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Sabour S, Bantle K, Bhatnagar A, Huang JY, Biggs A, Bodnar J, Dale JL, Gleason R, Klein L, Lasure M, Lee R, Nazarian E, Schneider E, Smith L, Snippes Vagnone P, Therrien M, Tran M, Valley A, Wang C, Young EL, Lutgring JD, Brown AC. Descriptive analysis of targeted carbapenemase genes and antibiotic susceptibility profiles among carbapenem-resistant Acinetobacter baumannii tested in the Antimicrobial Resistance Laboratory Network-United States, 2017-2020. Microbiol Spectr 2024; 12:e0282823. [PMID: 38174931 PMCID: PMC10845962 DOI: 10.1128/spectrum.02828-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacillus that can cause severe and difficult-to-treat healthcare-associated infections. A. baumannii can harbor mobile genetic elements carrying genes that produce carbapenemase enzymes, further limiting therapeutic options for infections. In the United States, the Antimicrobial Resistance Laboratory Network (AR Lab Network) conducts sentinel surveillance of carbapenem-resistant Acinetobacter baumannii (CRAB). Participating clinical laboratories sent CRAB isolates to the AR Lab Network for characterization, including antimicrobial susceptibility testing and molecular detection of class A (Klebsiella pneumoniae carbapenemase), class B (Active-on-Imipenem, New Delhi metallo-β-lactamase, and Verona integron-encoded metallo-β-lactamase), and class D (Oxacillinase, blaOXA-23-like, blaOXA-24/40-like, blaOXA-48-like, and blaOXA-58-like) carbapenemase genes. During 2017‒2020, 6,026 CRAB isolates from 45 states were tested for targeted carbapenemase genes; 1% (64 of 5,481) of CRAB tested for targeted class A and class B genes were positive, but 83% (3,351 of 4,041) of CRAB tested for targeted class D genes were positive. The number of CRAB isolates carrying a class A or B gene increased from 2 of 312 (<1%) tested in 2017 to 26 of 1,708 (2%) tested in 2020. Eighty-three percent (2,355 of 2,846) of CRAB with at least one of the targeted carbapenemase genes and 54% (271 of 500) of CRAB without were categorized as extensively drug resistant; 95% (42 of 44) of isolates carrying more than one targeted gene had difficult-to-treat susceptibility profiles. CRAB isolates carrying targeted carbapenemase genes present an emerging public health threat in the United States, and their rapid detection is crucial to improving patient safety.IMPORTANCEThe Centers for Disease Control and Prevention has classified CRAB as an urgent public health threat. In this paper, we used a collection of >6,000 contemporary clinical isolates to evaluate the phenotypic and genotypic properties of CRAB detected in the United States. We describe the frequency of specific carbapenemase genes detected, antimicrobial susceptibility profiles, and the distribution of CRAB isolates categorized as multidrug resistant, extensively drug-resistant, or difficult to treat. We further discuss the proportion of isolates showing susceptibility to Food and Drug Administration-approved agents. Of note, 84% of CRAB tested harbored at least one class A, B, or D carbapenemase genes targeted for detection and 83% of these carbapenemase gene-positive CRAB were categorized as extensively drug resistant. Fifty-four percent of CRAB isolates without any of these carbapenemase genes detected were still extensively drug-resistant, indicating that infections caused by CRAB are highly resistant and pose a significant risk to patient safety regardless of the presence of one of these carbapenemase genes.
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Affiliation(s)
- Sarah Sabour
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katie Bantle
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amelia Bhatnagar
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer Y. Huang
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela Biggs
- Maryland Department of Health, Baltimore, Maryland, USA
| | | | | | - Rachel Gleason
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Liore Klein
- Maryland Department of Health, Baltimore, Maryland, USA
| | - Megan Lasure
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA
| | - Rachel Lee
- Texas Department of State Health Services, Austin, Texas, USA
| | | | - Emily Schneider
- Washington State Department of Health Public Health Laboratories, Shoreline, Washington, USA
| | - Lori Smith
- Utah Public Health Laboratory, Taylorsville, Utah, USA
| | | | | | - Michael Tran
- Washington State Department of Health Public Health Laboratories, Shoreline, Washington, USA
| | - Ann Valley
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA
| | - Chun Wang
- Texas Department of State Health Services, Austin, Texas, USA
| | - Erin L. Young
- Utah Public Health Laboratory, Taylorsville, Utah, USA
| | - Joseph D. Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Allison C. Brown
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Barnes AMT, Frank KL, Dale JL, Manias DA, Powers JL, Dunny GM. Enterococcus faecalis colonizes and forms persistent biofilm microcolonies on undamaged endothelial surfaces in a rabbit endovascular infection model. FEMS Microbes 2021; 2:xtab014. [PMID: 34734186 PMCID: PMC8557322 DOI: 10.1093/femsmc/xtab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 09/23/2021] [Indexed: 01/03/2023] Open
Abstract
Infectious endocarditis (IE) is an uncommon disease with significant morbidity and mortality. The pathogenesis of IE has historically been described as a cascade of host-specific events beginning with endothelial damage and thrombus formation and followed by bacterial colonization of the nascent thrombus. Enterococcus faecalis is a Gram-positive commensal bacterial member of the gastrointestinal tract microbiota in most terrestrial animals and a leading cause of opportunistic biofilm-associated infections, including endocarditis. Here, we provide evidence that E. faecalis can colonize the endocardial surface without pre-existing damage and in the absence of thrombus formation in a rabbit endovascular infection model. Using previously described light and scanning electron microscopy techniques, we show that inoculation of a well-characterized E. faecalis lab strain in the marginal ear vein of New Zealand White rabbits resulted in rapid colonization of the endocardium throughout the heart within 4 days of administration. Unexpectedly, ultrastructural imaging revealed that the microcolonies were firmly attached directly to the endocardium in areas without morphological evidence of gross tissue damage. Further, the attached bacterial aggregates were not associated with significant cellular components of coagulation or host extracellular matrix damage repair (i.e. platelets). These results suggest that the canonical model of mechanical surface damage as a prerequisite for bacterial attachment to host sub-endothelial components is not required. Furthermore, these findings are consistent with a model of initial establishment of stable, endocarditis-associated E. faecalis biofilm microcolonies that may provide a reservoir for the eventual valvular infection characteristic of clinical endocarditis. The similarities between the E. faecalis colonization and biofilm morphologies seen in this rabbit endovascular infection model and our previously published murine gastrointestinal colonization model indicate that biofilm production and common host cell attachment factors are conserved in disparate mammalian hosts under both commensal and pathogenic contexts.
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Affiliation(s)
- Aaron M T Barnes
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Kristi L Frank
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Jennifer L Dale
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Dawn A Manias
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Jennifer L Powers
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Gary M Dunny
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
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3
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Karmarkar EN, O'Donnell K, Prestel C, Forsberg K, Gade L, Jain S, Schan D, Chow N, McDermott D, Rossow J, Toda M, Ruiz R, Hun S, Dale JL, Gross A, Maruca T, Glowicz J, Brooks R, Bagheri H, Nelson T, Gualandi N, Khwaja Z, Horwich-Scholefield S, Jacobs J, Cheung M, Walters M, Jacobs-Slifka K, Stone ND, Mikhail L, Chaturvedi S, Klein L, Vagnone PS, Schneider E, Berkow EL, Jackson BR, Vallabhaneni S, Zahn M, Epson E. Rapid Assessment and Containment of Candida auris Transmission in Postacute Care Settings-Orange County, California, 2019. Ann Intern Med 2021; 174:1554-1562. [PMID: 34487450 PMCID: PMC10984253 DOI: 10.7326/m21-2013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Candida auris, a multidrug-resistant yeast, can spread rapidly in ventilator-capable skilled-nursing facilities (vSNFs) and long-term acute care hospitals (LTACHs). In 2018, a laboratory serving LTACHs in southern California began identifying species of Candida that were detected in urine specimens to enhance surveillance of C auris, and C auris was identified in February 2019 in a patient in an Orange County (OC), California, LTACH. Further investigation identified C auris at 3 associated facilities. OBJECTIVE To assess the prevalence of C auris and infection prevention and control (IPC) practices in LTACHs and vSNFs in OC. DESIGN Point prevalence surveys (PPSs), postdischarge testing for C auris detection, and assessments of IPC were done from March to October 2019. SETTING All LTACHs (n = 3) and vSNFs (n = 14) serving adult patients in OC. PARTICIPANTS Current or recent patients in LTACHs and vSNFs in OC. INTERVENTION In facilities where C auris was detected, PPSs were repeated every 2 weeks. Ongoing IPC support was provided. MEASUREMENTS Antifungal susceptibility testing and whole-genome sequencing to assess isolate relatedness. RESULTS Initial PPSs at 17 facilities identified 44 additional patients with C auris in 3 (100%) LTACHs and 6 (43%) vSNFs, with the first bloodstream infection reported in May 2019. By October 2019, a total of 182 patients with C auris were identified by serial PPSs and discharge testing. Of 81 isolates that were sequenced, all were clade III and highly related. Assessments of IPC identified gaps in hand hygiene, transmission-based precautions, and environmental cleaning. The outbreak was contained to 2 facilities by October 2019. LIMITATION Acute care hospitals were not assessed, and IPC improvements over time could not be rigorously evaluated. CONCLUSION Enhanced laboratory surveillance and prompt investigation with IPC support enabled swift identification and containment of C auris. PRIMARY FUNDING SOURCE Centers for Disease Control and Prevention.
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Affiliation(s)
- Ellora N Karmarkar
- Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia, and the California Department of Public Health, Richmond, California (E.N.K.)
| | - Kathleen O'Donnell
- Orange County Health Care Agency, Santa Ana, California (K.O., D.S., J.J., M.C., L.M., M.Z.)
| | - Christopher Prestel
- Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia (C.P., J.R., M.T.)
| | - Kaitlin Forsberg
- Centers for Disease Control and Prevention and IHRC, Atlanta, Georgia (K.F.)
| | - Lalitha Gade
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Seema Jain
- California Department of Public Health, Richmond, California (S.J., H.B., T.N., Z.K., S.H., E.E.)
| | - Douglas Schan
- Orange County Health Care Agency, Santa Ana, California (K.O., D.S., J.J., M.C., L.M., M.Z.)
| | - Nancy Chow
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Darby McDermott
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - John Rossow
- Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia (C.P., J.R., M.T.)
| | - Mitsuru Toda
- Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia (C.P., J.R., M.T.)
| | - Ryan Ruiz
- Washington State Public Health Laboratories, Shoreline, Washington (R.R., S.H., E.S.)
| | - Sopheay Hun
- Washington State Public Health Laboratories, Shoreline, Washington (R.R., S.H., E.S.)
| | - Jennifer L Dale
- Minnesota Department of Health Public Health Laboratory, St. Paul, Minnesota (J.L.D., A.G., P.S.V.)
| | - Annastasia Gross
- Minnesota Department of Health Public Health Laboratory, St. Paul, Minnesota (J.L.D., A.G., P.S.V.)
| | - Tyler Maruca
- Maryland Department of Health Laboratories Administration, Baltimore, Maryland (T.M., L.K.)
| | - Janet Glowicz
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Richard Brooks
- Centers for Disease Control and Prevention, Atlanta, Georgia, and the Maryland Department of Health, Infectious Disease Epidemiology and Outbreak Response Bureau, Baltimore, Maryland (R.B.)
| | - Hosniyeh Bagheri
- California Department of Public Health, Richmond, California (S.J., H.B., T.N., Z.K., S.H., E.E.)
| | - Teresa Nelson
- California Department of Public Health, Richmond, California (S.J., H.B., T.N., Z.K., S.H., E.E.)
| | - Nicole Gualandi
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Zenith Khwaja
- California Department of Public Health, Richmond, California (S.J., H.B., T.N., Z.K., S.H., E.E.)
| | - Sam Horwich-Scholefield
- California Department of Public Health, Richmond, California (S.J., H.B., T.N., Z.K., S.H., E.E.)
| | - Josh Jacobs
- Orange County Health Care Agency, Santa Ana, California (K.O., D.S., J.J., M.C., L.M., M.Z.)
| | - Michele Cheung
- Orange County Health Care Agency, Santa Ana, California (K.O., D.S., J.J., M.C., L.M., M.Z.)
| | - Maroya Walters
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Kara Jacobs-Slifka
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Nimalie D Stone
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Lydia Mikhail
- Orange County Health Care Agency, Santa Ana, California (K.O., D.S., J.J., M.C., L.M., M.Z.)
| | | | - Liore Klein
- Maryland Department of Health Laboratories Administration, Baltimore, Maryland (T.M., L.K.)
| | - Paula Snippes Vagnone
- Minnesota Department of Health Public Health Laboratory, St. Paul, Minnesota (J.L.D., A.G., P.S.V.)
| | - Emily Schneider
- Washington State Public Health Laboratories, Shoreline, Washington (R.R., S.H., E.S.)
| | - Elizabeth L Berkow
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Brendan R Jackson
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Snigdha Vallabhaneni
- Centers for Disease Control and Prevention, Atlanta, Georgia (L.G., N.C., D.M., J.G., N.G., M.W., K.J., N.D.S., E.L.B., B.R.J., S.V.)
| | - Matthew Zahn
- Orange County Health Care Agency, Santa Ana, California (K.O., D.S., J.J., M.C., L.M., M.Z.)
| | - Erin Epson
- California Department of Public Health, Richmond, California (S.J., H.B., T.N., Z.K., S.H., E.E.)
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McKinsey DS, Gasser C, McKinsey JP, Ditto G, Agard A, Zellmer B, Poteete C, Vagnone PS, Dale JL, Bos J, Hahn R, Turabelidze G, Poiry M, Franklin P, Vlachos N, McAllister GA, Halpin AL, Glowicz J, Ham DC, Epstein L. A comprehensive approach to ending an outbreak of rare bla OXA-72 gene-positive carbapenem-resistant Acinetobacter baumannii at a Community Hospital, Kansas City, MO, 2018. Am J Infect Control 2021; 49:1183-1185. [PMID: 33839188 DOI: 10.1016/j.ajic.2021.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/01/2023]
Abstract
We identified a cluster of extensively drug-resistant, carbapenemase gene-positive, carbapenem-resistant Acinetobacter baumannii (CP-CRAB) at a teaching hospital in Kansas City. Extensively drug-resistant CRAB was identified from eight patients and 3% of environmental cultures. We used patient cohorting and targeted environmental disinfection to stop transmission. After implementation of these measures, no additional cases were identified.
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Affiliation(s)
| | | | | | - Geri Ditto
- Research Medical Center, Kansas City, MO
| | | | | | | | - Paula Snippes Vagnone
- Minnesota Department of Health Public Health Laboratory, Infectious Disease Section, St. Paul, MN
| | - Jennifer L Dale
- Minnesota Department of Health Public Health Laboratory, Infectious Disease Section, St. Paul, MN
| | - John Bos
- Missouri Department of Health and Senior Services, Jefferson City MO
| | - Rachael Hahn
- Missouri Department of Health and Senior Services, Jefferson City MO
| | | | - Madison Poiry
- Missouri Department of Health and Senior Services, Jefferson City MO
| | - Patrick Franklin
- Missouri Department of Health and Senior Services, Jefferson City MO
| | - Nicholas Vlachos
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Gillian A McAllister
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA; Commissioned Corps, U.S. Public Health Service, Rockville MD
| | - Janet Glowicz
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - D Cal Ham
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Lauren Epstein
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
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Dale JL, Raynor MJ, Ty MC, Hadjifrangiskou M, Koehler TM. A Dual Role for the Bacillus anthracis Master Virulence Regulator AtxA: Control of Sporulation and Anthrax Toxin Production. Front Microbiol 2018; 9:482. [PMID: 29599764 PMCID: PMC5862856 DOI: 10.3389/fmicb.2018.00482] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
Bacillus anthracis is an endemic soil bacterium that exhibits two different lifestyles. In the soil environment, B. anthracis undergoes a cycle of saprophytic growth, sporulation, and germination. In mammalian hosts, the pathogenic lifestyle of B. anthracis is spore germination followed by vegetative cell replication, but cells do not sporulate. During infection, and in specific culture conditions, transcription of the structural genes for the anthrax toxin proteins and the biosynthetic operon for capsule synthesis is positively controlled by the regulatory protein AtxA. A critical role for the atxA gene in B. anthracis virulence has been established. Here we report an inverse relationship between toxin production and sporulation that is linked to AtxA levels. During culture in conditions favoring sporulation, B. anthracis produces little to no AtxA. When B. anthracis is cultured in conditions favoring toxin gene expression, AtxA is expressed at relatively high levels and sporulation rate and efficiency are reduced. We found that a mutation within the atxA promoter region resulting in AtxA over-expression leads to a marked sporulation defect. The sporulation phenotype of the mutant is dependent upon pXO2-0075, an atxA-regulated open reading frame located on virulence plasmid pXO2. The predicted amino acid sequence of the pXO2-0075 protein has similarity to the sensor domain of sporulation sensor histidine kinases. It was shown previously that pXO2-0075 overexpression suppresses sporulation. We have designated pXO2-0075 “skiA” for “sporulation kinase inhibitor.” Our results indicate that in addition to serving as a positive regulator of virulence gene expression, AtxA modulates B. anthracis development.
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Affiliation(s)
- Jennifer L Dale
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
| | - Malik J Raynor
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
| | - Maureen C Ty
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Maria Hadjifrangiskou
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
| | - Theresa M Koehler
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,MD Anderson Cancer Center and UTHealth Graduate School of Biomedical Sciences, The University of Texas, Houston, TX, United States
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Keogh D, Tay WH, Ho YY, Dale JL, Chen S, Umashankar S, Williams RBH, Chen SL, Dunny GM, Kline KA. Enterococcal Metabolite Cues Facilitate Interspecies Niche Modulation and Polymicrobial Infection. Cell Host Microbe 2017; 20:493-503. [PMID: 27736645 DOI: 10.1016/j.chom.2016.09.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/25/2016] [Accepted: 09/07/2016] [Indexed: 01/04/2023]
Abstract
Enterococcus faecalis is frequently associated with polymicrobial infections of the urinary tract, indwelling catheters, and surgical wound sites. E. faecalis co-exists with Escherichia coli and other pathogens in wound infections, but mechanisms that govern polymicrobial colonization and pathogenesis are poorly defined. During infection, bacteria must overcome multiple host defenses, including nutrient iron limitation, to persist and cause disease. In this study, we investigated the contribution of E. faecalis to mixed-species infection when iron availability is restricted. We show that E. faecalis significantly augments E. coli biofilm growth and survival in vitro and in vivo by exporting L-ornithine. This metabolic cue facilitates E. coli biosynthesis of the enterobactin siderophore, allowing E. coli growth and biofilm formation in iron-limiting conditions that would otherwise restrict its growth. Thus, E. faecalis modulates its local environment by contributing growth-promoting cues that allow co-infecting organisms to overcome iron limitation and promotes polymicrobial infections.
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Affiliation(s)
- Damien Keogh
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Wei Hong Tay
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yao Yong Ho
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jennifer L Dale
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Siyi Chen
- Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074, Singapore
| | - Shivshankar Umashankar
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore 114756, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore 114756, Singapore
| | - Swaine L Chen
- Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074, Singapore; GERMS and Infectious Disease Group, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
| | - Gary M Dunny
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Kimberly A Kline
- Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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Bhatty M, Camacho MI, Gonzalez-Rivera C, Frank KL, Dale JL, Manias DA, Dunny GM, Christie PJ. PrgU: a suppressor of sex pheromone toxicity in Enterococcus faecalis. Mol Microbiol 2016; 103:398-412. [PMID: 27785854 DOI: 10.1111/mmi.13563] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Upon sensing of the peptide pheromone cCF10, Enterococcus faecalis cells carrying pCF10 produce three surface adhesins (PrgA, PrgB or Aggregation Substance, PrgC) and the Prg/Pcf type IV secretion system and, in turn, conjugatively transfer the plasmid at high frequencies to recipient cells. Here, we report that cCF10 induction is highly toxic to cells sustaining a deletion of prgU, a small orf located immediately downstream of prgB on pCF10. Upon pheromone exposure, these cells overproduce the Prg adhesins and display impaired envelope integrity, as evidenced by antibiotic susceptibility, misplaced division septa and cell lysis. Compensatory mutations in regulatory loci controlling expression of pCF10-encoded prg/pcf genes, or constitutive PrgU overproduction, block production of the Prg adhesins and render cells insensitive to pheromone. Cells engineered to overproduce PrgB, even independently of other pCF10-encoded proteins, have severely compromised cell envelopes and strong growth defects. PrgU has an RNA-binding fold, and prgB-prgU gene pairs are widely distributed among E. faecalis isolates and other enterococcal and staphylococcal species. Together, our findings support a model in which PrgU proteins represent a novel class of RNA-binding regulators that act to mitigate toxicity accompanying overproduction of PrgB-like adhesins in E. faecalis and other clinically-important Gram-positive species.
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Affiliation(s)
- Minny Bhatty
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, Texas, 77030, USA
| | - Martha I Camacho
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, Texas, 77030, USA
| | - Christian Gonzalez-Rivera
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, Texas, 77030, USA
| | - Kristi L Frank
- Department of Microbiology and Immunology, University of Minnesota Medical School, Microbiology Research Facility, 689 23rd Ave, S.E, Minneapolis, Minnesota, 55455, USA
| | - Jennifer L Dale
- Department of Microbiology and Immunology, University of Minnesota Medical School, Microbiology Research Facility, 689 23rd Ave, S.E, Minneapolis, Minnesota, 55455, USA
| | - Dawn A Manias
- Department of Microbiology and Immunology, University of Minnesota Medical School, Microbiology Research Facility, 689 23rd Ave, S.E, Minneapolis, Minnesota, 55455, USA
| | - Gary M Dunny
- Department of Microbiology and Immunology, University of Minnesota Medical School, Microbiology Research Facility, 689 23rd Ave, S.E, Minneapolis, Minnesota, 55455, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, Texas, 77030, USA
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Barnes AMT, Dale JL, Chen Y, Manias DA, Greenwood Quaintance KE, Karau MK, Kashyap PC, Patel R, Wells CL, Dunny GM. Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model. Virulence 2016; 8:282-296. [PMID: 27562711 DOI: 10.1080/21505594.2016.1208890] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The mammalian gastrointestinal (GI) tract is a complex organ system with a twist-a significant portion of its composition is a community of microbial symbionts. The microbiota plays an increasingly appreciated role in many clinically-relevant conditions. It is important to understand the details of biofilm development in the GI tract since bacteria in this state not only use biofilms to improve colonization, biofilm bacteria often exhibit high levels of resistance to common, clinically relevant antibacterial drugs. Here we examine the initial colonization of the germ-free murine GI tract by Enterococcus faecalis-one of the first bacterial colonizers of the naïve mammalian gut. We demonstrate strong morphological similarities to our previous in vitro E. faecalis biofilm microcolony architecture using 3 complementary imaging techniques: conventional tissue Gram stain, immunofluorescent imaging (IFM) of constitutive fluorescent protein reporter expression, and low-voltage scanning electron microscopy (LV-SEM). E. faecalis biofilm microcolonies were readily identifiable throughout the entire lower GI tract, from the duodenum to the colon. Notably, biofilm development appeared to occur as discrete microcolonies directly attached to the epithelial surface rather than confluent sheets of cells throughout the GI tract even in the presence of high (>109) fecal bacterial loads. An in vivo competition experiment using a pool of 11 select E. faecalis mutant strains containing sequence-defined transposon insertions showed the potential of this model to identify genetic factors involved in E. faecalis colonization of the murine GI tract.
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Affiliation(s)
- Aaron M T Barnes
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Jennifer L Dale
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Yuqing Chen
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Dawn A Manias
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Kerryl E Greenwood Quaintance
- b Department of Laboratory Medicine and Pathology , Division of Clinical Microbiology, Mayo Clinic , Rochester , MN , USA
| | - Melissa K Karau
- b Department of Laboratory Medicine and Pathology , Division of Clinical Microbiology, Mayo Clinic , Rochester , MN , USA
| | - Purna C Kashyap
- c Division of Gastroenterology , Department of Medicine , Mayo Clinic , Rochester , MN , USA
| | - Robin Patel
- b Department of Laboratory Medicine and Pathology , Division of Clinical Microbiology, Mayo Clinic , Rochester , MN , USA.,d Department of Medicine , Division of Infectious Disease, Mayo Clinic , Rochester , MN , USA
| | - Carol L Wells
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA.,e Laboratory Medicine and Pathology , University of Minnesota Medical School , Minneapolis , MN , USA
| | - Gary M Dunny
- a Departments of Microbiology & Immunology , University of Minnesota Medical School , Minneapolis , MN , USA
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9
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Dale JL, Cagnazzo J, Phan CQ, Barnes AMT, Dunny GM. Multiple roles for Enterococcus faecalis glycosyltransferases in biofilm-associated antibiotic resistance, cell envelope integrity, and conjugative transfer. Antimicrob Agents Chemother 2015; 59:4094-105. [PMID: 25918141 PMCID: PMC4468649 DOI: 10.1128/aac.00344-15] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [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: 02/09/2015] [Accepted: 04/21/2015] [Indexed: 12/31/2022] Open
Abstract
The emergence of multidrug-resistant bacteria and the limited availability of new antibiotics are of increasing clinical concern. A compounding factor is the ability of microorganisms to form biofilms (communities of cells encased in a protective extracellular matrix) that are intrinsically resistant to antibiotics. Enterococcus faecalis is an opportunistic pathogen that readily forms biofilms and also has the propensity to acquire resistance determinants via horizontal gene transfer. There is intense interest in the genetic basis for intrinsic and acquired antibiotic resistance in E. faecalis, since clinical isolates exhibiting resistance to multiple antibiotics are not uncommon. We performed a genetic screen using a library of transposon (Tn) mutants to identify E. faecalis biofilm-associated antibiotic resistance determinants. Five Tn mutants formed wild-type biofilms in the absence of antibiotics but produced decreased biofilm biomass in the presence of antibiotic concentrations that were subinhibitory to the parent strain. Genetic determinants responsible for biofilm-associated antibiotic resistance include components of the quorum-sensing system (fsrA, fsrC, and gelE) and two glycosyltransferase (GTF) genes (epaI and epaOX). We also found that the GTFs play additional roles in E. faecalis resistance to detergent and bile salts, maintenance of cell envelope integrity, determination of cell shape, polysaccharide composition, and conjugative transfer of the pheromone-inducible plasmid pCF10. The epaOX gene is located in a variable extended region of the enterococcal polysaccharide antigen (epa) locus. These data illustrate the importance of GTFs in E. faecalis adaptation to diverse growth conditions and suggest new targets for antimicrobial design.
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Affiliation(s)
- Jennifer L Dale
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Julian Cagnazzo
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Chi Q Phan
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Aaron M T Barnes
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Gary M Dunny
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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10
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James AP, Geijskes RJ, Dale JL, Harding RM. Development of a Novel Rolling-Circle Amplification Technique to Detect Banana streak virus that also Discriminates Between Integrated and Episomal Virus Sequences. Plant Dis 2011; 95:57-62. [PMID: 30743660 DOI: 10.1094/pdis-07-10-0519] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Banana plants are hosts to a large number of Banana streak virus (BSV) species. However, diagnostic methods for BSV are inadequate because of the considerable genetic and serological diversity among BSV isolates and the presence of integrated BSV sequences in some banana cultivars which leads to false positives. In this study, a sequence-nonspecific, rolling-circle amplification (RCA) technique was developed and shown to overcome these limitations for the detection and subsequent characterization of BSV isolates infecting banana. This technique was shown to discriminate between integrated and episomal BSV DNA, specifically detecting the latter in several banana cultivars known to contain episomal or integrated sequences of Banana streak Mysore virus (BSMyV), Banana streak OL virus (BSOLV), and Banana streak GF virus (BSGFV). Using RCA, the presence of BSMyV and BSOLV was confirmed in Australia, while BSOLV, BSGFV, Banana streak Uganda I virus (BSUgIV), Banana streak Uganda L virus (BSUgLV), and Banana streak Uganda M virus (BSUgMV) were detected in Uganda. This is the first confirmed report of episomally-derived BSUglV, BSUgLV, and BSUgMV in Uganda. As well as its ability to detect BSV, RCA was shown to detect two other pararetroviruses, Sugarcane bacilliform virus in sugarcane and Cauliflower mosaic virus in turnip.
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Affiliation(s)
- A P James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - R J Geijskes
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - J L Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - R M Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
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11
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Ha C, Revill P, Harding RM, Vu M, Dale JL. Identification and sequence analysis of potyviruses infecting crops in Vietnam. Arch Virol 2007; 153:45-60. [PMID: 17906829 DOI: 10.1007/s00705-007-1067-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 08/27/2007] [Indexed: 10/22/2022]
Abstract
Fifty-two virus isolates from 13 distinct potyvirus species infecting crops in Vietnam were identified and the 3' region of each genome was sequenced. The viruses were: bean common mosaic virus (BCMV), potato virus Y (PVY), sugarcane mosaic virus (SCMV), sorghum mosaic virus (SrMV), chilli veinal mottle virus (ChiVMV), zucchini yellow mosaic virus (ZYMV), leek yellow stripe virus (LYMV), shallot yellow stripe virus (SYSV), onion yellow dwarf virus (OYDV), turnip mosaic virus (TuMV), dasheen mosaic virus (DsMV), sweet potato feathery mottle virus (SPFMV) and a novel potyvirus infecting chilli, tentatively named chilli ringspot virus (ChiRSV). With the exception of BCMV and PVY, this is first report of these viruses in Vietnam. Further, rabbit bell (Crotalaria anagyroides) and typhonia (Typhonium trilobatum) were identified as new natural hosts of the peanut stunt virus (PStV) strain of BCMV and of DsMV, respectively. Sequence and phylogenetic analyses of the entire CP-coding region revealed considerable variability in BCMV, SCMV, PVY, ZYMV and DsMV.
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Affiliation(s)
- C Ha
- Tropical Crops and Biocommodities Domain, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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12
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Ha C, Coombs S, Revill PA, Harding RM, Vu M, Dale JL. Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Arch Virol 2007; 153:25-36. [PMID: 17906831 DOI: 10.1007/s00705-007-1053-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 08/06/2007] [Indexed: 10/22/2022]
Abstract
Two pairs of degenerate primers were designed from sequences within the potyviral CI (CIFor/CIRev) and HC-Pro-coding regions (HPFo/HPRev), and these were shown to be highly specific to members of the genus Potyvirus. Using the CIFor and CIRev primers, three novel potyviruses infecting crop and weed species from Vietnam were detected, namely telosma mosaic virus (TelMV) infecting telosma (Telosma cordata, Asclepiadaceae), peace lily mosaic virus (PeLMV) infecting peace lily (Spathiphyllum patinii, Araceae) and wild tomato mosaic virus (WTMV) infecting wild tomato (Solanum torvum, Solanaceae). The fragments amplified by the two sets of primers enabled additional PCR and complete genomic sequencing of these viruses and a banana bract mosaic virus (BBrMV) isolate from the Philippines. All four viruses shared genomic features typical of potyviruses. Sequence comparisons and phylogenetic analyses indicated that WTMV was most closely related to chilli veinal mottle virus (ChiVMV) and pepper veinal mottle virus (PVMV), while PeLMV, TelMV and BBrMV were related to different extents to members of the bean common mosaic virus (BCMV) subgroup.
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Affiliation(s)
- C Ha
- Tropical Crops and Biocommodities Domain, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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13
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Herrera-Valencia VA, Dugdale B, Harding RM, Dale JL. Mapping the 5' ends of banana bunchy top virus gene transcripts. Arch Virol 2006; 152:615-20. [PMID: 17187296 DOI: 10.1007/s00705-006-0889-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 11/06/2006] [Indexed: 10/23/2022]
Abstract
Banana bunchy top virus (BBTV), a multi-component circular ssDNA virus, replicates via a dsDNA intermediate that also serves as a template for virion sense transcription. Seven virus-derived transcripts have been previously identified and analysed in BBTV-infected bananas by northern analysis and 3' rapid amplification of cDNA ends (3' RACE). In this study, we have used RNA ligase-mediated rapid amplification of 5' cDNA ends (RLM-RACE) to complete the mapping of the BBTV gene transcripts and have now fully mapped the transcribed regions of each BBTV component and effectively defined the upstream regulatory region.
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Affiliation(s)
- V A Herrera-Valencia
- Centre for Tropical Crops and Biocommodities, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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14
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McQualter RB, Burns P, Smith GR, Dale JL, Harding RM. Molecular analysis of Fiji disease virus genome segments 5, 6, 8 and 10. Arch Virol 2004; 149:713-21. [PMID: 15045559 DOI: 10.1007/s00705-003-0243-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2003] [Accepted: 10/01/2003] [Indexed: 10/26/2022]
Abstract
The complete sequences of Fiji disease virus (FDV) genome segments 5 (S5), S6, S8 and S10 were obtained and comprised 3150 nt, 2831 nt, 1959 nt and 1819 nt, respectively. Each segment contained a single ORF which encoded putative proteins of 115 kDa, 97 kDa, 69 kDa and 63.0 kDa, respectively. The putative amino acid sequences encoded by S5 and S6 contained putative leucine zipper motifs while FDV S5 and S8 each contained an ATP-GTP-binding motif. At the amino acid level, FDV S5, S6, S8 and S10 showed most similarity to the corresponding segments of Rice black-streaked dwarf virus. Based on sequence similarities, it is predicted that FDV S8 encodes a minor core protein, while FDV S10 encodes an outer capsid protein. The evolutionary relationships of FDV to other reoviruses are discussed.
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Affiliation(s)
- R B McQualter
- Plant Biotechnology Program, Science Research Centre, Queensland University of Technology, Brisbane, Australia
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15
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Geijskes RJ, Braithwaite KS, Smith GR, Dale JL, Harding RM. Sugarcane bacilliform virus encapsidates genome concatamers and does not appear to integrate into the Saccharum officinarum genome. Arch Virol 2004; 149:791-8. [PMID: 15045565 DOI: 10.1007/s00705-003-0260-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Accepted: 10/16/2003] [Indexed: 10/26/2022]
Abstract
Sugarcane bacilliform virus (SCBV) DNA molecules larger than the complete genome length of 7.6 kbp were detected in infected plants and in virions. We have confirmed that these high molecular weight nucleic acids were open circular DNA and viral in origin. Due to their open circular conformation, accurate size determination of the DNA molecules was not possible using conventional electrophoresis. Using field inversion gel electrophoresis (FIGE), however, the DNA appeared to increase in genome size increments, with sizes ranging from 1 to 4 genomes (31 kbp) detected. The DNA was packaged into virions, which may explain the observation of purified virions with lengths corresponding to one, two or three times the modal length of 130 nm. The DNA products were possibly concatamers formed during replication as a result of a terminal overlap on the sense strand, and were shown to be overlapped individual genome-length molecules and not covalently-bonded continuous DNA strands. Southern analysis indicated that SCBV sequences are not integrated into the sugarcane genome and that the high molecular weight DNA observed in the sugarcane accessions analysed represents SCBV concatamers.
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Affiliation(s)
- R J Geijskes
- David North Plant Research Centre, Bureau of Sugar Experiment Stations, Indooroopilly, Queensland, Australia
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16
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Yang IC, Hafner GJ, Revill PA, Dale JL, Harding RM. Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test. Arch Virol 2003; 148:1957-68. [PMID: 14551818 DOI: 10.1007/s00705-003-0163-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have analysed the sequence variability in the putative reverse transcriptase (RT)/ribonuclease H (RNaseH) and the C-terminal coat protein (CP)-coding regions from Taro bacilliform virus (TaBV) isolates collected throughout the Pacific Islands. When the RT/RNaseH-coding region of 22 TaBV isolates from Fiji, French Polynesia, New Caledonia, Papua New Guinea (PNG), Samoa, Solomon Islands and Vanuatu was examined, maximum variability at the nucleotide and amino acid level was 22.9% and 13.6%, respectively. Within the CP-coding region of 13 TaBV isolates from Fiji, New Caledonia, PNG, Samoa and the Solomon Islands, maximum variability at the nucleotide and amino acid level was 30.7% and 19.5%, respectively. Phylogenetic analysis showed that TaBV isolates from the Solomon Islands showed greatest variability while those from New Caledonia and PNG showed least variability. Based on the sequences of the TaBV RT/RNaseH-coding region, we have developed a PCR-based diagnostic test that specifically detects all known TaBV isolates. Preliminary indexing has revealed that TaBV is widespread throughout Pacific Island countries. A sequence showing approximately 50% nucleotide identity to TaBV in the RT/RNaseH-coding region was also detected in all taro samples tested. The possibility that this may represent either an integrated sequence or the genome of an additional badnavirus infecting taro is discussed.
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Affiliation(s)
- I C Yang
- Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane, Queensland, Australia
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17
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Abstract
We have characterised two distinct geminiviruses that infect cucurbit cultivars in Vietnam. The genomes of both viruses consisted of two circular ssDNA components (DNA-A and DNA-B), with a genome arrangement and coding sequence typical of viruses in the Begomovirus genus in the family Geminiviridae. The sequence of DNA-A of one of the viruses was approximately 97% similar to Squash leaf curl virus-China (SLCV-Ch), for which a DNA-B has yet to be identified. We have named this virus Squash leaf curl virus-Vietnam (SLCV-Vn). The intergenic region of the SLCV-Vn DNA-B contained a 40 nt deletion between the putative AC1 TATA box and the stem loop. A second virus isolated from loofa in southern Vietnam was only 80% similar to SLCV-Vn over the complete DNA-A sequence, however the nucleotide sequence in the coat protein coding regions was 95% similar. We have named this virus Loofa yellow mosaic virus-Vietnam (LYMV-Vn). Other regions of the SLCV-Vn and LYMV-Vn genomes differed markedly, suggesting the coat protein coding region was recombinant. The DNA-B of both viruses were only 60% similar over the complete nucleotide sequence, although the encoded amino acid sequence of the BC1 gene was 90% identical.
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Affiliation(s)
- P A Revill
- Plant Biotechnology, Science Research Centre, Queensland University of Technology, Brisbane, Australia.
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18
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Yang IC, Iommarini JP, Becker DK, Hafner GJ, Dale JL, Harding RM. A promoter derived from taro bacilliform badnavirus drives strong expression in transgenic banana and tobacco plants. Plant Cell Rep 2003; 21:1199-206. [PMID: 12910370 DOI: 10.1007/s00299-003-0621-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Revised: 02/24/2003] [Accepted: 02/28/2003] [Indexed: 05/19/2023]
Abstract
Taro bacilliform virus (TaBV) is a pararetrovirus of the genus Badnavirus which infects the monocotyledonous plant, taro ( Colocasia esculenta). A region of the TaBV genome spanning nucleotides 6,281 to 12 (T1200), including the 3' end of open reading frame 3 (ORF 3) and the intergenic region to the end of the tRNA(met)-binding site, was tested for promoter activity along with four different 5' deletion fragments (T600, T500, T250 and T100). In transient assays, only the T1200, T600, T500 fragments were shown to have promoter activity in taro leaf, banana suspension cells and tobacco callus. When these three promoters were evaluated in stably transformed, in vitro-grown transgenic banana and tobacco plants, all were found to drive near-constitutive expression of either the green fluorescent protein or beta-glucuronidase (GUS) reporter gene in the stem (or pseudostem), leaves and roots, with strongest expression observed in the vascular tissue. In transgenic banana leaves, the T600 promoter directed four-fold greater GUS activity than that of the T1200, T500 and the maize polyubiquitin-1 promoters. In transgenic tobacco leaves, the levels of GUS expression directed by the three promoters was between four- and ten-fold lower than that of the double Cauliflower mosaic virus 35S promoter. These results indicate that the TaBV-derived promoters may be useful for the high-level constitutive expression of transgenes in either monocotyledonous or dicotyledonous species.
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Affiliation(s)
- I C Yang
- Centre for Molecular Biotechnology, Queensland University of Technology, GPO Box 2434, 4001, Brisbane, Australia
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19
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Abstract
Taro bacilliform virus (TaBV) has been classified as a putative badnavirus based on its non-enveloped, bacilliform virion morphology and transmission by mealybugs. The complete nucleotide sequence of a Papua New Guinea isolate of TaBV has now been determined and comprises 7458 bp. The genome contains four open reading frames (ORFs) on the plus-strand that potentially encode proteins of 17, 16, 214 and 13 kDa. The size and organisation of TaBV ORFs 1-3 is similar to that of most other badnaviruses, while the location of ORF 4 is similar to that of ORF 4 and ORF X of the atypical badnaviruses Citrus yellow mosaic virus and Cacao swollen shoot virus, respectively. The putative amino acid sequence of TaBV ORF 3 contained motifs that are conserved amongst badnavirus proteins including aspartic protease, reverse transcriptase (RT) and ribonuclease H (RNase H). The highly conserved putative plant tRNA(met)-binding site was also present in the 935 bp intergenic region of TaBV. Phylogenetic analysis using the amino acid sequence of ORF 3 showed that TaBV branched most closely to Dioscorea bacilliform virus. These results confirm that TaBV is a pararetrovirus of the genus Badnavirus, family Caulimoviridae.
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Affiliation(s)
- I C Yang
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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20
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Abstract
The genome of an Australian isolate of Sugarcane bacilliform virus (SCBV-IM) was cloned, sequenced and analysed. The genome consisted of 7687 nucleotides and contained three open reading frames which were similar in size and organisation to those of other badnaviruses. SCBV-IM was found to be most similar to the SCBV-Morocco isolate with amino acid sequence similarity of 91.4 %, 83.8 % and 85.3 % in the ORF I, II and III coding regions, respectively. Phylogenetic analysis of the SCBV-IM ORF III deduced amino acid sequence showed that SCBV isolates were more closely related to each other than to other badnaviruses. Amplification of SCBV sequences from three different sugarcane varieties revealed considerable variability in the viral populations, both within single infected plants as well as between infected plants, suggesting that the SCBV isolates sequenced to date may not be representative of the range of virus variability.
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Affiliation(s)
- R J Geijskes
- David North Plant Research Centre, Bureau of Sugar Experiment Stations, Indooroopilly, Queensland, Australia.
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21
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Abstract
We have analysed the sequence variability of the banana bunchy top nanovirus (BBTV) DNA-1 sequence from 17 isolates collected throughout Vietnam, and showed that the level of DNA-1 sequence variation within Vietnam was approximately double that previously reported for Asian BBTV isolates. Furthermore, the sequences separated into two geographical subgroups that generally correlated to the northern or southern regions of Vietnam. We have also characterised an additional putative Rep-encoding component associated with some BBTV isolates from Vietnam. This component, which we have named BBTV-S3, shared 47%, 69%, 56% and 65% nucleotide sequence identity with the previously reported Rep-encoding components BBTV DNA-1, S1, S2 and Y1 respectively.
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Affiliation(s)
- K E Bell
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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22
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Abstract
Banana bunchy top nanovirus (BBTV) has a multicomponent circular single-stranded DNA (cssDNA) genome consisting of at least six components. We have cloned, sequenced and analysed two additional cssDNA components, designated BBTV-S1 and S2, associated with a Taiwanese BBTV isolate. The sequences of BBTV-S1 and S2 comprised 1109 and 1095 nucleotides (nt), respectively, and like BBTV DNA-1, potentially encoded replication initiation proteins (Reps). However, the genome organisation of BBTV-S1 and S2 differed from that of BBTV DNA-1 in that (i) the stem sequence of the CR-SL was not conserved, (ii) the internal gene was absent and (iii) the probable TATA boxes were located 5' of the stem-loop. Further, sequence and phylogenetic analysis of the Rep genes indicated that BBTV DNA-S1 and S2 were distinct from BBTV DNA-1. When different geographical isolates of BBTV were tested for the presence of BBTV-S1/S2, these components were detected in various isolates from Vietnam, Taiwan, the Philippines, Tonga and Samoa but were not detected in isolates from Australia, Egypt, Fiji, and India. Based on these results, BBTV-S1 and S2 do not appear to be integral components of the BBTV genome and represent additional Rep-encoding DNAs associated with BBTV.
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Affiliation(s)
- C L Horser
- Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane, Australia
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23
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Affiliation(s)
- S R Hermann
- Queensland University of Technology, Brisbane, Australia
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Dugdale B, Becker DK, Beetham PR, Harding RM, Dale JL. Promoters derived from banana bunchy top virus DNA-1 to -5 direct vascular-associated expression in transgenic banana (Musa spp.). Plant Cell Rep 2000; 19:810-814. [PMID: 30754874 DOI: 10.1007/s002999900185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The intergenic regions of banana bunchy top virus (BBTV) DNA-1 to -5 were fused to the green fluorescent protein (GFP) and uidA reporter genes and assessed for promoter activity in transgenic banana (Musa spp. cv. Bluggoe). Promoter activity associated with the BBTV-derived promoters was transgene dependent with greatest activity observed using the GFP reporter. The BBTV promoters (BT1 to BT5) directed expression primarily in vascular-associated cells, although levels of activity varied between individual promoters. Promoters BT4 and BT5 directed the highest levels of GFP expression, while activity from BT1, BT2 and BT3 promoters was considerably weaker. Intron-mediated enhancement, using the maize polyubiquitin 1 (ubi1) intron, generated a significant increase in GUS expression directed by the BBTV promoters in transgenic plants.
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Affiliation(s)
- B Dugdale
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland, Australia 4001 e-mail: Tel: +61-7-38642819 Fax: +61-7-38641524, , , , , , AU
| | - D K Becker
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland, Australia 4001 e-mail: Tel: +61-7-38642819 Fax: +61-7-38641524, , , , , , AU
| | - P R Beetham
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland, Australia 4001 e-mail: Tel: +61-7-38642819 Fax: +61-7-38641524, , , , , , AU
| | - R M Harding
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland, Australia 4001 e-mail: Tel: +61-7-38642819 Fax: +61-7-38641524, , , , , , AU
| | - J L Dale
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland, Australia 4001 e-mail: Tel: +61-7-38642819 Fax: +61-7-38641524, , , , , , AU
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25
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Abstract
Complete nucleotide sequences of the coat protein gene (DNA-3) of banana bunchy top virus (BBTV) were obtained from five geographical isolates by PCR. Analysis of these sequences revealed two distinct groups of BBTV isolates with those from the Philippines, Taiwan and Vietnam forming the Asian group while the South Pacific/African group consisted of isolates from Australia, Burundi and Fiji. At the nucleotide level, the sequences of DNA-3 were more similar between isolates from the same group (maximum 5.86%) than between members of the two different groups (maximum 13.05%). At the amino acid level, the BBTV coat protein remained highly conserved, with a maximum of < 3% sequence variation between all isolates in this study. There was a significantly higher degree of divergence between the Asian isolates, which may indicate that BBTV has been present in this region for an extended period of time or that there have been multiple introductions of BBTV into bananas. The high level of conservation in the BBTV coat protein suggests that any of the DNA-3 sequences presented in this study would probably be equally effective as transgene in attempts to generate transgenic banana plants with resistance to both groups of BBTV isolates.
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Affiliation(s)
- R Wanitchakorn
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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26
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Becker DK, Dugdale B, Smith MK, Harding RM, Dale JL. Genetic transformation of Cavendish banana (Musa spp. AAA group) cv 'Grand Nain' via microprojectile bombardment. Plant Cell Rep 2000; 19:229-234. [PMID: 30754900 DOI: 10.1007/s002990050004] [Citation(s) in RCA: 35] [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] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An effective method has been developed for the stable transformation and regeneration of Cavendish banana (Musa spp. AAA group) cv 'Grand Nain' by microprojectile bombardment. Embryogenic cell suspensions were initiated using immature male flowers as the explant. Cells were co-bombarded with the neomycin phosphotransferase (nptII) selectable marker gene under the control of a banana bunchy top virus (BBTV) promoter or the CaMV 35S promoter, and either the β-glucuronidase (uidA) reporter gene or BBTV genes under the control of the maize polyubiquitin promoter. Plants were regenerated, under selection with kanamycin, that were co-transformed with nptII and either the uidA or BBTV genes. Molecular characterisation of transformants demonstrated that the transgenes had been stably integrated into the banana genome.
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Affiliation(s)
- D K Becker
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia e-mail: Fax: (+61) 7 3864 1534, , , , , , AU
| | - B Dugdale
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia e-mail: Fax: (+61) 7 3864 1534, , , , , , AU
| | - M K Smith
- Maroochy Research Station, Queensland Horticulture Institute, Department of Primary Industries, Queensland, Australia, , , , , , AU
| | - R M Harding
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia e-mail: Fax: (+61) 7 3864 1534, , , , , , AU
| | - J L Dale
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia e-mail: Fax: (+61) 7 3864 1534, , , , , , AU
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27
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Abstract
Green fluorescent protein (GFP)-tagging was used to determine the intracellular localization pattern of the proteins encoded by banana bunchy top virus (BBTV) DNA-3, -4 and -6. The protein encoded by BBTV DNA-4, which possesses a hydrophobic N terminus, was found to localize exclusively to the cell periphery while the proteins encoded by BBTV DNA-3 and -6 were found in both the nucleus and the cytoplasm. Co-expression of the DNA-4 protein and the proteins encoded by BBTV DNA-3 and -6 revealed that the DNA-4 protein was able to re-locate the DNA-6 protein, but not the DNA-3 protein, to the cell periphery. The 29 amino acid N-terminal hydrophobic region of the DNA-4 gene product appeared to be essential for specific localization of this protein since deletion of this region abolished its ability to localize to the cell periphery. These results indicate that BBTV may utilize a system analogous to that of the begomoviruses with the BBTV DNA-6 protein acting as a nuclear shuttle protein (NSP) while the DNA-4 protein transports the NSP-DNA complexes to the cell periphery for intercellular transport. The protein encoded by BBTV DNA-5 was found to contain an LXCXE motif and yeast two-hybrid analysis revealed that the DNA-5 protein has retinoblastoma (Rb)-binding activity. This activity was dependent on an intact LXCXE motif since specific mutations to either the C or E residue completely abolished Rb-binding activity. These results indicate that the gene product of BBTV DNA-5 is an Rb-binding-like protein and may play an important role in host-cell cycle manipulation.
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Affiliation(s)
- R Wanitchakorn
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, George Street, Brisbane 4001, Australia
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28
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Abstract
The 5' and 3' terminal sequences of the plus strand of Fiji disease fijivirus (FDV) segments 2, 3, 9 and 10 possess the conserved terminal sequences, 5'AAGUUUUU.....CAGCAGAUGUC 3'. The 5' sequence is identical to that of maize rough dwarf fijivirus (MRDV) and rice black-streaked dwarf fijivirus (RBSDV), whereas the FDV 3' sequence shares the consensus, CAGCNNNNGUC, with MRDV and RBSDV. The FDV terminal sequences, and the amino acid sequences from FDV segment 9, are more closely related to those from MRDV and RBSDV than to those from oat sterile dwarf fijivirus (OSDV) and Nilaparvata lugens reovirus (NLRV; a putative Fijivirus).
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Affiliation(s)
- J A McMahon
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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Rodoni BC, Dale JL, Harding RM. Characterization and expression of the coat protein-coding region of banana bract mosaic potyvirus, development of diagnostic assays and detection of the virus in banana plants from five countries in southeast Asia. Arch Virol 1999; 144:1725-37. [PMID: 10542022 DOI: 10.1007/s007050050700] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We have sequenced the entire coat protein (CP)-coding region and 5' 162 nucleotides of the 3' untranslated region (UTR) of nine different isolates of banana bract mosaic virus (BBrMV) from five different countries. Further, we have sequenced the 3' 621 nucleotides of the NIb-coding region of a Philippines isolate. This is the first report of BBrMV in Thailand, Vietnam and Western Samoa. When the sequences of the CP-coding region and 3' UTR were compared to each other, variability of between 0.3% and 5.6%, and 0.3% and 4. 3%, was observed at the nucleotide and amino acid levels, respectively. Phylogenetic analysis of the BBrMV isolates did not reveal any relationship between the geographic location of the isolates. The BBrMV CP was expressed in Escherichia coli as a fusion protein and the purified recombinant protein was used to produce a high titre BBrMV-specific polyclonal antiserum. This antiserum was used to develop a F(ab')(2) indirect double antibody sandwich ELISA and compared with immuno-capture PCR (IC-PCR) and reverse transcription PCR (RT-PCR) assays for BBrMV detection. RT-PCR was shown to be the most sensitive test followed by ELISA and IC-PCR. http://link.springer. de/link/service/journals/00705/bibs/9144009/91441725.htm</++ +HEA
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Affiliation(s)
- B C Rodoni
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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30
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Abstract
Banana bunchy top virus (BBTV) DNA-3 to 6 have each previously been shown to contain one large open reading frame in the virion sense, whereas no large ORF had been identified in BBTV DNA-2. RNAs transcribed from the BBTV genome were mapped using northern hybridisation and 3' RACE. One mRNA was transcribed from each of BBTV DNA-2 to 6 and four of these mRNAs mapped to the ORFs previously identified in BBTV DNA-3 to 6. The mRNA of BBTV DNA-2 was transcribed from a virion sense ORF probably using a TATA box sequence different to that in BBTV DNA-1, and DNA-3 to 6. This ORF encoded a 10 kDa protein of unknown function. The 3' untranslated region of the five mRNAs varied from 25 nucleotides (BBTV DNA-6) to 167 nucleotides (BBTV DNA-4) and each contained putative polyadenylation signals with associated GT rich sequence together with a possible termination signal (C/T/A)TGTAA conserved in all five mRNAs.
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Affiliation(s)
- P R Beetham
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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31
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Soo HM, Handley JA, Maugeri MM, Burns P, Smith GR, Dale JL, Harding RM. Molecular characterization of Fiji disease fijivirus genome segment 9. J Gen Virol 1998; 79 ( Pt 12):3155-61. [PMID: 9880035 DOI: 10.1099/0022-1317-79-12-3155] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This is the first report of sequence from Fiji disease fijivirus (FDV), the type member of the genus Fijivirus of the family Reoviridae. FDV genome segment (S9) comprised 1843 nt and contained two non-overlapping ORFs, separated by a 57 nt intergenic region. S9 ORF 1 comprised 1008 nt and encoded a 335-amino-acid polypeptide (predicted molecular mass 38.6 kDa), while ORF 2 comprised 627 nt and encoded a 208-amino-acid polypeptide (predicted molecular mass 23.8 kDa). The 5' and 3' non-coding regions were 49 and 102 nt, respectively. The S9 terminal sequences were 5' AAGUUUUU------UGUC 3', and located immediately adjacent to these sequences were 12 bp imperfect inverted repeats. The entire S9 ORF 1 and the hydrophilic regions of S9 ORF 2 were each expressed as a fusion protein with the maltose-binding protein in Escherichia coli. Antibodies produced against the ORF 1 fusion protein reacted strongly with a protein of approximately 39 kDa present in both crude extracts of FDV-infected sugarcane and partially purified FDV preparations. In contrast, antibodies raised against the modified ORF 2 fusion protein did not react with any proteins in the same samples. Further, polyclonal antibodies produced against partially purified FDV reacted with the ORF 1, but not the modified ORF 2, fusion protein. These results indicate that FDV S9 ORF 1 encodes a major structural protein, while ORF 2 probably encodes a non-structural protein.
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Affiliation(s)
- H M Soo
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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32
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Dugdale B, Beetham PR, Becker DK, Harding RM, Dale JL. Promoter activity associated with the intergenic regions of banana bunchy top virus DNA-1 to -6 in transgenic tobacco and banana cells. J Gen Virol 1998; 79 ( Pt 10):2301-11. [PMID: 9780033 DOI: 10.1099/0022-1317-79-10-2301] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Promoter regions associated with each of the six ssDNA components of banana bunchy top virus (BBTV) have been characterized. DNA segments incorporating the intergenic regions of BBTV DNA-1 to -6 were isolated and fused to the uidA (beta-glucuronidase) reporter gene to assess promoter activity. In tobacco cell suspensions, the BBTV DNA-2 and -6 promoters generated levels of GUS expression 2-fold greater and similar to the 800 bp CaMV 35S promoter, respectively. Deletion analysis of the BBTV DNA-6 promoter suggested all the necessary promoter elements required for strong expression were located within 239 nucleotides upstream of the translational start codon. In transgenic tobacco plants, the BBTV-derived promoters generally provided a weak, tissue-specific GUS expression pattern restricted to phloem-associated cells. However, in callus derived from tobacco leaf tissue, GUS expression directed by the BBTV DNA-6 promoter was strong and, in some lines, comparable to the CaMV 35S promoter. Detectable promoter activity associated with the BBTV promoters in banana embryogenic cells was only observed using a sensitive green fluorescent protein (GFP) reporter. Promoters derived from BBTV DNA-4 and -5 generated the highest levels of transient activity, which were greater than that of the maize ubi-1 promoter. In transgenic banana plants, the activity of the BBTV DNA-6 promoter was restricted to the phloem of leaves and roots, stomata and root meristems.
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Affiliation(s)
- B Dugdale
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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33
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Handley JA, Smith GR, Dale JL, Harding RM. Sequence diversity in the coat protein coding region of twelve sugarcane mosaic potyvirus isolates from Australia, USA and South Africa. Arch Virol 1998; 143:1145-53. [PMID: 9687871 DOI: 10.1007/s007050050362] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have sequenced the coat protein (CP) coding region of 11 field isolates of SCMV from Australia, USA and South Africa. The differences between the nucleotide sequences of the isolates was 0.2 to 4.1% and the encoded amino acid sequences differed by 0.0 to 3.5%. Phylogenetic analysis of the CP coding sequences of the SCMV isolates and the related potyviruses SCMV-MDB, JGMV, SrMV, MDMV-A and PVY showed that the SCMV isolates formed a tightly clustered group, with SCMV-MDB forming a separate branch. This indicated that (i) the SCMV isolates are of one strain (SCMV-A) and not geographically distinct species and (ii) SCMV-MDB is clearly distinct, and may represent another potyvirus species.
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Affiliation(s)
- J A Handley
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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34
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Abstract
Banana bunchy top virus (BBTV) has a multicomponent genome consisting of at least six circular single-stranded DNAs each with a single large open reading frame (ORF) in the virion sense. A protein of approximately 20 kDa has been associated with purified virions and is assumed to be the viral coat protein. The N-terminus of this protein was sequenced and compared to the predicted amino acid sequence of the large ORF of BBTV DNA-1 to 6. This comparison indicated that the ORF of BBTV DNA-3, which potentially encodes a protein of 19.3 kDa, was the coat protein gene of BBTV. The ORF sequence of BBTV DNA-3 was cloned into a prokaryotic expression vector, pMAL-c2, and the resulting maltose binding-BBTV coat protein fusion product was purified and used for the production of polyclonal antiserum in a rabbit. The resultant antiserum was able to detect the presence of BBTV in infected leaf tissue confirming that the large virion sense ORF of BBTV DNA-3 encodes the viral coat protein.
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Affiliation(s)
- R Wanitchakorn
- Centre for Molecular Biotechnology, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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35
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Handley JA, Smith GR, Dale JL, Harding RM. Sequence diversity in the NIb coding region of eight sugarcane mosaic potyvirus isolates infecting sugarcane in Australia. Arch Virol 1998; 141:2289-300. [PMID: 9526537 DOI: 10.1007/bf01718631] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have sequenced the NIb coding region of sugarcane mosaic potyvirus strain SC (SCMV-SC) and eight field isolates of SCMV from Australia. This region comprised 1563 nucleotides and encoded a putative protein of 521 amino acids containing the consensus motif GDD. The protease cleavage sites between the NIa/NIb and the NIb/coat protein were found to be Q/C and Q/A, respectively. The SCMV sequences were most similar to sorghum mosaic potyvirus with identities of 70% and 78% at the nucleotide and amino acid levels, respectively. When the sequences were compared to each other, there was a maximum of 3.3% variation between isolates at the nucleotide level and a maximum of 0.8% at the amino acid level. Phylogenetic analysis of the sequences indicated the field isolates were grouped according to their geographical location. The SCMV sequence with most homology to all other isolates has been selected to generate constructs for replicase-mediated resistance.
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Affiliation(s)
- J A Handley
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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Pecheniuk NM, Marsh NA, Walsh TP, Dale JL. Use of first nucleotide change technology to determine the frequency of factor V Leiden in a population of Australian blood donors. Blood Coagul Fibrinolysis 1997; 8:491-5. [PMID: 9491266 DOI: 10.1097/00001721-199711000-00002] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Activated protein C resistance (APCR), the most common risk factor for venous thrombosis, is the result of a G to A base substitution at nucleotide 1691 (R506Q) in the factor V gene. Current techniques to detect the factor V Leiden mutation, such as determination of restriction length polymorphisms, do not have the capacity to screen large numbers of samples in a rapid, cost-effective test. The aim of this study was to apply the first nucleotide change (FNC) technology, to the detection of the factor V Leiden mutation. After preliminary amplification of genomic DNA by polymerase chain reaction (PCR), an allele-specific primer was hybridised to the PCR product and extended using fluorescent terminating dideoxynucleotides which were detected by colorimetric assay. Using this ELISA-based assay, the prevalence of the factor V Leiden mutation was determined in an Australian blood donor population (n = 500). A total of 18 heterozygotes were identified (3.6%) and all of these were confirmed with conventional MnlI restriction digest. No homozygotes for the variant allele were detected. We conclude from this study that the frequency of 3.6% is compatible with others published for Caucasian populations. In addition, the FNC technology shows promise as the basis for a rapid, automated DNA based test for factor V Leiden.
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Affiliation(s)
- N M Pecheniuk
- Co-operative Research Centre for Diagnostic Technologies, School of Life Sciences, Queensland University of Technology, Brisbane, Australia
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37
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Hafner GJ, Stafford MR, Wolter LC, Harding RM, Dale JL. Nicking and joining activity of banana bunchy top virus replication protein in vitro. J Gen Virol 1997; 78 ( Pt 7):1795-9. [PMID: 9225058 DOI: 10.1099/0022-1317-78-7-1795] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The major open reading frame of banana bunchy top virus (BBTV) DNA-1 encodes a putative replication initiation protein (Rep). In vitro, a fusion protein of BBTV Rep linked to a maltose-binding protein exhibited both site-specific nicking and joining activities. These activities were dependent on the presence of Mg2+ or Mn2+, but did not require ATP. The fusion protein specifically cleaved ssDNA between bases +7 and +8 of a conserved nonanucleotide loop sequence which is present in the virion-strand of the stem-loop common region of each BBTV component. During this reaction, the fusion protein became covalently attached to the 5' end of the 3'cleavage product. After the nicking reactions, the fusion protein was also capable of catalysing the joining of two nicked ssDNA fragments in a site-specific manner. Based on these activities, BBTV Rep would appear to be very similar to the Rep proteins of the geminiviruses.
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Affiliation(s)
- G J Hafner
- Centre for Molecular Biotechnology, School of Life Sciences, Brisbane, Queensland, Australia
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38
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Rodoni BC, Ahlawat YS, Varma A, Dale JL, Harding RM. Identification and Characterization of Banana Bract Mosaic Virus in India. Plant Dis 1997; 81:669-672. [PMID: 30861856 DOI: 10.1094/pdis.1997.81.6.669] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We have identified banana bract mosaic potyvirus (BBMV) in banana plants growing in the Coimbatore and Tiruchchirappalli regions of southern India based on symptomatology, particle morphology, sequence homology, and nucleic acid hybridization assays. Potyvirus-like particles typical of BBMV also were detected in sap dips from banana plants growing in Maharashtra State. Sequence comparisons of the C terminus of the coat protein-coding and 3' untranslated regions revealed that the Indian isolates of BBMV had greater than 96.6 and 97.2% homology with a Philippines isolate at the nucleotide and amino acid levels, respectively. BBMV-infected banana cultivars from the Coimbatore region showed the characteristic mosaic on the bract of the banana inflorescence. In contrast, infected plants growing in the Tiruchchirappalli region and Maharashtra State displayed symptoms similar to those associated with cucumber mosaic cucumovirus and not the characteristic bract mosaic symptom. These results indicate that BBMV is more widespread than previously thought.
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Affiliation(s)
- B C Rodoni
- Centre for Molecular Biotechnology, Queensland University of Technology (QUT), GPO Box 2434, Brisbane, Australia, 4001
| | - Y S Ahlawat
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi-110 012, India
| | - A Varma
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi-110 012, India
| | - J L Dale
- Centre for Molecular Biotechnology, QUT, GPO Box 2434, Brisbane, Australia, 4001
| | - R M Harding
- Centre for Molecular Biotechnology, QUT, GPO Box 2434, Brisbane, Australia, 4001
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39
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Abstract
Banana bunchy top virus (BBTV) genomic ssDNA is capable of complementary strand synthesis in vitro without the addition of exogenous primers. We have demonstrated that the self-priming of BBTV can be attributed to a population of endogenous primers which are bound to the genomic DNA within the virions. The primer molecules appeared to be composed entirely of DNA and are heterogeneous in size. The primers were cloned, sequenced and shown to map to a region within the major common region and extend 5' of this conserved region. These primers were found to be associated with multiple components of the genome and were capable of full-length complementary strand synthesis in vitro. Interestingly, most of the cloned primers appeared to be derived from BBTV DNA-5; no function has yet been determined for the putative protein of the large ORF within this component.
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Affiliation(s)
- G J Hafner
- Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane, Australia
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40
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Abstract
We have mapped the mRNA transcripts of banana bunchy top virus (BBTV) DNA-1. Northern hybridization and 3' RACE analysis identified two poly-adenylated RNAs associated with BBTV DNA-1. Previously, one major ORF in the virion sense of DNA-1 had been identified, which encoded a putative replication protein (Rep). An mRNA was identified in BBTV infected bananas that was clearly transcribed from this Rep ORF. Further, a second transcript was identified which mapped to an ORF completely within the Rep ORF. This encoded a putative 5 kDa protein of unknown function. Both these transcripts were also identified in a tobacco plant that had been transformed with Agrobacterium tumefaciens harbouring a binary construct containing the Rep ORF from BBTV DNA-1. This Rep ORF was inserted 3' of a cauliflower mosaic virus 35S promoter and 5' of a vegetable storage protein terminator. The transcripts mapped from these tobacco plants were identical at the 3' end to the transcripts from BBTV infected banana plants. The site of polyadenylation for the Rep ORF was at base 963 immediately 3' of the translational stop codon confirming that the polyadenylation signals for this transcript were all within the ORF. However, the internal ORF had a large untranslated region of 272 bases with its site of polyadenylation at nucleotide 803 and a polyadenylation signal 3' of the translational stop codon. A possible upstream termination signal (A/TTGTAA) was identified and was conserved within BBTV DNA-1 sequences from different international isolates.
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Affiliation(s)
- P R Beetham
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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41
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Smith GR, Ford R, Bryant JD, Gambley RL, McGhie TK, Harding RM, Dale JL. Expression, purification, and use as an antigen of recombinant sugarcane mosaic virus coat protein. Arch Virol 1995; 140:1817-31. [PMID: 7503681 DOI: 10.1007/bf01384344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A high titre (1:10,000) antiserum was raised in a rabbit against the coat protein of sugarcane mosaic potyvirus (SCMV), by injecting a preparation of recombinant coat protein purified from a fusion protein expressed in E. coli. The fusion protein consisted of the MalE maltose binding protein (MBP) and the viral coat protein separated by the protease factor Xa cleavage site. The fusion protein was encoded by the plasmid pMAL-cCPM, which was constructed by cloning a modified coat protein gene to the 3' end of the MBP/factor Xa coding region. The coat protein gene was modified by site-directed mutagenesis so that the ATG start codon in the original construct was replaced by the codon AGC, deleting the NcoI restriction site (C/CATGG) and creating a unique Eco47III site (AGC/GCT). Endonuclease restriction with Eco47III resulted in a DNA fragment with GCT as the first three nucleotides. This triplet encodes alanine, which is the proposed N-terminal amino acid residue of the mature native coat protein. This modified coat protein coding region was ligated directly behind the nucleotide code for the amino acid recognition sequence for factor Xa. Expression was induced with IPTG and the recombinant fusion protein was extracted from the bacterial lysate by amylose resin column affinity chromatography and the two domains separated by factor Xa proteolysis. The coat protein was then purified from the maltose binding protein by ion exchange chromatography in buffer containing 6 M urea. A highly purified sample which contained 150 micrograms of both full-length and truncated coat proteins, was recovered from a litre of bacterial broth. The antiserum reacted with native coat protein in SCMV-infected sugarcane, and with recombinant coat proteins expressed in E. coli and sugarcane protoplasts with little or no cross-reaction with sugarcane proteins.
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Affiliation(s)
- G R Smith
- David North Plant Research Centre, Bureau of Sugar Experiment Stations, Brisbane, Queensland, Australia
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Abstract
The systemic movement and replication of banana bunchy top virus (BBTV) DNA component one were investigated. Strand-specific RNA probes and PCR were used to indicate the presence of the virus in various parts of infected banana plants during infection on the basis of dsDNA replicative intermediates of BBTV. The strand-specific probes were not only able to detect the presence of the virus but also gave an indication of where the virus replicated. The results using both the virion sense and complementary to virion sense specific probes were essentially the same indicating that BBTV initially replicated for a short period at the site of inoculation, and subsequently moved down the pseudostem to the basal meristematic region and ultimately into the roots and newly formed leaves. The virus was detected in the leaves formed prior to inoculation after 21 days using PCR but was not detected by the RNA probes. This indicated that the virus had the ability to move into these leaves but may not have replicated or accumulated to significant levels. The appearance of multimeric forms of BBTV suggested that the virus may have replicated via a rolling circle mechanism. Additionally, BBTV DNA component one did not appear to replicate in its aphid vector, Pentalonia nigronervosa.
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Affiliation(s)
- G J Hafner
- Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane, Australia
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Abstract
We have cloned, sequenced and analysed an additional five circular ssDNA components of banana bunchy top virus (BBTV) which we have called components 2, 3, 4, 5 and 6. These components were present in all BBTV infections tested. Four of these components (components 3, 4, 5 and 6) had one large open reading frame (ORF) in the virion sense located 3' of a stem-loop structure. Each ORF had a potential TATA box and one or two potential polyadenylation signals associated with it and each polyadenylation signal had an associated GC-rich region containing the trinucleotide sequence TTG. A number of ORFs were identified in component 2 but none of these had appropriately located potential TATA boxes and polyadenylation signals associated with them. None of the ORF amino acid sequences nor the full DNA sequences of any of the components had significant sequence identity with any known protein or nucleic acid sequences. However, the ORF of component 4 encoded a 30 residue hydrophobic domain which may indicate that this ORF encoded a transmembrane protein. Further, the ORFs of components 3 and 5 potentially encoded proteins of about 20 kDa, the size of the BBTV coat protein. There were two regions of sequence identity between the five components described here and the previously described component 1. Each component contained a conserved stem-loop structure and a nonanucleotide potential TATA box which was 5' of the large virion-sense ORF in five of the components. The stem-loop structures were incorporated in a common region (CR-SL) of 69 nucleotides which was 62% identical between components. All six BBTV components also contained a major common region (CR-M) which was located 5' of the CR-SL in each component, in the non-coding region and was 76% identical over 92 nucleotides. Each CR-M contained a near-complete 16 nucleotide direct repeat and a GC-box which was similar to the rightward promoter element found in wheat dwarf geminivirus. From these results, BBTV appears to belong to an undescribed plant virus group which could also include subterranean clover stunt virus, coconut foliar decay virus, faba bean necrotic yellows virus and milk vetch dwarf virus.
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Affiliation(s)
- T M Burns
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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Wilcox CS, Heiser JF, Crowder AM, Wassom NJ, Katz BB, Dale JL. Comparison of the effects on pupil size and accommodation of three regimens of topical dapiprazole. Br J Ophthalmol 1995; 79:544-8. [PMID: 7626570 PMCID: PMC505162 DOI: 10.1136/bjo.79.6.544] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Patients who have their pupils dilated for an eye examination traditionally have to wait several hours before their pupils return to normal size and their blurred vision (caused by paralysis of accommodation) resolves. Earlier studies with dapiprazole have demonstrated an accelerated reversal of dilatation. METHODS Three regimens of dapiprazole were studied to determine the effects on pupil diameter and accommodation after mydriasis produced by 2.5% phenylephrine and 0.5% tropicamide. Test regimens included one drop and 1 + 1 drop regimens, compared with a 2 + 2 drop reference regimen. Dapiprazole was administered in one eye and placebo in the other. Mean change from baseline was analysed for pupil diameter and accommodation at various time points after drug administration. Also, for the same variables, 90% confidence intervals for the areas under the curve (AUC) were computed. RESULTS Both test regimens were equivalent to the reference regimen on the basis of mean change from baseline for pupil diameter and accommodation at individual time points, and for the mean AUC. Most signs and symptoms (injection, stinging, burning, lid oedema, and ptosis) were less frequent in the test regimen treated eyes. There was no significant interaction between regimen and eye colour. CONCLUSION This study indicates that a lower dosage (for example, one drop) is also efficacious and has the added benefit of fewer side effects.
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Affiliation(s)
- C S Wilcox
- Pharmacology Research Institute, Irvine, California, USA
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45
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Abstract
Banana bract mosaic (BBMV) is a relatively new, non-persistently aphid transmitted disease of bananas in the Philippines. Partially purified preparations from infected plants contained low numbers of flexuous virions, 660 to 760 nm in length, and a 38kDa protein, possibly the coat protein, which reacted with a general potyvirus antiserum in western blots. There were insufficient virions for conventional antiserum production or cDNA synthesis. Therefore, DNA was amplified using potyvirus-specific degenerate primers and reverse transcriptase PCR. The PCR products were cloned, sequenced and analysed and contained a 5' open reading frame of up to 150 amino acids and a 3' untranslated region of up to 190 nucleotides which were clearly related to the C-terminal half of the coat proteins and the 3' untranslated regions, respectively of potyviruses. The BBMV open reading frame amino acid sequence was most similar to the C-terminal half of the maize dwarf mosaic potyvirus coat protein (71.3% similarity) and the BBMV 3' untranslated region was most similar to that of ornithogalum mosaic potyvirus (39.6% similarity). Our results show that BBMV is a distinct potyvirus and also demonstrate the application of virus group specific primers in the characterisation of previously undescribed viruses.
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Affiliation(s)
- M F Bateson
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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46
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Abstract
Banana bunchy top virus (BBTV) DNA component 1 from isolates from 10 different countries was cloned and sequenced and the sequences were aligned and compared. This analysis indicated two groups: the South Pacific group (isolates from Australia, Burundi, Egypt, Fiji, India, Tonga and Western Samoa) and the Asian group (isolates from the Philippines, Taiwan and Vietnam). The mean sequence difference within each group was 1.9 to 3.0% and between isolates from the two groups was approximately 10%, but some parts of the sequences differed more than others. However, the protein encoded by the major open reading frame, which is probably a replicase, differed by approximately 5%. The region from the beginning of the stem-loop sequence to the potential TATA box was identical in all isolates except for a two nucleotide change in the Western Samoan isolate and a single change in that of the NSW isolate. These results, together with other evidence, suggest that BBTV has spread to bananas after the initial movement of bananas from the Asian Pacific regions to Africa and the Americas.
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Affiliation(s)
- M Karan
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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47
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Bateson MF, Henderson J, Chaleeprom W, Gibbs AJ, Dale JL. Papaya ringspot potyvirus: isolate variability and the origin of PRSV type P (Australia). J Gen Virol 1994; 75 ( Pt 12):3547-53. [PMID: 7996146 DOI: 10.1099/0022-1317-75-12-3547] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We have sequenced the coat protein gene of nine isolates of papaya ringspot virus (PRSV) including six Australian and three Asian isolates and compared these with four previously reported sequences of PRSV. There was up to 12% sequence variation between isolates at the nucleotide level. However, there was no significant difference between the sequences obtained from Australian isolates irrespective of whether they were PRSV type P (cucurbit or papaya infecting) or PRSV type W (cucurbit infecting) and these isolates were more closely related to one another than to any other isolate. These results imply that PRSV-P, first recorded in Australia in 1991, arose locally from PRSV-W (first recorded in Australia in 1978) rather than being introduced. Further, there was no consistent sequence difference between PRSV-P and PRSV-W isolates that would obviously account for their host range difference.
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Affiliation(s)
- M F Bateson
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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Karan M, Dale JL, Bateson MF, Harding RM, Teakle DS. Detection and characterization of pangola stunt Fijivirus from Australia using cloned cDNA probes. Arch Virol 1994; 135:397-404. [PMID: 7979975 DOI: 10.1007/bf01310023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Four cDNA clones were generated from the genomic dsRNA of an Australian isolate of pangola stunt Fijivirus (PaSV). Each clone hybridized with nucleic acid extracts from PaSV infected plants but not healthy plants. Further, each clone hybridized with more than one segment of the PaSV dsRNA genome. One clone was used to demonstrate that homology existed between the Australian isolate of PaSV and a South American isolate of PaSV although the isolates differed in the sizes of the genomic dsRNAs and in the vector species. The clone also hybridized with some segments of the maize rough dwarf Fijivirus genome.
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Affiliation(s)
- M Karan
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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49
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Abstract
A 93 nucleotide sequence was found to be strongly conserved between two ssDNA genomic components of banana bunchy top virus (BBTV). Two outwardly extending degenerate primers were designed from this sequence and used in a polymerase chain reaction (PCR) with DNA extracted from purified BBTV virions. PCR amplified products consisting of at least seven distinct bands all approximately 1 kb and possibly representing full-length BBTV dsDNA were resolved. The PCR amplified products were cloned and the clones screened by restriction enzyme analysis. Four distinct restriction analysis groups were identified. These results confirm that the genome of BBTV contains at least five components and that it belongs to a previously undescribed group of plant viruses which may also contain subterranean clover stunt virus.
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Affiliation(s)
- T M Burns
- Centre for Molecular Biotechnology, School of Life Science, Queensland University of Technology, Brisbane, Australia
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50
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Abstract
Biotinylated Fiji disease fijivirus specific cDNA probes detected the presence of the virus in total nucleic acid extracts from infected sugarcane plants. Hybridised biotinylated probes were detected with streptavidin-alkaline phosphatase conjugate and the light generating substrate AMPPD. Samples were either blotted manually, or by alkaline capillary transfer using 100 mM NaOH. Transfer of nucleic acids to charge modified nylon with sodium hydroxide was superior to denaturation with glyoxal or formamide and salt-citrate buffer transfer as the bands were clearly resolved and no degradation of the FDV dsRNA was observed. Transfer of either total nucleic acid extracts or purified dsRNA in manifold blots generated false positive signals with the non-radio-active chemiluminescent detection systems tested. Manual or northern blots had a limit of detection for purified target double-stranded RNA of approximately 10 pg and 0.5 pg respectively. Manual blots were tested for practical application to screen germplasma for FDV infection. The virus was detected in leaf samples from FDV-infected plants, in some instances prior to development of the characteristic gall symptom.
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Affiliation(s)
- G R Smith
- David North Plant Research Centre, Bureau of Sugar Experiment Stations, Indooroopilly, Queensland, Australia
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