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Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol 2015; 16:234. [PMID: 26498365 PMCID: PMC4620651 DOI: 10.1186/s13059-015-0790-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0790-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland.
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,Department of Animal Science, University of Connecticut, Storrs, CT, 06029, USA.
| | - Paul A McGettigan
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Ceiridwen J Edwards
- Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Rd, Oxford, OX1 3QY, UK.
| | - Amanda J Lohan
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Alison Murphy
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Martin Braud
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Mark T Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Yuan Liu
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Andrew T Chamberlain
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Steven Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA.
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Shuaishuai Tai
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA. .,Recombinetics Inc., St. Paul, MN, 55104, USA.
| | - Brendan J Loftus
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. .,UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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Lanigan F, Brien GL, Fan Y, Madden SF, Jerman E, Maratha A, Aloraifi F, Hokamp K, Dunne EJ, Lohan AJ, Flanagan L, Garbe JC, Stampfer MR, Fridberg M, Jirstrom K, Quinn CM, Loftus B, Gallagher WM, Geraghty J, Bracken AP. Delineating transcriptional networks of prognostic gene signatures refines treatment recommendations for lymph node-negative breast cancer patients. FEBS J 2015; 282:3455-73. [DOI: 10.1111/febs.13354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/02/2015] [Accepted: 06/17/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Fiona Lanigan
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Gerard L. Brien
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Yue Fan
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Stephen F. Madden
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Emilia Jerman
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Ashwini Maratha
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Fatima Aloraifi
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Karsten Hokamp
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Eiseart J. Dunne
- The Smurfit Institute of Genetics; Trinity College Dublin; Ireland
| | - Amanda J. Lohan
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - Louise Flanagan
- Department of Histopathology; St Vincent's University Hospital; Dublin Ireland
| | - James C. Garbe
- Life Science Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Martha R. Stampfer
- Life Science Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Marie Fridberg
- Department of Clinical Sciences, Division of Oncology and Pathology; Lund University; Sweden
| | - Karin Jirstrom
- Department of Clinical Sciences, Division of Oncology and Pathology; Lund University; Sweden
| | - Cecily M. Quinn
- Department of Histopathology; St Vincent's University Hospital; Dublin Ireland
| | - Brendan Loftus
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - William M. Gallagher
- UCD School of Biomolecular and Biomedical Science; UCD Conway Institute; University College Dublin; Ireland
| | - James Geraghty
- Department of Histopathology; St Vincent's University Hospital; Dublin Ireland
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Firdessa R, Berg S, Hailu E, Schelling E, Gumi B, Erenso G, Gadisa E, Kiros T, Habtamu M, Hussein J, Zinsstag J, Robertson BD, Ameni G, Lohan AJ, Loftus B, Comas I, Gagneux S, Tschopp R, Yamuah L, Hewinson G, Gordon SV, Young DB, Aseffa A. Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg Infect Dis 2013; 19:460-3. [PMID: 23622814 PMCID: PMC3647644 DOI: 10.3201/eid1903.120256] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Molecular typing of 964 specimens from patients in Ethiopia with lymph node or pulmonary tuberculosis showed a similar distribution of Mycobacterium tuberculosis strains between the 2 disease manifestations and a minimal role for M. bovis. We report a novel phylogenetic lineage of M. tuberculosis strongly associated with the Horn of Africa.
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4
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Ó’Maoiléidigh DS, Wuest SE, Rae L, Raganelli A, Ryan PT, Kwaśniewska K, Das P, Lohan AJ, Loftus B, Graciet E, Wellmer F. Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS. Plant Cell 2013; 25:2482-503. [PMID: 23821642 PMCID: PMC3753378 DOI: 10.1105/tpc.113.113209] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/05/2013] [Accepted: 06/17/2013] [Indexed: 05/18/2023]
Abstract
The floral organ identity factor AGAMOUS (AG) is a key regulator of Arabidopsis thaliana flower development, where it is involved in the formation of the reproductive floral organs as well as in the control of meristem determinacy. To obtain insights into how AG specifies organ fate, we determined the genes and processes acting downstream of this C function regulator during early flower development and distinguished between direct and indirect effects. To this end, we combined genome-wide localization studies, gene perturbation experiments, and computational analyses. Our results demonstrate that AG controls flower development to a large extent by controlling the expression of other genes with regulatory functions, which are involved in mediating a plethora of different developmental processes. One aspect of this function is the suppression of the leaf development program in emerging floral primordia. Using trichome initiation as an example, we demonstrate that AG inhibits an important aspect of leaf development through the direct control of key regulatory genes. A comparison of the gene expression programs controlled by AG and the B function regulators APETALA3 and PISTILLATA, respectively, showed that while they control many developmental processes in conjunction, they also have marked antagonistic, as well as independent activities.
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Affiliation(s)
| | - Samuel E. Wuest
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Liina Rae
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Andrea Raganelli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Patrick T. Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Kamila Kwaśniewska
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pradeep Das
- École Normale Supérieure, 69364 Lyon, cedex 07, France
| | - Amanda J. Lohan
- Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Brendan Loftus
- Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Address correspondence to
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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Nalpas NC, Park SDE, Magee DA, Taraktsoglou M, Browne JA, Conlon KM, Rue-Albrecht K, Killick KE, Hokamp K, Lohan AJ, Loftus BJ, Gormley E, Gordon SV, MacHugh DE. Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro. BMC Genomics 2013; 14:230. [PMID: 23565803 PMCID: PMC3640917 DOI: 10.1186/1471-2164-14-230] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 03/08/2013] [Indexed: 12/20/2022] Open
Abstract
Background Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA. Results A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology. Conclusions This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA.
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Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JSC, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol 2013; 14:R11. [PMID: 23375108 PMCID: PMC4053784 DOI: 10.1186/gb-2013-14-2-r11] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 02/01/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan. RESULTS Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms. CONCLUSIONS Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.
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7
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Brien GL, Gambero G, O'Connell DJ, Jerman E, Turner SA, Egan CM, Dunne EJ, Jurgens MC, Wynne K, Piao L, Lohan AJ, Ferguson N, Shi X, Sinha KM, Loftus BJ, Cagney G, Bracken AP. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. Nat Struct Mol Biol 2012; 19:1273-81. [DOI: 10.1038/nsmb.2449] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Accepted: 10/17/2012] [Indexed: 12/21/2022]
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8
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Kröger C, Dillon SC, Cameron ADS, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JCD. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A 2012; 109:E1277-86. [PMID: 22538806 PMCID: PMC3356629 DOI: 10.1073/pnas.1201061109] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ(70) (including phoP, slyA, and invF) from which we identified the -10 and -35 motifs of σ(70)-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and <20% were found throughout the Enterobacteriaceae. This description of the transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Shane C. Dillon
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Andrew D. S. Cameron
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Kai Papenfort
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Sathesh K. Sivasankaran
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Karsten Hokamp
- Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Yanjie Chao
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Alexandra Sittka
- Molecular Pulmonology, Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Philipps University, 35043 Marburg, Germany
| | - Magali Hébrard
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Kristian Händler
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Aoife Colgan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Pimlapas Leekitcharoenphon
- Department of Systems Biology, Center for Biological Sequence Analysis, and
- National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gemma C. Langridge
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Amanda J. Lohan
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin 4, Ireland; and
| | - Brendan Loftus
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin 4, Ireland; and
| | - Sacha Lucchini
- Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - David W. Ussery
- Department of Systems Biology, Center for Biological Sequence Analysis, and
| | - Charles J. Dorman
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
| | - Nicholas R. Thomson
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jay C. D. Hinton
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, and
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Pozzi C, Waters EM, Rudkin JK, Schaeffer CR, Lohan AJ, Tong P, Loftus BJ, Pier GB, Fey PD, Massey RC, O'Gara JP. Methicillin resistance alters the biofilm phenotype and attenuates virulence in Staphylococcus aureus device-associated infections. PLoS Pathog 2012; 8:e1002626. [PMID: 22496652 PMCID: PMC3320603 DOI: 10.1371/journal.ppat.1002626] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 02/23/2012] [Indexed: 01/15/2023] Open
Abstract
Clinical isolates of Staphylococcus aureus can express biofilm phenotypes promoted by the major cell wall autolysin and the fibronectin-binding proteins or the icaADBC-encoded polysaccharide intercellular adhesin/poly-N-acetylglucosamine (PIA/PNAG). Biofilm production in methicillin-susceptible S. aureus (MSSA) strains is typically dependent on PIA/PNAG whereas methicillin-resistant isolates express an Atl/FnBP-mediated biofilm phenotype suggesting a relationship between susceptibility to β-lactam antibiotics and biofilm. By introducing the methicillin resistance gene mecA into the PNAG-producing laboratory strain 8325-4 we generated a heterogeneously resistant (HeR) strain, from which a homogeneous, high-level resistant (HoR) derivative was isolated following exposure to oxacillin. The HoR phenotype was associated with a R602H substitution in the DHHA1 domain of GdpP, a recently identified c-di-AMP phosphodiesterase with roles in resistance/tolerance to β-lactam antibiotics and cell envelope stress. Transcription of icaADBC and PNAG production were impaired in the 8325-4 HoR derivative, which instead produced a proteinaceous biofilm that was significantly inhibited by antibodies against the mecA-encoded penicillin binding protein 2a (PBP2a). Conversely excision of the SCCmec element in the MRSA strain BH1CC resulted in oxacillin susceptibility and reduced biofilm production, both of which were complemented by mecA alone. Transcriptional activity of the accessory gene regulator locus was also repressed in the 8325-4 HoR strain, which in turn was accompanied by reduced protease production and significantly reduced virulence in a mouse model of device infection. Thus, homogeneous methicillin resistance has the potential to affect agr- and icaADBC-mediated phenotypes, including altered biofilm expression and virulence, which together are consistent with the adaptation of healthcare-associated MRSA strains to the antibiotic-rich hospital environment in which they are frequently responsible for device-related infections in immuno-compromised patients. The acquisition of mecA, which encodes penicillin binding protein 2a (PBP2a) and methicillin resistance, by Staphylococcus aureus has added to an already impressive array of virulence mechanisms including enzyme and toxin production, biofilm forming capacity and immune evasion. And yet clinical data does not indicate that healthcare-associated methicillin resistant S. aureus (MRSA) strains are more virulent than their methicillin-susceptible counterparts. Here our findings suggest that MRSA sacrifices virulence potential for antibiotic resistance and that expression of methicillin resistance alters the biofilm phenotype but does not interfere with the colonization of implanted medical devices in vivo. High level expression of PBP2a, which was associated with a mutation in the c-di-AMP phosphodiesterase gene gdpP, resulted in these pleiotrophic effects by blocking icaADBC-dependent polysaccharide type biofilm development and promoting an alternative PBP2a-mediated biofilm, repressing the accessory gene regulator and extracellular protease production, and attenuating virulence in a mouse device-infection model. Thus the adaptation of MRSA to the hospital environment has apparently focused on the acquisition of antibiotic resistance and retention of biofilm forming capacity, which are likely to be more advantageous than metabolically-expensive enzyme and toxin production in immunocompromised patients with implanted medical devices offering a route to infection.
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Affiliation(s)
- Clarissa Pozzi
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Elaine M. Waters
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Justine K. Rudkin
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Carolyn R. Schaeffer
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Amanda J. Lohan
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Pin Tong
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Brendan J. Loftus
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Gerald B. Pier
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ruth C. Massey
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - James P. O'Gara
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- * E-mail:
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10
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Weissenmayer BA, Prendergast JGD, Lohan AJ, Loftus BJ. Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs. PLoS One 2011; 6:e17570. [PMID: 21408607 PMCID: PMC3048289 DOI: 10.1371/journal.pone.0017570] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 02/03/2011] [Indexed: 11/18/2022] Open
Abstract
Second generation sequencing has prompted a number of groups to re-interrogate the transcriptomes of several bacterial and archaeal species. One of the central findings has been the identification of complex networks of small non-coding RNAs that play central roles in transcriptional regulation in all growth conditions and for the pathogen's interaction with and survival within host cells. Legionella pneumophila is a Gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila during exponential and post-exponential broth growth and during the replicative and transmissive phase of infection inside A. castellanii. We extend previous microarray based studies as well as uncovering evidence of a complex regulatory architecture underpinned by numerous non-coding RNAs. Over seventy new non-coding RNAs could be identified; many of them appear to be strain specific and in configurations not previously reported. We discover a family of non-coding RNAs preferentially expressed during infection conditions and identify a second copy of 6S RNA in L. pneumophila. We show that the newly discovered putative 6S RNA as well as a number of other non-coding RNAs show evidence for antisense transcription. The nature and extent of the non-coding RNAs and their expression patterns suggests that these may well play central roles in the regulation of Legionella spp. specific traits and offer clues as to how L. pneumophila adapts to its intracellular niche. The expression profiles outlined in the study have been deposited into Genbank's Gene Expression Omnibus (GEO) database under the series accession GSE27232.
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Affiliation(s)
| | | | - Amanda J. Lohan
- UCD Conway Institute for Biomolecular and Biomedical Research, Dublin, Ireland
| | - Brendan J. Loftus
- UCD Conway Institute for Biomolecular and Biomedical Research, Dublin, Ireland
- * E-mail:
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11
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Tong P, Prendergast JGD, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF, Loftus B. Sequencing and analysis of an Irish human genome. Genome Biol 2010; 11:R91. [PMID: 20822512 PMCID: PMC2965383 DOI: 10.1186/gb-2010-11-9-r91] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Revised: 07/13/2010] [Accepted: 09/07/2010] [Indexed: 11/10/2022] Open
Abstract
Background Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci. Here, choosing a DNA sample from a population of interest due to its relative geographical isolation and genetic impact on further populations, we extend the above studies through the generation of 11-fold coverage of the first Irish human genome sequence. Results Using sequence data from a branch of the European ancestral tree as yet unsequenced, we identify variants that may be specific to this population. Through comparisons with HapMap and previous genetic association studies, we identified novel disease-associated variants, including a novel nonsense variant putatively associated with inflammatory bowel disease. We describe a novel method for improving SNP calling accuracy at low genome coverage using haplotype information. This analysis has implications for future re-sequencing studies and validates the imputation of Irish haplotypes using data from the current Human Genome Diversity Cell Line Panel (HGDP-CEPH). Finally, we identify gene duplication events as constituting significant targets of recent positive selection in the human lineage. Conclusions Our findings show that there remains utility in generating whole genome sequences to illustrate both general principles and reveal specific instances of human biology. With increasing access to low cost sequencing we would predict that even armed with the resources of a small research group a number of similar initiatives geared towards answering specific biological questions will emerge.
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Affiliation(s)
- Pin Tong
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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12
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Edwards CJ, Magee DA, Park SDE, McGettigan PA, Lohan AJ, Murphy A, Finlay EK, Shapiro B, Chamberlain AT, Richards MB, Bradley DG, Loftus BJ, MacHugh DE. A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius). PLoS One 2010; 5:e9255. [PMID: 20174668 PMCID: PMC2822870 DOI: 10.1371/journal.pone.0009255] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 01/29/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.
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Affiliation(s)
| | - David A. Magee
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
| | - Stephen D. E. Park
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
| | - Paul A. McGettigan
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
| | - Amanda J. Lohan
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alison Murphy
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Emma K. Finlay
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Beth Shapiro
- Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, Oxford, United Kingdom
| | | | - Martin B. Richards
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Brendan J. Loftus
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- * E-mail:
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13
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Abstract
Editing processes that result in the structural retailoring of the aminoacyl acceptor stems of mitochondrial tRNAs are the focus of this chapter. This type of tRNA editing is the most frequently observed and widely distributed and involves nucleotide replacement within the 5' or 3' half of the aminoacyl acceptor stem in either a template-directed or a template-independent fashion. We provide a detailed protocol that allows demarcation of 5'-terminal tRNA editing events from those occurring on the 3' side of the acceptor stem. We present the mitochondrial 5' tRNA editing system in Acanthamoeba castellanii as the exemplar of terminal tRNA editing. The methodology involves RNA ligase-mediated circularization of tRNAs, cDNA synthesis primed by tRNA-specific oligonucleotides, amplification of cDNA via polymerase chain reaction, and cloning and sequencing of multiple products. This approach permits (1) simultaneous determination of 5' and 3' acceptor stem sequences, (2) delineation of 5' or 3' editing, (3) identification of mature tRNAs (characterized by having a 3'-CCA(OH) motif), (4) identification of processing/editing intermediates, and (5) mechanistic insights.
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Affiliation(s)
- Amanda J Lohan
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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14
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Abstract
We present here methodology for assaying 5'-terminal editing of mitochondrial tRNAs in the amoeboid protist Acanthamoeba castellanii. This type of editing involves replacement of one or more nucleotides within the first three positions at the 5' end of a tRNA substrate. The assay procedure involves RNA ligase-mediated joining of the 5' and 3' ends of a tRNA, use of the resulting circularized tRNA as template for cDNA synthesis primed by tRNA-specific primers over a region that encompasses the ligated 5' and 3' halves of the acceptor stem, amplification of cDNA via polymerase chain reaction, and cloning and sequencing of double-stranded cDNA product. This approach has the advantage that it simultaneously reveals potential editing events on the 5' and 3' side of an acceptor stem, as well as serves to identify mature tRNAs (characterized by having a 3'-CCAOH motif) and partially processed intermediates.
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Affiliation(s)
- Amanda J Lohan
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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15
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Gu W, Jackman JE, Lohan AJ, Gray MW, Phizicky EM. tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Genes Dev 2003; 17:2889-901. [PMID: 14633974 PMCID: PMC289149 DOI: 10.1101/gad.1148603] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
All tRNAHis molecules are unusual in having an extra 5' GMP residue (G(-1)) that, in eukaryotes, is added after transcription and RNase P cleavage. Incorporation of this G(-1) residue is a rare example of nucleotide addition occurring at an RNA 5' end in a normal phosphodiester linkage. We show here that the essential Saccharomyces cerevisiae ORF YGR024c (THG1) is responsible for this guanylyltransferase reaction. Thg1p was identified by survey of a genomic collection of yeast GST-ORF fusion proteins for addition of [alpha-32P]GTP to tRNAHis. End analysis confirms the presence of G(-1). Thg1p is required for tRNAHis guanylylation in vivo, because cells depleted of Thg1p lack G(-1) in their tRNAHis. His6-Thg1p purified from Escherichia coli catalyzes the guanylyltransferase step of G(-1) addition using a ppp-tRNAHis substrate, and appears to catalyze the activation step using p-tRNAHis and ATP. Thg1p is highlye conserved in eukaryotes, where G(-1) addition is necessary, and is not found in eubacteria, where G(-1) is genome-encoded. Thus, Thg1p is the first member of a new family of enzymes that can catalyze phosphodiester bond formation at the 5' end of RNAs, formally in a 3'-5' direction. Surprisingly, despite its varied activities, Thg1p contains no recognizable catalytic or functional domains.
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Affiliation(s)
- Weifeng Gu
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
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16
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Abstract
The plastid genome of the nonphotosynthetic parasitic plant Epifagus virginiana contains only 17 of the 30 tRNA genes normally found in angiosperm plastid DNA. Although this is insufficient for translation, the genome is functional, so import of cytosolic tRNAs into plastids has been suggested. This raises the question of whether the tRNA genes that remain in E. virginiana plastid DNA are active or have just fortuitously escaped deletion. We report the sequences of 20 plastid tRNA loci from Orobanche minor, which shares a nonphotosynthetic ancestor with E. virginiana. The two species have 9 intact tRNA genes in common, the others being defunct in one or both species. The intron-containing trnLUAA gene is absent from E. virginiana, but it is intact, transcribed, and spliced in O. minor. The shared intact genes are better conserved than intergenic sequences, which indicates that these genes are being maintained by natural selection and, therefore, must be functional. For the most part, the tRNA species conserved in nonphotosynthetic plastids are also those that have never been found to be imported in plant mitochondria, which suggests that the same rules may govern tRNA import in the two organelles. A small photosynthesis gene, psbI, is still intact in O. minor, and computer simulations show that some small nonessential genes have an appreciable chance of escaping deletion.
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Affiliation(s)
- A J Lohan
- Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
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17
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Feldmann H, Aigle M, Aljinovic G, André B, Baclet MC, Barthe C, Baur A, Bécam AM, Biteau N, Boles E, Brandt T, Brendel M, Brückner M, Bussereau F, Christiansen C, Contreras R, Crouzet M, Cziepluch C, Démolis N, Delaveau T, Doignon F, Domdey H, Düsterhus S, Dubois E, Dujon B, El Bakkoury M, Entian KD, Feurmann M, Fiers W, Fobo GM, Fritz C, Gassenhuber H, Glandsdorff N, Goffeau A, Grivell LA, de Haan M, Hein C, Herbert CJ, Hollenberg CP, Holmstrøm K, Jacq C, Jacquet M, Jauniaux JC, Jonniaux JL, Kallesøe T, Kiesau P, Kirchrath L, Kötter P, Korol S, Liebl S, Logghe M, Lohan AJ, Louis EJ, Li ZY, Maat MJ, Mallet L, Mannhaupt G, Messenguy F, Miosga T, Molemans F, Müller S, Nasr F, Obermaier B, Perea J, Piérard A, Piravandi E, Pohl FM, Pohl TM, Potier S, Proft M, Purnelle B, Ramezani Rad M, Rieger M, Rose M, Schaaff-Gerstenschläger I, Scherens B, Schwarzlose C, Skala J, Slonimski PP, Smits PH, Souciet JL, Steensma HY, Stucka R, Urrestarazu A, van der Aart QJ, van Dyck L, Vassarotti A, Vetter I, Vierendeels F, Vissers S, Wagner G, de Wergifosse P, Wolfe KH, Zagulski M, Zimmermann FK, Mewes HW, Kleine K. Complete DNA sequence of yeast chromosome II. EMBO J 1994; 13:5795-809. [PMID: 7813418 PMCID: PMC395553 DOI: 10.1002/j.1460-2075.1994.tb06923.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.
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Affiliation(s)
- H Feldmann
- Institut für Physiologische Chemie, Physikalische Biochemie und Zellbiologie, Universität München, Germany
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18
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Abstract
We report the sequence of a 12 kilobase region spanning the centromere of Saccharomyces cerevisiae chromosome II. The sequence from the left arm includes genes for histones H2A and H2B. The sequence from the right arm includes a gene that probably encodes a novel trehalase, as well as the COQ1 gene (for an enzyme involved in coenzyme Q biosynthesis), and an open reading frame with significant similarity to bacterial genes of unknown function. The trehalase gene (YBR0106) on chromosome II is located beside the centromere and transcribed towards it. This is identical to the arrangement of the neutral trehalase gene (NTH1) beside the centromere of chromosome IV. The centromere regions of chromosomes II and IV may therefore have arisen through a duplication of the centromere region of an ancestral chromosome. The YBR0106 and NTH1 proteins are 77% identical in predicted amino acid sequence, but there is no pronounced sequence similarity between the two centromeres (CEN2 and CEN4) outside of the universally conserved CDE I and CDE III elements. The genes flanking the centromere and trehalase genes differ between the two chromosomes, so the similarity between chromosomes II and IV may be less extensive than that recently reported between chromosomes III and XIV.
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Affiliation(s)
- K H Wolfe
- Department of Genetics, University of Dublin, Trinity College, Ireland
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