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Unraveling Protein Interactions between the Temperate Virus Bam35 and Its Bacillus Host Using an Integrative Yeast Two Hybrid-High Throughput Sequencing Approach. Int J Mol Sci 2021; 22:ijms222011105. [PMID: 34681765 PMCID: PMC8539640 DOI: 10.3390/ijms222011105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Bacillus virus Bam35 is the model Betatectivirus and member of the family Tectiviridae, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. Interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, which are known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein–protein interactions (PPIs) network for a tectivirus–host system by studying the Bam35–Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and high-throughput sequencing (Y2H-HTS). We generated and thoroughly analyzed a genomic library of Bam35′s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait–prey couples. Initial analysis of the raw data enabled the identification of over 4000 candidate interactions, which were sequentially filtered to produce 182 high-confidence interactions that were defined as part of the core virus–host interactome. Overall, host metabolism proteins and peptidases were particularly enriched within the detected interactions, distinguishing this host–phage system from the other reported host–phage PPIs. Our approach also suggested biological roles for several Bam35 proteins of unknown function, including the membrane structural protein P25, which may be a viral hub with a role in host membrane modification during viral particle morphogenesis. This work resulted in a better understanding of the Bam35–B. thuringiensis interaction at the molecular level and holds great potential for the generalization of the Y2H-HTS approach for other virus–host models.
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De Smet J, Wagemans J, Hendrix H, Staes I, Visnapuu A, Horemans B, Aertsen A, Lavigne R. Bacteriophage-mediated interference of the c-di-GMP signalling pathway in Pseudomonas aeruginosa. Microb Biotechnol 2021; 14:967-978. [PMID: 33314648 PMCID: PMC8085984 DOI: 10.1111/1751-7915.13728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/19/2020] [Accepted: 11/22/2020] [Indexed: 01/10/2023] Open
Abstract
C-di-GMP is a key signalling molecule which impacts bacterial motility and biofilm formation and is formed by the condensation of two GTP molecules by a diguanylate cyclase. We here describe the identification and characterization of a family of bacteriophage-encoded peptides that directly impact c-di-GMP signalling in Pseudomonas aeruginosa. These phage proteins target Pseudomonas diguanylate cyclase YfiN by direct protein interaction (termed YIPs, YfiN Interacting Peptides). YIPs induce an increase of c-di-GMP production in the host cell, resulting in a decrease in motility and an increase in biofilm mass in P. aeruginosa. A dynamic analysis of the biofilm morphology indicates a denser biofilm structure after induction of the phage protein. This intracellular signalling interference strategy by a lytic phage constitutes an unexplored phage-based mechanism of metabolic regulation and could potentially serve as inspiration for the development of molecules that interfere with biofilm formation in P. aeruginosa and other pathogens.
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Affiliation(s)
- Jeroen De Smet
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
- Present address:
Lab4FoodDepartment of Microbial and Molecular Systems (M2S)KU Leuven Campus GeelGeel2440Belgium
| | - Jeroen Wagemans
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Hanne Hendrix
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Ines Staes
- Laboratory of Food MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenHeverlee3001Belgium
| | - Annegrete Visnapuu
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Benjamin Horemans
- Department of Earth and Environmental SciencesKU LeuvenHeverlee3001Belgium
| | - Abram Aertsen
- Laboratory of Food MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenHeverlee3001Belgium
| | - Rob Lavigne
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
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Uytterhoeven B, Lathouwers T, Voet M, Michiels CW, Lavigne R. A Protein Interaction Map of the Kalimantacin Biosynthesis Assembly Line. Front Microbiol 2016; 7:1726. [PMID: 27853452 PMCID: PMC5089993 DOI: 10.3389/fmicb.2016.01726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/17/2016] [Indexed: 12/04/2022] Open
Abstract
The antimicrobial secondary metabolite kalimantacin (also called batumin) is produced by a hybrid polyketide/non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein–protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites. This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.
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Affiliation(s)
- Birgit Uytterhoeven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Thomas Lathouwers
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Chris W Michiels
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems, KU Leuven Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
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Wang JB, Lin NT, Tseng YH, Weng SF. Genomic Characterization of the Novel Aeromonas hydrophila Phage Ahp1 Suggests the Derivation of a New Subgroup from phiKMV-Like Family. PLoS One 2016; 11:e0162060. [PMID: 27603936 PMCID: PMC5014404 DOI: 10.1371/journal.pone.0162060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/16/2016] [Indexed: 12/15/2022] Open
Abstract
Aeromonas hydrophila is an opportunistic pathogenic bacterium causing diseases in human and fish. The emergence of multidrug-resistant A. hydrophila isolates has been increasing in recent years. In this study, we have isolated a novel virulent podophage of A. hydrophila, designated as Ahp1, from waste water. Ahp1 has a rapid adsorption (96% adsorbed in 2 min), a latent period of 15 min, and a burst size of 112 PFU per infected cell. At least eighteen Ahp1 virion proteins were visualized in SDS-polyacrylamide gel electrophoresis, with a 36-kDa protein being the predicted major capsid protein. Genome analysis of Ahp1 revealed a linear doubled-stranded DNA genome of 42,167 bp with a G + C content of 58.8%. The genome encodes 46 putative open reading frames, 5 putative phage promoters, and 3 transcriptional terminators. Based on high degrees of similarity in overall genome organization and among most of the corresponding ORFs, as well as phylogenetic relatedness among their DNAP, RNAP and major capsid proteins, we propose a new subgroup, designated Ahp1-like subgroup. This subgroup contains Ahp1 and members previously belonging to phiKMV-like subgroup, phiAS7, phi80-18, GAP227, phiR8-01, and ISAO8. Since Ahp1 has a narrow host range, for effective phage therapy, different phages are needed for preparation of cocktails that are capable of killing the heterogeneous A. hydrophila strains.
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Affiliation(s)
- Jian-Bin Wang
- Institute of Medical Sciences, Tzu Chi University, Hualien 970, Taiwan
| | - Nien-Tsung Lin
- Institute of Medical Sciences, Tzu Chi University, Hualien 970, Taiwan
- Master Program in Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien 970, Taiwan
| | - Yi-Hsiung Tseng
- Institute of Medical Sciences, Tzu Chi University, Hualien 970, Taiwan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
- * E-mail: (YHT); (SFW)
| | - Shu-Fen Weng
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
- * E-mail: (YHT); (SFW)
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De Smet J, Zimmermann M, Kogadeeva M, Ceyssens PJ, Vermaelen W, Blasdel B, Bin Jang H, Sauer U, Lavigne R. High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection. ISME JOURNAL 2016; 10:1823-35. [PMID: 26882266 DOI: 10.1038/ismej.2016.3] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 11/26/2015] [Accepted: 12/16/2015] [Indexed: 12/19/2022]
Abstract
Phage-mediated metabolic changes in bacteria are hypothesized to markedly alter global nutrient and biogeochemical cycles. Despite their theoretic importance, experimental data on the net metabolic impact of phage infection on the bacterial metabolism remains scarce. In this study, we tracked the dynamics of intracellular metabolites using untargeted high coverage metabolomics in Pseudomonas aeruginosa cells infected with lytic bacteriophages from six distinct phage genera. Analysis of the metabolomics data indicates an active interference in the host metabolism. In general, phages elicit an increase in pyrimidine and nucleotide sugar metabolism. Furthermore, clear phage-specific and infection stage-specific responses are observed, ranging from extreme metabolite depletion (for example, phage YuA) to complete reorganization of the metabolism (for example, phage phiKZ). As expected, pathways targeted by the phage-encoded auxiliary metabolic genes (AMGs) were enriched among the metabolites changing during infection. The effect on pyrimidine metabolism of phages encoding AMGs capable of host genome degradation (for example, YuA and LUZ19) was distinct from those lacking nuclease-encoding genes (for example, phiKZ), which demonstrates the link between the encoded set of AMGs of a phage and its impact on host physiology. However, a large fraction of the profound effect on host metabolism could not be attributed to the phage-encoded AMGs. We suggest a potentially crucial role for small, 'non-enzymatic' peptides in metabolism take-over and hypothesize on potential biotechnical applications for such peptides. The highly phage-specific nature of the metabolic impact emphasizes the potential importance of the 'phage diversity' parameter when studying metabolic interactions in complex communities.
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Affiliation(s)
- Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Michael Zimmermann
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Maria Kogadeeva
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium.,Unit Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Wesley Vermaelen
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Bob Blasdel
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Ho Bin Jang
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
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Wagemans J, Delattre AS, Uytterhoeven B, De Smet J, Cenens W, Aertsen A, Ceyssens PJ, Lavigne R. Antibacterial phage ORFans of Pseudomonas aeruginosa phage LUZ24 reveal a novel MvaT inhibiting protein. Front Microbiol 2015; 6:1242. [PMID: 26594207 PMCID: PMC4635203 DOI: 10.3389/fmicb.2015.01242] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
The functional elucidation of small unknown phage proteins (‘ORFans’) presents itself as one of the major challenges of bacteriophage molecular biology. In this work, we mined the Pseudomonas aeruginosa-infecting phage LUZ24 proteome for antibacterial and antibiofilm proteins against its host. Subsequently, their putative host target was identified. In one example, we observed an interaction between LUZ24 gp4 and the host transcriptional regulator MvaT. The polymerization of MvaT across AT-rich DNA strands permits gene silencing of foreign DNA, thereby limiting any potentially adverse effects of such DNA. Gel shift assays proved the inhibitory effect of LUZ24 gp4 on MvaT DNA binding activity. Therefore, we termed this gene product as Mip, the MvaT inhibiting protein. We hypothesize Mip prevents the AT-rich LUZ24 DNA from being physically blocked by MvaT oligomers right after its injection in the host cell, thereby allowing phage transcription and thus completion of the phage infection cycle.
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Affiliation(s)
- Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Anne-Sophie Delattre
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Birgit Uytterhoeven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - William Cenens
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven Leuven, Belgium
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
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7
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Solteszova B, Halgasova N, Bukovska G. Interaction between phage BFK20 helicase gp41 and its host Brevibacterium flavum primase DnaG. Virus Res 2015; 196:150-6. [DOI: 10.1016/j.virusres.2014.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/12/2014] [Accepted: 11/17/2014] [Indexed: 11/24/2022]
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Wagemans J, Blasdel BG, Van den Bossche A, Uytterhoeven B, De Smet J, Paeshuyse J, Cenens W, Aertsen A, Uetz P, Delattre AS, Ceyssens PJ, Lavigne R. Functional elucidation of antibacterial phage ORFans targetingPseudomonas aeruginosa. Cell Microbiol 2014; 16:1822-35. [DOI: 10.1111/cmi.12330] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Jeroen Wagemans
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Bob G. Blasdel
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - An Van den Bossche
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Birgit Uytterhoeven
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Jeroen De Smet
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Jan Paeshuyse
- Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Minderbroedersstraat 10 - box 1030 3000 Leuven Belgium
| | - William Cenens
- Department of Microbial and Molecular Systems; Katholieke Universiteit Leuven; Kasteelpark Arenberg 22 - box 2457 3001 Leuven Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems; Katholieke Universiteit Leuven; Kasteelpark Arenberg 22 - box 2457 3001 Leuven Belgium
| | - Peter Uetz
- Centre for the Study of Biological Complexity; Virginia Commonwealth University; 1000 West Cary Street - room 333 Richmond VA 23284 USA
| | - Anne-Sophie Delattre
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Pieter-Jan Ceyssens
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
- Bacterial Diseases Division; Scientific Institute of Public Health (WIV-ISP); J. Wytsmanstraat 14 1050 Brussels Belgium
| | - Rob Lavigne
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
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Houot L, Fanni A, de Bentzmann S, Bordi C. A bacterial two-hybrid genome fragment library for deciphering regulatory networks of the opportunistic pathogen Pseudomonas aeruginosa. Microbiology (Reading) 2012; 158:1964-1971. [DOI: 10.1099/mic.0.057059-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Laetitia Houot
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255 CNRS – Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Adeline Fanni
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255 CNRS – Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Sophie de Bentzmann
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255 CNRS – Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Christophe Bordi
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255 CNRS – Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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Barret M, Egan F, Fargier E, Morrissey JP, O'Gara F. Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. MICROBIOLOGY-SGM 2011; 157:1726-1739. [PMID: 21474537 DOI: 10.1099/mic.0.048645-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacteria encode multiple protein secretion systems that are crucial for interaction with the environment and with hosts. In recent years, attention has focused on type VI secretion systems (T6SSs), which are specialized transporters widely encoded in Proteobacteria. The myriad of processes associated with these secretion systems could be explained by subclasses of T6SS, each involved in specialized functions. To assess diversity and predict function associated with different T6SSs, comparative genomic analysis of 34 Pseudomonas genomes was performed. This identified 70 T6SSs, with at least one locus in every strain, except for Pseudomonas stutzeri A1501. By comparing 11 core genes of the T6SS, it was possible to identify five main Pseudomonas phylogenetic clusters, with strains typically carrying T6SSs from more than one clade. In addition, most strains encode additional vgrG and hcp genes, which encode extracellular structural components of the secretion apparatus. Using a combination of phylogenetic and meta-analysis of transcriptome datasets it was possible to associate specific subsets of VgrG and Hcp proteins with each Pseudomonas T6SS clade. Moreover, a closer examination of the genomic context of vgrG genes in multiple strains highlights a number of additional genes associated with these regions. It is proposed that these genes may play a role in secretion or alternatively could be new T6S effectors.
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Affiliation(s)
- Matthieu Barret
- BIOMERIT Research Centre, Department of Microbiology, University College Cork, Cork, Ireland
| | - Frank Egan
- BIOMERIT Research Centre, Department of Microbiology, University College Cork, Cork, Ireland
| | - Emilie Fargier
- BIOMERIT Research Centre, Department of Microbiology, University College Cork, Cork, Ireland
| | - John P Morrissey
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, Department of Microbiology, University College Cork, Cork, Ireland
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11
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Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA. Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res 2011; 21:126-36. [PMID: 21149389 PMCID: PMC3012920 DOI: 10.1101/gr.111732.110] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 10/28/2010] [Indexed: 01/06/2023]
Abstract
Viruses may play an important role in the evolution of human microbial communities. Clustered regularly interspaced short palindromic repeats (CRISPRs) provide bacteria and archaea with adaptive immunity to previously encountered viruses. Little is known about CRISPR composition in members of human microbial communities, the relative rate of CRISPR locus change, or how CRISPR loci differ between the microbiota of different individuals. We collected saliva from four periodontally healthy human subjects over an 11- to 17-mo time period and analyzed CRISPR sequences with corresponding streptococcal repeats in order to improve our understanding of the predominant features of oral streptococcal adaptive immune repertoires. We analyzed a total of 6859 CRISPR bearing reads and 427,917 bacterial 16S rRNA gene sequences. We found a core (ranging from 7% to 22%) of shared CRISPR spacers that remained stable over time within each subject, but nearly a third of CRISPR spacers varied between time points. We document high spacer diversity within each subject, suggesting constant addition of new CRISPR spacers. No greater than 2% of CRISPR spacers were shared between subjects, suggesting that each individual was exposed to different virus populations. We detect changes in CRISPR spacer sequence diversity over time that may be attributable to locus diversification or to changes in streptococcal population structure, yet the composition of the populations within subjects remained relatively stable. The individual-specific and traceable character of CRISPR spacer complements could potentially open the way for expansion of the domain of personalized medicine to the oral microbiome, where lineages may be tracked as a function of health and other factors.
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Affiliation(s)
- David T Pride
- Department of Pathology, University of California, San Diego, La Jolla, California 92093, USA
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12
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Abstract
Pseudomonas species and their bacteriophages have been studied intensely since the beginning of the 20th century, due to their ubiquitous nature, and medical and ecological importance. Here, we summarize recent molecular research performed on Pseudomonas phages by reviewing findings on individual phage genera. While large phage collections are stored and characterized worldwide, the limits of their genomic diversity are becoming more and more apparent. Although this article emphasizes the biological background and molecular characteristics of these phages, special attention is given to emerging studies in coevolutionary and in therapeutic settings.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, bus 2462, B-3001 Leuven, Belgium
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13
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Roucourt B, Lavigne R. The role of interactions between phage and bacterial proteins within the infected cell: a diverse and puzzling interactome. Environ Microbiol 2009; 11:2789-805. [PMID: 19691505 DOI: 10.1111/j.1462-2920.2009.02029.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Interactions between bacteriophage proteins and bacterial proteins are important for efficient infection of the host cell. The phage proteins involved in these bacteriophage-host interactions are often produced immediately after infection. A survey of the available set of published bacteriophage-host interactions reveals the targeted host proteins are inhibited, activated or functionally redirected by the phage protein. These interactions protect the bacteriophage from bacterial defence mechanisms or adapt the host-cell metabolism to establish an efficient infection cycle. Regrettably, a large majority of bacteriophage early proteins lack any identified function. Recent research into the antibacterial potential of bacteriophage-host interactions indicates that phage early proteins seem to target a wide variety of processes in the host cell - many of them non-essential. Since a clear understanding of such interactions may become important for regulations involving phage therapy and in biotechnological applications, increased scientific emphasis on the biological elucidation of such proteins is warranted.
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Affiliation(s)
- Bart Roucourt
- Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21 box 2462, B-3001 Leuven, Belgium
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Roucourt B, Minnebo N, Augustijns P, Hertveldt K, Volckaert G, Lavigne R. Biochemical characterization of malate synthase G of P. aeruginosa. BMC BIOCHEMISTRY 2009; 10:20. [PMID: 19549344 PMCID: PMC2708195 DOI: 10.1186/1471-2091-10-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 06/24/2009] [Indexed: 11/10/2022]
Abstract
Background Malate synthase catalyzes the second step of the glyoxylate bypass, the condensation of acetyl coenzyme A and glyoxylate to form malate and coenzyme A (CoA). In several microorganisms, the glyoxylate bypass is of general importance to microbial pathogenesis. The predicted malate synthase G of Pseudomonas aeruginosa has also been implicated in virulence of this opportunistic pathogen. Results Here, we report the verification of the malate synthase activity of this predicted protein and its recombinant production in E. coli, purification and biochemical characterization. The malate synthase G of P. aeruginosa PAO1 has a temperature and pH optimum of 37.5°C and 8.5, respectively. Although displaying normal thermal stability, the enzyme was stable up to incubation at pH 11. The following kinetic parameters of P. aeruginosa PAO1 malate synthase G were obtained: Km glyoxylate (70 μM), Km acetyl CoA (12 μM) and Vmax (16.5 μmol/minutes/mg enzyme). In addition, deletion of the corresponding gene showed that it is a prerequisite for growth on acetate as sole carbon source. Conclusion The implication of the glyoxylate bypass in the pathology of various microorganisms makes malate synthase G an attractive new target for antibacterial therapy. The purification procedure and biochemical characterization assist in the development of antibacterial components directed against this target in P. aeruginosa.
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Affiliation(s)
- Bart Roucourt
- Department of Biosystems, Katholieke Universiteit Leuven, Belgium.
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