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Ohdera AH, Mansbridge M, Wang M, Naydenkov P, Kamel B, Goentoro L. The microbiome of a Pacific moon jellyfish Aurelia coerulea. PLoS One 2024; 19:e0298002. [PMID: 38635587 PMCID: PMC11025843 DOI: 10.1371/journal.pone.0298002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/16/2024] [Indexed: 04/20/2024] Open
Abstract
The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.
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Affiliation(s)
- Aki H. Ohdera
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
- National Museum of Natural History, Smithsonian Institute, Washington, D.C., United States of America
| | | | - Matthew Wang
- Flintridge Preparatory School, La Cañada Flintridge, CA, United States of America
| | - Paulina Naydenkov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Bishoy Kamel
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Lea Goentoro
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
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Broto A, Gaspari E, Miravet-Verde S, Dos Santos VAPM, Isalan M. A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications. Nat Commun 2022; 13:1910. [PMID: 35393441 PMCID: PMC8991246 DOI: 10.1038/s41467-022-29574-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/24/2022] [Indexed: 12/18/2022] Open
Abstract
Mycoplasmas have exceptionally streamlined genomes and are strongly adapted to their many hosts, which provide them with essential nutrients. Owing to their relative genomic simplicity, Mycoplasmas have been used to develop chassis for biotechnological applications. However, the dearth of robust and precise toolkits for genomic manipulation and tight regulation has hindered any substantial advance. Herein we describe the construction of a robust genetic toolkit for M. pneumoniae, and its successful deployment to engineer synthetic gene switches that control and limit Mycoplasma growth, for biosafety containment applications. We found these synthetic gene circuits to be stable and robust in the long-term, in the context of a minimal cell. With this work, we lay a foundation to develop viable and robust biosafety systems to exploit a synthetic Mycoplasma chassis for live attenuated vectors for therapeutic applications.
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Affiliation(s)
- Alicia Broto
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Erika Gaspari
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- European & Developing Countries Clinical Trials Partnership (EDCTP), The Hague, The Netherlands
| | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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SARS-CoV-2, Zika viruses and mycoplasma: Structure, pathogenesis and some treatment options in these emerging viral and bacterial infectious diseases. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166264. [PMID: 34481867 PMCID: PMC8413106 DOI: 10.1016/j.bbadis.2021.166264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/22/2021] [Accepted: 08/30/2021] [Indexed: 01/28/2023]
Abstract
The molecular evolution of life on earth along with changing environmental, conditions has rendered mankind susceptible to endemic and pandemic emerging infectious diseases. The effects of certain systemic viral and bacterial infections on morbidity and mortality are considered as examples of recent emerging infections. Here we will focus on three examples of infections that are important in pregnancy and early childhood: SARS-CoV-2 virus, Zika virus, and Mycoplasma species. The basic structural characteristics of these infectious agents will be examined, along with their general pathogenic mechanisms. Coronavirus infections, such as caused by the SARS-CoV-2 virus, likely evolved from zoonotic bat viruses to infect humans and cause a pandemic that has been the biggest challenge for humanity since the Spanish Flu pandemic of the early 20th century. In contrast, Zika Virus infections represent an expanding infectious threat in the context of global climate change. The relationship of these infections to pregnancy, the vertical transmission and neurological sequels make these viruses highly relevant to the topics of this special issue. Finally, mycoplasmal infections have been present before mankind evolved, but they were rarely identified as human pathogens until recently, and they are now recognized as important coinfections that are able to modify the course and prognosis of various infectious diseases and other chronic illnesses. The infectious processes caused by these intracellular microorganisms are examined as well as some general aspects of their pathogeneses, clinical presentations, and diagnoses. We will finally consider examples of treatments that have been used to reduce morbidity and mortality of these infections and discuss briefly the current status of vaccines, in particular, against the SARS-CoV-2 virus. It is important to understand some of the basic features of these emerging infectious diseases and the pathogens involved in order to better appreciate the contributions of this special issue on how infectious diseases can affect human pregnancy, fetuses and neonates.
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Giacobbo FCN, Eyng C, Nunes RV, de Souza C, Teixeira LV, Pilla R, Suchodolski JS, Bortoluzzi C. Influence of Enzyme Supplementation in the Diets of Broiler Chickens Formulated with Different Corn Hybrids Dried at Various Temperatures. Animals (Basel) 2021; 11:ani11030643. [PMID: 33671022 PMCID: PMC7997286 DOI: 10.3390/ani11030643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary The use of exogenous enzymes is a common nutrition strategy of the poultry industry. However, the influence of this additive on the microbiota and its efficiency when the diets are formulated with different hybrids of corn dried under high temperature are still unclear. From a practical point of view, evaluating the mode of action of enzymes in different situations is crucial to ensure competitive performance results with low production costs. The current study confirmed that regardless of corn hybrids and drying temperature, dietary supplementation with amylase, xylanase, and protease was beneficial for intestinal morphology and allowed a modulation of the cecal microbiota. This influence may have changed the digestive process and use of nutrients by the broilers, resulting in better animal performance. Abstract We evaluated the influence of enzymatic supplementation on the growth performance and cecal microbiota of broilers. A total of 2160 1-day-old male chicks were used in a 3 × 2 × 2 factorial arrangement (three corn hybrids, two drying temperatures −80 and 110 °C, with or without the inclusion of an enzymatic blend (amylase, xylanase, and protease) (20 birds/pen, n = 9). For all performance and digestibility parameters, we observed, in general, isolated effects of the corn hybrids and drying temperature. Birds that received the enzymatic blend in the diet showed better weight gain from 1 to 21 days (d) and better digestibility coefficients of nutrients at 42 d. Birds fed diets with corn dried at 80 °C showed a better feed conversion ratio from 1 to 42 d. At 21 d of age, enzymatic supplementation had positive effects on jejunum morphology. Enzyme supplementation increased the abundance of the phylum Tenericutes, class Bacilli and Mollicutes, reduced Clostridia, and increased the abundances of the families Lactobacillaceae, Anaeroplasmataceae, and O_RF39;F. In conclusion, the addition of amylase, xylanase, and protease led to a better nutrient digestibility, performance, and intestinal morphology. In addition, enzyme supplementation changed the diversity, composition, and predicted function of the cecal microbiota at d 21.
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Affiliation(s)
- Franciele C. N. Giacobbo
- Ciências Agrárias, Universidade Estadual do Oeste do Paraná, 85960-000 Mal. C. Rondon, Brazil; (F.C.N.G.); (R.V.N.); (C.d.S.)
| | - Cinthia Eyng
- Ciências Agrárias, Universidade Estadual do Oeste do Paraná, 85960-000 Mal. C. Rondon, Brazil; (F.C.N.G.); (R.V.N.); (C.d.S.)
- Correspondence: ; Tel.: +55-45-99800-0893
| | - Ricardo V. Nunes
- Ciências Agrárias, Universidade Estadual do Oeste do Paraná, 85960-000 Mal. C. Rondon, Brazil; (F.C.N.G.); (R.V.N.); (C.d.S.)
| | - Cleison de Souza
- Ciências Agrárias, Universidade Estadual do Oeste do Paraná, 85960-000 Mal. C. Rondon, Brazil; (F.C.N.G.); (R.V.N.); (C.d.S.)
| | | | - Rachel Pilla
- Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (R.P.); (J.S.S.)
| | - Jan S. Suchodolski
- Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (R.P.); (J.S.S.)
| | - Cristiano Bortoluzzi
- Department of Poultry Science, Texas A&M University, College Station, TX 77845, USA;
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Santos Junior MN, de Macêdo Neres NS, Campos GB, Bastos BL, Timenetsky J, Marques LM. A Review of Ureaplasma diversum: A Representative of the Mollicute Class Associated With Reproductive and Respiratory Disorders in Cattle. Front Vet Sci 2021; 8:572171. [PMID: 33681318 PMCID: PMC7930009 DOI: 10.3389/fvets.2021.572171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/13/2021] [Indexed: 12/22/2022] Open
Abstract
The Mollicutes class encompasses wall-less microbes with a reduced genome. They may infect plants, insects, humans, and animals including those on farms and in livestock. Ureaplasma diversum is a mollicute associated with decreased reproduction mainly in the conception rate in cattle, as well as weight loss and decreased quality in milk production. Therefore, U. diversum infection contributes to important economic losses, mainly in large cattle-producing countries such as the United States, China, Brazil, and India. The characteristics of Mollicutes, virulence, and pathogenic variations make it difficult to control their infections. Genomic analysis, prevalence studies, and immunomodulation assays help better understand the pathogenesis of bovine ureaplasma. Here we present the main features of transmission, virulence, immune response, and pathogenesis of U. diversum in bovines.
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Affiliation(s)
- Manoel Neres Santos Junior
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
- Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil
| | - Nayara Silva de Macêdo Neres
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | - Guilherme Barreto Campos
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | - Bruno Lopes Bastos
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | - Jorge Timenetsky
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Lucas Miranda Marques
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
- Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
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Silva JK, Marques LM, Timenetsky J, de Farias ST. Ureaplasma diversum protein interaction networks: evidence of horizontal gene transfer and evolution of reduced genomes among Mollicutes. Can J Microbiol 2019; 65:596-612. [PMID: 31018106 DOI: 10.1139/cjm-2018-0688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ureaplasma diversum is a member of the Mollicutes class responsible for urogenital tract infection in cattle and small ruminants. Studies indicate that the process of horizontal gene transfer, the exchange of genetic material among different species, has a crucial role in mollicute evolution, affecting the group's characteristic genomic reduction process and simplification of metabolic pathways. Using bioinformatics tools and the STRING database of known and predicted protein interactions, we constructed the protein-protein interaction network of U. diversum and compared it with the networks of other members of the Mollicutes class. We also investigated horizontal gene transfer events in subnetworks of interest involved in purine and pyrimidine metabolism and urease function, chosen because of their intrinsic importance for host colonization and virulence. We identified horizontal gene transfer events among Mollicutes and from Ureaplasma to Staphylococcus aureus and Corynebacterium, bacterial groups that colonize the urogenital niche. The overall tendency of genome reduction and simplification in the Mollicutes is echoed in their protein interaction networks, which tend to be more generalized and less selective. Our data suggest that the process was permitted (or enabled) by an increase in host dependence and the available gene repertoire in the urogenital tract shared via horizontal gene transfer.
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Affiliation(s)
- Joana Kästle Silva
- a Department of Molecular Biology, Federal University of Paraíba, João Pessoa, Brazil
| | - Lucas Miranda Marques
- b Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil.,c Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Jorge Timenetsky
- c Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
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Nucleotide composition bias and codon usage trends of gene populations in Mycoplasma capricolum subsp. capricolum and M. Agalactiae. J Genet 2016; 94:251-60. [PMID: 26174672 DOI: 10.1007/s12041-015-0512-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Because of the low GC content of the gene population, amino acids of the two mycoplasmas tend to be encoded by synonymous codons with an A or T end. Compared with the codon usage of ovine, Mycoplasma capricolum and M. agalactiae tend to select optimal codons, which are rare codons in ovine. Due to codon usage pattern caused by genes with key biological functions, the overall codon usage trends represent a certain evolutionary direction in the life cycle of the two mycoplasmas. The overall codon usage trends of a gene population of M. capricolum subsp. capricolum can be obviously separated from other mycoplasmas, and the overall codon usage trends of M. agalactiae are highly similar to those of M. bovis. These results partly indicate the independent evolution of the two mycoplasmas without the limits of the host cell's environment. The GC and AT skews estimate nucleotide composition bias at different positions of nucleotide triplets and the protein consideration caused by the nucleotide composition bias at codon positions 1 and 2 largely take part in synonymous codon usage patterns of the two mycoplasmas. The correlation between the codon adaptation index and codon usage variation indicates that the effect of codon usage on gene expression in M. capricolum subsp. capricolum is opposite to that of M. agalactiae, further suggesting independence of the evolutionary process influencing the overall codon usage trends of gene populations of mycoplasmas.
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8
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Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population. Appl Environ Microbiol 2015; 81:6038-52. [PMID: 26116680 DOI: 10.1128/aem.01601-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/19/2015] [Indexed: 01/25/2023] Open
Abstract
The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle.
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Robinson JW, Dando SJ, Nitsos I, Newnham J, Polglase GR, Kallapur SG, Pillow JJ, Kramer BW, Jobe AH, Payton D, Knox CL. Ureaplasma parvum serovar 3 multiple banded antigen size variation after chronic intra-amniotic infection/colonization. PLoS One 2013; 8:e62746. [PMID: 23638142 PMCID: PMC3637154 DOI: 10.1371/journal.pone.0062746] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 03/28/2013] [Indexed: 12/21/2022] Open
Abstract
Ureaplasma species are the microorganisms most frequently associated with adverse pregnancy outcomes. The multiple banded antigen (MBA), a surface-exposed lipoprotein, is a key virulence factor of ureaplasmas. The MBA demonstrates size variation, which we have shown previously to be correlated with the severity of chorioamnion inflammation. We aimed to investigate U. parvum serovar 3 pathogenesis in vivo, using a sheep model, by investigating: MBA variation after long term (chronic) and short term (acute) durations of in utero ureaplasma infections, and the severity of chorioamnionitis and inflammation in other fetal tissues. Inocula of 2×107 colony-forming-units (CFU) of U. parvum serovar 3 (Up) or media controls (C) were injected intra-amniotically into pregnant ewes at one of three time points: day 55 (69d Up, n = 8; C69, n = 4); day 117 (7d Up, n = 8; C7, n = 2); and day 121 (3d Up, n = 8; C3, n = 2) of gestation (term = 145–150d). At day 124, preterm fetuses were delivered surgically. Samples of chorioamnion, fetal lung, and umbilical cord were: (i) snap frozen for subsequent ureaplasma culture, and (ii) fixed, embedded, sectioned and stained by haematoxylin and eosin stain for histological analysis. Selected fetal lung clinical ureaplasma isolates were cloned and filtered to obtain cultures from a single CFU. Passage 1 and clone 2 ureaplasma cultures were tested by western blot to demonstrate MBA variation. In acute durations of ureaplasma infection no MBA variants (3d Up) or very few MBA variants (7d Up) were present when compared to the original inoculum. However, numerous MBA size variants were generated in vivo (alike within contiguous tissues, amniotic fluid and fetal lung, but different variants were present within chorioamnion), during chronic, 69d exposure to ureaplasma infection. For the first time we have shown that the degree of ureaplasma MBA variation in vivo increased with the duration of gestation.
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Affiliation(s)
- James W. Robinson
- Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Samantha J. Dando
- Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Ilias Nitsos
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Western Australia, Australia
| | - John Newnham
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Graeme R. Polglase
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Suhas G. Kallapur
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Western Australia, Australia
- Department of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - J. Jane Pillow
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Western Australia, Australia
| | - Boris W. Kramer
- Department of Pediatrics, School of Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Alan H. Jobe
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Western Australia, Australia
- Department of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Diane Payton
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Christine L. Knox
- Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- * E-mail:
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Párraga-Niño N, Colomé-Calls N, Canals F, Querol E, Ferrer-Navarro M. A comprehensive proteome of Mycoplasma genitalium. J Proteome Res 2012; 11:3305-16. [PMID: 22582988 DOI: 10.1021/pr300084c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycoplasma genitalium is a human pathogen associated with several sexually transmitted diseases. Proteomic technologies, along with other methods for global gene expression analysis, play a key role in understanding the mechanisms of bacterial pathogenesis and physiology. The proteome of M. genitalium, model of a minimal cell, has been extended using a combination of different proteomic approaches and technologies. The total proteome of this microorganism has been analyzed using gel-based and gel-free approaches, achieving the identification of 85.3% of the predicted ORFs. In addition, a comprehensive analysis of membrane subproteome has been performed. For this purpose, the TX-114 soluble fraction has been analyzed as well as the surface proteins, using cell-surface protein labeling with CyDye. Finally, the serological response of M. genitalium-infected patients and healthy donors has been analyzed to identify proteins that trigger immunological response. Here, we present the most extensive M. genitalium proteome analysis (85.3% of predicted ORFs), a comprehensive M. genitalium membrane analysis, and a study of the human serological response to M. genitalium.
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Affiliation(s)
- Noemí Párraga-Niño
- Institut de Biotecnologia i de Biomedicina (IBB) and Dpt Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona (UAB), E-08193 Cerdanyola del Vallès (Barcelona), Spain
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11
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Yamaguti M, Muller EE, Piffer AI, Kich JD, Klein CS, Kuchiishi SS. Detection of Mycoplasma hyopneumoniae by polymerase chain reaction in swine presenting respiratory problems. Braz J Microbiol 2008; 39:471-6. [PMID: 24031248 PMCID: PMC3768421 DOI: 10.1590/s1517-838220080003000011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Indexed: 11/21/2022] Open
Abstract
Since Mycoplasma hyopneumoniae isolation in appropriate media is a difficult task and impractical for daily routine diagnostics, Nested-PCR (N-PCR) techniques are currently used to improve the direct diagnostic sensitivity of Swine Enzootic Pneumonia. In a first experiment, this paper describes a N-PCR technique optimization based on three variables: different sampling sites, sample transport media, and DNA extraction methods, using eight pigs. Based on the optimization results, a second experiment was conducted for testing validity using 40 animals. In conclusion, the obtained results of the N-PCR optimization and validation allow us to recommend this test as a routine monitoring diagnostic method for Mycoplasma hyopneumoniae infection in swine herds.
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Affiliation(s)
- M Yamaguti
- Universidade Estadual de Londrina, Campus Universitário , Londrina, PR , Brasil
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12
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Park SC, Yibchok-Anun S, Cheng H, Young TF, Thacker EL, Minion FC, Ross RF, Hsu WH. Mycoplasma hyopneumoniae increases intracellular calcium release in porcine ciliated tracheal cells. Infect Immun 2002; 70:2502-6. [PMID: 11953388 PMCID: PMC127901 DOI: 10.1128/iai.70.5.2502-2506.2002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the effects of intact pathogenic Mycoplasma hyopneumoniae, nonpathogenic M. hyopneumoniae, and Mycoplasma flocculare on intracellular free Ca2+ concentrations ([Ca2+]i) in porcine ciliated tracheal epithelial cells. The ciliated epithelial cells had basal [Ca2+]i of 103 +/- 3 nM (n = 217 cells). The [Ca2+]i increased by 250 +/- 19 nM (n = 47 cells) from the basal level within 100 s of the addition of pathogenic M. hyopneumoniae strain 91-3 (300 microg/ml), and this increase lasted approximately 60 s. In contrast, nonpathogenic M. hyopneumoniae and M. flocculare at concentrations of 300 microg/ml failed to increase [Ca2+]i. In Ca2+-free medium, pathogenic M. hyopneumoniae still increased [Ca2+]i in tracheal cells. Pretreatment with thapsigargin (1 microM for 30 min), which depleted the Ca2+ store in the endoplasmic reticulum, abolished the effect of M. hyoneumoniae. Pretreatment with pertussis toxin (100 ng/ml for 3 h) or U-73122 (2 microM for 100 s), an inhibitor of phospholipase C, also abolished the effect of M. hyopneumoniae. The administration of mastoparan 7, an activator of pertussis toxin-sensitive proteins G(i) and G(o), increased [Ca2+]i in ciliated tracheal cells. These results suggest that pathogenic M. hyopneumoniae activates receptors that are coupled to G(i) or G(o), which in turn activates a phospholipase C pathway, thereby releasing Ca2+ from the endoplasmic reticulum. Thus, an increase in Ca2+ may serve as a signal for the pathogenesis of M. hyopneumoniae.
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Affiliation(s)
- Seung-Chun Park
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, USA
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13
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Forsyth RA, Haselbeck RJ, Ohlsen KL, Yamamoto RT, Xu H, Trawick JD, Wall D, Wang L, Brown-Driver V, Froelich JM, C KG, King P, McCarthy M, Malone C, Misiner B, Robbins D, Tan Z, Zhu Zy ZY, Carr G, Mosca DA, Zamudio C, Foulkes JG, Zyskind JW. A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 2002; 43:1387-400. [PMID: 11952893 DOI: 10.1046/j.1365-2958.2002.02832.x] [Citation(s) in RCA: 368] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To address the need for new approaches to antibiotic drug development, we have identified a large number of essential genes for the bacterial pathogen, Staphylococcus aureus, using a rapid shotgun antisense RNA method. Staphylococcus aureus chromosomal DNA fragments were cloned into a xylose-inducible expression plasmid and transformed into S. aureus. Homology comparisons between 658 S. aureus genes identified in this particular antisense screen and the Mycoplasma genitalium genome, which contains 517 genes in total, yielded 168 conserved genes, many of which appear to be essential in M. genitalium and other bacteria. Examples are presented in which expression of an antisense RNA specifically reduces its cognate mRNA. A cell-based, drug-screening assay is also described, wherein expression of an antisense RNA confers specific sensitivity to compounds targeting that gene product. This approach enables facile assay development for high throughput screening for any essential gene, independent of its biochemical function, thereby greatly facilitating the search for new antibiotics.
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14
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Fraser CM, Eisen J, Fleischmann RD, Ketchum KA, Peterson S. Comparative genomics and understanding of microbial biology. Emerg Infect Dis 2000; 6:505-12. [PMID: 10998382 PMCID: PMC2627966 DOI: 10.3201/eid0605.000510] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The sequences of close to 30 microbial genomes have been completed during the past 5 years, and the sequences of more than 100 genomes should be completed in the next 2 to 4 years. Soon, completed microbial genome sequences will represent a collection of >200,000 predicted coding sequences. While analysis of a single genome provides tremendous biological insights on any given organism, comparative analysis of multiple genomes provides substantially more information on the physiology and evolution of microbial species and expands our ability to better assign putative function to predicted coding sequences.
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Affiliation(s)
- C M Fraser
- The Institute for Genomic Research, Rockville, Maryland 20850, USA.
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15
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Kokotovic B, Friis NF, Jensen JS, Ahrens P. Amplified-fragment length polymorphism fingerprinting of Mycoplasma species. J Clin Microbiol 1999; 37:3300-7. [PMID: 10488196 PMCID: PMC85551 DOI: 10.1128/jcm.37.10.3300-3307.1999] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including Mycoplasma genitalium (n = 11), Mycoplasma pneumoniae (n = 5), Mycoplasma hominis (n = 5), Mycoplasma hyopneumoniae (n = 9), Myco plasma flocculare (n = 5), Mycoplasma hyosynoviae (n = 10), and Mycoplasma dispar (n = 5). AFLP templates were prepared by the digestion of mycoplasmal DNA with BglII and MfeI restriction endonucleases and subsequent ligation of corresponding site-specific adapters. The amplification of AFLP templates with a single set of nonselective primers resulted in reproducible fingerprints of approximately 60 to 80 fragments in the size range of 50 to 500 bp. The method was able to discriminate the analyzed strains at species and intraspecies levels as well. Each of the tested Mycoplasma species developed a banding pattern entirely different from those obtained from other species under analysis. Subtle intraspecies genomic differences were detected among strains of all of the Mycoplasma species analyzed. The extent of polymorphism varied markedly between the analyzed mycoplasmas, comprising pattern similarity levels from 61.7% detected among M. dispar strains to 95.9% detected among M. genitalium strains. The results of the present study provide evidence of the high discriminatory power of AFLP analysis, suggesting the possible applicability of this method to the molecular characterization of mycoplasmas.
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Affiliation(s)
- B Kokotovic
- Danish Veterinary Laboratory, DK-1790 Copenhagen V, Denmark.
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16
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Abstract
The recent sequencing of the entire genomes of Mycoplasma genitalium and M. pneumoniae has attracted considerable attention to the molecular biology of mycoplasmas, the smallest self-replicating organisms. It appears that we are now much closer to the goal of defining, in molecular terms, the entire machinery of a self-replicating cell. Comparative genomics based on comparison of the genomic makeup of mycoplasmal genomes with those of other bacteria, has opened new ways of looking at the evolutionary history of the mycoplasmas. There is now solid genetic support for the hypothesis that mycoplasmas have evolved as a branch of gram-positive bacteria by a process of reductive evolution. During this process, the mycoplasmas lost considerable portions of their ancestors' chromosomes but retained the genes essential for life. Thus, the mycoplasmal genomes carry a high percentage of conserved genes, greatly facilitating gene annotation. The significant genome compaction that occurred in mycoplasmas was made possible by adopting a parasitic mode of life. The supply of nutrients from their hosts apparently enabled mycoplasmas to lose, during evolution, the genes for many assimilative processes. During their evolution and adaptation to a parasitic mode of life, the mycoplasmas have developed various genetic systems providing a highly plastic set of variable surface proteins to evade the host immune system. The uniqueness of the mycoplasmal systems is manifested by the presence of highly mutable modules combined with an ability to expand the antigenic repertoire by generating structural alternatives, all compressed into limited genomic sequences. In the absence of a cell wall and a periplasmic space, the majority of surface variable antigens in mycoplasmas are lipoproteins. Apart from providing specific antimycoplasmal defense, the host immune system is also involved in the development of pathogenic lesions and exacerbation of mycoplasma induced diseases. Mycoplasmas are able to stimulate as well as suppress lymphocytes in a nonspecific, polyclonal manner, both in vitro and in vivo. As well as to affecting various subsets of lymphocytes, mycoplasmas and mycoplasma-derived cell components modulate the activities of monocytes/macrophages and NK cells and trigger the production of a wide variety of up-regulating and down-regulating cytokines and chemokines. Mycoplasma-mediated secretion of proinflammatory cytokines, such as tumor necrosis factor alpha, interleukin-1 (IL-1), and IL-6, by macrophages and of up-regulating cytokines by mitogenically stimulated lymphocytes plays a major role in mycoplasma-induced immune system modulation and inflammatory responses.
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Affiliation(s)
- S Razin
- Department of Membrane and Ultrastructure Research, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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18
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Kuboyama T, Huang CC, Lu X, Sawayanagi T, Kanazawa T, Kagami T, Matsuda I, Tsuchizaki T, Namba S. A plasmid isolated from phytopathogenic onion yellows phytoplasma and its heterogeneity in the pathogenic phytoplasma mutant. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1998; 11:1031-1037. [PMID: 9805390 DOI: 10.1094/mpmi.1998.11.11.1031] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A 3.6-kbp DNA fragment was cloned from the extrachromosomal DNA of a pathogenic plant mollicute, onion yellows phytoplasma (OY-W). Sequence analysis of the fragment revealed an open reading frame (ORF) encoding the replication (Rep) protein of rolling-circle replication (RCR)-type plasmids. This result suggests the existence of a plasmid (pOYW1) in OY-W that uses the RCR mechanism. This assumption was confirmed by detecting the single-stranded DNA (ssDNA) of a replication intermediate that is specifically produced by the RCR mechanism. This is the first report on the identification of the replication system of this plasmid and the genes encoded in it. With a DNA fragment including the Rep gene region of pOYW1 used as a probe, Southern and Northern (RNA) blot hybridizations were employed to examine the heterogeneity between the plasmids found in OY-W and a pathogenic mutant (OY-M) isolated from OY-W. Multiple bands were detected in the DNA and RNA extracted from both OY-W and OY-M infected plants, although the banding patterns were different. Moreover, the copy number of plasmids from OY-W was about 4.2 times greater than that from OY-M. These results indicate constructive heterogeneity between OY-W and OY-M plasmids, and the possibility of a relationship between the plasmid-encoded genes and the pathogenicity of the phytoplasma was suggested.
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Affiliation(s)
- T Kuboyama
- Laboratory of Bioresource Technology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
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19
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Poonia B, Sharma AK. Modulation of lympho-proliferative responses of ovine peripheral blood mononuclear cells by Mycoplasma mycoides ssp. mycoides (LC type). Vet Immunol Immunopathol 1998; 64:323-35. [PMID: 9764725 DOI: 10.1016/s0165-2427(98)00141-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present study was carried out to investigate the immunomodulating potential of M. mycoides ssp. mycoides (Mmm) (LC): a standard strain (Y-Goat, YG) and a local strain (M30) isolated from the pneumonic lung of a lamb during an outbreak of respiratory disease. The study was conducted in two parts to determine in vitro and in vivo aspects of the Mmm-induced modulation of cellular immune responses. In vitro experiments, using peripheral blood mononuclear cells (PBMC) of naive lambs, showed that live (Lv) or inactivated (Ina) antigens of Mmm (strains YG and M30) were not mitogenic for PBMC. Live antigens of both the strains, however, induced significant suppression of the PHA-driven lympho-proliferative (LP) responses. Suppression of LP responses by infectious Mmm (both strains) was restored in the presence of exogenous recombinant human interleukin-2 (rhIL-2). Following experimental inoculation of lambs with Mmm (YG), a significant reduction in non-specific LP responses was observed on days 6, 10 and 14 post inoculation (p.i.). There was a slow but significant rise in memory LP responses to Mmm strains (YG and M30). Specific subset depletion studies, using immunomagnetic cell separation (IMCS) technique, carried out on days 10 and 14 p.i., revealed that the OvCD4+ cell population was the main proliferating lymphocyte subset following an infection with Mmm (LC type).
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Affiliation(s)
- B Poonia
- Department of Veterinary Microbiology, CCS Haryana Agricultural University, India
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20
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Miyata M, Fukumura T. Asymmetrical progression of replication forks just after initiation on Mycoplasma capricolum chromosome revealed by two-dimensional gel electrophoresis. Gene X 1997; 193:39-47. [PMID: 9249065 DOI: 10.1016/s0378-1119(97)00075-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Previously, we mapped the replication initiation site of the Mycoplasma capricolum chromosome into a region containing the dnaA gene [M. Miyata et al., 1993a. Nucleic Acids Res. 21, 4816-4823]. In this study, various regions including this functional domain were analyzed by two complementary two-dimensional (2D) gel electrophoretic methods. Sizes of nascent strands in a 10.7-kb and a 5.6-kb region were examined by a neutral/alkaline (N/A) method. The shortest nascent strand was detected in an 875-bp region composed of the 3' end of the dnaA gene and its downstream non-coding sequence. The shortest nascent strand detected became longer in an asymmetrical manner as position of the probe became further from the putative initiation site in both directions. The intermediate forms of eight regions restricted at different sites were examined by a neutral/neutral (N/N) method. Bubble arcs were observed in four regions including the 875-bp region. The region containing the 875-bp region at about its center showed an asymmetrical arc, although that containing the 875-bp region at its end showed a symmetrical arc. These results show that the replication forks develop in the 875-bp region and proceed bidirectionally in an asymmetrical manner around the initiation site. The results of N/A analysis of the 5.6-kb region showed a shift of intensity in the nascent strand signal, which suggests an upshift of fork progression velocity.
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Affiliation(s)
- M Miyata
- Department of Biology, Faculty of Science, Osaka City University, Sumiyoshi-ku, Japan.
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21
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Zhu PP, Nosworthy N, Ginsburg A, Miyata M, Seok YJ, Peterkofsky A. Expression, purification, and characterization of enzyme IIA(glc) of the phosphoenolpyruvate:sugar phosphotransferase system of Mycoplasma capricolum. Biochemistry 1997; 36:6947-53. [PMID: 9188690 DOI: 10.1021/bi963090m] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The gene encoding enzyme IIA(glc) (EIIA) of the phosphoenolpyruvate:sugar phosphotransferase system of Mycoplasma capricolum was cloned into a regulated expression vector. The purified protein product of the overexpressed gene was characterized as an active phosphoacceptor from HPr with a higher pI than previously described EIIAs. M. capricolum EIIA was unreactive with antibodies directed against the corresponding proteins from either Gram-positive or Gram-negative bacteria. Enzyme IIA(glc) behaved as a homogeneous, monomeric species of 16,700 Mr in analytical ultracentrifugation. The circular dichroism far-UV spectrum of EIIA reflects a low alpha-helical content and predominantly beta-sheet structural content: temperature-induced changes in ellipticity at 205 nm showed that the protein undergoes reversible, two-state thermal unfolding with Tm = 70.0 +/- 0.3 degrees C and a van't Hoff deltaH of 90 kcal/mol. Enzyme I (64,600 Mr) from M. capricolum exhibited a monomer-dimer-tetramer association at 4 and 20 degrees C with dimerization constants of log K(A) = 5.6 and 5.1 [M(-1)], respectively, in sedimentation equilibrium experiments. A new vector, capable of introducing an N-terminal His tag on a protein, was developed in order to generate highly purified heat-stable protein (HPr). No significant interaction of EIIA with HPr was detected by gel-filtration chromatography, intrinsic tryptophanyl residue fluorescence changes, titration calorimetry, biomolecular interaction, or sedimentation equilibrium studies. While Escherichia coli EIIA inhibits Gram-negative glycerol kinase activity, the M. capricolum EIIA has no effect on the homologous glycerol kinase. The probable regulator of sugar transport systems, HPr(Ser) kinase, was demonstrated in extracts of M. capricolum and Mycoplasma genitalium. Gene mapping studies demonstrated that, in contrast to the clustered arrangement of genes encoding HPr and enzyme I in E. coli, these genes are located diametrically opposite in the M. capricolum chromosome.
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Affiliation(s)
- P P Zhu
- Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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22
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Athamna A, Rosengarten R, Levisohn S, Kahane I, Yogev D. Adherence of Mycoplasma gallisepticum involves variable surface membrane proteins. Infect Immun 1997; 65:2468-71. [PMID: 9169793 PMCID: PMC175345 DOI: 10.1128/iai.65.6.2468-2471.1997] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Adherence of Mycoplasma gallisepticum to erythrocytes was examined by colony immunoblotting, detergent phase fractionation, trypsin treatment, comparison of protein profiles, and comparison of erythrocyte-bound mycoplasma protein fractions of hemadsorption-positive and -negative mutants. The binding of M. gallisepticum to chicken or human erythrocytes was found to be mediated via surface-exposed membrane proteins undergoing high-frequency phase variation.
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Affiliation(s)
- A Athamna
- Department of Membrane and Ultrastructure Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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23
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Gruber TM, Bryant DA. Molecular systematic studies of eubacteria, using sigma70-type sigma factors of group 1 and group 2. J Bacteriol 1997; 179:1734-47. [PMID: 9045836 PMCID: PMC178889 DOI: 10.1128/jb.179.5.1734-1747.1997] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Sigma factors of the sigma70 family were used as a phylogenetic tool to compare evolutionary relationships among eubacteria. Several new sigma factor genes were cloned and sequenced to increase the variety of available sequences. Forty-two group 1 sigma factor sequences of various species were analyzed with the help of a distance matrix method to establish a phylogenetic tree. The tree derived by using sigma factors yielded subdivisions, including low-G+C and high-G+C gram-positive bacteria, cyanobacteria, and the alpha, beta, gamma, and delta subdivisions of proteobacteria, consistent with major bacterial groups found in trees derived from analyses with other molecules. However, some groupings (e.g., the chlamydiae, mycoplasmas, and green sulfur bacteria) are found in different positions than for trees obtained by using other molecular markers. A direct comparison to the most extensively used molecule in systematic studies, small-subunit rRNA, was made by deriving trees from essentially the same species set and using similar phylogenetic methods. Differences and similarities based on the two markers are discussed. Additionally, 31 group 2 sigma factors were analyzed in combination with the group 1 proteins in order to detect functional groupings of these alternative sigma factors. The data suggest that promoters recognized by the major vegetative sigma factors of eubacteria will contain sequence motifs and spacing very similar to those for the sigma70 sigma factors of Escherichia coli.
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Affiliation(s)
- T M Gruber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA
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24
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Liefting LW, Andersen MT, Beever RE, Gardner RC, Forster RL. Sequence heterogeneity in the two 16S rRNA genes of Phormium yellow leaf phytoplasma. Appl Environ Microbiol 1996; 62:3133-9. [PMID: 8795200 PMCID: PMC168106 DOI: 10.1128/aem.62.9.3133-3139.1996] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Phormium yellow leaf (PYL) phytoplasma causes a lethal disease of the monocotyledon, New Zealand flax (Phormium tenax). The 16S rRNA genes of PYL phytoplasma were amplified from infected flax by PCR and cloned, and the nucleotide sequences were determined. DNA sequencing and Southern hybridization analysis of genomic DNA indicated the presence of two copies of the 16S rRNA gene. The two 16S rRNA genes exhibited sequence heterogeneity in 4 nucleotide positions and could be distinguished by the restriction enzymes BpmI and BsrI. This is the first record in which sequence heterogeneity in the 16S rRNA genes of a phytoplasma has been determined by sequence analysis. A phylogenetic tree based on 16S rRNA gene sequences showed that PYL phytoplasma is most closely related to the stolbur and German grapevine yellows phytoplasmas, which form the stolbur subgroup of the aster yellows group. This phylogenetic position of PYL phytoplasma was supported by 16S/23S spacer region sequence data.
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Affiliation(s)
- L W Liefting
- Horticulture and Food Research Institute of New Zealand Ltd., Auckland, New Zealand.
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25
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Zhu PP, Peterkofsky A. Sequence and organization of genes encoding enzymes involved in pyruvate metabolism in Mycoplasma capricolum. Protein Sci 1996; 5:1719-36. [PMID: 8844861 PMCID: PMC2143489 DOI: 10.1002/pro.5560050825] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The region of the genome of Mycoplasma capricolum upstream of the portion encompassing the genes for Enzymes I and IIAglc of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) was cloned and sequenced. Examination of the sequence revealed open reading frames corresponding to numerous genes involved with the oxidation of pyruvate. The deduced gene organization is naox (encoding NADH oxidase)-lplA (encoding lipoate-protein ligase)-odpA (encoding pyruvate dehydrogenase EI alpha)-odpB (encoding pyruvate dehydrogenase EI beta)-odp2(encoding pyruvate dehydrogenase EII)-dldH (encoding dihydrolipoamide dehydrogenase)-pta (encoding phosphotransacetylase)-ack (encoding acetate kinase)-orfA (an unknown open reading frame)-kdtB-ptsI-crr. Analysis of the DNA sequence suggests that the naox and lplA genes are part of a single operon, odpA and odpB constitute an additional operon, odp2 and dldH a third operon, and pta and ack an additional transcription unit. Phylogenetic analyses of the protein products of the odpA and odpB genes indicate that they are most similar to the corresponding proteins from Mycoplasma genitalium, Acholeplasma laidlawii, and Gram-positive organisms. The product of the odp2 gene contains a single lipoyl domain, as is the case with the corresponding proteins from M. genitalium and numerous other organisms. An evolutionary tree places the M. capricolum odp2 gene product in close relationship to the corresponding proteins from A. laidlawii and M.genitalium. The dldH gene encodes an unusual form of dihydrolipoamide dehydrogenase that contains an aminoterminal extension corresponding to a lipoyl domain, a property shared by the corresponding proteins from Alcaligenes eutrophus and Clostridium magnum. Aside from that feature, the protein is related phylogenetically to the corresponding proteins from A. laidlawii and M. genitalium. The phosphotransacetylase from M. capricolum is related most closely to the corresponding protein from M. genitalium and is distinguished easily from the enzymes from Escherichia coli and Haemophilus influenzae by the absence of the characteristic amino-terminal extension. The acetate kinase from M. capricolum is related evolutionarily to the homologous enzyme from M. genitalium. Map position comparisons of genes encoding proteins involved with pyruvate metabolism show that, whereas all the genes are clustered in M. capricolum, they are scattered in M. genitalium.
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Affiliation(s)
- P P Zhu
- Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
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26
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Hilbert H, Himmelreich R, Plagens H, Herrmann R. Sequence analysis of 56 kb from the genome of the bacterium Mycoplasma pneumoniae comprising the dnaA region, the atp operon and a cluster of ribosomal protein genes. Nucleic Acids Res 1996; 24:628-39. [PMID: 8604303 PMCID: PMC145699 DOI: 10.1093/nar/24.4.628] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
To sequence the entire 800 kilobase pair genome of the bacterium Mycoplasma pneumoniae, a plasmid library was established with contained the majority of the EcoR1 fragments from M.pneumoniae. The EcoR1 fragments were subcloned from an ordered cosmid library comprising the complete M.pneumoniae genome. Individual plasmid clones were sequenced in an ordered fashion mainly by primer walking. We report here the initial results from the sequence analysis of -56 kb comprising the dnaA region as a potential origin of replication, the ATPase operon and a region coding for a cluster of ribosomal protein genes. The data were compared with the corresponding genes/operons from Bacillus subtilis, Escherichia coli, Mycoplasma capricolum and Mycoplasma gallisepticum.
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Affiliation(s)
- H Hilbert
- Zentrum für Molekulare Biologie Heidelberg, Universität Heidelberg, Germany
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27
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Neyrolles O, Ferris S, Behbahani N, Montagnier L, Blanchard A. Organization of Ureaplasma urealyticum urease gene cluster and expression in a suppressor strain of Escherichia coli. J Bacteriol 1996; 178:647-55. [PMID: 8550495 PMCID: PMC177707 DOI: 10.1128/jb.178.3.647-655.1996] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Ureaplasma urealyticum is a pathogenic ureolytic mollicute which colonizes the urogenital tracts of humans. A genetic polymorphism between the two biotypes of U. urealyticum at the level of the urease genes was found. The urease gene cluster from a biotype 1 representative of U. urealyticum (serotype I) was cloned and sequenced. Seven genes were found, with ureA, ureB, and ureC encoding the structural subunits and ureE, ureF, ureG, and a truncated ureI) gene encoding accessory proteins. Urease expression was not obtained when the plasmid containing these genes was incorporated into an opal suppressor strain of Escherichia coli, although this enzymatic activity was found in the same E. coli strain transformed with pC6b, a plasmid with previously cloned urease genes from the U. urealyticum T960 strain of biotype 2 (serotype 8). Although there are 12 TGA triplets encoding tryptophan within urease genes, the level of expression obtained was comparable to the levels reported for other bacterial genes expressed in E. coli. Nested deletion experiments allowed us to demonstrate that ureD is necessary for urease activity whereas another open reading frame located downstream is not. The promoter for ureA and possibly other urease genes was identified for both serotypes.
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Affiliation(s)
- O Neyrolles
- Unité d'Oncologie Virale, Institut Pasteur, Paris, France
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28
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Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA, Venter JC. The minimal gene complement of Mycoplasma genitalium. Science 1995; 270:397-403. [PMID: 7569993 DOI: 10.1126/science.270.5235.397] [Citation(s) in RCA: 1638] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.
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Affiliation(s)
- C M Fraser
- Institute for Genomic Research, Rockville, MD 20850, USA
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29
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Abstract
A putative retrovirus called LM7 was recently isolated from a patient with MS. This retrovirus was detected in LM7 and LM711 cultured human leptomeningeal cells. In the present work, nucleic acids from LM711 cell culture supernatants were purified and subjected to avian myeloblastosis viral (AMV) reverse transcriptase and to random polymerase chain reaction (rPCR) in order to characterize the genomic material of LM7 virions. Analysis of reverse transcription products allowed the detection of an approximately 14 kb ribonucleic acid in all LM711 cell culture supernatants. However, sequencing of rPCR-amplified molecules as well as RNA blotting data showed essentially that all tested cells producing LM7 particles were infected with mycoplasma. Moreover, purification of LM7 particles onto a linear sucrose density gradient established that the 14 kb nucleic acid was always associated with the 1.19-1.21 g ml-1 sucrose fractions, which are known to correspond to the buoyant density of mycoplasma. In addition, no viral genomic RNA was detected in the 1.17 g ml-1 sucrose fraction containing the low reverse transcription activity. These results strongly suggest that microscopic images and serological data could be related to mycoplasma and/or to a virion associated with the bacteria. The LM7 particle might be a new and additional enveloped virus able to infect Mycoplasma hyorhinis hosts. Thus, for instance, it would be presumptuous to assert, with our current understanding, that the LM7 virion is one of the causal agents of MS in humans.
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Affiliation(s)
- P Froussard
- Département des Rétrovirus, Institut Pasteur, Paris, France
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30
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Ladefoged SA, Birkelund S, Hauge S, Brock B, Jensen LT, Christiansen G. A 135-kilodalton surface antigen of Mycoplasma hominis PG21 contains multiple directly repeated sequences. Infect Immun 1995; 63:212-23. [PMID: 7806360 PMCID: PMC172980 DOI: 10.1128/iai.63.1.212-223.1995] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A monoclonal antibody was used to characterize a 135-kDa surface-located membrane protein (Lmp1) generally present in Mycoplasma hominis strains. The monoclonal antibody, 552, was applied to identify the corresponding gene in an expression library of M. hominis PG21 DNA. The M. hominis PG21 lmp1 gene was sequenced, and its gene product was characterized with the goal of elucidating the structure and function of Lmp1. A total of 7,196 bp in the lmp1 region was sequenced. An open reading frame of 4,032 bp, encoding a protein of 1,344 amino acids with a calculated molecular weight of 147,000, was identified. Analysis of the deduced amino acid sequence predicted a hydrophilic protein with a basic pI (10.0). The N-terminal 24 amino acids were a typical leader sequence. Downstream from the first 726 nucleotides, six similar direct repeats of 471 nucleotides were found. In repeat 7, a single-base substitution, C-->A, gave rise to the stop codon of lmp1. Thus, the C-terminal 945 amino acids were encoded by the 471-bp direct repeats. As evidenced by Southern blot analysis, the gene encoding the 135-kDa antigen is part of a multigene family. One of the genes, lmp2, was situated directly downstream from lmp1 where the direct repeats continued.
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Affiliation(s)
- S A Ladefoged
- Department of Medical Microbiology and Immunology, University of Aarhus, Denmark
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31
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Chastel C. Links and interactions between mycoplasmas and viruses: past confusions and present realities. Arch Virol 1995; 140:811-26. [PMID: 7605196 PMCID: PMC7087232 DOI: 10.1007/bf01314960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/1994] [Accepted: 01/30/1995] [Indexed: 01/26/2023]
Abstract
Links between mycoplasmas and viruses are ancient, multiple and complex, from past confusions during the first decades of the virus era to present realities illustrated by the possible implication of mycoplasmas as co-factors in natural infections of AIDS. Mycoplasma viruses (phages) may also be responsible for modifying the pathogenic power of mycoplasmas, at least for plants and insects. In addition, several mycoplasmas are able to act as undesirable cell culture contaminants that induce erroneous results in both applied and general virology. These problems are examined within a historical context.
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Affiliation(s)
- C Chastel
- Virus Laboratory, Faculty of Medicine, Brest, France
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32
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Yogev D, Menaker D, Strutzberg K, Levisohn S, Kirchhoff H, Hinz KH, Rosengarten R. A surface epitope undergoing high-frequency phase variation is shared by Mycoplasma gallisepticum and Mycoplasma bovis. Infect Immun 1994; 62:4962-8. [PMID: 7523302 PMCID: PMC303213 DOI: 10.1128/iai.62.11.4962-4968.1994] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have recently reported that three distinct size- and phase-variable surface lipoproteins (Vsps) of the bovine pathogen Mycoplasma bovis possess a common epitope recognized by monoclonal antibody 1E5. In the present study, we show that this epitope is also present on a size-variant protein (PvpA) of the avian pathogen Mycoplasma gallisepticum. Application of monoclonal antibody 1E5 in Western immunoblot analysis of Triton X-114 phase-fractionated proteins and in colony immunoblots, as well as in trypsin and carboxypeptidase digestion experiments, has demonstrated that (i) PvpA is an integral membrane protein with a free C terminus, (ii) the shared epitope is surface exposed, and (iii) PvpA is subjected to high-frequency phase variation in expression. By using serum antibodies from M. gallisepticum-infected chickens, we were able to demonstrate the immunogenic nature of PvpA and identify three additional highly immunogenic Triton X-114 phase proteins (p67, p72, and p75) also undergoing high-frequency phase variation spontaneously and independently. Metabolic labeling experiments with [14C]palmitate and [14C]oleate revealed that PvpA, in contrast to p67, p72, and p75, is not lipid modified. Southern blot hybridization with restriction fragments carrying the pvpA gene of M. gallisepticum or the vspA gene of M. bovis against digested genomic DNA of the two Mycoplasma species indicated the absence of genetic relatedness between the pvpA and vspA genes. The apparent complexity of the antigenic variation phenomenon in M. gallisepticum is discussed.
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Affiliation(s)
- D Yogev
- Department of Membrane and Ultrastructure Research, Hebrew University-Hadassah Medical School, Jerusalem
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33
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Zhu PP, Reizer J, Peterkofsky A. Unique dicistronic operon (ptsI-crr) in Mycoplasma capricolum encoding enzyme I and the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system: cloning, sequencing, promoter analysis, and protein characterization. Protein Sci 1994; 3:2115-28. [PMID: 7703858 PMCID: PMC2142656 DOI: 10.1002/pro.5560031125] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The region of the genome of Mycoplasma capricolum encompassing the genes for Enzymes I and IIAglc of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) was cloned and sequenced. Examination of the sequence revealed a unique arrangement of the pts operon. In all other bacterial species characterized thus far, the gene encoding Enzyme I (ptsI) in the pts operon is located immediately downstream of the gene (ptsH) encoding HPr, a general energy coupling protein of the PTS. In M. capricolum, ptsH and ptsI reside on 2 distinct operons at separate loci on the chromosome (Zhu PP, Reizer J, Reizer A, Peterkofsky A, 1993, J Biol Chem 268:26531-26540). In the present work, it is shown that the Mycoplasma Enzyme I gene is preceded by an open reading frame homologous to the product of the Escherichia coli kdtB gene and is followed by the gene (crr) encoding Enzyme IIAglc. Northern blot analysis indicated that ptsI and crr constitute a dicistronic operon that includes an independent promoter for the crr gene. Primer extension studies established the transcription start sites for the ptsI and crr genes. The products of the ptsI and crr genes are homologous to previously sequenced Enzymes I and IIAglc proteins but are more similar to the counterpart proteins from gram-positive than to those from gram-negative organisms. The deduced amino acid sequence of the Mycoplasma Enzyme I shows that it differs from other Enzymes I by having fewer acidic amino acids and more basic, amidated, and aromatic amino acids. The deduced amino acid sequence of the Mycoplasma Enzyme IIAglc indicates that it is the shortest (154 residues) of the proteins in this class and it is the only Enzyme IIAglc with a tryptophan and a cysteine residue. In vitro sugar phosphorylation studies with extracts from E. coli and Bacillus subtilis and purified proteins indicated that the Mycoplasma HPr is not a phosphoacceptor from the E. coli Enzyme I, whereas the Mycoplasma Enzyme IIAglc accepts and transfers phosphate from both E. coli and B. subtilis PTS components.
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Affiliation(s)
- P P Zhu
- Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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34
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Bailey CC, Bott KF. An unusual gene containing a dnaJ N-terminal box flanks the putative origin of replication of Mycoplasma genitalium. J Bacteriol 1994; 176:5814-9. [PMID: 8083173 PMCID: PMC196786 DOI: 10.1128/jb.176.18.5814-5819.1994] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Origins of replication are known to be highly conserved among widely divergent microbial species, with the gene order in those regions being dnaA-dnaN-recF-gyrB. On the basis of sequence identities to entries in GenBank, the gene order of a 6-kb fragment of Mycoplasma genitalium DNA was determined to be dnaN-orf311-gyrB-gyrA-serS, which is structurally similar to the ancestral origin of replication. We have directly linked the dnaN gene to the M. genitalium dnaA gene by PCR amplification. However, we found a novel open reading frame, designated orf311, in place of an expected sequence encoding recF. Orf311 contains a DnaJ box motif at its N terminus, but it has no overall homology to any other protein or sequence in the database. We are unable to detect any recF homolog in M. genitalium by hybridization or during a random sequencing survey of the genome.
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Affiliation(s)
- C C Bailey
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
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35
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Pettersson B, Johansson KE, Uhlén M. Sequence analysis of 16S rRNA from mycoplasmas by direct solid-phase DNA sequencing. Appl Environ Microbiol 1994; 60:2456-61. [PMID: 7521158 PMCID: PMC201670 DOI: 10.1128/aem.60.7.2456-2461.1994] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Automated solid-phase DNA sequencing was used for determination of partial 16S ribosomal DNA sequences of mycoplasmas. The sequence information was used to establish phylogenetic relationships of 11 different mycoplasmas whose 16S rRNA sequences had not been determined earlier. A biotinylated fragment corresponding to positions 344 to 939 in the Escherichia coli sequence was generated by PCR. The PCR product was immobilized onto streptavidin-coated paramagnetic beads, and direct sequencing was performed in both directions. One previously unclassified avian mycoplasma was found to belong to the Mycoplasma lipophilum cluster of the hominis group. Microheterogeneities were discovered in the rRNA operons of Mycoplasma mycoides subsp. mycoides (SC type), confirming the existence of two different rRNA operons. The 16S rRNA sequence of M. mycoides subsp. capri was identical to that of M. mycoides subsp. mycoides (type SC), except that no microheterogeneities were revealed. Furthermore, automated solid-phase DNA sequencing was used to identify a mycoplasmal contamination of a cell culture as Mycoplasma hyorhinis, which proved to be very difficult by conventional methods. The results suggest that the direct solid-phase DNA sequencing procedure is a powerful tool for identification of mycoplasmas and is also useful in taxonomic studies.
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Affiliation(s)
- B Pettersson
- Department of Biochemistry and Biotechnology, Royal Institute of Technology, Stockholm, Sweden
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36
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Knudtson KL, Minion FC. Use of lac gene fusions in the analysis of Acholeplasma upstream gene regulatory sequences. J Bacteriol 1994; 176:2763-6. [PMID: 8169231 PMCID: PMC205422 DOI: 10.1128/jb.176.9.2763-2766.1994] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The objective of this study was to develop a means of identifying and analyzing mycoplasma gene regulatory elements. Analysis of Acholeplasma oculi ISM1499 transcriptional sequences was accomplished using a promoterless lacZ reporter gene and an integrative vector strategy. Seven promoter-containing fragments were identified, levels of beta-galactosidase were determined, and transcriptional start sites were mapped.
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Affiliation(s)
- K L Knudtson
- Department of Microbiology, Immunology and Preventive Medicine, Iowa State University, Ames 50011
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37
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Tigges E, Minion FC. Physical map of the genome of Acholeplasma oculi ISM1499 and construction of a Tn4001 derivative for macrorestriction chromosomal mapping. J Bacteriol 1994; 176:1180-3. [PMID: 8106329 PMCID: PMC205171 DOI: 10.1128/jb.176.4.1180-1183.1994] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A physical chromosomal map of Acholeplasma oculi ISM1499 was constructed by using field inversion gel electrophoresis. To assist in the ordering of the chromosomal fragments, a modified transposon, Tn4001.1064, was constructed. It was also used to rescue mycoplasmal chromosomal sequences adjacent to transposon insertion sites in a one-step cloning procedure. The total size of the A. oculi ISM1499 genome was estimated to be 1,633 kb. The restriction enzyme sites for ApaI, BssHII, EagI, and SmaI were positioned on the map along with several transposon insertion sites.
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Affiliation(s)
- E Tigges
- Veterinary Medical Research Institute, Iowa State University, Ames 50011
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38
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Zhu PP, Reizer J, Reizer A, Peterkofsky A. Unique monocistronic operon (ptsH) in Mycoplasma capricolum encoding the phosphocarrier protein, HPr, of the phosphoenolpyruvate:sugar phosphotransferase system. Cloning, sequencing, and characterization of ptsH. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74345-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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39
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Peterson SN, Hu PC, Bott KF, Hutchison CA. A survey of the Mycoplasma genitalium genome by using random sequencing. J Bacteriol 1993; 175:7918-30. [PMID: 8253680 PMCID: PMC206970 DOI: 10.1128/jb.175.24.7918-7930.1993] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A total of 508 random clones from five Mycoplasma genitalium genomic libraries were partially sequenced and analyzed. This resulted in the identification of 291 unique contigs. Sequence information from these clones (100,993 nucleotides), representing approximately 17% of this pathogen's genome, was analyzed by comparison to the DNA and protein sequence data bases. The frequency with which clones could be identified, by virtue of possessing homology to another data base entry, was 46%. Sequence analysis indicated the following. (i) The M. genitalium genome contains many genes involved in various metabolic processes. (ii) Repetitive DNA may comprise as much as 4% of this genome. (iii) The MgPa adhesin gene may be the result of horizontal transfer from an unknown origin. (iv) Not all dinucleotide pairs are present in this genome at the expected frequency. (v) This genome potentially encodes approximately 390 proteins and makes very efficient use of its limited amount of DNA. In addition, this study allowed us to estimate the number of genes involved with various cellular functions.
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Affiliation(s)
- S N Peterson
- Curriculum in Genetics, University of North Carolina at Chapel Hill 27599
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40
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Simoneau P, Li CM, Loechel S, Wenzel R, Herrmann R, Hu PC. Codon reading scheme in Mycoplasma pneumoniae revealed by the analysis of the complete set of tRNA genes. Nucleic Acids Res 1993; 21:4967-74. [PMID: 7513847 PMCID: PMC311414 DOI: 10.1093/nar/21.21.4967] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The 33 genes encoding the complete set of tRNA species in Mycoplasma pneumoniae have been cloned and sequenced. They are organized into 5 clusters in addition to 9 single genes. No redundant gene was found, indicating that 33 tRNAs correspond to 32 different anticodons and decode all 62 codons used in this organism. There is only one single tRNA for each of the Ala, Leu, Pro, and Val family boxes. Therefore, a simplified decoding system resembling that recently described for Mycoplasma capricolum (1) has to also exist in M.pneumoniae. However, analysis of the anticodon set and codon usage revealed features characteristic of the latter: (i) there is no obvious preference toward AT rich synonymous codons, (ii) CGG codons are assigned for arginine and are translated by tRNA Arg(UCG), and (iii) CNN or GNN anticodons are encountered in the Ser, Thr, Arg, and Gly family boxes. We thus propose that this codon-anticodon recognition pattern has emerged in the 'M.pneumoniae cluster' under a genomic economization strategy but without the influence of AT pressure.
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Affiliation(s)
- P Simoneau
- Department of Pediatrics, University of North Carolina, Chapel Hill 27599
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41
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Miyata M, Sano K, Okada R, Fukumura T. Mapping of replication initiation site in Mycoplasma capricolum genome by two-dimensional gel-electrophoretic analysis. Nucleic Acids Res 1993; 21:4816-23. [PMID: 8233831 PMCID: PMC331511 DOI: 10.1093/nar/21.20.4816] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The homolog of the dnaA gene, which has been reported to be present in the vicinity of the initiation site of replication in the genome of Mycoplasma capricolum (M.Miyata, L.Wang, and T.Fukumura, J. Bacteriol. 175: 655-660, 1993) was mapped precisely. A 9540-bp region containing the dnaA gene was cloned and the entire region was sequenced with the exception of a previously reported region of 2517 bp (Fujita, M.Q., Yoshikawa, H. and Ogasawara, N. Gene 93: 73-78, 1992). The organization of the 9540-bp region was compared with that of corresponding regions in other bacteria. The arrangement and directions of rnpA, rpmH, dnaA, dnaN were conserved, but no other open reading frames were found that were homologous to those that are commonly found around dnaA genes in other bacteria. The directions of movement of the replication fork around the dnaA gene were analyzed by neutral/alkaline two-dimensional gel electrophoresis. The forks developed in a 1569-bp region that consisted of the dnaA structural gene and its downstream non-coding region, and then they proceeded bidirectionally.
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Affiliation(s)
- M Miyata
- Department of Biology, Faculty of Science, Osaka City University, Japan
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42
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Ushida C, Muto A. A small RNA of Mycoplasma capricolum that resembles eukaryotic U6 small nuclear RNA. Nucleic Acids Res 1993; 21:2649-53. [PMID: 7687343 PMCID: PMC309594 DOI: 10.1093/nar/21.11.2649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Mycoplasma capricolum, a parasitic prokaryote, contains several small stable RNAs, besides rRNAs and tRNAs. One of them, designated MCS4 RNA (125 nucleotides in length), has been isolated and sequenced. This RNA is abundant in the cell, and is encoded by two genes. Unexpectedly, MCS4 RNA has been found to reveal extensive sequence similarity to eukaryotic U6 snRNAs. This finding suggests that MCS4 and U6 snRNAs are derived from a common ancestral RNA that has existed before the divergence of prokaryotes and eukaryotes.
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Affiliation(s)
- C Ushida
- Department of Biology, Faculty of Science, Hirosaki University, Aomori, Japan
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43
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Washburn LR, Hirsch S, Voelker LL. Mechanisms of attachment of Mycoplasma arthritidis to host cells in vitro. Infect Immun 1993; 61:2670-80. [PMID: 8500906 PMCID: PMC280899 DOI: 10.1128/iai.61.6.2670-2680.1993] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Although other investigators have reported that Mycoplasma arthritidis failed to attach to several types of mammalian cells in vitro, we showed that it attached well to rat synovial fibroblasts, lung cells, and skin cells but not to kidney cells, suggesting that receptor sites are unequally expressed or distributed among different rat tissues. M. arthritidis also attached poorly to canine kidney and to baby hamster kidney cells, although it did attach to human fetal lung and fetal amnion cells. Four M. arthritidis strains, two virulent and two avirulent, all attached equally well to rat lung cells. Attachment was inhibited by trypsinization, suggesting that the major adhesins are protein. Fab' fractions of rabbit antisera against four M. arthritidis strains partially inhibited adherence of both homologous and heterologous strains, although not to the same extent, indicating some degree of antigenic heterogeneity among their adhesins. A filter-cloned variant of M. arthritidis 158p10p9, designated LC1, attached poorly compared with the parent strain. Missing from this variant were two proteins migrating within the 81- to 90-kDa range by polyacrylamide gel electrophoresis; in their place was a 24-kDa antigen that may be a truncated version of one of these proteins. A monoclonal antibody that partially inhibited attachment recognized all these peptides by Western immunoblotting. An additional attachment-inhibiting monoclonal antibody recognized a 71-kDa antigen present in both low-adherence and fully adherent populations. The low-adherence variant LC1 induced slightly but significantly less arthritis in Lewis rats than did a fully adherent clone.
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Affiliation(s)
- L R Washburn
- Department of Microbiology, University of South Dakota School of Medicine, Vermillion 57069
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44
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Schaeffer WI, Melamede R. Fluorometric quantitation of broth-cultured mycoplasmas by using alkaline ethidium bromide. J Clin Microbiol 1993; 31:1303-7. [PMID: 8501232 PMCID: PMC262923 DOI: 10.1128/jcm.31.5.1303-1307.1993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We developed a fluorometric system which does for broth-grown mycoplasmas what turbidimetric analysis does for broth-grown bacteria. It allows one to monitor the growth of broth-grown mycoplasmas at any interval desired. The entire procedure is quick, taking not more than 20 min. The fluorometric readings correlate with colonial growth on agar, making it possible, for the first time, to take readings which closely estimate the CFU present in the culture at a given moment in time. We show that this system can be used to assess the effectiveness of an antimycoplasmal antibiotic and to optimize medium components and that fluorometer readings taken during the logarithmic phase of growth correlate with the DNA content of the viable cells. Use of this methodology will permit investigators to know absolutely the phase of the growth cycle of the culture concomitant with the growth of the culture itself, and since fluorometer readings of culture aliquots can be converted to DNA equivalents, the standardization of mycoplasmal cultures within and between laboratories will be a possibility.
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Affiliation(s)
- W I Schaeffer
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington 05405
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45
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Su CJ, Dallo SF, Chavoya A, Baseman JB. Possible origin of sequence divergence in the P1 cytadhesin gene of Mycoplasma pneumoniae. Infect Immun 1993; 61:816-22. [PMID: 8432602 PMCID: PMC302806 DOI: 10.1128/iai.61.3.816-822.1993] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Specific regions of the P1 adhesin structural gene of Mycoplasma pneumoniae hybridize to various parts of the mycoplasma genome, indicating their multiple-copy nature. In addition, restriction fragment length polymorphisms and sequence divergence have been observed in the P1 gene, permitting the classification of clinical isolates of M. pneumoniae into two groups, I and II. These data suggest that the observed P1 gene diversity may be explained by homologous recombination between similar but not identical multicopy P1-related sequences and the P1 structural gene. We used oligonucleotide probes specific to the diverged regions of the group I and group II P1 structural genes to clone and sequence multicopy P1-related DNA segments. We detected sequences in group I M. pneumoniae isolates that were homologous not only to the group I P1 structural gene but also to the diverged regions of the group II P1 structural gene. Likewise, sequences in group II clinical isolates that were homologous both to the group II P1 structural gene and the diverged regions of the group I P1 structural gene were detected.
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Affiliation(s)
- C J Su
- Department of Microbiology, University of Texas Health Science Center, San Antonio 78284
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46
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Miyata M, Wang L, Fukumura T. Localizing the replication origin region on the physical map of the Mycoplasma capricolum genome. J Bacteriol 1993; 175:655-60. [PMID: 8423141 PMCID: PMC196202 DOI: 10.1128/jb.175.3.655-660.1993] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Four lines of evidence argue that the replication origin of the Mycoplasma capricolum genome lies within the 46-kb BamHI fragment bordered by two BamHI sites of the total of nine BamHI sites that have been located on the physical map (M. Miyata, L. Wang, and T. Fukumura, FEMS Microbiol. Lett. 79:329-334, 1991). First, this fragment lost its labeling in preference to other fragments when log-phase cultures were incubated in the presence of chloramphenicol for various times to inhibit the initiation of new rounds of replication and then further incubated with radioactive dTMP to allow DNA elongation to continue. Second, the relative frequencies of various restriction fragments of the genome DNA from exponentially growing cells decreased with increasing distance from the putative origin. Third, preferential labeling occurred when radioactive dTMP was added to cultures of a DNA elongation-defective, temperature-sensitive mutant with a simultaneous temperature downshift. Fourth, the M. capricolum homolog of the dnaA gene, which is located near the replication origin in many other bacteria, was found in the 46-kb fragment.
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Affiliation(s)
- M Miyata
- Department of Biology, Faculty of Science, Osaka City University, Japan
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47
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48
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Samuelsson T. A Mycoplasma protein homologous to mammalian SRP54 recognizes a highly conserved domain of SRP RNA. Nucleic Acids Res 1992; 20:5763-70. [PMID: 1280809 PMCID: PMC334414 DOI: 10.1093/nar/20.21.5763] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A protein homologous to SRP54, a subunit of the mammalian signal recognition particle (SRP), was identified in Mycoplasma mycoides. The mycoplasma protein was expressed in E.coli and purified to near homogeneity. It was shown to bind specifically in vitro to a small mycoplasma RNA with structural features related to the RNA component of SRP. These findings provide evidence of a ribonucleoprotein complex in mycoplasma reminiscent of SRP. A part of the RNA was protected from ribonuclease digestion in the presence of the SRP54 homologue. The protected region contains structural elements that have been highly conserved in SRP RNAs during evolution.
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Affiliation(s)
- T Samuelsson
- Department of Medical Biochemistry, University of Göteborg, Sweden
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49
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Wenzel R, Pirkl E, Herrmann R. Construction of an EcoRI restriction map of Mycoplasma pneumoniae and localization of selected genes. J Bacteriol 1992; 174:7289-96. [PMID: 1429453 PMCID: PMC207423 DOI: 10.1128/jb.174.22.7289-7296.1992] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A restriction map of the genome of Mycoplasma pneumoniae, a small human pathogenic bacterium, was constructed by means of an ordered cosmid library which spans the complete bacterial chromosome. The positions of 143 endonuclease EcoRI restriction fragments were determined and aligned with the physical map. In addition, restriction sites for the rare-cutting enzymes XhoI (25 sites), ApaI (13 sites), NotI (2 sites), and SfiI (2 sites) were included. The resulting map consists of 185 restriction sites, has a mean resolution of 4.4 kbp, and predicts a genome size of 809 kbp. In addition, several genes were identified and mapped to their respective genomic EcoRI restriction fragments.
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Affiliation(s)
- R Wenzel
- ZMBH, University of Heidelberg, Germany
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Salman M, Tarshis M, Rottem S. Fusion-mediated transfer of plasmids into Spiroplasma floricola cells. J Bacteriol 1992; 174:4410-5. [PMID: 1624433 PMCID: PMC206226 DOI: 10.1128/jb.174.13.4410-4415.1992] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have developed and characterized a system for the transfer of plasmids encapsulated in large unilamellar vesicles (LUV) into Spiroplasma floricola BNR1 cells. The approach is based on the ability of S. floricola-derived LUV to fuse with S. floricola cells. The fusion was continuously monitored by an assay for lipid mixing based on the dequenching of the fluorescent probe octadecylrhodamine B (R18) that was incorporated into LUV at self-quenching concentrations. The fusion was also evaluated by fluorescence-activated cell sorter measurements and by sucrose density gradient analysis. LUV-cell fusion occurred only in the presence of low concentrations (5%) of polyethylene glycol (polyethylene glycol 8000) and depended on temperature, the LUV/cell ratio, and divalent cations in the incubation medium. Throughout the fusion process, spiroplasma cells remained intact and viable. Under optimal fusion conditions, the plasmid pACYC, encapsulated in LUV by reversed-phase evaporation, was transferred into live S. floricola cells and expressed chloramphenicol acetyltransferase activity. The expression was transient with maximal chloramphenicol acetyltransferase activity observed after 6 h of incubation of the transfected cells.
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Affiliation(s)
- M Salman
- Department of Membrane and Ultrastructure Research, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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