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Santiago-Rodriguez TM, Garoutte A, Adams E, Nasser W, Ross MC, La Reau A, Henseler Z, Ward T, Knights D, Petrosino JF, Hollister EB. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. Genes (Basel) 2020; 11:E1380. [PMID: 33233349 PMCID: PMC7700633 DOI: 10.3390/genes11111380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.
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Affiliation(s)
| | - Aaron Garoutte
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Emmase Adams
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Waleed Nasser
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alex La Reau
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Zachariah Henseler
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Tonya Ward
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Dan Knights
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph F. Petrosino
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily B. Hollister
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
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2
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Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Cantwell L, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Valladares O, Vardarajan B, Wang LS, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA. Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry 2020; 25:1859-1875. [PMID: 30108311 PMCID: PMC6375806 DOI: 10.1038/s41380-018-0112-7] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/01/2018] [Accepted: 05/14/2018] [Indexed: 12/21/2022]
Abstract
The Alzheimer's Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. We tested ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants. Sixteen single variants and 19 genes that met criteria for significant or suggestive associations after multiple-testing correction were evaluated for replication in four independent samples; three with whole exome sequencing (2,778 cases, 7,262 controls) and one with genome-wide genotyping imputed to the Haplotype Reference Consortium panel (9,343 cases, 11,527 controls). The top findings in the discovery sample were also followed-up in the ADSP whole-genome sequenced family-based dataset (197 members of 42 EA families and 501 members of 157 CH families). We identified novel and predicted functional genetic variants in genes previously associated with AD. We also detected associations in three novel genes: IGHG3 (p = 9.8 × 10-7), an immunoglobulin gene whose antibodies interact with β-amyloid, a long non-coding RNA AC099552.4 (p = 1.2 × 10-7), and a zinc-finger protein ZNF655 (gene-based p = 5.0 × 10-6). The latter two suggest an important role for transcriptional regulation in AD pathogenesis.
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Affiliation(s)
- Joshua C Bis
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
| | - Xueqiu Jian
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Yuning Chen
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William S Bush
- Case Western Reserve University, Cleveland Heights, OH, USA
| | - William J Salerno
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Lancour
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Yiyi Ma
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Alan E Renton
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Yi Zhao
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Liming Qu
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shahzad Ahmad
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - Najaf Amin
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Philippe Amouyel
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dominique Campion
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
- Department of Research, Centre Hospitalier du Rouvray, Sotteville-lès-, Rouen, France
| | - Laura Cantwell
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Camille Charbonnier
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Paul K Crane
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - L Adrienne Cupples
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Jean-François Dartigues
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
| | - Stéphanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
- Department of Neurology and Institute for Neurodegenerative Diseases, Bordeaux University Hospital, Memory Clinic, F-33000, Bordeaux, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, Direction de le Recherche Fondamentale, CEA, Evry, France
| | - Lucinda Fulton
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | | | | | - Richard A Gibbs
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alison Goate
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Grenier-Boley
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Seppo Helisalmi
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Daniel P Howrigan
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - M Arfan Ikram
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jan Konrad
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Amanda Kuzma
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Honghuang Lin
- Department of Medicine (Computational Biomedicine), Boston University School of Medicine, Boston, MA, USA
| | - Kari Mattila
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | - Donna M Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Waleed Nasser
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin Neale
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kwangsik Nho
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gaël Nicolas
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Devanshi Patel
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
- University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Bruce M Psaty
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Richard Redon
- Inserm, CNRS, Univ. Nantes, CHU Nantes, l'institut du thorax, Nantes, France
| | | | - Anne M Remes
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
- Unit of Clinical Neuroscience, Neurology, University of Oulu and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Chloe Sarnowski
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Helena Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Michael Schmidt
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | | | | | - Christophe Tzourio
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
| | | | | | - Otto Valladares
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Li-San Wang
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Weixin Wang
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ellen Wijsman
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Daniela Witten
- Department of Statistics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kim C Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaoling Zhang
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Celine Bellenguez
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Jean-Charles Lambert
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kathryn L Lunetta
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Anita L Destefano
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Josée Dupuis
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Sudha Seshadri
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Adam C Naj
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lindsay A Farrer
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA.
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA.
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3
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Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Cantwell L, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Valladares O, Vardarajan B, Wang LS, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA. Correction: Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry 2020; 25:1901-1903. [PMID: 31636380 PMCID: PMC7387240 DOI: 10.1038/s41380-019-0529-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A correction to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Joshua C. Bis
- 0000000122986657grid.34477.33Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA USA
| | - Xueqiu Jian
- 0000 0000 9206 2401grid.267308.8Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Brian W. Kunkle
- 0000 0004 1936 8606grid.26790.3aJohn P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL USA
| | - Yuning Chen
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Kara L. Hamilton-Nelson
- 0000 0004 1936 8606grid.26790.3aJohn P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL USA
| | - William S. Bush
- 0000 0001 2164 3847grid.67105.35Case Western Reserve University, Cleveland Heights, OH USA
| | - William J. Salerno
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Daniel Lancour
- 0000 0004 0367 5222grid.475010.7Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA USA
| | - Yiyi Ma
- 0000 0004 0367 5222grid.475010.7Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA USA
| | - Alan E. Renton
- 0000 0001 0670 2351grid.59734.3cDepartment of Neuroscience and Ronald M Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Edoardo Marcora
- 0000 0001 0670 2351grid.59734.3cDepartment of Neuroscience and Ronald M Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA ,0000 0001 0670 2351grid.59734.3cDepartment of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - John J. Farrell
- 0000 0004 0367 5222grid.475010.7Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA USA
| | - Yi Zhao
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Liming Qu
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Shahzad Ahmad
- 000000040459992Xgrid.5645.2Erasmus University Medical Center, Rotterdam, Netherlands
| | - Najaf Amin
- grid.457380.dInserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Philippe Amouyel
- grid.457380.dInserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France ,0000 0001 2159 9858grid.8970.6Institut Pasteur de Lille, Lille, France ,0000 0001 2242 6780grid.503422.2University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Gary W. Beecham
- 0000 0004 1936 8606grid.26790.3aJohn P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL USA
| | - Jennifer E. Below
- 0000 0004 1936 9916grid.412807.8Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN USA
| | - Dominique Campion
- 0000 0004 1785 9671grid.460771.3Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France ,0000 0004 1765 2814grid.477068.aDepartment of Research, Centre Hospitalier du Rouvray, Sotteville-lès-, Rouen, France
| | - Laura Cantwell
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Camille Charbonnier
- 0000 0004 1785 9671grid.460771.3Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Jaeyoon Chung
- 0000 0004 0367 5222grid.475010.7Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA USA
| | - Paul K. Crane
- 0000000122986657grid.34477.33Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA USA
| | - Carlos Cruchaga
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University, St. Louis, MO USA
| | - L. Adrienne Cupples
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA ,0000 0001 2293 4638grid.279885.9National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA USA
| | - Jean-François Dartigues
- 0000 0001 2106 639Xgrid.412041.2University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Stéphanie Debette
- 0000 0001 2106 639Xgrid.412041.2University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France ,0000 0004 0593 7118grid.42399.35Department of Neurology and Institute for Neurodegenerative Diseases, Bordeaux University Hospital, Memory Clinic, F-33000 Bordeaux, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, Direction de le Recherche Fondamentale, CEA, Evry, France
| | - Lucinda Fulton
- 0000 0001 2355 7002grid.4367.6McDonnell Genome Institute, Washington University, St. Louis, MO USA
| | | | | | - Richard A. Gibbs
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Alison Goate
- 0000 0001 0670 2351grid.59734.3cDepartment of Neuroscience and Ronald M Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY USA ,0000 0001 0670 2351grid.59734.3cDepartment of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Benjamin Grenier-Boley
- grid.457380.dInserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Namrata Gupta
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jonathan L. Haines
- 0000 0001 2164 3847grid.67105.35Case Western Reserve University, Cleveland Heights, OH USA
| | - Aki S. Havulinna
- 0000 0004 0410 2071grid.7737.4Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland ,0000 0001 1013 0499grid.14758.3fNational Institute for Health and Welfare, Helsinki, Finland
| | - Seppo Helisalmi
- 0000 0001 0726 2490grid.9668.1Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- 0000 0001 0726 2490grid.9668.1Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Daniel P. Howrigan
- grid.66859.34Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - M. Arfan Ikram
- 000000040459992Xgrid.5645.2Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jaakko Kaprio
- 0000 0004 0410 2071grid.7737.4Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jan Konrad
- 0000 0001 2355 7002grid.4367.6Department of Psychiatry, Washington University, St. Louis, MO USA
| | - Amanda Kuzma
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Eric S. Lander
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Mark Lathrop
- grid.411640.6McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Terho Lehtimäki
- 0000 0001 2314 6254grid.502801.eDepartment of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Honghuang Lin
- 0000 0004 0367 5222grid.475010.7Department of Medicine (Computational Biomedicine), Boston University School of Medicine, Boston, MA USA
| | - Kari Mattila
- 0000 0001 2314 6254grid.502801.eDepartment of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard Mayeux
- 0000000419368729grid.21729.3fColumbia University, New York, NY USA
| | - Donna M. Muzny
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Waleed Nasser
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Benjamin Neale
- grid.66859.34Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Kwangsik Nho
- 0000 0001 2287 3919grid.257413.6Indiana University School of Medicine, Indianapolis, IN USA
| | - Gaël Nicolas
- 0000 0004 1785 9671grid.460771.3Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Devanshi Patel
- 0000 0004 0367 5222grid.475010.7Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA USA
| | - Margaret A. Pericak-Vance
- 0000 0004 1936 8606grid.26790.3aJohn P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL USA
| | - Markus Perola
- 0000 0004 0410 2071grid.7737.4Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland ,0000 0001 1013 0499grid.14758.3fNational Institute for Health and Welfare, Helsinki, Finland ,0000 0001 0943 7661grid.10939.32University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Bruce M. Psaty
- 0000000122986657grid.34477.33Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA USA ,0000000122986657grid.34477.33Department of Epidemiology, University of Washington, Seattle, WA USA ,0000000122986657grid.34477.33Department of Health Services, University of Washington, Seattle, WA USA ,0000 0004 0615 7519grid.488833.cKaiser Permanente Washington Health Research Institute, Seattle, WA USA
| | - Olivier Quenez
- 0000 0004 1785 9671grid.460771.3Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Farid Rajabli
- 0000 0004 1936 8606grid.26790.3aJohn P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL USA
| | - Richard Redon
- 0000 0004 0472 0371grid.277151.7Inserm, CNRS, Univ. Nantes, CHU Nantes, l’institut du thorax, Nantes, France
| | - Christiane Reitz
- 0000000419368729grid.21729.3fColumbia University, New York, NY USA
| | - Anne M. Remes
- 0000 0001 0726 2490grid.9668.1Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland ,0000 0004 4685 4917grid.412326.0Unit of Clinical Neuroscience, Neurology, University of Oulu and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Veikko Salomaa
- 0000 0001 1013 0499grid.14758.3fNational Institute for Health and Welfare, Helsinki, Finland
| | - Chloe Sarnowski
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Helena Schmidt
- 0000 0000 8988 2476grid.11598.34Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Michael Schmidt
- 0000 0004 1936 8606grid.26790.3aJohn P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL USA
| | - Reinhold Schmidt
- 0000 0000 8988 2476grid.11598.34Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Hilkka Soininen
- 0000 0001 0726 2490grid.9668.1Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland ,0000 0004 0628 207Xgrid.410705.7Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Timothy A. Thornton
- 0000000122986657grid.34477.33Department of Statistics, University of Washington, Seattle, WA USA
| | - Giuseppe Tosto
- 0000000419368729grid.21729.3fColumbia University, New York, NY USA
| | - Christophe Tzourio
- 0000 0001 2106 639Xgrid.412041.2University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Sven J. van der Lee
- 000000040459992Xgrid.5645.2Erasmus University Medical Center, Rotterdam, Netherlands
| | - Cornelia M. van Duijn
- 000000040459992Xgrid.5645.2Erasmus University Medical Center, Rotterdam, Netherlands
| | - Otto Valladares
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Badri Vardarajan
- 0000000419368729grid.21729.3fColumbia University, New York, NY USA
| | - Li-San Wang
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Weixin Wang
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Ellen Wijsman
- 0000000122986657grid.34477.33Department of Medicine (Medical Genetics), University of Washington, Seattle, WA USA ,0000000122986657grid.34477.33Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Richard K. Wilson
- 0000 0001 2355 7002grid.4367.6McDonnell Genome Institute, Washington University, St. Louis, MO USA
| | - Daniela Witten
- 0000000122986657grid.34477.33Department of Statistics, University of Washington, Seattle, WA USA ,0000000122986657grid.34477.33Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Kim C. Worley
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Xiaoling Zhang
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA ,0000 0004 0367 5222grid.475010.7Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA USA
| | | | - Celine Bellenguez
- grid.457380.dInserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Jean-Charles Lambert
- grid.457380.dInserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Mitja I. Kurki
- 0000 0004 0410 2071grid.7737.4Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland ,grid.66859.34Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Aarno Palotie
- 0000 0004 0410 2071grid.7737.4Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland ,grid.66859.34Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Mark Daly
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0410 2071grid.7737.4Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland ,0000 0004 0386 9924grid.32224.35Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Eric Boerwinkle
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA ,0000 0000 9206 2401grid.267308.8School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Kathryn L. Lunetta
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Anita L. Destefano
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA ,0000 0004 0367 5222grid.475010.7Departments of Neurology, Boston University School of Medicine, Boston, MA USA
| | - Josée Dupuis
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Eden R. Martin
- 0000 0004 1936 8606grid.26790.3aJohn P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL USA
| | - Gerard D. Schellenberg
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Sudha Seshadri
- 0000 0001 2293 4638grid.279885.9National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA USA ,0000 0004 0367 5222grid.475010.7Departments of Neurology, Boston University School of Medicine, Boston, MA USA ,0000 0001 0629 5880grid.267309.9Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX USA
| | - Adam C. Naj
- 0000 0004 1936 8972grid.25879.31University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - Myriam Fornage
- 0000 0000 9206 2401grid.267308.8Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX USA ,0000 0000 9206 2401grid.267308.8School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Lindsay A. Farrer
- 0000 0004 1936 7558grid.189504.1Departments of Biostatistics, Boston University School of Public Health, Boston, MA USA ,0000 0004 0367 5222grid.475010.7Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA USA ,0000 0004 0367 5222grid.475010.7Departments of Neurology, Boston University School of Medicine, Boston, MA USA ,0000 0004 1936 7558grid.189504.1Department of Epidemiology, Boston University School of Public Health, Boston, MA USA ,0000 0004 0367 5222grid.475010.7Department of Ophthalmology, Boston University School of Medicine, Boston, MA USA
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4
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Poutsiaka D, Stern L, Riquelme V, Hollister E, Cope J, Nasser W, Dinh D, Nassif J, Thorpe C, Kane A, McDermott L, Snydman D. Impact of Body Mass Index (BMI) on the Effect of a Lactobacillus Rhamnosus GG (LGG)/Bifidobacterium Animalis Subspecies Lactis BB-12 (BB-12) Combination on Gut Microbiota (P20-023-19). Curr Dev Nutr 2019. [DOI: 10.1093/cdn/nzz040.p20-023-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
This exploratory study builds upon an earlier study of probiotic supplementation1 to assess the effects of a probiotic combination (P) of LGG and BB-12 on human gut microbiota composition and function, and to uncover an association with BMI.
Methods
Healthy subjects ingested P for 21 days (n = 18, P group) or did not (n = 7, C group).
Fecal samples obtained at baseline (D_0) and after 21 days of supplementation (D_21) underwent 16S ribosomal RNA gene and shotgun metagenomics sequencing to characterize the bacterial and archaeal communities to the genus/species level and identify functional community genes.
Results
Following P ingestion, no global differences in microbiota community structure or relative gene abundance were detected. In targeted analyses, the abundances of LGG and BB-12 in the P group at D_21 increased in a statistically significant manner as the BMI decreased (Spearman correlation, P = 0.04 and P = 0.01, respectively). The relative abundance of LGG but not BB-12 appeared increased in P subjects at D_21 with BMI < 25 compared to BMI > 25 (P = 0.09). P group subjects with BMI < 25 demonstrated trends toward or statistically significant increases in the relative abundances of 5 genes involved with flagellar structure (KEGG orthologs K02422, P = 0.04; K03406, P = 0.06; K02407, P = 0.08; K02397, P = 0.08; K02396, P = 0.09) at D_21 compared to those with BMI > 25. No such differences were observed for the C group nor were there differences in relative gene abundance at D_0 in the P group with BMI < 25 vs BMI > 25.
Conclusions
We observed no global changes in the fecal microbial community structure or function with P ingestion in this sample of healthy persons. However, we did observe patterns suggestive of a potential link between BMI and the response of the gut microbiota to P. Although our results are based on a small number of subjects, they are in line with previous findings related to LGG supplementation and the expression of flagellar genes2. We agree with other recent reports that future studies would benefit from a detailed examination of the transcriptome, proteome and/or metabolome to better understand the potential impact of probiotics on the gut microbiota, and the mechanism of the effect of BMI.
Funding Sources
Pfizer Inc.
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5
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Latronico F, Nasser W, Puhakainen K, Ollgren J, Hyyryläinen HL, Beres SB, Lyytikäinen O, Jalava J, Musser JM, Vuopio J. Genomic Characteristics Behind the Spread of Bacteremic Group A Streptococcus Type emm89 in Finland, 2004-2014. J Infect Dis 2016; 214:1987-1995. [PMID: 27707808 PMCID: PMC5142090 DOI: 10.1093/infdis/jiw468] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/27/2016] [Indexed: 12/20/2022] Open
Abstract
Background. Many countries worldwide have reported increasing numbers of emm89 group A Streptococcus (GAS) infections during last decade. Pathogen genetic factors linked to this increase need assessment. Methods. We investigated epidemiological characteristics of emm89 GAS bacteremic infections, including 7-day and 30-day case-fatality rates, in Finland during 2004–2014 and linked them to whole-genome sequencing data obtained from corresponding strains. The Fisher exact test and exact logistic regression were used to compare differences between bacteremic infections due to emm89 GAS belonging to different genetic clades and subclades. Results. Out of 1928 cases of GAS bacteremic infection, 278 were caused by emm89 GAS. We identified 2 genetically distinct clades, arbitrarily designated clade 2 and clade 3. Both clades were present during 2004–2008, but clade 3 increased rapidly from 2009 onward. Six subclades (designated subclades A–F) were identified within clade 3, based on phylogenetic core genome analysis. The case-fatality rate differed significantly between subclades (P < .05), with subclade D having the highest 30-day estimated case-fatality rate (19% vs 3%–14%). Conclusions. A new emm89 clone, clade 3, emerged in 2009 and spread rapidly in Finland. Patients infected with certain subclades of clade 3 were significantly more likely to die. A specific polymerase chain reaction assay was developed to follow the spread of subclade D in 2015.
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Affiliation(s)
- Francesca Latronico
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki.,European Programme for Public Health Microbiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Waleed Nasser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Texas
| | - Kai Puhakainen
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki.,Department of Medical Microbiology and Immunology, University of Turku, Finland
| | - Jukka Ollgren
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki
| | | | - Stephen B Beres
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Texas
| | - Outi Lyytikäinen
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki
| | - Jari Jalava
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Texas
| | - Jaana Vuopio
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki.,Department of Medical Microbiology and Immunology, University of Turku, Finland
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6
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Abstract
The pectinolytic Dickeya spp. are Gram-negative bacteria causing severe disease in a wide range of plant species. Although the Dickeya genus was initially restricted to tropical and subtropical areas, two Dickeya species (D. dianthicola and D. solani) emerged recently in potato cultures in Europe. Soft-rot, the visible symptoms, is caused by plant cell wall degrading enzymes, mainly pectate lyases (Pels) that cleave the pectin polymer. However, an efficient colonization of the host requires many additional elements including early factors (eg, flagella, lipopolysaccharide, and exopolysaccharide) that allow adhesion of the bacteria and intermediate factors involved in adaptation to new growth conditions encountered in the host (eg, oxidative stress, iron starvation, and toxic compounds). To facilitate this adaptation, Dickeya have developed complex regulatory networks ensuring appropriate expression of virulence genes. This review presents recent advances in our understanding of the signals and genetic circuits impacting the expression of virulence determinants. Special attention is paid to integrated control of virulence functions by variations in the superhelical density of chromosomal DNA, and the global and specific regulators, making the regulation of Dickeya virulence an especially attractive model for those interested in relationships between the chromosomal dynamics and gene regulatory networks.
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Affiliation(s)
- S Reverchon
- Department of Biology, University of Lyon, INSA-Lyon, Villeurbanne, Lyon, France.
| | - G Muskhelisvili
- Department of Biology, University of Lyon, INSA-Lyon, Villeurbanne, Lyon, France
| | - W Nasser
- Department of Biology, University of Lyon, INSA-Lyon, Villeurbanne, Lyon, France
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7
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Novelli F, Lena AM, Panatta E, Nasser W, Shalom-Feuerstein R, Candi E, Melino G. Allele-specific silencing of EEC p63 mutant R304W restores p63 transcriptional activity. Cell Death Dis 2016; 7:e2227. [PMID: 27195674 PMCID: PMC4917656 DOI: 10.1038/cddis.2016.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 03/03/2016] [Accepted: 03/08/2016] [Indexed: 01/01/2023]
Abstract
EEC (ectrodactily-ectodermal dysplasia and cleft lip/palate) syndrome is a rare genetic disease, autosomal dominant inherited. It is part of the ectodermal dysplasia disorders caused by heterozygous mutations in TP63 gene. EEC patients present limb malformations, orofacial clefting, skin and skin's appendages defects, ocular abnormalities. The transcription factor p63, encoded by TP63, is a master gene for the commitment of ectodermal-derived tissues, being expressed in the apical ectodermal ridge is critical for vertebrate limb formation and, at a later stage, for skin and skin's appendages development. The ΔNp63α isoform is predominantly expressed in epithelial cells and it is indispensable for preserving the self-renewal capacity of adult stem cells and to engage specific epithelial differentiation programs. Small interfering RNA (siRNA) offers a potential therapy approach for EEC patients by selectively silencing the mutant allele. Here, using a systemic screening based on a dual-luciferase reported gene assay, we have successfully identified specific siRNAs for repressing the EEC-causing p63 mutant, R304W. Upon siRNA treatment, we were able to restore ΔNp63-WT allele transcriptional function in induced pluripotent stem cells that were derived from EEC patient biopsy. This study demonstrates that siRNAs approach is promising and, may pave the way for curing/delaying major symptoms, such as cornea degeneration and skin erosions in young EEC patients.
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Affiliation(s)
- F Novelli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - A M Lena
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - E Panatta
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - W Nasser
- Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - R Shalom-Feuerstein
- Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - E Candi
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - G Melino
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy.,Medical Research Council, Toxicology Unit, Leicester University, Hodgkin Building, Leicester, UK
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8
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Zhu L, Olsen RJ, Nasser W, Beres SB, Vuopio J, Kristinsson KG, Gottfredsson M, Porter AR, DeLeo FR, Musser JM. A molecular trigger for intercontinental epidemics of group A Streptococcus. J Clin Invest 2015; 125:3545-59. [PMID: 26258415 DOI: 10.1172/jci82478] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/02/2015] [Indexed: 01/01/2023] Open
Abstract
The identification of the molecular events responsible for strain emergence, enhanced virulence, and epidemicity has been a long-pursued goal in infectious diseases research. A recent analysis of 3,615 genomes of serotype M1 group A Streptococcus strains (the so-called "flesh-eating" bacterium) identified a recombination event that coincides with the global M1 pandemic beginning in the early 1980s. Here, we have shown that the allelic variation that results from this recombination event, which replaces the chromosomal region encoding secreted NADase and streptolysin O, is the key driver of increased toxin production and enhanced infection severity of the M1 pandemic strains. Using isoallelic mutant strains, we found that 3 polymorphisms in this toxin gene region increase resistance to killing by human polymorphonuclear leukocytes, increase bacterial proliferation, and increase virulence in animal models of pharyngitis and necrotizing fasciitis. Genome sequencing of an additional 1,125 streptococcal strains and virulence studies revealed that a highly similar recombinational replacement event underlies an ongoing intercontinental epidemic of serotype M89 group A Streptococcus infections. By identifying the molecular changes that enhance upper respiratory tract fitness, increased resistance to innate immunity, and increased tissue destruction, we describe a mechanism that underpins epidemic streptococcal infections, which have affected many millions of people.
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9
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Abou Abbas L, Salameh P, Nasser W, Nasser Z, Godin I. Obesity and symptoms of depression among adults in selected countries of the Middle East: a systematic review and meta-analysis. Clin Obes 2015; 5:2-11. [PMID: 25504829 DOI: 10.1111/cob.12082] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/28/2014] [Accepted: 10/15/2014] [Indexed: 01/22/2023]
Abstract
Although obesity has been widely recognized for its consequences on physical health, its psychological burden in the adult populations in the Middle East remains unclear. This meta-analysis synthesized data from observational studies to investigate the association between obesity and depression among adult populations in Middle Eastern countries. Five bibliographical electronic databases were searched for studies published up to April 2014. Pooled meta-analytic estimates were derived using the random-effect models. Three case-control studies and five cross-sectional studies were identified. Meta-analysis showed significant positive associations between obesity and depression across study designs, with an overall effect of odds ratio 1.27 (95% confidence interval 1.11-1.44). The association between obesity and depression was more marked in women than men although that difference was not statistically significant. Other subgroup analysis showed that none of the potential factors including the assessment for obesity or depression, confounder control and study quality had a modification effect on the studied association. Meta-analysis of eight observational studies from five countries in the Middle East suggests an evidence of a positive association between obesity and depression among adult populations, which appeared to be more marked among women. Future research should examine the causal pathways between obesity and depression.
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Affiliation(s)
- L Abou Abbas
- School of Public Health, Free University of Brussels, Brussels, Belgium; Clinical and Epidemiological Research Laboratory (LCER), Doctoral School of Sciences and Technology, Lebanese University, Beirut, Lebanon
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10
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Nasser W, Santhanam B, Miranda ER, Parikh A, Juneja K, Rot G, Dinh C, Chen R, Zupan B, Shaulsky G, Kuspa A. Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Curr Biol 2013; 23:862-72. [PMID: 23664307 DOI: 10.1016/j.cub.2013.04.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/12/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Amoebae and bacteria interact within predator-prey and host-pathogen relationships, but the general response of amoeba to bacteria is not well understood. The amoeba Dictyostelium discoideum feeds on, and is colonized by, diverse bacterial species, including Gram-positive [Gram(+)] and Gram-negative [Gram(-)] bacteria, two major groups of bacteria that differ in structure and macromolecular composition. RESULTS Transcriptional profiling of D. discoideum revealed sets of genes whose expression is enriched in amoebae interacting with different species of bacteria, including sets that appear specific to amoebae interacting with Gram(+) or with Gram(-) bacteria. In a genetic screen utilizing the growth of mutant amoebae on a variety of bacteria as a phenotypic readout, we identified amoebal genes that are only required for growth on Gram(+) bacteria, including one that encodes the cell-surface protein gp130, as well as several genes that are only required for growth on Gram(-) bacteria, including one that encodes a putative lysozyme, AlyL. These genes are required for parts of the transcriptional response of wild-type amoebae, and this allowed their classification into potential response pathways. CONCLUSIONS We have defined genes that are critical for amoebal survival during feeding on Gram(+), or Gram(-), bacteria that we propose form part of a regulatory network that allows D. discoideum to elicit specific cellular responses to different species of bacteria in order to optimize survival.
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Affiliation(s)
- Waleed Nasser
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Sibai AM, Nasser W, Ammar W, Khalife MJ, Harb H, Fuleihan GEH. Hip fracture incidence in Lebanon: a national registry-based study with reference to standardized rates worldwide. Osteoporos Int 2011; 22:2499-506. [PMID: 21069293 DOI: 10.1007/s00198-010-1468-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 10/13/2010] [Indexed: 11/24/2022]
Abstract
UNLABELLED Crude incidence rates for hip fractures in individuals aged 50 and above in Lebanon were determined using data from the national hip fracture registry. For the years 2006-2008, crude rates varied between 164 and 188/100,000 for females and between 88 and 106 per 100,000 for males. Using the US 2000 white population as a reference, the calculated age-standardized rates were closest to rates derived for southern Europe. INTRODUCTION Owing to the demographic explosion, it is projected that the rates of hip fractures would increase the most in the Middle East and Asia. Few are the population-based studies investigating the incidence of hip fractures in the region. METHODS Using the Ministry of Health registry data, this population-based study evaluated the incidence of hip fractures in individuals aged 50 and above in Lebanon for the years 2006, 2007, and 2008. RESULTS Hip fracture crude incidence rates varied across the years between 164 and 188 per 100,000 for females and between 88 and 106 per 100,000 for males, with a female/male ratio of 1.6-2.1. The overall mean age (SD) for hip fractures was 75.9 (9.2), 76.8 (9.0), and 77.0 (9.9) years in females in 2006, 2007, and 2008, respectively, and 74.4 (11.6), 76.3 (10.3), and 74.0 (12.1) years in males, respectively. Using the US 2000 white population as a reference, the age-standardized rates were 370.4, 335.1, and 329.0 for females and 109.7, 134.1, and 128.7 for males, for the years 2006, 2007, and 2008, respectively. CONCLUSIONS The hip fracture age-standardized incidence rates in the Lebanese subjects receiving Ministry of Health coverage were lower than those found in northern Europe and the US and closest to rates derived for southern Europe.
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Affiliation(s)
- A M Sibai
- Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut (AUB), PO BOX: 11-0236, Riad El Solh, 1107 2020, Beirut, Lebanon.
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Dishmon DA, Khouzam RN, Hajjar A, Cross J, Khan M, Chishti W, Nasser W, Weber KT, Carbone LD. 263 HIP FRACTURES IN MALE VETERANS WITH CONGESTIVE HEART FAILURE. J Investig Med 2006. [DOI: 10.2310/6650.2005.x0008.262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Koomen JM, Zhao H, Li D, Nasser W, Hawke DH, Abbruzzese JL, Baggerly KA, Kobayashi R. Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting. Rapid Commun Mass Spectrom 2005; 19:1624-36. [PMID: 15915451 DOI: 10.1002/rcm.1963] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A peptide targeting method has been developed for diagnostic protein discovery, which combines proteolytic digestion of fractionated plasma proteins and liquid chromatography coupled to electrospray time-of-flight mass spectrometry (LC/ESI-TOFMS) profiling. Proteolysis prior to profiling overcomes molecular weight limitations and compensates for the poor sensitivity of matrix-assisted laser desorption/ionization (MALDI) protein profiling. LC/MS increases the peak capacity compared to crude fractionation techniques or single sample MALDI analysis. Differentially expressed peptides are targeted in the mass chromatograms using bioinformatic techniques and subsequently sequenced with MALDI tandem MS. In a model study comparing pancreatic cancer patients to controls, 74% of the peptide targets were successfully sequenced. This profiling method was superior to previous experiments using single sample MALDI analysis for protein profiling or proteolytic peptide profiling, because more potential protein markers were identified.
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Affiliation(s)
- John M Koomen
- Molecular Pathology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA
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Nasser W, Schneider R, Travers A, Muskhelishvili G. CRP modulates fis transcription by alternate formation of activating and repressing nucleoprotein complexes. J Biol Chem 2001; 276:17878-86. [PMID: 11279109 DOI: 10.1074/jbc.m100632200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA architectural proteins FIS and CRP are global regulators of transcription in Escherichia coli involved in the adjustment of cellular metabolism to varying growth conditions. We have previously demonstrated that FIS modulates the expression of the crp gene by functioning as its transcriptional repressor. Here we show that in turn, CRP is required to maintain the growth phase pattern of fis expression. We demonstrate the existence of a divergent promoter in the fis regulatory region, which reduces transcription of the fis promoter. In the absence of FIS, CRP activates fis transcription, thereby displacing the polymerase from the divergent promoter, whereas together FIS and CRP synergistically repress fis gene expression. These results provide evidence for a direct cross-talk between global regulators of cellular transcription during the growth phase. This cross-talk is manifested in alternate formation of functional nucleoprotein complexes exerting either activating or repressing effects on transcription.
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Affiliation(s)
- W Nasser
- Institut für Genetik und Mikrobiologie, Ludwig-Maximilians-Univesitaet, Maria-Ward-Strasse 1a, 80638 München, Germany
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Rouanet C, Nasser W. The PecM protein of the phytopathogenic bacterium Erwinia chrysanthemi, membrane topology and possible involvement in the efflux of the blue pigment indigoidine. J Mol Microbiol Biotechnol 2001; 3:309-18. [PMID: 11321588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
The pecS regulatory locus negatively modulates the expression of many virulence genes in Erwinia chrysanthemi. This locus consists of two genes, pecS and pecM, divergently transcribed. Previous studies have shown that PecS down-regulates the expression of both pecSand pecMgenes and that PecM is required for full PecS activity. Computer-aided hydropathy analysis of PecM predicted the presence of between 8 to 10 potential transmembrane segments. We analyzed the membrane topology of PecM using the beta-lactamase gene fusion system and obtained the following unique characteristics. PecM contains 10 membrane spanning segments, with both the amino and carboxyl termini located in the cytoplasmic side of the inner membrane. The fourth periplasmic loop, which has a relatively long hydrophilic domain containing 17 amino acid residues, may play an important role in PecM function. The topological model obtained for PecM can be applied to PecM homologues in other bacteria. Measurement of the extrusion of the blue pigment indigoidine by the E. chrysanthemi derivative isogenic mutants pecS, pecM and pecS-pecM revealed that PecM is required for complete efflux of the pigment. Its relation to other efflux systems and its potential physiological role are discussed.
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Affiliation(s)
- C Rouanet
- Unité de Microbiologie et Génétique, ERS-CNRS 2009, INSA, Villeurbanne, France.
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Kramer U, Spector S, Nasser W, Siomin V, Fried I, Constantini S. Surgical treatment of hypothalamic hamartoma and refractory seizures: a case report and review of the literature. Pediatr Neurosurg 2001; 34:40-2. [PMID: 11275785 DOI: 10.1159/000055990] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Refractory gelastic seizures are often associated with hypothalamic hamartoma (HH). Presurgical evaluation in such children often points to a distinct cortical region as the source of the seizures. A case of a child with HH and refractory seizures is presented. Video-EEG monitoring revealed a well-defined epileptic focus in the left frontal region. In accordance with the current understanding of the nature of hamartoma-related seizures, the hamartoma was resected. Follow-up evaluations revealed a marked improvement in seizure frequency and global functioning.
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Affiliation(s)
- U Kramer
- Child Developmental Center and Pediatric Neurology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Nasser W, Faelen M, Hugouvieux-Cotte-Pattat N, Reverchon S. Role of the nucleoid-associated protein H-NS in the synthesis of virulence factors in the phytopathogenic bacterium Erwinia chrysanthemi. Mol Plant Microbe Interact 2001; 14:10-20. [PMID: 11194867 DOI: 10.1094/mpmi.2001.14.1.10] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The ability of the enterobacterium Erwinia chrysanthemi to induce pathogenesis in plant tissue is strongly related to the massive production of plant-cell-wall-degrading enzymes (pectinases, cellulases, and proteases). Additional factors, including flagellar proteins and exopolysaccharides (EPS), also are required for the efficient colonization of plants. Production of these virulence factors, particularly pectate lyases, the main virulence determinant, is tightly regulated by environmental conditions. The possible involvement of the protein H-NS in this process was investigated. The E. chrysanthemi hns gene was cloned by complementation of an Escherichia coli hns mutation. Its nucleotide sequence contains a 405-bp open reading frame that codes for a protein with 85% identity to the E. coli H-NS protein. An E. chrysanthemi hns mutant was constructed by reverse genetics. This mutant displays a reduced growth rate and motility but an increased EPS synthesis and sensitivity toward high osmolarity. Furthermore, pectate lyase production is dramatically reduced in this mutant. The hns mutation acts on at least two conditions affecting pectate lyase synthesis: induction of pectate lyase synthesis at low temperatures (25 degrees C) is no longer observed in the hns mutant and induction of pectate lyase production occurs in the late stationary growth phase in the hns background, instead of in the late exponential growth phase as it does in the parental strain. Moreover, the E. chrysanthemi hns mutant displays reduced virulence on plants. Taken together, these data suggest that H-NS plays a crucial role in the expression of the virulence genes and in the pathogenicity of E. chrysanthemi.
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Affiliation(s)
- W Nasser
- Unité de Microbiologie et Génétique, ERS-CNRS 2009, INSA, Villeurbanne, France.
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Nasser W, Shevchik VE, Hugouvieux-Cotte-Pattat N. Analysis of three clustered polygalacturonase genes in Erwinia chrysanthemi 3937 revealed an anti-repressor function for the PecS regulator. Mol Microbiol 1999; 34:641-50. [PMID: 10564505 DOI: 10.1046/j.1365-2958.1999.01609.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Erwinia chrysanthemi 3937 secretes an arsenal of pectinolytic enzymes including several pectate lyases encoded by the pel genes. We characterized a novel cluster of pectinolytic genes consisting of the three adjacent genes pehV, pehW and pehX, whose products have polygalacturonase activity. The high similarity between the three genes suggests that they result from duplication of an ancestral gene. The transcription of pehV, pehW and pehX is dependent on several environmental conditions. They are induced by pectin catabolic products and this induction results from inactivation of the KdgR repressor which controls almost all the steps of pectin catabolism. The presence of calcium ions strongly reduced the transcription of the three peh genes. Their expression was also affected by growth phase, osmolarity, oxygen limitation and nitrogen starvation. In addition, the pehX transcription is affected by catabolite repression and controlled by the activator protein CRP. PecS, which was initially isolated as a repressor of virulence factors, acts as an activator of the peh transcription. We showed that the three regulators KdgR, PecS and CRP act by direct interaction with the promoter regions of the peh genes. Analysis of simultaneous binding of KdgR, PecS, CRP and RNA polymerase indicated that the activator effect of PecS results from a competition between PecS and KdgR for the occupation of overlapping binding sites. Thus, to activate peh transcription, PecS behaves as an anti-repressor against KdgR.
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Affiliation(s)
- W Nasser
- Unité Microbiologie et Génétique - composante INSA, UMR INSA-UCB-CNRS 5577, Bat 406, INSA, 20, Avenue Albert Einstein, F-69621 Villeurbanne Cedex, France
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Buchet A, Nasser W, Eichler K, Mandrand-Berthelot MA. Positive co-regulation of the Escherichia coli carnitine pathway cai and fix operons by CRP and the CaiF activator. Mol Microbiol 1999; 34:562-75. [PMID: 10564497 DOI: 10.1046/j.1365-2958.1999.01622.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Activation of the two divergent Escherichia coli cai and fix operons involved in anaerobic carnitine metabolism is co-dependent on the cyclic AMP receptor protein (CRP) and on CaiF, the specific carnitine-sensitive transcriptional regulator. CaiF was overproduced using a phage T7 system, purified on a heparin column and ran as a 15 kDa protein on SDS-PAGE. DNase I footprinting and interference experiments identified two sites, F1 and F2, with apparently comparable affinities for the binding of CaiF in the cai-fix regulatory region. These sites share a common perfect inverted repeat comprising two 11 bp half-sites separated by 13 bp, and centred at -70 and -127 from the fix transcription start site. They were found to overlap the two low-affinity binding sites, CRP2 and CRP3, determined previously for CRP. Gel shift assays and footprinting experiments suggest that CaiF and CRP bind co-operatively to the F1/CRP2 and F2/CRP3 sites of the intergenic cai-fix region. Moreover, they appeared to serve the simultaneous binding of each other, giving rise to an original multiprotein CRP-CaiF complex enabling RNA polymerase recruitment and local DNA untwisting, at least at the fix promoter. Using random mutagenesis, two CaiF mutants impaired in transcription activation were isolated. The N-terminal A27V mutation affected the structural organization of the activator, whereas the central I62N mutation was suggested to interfere with DNA binding.
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Affiliation(s)
- A Buchet
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, CNRS UMR 5577, Institut National des Sciences Appliquées, Bâtiment 406, 20, avenue Albert Einstein, F-69621 Villeurbanne Cedex, France
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Rouanet C, Nomura K, Tsuyumu S, Nasser W. Regulation of pelD and pelE, encoding major alkaline pectate lyases in Erwinia chrysanthemi: involvement of the main transcriptional factors. J Bacteriol 1999; 181:5948-57. [PMID: 10498706 PMCID: PMC103621 DOI: 10.1128/jb.181.19.5948-5957.1999] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The main virulence factors of the phytopathogenic bacterium Erwinia chrysanthemi are pectinases which attack pectin, the major constituent of the plant cell wall. Of these enzymes, the alkaline isoenzyme named PelD in strain 3937 and PelE in strain EC16 has been described as being particularly important, based on virulence studies of plants. Expression of the pelD and pelE genes is tightly modulated by various regulators, including the KdgR repressor and the cyclic AMP-cyclic AMP receptor protein (CRP) activator complex. The use of a lacZ reporter gene allowed us to quantify the repression of E. chrysanthemi 3937 pelD expression exerted by PecS, another repressor of pectinase synthesis. In vitro DNA-protein interaction experiments, centered on the pelD and pelE wild-type or pelE mutated promoter regions, allowed us to define precisely the sequences involved in the binding of these three regulators and of RNA polymerase (RNAP). These studies revealed an unusual binding of the KdgR repressor and suggested the presence of a UP (upstream) element in the pelD and pelE genes. Investigation of the simultaneous binding of CRP, KdgR, PecS, and the RNAP to the regulatory region of the pelD and pelE genes showed that (i) CRP and RNAP bind cooperatively, (ii) PecS partially inhibits binding of the CRP activator and of the CRP-RNAP complex, and (iii) KdgR stabilizes the binding of PecS and prevents transcriptional initiation by RNAP. Taken together, our data suggest that PecS attenuates pelD and pelE expression rather than acting as a true repressor like KdgR. Overall, control of the pelD and pelE genes of E. chrysanthemi appears to be both complex and novel.
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Affiliation(s)
- C Rouanet
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, CNRS-UMR 5577, 69621 Villeurbanne Cedex, France
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Nomura K, Nasser W, Tsuyumu S. Self-regulation of pir, a regulatory protein responsible for hyperinduction of pectate lyase in Erwinia chrysanthemi EC16. Mol Plant Microbe Interact 1999; 12:385-390. [PMID: 10226371 DOI: 10.1094/mpmi.1999.12.5.385] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Previously, we have cloned and characterized the pir (plant inducible regulator) gene, which is responsible for hyperinduction of the synthesis of an isozyme of pectate lyase (PLe) in Erwinia chrysanthemi EC16 in the presence of potato extract and sodium polypectate (NaPP). The Pir protein purified from Escherichia coli overexpressing pir is able to bind to the promoter region of pir as a dimer. Self-regulation of pir by its own translational product (Pir) was suggested from the findings that Pir binds at the promoter region of pir and that the hyperinduction of the pirlux construct in response to plant extract was observed only in pir+ but not in pir mutant EC16. Thus, hyperinduction of PLe was thought to be mainly due to overproduction of Pir. On the other hand, KdgR and PecS, which have been reported to be the major regulatory proteins for the synthesis of pectic enzymes, did not bind to the promoter region of pir. Thus, the regulation of Pir synthesis seems to be independent of KdgR and PecS. Also, its expression was insensitive to catabolite repression as predicted from failure of cyclic AMP (cAMP)-CRP (cAMP recognizing protein) to bind at the pir promoter region.
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Affiliation(s)
- K Nomura
- Faculty of Agriculture, Shizuoka University, Japan
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Nomura K, Nasser W, Kawagishi H, Tsuyumu S. The pir gene of Erwinia chrysanthemi EC16 regulates hyperinduction of pectate lyase virulence genes in response to plant signals. Proc Natl Acad Sci U S A 1998; 95:14034-9. [PMID: 9826648 PMCID: PMC24321 DOI: 10.1073/pnas.95.24.14034] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The plant pathogenic bacterium Erwinia chrysanthemi secretes pectate lyase proteins that are important virulence factors attacking the cell walls of plant hosts. Bacterial production of these enzymes is induced by the substrate polypectate-Na (NaPP) and further stimulated by the presence of plant extracts. The bacterial regulator responsible for induction by plant extracts was identified and purified by using a DNA-binding assay with the promoter region of pelE that encodes a major pectate lyase. A novel bacterial protein, called Pir, was isolated that produced a specific gel shift of the pelE promoter DNA, and the corresponding pir gene was cloned and sequenced. The Pir protein contains 272 amino acids with a molecular mass of 30 kDa and appears to function as a dimer. A homology search indicates that Pir belongs to the IclR family of transcriptional regulators. Pir bound to a 35-bp DNA sequence in the promoter region of pelE. This site overlaps that of a previously described negative regulator, KdgR. Gel shift experiments showed that the binding of either Pir or KdgR interfered with binding of the other protein.
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Affiliation(s)
- K Nomura
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Shizuoka 422-8529 Japan
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Castillo A, Nasser W, Condemine G, Reverchon S. The PecT repressor interacts with regulatory regions of pectate lyase genes in Erwinia chrysanthemi. Biochim Biophys Acta 1998; 1442:148-60. [PMID: 9804934 DOI: 10.1016/s0167-4781(98)00158-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Erwinia chrysanthemi is a broad host range phytopathogenic enterobacterium responsible for soft-rot disease of many plant species. The pecT gene encodes a repressor that negatively regulates the expression of virulence factors, such as pectinases, motility or exopolysaccharide synthesis. The cloned pecT gene was overexpressed using a phage T7 system. The purification of PecT involved the use of a TSK-heparin column and delivered the PecT protein that was purified to near homogeneity. The purified repressor displayed a 34 kDa apparent molecular mass. Gel-filtration experiments revealed that the PecT protein is a dimer. Band-shift assays demonstrated that the tetramer of the PecT protein could specifically bind in vitro to the regulatory regions of the pectate lyase genes with variable affinities. In addition, we demonstrated that PecT represses its own synthesis by interacting independently with two 200 bp regions, R1 and R2, located from -382 to -632 and -17 to -234, respectively, from the distal P1 promoter and from -465 to -715 and -100 to -317 from the P2 proximal promoter. We propose a model that explains the regulation exerted by PecT on its target genes and that integrates the phenotype obtained with a PecT overproducing pec-1 mutant or a pecT mutant.
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Affiliation(s)
- A Castillo
- Laboratoire de Génétique Moléculaire des Microorganismes, CNRS UMR 5577 INSA, Bat 406, 20 Avenue Albert Einstein, 69621 Villeurbanne, France
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Nasser W, Bouillant ML, Salmond G, Reverchon S. Characterization of the Erwinia chrysanthemi expI-expR locus directing the synthesis of two N-acyl-homoserine lactone signal molecules. Mol Microbiol 1998; 29:1391-405. [PMID: 9781877 DOI: 10.1046/j.1365-2958.1998.01022.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The plant pathogen Erwinia chrysanthemi produces three acyl-homoserine lactones (acyl-HSLs). One has been identified as N-(3-oxohexanoyl)-homoserine lactone (OHHL), and the two others were supposed to be N (hexanoyl)-homoserine lactone (HHL) and N-(decanoyl)-homoserine lactone (DHL). The genes for a quorum-sensing signal generator (expI) and a response regulator (expR) were cloned. These genes are convergently transcribed and display high similarity to the expI-expR genes of Erwinia carotovora. ExpI is responsible for both OHHL and HHL production. Inactivation of expl had little effect on pectinase synthesis in E. chrysanthemi, as expression of only two of the pectate lyase genes, pelA and pelB, was decreased. E. chrysanthemi expR mutants still produced acyl-HSL and pectinases. However, gel shift and DNAse I footprinting experiments showed that the purified E. chrysanthemi ExpR protein binds specifically to the promoter regions of the five major pel genes. Addition of OHHL modified the ExpR-DNA bandshift profiles, indicating that ExpR interacts with OHHL and binds to DNA in different ways, depending on the OHHL concentration. Localization of the ExpR binding sites just upstream of promoter regions suggests that ExpR functions as an activator of pel expression in the presence of OHHL. The absence of a phenotype in expR mutants strongly suggests that at least an additional interchangeable ExpR homologue exists in E. chrysanthemi. Finally, transcription of expI::uidA and expR::uidA fusions is dependent on the population density, suggesting the existence of a quorum-sensing hierarchy in E. chrysanthemi. These results suggest that the expI-expR locus is part of a complex autoregulatory system that controls quorum sensing in E. chrysanthemi.
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Affiliation(s)
- W Nasser
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, UMR-CNRS 5577, INSA, Villeurbanne, France.
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Reverchon S, Bouillant ML, Salmond G, Nasser W. Integration of the quorum-sensing system in the regulatory networks controlling virulence factor synthesis in Erwinia chrysanthemi. Mol Microbiol 1998; 29:1407-18. [PMID: 9781878 DOI: 10.1046/j.1365-2958.1998.01023.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The expI-expR locus drives a quorum-sensing system in the phytopathogenic bacterium, Erwinia chrysanthemi. Purified ExpR, an N-acyl homoserine lactone-responsive regulatory protein, binds to the promoter/operator region of the expI and expR genes. DNase I footprinting experiments showed that ExpR protects the regions between -66 and -40 from the P1 transcription initiation site of expl and between -54 and -18 from the expR transcription initiation site P1. The protected region overlaps the two expR promoters, P1 and P2, suggesting that ExpR exerts a negative control on its own gene expression. This assertion is reinforced by the fact that the addition of OHHL dissociates the ExpR-expR DNA complex. In contrast, the location of the ExpR binding site on the expI gene suggests an activator function, as reported for the pel genes. Moreover, ExpR is able to induce DNA bending. In vivo and in vitro studies revealed that CRP functions as an activator of expR expression, but as a repressor of expI transcription. A second level of control of expR and expI occurs through the PecS repressor, a regulator of pectinase synthesis. PecS represses expI expression, while ExpR activates pecS transcription, suggesting the existence of a mutual control between pecS and the expI-expR system in E. chrysanthemi. Regulation of pectinase synthesis in soft rot Erwinia appears to be a complex network of multiple cross-acting regulatory elements. A model that integrates these regulatory elements is proposed.
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Affiliation(s)
- S Reverchon
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, UMR-CNRS 5577, INSA, Villeurbanne, France.
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Abstract
The main virulence factors of the phytopathogenic bacteria Erwinia chrysanthemi are pectinases that cleave pectin, a major constituent of the plant cell wall. The cyclic AMP receptor protein (CRP) was identified as the main activator of the pectinolysis genes. Gel shift and DNase I footprinting experiments showed that the purified E. chrysanthemi CRP protein binds specifically to the promoter regions of seven pectinolysis genes (pelB, pelC, pelD, pelE, ogl, kduI and kdgT) whose expression is positively regulated in vivo by CRP. In contrast, no interaction was observed between CRP and the promoter-operator region of pelA, whose expression is negatively regulated in vivo by CRP. Primer extension experiments demonstrated that each of the pelB, pelC, pelE and kduI genes is expressed from a unique sigma70 promoter, whereas ogl and kdgT possess three and two functional promoters respectively. The position of the CRP binding site relative to the transcription start site suggests that CRP acts as a primary activator at the pelB (via the CRP binding site 1), pelC, pelE, pelD, kdgTP1 and oglP2 promoters. In contrast, transcription at the kduI, oglP1 promoters seems to require another transcriptional activator in synergy with CRP. Investigation of the simultaneous binding of CRP and KdgR, the main repressor of pectinolysis genes, to the regulatory regions of pelB, pelC, pelD, pelE, ogl, kduI and kdgT genes showed that binding of KdgR is preferential and exclusive in the case of ogl and kdgT, whereas the binding of these two regulators is independent in the case of pelB, pelC, pelD, pelE and kduI. Taken together, our data suggest that the antagonistic effects of CRP and KdgR on the expression of the pectinolysis genes occur by different mechanisms, including direct competition between the two regulators or between the repressor and RNA polymerase for the occupation of a common DNA region on the target genes.
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Affiliation(s)
- W Nasser
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, CNRS UMR 5577, Villeurbanne, France
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Praillet T, Reverchon S, Robert-Baudouy J, Nasser W. The PecM protein is necessary for the DNA-binding capacity of the PecS repressor, one of the regulators of virulence-factor synthesis in Erwinia chrysanthemi. FEMS Microbiol Lett 1997; 154:265-70. [PMID: 9311123 DOI: 10.1111/j.1574-6968.1997.tb12654.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The pecS regulatory locus is responsible for the down-expression of many virulence genes in Erwinia chrysanthemi. This locus consists of two genes, pecS and pecM, divergently transcribed. Genetic evidence indicates that the PecM protein modulates the regulatory activity of PecS. Purification and characterization of PecS, expressed either from E. coli, from the wild-type E. chrysanthemi strain or from a pecM mutant, showed that the PecS protein produced in these three genetic backgrounds displays the same biochemical properties. Band-shift assay analysis with the three PecS isoforms confirmed the involvement of the PecM protein in modulating the PecS DNA-binding capacity. Moreover, determination of the Kdapp for operator regions of the PecS protein, produced either by the wild-type E. chrysanthemi or by E. coli, reveals similar affinities. Thus, in E. coli, there is likely to be at least one other PecM-like protein able to cross-react with the E. chrysanthemi PecS protein.
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Affiliation(s)
- T Praillet
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, CNRS UMR 5577, INSA Lyon, France.
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Reverchon S, Expert D, Robert-Baudouy J, Nasser W. The cyclic AMP receptor protein is the main activator of pectinolysis genes in Erwinia chrysanthemi. J Bacteriol 1997; 179:3500-8. [PMID: 9171393 PMCID: PMC179141 DOI: 10.1128/jb.179.11.3500-3508.1997] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The main virulence factors of the phytopathogenic bacterium Erwinia chrysanthemi are pectinases that cleave pectin, a major constituent of the plant cell wall. Although physiological studies suggested that pectinase production in Erwinia species is subjected to catabolite repression, the direct implication of the cyclic AMP receptor protein (CRP) in this regulation has never been demonstrated. To investigate the role of CRP in pectin catabolism, we cloned the E. chrysanthemi crp gene by complementation of an Escherichia coli crp mutation and then constructed E. chrysanthemi crp mutants by reverse genetics. The carbohydrate fermentation phenotype of the E. chrysanthemi crp mutants is similar to that of an E. coli crp mutant. Furthermore, these mutants are unable to grow on pectin or polygalacturonate as the sole carbon source. Analysis of the nucleotide sequence of the E. chrysanthemi crp gene revealed the presence of a 630-bp open reading frame (ORF) that codes for a protein highly similar to the CRP of E. coli. Using a crp::uidA transcriptional fusion, we demonstrated that the E. chrysanthemi CRP represses its own expression, probably via a mechanism similar to that described for the E. coli crp gene. Moreover, in the E. chrysanthemi crp mutants, expression of pectinase genes (pemA, pelB, pelC, pelD, and pelE) and of genes of the intracellular part of the pectin degradation pathway (ogl, kduI, and kdgT), which are important for inducer formation and transport, is dramatically reduced in induced conditions. In contrast, expression of pelA, which encodes a pectate lyase important for E. chrysanthemi pathogenicity, seems to be negatively regulated by CRP. The E. chrysanthemi crp mutants have greatly decreased maceration capacity in potato tubers, chicory leaves, and celery petioles as well as highly diminished virulence on saintpaulia plants. These findings demonstrate that CRP plays a crucial role in expression of the pectinolysis genes and in the pathogenicity of E. chrysanthemi.
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Affiliation(s)
- S Reverchon
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, CNRS UMR 5577, INSA Bat 406, Villeurbanne, France
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Abstract
The Erwinia chrysanthemi pecS mutant displays constitutive production of virulence factors, such as pectinases or cellulases. Complementation of the pecS mutation can be obtained in the presence of the pecS wild-type gene on a low-copy-number plasmid. Moreover, the resulting plasmid decreases the expression of a pecS::uidA chromosomal fusion, indicating the existence of an autoregulation mechanism. This negative autoregulation was confirmed and quantified by analysis of the pecS transcripts using primer-extension experiments. Band-shift assays and DNase I footprinting experiments demonstrated that the PecS protein could bind to the intergenic regulatory region, located between the pecS and pecM genes, with a relatively high affinity (apparent dissociation constant (K'[d]) close to 4nM). These PecS-binding sites overlap the pecS and pecM promoters. The comparison of these new PecS-binding sites with those previously characterized on the target genes confirms the absence of a consensus. This observation was in accordance with the results of the missing-contact experiments performed on the pecS-pecM intergenic regulatory region and the celZ operator. Concurrently, we demonstrated that the PecS protein negatively controls the expression of the divergently transcribed pecM gene located 400bp upstream from the pecS gene. By following the efficiency of pecS autoregulation in a double E. chrysanthemi pecM-pecS mutant, we established that the PecM protein potentiates PecS activity in vivo.
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Affiliation(s)
- T Praillet
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, CNRS-UMR 5577, INSA Bâtiment 406, Villeurbanne, France
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Tardy F, Nasser W, Robert-Baudouy J, Hugouvieux-Cotte-Pattat N. Comparative analysis of the five major Erwinia chrysanthemi pectate lyases: enzyme characteristics and potential inhibitors. J Bacteriol 1997; 179:2503-11. [PMID: 9098045 PMCID: PMC178996 DOI: 10.1128/jb.179.8.2503-2511.1997] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In Erwinia chrysanthemi 3937, pectate lyase activity mainly results from the cumulative action of five major isoenzymes, PelA to PelE. Comparison of their amino acid sequences revealed two families, PelB-C and PelA-D-E. Molecular cloning permitted expression of the different pel genes in Escherichia coli and the isolation of each Pel independently from the other isoenzymes. We used similar experimental conditions to overproduce and purify the five Pels in a one-step chromatography method. We analyzed some of the basic enzymatic properties of these five isoenzymes. PelA has a low specific activity compared to the other four enzymes. PelB and PelC have a high affinity for their substrate: about 10-fold higher than the enzymes of the PelA-D-E group. The optimum pH is more alkaline for PelB and PelC (about 9.2) than for PelA, PelD, and PelE (from 8 to 8.8). Below pH 7, activity was negligible for PelB and PelC, while PelA, PelD, and PelE retained 25 to 30% of their activities. The temperature optima were determined to be 50 degrees C for PelD and PelE, 55 degrees C for PelA, and 60 degrees C for PelB and PelC. Enzymes of the PelB-C group are more stable than those of the PelA-D-E group. Use of substrates presenting various degrees of methylation revealed that PelA, PelD, and PelE are active only for very low levels of methylation, while PelB and PelC are more active on partially methylated pectins (up to 22% for PelC and up to 45% for PelB). Pectate lyases have an absolute requirement for Ca2+ ions. For the five isoenzymes, maximal activity was obtained at a Ca2+ concentration of 0.1 mM. None of the tested cations (Ba2+, Co2+, Cu2+, Mg2+, Mn2+, Sr2+, Zn2+) can substitute for Ca2+. At a high concentration (1 mM), most of the divalent cations inhibited pectate lyase activity. In addition, we demonstrated that two compounds present in plant tissues, epicatechin and salicylic acid, inhibit the pectate lyases at a concentration of 0.2 mM.
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Affiliation(s)
- F Tardy
- Laboratoire de Génétique Moléculaire des Microorganismes, UMR-CNRS 5577, INSA, Villeurbanne, France
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Abstract
Erwinia chrysanthemi is an enterobacterium that causes various plant diseases. Its pathogenicity results from the secretion of pectinolytic enzymes responsible for the disorganization of the plant cell wall. The E. chrysanthemi strain 3937 produces two pectin methylesterases, at least seven pectate lyases, a polygalacturonase, and a pectin lyase. The extracellular degradation of the pectin leads to the formation of oligogalacturonides that are catabolized through an intracellular pathway. The pectinase genes are expressed from independent cistrons, and their transcription is favored by environmental conditions such as presence of pectin and plant extracts, stationary growth phase, low temperature, oxygen or iron limitation, and so on. Moreover, transcription of the pectin lyase gene responds to DNA-damaging agents. The differential expressions of individual pectinase genes presumably reflect their role during plant infection. The regulation of pel genes requires several regulatory systems, including the KdgR repressor, which mediates the induction of all the pectinolysis genes in the presence of pectin catabolites. KdgR also controls the genes necessary for pectinase secretion and other pectin-inducible genes not yet characterized. PecS, a cytoplasmic protein homologous to other transcriptional regulators, can bind in vitro to the regulatory regions of pectinase and cellulase genes. The PecT protein, a member of the LysR family of transcriptional regulators, represses the expression of some pectinase genes and also affects other metabolic pathways of the bacteria. Other proteins involved in global regulations, such as CRP or HNS, can bind to the regulatory regions of the pectinase genes and affect their transcription.
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Praillet T, Nasser W, Robert-Baudouy J, Reverchon S. Purification and functional characterization of PecS, a regulator of virulence-factor synthesis in Erwinia chrysanthemi. Mol Microbiol 1996; 20:391-402. [PMID: 8733237 DOI: 10.1111/j.1365-2958.1996.tb02626.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Erwinia chrysanthemi pecS gene encodes a repressor that negatively regulates the expression of virulence factors such as pectinases or cellulases. The cloned pecS gene was overexpressed using a phage T7 system. The purification of PecS involved DEAE-anion exchange and TSK-heparin columns and delivered the PecS protein that was purified to homogeneity. The purified repressor displayed an 18 kDa apparent molecular mass and an isoelectric point near to neutrality (pl = 6.5). Gel-filtration experiments revealed that the PecS protein is a dimer. Bandshift assays demonstrated that the PecS protein could specifically bind in vitro to the regulatory sites of the in vivo PecS-regulated genes. The interaction between the PecS protein and its DNA-binding site was characterized by a relatively low affinity (about 10(-8) M). DNase I footprintings revealed short protected sequences only with the most in vivo PecS-regulated genes. Alignment of these PecS-binding sites did not show a well-conserved consensus sequence. Immunoblotting demonstrated that the copy number of the PecS protein was approximately 50 dimers per cell. The low affinity of the PecS repressor for its DNA targets and the low cellular PecS content suggest the existence of E. chrysanthemi-specific factors able to potentiate PecS protein activity in vivo.
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Affiliation(s)
- T Praillet
- Laboratoire de Génétique Moléculaire des Microorganismes, CNRS-UMR 5577, Villeurbanne, France
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Didierjean L, Frendo P, Nasser W, Genot G, Marivet J, Burkard G. Heavy-metal-responsive genes in maize: identification and comparison of their expression upon various forms of abiotic stress. Planta 1996; 199:1-8. [PMID: 8680303 DOI: 10.1007/bf00196874] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
To identify genes involved in defense against heavy-metal stresses, a cDNA library originating from mercuric chloride-treated maize (Zea mays L. cv. INRA 258) leaves was constructed and analysed by differential screening using cDNAs derived from treated and untreated plants. Transcriptionally activated cDNA clones, designated CHEM (chemically-activated), were isolated and characterized. They represent various known proteins, such as glycine-rich proteins, pathogenesis-related proteins, chaperones and membrane proteins. The expression of the genes encoding these proteins was studied in maize subjected to other forms of abiotic stress. Expression of glycine-rich proteins was greatly enhanced by heat stress, and also stimulated by NaCl, polluted rainwater, wounding and cold stress. Pathogenesis-related proteins were strongly induced by ultraviolet light and to a lesser extent by NaCl, polluted rainwater and wounding. Heat-shock protein was mainly induced by heat and cold, and ubiquitin by wounding. Expression of the membrane channel protein was stimulated by heat stress, NaCl, polluted rainwater and ultraviolet-light irradiation.
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Affiliation(s)
- L Didierjean
- Institut de Biologie Moléculaire des Plantes, Strasbourg, France
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Moulard M, Condemine G, Nasser W, Robert-Baudouy J. Purification and characterization of the nuclease NucM of Erwinia chrysanthemi. Biochim Biophys Acta 1995; 1262:133-8. [PMID: 7599187 DOI: 10.1016/0167-4781(95)00061-k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The major periplasmic nuclease of Erwinia chrysanthemi strain 3937, NucM, has been purified near to homogeneity by a one step purification procedure, using chromatography on a sulfopropyl column. NucM cleaves randomly single and double-stranded DNA and RNA. It does not need divalent cations for its action, and is more active in low salt buffers. A serine and a histidine residue could be present in the catalytic site. Formation of disulfide bonds is necessary for NucM activity. NucM is probably synthesized as a reduced inactive polypeptide and becomes active in the periplasm once disulfide bonds are formed.
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Affiliation(s)
- M Moulard
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, URA CNRS 1486, Institut National des Sciences Appliquées, Villeurbanne, France
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Pickersgill R, Jenkins J, Harris G, Nasser W, Robert-Baudouy J. The structure of Bacillus subtilis pectate lyase in complex with calcium. Nat Struct Biol 1994; 1:717-23. [PMID: 7634076 DOI: 10.1038/nsb1094-717] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have solved the structure of the Bacillus subtilis pectate lyase (BsPel) in complex with calcium. The structure consists of a parallel beta-helix domain and a loop region. The alpha L-bounded beta-strand seen in BsPel is a new element of protein structure and its frequent occurrence suggests it is an important characteristic of the parallel beta-helix. A pronounced cleft is formed between the loops and the parallel beta-helix domain and we propose that this is the active site cleft. Calcium, essential for the activity of the enzyme, binds at the bottom of this cleft and an arginine residue close to the calcium, which is conserved across all pectin and pectate lyases, may be involved in catalysis.
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Affiliation(s)
- R Pickersgill
- Department of Protein Engineering, Institute of Food Research, Reading, UK
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Hugouvieux-Cotte-Pattat N, Nasser W, Robert-Baudouy J. Molecular characterization of the Erwinia chrysanthemi kdgK gene involved in pectin degradation. J Bacteriol 1994; 176:2386-92. [PMID: 8157608 PMCID: PMC205363 DOI: 10.1128/jb.176.8.2386-2392.1994] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The pathways of pectin and galacturonate catabolism in Erwinia chrysanthemi converge to form a common intermediate, 2-keto-3-deoxygluconate (KDG), which is phosphorylated by KDG kinase encoded by the kdgK gene. We cloned the kdgK gene of E. chrysanthemi 3937 by complementing an Escherichia coli kdgK mutation, using an RP4-derivative plasmid. One of the kdgK R-prime plasmids harbored a DNA insert of about 80 kb and carried the uxuA and uxuB genes involved in glucuronate catabolism and the celY gene coding for an E. chrysanthemi cellulase. The kdgK and celY genes were precisely located on this plasmid, and their respective transcriptional directions were determined. The nucleotide sequence of the kdgK region indicated that the kdgK reading frame is 981 bases long, corresponding to a protein of 329 amino acids with a molecular mass of 36,377 Da. Analysis of the deduced primary amino acid sequence showed that this enzyme is a new member of the PfkB family of carbohydrate kinases. Expression of kdgK is controlled by a negative regulatory gene, kdgR, which represses all the steps of pectin degradation. Near the putative promoter of the kdgK gene, we identified a putative KdgR-binding site and demonstrated that the KdgR protein specifically binds in vitro to this DNA region. The KdgR-KDG couple directly mediates the phenomenon of repression or induction. The KDG kinase, by limiting the intracellular inducer concentration, appears to be a key enzyme in induction of the whole catabolic pathway.
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Affiliation(s)
- N Hugouvieux-Cotte-Pattat
- Laboratoire de Généteique Moléculaire des Microorganismes, CNRS URA-1486, INSA de Lyon, Villeurbanne, France
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Abstract
Erwinia chrysanthemi mutants (designated as pecS) displaying derepressed pectate lyase and cellulase synthesis were isolated. In addition, the pecS mutation is responsible for production of an extracellular insoluble blue pigment whose synthesis is cryptic in the wild-type 3937 strain. Transduction analysis indicates that the phenotype is due to a single mutation located near the xyl marker on the strain 3937 chromosome. This mutation was complemented by an R-prime plasmid carrying the xyl and argG genes of E. chrysanthemi, suggesting that the pecS product acts in trans to modulate pectinase, cellulase and blue pigment production. Insertion mutagenesis of the cloned region and recombination of the corresponding mutations in the bacterial chromosome by marker exchange revealed the existence of two divergently transcribed genes, pecS and pecM, that are both involved in the pectate lyase and cellulase regulation. The nucleotide sequences of pecS and pecM were determined. The pecS gene encodes a 166 amino acid polypeptide that shows similarity to the MprA regulatory protein of Escherichia coli whereas the pecM gene encodes a 297 amino acid polypeptide that was shown to be an integral membrane protein. The possible functions of the PecS and PecM proteins derived from the mutant phenotype and sequence analysis are discussed in terms of signal transduction and transcription regulation.
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Affiliation(s)
- S Reverchon
- Laboratoire de Génétique Moléculaire des Microorganismes, CNRS-URA 1486, INSA Bâtiment 406, Villeurbanne, France
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Nasser W, Reverchon S, Condemine G, Robert-Baudouy J. Specific interactions of Erwinia chrysanthemi KdgR repressor with different operators of genes involved in pectinolysis. J Mol Biol 1994; 236:427-40. [PMID: 8107132 DOI: 10.1006/jmbi.1994.1155] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Erwinia chrysanthemi kdgR gene encodes a repressor that negatively regulates the expression of genes involved in pectinolysis and in pectinase secretion. The cloned kdgR gene was overexpressed in Escherichia coli by using a phage T7 system. Overproduced repressor was purified to homogeneity by two chromatographic steps. Gel retardation and DNase I protection experiments demonstrated the specific binding of the KdgR protein to the operators of pectinase genes (pelA, pelB, pelC, pelE), to the operator of genes involved in pectin catabolism (kdgT, ogl, kduI-kdgF) and to that of the outT gene involved in pectinase secretion. These interactions involved one (pelA, pelB, kduI-kdgF, outT) or several operator sites (pelC, pelE, ogl, kdgT) that generally overlap the promoter. Despite the presence of potential KdgR binding sites (KdgR-box) in the regulatory regions of four genes involved in pectin catabolism (kdgC, kduD, pem, kdgA) and in a pectinase secretion gene outC, no DNA-repressor complex could be observed by in vitro experiments. By using a missing contact experiment on the coding strand of ogl and pelE regulatory regions, a new KdgR-binding consensus was proposed. This new consensus, constituted by two half motifs (AATGAAAACT)N(NTCGATTTCTA), is well conserved in the operators which interact in vitro with the KdgR repressor. In contrast, this repressor-recognized motif is degenerated in the other operators that cannot interact in vitro with the repressor. These results suggest the existence of different regulation mechanisms mediated by the KdgR protein for the two classes of operators.
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Affiliation(s)
- W Nasser
- Laboratoire de Génétique Moléculaire des Microorganismes et des Interactions Cellulaires, URA CNRS 1486, Institut National des Sciences Appliqées, Villeurbanne, France
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Nasser W, Awadé AC, Reverchon S, Robert-Baudouy J. Pectate lyase from Bacillus subtilis: molecular characterization of the gene, and properties of the cloned enzyme. FEBS Lett 1993; 335:319-26. [PMID: 8262178 DOI: 10.1016/0014-5793(93)80410-v] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Pectate lyases (PL) initiate soft-rot diseases in plants by cleaving pectin which is the major component of the plant cell wall. The present paper reports the first cloning and characterization of a pectate lyase (pel) gene from the Bacillus genus. This gene was isolated from a Bacillus subtilis genomic library constructed in pUC18 as vector and Escherichia coli as host. By Southern hybridization this gene was shown to be present in a single copy in the B. subtilis genome. The nucleotide sequence of a 1.6 kb-pair HindIII restriction fragment, which confers pectate lyase activity to E. coli, indicated a 1,260 bp open reading frame encoding a 420 amino acid polypeptide which includes a 21 amino acid signal sequence. The 45,605 Da deduced protein displays homologies to PLs from Erwinia chrysanthemi. The B. subtilis PL cloned in E. coli was located in the periplasm. It was purified to homogeneity in a one-step procedure from the E. coli periplasmic fluid after overproduction using the pT7 system. Biochemical properties of the purified enzyme were similar to those found for the PL isolated from B. subtilis extracellular media.
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Affiliation(s)
- W Nasser
- Laboratoire de Génétique Moléculaire des Microorganismes, URA CNRS 1486, Villeurbanne, France
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Jenkins J, Nasser W, Scott M, Pickersgill R, Vignon JC, Robert-Baudouy J. Crystallization and preliminary X-ray studies of the pectate lyase from Bacillus subtilis. J Mol Biol 1992; 228:1255-8. [PMID: 1474589 DOI: 10.1016/0022-2836(92)90330-m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The pectate lyase (EC 4.2.2.9) from Bacillus subtilis has been crystallized. Crystals of form 1, grown by the hanging drop method using polyethylene glycol as precipitant, diffract to at least 2.4 A resolution. They belong to the spacegroup P2(1) with a = 132.9 A, b = 41.2 A, c = 156.8 A and beta = 114.9 degrees with probably four molecules in the asymmetric unit. A second crystal form grown from 2-methyl-2,4-pentandiol also belongs to the spacegroup P2(1) with a = 55.0 A, b = 88.1 A, c = 50.2 A and beta = 109.0 degrees. These crystals diffract to at least 2.0 A and have one molecule in the asymmetric unit. Both crystal forms are suitable for the determination of high-resolution structures.
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Affiliation(s)
- J Jenkins
- Department of Protein Engineering, AFRC Institute of Food Research, Reading, U.K
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Nasser W, Reverchon S, Robert-Baudouy J. Purification and functional characterization of the KdgR protein, a major repressor of pectinolysis genes of Erwinia chrysanthemi. Mol Microbiol 1992; 6:257-65. [PMID: 1545709 DOI: 10.1111/j.1365-2958.1992.tb02007.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The phytopathogenicity of the enterobacterium Erwinia chrysanthemi chiefly results from its capacity to degrade pectin, which is the major component of plant cell walls. This degradation requires the product of 12 genes which constitute independent transcriptional units. All these genes, including kdgT which encodes the 2-keto-3-deoxygluconate (KDG) transport system, are negatively regulated by the KdgR protein. The E. chrysanthemi kdgR gene was cloned into an expression vector and overexpressed in Escherichia coli. KdgR was then purified to homogeneity by two chromatographic steps as a dimer of approximately 62 kDa. Using gel retardation assays, we demonstrated that this purified repressor binds to the 25bp oligonucleotide (AAAAAAGAAACATTGTTTCATTTGT) present in the kdgT regulatory region. Dimethyl sulphate interference experiments revealed that the repressor interacts with four guanine bases and 10 adenine bases in the two strands of this KdgR box. KDG, an actual inducer of pectinolysis, releases the repressor from the operator complexes, whereas galacturonate, which is the precursor of the actual inducer, does not. These results suggest the existence of a specific interaction between KDG and KdgR protein. This study opens discussion on the relative affinity of the KdgR protein for the different operators of pectinolysis genes which are interpreted in terms of differential regulation.
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Affiliation(s)
- W Nasser
- Laboratoire de Génétique Moléculaire des Microorganismes, Institut National des Sciences Apliquées, Villeurbanne, France
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Abstract
Erwinia chrysanthemi is a phytopathogenic enterobacterium able to degrade the pectic fraction of plant cell walls. The kdgR negative regulatory gene controls all the genes involved in pectin catabolism, including the pel genes encoding pectate lyases. The E. chrysanthemi kdgR regulatory gene was subcloned in Escherichia coli where it was shown to be functional, since it repressed the expression of a pelE::uidA fusion. The nucleotide sequence of kdgR contained an open reading frame of 918bp preceded by classical transcriptional initiation signals. KdgR shows similarity to two other regulatory proteins, namely GylR, encoding an activator protein of the glycerol operon in Streptomyces coelicolor, and IclR, encoding a repressor of the acetate operon in Salmonella typhimurium and in Escherichia coli. Previously, comparison of regulatory regions of several genes controlled by kdgR revealed the existence of a conserved region which was proposed as a KdgR-binding site. The 25 bp oligonucleotide AAAAAAGAAACATTGTTTCATTTGT corresponding to this consensus was substituted to the lac operator, at the beginning of transcription of the lacZ gene. This construct functioned as an operator for binding of the KdgR protein in vivo.
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Affiliation(s)
- S Reverchon
- Laboratoire de Génétique Moléculaire des Microorganismes, Institut National des Sciences Appliquées, Villeurbanne, France
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Nasser W, Condemine G, Plantier R, Anker D, Robert-Baudouy J. Inducing properties of analogs of 2-keto-3-deoxygluconate on the expression of pectinase genes of Erwinia chrysanthemi. FEMS Microbiol Lett 1991; 65:73-8. [PMID: 1874406 DOI: 10.1016/0378-1097(91)90474-o] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In Erwinia chrysanthemi, all the genes involved in pectin degradation are controlled by the negative regulatory gene kdgR. 2-keto-3-deoxy-gluconate (KDG) is the inducing molecule that interacts with KdgR to allow the expression of all the genes of the kdg regulon. The inducing properties on the expression of genes regulated by kdgR of various analogs and derivatives of KDG were tested. All the inducers share the common moiety COOH-CO-CH2-CHOH-C-C included in a pyranic cycle. Our results show that esterification of C1 prevents induction. Presence of a ketone function on C2 and absence of hydroxyl on C3 are necessary for induction. The nature and the configuration of substituent on C5 has no influence on induction. Two compounds have interesting properties: 5-O-methyl-KDG is a gratuitous inducer, and gluconic acid can prevent induction.
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Affiliation(s)
- W Nasser
- Laboratoire de Génétique Moléculaire des Microorganismes, INSA, Villeurbanne, France
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Abstract
Bacillus subtilis strain SO113 secretes a pectate lyase which is produced during the exponential death phase of growth, just before sporulation. This extracellular pectate lyase, which produces unsaturated products from polygalacturonate, was purified 35-fold from the culture supernatant of Bacillus subtilis by a CM Sephadex chromatography. It has an isoelectric point of about 9.6 and an Mr of 42,000. Optimum activity occurred at pH 8.4 and at 42 degrees C. Calcium has a stimulative effect on the enzyme activity while EDTA leads to enzyme inactivation. The pectate lyase has a specific activity of 131 mumol of aldehyde groups per min and per mg of protein. The Km of the purified enzyme for polygalacturonic acid was 0.862 g.l-1 and the Vmax for polygalacturonic acid hydrolysis was 1.475 mumol of unsaturated products per min and per mg of protein. By using monoclonal antibodies raised against Erwinia chrysanthemi 3937 pectate lyases, it was shown that pectate lyases b and c of this strain are immunologically closely related to the Bacillus subtilis pectate lyase.
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Affiliation(s)
- W Nasser
- Laboratoire de Génétique Moléculaire des Microorganismes, Institut National des Sciences Appliquées, Villeurbanne, France
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Nasser W, de Tapia M, Kauffmann S, Montasser-Kouhsari S, Burkard G. Identification and characterization of maize pathogenesis-related proteins. Four maize PR proteins are chitinases. Plant Mol Biol 1988; 11:529-538. [PMID: 24272409 DOI: 10.1007/bf00039033] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/1988] [Accepted: 07/25/1988] [Indexed: 06/02/2023]
Abstract
Eight pathogenesis-related proteins extractable at pH 2.8 were found to accumulate in maize leaves after mercuric chloride treatment or brome mosaic virus infection. These proteins were called PRm (pathogenesis-related maize) proteins. Seven PRm proteins were purified to homogeneity by preparative polyacrylamide gel electrophoresis and their amino acid compositions determined. Estimated molecular weights in SDS-containing gels were: PRm 1 14.2 kDa; Prm 2 16.5 kDa; PRm 3 and PRm 4 25 kDa; PRm 6b 30.5 kDa; PRm 6a 32 kDa; PRm 7 34.5 kDa. Antisera raised against either PRm 3 or PRm 4 reacted specifically each with PRm 3 or PRm 4. Antisera raised against PRm 6b reacted with PRm 6b as well as with PRm 6a and antisera against PRm 7 reacted with PRm 7 and PRm 5. Tobacco anti-PR 1b antisera reacted with maize PRm 2.Chitinase (poly[1,4-(N-acetyl-β-D-glucosamide)]glycanhydrolase, EC 3.2.1.14) activity was found for PRm 3, PRm 4, PRm 5, and PRm 7.
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Affiliation(s)
- W Nasser
- Institut de Biologie Moléculaire des Plantes, 12 rue du Général Zimmer, 67000, Strasbourg, France
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Farah M, Hélou E, Nasser W, Tabbara W. [A further case of Caroli's disease with segmentary bilobar giant dilations, complicated by lithiasis and surgically cured]. Rev Med Chir Mal Foie 1966; 41:305-28. [PMID: 5992831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Abstract
A case of complete absence of the left pericardium, suspected from plain chest x-rays and proved by diagnostic left pneumothorax, has been reported. The significance of the pericardium in relation to cardiac function is discussed. Because absence of the left pericardium is a benign and relatively asymptomatic anomaly that usually requires no treatment, it behooves the clinician and radiologist to become cognizant of its presence.
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