Medical Microbiology, Fudan University, Shanghai, People's Republic of China
| | - Amer E. Villaruz
- National Institute of Allergy and Infectious Diseases, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Min Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Michael Otto
- National Institute of Allergy and Infectious Diseases, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, Institutes of Biomedical Sciences, and Institute of Medical Microbiology, Fudan University, Shanghai, People's Republic of China
- * E-mail:
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20
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Suzuki N, Inui M, Yukawa H. High-throughput transposon mutagenesis of Corynebacterium glutamicum. Methods Mol Biol 2011; 765:409-417. [PMID: 21815106 DOI: 10.1007/978-1-61779-197-0_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Construction of gene disruption mutants and analysis of the resultant phenotypes are an important strategy to study gene function. A simple and high-throughput method developed for microorganisms combines two different types of transposons, direct genomic DNA amplification and thermal asymmetric interlaced-PCR. The considerable utility of this approach is demonstrable in Corynebacterium glutamicum, where 18,000 transposon disruptants enabled the generation of an insertion library covering nearly 80% of the organism's 2,990 ORFs.
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Affiliation(s)
- Nobuaki Suzuki
- Research Institute of Innovative Technology for the Earth (RITE), Kizugawa-Shi, Kyoto, Japan
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21
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ygs is a novel gene that influences biofilm formation and the general stress response of Staphylococcus epidermidis. Infect Immun 2010; 79:1007-15. [PMID: 21173311 DOI: 10.1128/iai.00916-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Infections caused by the nosocomial pathogen Staphylococcus epidermidis frequently develop on implanted medical devices and involve biofilm formation. Biofilms are surface-attached microbial communities that show increased resistance to drug treatment and mechanisms of innate host defense. In this study, a mutant library of the clinical isolate S. epidermidis 1457 was constructed using mariner-based transposon mutagenesis. About a thousand mutants were screened, and 12 mutants were identified as significantly defective in biofilm formation. We focused on a mutant in which the transposon had inserted in a gene with unknown function, SERP0541, which is annotated as a gene encoding a GSP13-like general stress response protein. The gene was named ygs (encoding an unknown general stress protein). Various stresses, including heat, pH, high osmolarity, and ethanol affected the survival of the ygs mutant to a significantly higher degree than the wild-type strain and led to increased expression of ygs. Furthermore, synthesis of polysaccharide intercellular adhesin (PIA) and transcription of the PIA biosynthetic operon were significantly decreased in the ygs mutant. These results are in accordance with the putative involvement of ygs in stress-response gene regulation and indicate that ygs influences biofilm development by controlling PIA-dependent biofilm accumulation. Moreover, ygs had a significant impact on the formation of biofilms and metastatic disease in two catheter-related rat infection models. Our study shows that the ygs gene controls S. epidermidis biofilm accumulation and stress resistance, representing a key regulator of both structural and physiological biofilm characteristics with a significant impact on biofilm-associated infection.
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22
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Carlyon RE, Ryther JL, VanYperen RD, Griffitts JS. FeuN, a novel modulator of two-component signalling identified in Sinorhizobium meliloti. Mol Microbiol 2010; 77:170-82. [PMID: 20487268 DOI: 10.1111/j.1365-2958.2010.07198.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sinorhizobium meliloti is a nitrogen-fixing bacterial symbiont of alfalfa and related legumes. Symbiotic infection by S. meliloti requires an osmosensory two-component system composed of the response regulator FeuP and the sensor kinase FeuQ. The FeuPQ pathway positively regulates transcription of multiple genes including ndvA, which encodes the cyclic glucan exporter. Here we show that proper regulation of this signalling pathway is essential for cell viability. Without the small 83 amino acid protein FeuN, S. meliloti cells are unable to grow, and this phenotype is dependent on the FeuPQ pathway. Using Escherichia coli as a heterologous system, we show that expression of feuP and feuQ leads to a dramatic increase in ndvA promoter activity, but that simultaneous expression of feuN abrogates this effect. Random mutagenesis of the feuPQ bicistron revealed a defined region of the FeuQ protein in and around its two predicted transmembrane domains that are required for FeuN-dependent signalling modulation. Marker enzyme fusion experiments indicate that most of the FeuN polypeptide is localized to the periplasm. Our data support a model in which FeuN interacts directly with FeuQ to attenuate phosphorylation of FeuP, and that without this activity, hyperactive signalling through FeuPQ results in cessation of growth or death.
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Affiliation(s)
- Rebecca E Carlyon
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
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23
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Amarelle V, Koziol U, Rosconi F, Noya F, O'Brian MR, Fabiano E. A new small regulatory protein, HmuP, modulates haemin acquisition in Sinorhizobium meliloti. MICROBIOLOGY-SGM 2010; 156:1873-1882. [PMID: 20167620 PMCID: PMC3068671 DOI: 10.1099/mic.0.037713-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sinorhizobium meliloti has multiple systems for iron acquisition, including the use of haem as an iron source. Haem internalization involves the ShmR haem outer membrane receptor and the hmuTUV locus, which participates in haem transport across the cytoplasmic membrane. Previous studies have demonstrated that expression of the shmR gene is negatively regulated by iron through RirA. Here, we identify hmuP in a genetic screen for mutants that displayed aberrant control of shmR. The normal induction of shmR in response to iron limitation was lost in the hmuP mutant, showing that this gene positively affects shmR expression. Moreover, the HmuP protein is not part of the haemin transporter system. Analysis of gene expression and siderophore production indicates that disruption of hmuP does not affect other genes related to the iron-restriction response. Our results strongly indicate that the main function of HmuP is the transcriptional regulation of shmR. Sequence alignment of HmuP homologues and comparison with the NMR structure of Rhodopseudomonas palustris CGA009 HmuP protein revealed that certain amino acids localized within predicted β-sheets are well conserved. Our data indicate that at least one of the β-sheets is important for HmuP activity.
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Affiliation(s)
- Vanesa Amarelle
- Laboratorio de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Av. Italia 3318, Montevideo 11600, Uruguay
| | - Uriel Koziol
- Sección Bioquímica, Facultad de Ciencias, Iguá 4225, Montevideo 11400, Uruguay.,Laboratorio de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Av. Italia 3318, Montevideo 11600, Uruguay
| | - Federico Rosconi
- Laboratorio de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Av. Italia 3318, Montevideo 11600, Uruguay
| | - Francisco Noya
- Laboratorio de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Av. Italia 3318, Montevideo 11600, Uruguay
| | - Mark R O'Brian
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Elena Fabiano
- Laboratorio de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Unidad Asociada a la Facultad de Ciencias, Av. Italia 3318, Montevideo 11600, Uruguay
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Christner M, Franke GC, Schommer NN, Wendt U, Wegert K, Pehle P, Kroll G, Schulze C, Buck F, Mack D, Aepfelbacher M, Rohde H. The giant extracellular matrix-binding protein of Staphylococcus epidermidis mediates biofilm accumulation and attachment to fibronectin. Mol Microbiol 2009; 75:187-207. [PMID: 19943904 DOI: 10.1111/j.1365-2958.2009.06981.x] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Virulence of nosocomial pathogen Staphylococcus epidermidis is essentially related to formation of adherent biofilms, assembled by bacterial attachment to an artificial surface and subsequent production of a matrix that mediates interbacterial adhesion. Growing evidence supports the idea that proteins are functionally involved in S. epidermidis biofilm accumulation. We found that in S. epidermidis 1585v overexpression of a 460 kDa truncated isoform of the extracellular matrix-binding protein (Embp) is necessary for biofilm formation. Embp is a giant fibronectin-binding protein harbouring 59 Found In Various Architectures (FIVAR) and 38 protein G-related albumin-binding (GA) domains. Studies using defined Embp-positive and -negative S. epidermidis strains proved that Embp is sufficient and necessary for biofilm formation. Further data showed that the FIVAR domains of Embp mediate binding of S. epidermidis to solid-phase attached fibronectin, constituting the first step of biofilm formation on conditioned surfaces. The binding site in fibronectin was assigned to the fibronectin domain type III12. Embp-mediated biofilm formation also protected S. epidermidis from phagocytosis by macrophages. Thus, Embp is a multifunctional cell surface protein that mediates attachment to host extracellular matrix, biofilm accumulation and escape from phagocytosis, and therefore is well suited for promoting implant-associated infections.
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Affiliation(s)
- Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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25
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Interconnections between Sigma B, agr, and proteolytic activity in Staphylococcus aureus biofilm maturation. Infect Immun 2009; 77:1623-35. [PMID: 19188357 DOI: 10.1128/iai.01036-08] [Citation(s) in RCA: 202] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Staphylococcus aureus is a proficient biofilm former on host tissues and medical implants. We mutagenized S. aureus strain SH1000 to identify loci essential for ica-independent mechanisms of biofilm maturation and identified multiple insertions in the rsbUVW-sigB operon. Following construction and characterization of a sigB deletion, we determined that the biofilm phenotype was due to a lack of sigma factor B (SigB) activity. The phenotype was conserved in a sigB mutant of USA300 strain LAC, a well-studied community-associated methicillin-resistant S. aureus isolate. We determined that agr RNAIII levels were elevated in the sigB mutants, and high levels of RNAIII expression are known to have antibiofilm effects. By introducing an agr mutation into the SH1000 or LAC sigB deletion strain, S. aureus regained biofilm capacity, indicating that the biofilm phenotype was agr dependent. Protease activity is linked to agr activity and ica-independent biofilm formation, and we observed that the protease inhibitors phenylmethylsulfonyl fluoride and alpha-macroglobulin could reverse the sigB biofilm defect. Similarly, inactivating genes encoding both the aureolysin and Spl extracellular proteases in the sigB mutant restored biofilm capacity. Due to the growing link between murein hydrolase activity and biofilm maturation, autolysin zymography was performed, which revealed an altered profile in the sigB mutant; again, the phenotype could be repaired through protease inactivation. These findings indicate that the lack of SigB activity results in increased RNAIII expression, thus elevating extracellular protease levels and altering the murein hydrolase activity profile. Altogether, our observations demonstrate that SigB is an essential regulator of S. aureus biofilm maturation.
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26
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Costa AR, Henriques M, Oliveira R, Azeredo J. The role of polysaccharide intercellular adhesin (PIA) in Staphylococcus epidermidis adhesion to host tissues and subsequent antibiotic tolerance. Eur J Clin Microbiol Infect Dis 2009; 28:623-9. [PMID: 19130107 DOI: 10.1007/s10096-008-0684-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 12/01/2008] [Indexed: 10/21/2022]
Abstract
The aim of this study was to determine the role of polysaccharide intercellular adhesin (PIA) in Staphylococcus epidermidis adhesion to host tissues and subsequent antibiotic tolerance. The adherence of S. epidermidis 1457 and the mutant defective in PIA production (1457-M10) to urinary epithelium and endothelium was estimated by colony counting. Minimum bactericidal concentration and mean reduction of cellular activity (XTT) following antibiotic exposure was determined for planktonic and adhered bacteria. S. epidermidis 1457 adhered to a greater extent to both cells than the mutant strain. The adhered strains had a significantly higher antimicrobial tolerance than their planktonic counterparts. The mutant strain was, in general, the most susceptible to the antibiotics assayed. In conclusion, PIA may influence S. epidermidis adherence to host tissues and their antimicrobial susceptibility. Initial adhesion may be the main step for the acquisition of resistance in S. epidermidis.
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Affiliation(s)
- A R Costa
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, 4710-057, Braga, Portugal
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Regulatory and DNA repair genes contribute to the desiccation resistance of Sinorhizobium meliloti Rm1021. Appl Environ Microbiol 2008; 75:446-53. [PMID: 19028909 DOI: 10.1128/aem.02207-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti can form a nitrogen-fixing symbiotic relationship with alfalfa after bacteria in the soil infect emerging root hairs of the growing plant. To be successful at this, the bacteria must be able to survive in the soil between periods of active plant growth, including when conditions are dry. The ability of S. meliloti to withstand desiccation has been known for years, but genes that contribute to this phenotype have not been identified. Transposon mutagenesis was used in combination with novel screening techniques to identify four desiccation-sensitive mutants of S. meliloti Rm1021. DNA sequencing of the transposon insertion sites identified three genes with regulatory functions (relA, rpoE2, and hpr) and a DNA repair gene (uvrC). Various phenotypes of the mutants were determined, including their behavior on several indicator media and in symbiosis. All of the mutants formed an effective symbiosis with alfalfa. To test the hypothesis that UvrC-related excision repair was important in desiccation resistance, uvrA, uvrB, and uvrC deletion mutants were also constructed. These strains were sensitive to DNA damage induced by UV light and 4-NQO and were also desiccation sensitive. These data indicate that uvr gene-mediated DNA repair and the regulation of stress-induced pathways are important for desiccation resistance.
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Spears PA, Suyemoto MM, Palermo AM, Horton JR, Hamrick TS, Havell EA, Orndorff PE. A Listeria monocytogenes mutant defective in bacteriophage attachment is attenuated in orally inoculated mice and impaired in enterocyte intracellular growth. Infect Immun 2008; 76:4046-54. [PMID: 18559424 PMCID: PMC2519439 DOI: 10.1128/iai.00283-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/09/2008] [Accepted: 06/09/2008] [Indexed: 11/20/2022] Open
Abstract
A Listeria monocytogenes bacteriophage was used to identify a phage-resistant Tn917 insertion mutant of the mouse-virulent listerial strain F6214-1. The mutant was attenuated when it was inoculated orally into female A/J mice and failed to replicate efficiently in cultured mouse enterocytes. Phage binding studies indicated that the mutant had a cell surface alteration that precluded phage attachment. All phenotypes associated with the mutation could be complemented in trans by a single open reading frame (ORF) that corresponded to the ORF interrupted by the Tn917 insertion. The complementation effected was, in all cases, at a level indistinguishable from that of the parent. The Tn917 insertion interrupted a gene that is predicted to encode a group 2 glycosyl transferase (provisionally designated glcV). A similar glcV gene is present in Listeria welshimeri and Listeria innocua and in some serotypes of L. monocytogenes. We speculate that the loss of the glcV product results in a defective phage receptor and that this alteration coincidentally influences a feature of the normal host-pathogen interaction required for virulence. Interestingly, the glcV lesion, while preventing phage attachment, did not alter the mutant's ability to bind to cultured mouse enterocyte monolayers. Rather, the mutation appeared to alter a subsequent step in intracellular replication measured by a reduction in plaque-forming efficiency and plaque size. In vivo, the mutant was undetectable in the liver and spleen 48 h after oral inoculation. The mutation is significant in part because it is one of the few that produce attenuation when the mutant is delivered orally.
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Affiliation(s)
- Patricia A Spears
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27606, USA
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Griffitts JS, Long SR. A symbiotic mutant of Sinorhizobium meliloti reveals a novel genetic pathway involving succinoglycan biosynthetic functions. Mol Microbiol 2008; 67:1292-306. [PMID: 18284576 DOI: 10.1111/j.1365-2958.2008.06123.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A large-scale screen for symbiotic mutants was carried out using the model root nodulating bacterium Sinorhizobium meliloti. Several mutations in the previously uncharacterized gene msbA2 were isolated. msbA2 encodes a member of the ATP-binding cassette exporter family. This protein family is known to export a wide variety of compounds from bacterial cells. S. meliloti MsbA2 is required for the invasion of nodule tissue, with msbA2 mutant cells stimulating nodule primordium morphogenesis, but failing to invade plant tissue beyond the epidermal cell layer. msbA2 mutants do not exhibit any of the free-living traits often found to correlate with symbiotic defects, suggesting that MsbA2 may take part in a specifically symbiotic function. In strains that overproduce the symbiotic signalling polysaccharide succinoglycan, loss of MsbA2 function is extremely deleterious. This synthetic lethal phenotype can be suppressed by disrupting the succinoglycan biosynthetic genes exoY or exoA. It can also be suppressed by disrupting putative glycosyltransferase-encoding genes found upstream of msbA2. Finally, the symbiotic phenotype of a msbA2 null mutant is suppressed by secondary mutations in these upstream transferase genes, indicating that the msbA2 mutant phenotype may be caused by an inhibitory accumulation of a novel polysaccharide that is synthesized from succinoglycan precursors.
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Affiliation(s)
- Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
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Yurgel SN, Berrocal J, Wilson C, Kahn ML. Pleiotropic effects of mutations that alter the Sinorhizobium meliloti cytochrome c respiratory system. MICROBIOLOGY-SGM 2007; 153:399-410. [PMID: 17259611 DOI: 10.1099/mic.0.2006/002634-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Using transposon mutagenesis, mutations have been isolated in several genes (ccdA, cycM, ccmC, ccmB and senC) that play a role in Sinorhizobium meliloti cytochrome metabolism. As in other bacteria, mutations in the S. meliloti ccdA, ccmB and ccmC genes resulted in the absence of all c-type cytochromes. However, the S. meliloti ccdA mutant also lacked cytochrome oxidase aa(3), a defect that does not appear to have been reported for other bacteria. The aa(3)-type cytochromes were also missing from a mutant strain with an insertion into the gene encoding the haem-containing subunit (SU)I of aa(3) cytochrome c oxidase, but not in mutants unable to make SUII or SUIII, indicating that CcdA probably plays a role in assembling SUI. The cytochrome-deficient mutants also had other free-living phenotypes, including a significant decrease in growth rate on rich media and increased motility on minimal media. A senC mutant also had significantly decreased motility, but the motility and growth properties of the cycM mutant were unchanged. Unlike similar mutants in Bradyrhizobium japonicum and Rhizobium leguminosarum, an S. meliloti Rm1021 cycM mutant contained cytochrome oxidase aa(3). Cytochrome maturation in strain Rm1021 appeared to be similar to maturation in other rhizobia, but there were some differences in the cytochrome composition of the strain, and respiration chain function and assembly.
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Affiliation(s)
- Svetlana N Yurgel
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Jhoanna Berrocal
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, USA
| | - Cynthia Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, USA
| | - Michael L Kahn
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, USA
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Mack D, Rohde H, Harris LG, Davies AP, Horstkotte MA, Knobloch JKM. Biofilm formation in medical device-related infection. Int J Artif Organs 2006; 29:343-59. [PMID: 16705603 DOI: 10.1177/039139880602900404] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Medical device-associated infections, most frequently caused by coagulase-negative staphylococci, especially Staphylococcus epidermidis, are of increasing importance in modern medicine. Regularly, antimicrobial therapy fails without removal of the implanted device. The most important factor in the pathogenesis of medical device-associated staphylococcal infections is the formation of adherent, multilayered bacterial biofilms. There is urgent need for an increased understanding of the functional factors involved in biofilm formation, the regulation of their expression, and the interaction of those potential virulence factors in device related infection with the host. Significant progress has been made in recent years which may ultimately lead to new rational approaches for better preventive, therapeutic, and diagnostic measures.
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Affiliation(s)
- D Mack
- Medical Microbiology and Infectious Diseases, The School of Medicine, University of Wales Swansea, Swansea, UK.
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Mack D, Davies AP, Harris LG, Rohde H, Horstkotte MA, Knobloch JKM. Microbial interactions in Staphylococcus epidermidis biofilms. Anal Bioanal Chem 2006; 387:399-408. [PMID: 16955256 DOI: 10.1007/s00216-006-0745-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 08/03/2006] [Accepted: 08/08/2006] [Indexed: 10/24/2022]
Abstract
Medical device-associated infections, most frequently caused by coagulase-negative staphylococci, especially Staphylococcus epidermidis, are of increasing importance in modern medicine. The formation of adherent, multilayered bacterial biofilms is the most important factor in the pathogenesis of these infections, which regularly fail to respond to appropriate antimicrobial therapy. Progress in elucidating the factors functional in elaboration of S. epidermidis biofilms and the regulation of their expression with a special emphasis on the role of quorum sensing are reviewed. Significant progress has been made in recent years, which provides the rationale for developing better preventive, therapeutic and diagnostic measures.
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Affiliation(s)
- Dietrich Mack
- Medical Microbiology and Infectious Diseases, The School of Medicine, Swansea University, Grove Building, Singleton Park, Swansea, SA2 8PP, UK.
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Suzuki N, Okai N, Nonaka H, Tsuge Y, Inui M, Yukawa H. High-throughput transposon mutagenesis of Corynebacterium glutamicum and construction of a single-gene disruptant mutant library. Appl Environ Microbiol 2006; 72:3750-5. [PMID: 16672528 PMCID: PMC1472376 DOI: 10.1128/aem.72.5.3750-3755.2006] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A simple and high-throughput transposon-mediated mutagenesis system employing two different types of transposons in combination with direct genomic DNA amplification and thermal asymmetric interlaced PCR (TAIL-PCR) was developed. Each of the two minitransposons based on IS31831 (ISL3 family) and Tn5 (IS4 family) was integrated into the Corynebacterium glutamicum R genome. By using BLAST and Perl, transposon insertion locations were automatically identified based on the sequences of TAIL-PCR products of mutant cells. Insertion locations of 18,000 mutants were analyzed, and a comprehensive insertion library covering nearly 80% of the 2,990 open reading frames of C. glutamicum R was generated. Eight thousand of the mutants, exhibiting disruption in 2,330 genes, survived on complex medium under normal laboratory conditions, indicating that the genes were not essential for cell survival. Of the 2,330 genes, 30 exhibited high similarity to essential genes of Escherichia coli or Bacillus subtilis. This approach could be useful in furthering genetic understanding of cellular life and facilitating the functional analysis of microorganisms.
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Affiliation(s)
- Nobuaki Suzuki
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizu-Cho, Soraku-Gun, Kyoto 619-0292, Japan
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N/A, 张 万. N/A. Shijie Huaren Xiaohua Zazhi 2006; 14:1714-1720. [DOI: 10.11569/wcjd.v14.i17.1714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Lane JM, Rubin EJ. Scaling down: a PCR-based method to efficiently screen for desired knockouts in a high density Mycobacterium tuberculosis picked mutant library. Tuberculosis (Edinb) 2006; 86:310-3. [PMID: 16527544 DOI: 10.1016/j.tube.2006.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 01/20/2006] [Indexed: 11/25/2022]
Abstract
Transposon mutagenesis produces random mycobacterial mutants at high frequency. Because they are random, however, it is difficult to isolate mutations in particular target genes. Here we describe the use of an arrayed library of Mycobacterium tuberculosis together with a PCR screening strategy to rapidly identify strains with defined insertion mutations. This method is useful for many genetic applications.
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Affiliation(s)
- James M Lane
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
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Jäger S, Mack D, Rohde H, Horstkotte MA, Knobloch JKM. Disintegration of Staphylococcus epidermidis biofilms under glucose-limiting conditions depends on the activity of the alternative sigma factor sigmaB. Appl Environ Microbiol 2005; 71:5577-81. [PMID: 16151151 PMCID: PMC1214654 DOI: 10.1128/aem.71.9.5577-5581.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To evaluate the role of the polysaccharide intercellular adhesin as an energy-storage molecule, we investigated the effect of nutrient limitation on S. epidermidis biofilms. The stability of established biofilms depends on sigma(B) activity; however, the slow decay of biofilms under conditions of nutrient limitation reveal its use as an energy-storage molecule to be unlikely.
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Affiliation(s)
- Sebastian Jäger
- Universitätsklinikum Hamburg-Eppendorf, Zentrum für Klinisch-Theoretische Medizin I, Institut für Infektionsmedizin, Martinistrasse 52, D-20246 Hamburg, Germany
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Rooney AP, Swezey JL, Wicklow DT, McAtee MJ. Bacterial species diversity in cigarettes linked to an investigation of severe pneumonitis in U.S. Military personnel deployed in operation iraqi freedom. Curr Microbiol 2005; 51:46-52. [PMID: 15942700 DOI: 10.1007/s00284-005-4491-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Accepted: 02/01/2005] [Indexed: 11/30/2022]
Abstract
This report presents results from a study on the bacterial diversity of cigarette brands collected from military personnel during the U.S. Army's investigation of a series of cases of acute eosinophilic pneumonitis in military personnel deployed in Operation Iraqi Freedom. Eight species of Bacillus, including five new species, and one new species of Kurthia were isolated from the cigarettes. Some of these species have been identified elsewhere as causes of hypersensitivity pneumonitis and other respiratory syndromes. All of the isolates were facultative anaerobes, and many displayed mucoid growth under anaerobic conditions. In addition, many isolates also displayed the ability to form surface biofilms under liquid culture. Although biofilm formation and mucoid growth were not correlated, the former was found to be much more pronounced under anaerobic conditions as opposed to aerobic ones. The implications of these findings are discussed.
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Affiliation(s)
- Alejandro P Rooney
- Microbial Genomics and Bioprocessing Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA.
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Das S, Noe JC, Paik S, Kitten T. An improved arbitrary primed PCR method for rapid characterization of transposon insertion sites. J Microbiol Methods 2005; 63:89-94. [PMID: 16157212 DOI: 10.1016/j.mimet.2005.02.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 01/20/2005] [Accepted: 02/11/2005] [Indexed: 11/19/2022]
Abstract
Modifications were made to published arbitrary primed polymerase chain reaction (AP-PCR) procedures that resulted in increased specificity and sensitivity. Several arbitrary primer sequences were also evaluated, resulting in recommendations for primer design.
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Affiliation(s)
- Sankar Das
- Philips Institute of Oral and Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298-0566, USA
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Rohde H, Kalitzky M, Kröger N, Scherpe S, Horstkotte MA, Knobloch JKM, Zander AR, Mack D. Detection of virulence-associated genes not useful for discriminating between invasive and commensal Staphylococcus epidermidis strains from a bone marrow transplant unit. J Clin Microbiol 2005; 42:5614-9. [PMID: 15583290 PMCID: PMC535265 DOI: 10.1128/jcm.42.12.5614-5619.2004] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Because of their biofilm-forming capacity, invasive Staphylococcus epidermidis isolates, which cause the majority of nosocomial catheter-related bloodstream infections (BSIs), are thought to be selected at the time of catheter insertion from a population of less virulent commensal strains. This fact allows the prediction that invasive and contaminating strains can be differentiated via detection of virulence-associated genes. However, the hospital environment may pave the way for catheter-related infections by promoting a shift in the commensal bacterial population toward strains with enhanced virulence. The distribution of virulence-associated genes (icaADBC, aap, atlE, bhp, fbe, embp, mecA, IS256, and IS257), polysaccharide intercellular adhesin synthesis, and biofilm formation were investigated in S. epidermidis strains from independent episodes of catheter-related BSIs in individuals who have received bone marrow transplantation (BMT). The results were compared with those obtained for commensal S. epidermidis isolates from hospitalized patients after BMT and from healthy individuals, respectively. The clonal relationships of the strains were investigated by pulsed-field gel electrophoresis. icaADBC, mecA, and IS256 were significantly more prevalent in BSI isolates than in commensal isolates from healthy individuals. However, the prevalence of any of the genes in clonally independent, endogenous commensal strains from BMT patients did not differ from that in invasive BSI strains. icaADBC and methicillin resistance, factors important for the establishment of catheter-related infections, already ensure survival of the organisms in their physiological habitat in the hospital environment, resulting in a higher probability of contamination of indwelling medical devices with virulent S. epidermidis strains. The dynamics of S. epidermidis populations reveal that detection of icaADBC and mecA is not suitable for discriminating invasive from contaminating S. epidermidis strains.
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Affiliation(s)
- Holger Rohde
- Institut für Infektionsmedizin, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
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Mack D, Becker P, Chatterjee I, Dobinsky S, Knobloch JKM, Peters G, Rohde H, Herrmann M. Mechanisms of biofilm formation in Staphylococcus epidermidis and Staphylococcus aureus: functional molecules, regulatory circuits, and adaptive responses. Int J Med Microbiol 2004; 294:203-12. [PMID: 15493831 DOI: 10.1016/j.ijmm.2004.06.015] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biomaterial-associated infections, most frequently caused by Staphylococcus epidermidis and Staphylococcus aureus, are of increasing importance in modern medicine. Regularly, antimicrobial therapy fails without removal of the implanted device. The most important factor in the pathogenesis of biomaterial-associated staphylococcal infections is the formation of adherent, multilayered bacterial biofilms. In this review, recent insights regarding factors functional in biofilm formation of S. epidermidis, their role in pathogenesis, and regulation of their expression are presented. Similarly, in S. aureus the biofilm mode of growth affects gene expression and the overall metabolic status. Experimental approaches for analysis of differential expression of genes involved in these adaptive responses and evolving patterns of gene expression are discussed.
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Affiliation(s)
- Dietrich Mack
- Institut für Infektionsmedizin, Zentrum für Klinisch-Theoretische Medizin I, Universitätsklinikum Hamburg-Eppendorf Martinistr 52, D-20246 Hamburg, Germany.
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