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Avadhanula V, Creighton C, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson E, Rajan A, Menon V, Doddapaneni H, Muzny D, Metcalf G, Cregeen SJ, Hoffman K, Gibbs R, Petrosino J, Piedra P. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. Res Sq 2023:rs.3.rs-2978272. [PMID: 37333115 PMCID: PMC10274945 DOI: 10.21203/rs.3.rs-2978272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
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Avadhanula V, Creighton CJ, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson EG, Rajan A, Menon VK, Doddapaneni H, Muzny DM, Metcalf G, Cregeen SJJ, Hoffman KL, Gibbs RA, Petrosino J, Piedra PA. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. bioRxiv 2023:2023.05.24.542181. [PMID: 37292999 PMCID: PMC10245966 DOI: 10.1101/2023.05.24.542181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
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Affiliation(s)
- Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Center for Health Data Science and Analytics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Divya Nagaraj
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Erin G. Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vipin Kumar Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Marie Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
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3
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Chou A, Sucgang R, Hamill RJ, Zechiedrich L, Trautner BW. Mortality difference from Klebsiella aerogenes vs Enterobacter cloacae bloodstream infections. Access Microbiol 2023; 5:acmi000421. [PMID: 36919079 PMCID: PMC10008348 DOI: 10.1099/acmi.0.000421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/17/2022] [Indexed: 03/02/2023] Open
Abstract
Members of the order Enterobacterales, including Escherichia coli , Klebsiella species and Enterobacter species, are important pathogens in healthcare-associated infections. Higher mortality has been reported from infections due to Klebsiella pneumoniae than from E. coli , but prior studies comparing Enterobacter aerogenes (recently renamed Klebsiella aerogenes ) bacteraemia and Enterobacter cloacae complex bacteraemia have yielded conflicting results regarding whether clinical outcomes differ. We found bacteraemia with K. aerogenes was independently associated with greater risk of 30-day mortality than bacteraemia with Enterobacter cloacae complex.
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Affiliation(s)
- Andrew Chou
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, 2450 Holcombe Blvd, Suite 01Y, Houston, Texas, USA.,Medical Care Line, Infectious Disease Section, Michael E. DeBakey VA Medical Center, Houston, Texas, 2002 Holcombe Blvd 111G/4B370, Houston, Texas, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.,Margaret M. and Albert B. Alkek Department of Medicine Section of Infectious Disease, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Richard Sucgang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.,Center for Health Data Science and Analytics, Houston Methodist Hospital, 6565 Fannin St, Houston, Texas, USA
| | - Richard J Hamill
- Medical Care Line, Infectious Disease Section, Michael E. DeBakey VA Medical Center, Houston, Texas, 2002 Holcombe Blvd 111G/4B370, Houston, Texas, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.,Margaret M. and Albert B. Alkek Department of Medicine Section of Infectious Disease, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Barbara W Trautner
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, 2450 Holcombe Blvd, Suite 01Y, Houston, Texas, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.,Section of Health Services Research, Departments of Medicine and Surgery, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
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4
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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5
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Chen F, Zhang Y, Sucgang R, Ramani S, Corry D, Kheradmand F, Creighton CJ. Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. Sci Rep 2021; 11:2459. [PMID: 33510359 PMCID: PMC7844278 DOI: 10.1038/s41598-021-82221-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
A deeper understanding of the molecular biology of SARS-CoV-2 infection, including the host response to the virus, is urgently needed. Commonalities exist between the host immune response to viral infections and cancer. Here, we defined transcriptional signatures of SARS-CoV-2 infection involving hundreds of genes common across lung adenocarcinoma cell lines (A549, Calu-3) and normal human bronchial epithelial cells (NHBE), with additional signatures being specific to one or both adenocarcinoma lines. Cross-examining eight transcriptomic databases, we found that host transcriptional responses of lung adenocarcinoma cells to SARS-CoV-2 infection shared broad similarities with host responses to multiple viruses across different model systems and patient samples. Furthermore, these SARS-CoV-2 transcriptional signatures were manifested within specific subsets of human cancer, involving ~ 20% of cases across a wide range of histopathological types. These cancer subsets show immune cell infiltration and inflammation and involve pathways linked to the SARS-CoV-2 response, such as immune checkpoint, IL-6, type II interferon signaling, and NF-κB. The cell line data represented immune responses activated specifically within the cancer cells of the tumor. Common genes and pathways implicated as part of the viral host response point to therapeutic strategies that may apply to both SARS-CoV-2 and cancer.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Corry
- Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey VA, Houston, TX, 77030, USA
- Departments of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Farrah Kheradmand
- Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey VA, Houston, TX, 77030, USA
- Departments of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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6
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals. bioRxiv 2020:2020.12.11.421057. [PMID: 33330863 PMCID: PMC7743067 DOI: 10.1101/2020.12.11.421057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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7
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. bioRxiv 2020:2020.07.27.223495. [PMID: 32766579 PMCID: PMC7402036 DOI: 10.1101/2020.07.27.223495] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
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8
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Narita TB, Kawabe Y, Kin K, Gibbs RA, Kuspa A, Muzny DM, Richards S, Strassmann JE, Sucgang R, Worley KC, Schaap P. Loss of the Polyketide Synthase StlB Results in Stalk Cell Overproduction in Polysphondylium violaceum. Genome Biol Evol 2020; 12:674-683. [PMID: 32386295 PMCID: PMC7259674 DOI: 10.1093/gbe/evaa079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Indexed: 11/12/2022] Open
Abstract
Major phenotypic innovations in social amoeba evolution occurred at the transition between the Polysphondylia and group 4 Dictyostelia, which comprise the model organism Dictyostelium discoideum, such as the formation of a new structure, the basal disk. Basal disk differentiation and robust stalk formation require the morphogen DIF-1, synthesized by the polyketide synthase StlB, the des-methyl-DIF-1 methyltransferase DmtA, and the chlorinase ChlA, which are conserved throughout Dictyostelia. To understand how the basal disk and other innovations evolved in group 4, we sequenced and annotated the Polysphondylium violaceum (Pvio) genome, performed cell type-specific transcriptomics to identify cell-type marker genes, and developed transformation and gene knock-out procedures for Pvio. We used the novel methods to delete the Pvio stlB gene. The Pvio stlB- mutants formed misshapen curly sorogens with thick and irregular stalks. As fruiting body formation continued, the upper stalks became more regular, but structures contained 40% less spores. The stlB- sorogens overexpressed a stalk gene and underexpressed a (pre)spore gene. Normal fruiting body formation and sporulation were restored in Pvio stlB- by including DIF-1 in the supporting agar. These data indicate that, although conserved, stlB and its product(s) acquired both a novel role in the group 4 Dictyostelia and a role opposite to that in its sister group.
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Affiliation(s)
- Takaaki B Narita
- School of Life Sciences, University of Dundee, United Kingdom,Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
| | | | - Koryu Kin
- School of Life Sciences, University of Dundee, United Kingdom
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Adam Kuspa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas,The Welch Foundation, Houston, TX
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Genome Sequencing Center, University of California Davis, Davis, CA
| | | | - Richard Sucgang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, United Kingdom,Corresponding author: E-mail:
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9
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Chou A, Sucgang R, Zechiedrich L, Trautner BW. 1822. Veterans Are Special: Clinical Decision Tree Misses ESBL Status in Bacteremic Veterans. Open Forum Infect Dis 2018. [PMCID: PMC6252509 DOI: 10.1093/ofid/ofy210.1478] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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Affiliation(s)
- Andrew Chou
- Medical Care Line, Infectious Disease Section, Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Richard Sucgang
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Department of Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Barbara W Trautner
- Department of Veterans Affairs, Health Services Research and Development Center of Excellence, Michael E. DeBakey VA Medical Center, Houston, Texas, Houston, Texas
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
- Baylor College of Medicine, Houston, Texas
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10
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Chou A, Rossi V, Sucgang R, Hamill R, Zechiedrich L, Trautner BW. 1051. Increased Mortality in Bacteremia by Enterobacter Species With Discordant Imipenem and Ertapenem Susceptibilities. Open Forum Infect Dis 2018. [PMCID: PMC6255083 DOI: 10.1093/ofid/ofy210.888] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Carbapenem-resistant Enterobacteriaceae (CRE) that are resistant only to one carbapenem have been reported, but the frequency of discordance between ertapenem and imipenem/meropenem is not known for Enterobacter species. We investigated the occurrence of discordant carbapenem susceptibilities in Enterobacter species bacteremia and the potential association with increased mortality. Methods We examined all cases of Enterobacter species bacteremia from January 2012 to December 2016 at the Michael E. DeBakey VA Medical Center in Houston, Texas, USA. Clinical and microbiological data were independently extracted by two investigators. Antibiotic susceptibility testing results were interpreted according to current CLSI breakpoints. Results We found 14/67 (20.9%) isolates had discordance between ertapenem and imipenem susceptibilities. Eight isolates were ertapenem susceptible/imipenem nonsusceptible and six isolates were ertapenem nonsusceptible/imipenem susceptible (table). Bacteremia cleared in 94.5% (52/55) of all patients who had follow-up cultures, including infection by all (13/13) isolates with discordant carbapenem susceptibilities tested. Thirty-day mortality was statistically higher in infection by isolates with discordant carbapenem susceptibilities than by isolates that were susceptible to all tested carbapenems (10% vs. 36%; P = 0.03, Fisher’s exact test). In-hospital mortality was also higher in the discordant cohort as well (12% vs. 36%; P = 0.04, Fisher’s exact test). Acute severity of illness at bacteremia onset did not differ between the groups (median Pitt bacteremia score 2 vs. 3; P = 0.11, Wilcoxon rank-sum test). Conclusion Bacteremia by Enterobacter species with discordant ertapenem and imipenem/meropenem susceptibilities is a relevant clinical issue, occurring in 20.9% of Enterobacter species bacteremias at our institution, and the discordance is associated with increased mortality. Whether such species can be safely treated with one carbapenem but not another is worth further investigation. MIC: minimum inhibitory concentration; S: susceptible; I: intermediate; R: resistant; Disclosures B. W. Trautner, Paratek: Consultant, Consulting fee. Zambon: Consultant, Consulting fee and Research grant.
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Affiliation(s)
- Andrew Chou
- Medical Care Line, Infectious Disease Section, Michael E. DeBakey VA Medical Center, Houston, Texas
- Department of Medicine Section of Infectious Diseases, Department of Microbiology and Molecular Virology, Baylor College of Medicine, Houston, Texas
| | - Vittoria Rossi
- School of Medicine, Baylor College of Medicine, Houston, Texas
| | - Richard Sucgang
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Richard Hamill
- Internal Medicine – Infectious Diseases, Baylor College of Medicine & Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Department of Pharmacology, Baylor College of Medicine, Houston, Texas
| | - Barbara W Trautner
- Department of Veterans Affairs, Health Services Research & Development Center of Excellence, Michael E. DeBakey VA Medical Center, Houston, Texas
- Department of Surgery, Baylor College of Medicine, Houston, Texas
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
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11
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Koire A, Gilbert BE, Sucgang R, Zechiedrich L. Correction: Repurposed Transcriptomic Data Reveal Small Viral RNA Produced by Influenza Virus during Infection in Mice. PLoS One 2017; 12:e0189384. [PMID: 29206873 PMCID: PMC5716586 DOI: 10.1371/journal.pone.0189384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0165729.].
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12
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Bodine TJ, Evangelista MA, Chang HT, Ayoub CA, Samuel BS, Sucgang R, Zechiedrich L. Escherichia coli DNA ligase B may mitigate damage from oxidative stress. PLoS One 2017; 12:e0180800. [PMID: 28700629 PMCID: PMC5507437 DOI: 10.1371/journal.pone.0180800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 06/21/2017] [Indexed: 01/02/2023] Open
Abstract
Escherichia coli encodes two DNA ligases, ligase A, which is essential under normal laboratory growth conditions, and ligase B, which is not. Here we report potential functions of ligase B. We found that across the entire Enterobacteriaceae family, ligase B is highly conserved in both amino acid identity and synteny with genes associated with oxidative stress. Deletion of ligB sensitized E. coli to specific DNA damaging agents and antibiotics resulted in a weak mutator phenotype, and decreased biofilm formation. Overexpression of ligB caused a dramatic extension of lag phase that eventually resumed normal growth. The ligase function of ligase B was not required to mediate the extended lag phase, as overexpression of a ligase-deficient ligB mutant also blocked growth. Overexpression of ligB during logarithmic growth caused an immediate block of cell growth and DNA replication, and death of about half of cells. These data support a potential role for ligase B in the base excision repair pathway or the mismatch repair pathway.
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Affiliation(s)
- Truston J. Bodine
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, United States of America
| | - Michael A. Evangelista
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Huan Ting Chang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Department of BioSciences, Rice University, Houston, TX, United States of America
| | - Christopher A. Ayoub
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Buck S. Samuel
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States of America
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Lynn Zechiedrich
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, United States of America
- * E-mail:
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13
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Chou A, Pritchard H, Sucgang R, Zechiedrich L. Discordant Ertapenem/Imipenem Susceptibilities in Enterobacter Bacteremia: Frequency and Outcomes. Open Forum Infect Dis 2017. [DOI: 10.1093/ofid/ofx163.248] [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: 11/12/2022] Open
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14
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Koire A, Gilbert BE, Sucgang R, Zechiedrich L. Repurposed Transcriptomic Data Reveal Small Viral RNA Produced by Influenza Virus during Infection in Mice. PLoS One 2016; 11:e0165729. [PMID: 27788253 PMCID: PMC5082947 DOI: 10.1371/journal.pone.0165729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022] Open
Abstract
Influenza virus, a highly infectious ssRNA virus, replicates in the nucleus of host cells. This unusual feature brings the possibility that the virus may hijack host small noncoding RNA metabolism. Influenza small viral RNA production has been examined in vitro but has not yet been studied in an in vivo setting. We assessed small RNA species from influenza virus during mouse infection by mining publicly available mouse small RNA transcriptome data. We uncovered 26 nt reads corresponding to svRNA, a small viral RNA previously detected in vitro that regulates the transition from transcription to replication during infection, and found a strong positive correlation between svRNA production and host susceptibility to influenza virus infection. We also detected significant overrepresentation of a non-coding 23 nt sequence that we speculate may behave like a miRNA and work with influenza protein NS1 to prevent the transcription and maturation of interferon-stimulated mRNAs.
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Affiliation(s)
- Amanda Koire
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Brian E. Gilbert
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lynn Zechiedrich
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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15
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Chou A, Roa M, Evangelista MA, Sulit AK, Lagamayo E, Torres BC, Klinzing DC, Daroy MLG, Navoa-Ng J, Sucgang R, Zechiedrich L. Emergence of Klebsiella pneumoniae ST273 Carrying bla NDM-7 and ST656 Carrying bla NDM-1 in Manila, Philippines. Microb Drug Resist 2016; 22:585-588. [PMID: 27032000 PMCID: PMC5073224 DOI: 10.1089/mdr.2015.0205] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We sought to determine the epidemiology of carbapenem-resistant Enterobacteriaceae and to investigate the emergence of carbapenem-resistant Klebsiella pneumoniae in two teaching hospitals in Manila, Philippines. We screened 364 Enterobacteriaceae for carbapenem resistance between 2012 and 2013 and detected four carbapenem-resistant K. pneumoniae isolates from three different patients. We used whole genome sequencing to determine the antibiotic resistance profiles and confirmed the presence of carbapenemase genes by multiplex PCR. We used multilocus sequence typing and PCR-based replicon typing to genetically characterize the carbapenem-resistant isolates. The carbapenemase gene blaNDM was detected in K. pneumoniae isolates from two patients. The first patient had ventilator-associated pneumonia and lumbar shunt infection from K. pneumoniae ST273 carrying blaNDM-7. The second patient had asymptomatic genitourinary colonization with K. pneumoniae ST656 carrying blaNDM-1. The third patient had a gluteal abscess with K. pneumoniae ST1 that did not carry a carbapenemase gene, but did carry blaDHA-1, blaOXA-1, and blaSHV-1. In this study, we report the first cases of blaNDM-carrying pathogens in the Philippines and add to the growing evidence of the worldwide spread of ST273 and NDM-7, a more efficient carbapenem hydrolyzer than NDM-1.
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Affiliation(s)
- Andrew Chou
- 1 Division of Infectious Diseases, Department of Medicine, Baylor College of Medicine , Houston, Texas.,2 Department of Molecular Virology and Microbiology, Baylor College of Medicine , Houston, Texas
| | - Marylette Roa
- 3 Research and Biotechnology Group, St. Luke's Medical Center , Quezon City, Philippines
| | - Michael A Evangelista
- 4 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston, Texas
| | - Arielle Kae Sulit
- 3 Research and Biotechnology Group, St. Luke's Medical Center , Quezon City, Philippines
| | - Evelina Lagamayo
- 5 Pathology Institute, St. Luke's Medical Center , Quezon City, Philippines
| | - Brian C Torres
- 3 Research and Biotechnology Group, St. Luke's Medical Center , Quezon City, Philippines
| | - David C Klinzing
- 3 Research and Biotechnology Group, St. Luke's Medical Center , Quezon City, Philippines .,6 Tahoe Research Initiative , Incline Village, Nevada
| | - Maria Luisa G Daroy
- 3 Research and Biotechnology Group, St. Luke's Medical Center , Quezon City, Philippines
| | - Josephine Navoa-Ng
- 5 Pathology Institute, St. Luke's Medical Center , Quezon City, Philippines .,7 Infection Control Service, St. Luke's Medical Center , Quezon City, Philippines
| | - Richard Sucgang
- 4 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston, Texas
| | - Lynn Zechiedrich
- 2 Department of Molecular Virology and Microbiology, Baylor College of Medicine , Houston, Texas.,4 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston, Texas.,8 Department of Pharmacology, Baylor College of Medicine , Houston, Texas
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16
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Ostrowski EA, Shen Y, Tian X, Sucgang R, Jiang H, Qu J, Katoh-Kurasawa M, Brock DA, Dinh C, Lara-Garduno F, Lee SL, Kovar CL, Dinh HH, Korchina V, Jackson L, Patil S, Han Y, Chaboub L, Shaulsky G, Muzny DM, Worley KC, Gibbs RA, Richards S, Kuspa A, Strassmann JE, Queller DC. Genomic signatures of cooperation and conflict in the social amoeba. Curr Biol 2015; 25:1661-5. [PMID: 26051890 DOI: 10.1016/j.cub.2015.04.059] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/01/2015] [Accepted: 04/22/2015] [Indexed: 12/14/2022]
Abstract
Cooperative systems are susceptible to invasion by selfish individuals that profit from receiving the social benefits but fail to contribute. These so-called "cheaters" can have a fitness advantage in the laboratory, but it is unclear whether cheating provides an important selective advantage in nature. We used a population genomic approach to examine the history of genes involved in cheating behaviors in the social amoeba Dictyostelium discoideum, testing whether these genes experience rapid evolutionary change as a result of conflict over spore-stalk fate. Candidate genes and surrounding regions showed elevated polymorphism, unusual patterns of linkage disequilibrium, and lower levels of population differentiation, but they did not show greater between-species divergence. The signatures were most consistent with frequency-dependent selection acting to maintain multiple alleles, suggesting that conflict may lead to stalemate rather than an escalating arms race. Our results reveal the evolutionary dynamics of cooperation and cheating and underscore how sequence-based approaches can be used to elucidate the history of conflicts that are difficult to observe directly.
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Affiliation(s)
- Elizabeth A Ostrowski
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY 10027, USA
| | - Xiangjun Tian
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Debra A Brock
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher Dinh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fremiet Lara-Garduno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - LaRonda Jackson
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shobha Patil
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lesley Chaboub
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adam Kuspa
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joan E Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David C Queller
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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17
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Swick MC, Evangelista MA, Bodine TJ, Easton-Marks JR, Barth P, Shah MJ, Bormann Chung CA, Stanley S, McLaughlin SF, Lee CC, Sheth V, Doan Q, Hamill RJ, Steffen D, Becnel LB, Sucgang R, Zechiedrich L. Novel Conserved Genotypes Correspond to Antibiotic Resistance Phenotypes of E. coli Clinical Isolates. PLoS One 2013; 8:e65961. [PMID: 23824211 PMCID: PMC3688849 DOI: 10.1371/journal.pone.0065961] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 05/03/2013] [Indexed: 11/20/2022] Open
Abstract
Current efforts to understand antibiotic resistance on the whole genome scale tend to focus on known genes even as high throughput sequencing strategies uncover novel mechanisms. To identify genomic variations associated with antibiotic resistance, we employed a modified genome-wide association study; we sequenced genomic DNA from pools of E. coli clinical isolates with similar antibiotic resistance phenotypes using SOLiD technology to uncover single nucleotide polymorphisms (SNPs) unanimously conserved in each pool. The multidrug-resistant pools were genotypically similar to SMS-3-5, a previously sequenced multidrug-resistant isolate from a polluted environment. The similarity was evenly spread across the entire genome and not limited to plasmid or pathogenicity island loci. Among the pools of clinical isolates, genomic variation was concentrated adjacent to previously reported inversion and duplication differences between the SMS-3-5 isolate and the drug-susceptible laboratory strain, DH10B. SNPs that result in non-synonymous changes in gyrA (encoding the well-known S83L allele associated with fluoroquinolone resistance), mutM, ligB, and recG were unanimously conserved in every fluoroquinolone-resistant pool. Alleles of the latter three genes are tightly linked among most sequenced E. coli genomes, and had not been implicated in antibiotic resistance previously. The changes in these genes map to amino acid positions in alpha helices that are involved in DNA binding. Plasmid-encoded complementation of null strains with either allelic variant of mutM or ligB resulted in variable responses to ultraviolet light or hydrogen peroxide treatment as markers of induced DNA damage, indicating their importance in DNA metabolism and revealing a potential mechanism for fluoroquinolone resistance. Our approach uncovered evidence that additional DNA binding enzymes may contribute to fluoroquinolone resistance and further implicate environmental bacteria as a reservoir for antibiotic resistance.
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Affiliation(s)
- Michelle C. Swick
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael A. Evangelista
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
| | - Truston J. Bodine
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jeremy R. Easton-Marks
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Biomedical Informatics Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Patrick Barth
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Minita J. Shah
- Life Technologies, Beverly, Massachusetts, United States of America
| | | | - Sarah Stanley
- Life Technologies, Beverly, Massachusetts, United States of America
| | | | - Clarence C. Lee
- Life Technologies, Beverly, Massachusetts, United States of America
| | - Vrunda Sheth
- Life Technologies, Beverly, Massachusetts, United States of America
| | - Quynh Doan
- Life Technologies, Foster City, California, United States of America
| | - Richard J. Hamill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Steffen
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Biomedical Informatics Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lauren B. Becnel
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Biomedical Informatics Group, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
- * E-mail: (RS); (LZ)
| | - Lynn Zechiedrich
- Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, Texas, United States of America
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (RS); (LZ)
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18
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Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, Dalin E, Tu H, Huang E, Barry K, Lindquist E, Shapiro H, Bruce D, Schmutz J, Salamov A, Fey P, Gaudet P, Anjard C, Babu MM, Basu S, Bushmanova Y, van der Wel H, Katoh-Kurasawa M, Dinh C, Coutinho PM, Saito T, Elias M, Schaap P, Kay RR, Henrissat B, Eichinger L, Rivero F, Putnam NH, West CM, Loomis WF, Chisholm RL, Shaulsky G, Strassmann JE, Queller DC, Kuspa A, Grigoriev IV. Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol 2011; 12:R20. [PMID: 21356102 PMCID: PMC3188802 DOI: 10.1186/gb-2011-12-2-r20] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [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: 07/20/2010] [Revised: 12/09/2010] [Accepted: 02/28/2011] [Indexed: 12/28/2022] Open
Abstract
Background The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Results We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. Conclusions The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.
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Affiliation(s)
- Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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19
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Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G. Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol 2010; 11:R35. [PMID: 20236529 PMCID: PMC2864575 DOI: 10.1186/gb-2010-11-3-r35] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [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: 12/16/2009] [Revised: 02/11/2010] [Accepted: 03/17/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Evolutionarily divergent organisms often share developmental anatomies despite vast differences between their genome sequences. The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish. RESULTS Here we show that the anatomical similarities are accompanied by extensive transcriptome conservation. Using RNA sequencing we compared the abundance and developmental regulation of all the transcripts in the two species. In both species, most genes are developmentally regulated and the greatest expression changes occur during the transition from unicellularity to multicellularity. The developmental regulation of transcription is highly conserved between orthologs in the two species. In addition to timing of expression, the level of mRNA production is also conserved between orthologs and is consistent with the intuitive notion that transcript abundance correlates with the amount of protein required. Furthermore, the conservation of transcriptomes extends to cell-type specific expression. CONCLUSIONS These findings suggest that developmental programs are remarkably conserved at the transcriptome level, considering the great evolutionary distance between the genomes. Moreover, this transcriptional conservation may be responsible for the similar developmental anatomies of Dictyostelium discoideum and Dictyostelium purpureum.
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Affiliation(s)
- Anup Parikh
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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20
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Benabentos R, Hirose S, Sucgang R, Curk T, Katoh M, Ostrowski EA, Strassmann JE, Queller DC, Zupan B, Shaulsky G, Kuspa A. Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium. Curr Biol 2009; 19:567-72. [PMID: 19285397 DOI: 10.1016/j.cub.2009.02.037] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 01/02/2009] [Accepted: 02/04/2009] [Indexed: 01/01/2023]
Abstract
Self and kin discrimination are observed in most kingdoms of life and are mediated by highly polymorphic plasma membrane proteins. Sequence polymorphism, which is essential for effective recognition, is maintained by balancing selection. Dictyostelium discoideum are social amoebas that propagate as unicellular organisms but aggregate upon starvation and form fruiting bodies with viable spores and dead stalk cells. Aggregative development exposes Dictyostelium to the perils of chimerism, including cheating, which raises questions about how the victims survive in nature and how social cooperation persists. Dictyostelids can minimize the cost of chimerism by preferential cooperation with kin, but the mechanisms of kin discrimination are largely unknown. Dictyostelium lag genes encode transmembrane proteins with multiple immunoglobulin (Ig) repeats that participate in cell adhesion and signaling. Here, we describe their role in kin discrimination. We show that lagB1 and lagC1 are highly polymorphic in natural populations and that their sequence dissimilarity correlates well with wild-strain segregation. Deleting lagB1 and lagC1 results in strain segregation in chimeras with wild-type cells, whereas elimination of the nearly invariant homolog lagD1 has no such consequences. These findings reveal an early evolutionary origin of kin discrimination and provide insight into the mechanism of social recognition and immunity.
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Affiliation(s)
- Rocio Benabentos
- Graduate Program in Cell and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Song J, Xu Q, Olsen R, Loomis WF, Shaulsky G, Kuspa A, Sucgang R. Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage. PLoS Comput Biol 2005; 1:e71. [PMID: 16362072 PMCID: PMC1314882 DOI: 10.1371/journal.pcbi.0010071] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Accepted: 11/07/2005] [Indexed: 11/26/2022] Open
Abstract
The Amoebozoa are a sister clade to the fungi and the animals, but are poorly sampled for completely sequenced genomes. The social amoeba Dictyostelium discoideum and amitochondriate pathogen Entamoeba histolytica are the first Amoebozoa with genomes completely sequenced. Both organisms are classified under the Conosa subphylum. To identify Amoebozoa-specific genomic elements, we compared these two genomes to each other and to other eukaryotic genomes. An expanded phylogenetic tree built from the complete predicted proteomes of 23 eukaryotes places the two amoebae in the same lineage, although the divergence is estimated to be greater than that between animals and fungi, and probably happened shortly after the Amoebozoa split from the opisthokont lineage. Most of the 1,500 orthologous gene families shared between the two amoebae are also shared with plant, animal, and fungal genomes. We found that only 42 gene families are distinct to the amoeba lineage; among these are a large number of proteins that contain repeats of the FNIP domain, and a putative transcription factor essential for proper cell type differentiation in D. discoideum. These Amoebozoa-specific genes may be useful in the design of novel diagnostics and therapies for amoebal pathologies. Most single-celled eukaryotes were lumped together in a single catchall classification until molecular sequencing revealed that they are a very diverse group that illustrates the different paths eukaryotic evolution has taken. Comparing a representative subset of genes indicates that one group in particular, the Amoebozoa, are a sister group to the animals and fungi, even more closely related than the plants. Despite their diversity, few simple eukaryotes have been the subject of complete genome sequencing. The genomes of two amoebozoa, Dictyostelium discoideum (a free-living social amoeba) and Entamoeba histolytica (a pathogenic amoeba), were recently completed. The authors compared the predicted proteins encoded by each organism to each other, and to other representative eukaryotes, and built a phylogenetic tree using not just a few representative genes, but the entire genomes of 23 organisms. The resulting tree closely re-created the relationships predicted from the sampled genes, including reinforcing the close relationship between the amoebozoa and the animals and fungi. The authors also found very few genes that are exclusively inherited by amoebozoa. Since some amoebozoa are important clinical pathogens, these genes are likely good targets for therapeutic agents that will not affect the animal host.
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Affiliation(s)
- Jie Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qikai Xu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rolf Olsen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Section of Cell and Developmental Biology, Division of Biology, University of California San Diego, La Jolla, California, United States of America
| | - William F Loomis
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Section of Cell and Developmental Biology, Division of Biology, University of California San Diego, La Jolla, California, United States of America
| | - Gad Shaulsky
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Adam Kuspa
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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22
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Eichinger L, Pachebat J, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Babu MM, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail M, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox E, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. The genome of the social amoeba Dictyostelium discoideum. Nature 2005; 435:43-57. [PMID: 15875012 PMCID: PMC1352341 DOI: 10.1038/nature03481] [Citation(s) in RCA: 947] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Accepted: 02/17/2005] [Indexed: 02/07/2023]
Abstract
The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
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Affiliation(s)
- L. Eichinger
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - J.A. Pachebat
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - G. Glöckner
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M.-A. Rajandream
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - M. Berriman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - R. Olsen
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - K. Szafranski
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Q. Xu
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - B. Tunggal
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - S. Kummerfeld
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - M. Madera
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - B. A. Konfortov
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - F. Rivero
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - A. T. Bankier
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - R. Lehmann
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - N. Hamlin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Davies
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Gaudet
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - P. Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - K. Pilcher
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - G. Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Saunders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - E. Sodergren
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kerhornou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - X. Nie
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Hall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Anjard
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - L. Hemphill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Bason
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Farbrother
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Desany
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - E. Just
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - T. Morio
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - R. Rost
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - C. Churcher
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Cooper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Haydock
- Biochemistry Department, University of Cambridge, Cambridge CB2 1QW, UK
| | - N. van Driessche
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Cronin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - I. Goodhead
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - T. Mourier
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Pain
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Harper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Lindsay
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - H. Hauser
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. James
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Quiles
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Madan Babu
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - T. Saito
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810 Japan
| | - C. Buchrieser
- Unité de Genomique des Microorganismes Pathogenes, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - A. Wardroper
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
- Department of Biology, University of York, York YO10 5YW, UK
| | - M. Felder
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M. Thangavelu
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
| | - D. Johnson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Knights
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Loulseged
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - K. Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. Oliver
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Price
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M.A. Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Urushihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - J. Hernandez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - E. Rabbinowitsch
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Steffen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Sanders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Ma
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Y. Kohara
- Centre for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - S. Sharp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Simmonds
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Spiegler
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Tivey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato, Tokyo 108-8639, Japan
| | - B. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Walker
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Woodward
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - T. Winckler
- Institut für Pharmazeutische Biologie, Universität Frankfurt (Biozentrum), Frankfurt am Main, 60439, Germany
| | - Y. Tanaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - G. Shaulsky
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - M. Schleicher
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - G. Weinstock
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Rosenthal
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - E.C. Cox
- Department of Molecular Biology, Princeton University, Princeton, NJ08544-1003, USA
| | - R. L. Chisholm
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - R. Gibbs
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - W. F. Loomis
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M. Platzer
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - R. R. Kay
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - J. Williams
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - P. H. Dear
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - A. A. Noegel
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Barrell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kuspa
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Sucgang R, Chen G, Liu W, Lindsay R, Lu J, Muzny D, Shaulsky G, Loomis W, Gibbs R, Kuspa A. Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucleic Acids Res 2003; 31:2361-8. [PMID: 12711681 PMCID: PMC154234 DOI: 10.1093/nar/gkg348] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a library of ordered YAC clones, we provide evidence for a chromosomal copy of the rDNA on chromosome 4. This locus may provide master copies for the stable transmission of the extrachromosomal elements. The extrachromosomal elements were also found to form chromosome-sized clusters of DNA within nuclei of nocodazole-treated cells arrested in mitosis. These clusters resemble true chromosomes and may allow the efficient segregation of the rDNA during mitosis. These rDNA clusters may also explain the cytological observations of a seventh chromosome in this organism.
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Affiliation(s)
- Richard Sucgang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Van Driessche N, Shaw C, Katoh M, Morio T, Sucgang R, Ibarra M, Kuwayama H, Saito T, Urushihara H, Maeda M, Takeuchi I, Ochiai H, Eaton W, Tollett J, Halter J, Kuspa A, Tanaka Y, Shaulsky G. A transcriptional profile of multicellular development inDictyostelium discoideum. Development 2002; 129:1543-52. [PMID: 11923193 DOI: 10.1242/dev.129.7.1543] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A distinct feature of development in the simple eukaryote Dictyostelium discoideum is an aggregative transition from a unicellular to a multicellular phase. Using genome-wide transcriptional analysis we show that this transition is accompanied by a dramatic change in the expression of more than 25% of the genes in the genome. We also show that the transcription patterns of these genes are not sensitive to the strain or the nutritional history, indicating that Dictyostelium development is a robust physiological process that is accompanied by stereotypical transcriptional events. Analysis of the two differentiated cell types, spores and stalk cells, and their precursors revealed a large number of differentially expressed genes as well as unexpected patterns of gene expression, which shed new light on the timing and possible mechanisms of cell-type divergence. Our findings provide new perspectives on the complexity of the developmental program and the fraction of the genome that is regulated during development.Supplemental data available on-line
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Affiliation(s)
- Nancy Van Driessche
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
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Abstract
The genome of Dictyostelium discoideum is being sequenced by an international consortium and is scheduled for completion in the next few years. The sequence will accelerate research into a number of phenomena carried out by these versatile soil amoebae, providing insight into analogous processes that operate in a wide range of eukaryotes. These include the dynamic regulation of the cytoskeleton during chemotaxis, intercellular communication during multicellular development and the intracellular growth of bacterial pathogens. The current state of the genome project is summarized and the challenges of sequencing a genome with unusually low guanine and cytosine content and with a bimodal base composition distribution are discussed. The prospects for functional analyses at the genomic scale are also considered.
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Affiliation(s)
- A Kuspa
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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Abstract
Dictyostelium discoideum is a useful model for molecular studies of cell biology and development. The 34-megabase Dictyostelium genome is currently being sequenced through the efforts of an international consortium. The genome is expected to encode 8-10,000 genes, including all those required for a free-living eukaryote capable of multicellular development. A complete description of the Dictyostelium genome will open the way toward the application of genome-based experimental approaches to studies of cell biology and development in this organism, and allow detailed physiological and evolutionary comparisons to other species.
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Affiliation(s)
- R Sucgang
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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de Hostos EL, McCaffrey G, Sucgang R, Pierce DW, Vale RD. A developmentally regulated kinesin-related motor protein from Dictyostelium discoideum. Mol Biol Cell 1998; 9:2093-106. [PMID: 9693369 PMCID: PMC25463 DOI: 10.1091/mbc.9.8.2093] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The cellular slime mold Dictyostelium discoideum is an attractive system for studying the roles of microtubule-based motility in cell development and differentiation. In this work, we report the first molecular characterization of kinesin-related proteins (KRPs) in Dictyostelium. A PCR-based strategy was used to isolate DNA fragments encoding six KRPs, several of which are induced during the developmental program that is initiated by starvation. The complete sequence of one such developmentally regulated KRP (designated K7) was determined and found to be a novel member of the kinesin superfamily. The motor domain of K7 is most similar to that of conventional kinesin, but unlike conventional kinesin, K7 is not predicted to have an extensive alpha-helical coiled-coil domain. The nonmotor domain is unusual and is rich in Asn, Gln, and Thr residues; similar sequences are found in other developmentally regulated genes in Dictyostelium. K7, expressed in Escherichia coli, supports plus end-directed microtubule motility in vitro at a speed of 0.14 micron/s, indicating that it is a bona fide motor protein. The K7 motor is found only in developing cells and reaches a peak level of expression between 12 and 16 h after starvation. By immunofluorescence microscopy, K7 localizes to a membranous perinuclear structure. To examine K7 function, we prepared a null cell line but found that these cells show no gross developmental abnormalities. However, when cultivated in the presence of wild-type cells, the K7-null cells are mostly absent from the prestalk zone of the slug. This result suggests that in a population composed largely of wild-type cells, the absence of the K7 motor protein interferes either with the ability of the cells to localize to the prestalk zone or to differentiate into prestalk cells.
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Affiliation(s)
- E L de Hostos
- Department of Biochemistry and Cell Biology, Rice University, Houston Texas 77005, USA
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Sucgang R, Weijer CJ, Siegert F, Franke J, Kessin RH. Null mutations of the Dictyostelium cyclic nucleotide phosphodiesterase gene block chemotactic cell movement in developing aggregates. Dev Biol 1997; 192:181-92. [PMID: 9405107 DOI: 10.1006/dbio.1997.8720] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Extracellular cAMP is a critical messenger in the multicellular development of the cellular slime mold Dictyostelium discoideum. The levels of cAMP are controlled by a cyclic nucleotide phosphodiesterase (PDE) that is secreted by the cells. The PDE gene (pdsA) is controlled by three promoters that permit expression during vegetative growth, during aggregation, and in prestalk cells of the older structures. Targeted disruption of the gene aborts development, and complementation with a modified pdsA restores development. Two distinct promoters must be used for full complementation, and an inhibitory domain of the PDE must be removed. We took advantage of newly isolated PDE-null cells and the natural chimerism of the organism to ask whether the absence of PDE affected individual cell behavior. PDE-null cells aggregated with isogenic wild-type cells in chimeric mixtures, but could not move in a coordinated manner in mounds. The wild-type cells move inward toward the center of the mound, leaving many of the PDE-null cells at the periphery of the aggregate. During the later stages of development, PDE-null cells in the chimera segregate to regions which correspond to the prestalk region and the rear of the slug. Participation in the prespore/spore population returns with the restoration of a modified pdsA to the null cells.
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Affiliation(s)
- R Sucgang
- College of Physicians and Surgeons, Columbia University, 630 West 168 Street, New York, New York 10032, USA
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