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Deng MZ, Liu Q, Cui SJ, Wang YX, Zhu G, Fu H, Gan M, Xu YY, Cai X, Wang S, Sha W, Zhao GP, Fortune SM, Lyu LD. An additional proofreader contributes to DNA replication fidelity in mycobacteria. Proc Natl Acad Sci U S A 2024; 121:e2322938121. [PMID: 39141351 PMCID: PMC11348249 DOI: 10.1073/pnas.2322938121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
Abstract
The removal of mis-incorporated nucleotides by proofreading activity ensures DNA replication fidelity. Whereas the ε-exonuclease DnaQ is a well-established proofreader in the model organism Escherichia coli, it has been shown that proofreading in a majority of bacteria relies on the polymerase and histidinol phosphatase (PHP) domain of replicative polymerase, despite the presence of a DnaQ homolog that is structurally and functionally distinct from E. coli DnaQ. However, the biological functions of this type of noncanonical DnaQ remain unclear. Here, we provide independent evidence that noncanonical DnaQ functions as an additional proofreader for mycobacteria. Using the mutation accumulation assay in combination with whole-genome sequencing, we showed that depletion of DnaQ in Mycolicibacterium smegmatis leads to an increased mutation rate, resulting in AT-biased mutagenesis and increased insertions/deletions in the homopolymer tract. Our results showed that mycobacterial DnaQ binds to the β clamp and functions synergistically with the PHP domain proofreader to correct replication errors. Furthermore, the loss of dnaQ results in replication fork dysfunction, leading to attenuated growth and increased mutagenesis on subinhibitory fluoroquinolones potentially due to increased vulnerability to fork collapse. By analyzing the sequence polymorphism of dnaQ in clinical isolates of Mycobacterium tuberculosis (Mtb), we demonstrated that a naturally evolved DnaQ variant prevalent in Mtb lineage 4.3 may enable hypermutability and is associated with drug resistance. These results establish a coproofreading model and suggest a division of labor between DnaQ and PHP domain proofreader. This study also provides real-world evidence that a mutator-driven evolutionary pathway may exist during the adaptation of Mtb.
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Affiliation(s)
- Ming-Zhi Deng
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Shu-Jun Cui
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Yi-Xin Wang
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Guoliang Zhu
- Shanghai Zelixir Biotech Company Ltd., Shanghai200030, China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Chinese Academy of Sciences Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai200032, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Mingyu Gan
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai201102, China
| | - Yuan-Yuan Xu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Xia Cai
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai200030, China
| | - Wei Sha
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai200433, China
| | - Guo-Ping Zhao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai200433, China
- Chinese Academy of Sciences Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai200032, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai200433, China
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Barela Hudgell MA, Momtaz F, Jafri A, Alekseyev MA, Smith LC. Local Genomic Instability of the SpTransformer Gene Family in the Purple Sea Urchin Inferred from BAC Insert Deletions. Genes (Basel) 2024; 15:222. [PMID: 38397211 PMCID: PMC10887614 DOI: 10.3390/genes15020222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The SpTransformer (SpTrf) gene family in the purple sea urchin, Strongylocentrotus purpuratus, encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the SpTrf gene cluster was tested by 10 days of growth of Escherichia coli harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing SpTrf genes. After the growth period, the BAC DNA inserts were analyzed for size and SpTrf gene content. Clones with multiple SpTrf genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single SpTrf gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of SpTrf genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among SpTrf genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes.
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Affiliation(s)
- Megan A. Barela Hudgell
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Farhana Momtaz
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Abiha Jafri
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
| | - Max A. Alekseyev
- Department of Mathematics and the Computational Biology Institute, George Washington University, Washington, DC 20052, USA;
| | - L. Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA; (M.A.B.H.); (F.M.)
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Deng MZ, Liu Q, Cui SJ, Fu H, Gan M, Xu YY, Cai X, Sha W, Zhao GP, Fortune SM, Lyu LD. Mycobacterial DnaQ is an Alternative Proofreader Ensuring DNA Replication Fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563508. [PMID: 37961690 PMCID: PMC10634781 DOI: 10.1101/2023.10.24.563508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Remove of mis-incorporated nucleotides ensures replicative fidelity. Although the ε-exonuclease DnaQ is a well-established proofreader in the model organism Escherichia coli, proofreading in mycobacteria relies on the polymerase and histidinol phosphatase (PHP) domain of replicative polymerase despite the presence of an alternative DnaQ homolog. Here, we show that depletion of DnaQ in Mycolicibacterium smegmatis results in increased mutation rate, leading to AT-biased mutagenesis and elevated insertions/deletions in homopolymer tract. We demonstrated that mycobacterial DnaQ binds to the b-clamp and functions synergistically with the PHP domain to correct replication errors. Further, we found that the mycobacterial DnaQ sustains replicative fidelity upon chromosome topological stress. Intriguingly, we showed that a naturally evolved DnaQ variant prevalent in clinical Mycobacterium tuberculosis isolates enables hypermutability and is associated with extensive drug resistance. These results collectively establish that the alternative DnaQ functions in proofreading, and thus reveal that mycobacteria deploy two proofreaders to maintain replicative fidelity.
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Affiliation(s)
- Ming-Zhi Deng
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- These authors contributed equally
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
- These authors contributed equally
| | - Shu-Jun Cui
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Mingyu Gan
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102, P.R.China
| | - Yuan-Yuan Xu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Xia Cai
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Wei Sha
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
| | - Guo-Ping Zhao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
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Pintado A, Domínguez-Cerván H, Pastor V, Vincent M, Lee SG, Flors V, Ramos C. Allelic variation in the indoleacetic acid-lysine synthase gene of the bacterial pathogen Pseudomonas savastanoi and its role in auxin production. FRONTIERS IN PLANT SCIENCE 2023; 14:1176705. [PMID: 37346122 PMCID: PMC10280071 DOI: 10.3389/fpls.2023.1176705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023]
Abstract
Indole-3-acetic acid (IAA) production is a pathogenicity/virulence factor in the Pseudomonas syringae complex, including Pseudomonas savastanoi. P. savastanoi pathovars (pvs.) genomes contain the iaaL gene, encoding an enzyme that catalyzes the biosynthesis of the less biologically active compound 3-indole-acetyl-ϵ-L-lysine (IAA-Lys). Previous studies have reported the identification of IAA-Lys in culture filtrates of P. savastanoi strains isolated from oleander (pv. nerii), but the conversion of IAA into a conjugate was not detectable in olive strains (pv. savastanoi). In this paper, we show the distribution of iaaL alleles in all available P. savastanoi genomes of strains isolated from woody hosts. Most strains encode two different paralogs, except for those isolated from broom (pv. retacarpa), which contain a single allele. In addition to the three previously reported iaaL alleles (iaaL Psv, iaaL Psn and iaaL Pto), we identified iaaL Psf, an exclusive allele of strains isolated from ash (pv. fraxini). We also found that the production of IAA-Lys in P. savastanoi pv. savastanoi and pv. nerii depends on a functional iaaL Psn allele, whereas in pv. fraxini depends on iaaL Psf. The production of IAA-Lys was detected in cultures of an olive strain heterologously expressing IaaLPsn-1, IaaLPsf-1 and IaaLPsf-3, but not when expressing IaaLPsv-1. In addition, Arabidopsis seedlings treated with the strains overproducing the conjugate, and thus reducing the free IAA content, alleviated the root elongation inhibitory effect of IAA. IAA-Lys synthase activity assays with purified allozymes confirmed the functionality and specificity of lysine as a substrate of IaaLPsn-1 and IaaLPsf-3, with IaaLPsf-3 showing the highest catalytic efficiency for both substrates. The IAA-Lys synthase activity of IaaLPsn-1 was abolished by the insertion of two additional tyrosine residues encoded in the inactive allozyme IaaLPsv-1. These results highlight the relevance of allelic variation in a phytohormone-related gene for the modulation of auxin production in a bacterial phytopathogen.
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Affiliation(s)
- Adrián Pintado
- Área de Genética, Facultad de Ciencias, Universidad de Málaga (UMA), Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Hilario Domínguez-Cerván
- Área de Genética, Facultad de Ciencias, Universidad de Málaga (UMA), Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Victoria Pastor
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I (UJI), Castelló de la Plana, Spain
| | - Marissa Vincent
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Soon Goo Lee
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, United States
| | - Víctor Flors
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I (UJI), Castelló de la Plana, Spain
| | - Cayo Ramos
- Área de Genética, Facultad de Ciencias, Universidad de Málaga (UMA), Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
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Karamycheva S, Wolf YI, Persi E, Koonin EV, Makarova KS. Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions. Biol Direct 2022; 17:22. [PMID: 36042479 PMCID: PMC9425974 DOI: 10.1186/s13062-022-00337-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background Evolutionary rate is a key characteristic of gene families that is linked to the functional importance of the respective genes as well as specific biological functions of the proteins they encode. Accurate estimation of evolutionary rates is a challenging task that requires precise phylogenetic analysis. Here we present an easy to estimate protein family level measure of sequence variability based on alignment column homogeneity in multiple alignments of protein sequences from Clade-Specific Clusters of Orthologous Genes (csCOGs). Results We report genome-wide estimates of variability for 8 diverse groups of bacteria and archaea and investigate the connection between variability and various genomic and biological features. The variability estimates are based on homogeneity distributions across amino acid sequence alignments and can be obtained for multiple groups of genomes at minimal computational expense. About half of the variance in variability values can be explained by the analyzed features, with the greatest contribution coming from the extent of gene paralogy in the given csCOG. The correlation between variability and paralogy appears to originate, primarily, not from gene duplication, but from acquisition of distant paralogs and xenologs, introducing sequence variants that are more divergent than those that could have evolved in situ during the lifetime of the given group of organisms. Both high-variability and low-variability csCOGs were identified in all functional categories, but as expected, proteins encoded by integrated mobile elements as well as proteins involved in defense functions and cell motility are, on average, more variable than proteins with housekeeping functions. Additionally, using linear discriminant analysis, we found that variability and fraction of genomes carrying a given gene are the two variables that provide the best prediction of gene essentiality as compared to the results of transposon mutagenesis in Sulfolobus islandicus. Conclusions Variability, a measure of sequence diversity within an alignment relative to the overall diversity within a group of organisms, offers a convenient proxy for evolutionary rate estimates and is informative with respect to prediction of functional properties of proteins. In particular, variability is a strong predictor of gene essentiality for the respective organisms and indicative of sub- or neofunctionalization of paralogs. Supplementary Information The online version contains supplementary material available at 10.1186/s13062-022-00337-7.
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Affiliation(s)
- Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Erez Persi
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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Yue J, Lu Q, Ni Y, Chen P, Liu C. Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp. Sci Rep 2022; 12:13931. [PMID: 35978085 PMCID: PMC9385723 DOI: 10.1038/s41598-022-18387-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 08/10/2022] [Indexed: 12/30/2022] Open
Abstract
Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.
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Affiliation(s)
- Jingwen Yue
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China ,grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
| | - Qianqi Lu
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China
| | - Yang Ni
- grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
| | - Pinghua Chen
- grid.256111.00000 0004 1760 2876Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, No.15, Shangxiadian Road, Fuzhou, 350002 Fujian People’s Republic of China
| | - Chang Liu
- grid.506261.60000 0001 0706 7839Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing, 100193 People’s Republic of China
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Goncharova YO, Bogun AG, Bahtejeva IV, Titareva GM, Mironova RI, Kravchenko TB, Ostarkov NA, Brushkov AV, Timofeev VS, Ignatov SG. Allelic Polymorphism of Anthrax Pathogenicity Factor Genes as a Means of Estimating Microbiological Risks Associated with Climate Change. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822040056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Climate change brings new risks of emergence of especially dangerous diseases. The paper reports the possibility of assessing the pathogenic potential of bacteria as demonstrated by studying the allelic polymorphism of anthrax bacterium pathogenicity factor genes, which is a prerequisite for assessing the associated microbiological risks. The allelic polymorphism of the capBCADE operon (capB, capC, capA, capD, and capE genes) encoding the capsule biosynthesis proteins of Bacillus anthracis, and the acpA and acpB genes encoding the expression regulators of this operon have been studied for the first time. A number of single nucleotide polymorphisms (SNPs) were described in the strains of the studied sample, including 5 SNPs in the capB gene, 3 in capC, 4 in capA, 14 in capD, 2 in capE, and 15 in acpB, as well as 7 SNPs and one insertion in the acpA gene. As a result, the sample has been divided into sequence types for each gene and 17 genotypes, which are combinations of the identified sequence types. In silico translation of the detected alleles of the studied genes revealed three isoforms of the CapB and CapA proteins, two isoforms of the CapC and CapE proteins, six isoforms of the CapD protein, five isoforms of the AcpA protein, and four isoforms in the AcpB protein. It has been demonstrated that the SNP in the 351A → G position of capC is a marker of A.Br.Aust94 group strains. Based on the results, A.Br.Vollum group strains were divided into two subgroups. The strains in the evolutionary lines B and C differed from the line A strains by the presence of an 853G → A SNP in the acpA gene. In addition, a previously unknown variable number tandem repeat (VNTR), has been found in the acpA gene and the possibility of using it for differentiating and genotyping of B. anthracis strains has been demonstrated.
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Sharpe JL, Harper NS, West RJH. Identification and Monitoring of Nucleotide Repeat Expansions Using Southern Blotting in Drosophila Models of C9orf72 Motor Neuron Disease and Frontotemporal Dementia. Bio Protoc 2022; 12:e4424. [PMID: 35813024 PMCID: PMC9183971 DOI: 10.21769/bioprotoc.4424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/29/2022] Open
Abstract
Repeat expansion diseases, including fragile X syndrome, Huntington's disease, and C9orf72-related motor neuron disease and frontotemporal dementia, are a group of disorders associated with polymorphic expansions of tandem repeat nucleotide sequences. These expansions are highly repetitive and often hundreds to thousands of repeats in length, making accurate identification and determination of repeat length via PCR or sequencing challenging. Here we describe a protocol for monitoring repeat length in Drosophila models carrying 1,000 repeat C9orf72-related dipeptide repeat transgenes using Southern blotting. This protocol has been used regularly to check the length of these lines for over 100 generations with robust and repeatable results and can be implemented for monitoring any repeat expansion in Drosophila.
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Affiliation(s)
- Joanne L. Sharpe
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
,Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
,Neuroscience Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Nikki S. Harper
- Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Ryan J. H. West
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
,Neuroscience Institute, The University of Sheffield, Sheffield, United Kingdom
,
*For correspondence:
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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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10
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Bachar A, Itzhaki E, Gleizer S, Shamshoom M, Milo R, Antonovsky N. Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes. Nucleic Acids Res 2020; 48:761-769. [PMID: 31777935 PMCID: PMC6954433 DOI: 10.1093/nar/gkz1100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/27/2019] [Accepted: 11/21/2019] [Indexed: 11/14/2022] Open
Abstract
Identifying the molecular mechanisms that give rise to genetic variation is essential for the understanding of evolutionary processes. Previously, we have used adaptive laboratory evolution to enable biomass synthesis from CO2 in Escherichia coli. Genetic analysis of adapted clones from two independently evolving populations revealed distinct enrichment for insertion and deletion mutational events. Here, we follow these observations to show that mutations in the gene encoding for DNA topoisomerase I (topA) give rise to mutator phenotypes with characteristic mutational spectra. Using genetic assays and mutation accumulation lines, we find that point mutations in topA increase the rate of sequence deletion and duplication events. Interestingly, we observe that a single residue substitution (R168C) results in a high rate of head-to-tail (tandem) short sequence duplications, which are independent of existing sequence repeats. Finally, we show that the unique mutation spectrum of topA mutants enhances the emergence of antibiotic resistance in comparison to mismatch-repair (mutS) mutators, and leads to new resistance genotypes. Our findings highlight a potential link between the catalytic activity of topoisomerases and the fundamental question regarding the emergence of de novo tandem repeats, which are known modulators of bacterial evolution.
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Affiliation(s)
- Amit Bachar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elad Itzhaki
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Melina Shamshoom
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.,Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
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11
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Singh YH, Sharma SK, Sinha B, Baranwal VK, Singh NB, Chanu NT, Roy SS, Ansari MA, Ningombam A, Devi PS, Das AK, Singh S, Singh KM, Prakash N. Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ' Candidatus Liberibacter asiaticus' Prevalent in North East India. THE PLANT PATHOLOGY JOURNAL 2019; 35:644-653. [PMID: 31832044 PMCID: PMC6901247 DOI: 10.5423/ppj.oa.03.2019.0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/23/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
The genetic variability of 'Candidatus Liberibacter asiaticus' (CLas) population associated with huanglongbing (HLB) disease of citrus in North Eastern (NE) region of India, a geographically locked region, and home for the diversity of many citrus species was analyzed on the basis of tandem repeat numbers (TRN) in variable CLIBASIA_01645 genomic loci. Fifty-five CLas strains sampled from different groves of NE Hill (NEH) region of India were in single amplicon group, but there was remarkable genetic variability in TRNs. The TRN in HLB-associated CLas strains varied from 0-21 and two novel repeat motifs were also identified. Among the NE population of CLas, TRN5 and TRN9 were most frequent (total frequency of 36.36%) followed by TRN4 (14.55%) and TRN6, TNR7 with a frequency of 12.73% each. Class II type CLas genotypes (5 < TRN ≤ 10) had highest prevalence (frequency of 60.00%) in the samples characterized in present study. Class I (TRN ≤ 5) genotypes were second highest prevalent (29.09%) in the NEH region. Further analysis of genetic diversity parameters using Nei's measure (H value) indicated wide genetic diversity in the CLas strains of NE India (H value of 0.58-0.86). Manipur CLas strains had highest genetic variability (0.86) as compared to Eastern, Southern and Central India. The R10 values (TRN ≤ 10/TRN > 10) of NE CLas population was 10.43 (73/7), higher from other regions of India. Present study conclusively reported the occurrence of high genetic variability in TRN of CLas population in North East Indian citrus groves which have evolved to adapt to the specific ecological niche.
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Affiliation(s)
- Yanglem Herojit Singh
- Department of Plant Pathology, College of Agriculture, Central Agricultural University, Imphal 795004,
India
| | | | - Bireswar Sinha
- Department of Plant Pathology, College of Agriculture, Central Agricultural University, Imphal 795004,
India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012,
India
| | | | - Ngathem Taibangnganbi Chanu
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004,
India
- College of Horticulture and Forestry, Central Agricultural University, Pasighat 791102,
India
| | - Subhra S. Roy
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004,
India
| | - Meraj A. Ansari
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004,
India
| | - Arati Ningombam
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004,
India
| | - Ph. Sobita Devi
- Department of Plant Pathology, College of Agriculture, Central Agricultural University, Imphal 795004,
India
| | - Ashis Kumar Das
- ICAR-Central Citrus Research Institute, Nagpur 440010,
India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013,
India
| | - K. Mamocha Singh
- Department of Entomology, College of Agriculture, Central Agricultural University, Imphal 795004,
India
| | - Narendra Prakash
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal 795004,
India
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12
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Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M, Yachie N. Fast and global detection of periodic sequence repeats in large genomic resources. Nucleic Acids Res 2019; 47:e8. [PMID: 30304510 PMCID: PMC6344855 DOI: 10.1093/nar/gky890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022] Open
Abstract
Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeating biomolecules of natural organisms. Despite the biological importance of periodically repeating sequences and the expectation that new genome editing modules could be discovered from such periodical repeats, no software that globally detects such structured elements in large genomic resources in a high-throughput and unsupervised manner has been developed. We developed new software, SPADE (Search for Patterned DNA Elements), that exhaustively explores periodic DNA and protein repeats from large-scale genomic datasets based on k-mer periodicity evaluation. With a simple constraint, sequence periodicity, SPADE captured reported genome-editing-associated sequences and other protein families involving repeating domains such as tetratricopeptide, ankyrin and WD40 repeats with better performance than the other software designed for limited sets of repetitive biomolecular sequences, suggesting the high potential of this software to contribute to the discovery of new biological events and new genome editing modules.
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Affiliation(s)
- Hideto Mori
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Daniel Evans-Yamamoto
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Soh Ishiguro
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan.,Department of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
| | - Nozomu Yachie
- Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan.,Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,PRESTO, Japan Science and Technology Agency (JST), Tokyo 153-8904, Japan
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13
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Genome-wide investigation of microsatellite polymorphism in coding region of the giant panda (Ailuropoda melanoleuca) genome: a resource for study of phenotype diversity and abnormal traits. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00418-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Repeat Instability in the Fragile X-Related Disorders: Lessons from a Mouse Model. Brain Sci 2019; 9:brainsci9030052. [PMID: 30832215 PMCID: PMC6468611 DOI: 10.3390/brainsci9030052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 12/21/2022] Open
Abstract
The fragile X-related disorders (FXDs) are a group of clinical conditions that result primarily from an unusual mutation, the expansion of a CGG-repeat tract in exon 1 of the FMR1 gene. Mouse models are proving useful for understanding many aspects of disease pathology in these disorders. There is also reason to think that such models may be useful for understanding the molecular basis of the unusual mutation responsible for these disorders. This review will discuss what has been learnt to date about mechanisms of repeat instability from a knock-in FXD mouse model and what the implications of these findings may be for humans carrying expansion-prone FMR1 alleles.
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15
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Adenovirus based HPV L2 vaccine induces broad cross-reactive humoral immune responses. Vaccine 2018; 36:4462-4470. [DOI: 10.1016/j.vaccine.2018.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 12/24/2022]
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16
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Thomas JD, Oliveira R, Sznajder ŁJ, Swanson MS. Myotonic Dystrophy and Developmental Regulation of RNA Processing. Compr Physiol 2018; 8:509-553. [PMID: 29687899 PMCID: PMC11323716 DOI: 10.1002/cphy.c170002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy (DM) is a multisystemic disorder caused by microsatellite expansion mutations in two unrelated genes leading to similar, yet distinct, diseases. DM disease presentation is highly variable and distinguished by differences in age-of-onset and symptom severity. In the most severe form, DM presents with congenital onset and profound developmental defects. At the molecular level, DM pathogenesis is characterized by a toxic RNA gain-of-function mechanism that involves the transcription of noncoding microsatellite expansions. These mutant RNAs disrupt key cellular pathways, including RNA processing, localization, and translation. In DM, these toxic RNA effects are predominantly mediated through the modulation of the muscleblind-like and CUGBP and ETR-3-like factor families of RNA binding proteins (RBPs). Dysfunction of these RBPs results in widespread RNA processing defects culminating in the expression of developmentally inappropriate protein isoforms in adult tissues. The tissue that is the focus of this review, skeletal muscle, is particularly sensitive to mutant RNA-responsive perturbations, as patients display a variety of developmental, structural, and functional defects in muscle. Here, we provide a comprehensive overview of DM1 and DM2 clinical presentation and pathology as well as the underlying cellular and molecular defects associated with DM disease onset and progression. Additionally, fundamental aspects of skeletal muscle development altered in DM are highlighted together with ongoing and potential therapeutic avenues to treat this muscular dystrophy. © 2018 American Physiological Society. Compr Physiol 8:509-553, 2018.
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Affiliation(s)
- James D. Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Ruan Oliveira
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Łukasz J. Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Maurice S. Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
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17
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Abstract
Diseases such as Huntington's disease and certain spinocerebellar ataxias are caused by the expansion of genomic cytosine-adenine-guanine (CAG) trinucleotide repeats beyond a specific threshold. These diseases are all characterised by neurological symptoms and central neurodegeneration, but our understanding of how expanded repeats drive neuronal loss is incomplete. Recent human genetic evidence implicates DNA repair pathways, especially mismatch repair, in modifying the onset and progression of CAG repeat diseases. Repair pathways might operate directly on repeat sequences by licensing or inhibiting repeat expansion in neurons. Alternatively, or in addition, because many of the genes containing pathogenic CAG repeats encode proteins that themselves have roles in the DNA damage response, it is possible that repeat expansions impair specific DNA repair pathways. DNA damage could then accrue in neurons, leading to further expansion at repeat loci, thus setting up a vicious cycle of pathology. In this review, we consider DNA damage and repair pathways in postmitotic neurons in the context of disease-causing CAG repeats. Investigating and understanding these pathways, which are clearly relevant in promoting and ameliorating disease in humans, is a research priority, as they are known to modify disease and therefore constitute prevalidated drug targets.
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Affiliation(s)
- Thomas H Massey
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Lesley Jones
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Hadyn Ellis Building, Cardiff University, Cardiff, CF24 4HQ, UK
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18
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Abstract
Huntington's disease (HD) is caused by a CAG repeat expansion in the HTT gene. Repeat length can change over time, both in individual cells and between generations, and longer repeats may drive pathology. Cellular DNA repair systems have long been implicated in CAG repeat instability but recent genetic evidence from humans linking DNA repair variants to HD onset and progression has reignited interest in this area. The DNA damage response plays an essential role in maintaining genome stability, but may also license repeat expansions in the context of HD. In this chapter we summarize the methods developed to assay CAG repeat expansion/contraction in vitro and in cells, and review the DNA repair genes tested in mouse models of HD. While none of these systems is currently ideal, new technologies, such as long-read DNA sequencing, should improve the sensitivity of assays to assess the effects of DNA repair pathways in HD. Improved assays will be essential precursors to high-throughput testing of small molecules that can alter specific steps in DNA repair pathways and perhaps ameliorate expansion or enhance contraction of the HTT CAG repeat.
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19
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Ye L, Jiao N, Tang X, Chen Y, Ye X, Ren L, Hu F, Wang S, Wen M, Zhang C, Tao M, Liu S. Chimeras Linked to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:401-409. [PMID: 28681105 DOI: 10.1007/s10126-017-9764-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/09/2017] [Indexed: 06/07/2023]
Abstract
The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species, and therefore, it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs benefit from the intervention of recombinases. In addition, TRs and TEs can also result in insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.
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Affiliation(s)
- Lihai Ye
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Ni Jiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Xiaojun Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Yiyi Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Xiaolan Ye
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
- College of Life Sciences, Hunan Normal University, Changsha, 410081, People's Republic of China.
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20
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Schlegel S, Genevaux P, de Gier JW. Isolating Escherichia coli strains for recombinant protein production. Cell Mol Life Sci 2016; 74:891-908. [PMID: 27730255 PMCID: PMC5306230 DOI: 10.1007/s00018-016-2371-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/22/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Escherichia coli has been widely used for the production of recombinant proteins. To improve protein production yields in E. coli, directed engineering approaches have been commonly used. However, there are only few reported examples of the isolation of E. coli protein production strains using evolutionary approaches. Here, we first give an introduction to bacterial evolution and mutagenesis to set the stage for discussing how so far selection- and screening-based approaches have been used to isolate E. coli protein production strains. Finally, we discuss how evolutionary approaches may be used in the future to isolate E. coli strains with improved protein production characteristics.
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Affiliation(s)
- Susan Schlegel
- Department of Environmental Systems Science, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusväg 16C, 106 91, Stockholm, Sweden.
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21
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Lin TY. Simple sequence repeat variations expedite phage divergence: Mechanisms of indels and gene mutations. Mutat Res 2016; 789:48-56. [PMID: 27133219 DOI: 10.1016/j.mrfmmm.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/26/2016] [Accepted: 04/11/2016] [Indexed: 12/27/2022]
Abstract
Phages are the most abundant biological entities and influence prokaryotic communities on Earth. Comparing closely related genomes sheds light on molecular events shaping phage evolution. Simple sequence repeat (SSR) variations impart over half of the genomic changes between T7M and T3, indicating an important role of SSRs in accelerating phage genetic divergence. Differences in coding and noncoding regions of phages infecting different hosts, coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2, frequently arise from SSR variations. Such variations modify noncoding and coding regions; the latter efficiently changes multiple amino acids, thereby hastening protein evolution. Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats. The categorization demonstrates the ways SSRs mutate in genomes during phage evolution. Indels are common constituents of genome variations and human diseases, yet, how they occur without preexisting repeat sequence is less understood. Non-repeat-unit-based misalignment-elongation (NRUBME) is proposed to be one mechanism for indels without adjacent repeats. NRUBME or consecutive NRUBME may also change repeat motifs or generate new repeats. NRUBME invoking a non-Watson-Crick base pair explains insertions that initiate mononucleotide repeats. Furthermore, NRUBME successfully interprets many inexplicable human di- to tetranucleotide repeat generations. This study provides the first evidence of SSR variations expediting phage divergence, and enables insights into the events and mechanisms of genome evolution. NRUBME allows us to emulate natural evolution to design indels for various applications.
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Affiliation(s)
- Tiao-Yin Lin
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsin Chu, Taiwan.
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22
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Rehm C, Wurmthaler LA, Li Y, Frickey T, Hartig JS. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp. PLoS One 2015; 10:e0144275. [PMID: 26695179 PMCID: PMC4692102 DOI: 10.1371/journal.pone.0144275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/16/2015] [Indexed: 12/04/2022] Open
Abstract
In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5
nucleotides (nt) are causative for phase and antigenic variation. Although an
increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs
of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity
to fold into G-quadruplex (G4) structures have received little attention. In silico
analysis of prokaryotic genomes show putative G4 forming sequences to be abundant.
This report focuses on a surprisingly enriched G-rich repeat of the type
GGGNATC in Xanthomonas and cyanobacteria
such as Nostoc. We studied in detail the genomes of
Xanthomonas campestris pv. campestris ATCC 33913
(Xcc), Xanthomonas axonopodis pv.
citri str. 306 (Xac), and Nostoc
sp. strain PCC7120 (Ana). In all three organisms repeats
are spread all over the genome with an over-representation in non-coding regions.
Extensive variation of the number of repetitive units was observed with repeat
numbers ranging from two up to 26 units. However a clear preference for four units
was detected. The strong bias for four units coincides with the requirement of four
consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus
repeat sequences was found in biophysical studies utilizing CD spectroscopy. The
G-rich repeats are preferably located between aligned open reading frames (ORFs) and
are under-represented in coding regions or between divergent ORFs. The G-rich repeats
are preferentially located within a distance of 50 bp upstream of an ORF on the
anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis
of whole transcriptome sequence data showed that the majority of repeat sequences are
transcribed. The genetic loci in the vicinity of repeat regions show increased
genomic stability. In conclusion, we introduce and characterize a special class of
highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.
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Affiliation(s)
- Charlotte Rehm
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Lena A Wurmthaler
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Yuanhao Li
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Tancred Frickey
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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Holder IT, Wagner S, Xiong P, Sinn M, Frickey T, Meyer A, Hartig JS. Intrastrand triplex DNA repeats in bacteria: a source of genomic instability. Nucleic Acids Res 2015; 43:10126-42. [PMID: 26450966 PMCID: PMC4666352 DOI: 10.1093/nar/gkv1017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
Repetitive nucleic acid sequences are often prone to form secondary structures distinct from B-DNA. Prominent examples of such structures are DNA triplexes. We observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. A systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the ITxF database available online at http://bioinformatics.uni-konstanz.de/utils/ITxF/. Next we investigated biophysical and biochemical properties of a particular G/C-rich triplex motif (TM) that occurs in many copies in more than 260 bacterial genomes by CD and nuclear magnetic resonance spectroscopy as well as in vivo footprinting techniques. A characterization of putative properties and functions of these unusually frequent nucleic acid motifs demonstrated that the occurrence of the TM is associated with a high degree of genomic instability. TM-containing genomic loci are significantly more rearranged among closely related Escherichia coli strains compared to control sites. In addition, we found very high frequencies of TM motifs in certain Enterobacteria and Cyanobacteria that were previously described as genetically highly diverse. In conclusion we link intrastrand triplex motifs with the induction of genomic instability. We speculate that the observed instability might be an adaptive feature of these genomes that creates variation for natural selection to act upon.
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Affiliation(s)
- Isabelle T Holder
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Stefanie Wagner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Peiwen Xiong
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Tancred Frickey
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Jäckel C, Hammerl JA, Reetz J, Kropinski AM, Hertwig S. Campylobacter group II phage CP21 is the prototype of a new subgroup revealing a distinct modular genome organization and host specificity. BMC Genomics 2015; 16:629. [PMID: 26296758 PMCID: PMC4546147 DOI: 10.1186/s12864-015-1837-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/13/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The application of phages is a promising tool to reduce the number of Campylobacter along the food chain. Besides the efficacy against a broad range of strains, phages have to be safe in terms of their genomes. Thus far, no genes with pathogenic potential (e.g., genes encoding virulence factors) have been detected in Campylobacter phages. However, preliminary studies suggested that the genomes of group II phages may be diverse and prone to genomic rearrangements. RESULTS We determined and analysed the genomic sequence (182,761 bp) of group II phage CP21 that is closely related to the already characterized group II phages CP220 and CPt10. The genomes of these phages are comprised of four modules separated by very similar repeat regions, some of which harbouring open reading frames (ORFs). Though, the arrangement of the modules and the location of some ORFs on the genomes are different in CP21 and in CP220/CPt10. In this work, a PCR system was established to study the modular genome organization of other group II phages demonstrating that they belong to different subgroups of the CP220-like virus genus, the prototypes of which are CP21 and CP220. The subgroups revealed different restriction patterns and, interestingly enough, also distinct host specificities, tail fiber proteins and tRNA genes. We additionally analysed the genome of group II phage vB_CcoM-IBB_35 (IBB_35) for which to date only five individual contigs could be determined. We show that the contigs represent modules linked by long repeat regions enclosing some yet not identified ORFs (e.g., for a head completion protein). The data suggest that IBB_35 is a member of the CP220 subgroup. CONCLUSION Campylobacter group II phages are diverse regarding their genome organization. Since all hitherto characterized group II phages contain numerous genes for transposases and homing endonucleases as well as similar repeat regions, it cannot be excluded that these phages are genetically unstable. To answer this question, further experiments and sequencing of more group II phages should be performed.
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Affiliation(s)
- Claudia Jäckel
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
| | - Jens A Hammerl
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
| | - Jochen Reetz
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
| | - Andrew M Kropinski
- Departments of Food Science & Molecular and Cellular Biology & Pathobiology, University of Guelph, Ontario, Canada.
| | - Stefan Hertwig
- ᅟ, Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany.
- Abteilung Biologische Sicherheit, Bundesinstitut für Risikobewertung, Diagnostik und Erregercharakterisierung, Diedersdorfer Weg 1, D-12277, Berlin, Germany.
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25
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Dominant short repeated sequences in bacterial genomes. Genomics 2015; 105:175-81. [PMID: 25561351 DOI: 10.1016/j.ygeno.2014.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 12/22/2014] [Accepted: 12/29/2014] [Indexed: 11/22/2022]
Abstract
We use a novel multidimensional searching approach to present the first exhaustive search for all possible repeated sequences in 166 genomes selected to cover the bacterial domain. We found an overrepresentation of repeated sequences in all but one of the genomes. The most prevalent repeats by far were related to interspaced short palindromic repeats (CRISPRs)—conferring bacterial adaptive immunity. We identified a deep branching clade of thermophilic Firmicutes containing the highest number of CRISPR repeats. We also identified a high prevalence of tandem repeated heptamers. In addition, we identified GC-rich repeats that could potentially be involved in recombination events. Finally, we identified repeats in a 16322 amino acid mega protein (involved in biofilm formation) and inverted repeats flanking miniature transposable elements (MITEs). In conclusion, the exhaustive search for repeated sequences identified new elements and distribution of these, which has implications for understanding both the ecology and evolution of bacteria.
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Yi H, Song H, Hwang J, Kim K, Nierman WC, Kim HS. The tandem repeats enabling reversible switching between the two phases of β-lactamase substrate spectrum. PLoS Genet 2014; 10:e1004640. [PMID: 25233343 PMCID: PMC4169377 DOI: 10.1371/journal.pgen.1004640] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/31/2014] [Indexed: 11/25/2022] Open
Abstract
Expansion or shrinkage of existing tandem repeats (TRs) associated with various biological processes has been actively studied in both prokaryotic and eukaryotic genomes, while their origin and biological implications remain mostly unknown. Here we describe various duplications (de novo TRs) that occurred in the coding region of a β-lactamase gene, where a conserved structure called the omega loop is encoded. These duplications that occurred under selection using ceftazidime conferred substrate spectrum extension to include the antibiotic. Under selective pressure with one of the original substrates (amoxicillin), a high level of reversion occurred in the mutant β-lactamase genes completing a cycle back to the original substrate spectrum. The de novo TRs coupled with reversion makes a genetic toggling mechanism enabling reversible switching between the two phases of the substrate spectrum of β-lactamases. This toggle exemplifies the effective adaptation of de novo TRs for enhanced bacterial survival. We found pairs of direct repeats that mediated the DNA duplication (TR formation). In addition, we found different duos of sequences that mediated the DNA duplication. These novel elements—that we named SCSs (same-strand complementary sequences)—were also found associated with β-lactamase TR mutations from clinical isolates. Both direct repeats and SCSs had a high correlation with TRs in diverse bacterial genomes throughout the major phylogenetic lineages, suggesting that they comprise a fundamental mechanism shaping the bacterial evolution. β-lactamases can adapt to new antibiotics by mutations in their genes. The original and the extended substrate spectrums of β-lactamases define two phases of catalytic activity, and the conversion by point mutations is unidirectional from the initial to the new spectrum. We describe duplication mutations that enable reversible switching between the substrate spectrums, increasing the adaptability of the bacterium. We provide evidence supporting that two distinct groups of short sequences mediated the formation of DNA duplications in β-lactamases: direct repeats and novel elements that we named, SCSs (same-strand complementary sequences). Our study suggests that DNA duplication processes mediated by both direct repeats and SCSs are not just limited to the β-lactamase genes but comprise a fundamental mechanism in bacterial genome evolution.
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Affiliation(s)
- Hyojeong Yi
- Department of Biosystems and Biotechnology, Korea University, Seoul, Korea
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Han Song
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Junghyun Hwang
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - Karan Kim
- Department of Biomedical Sciences, Korea University, Seoul, Korea
| | - William C. Nierman
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Heenam Stanley Kim
- Department of Biosystems and Biotechnology, Korea University, Seoul, Korea
- Department of Biomedical Sciences, Korea University, Seoul, Korea
- * E-mail:
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27
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Frascella A, Bettini PP, Kolařík M, Comparini C, Pazzagli L, Luti S, Scala F, Scala A. Interspecific variability of class II hydrophobin GEO1 in the genus Geosmithia. Fungal Biol 2014; 118:862-71. [PMID: 25442290 DOI: 10.1016/j.funbio.2014.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 07/04/2014] [Accepted: 07/28/2014] [Indexed: 11/24/2022]
Abstract
The genus Geosmithia Pitt (Ascomycota: Hypocreales) comprises cosmopolite fungi living in the galleries built by phloeophagous insects. Following the characterization in Geosmithia species 5 of the class II hydrophobin GEO1 and of the corresponding gene, the presence of the geo1 gene was investigated in 26 strains derived from different host plants and geographic locations and representing the whole phylogenetic diversity of the genus. The geo1 gene was detected in all the species tested where it maintained the general organization shown in Geosmithia species 5, comprising three exons and two introns. Size variations were found in both introns and in the first exon, the latter being due to the presence of an intragenic tandem repeat sequence corresponding to a stretch of glycine residues in the deduced proteins. At the amino acid level the deduced proteins had 44.6 % identity and no major differences in the biochemical parameters (pI, GRAVY index, hydropathy plots) were found. GEO1 release in the fungal culture medium was also assessed by turbidimetric assay and SDS-PAGE, and showed high variability between species. The phylogeny based on the geo1 sequences did not correspond to that generated from a neutral marker (ITS rDNA), suggesting that sequence similarities could be influenced by other factors than phylogenetic relatedness, such as the intimacy of the symbiosis with insect vectors. The hypothesis of a strong selection pressure on the geo1 gene was sustained by the low values (<1) of non synonymous to synonymous nucleotide substitutions ratios (Ka/Ks), which suggest that purifying selection might act on this gene. These results are compatible with either a birth-and-death evolution scenario or horizontal transfer of the gene between Geosmithia species.
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Affiliation(s)
- Arcangela Frascella
- Dipartimento di Biologia, Università di Firenze, via Madonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy; Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Università di Firenze, via della Lastruccia 10, 50019 Sesto Fiorentino, FI, Italy.
| | - Priscilla P Bettini
- Dipartimento di Biologia, Università di Firenze, via Madonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
| | - Miroslav Kolařík
- Institute of Microbiology of the ASCR, v.v.i, Videnská 1083, 142 20 Praha 4, Czech Republic.
| | - Cecilia Comparini
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Università di Firenze, via della Lastruccia 10, 50019 Sesto Fiorentino, FI, Italy.
| | - Luigia Pazzagli
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università di Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Simone Luti
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche, Università di Firenze, Viale Morgagni 50, 50134 Florence, Italy.
| | - Felice Scala
- Dipartimento di Arboricoltura, Botanica e Patologia Vegetale, Sezione di Patologia Vegetale, Università di Napoli "Federico II", via Università 100, 80055 Portici, NA, Italy.
| | - Aniello Scala
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), Università di Firenze, via della Lastruccia 10, 50019 Sesto Fiorentino, FI, Italy.
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Abstract
Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.
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Graves CJ, Ros VID, Stevenson B, Sniegowski PD, Brisson D. Natural selection promotes antigenic evolvability. PLoS Pathog 2013; 9:e1003766. [PMID: 24244173 PMCID: PMC3828179 DOI: 10.1371/journal.ppat.1003766] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 09/30/2013] [Indexed: 01/16/2023] Open
Abstract
The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.
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Affiliation(s)
| | - Vera I. D. Ros
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Brian Stevenson
- University of Kentucky, Lexington, Kentucky, United States of America
| | - Paul D. Sniegowski
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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30
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Halkilahti J, Haukka K, Siitonen A. Genotyping of outbreak-associated and sporadic Yersinia pseudotuberculosis strains by novel multilocus variable-number tandem repeat analysis (MLVA). J Microbiol Methods 2013; 95:245-50. [DOI: 10.1016/j.mimet.2013.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/09/2013] [Accepted: 09/09/2013] [Indexed: 01/03/2023]
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Marvig RL, Johansen HK, Molin S, Jelsbak L. Genome analysis of a transmissible lineage of pseudomonas aeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators. PLoS Genet 2013; 9:e1003741. [PMID: 24039595 PMCID: PMC3764201 DOI: 10.1371/journal.pgen.1003741] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/08/2013] [Indexed: 11/18/2022] Open
Abstract
Genome sequencing of bacterial pathogens has advanced our understanding of their evolution, epidemiology, and response to antibiotic therapy. However, we still have only a limited knowledge of the molecular changes in in vivo evolving bacterial populations in relation to long-term, chronic infections. For example, it remains unclear what genes are mutated to facilitate the establishment of long-term existence in the human host environment, and in which way acquisition of a hypermutator phenotype with enhanced rates of spontaneous mutations influences the evolutionary trajectory of the pathogen. Here we perform a retrospective study of the DK2 clone type of P. aeruginosa isolated from Danish patients suffering from cystic fibrosis (CF), and analyze the genomes of 55 bacterial isolates collected from 21 infected individuals over 38 years. Our phylogenetic analysis of 8,530 mutations in the DK2 genomes shows that the ancestral DK2 clone type spread among CF patients through several independent transmission events. Subsequent to transmission, sub-lineages evolved independently for years in separate hosts, creating a unique possibility to study parallel evolution and identification of genes targeted by mutations to optimize pathogen fitness (pathoadaptive mutations). These genes were related to antibiotic resistance, the cell envelope, or regulatory functions, and we find that the prevalence of pathoadaptive mutations correlates with evolutionary success of co-evolving sub-lineages. The long-term co-existence of both normal and hypermutator populations enabled comparative investigations of the mutation dynamics in homopolymeric sequences in which hypermutators are particularly prone to mutations. We find a positive exponential correlation between the length of the homopolymer and its likelihood to acquire mutations and identify two homopolymer-containing genes preferentially mutated in hypermutators. This homopolymer facilitated differential mutagenesis provides a novel genome-wide perspective on the different evolutionary trajectories of hypermutators, which may help explain their emergence in CF infections. Pseudomonas aeruginosa is the dominating pathogen of chronic airway infections in patients with cystic fibrosis (CF). Although bacterial long-term persistence in CF hosts involves mutation and selection of genetic variants with increased fitness in the CF lung environment, our understanding of the within-host evolutionary processes is limited. Here, we performed a retrospective study of the P. aeruginosa DK2 clone type, which is a transmissible clone isolated from chronically infected Danish CF patients over a period of 38 years. Whole-genome analysis of DK2 isolates enabled a fine-grained reconstruction of the recent evolutionary history of the DK2 lineage and an identification of bacterial genes targeted by mutations to optimize pathogen fitness. The identification of such pathoadaptive genes gives new insight into how the pathogen evolves under the selective pressures of the host immune system and drug therapies. Furthermore, isolates with increased rates of mutation (hypermutator phenotype) emerged in the DK lineage. While this phenotype may accelerate evolution, we also show that hypermutators display differential mutagenesis of certain genes which enable them to follow alternative evolutionary pathways. Overall, our study identifies genes important for bacterial persistence and provides insight into the different mutational mechanisms that govern the adaptive genetic changes.
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Affiliation(s)
- Rasmus Lykke Marvig
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Søren Molin
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail: (SM); (LJ)
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail: (SM); (LJ)
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32
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Zhou K, Aertsen A, Michiels CW. The role of variable DNA tandem repeats in bacterial adaptation. FEMS Microbiol Rev 2013; 38:119-41. [PMID: 23927439 DOI: 10.1111/1574-6976.12036] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/13/2013] [Accepted: 07/26/2013] [Indexed: 01/05/2023] Open
Abstract
DNA tandem repeats (TRs), also designated as satellite DNA, are inter- or intragenic nucleotide sequences that are repeated two or more times in a head-to-tail manner. Because TR tracts are prone to strand-slippage replication and recombination events that cause the TR copy number to increase or decrease, loci containing TRs are hypermutable. An increasing number of examples illustrate that bacteria can exploit this instability of TRs to reversibly shut down or modulate the function of specific genes, allowing them to adapt to changing environments on short evolutionary time scales without an increased overall mutation rate. In this review, we discuss the prevalence and distribution of inter- and intragenic TRs in bacteria and the mechanisms of their instability. In addition, we review evidence demonstrating a role of TR variations in bacterial adaptation strategies, ranging from immune evasion and tissue tropism to the modulation of environmental stress tolerance. Nevertheless, while bioinformatic analysis reveals that most bacterial genomes contain a few up to several dozens of intra- and intergenic TRs, only a small fraction of these have been functionally studied to date.
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Affiliation(s)
- Kai Zhou
- Department of Microbial and Molecular Systems (M²S), Faculty of Bioscience Engineering, Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Leuven, Belgium
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Gunka K, Stannek L, Care RA, Commichau FM. Selection-driven accumulation of suppressor mutants in bacillus subtilis: the apparent high mutation frequency of the cryptic gudB gene and the rapid clonal expansion of gudB(+) suppressors are due to growth under selection. PLoS One 2013; 8:e66120. [PMID: 23785476 PMCID: PMC3681913 DOI: 10.1371/journal.pone.0066120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/01/2013] [Indexed: 11/25/2022] Open
Abstract
Soil bacteria like Bacillus subtilis can cope with many growth conditions by adjusting gene expression and metabolic pathways. Alternatively, bacteria can spontaneously accumulate beneficial mutations or shape their genomes in response to stress. Recently, it has been observed that a B. subtilis mutant lacking the catabolically active glutamate dehydrogenase (GDH), RocG, mutates the cryptic gudBCR gene at a high frequency. The suppressor mutants express the active GDH GudB, which can fully replace the function of RocG. Interestingly, the cryptic gudBCR allele is stably inherited as long as the bacteria synthesize the functional GDH RocG. Competition experiments revealed that the presence of the cryptic gudBCR allele provides the bacteria with a selective growth advantage when glutamate is scarce. Moreover, the lack of exogenous glutamate is the driving force for the selection of mutants that have inactivated the active gudB gene. In contrast, two functional GDHs are beneficial for the cells when glutamate was available. Thus, the amount of GDH activity strongly affects fitness of the bacteria depending on the availability of exogenous glutamate. At a first glance the high mutation frequency of the cryptic gudBCR allele might be attributed to stress-induced adaptive mutagenesis. However, other loci on the chromosome that could be potentially mutated during growth under the selective pressure that is exerted on a GDH-deficient mutant remained unaffected. Moreover, we show that a GDH-proficient B. subtilis strain has a strong selective growth advantage in a glutamate-dependent manner. Thus, the emergence and rapid clonal expansion of the active gudB allele can be in fact explained by spontaneous mutation and growth under selection without an increase of the mutation rate. Moreover, this study shows that the selective pressure that is exerted on a maladapted bacterium strongly affects the apparent mutation frequency of mutational hot spots.
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Affiliation(s)
- Katrin Gunka
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Lorena Stannek
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Rachel A. Care
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Fabian M. Commichau
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail:
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Roos S, Macao B, Fusté JM, Lindberg C, Jemt E, Holme E, Moslemi AR, Oldfors A, Falkenberg M. Subnormal levels of POLγA cause inefficient initiation of light-strand DNA synthesis and lead to mitochondrial DNA deletions and progressive external ophthalmoplegia [corrected]. Hum Mol Genet 2013; 22:2411-22. [PMID: 23446635 DOI: 10.1093/hmg/ddt094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The POLG1 gene encodes the catalytic subunit of mitochondrial DNA (mtDNA) polymerase γ (POLγ). We here describe a sibling pair with adult-onset progressive external ophthalmoplegia, cognitive impairment and mitochondrial myopathy characterized by DNA depletion and multiple mtDNA deletions. The phenotype is due to compound heterozygous POLG1 mutations, T914P and the intron mutation c.3104 + 3A > T. The mutant genes produce POLγ isoforms with heterozygous phenotypes that fail to synthesize longer DNA products in vitro. However, exon skipping in the c.3104 + 3A > T mutant is not complete, and the presence of low levels of wild-type POLγ explains patient survival. To better understand the underlying pathogenic mechanisms, we characterized the effects of POLγ depletion in vitro and found that leading-strand DNA synthesis is relatively undisturbed. In contrast, initiation of lagging-strand DNA synthesis is ineffective at lower POLγ concentrations that uncouples leading strand from lagging-strand DNA synthesis. In vivo, this effect leads to prolonged exposure of the heavy strand in its single-stranded conformation that in turn can cause the mtDNA deletions observed in our patients. Our findings, thus, suggest a molecular mechanism explaining how POLγ mutations can cause mtDNA deletions in vivo.
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Affiliation(s)
- Sara Roos
- Department of Pathology, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gula Stråket 8, Gothenburg SE-413 45, Sweden.
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Zhou K, Michiels CW, Aertsen A. Variation of intragenic tandem repeat tract of tolA modulates Escherichia coli stress tolerance. PLoS One 2012; 7:e47766. [PMID: 23094082 PMCID: PMC3477136 DOI: 10.1371/journal.pone.0047766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/20/2012] [Indexed: 11/18/2022] Open
Abstract
In recent work we discovered that the intragenic tandem repeat (TR) region of the tolA gene is highly variable among different Escherichia coli strains. The aim of this study was therefore to investigate the biological function and dynamics of TR variation in E. coli tolA. The biological impact of TR variation was examined by comparing the ability of a set of synthetic tolA variants with in frame repeat copies varying from 2 to 39 to rescue the altered susceptibility of an E. coli ΔtolA mutant to deoxycholic acid, sodium dodecyl sulfate, hyperosmolarity, and infection with filamentous bacteriophage. Interestingly, although each of the TolA variants was able to at least partly rescue the ΔtolA mutant, the extent was clearly dependent on both the repeat number and the type of stress imposed, indicating the existence of opposing selective forces with regard to the optimal TR copy number. Subsequently, TR dynamics in a clonal population were assayed, and we could demonstrate that TR contractions are RecA dependent and enhanced in a DNA repair deficient uvrD background, and can occur at a frequency of 6.9×10−5.
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Affiliation(s)
- Kai Zhou
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department of Microbial and Molecular Systems (MS), Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Chris W. Michiels
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department of Microbial and Molecular Systems (MS), Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department of Microbial and Molecular Systems (MS), Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
- * E-mail:
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Common fragile sites: genomic hotspots of DNA damage and carcinogenesis. Int J Mol Sci 2012; 13:11974-11999. [PMID: 23109895 PMCID: PMC3472787 DOI: 10.3390/ijms130911974] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/09/2012] [Accepted: 09/05/2012] [Indexed: 01/08/2023] Open
Abstract
Genomic instability, a hallmark of cancer, occurs preferentially at specific genomic regions known as common fragile sites (CFSs). CFSs are evolutionarily conserved and late replicating regions with AT-rich sequences, and CFS instability is correlated with cancer. In the last decade, much progress has been made toward understanding the mechanisms of chromosomal instability at CFSs. However, despite tremendous efforts, identifying a cancer-associated CFS gene (CACG) remains a challenge and little is known about the function of CACGs at most CFS loci. Recent studies of FATS (for Fragile-site Associated Tumor Suppressor), a new CACG at FRA10F, reveal an active role of this CACG in regulating DNA damage checkpoints and suppressing tumorigenesis. The identification of FATS may inspire more discoveries of other uncharacterized CACGs. Further elucidation of the biological functions and clinical significance of CACGs may be exploited for cancer biomarkers and therapeutic benefits.
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Ryall B, Eydallin G, Ferenci T. Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition. Microbiol Mol Biol Rev 2012; 76:597-625. [PMID: 22933562 PMCID: PMC3429624 DOI: 10.1128/mmbr.05028-11] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior.
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Affiliation(s)
- Ben Ryall
- School of Molecular Bioscience, University of Sydney, New South Wales, Australia
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Samy M, Gattolliat CH, Pendino F, Hillion J, Nguyen E, Bombard S, Douc-Rasy S, Bénard J, Ségal-Bendirdjian E. Loss of the malignant phenotype of human neuroblastoma cells by a catalytically inactive dominant-negative hTERT mutant. Mol Cancer Ther 2012; 11:2384-93. [PMID: 22933702 DOI: 10.1158/1535-7163.mct-12-0281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Telomerase, a ribonucleoprotein complex mainly composed of the reverse transcriptase catalytic subunit (human telomerase reverse transcriptase, hTERT) and the RNA component (hTR), is a key enzyme of cancer progression. That aggressive stage 4-neuroblastoma expressed high levels of telomerase activity, whereas favorable tumors had no or little telomerase expression and activity, prompted us to investigate the role of this enzyme in this tumor model of altered proliferation, neuronal differentiation, and apoptosis. A human MYCN-amplified neuroblastoma cell line (IGR-N-91) was engineered to stably express either the normal hTERT protein (WT-hTERT) or a catalytically inactive dominant-negative mutant of this protein (DN-hTERT). We showed that DN-hTERT expression inhibited the endogenous hTERT in the malignant neuroblasts without telomere shortening nor loss of in vitro proliferative capacity. Importantly, DN-hTERT expression induced major changes in cell morphology of neuroblasts that switched them from a neuronal to a substrate adherent phenotype, which was more prone to apoptosis and lost their tumorigenic properties in nude mice. These biologic effects arose from modifications in the expression of genes involved in both apoptosis and neuroblastoma biology. Taken together these results highlighted the functional relevance of noncanonical functions of hTERT in the determination of neuroblast cell fate. Therefore, our results envision new therapeutic strategies for metastatic neuroblastoma therapeutic management.
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Affiliation(s)
- Mona Samy
- INSERM UMR-S 1007, Université Paris-Descartes, 45 rue des Saints-Pères, 75006 Paris, France
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39
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Variability of the tandem repeat region of the Escherichia coli tolA gene. Res Microbiol 2012; 163:316-22. [DOI: 10.1016/j.resmic.2012.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 05/03/2012] [Indexed: 11/23/2022]
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40
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Lindeberg M. Genome-enabled perspectives on the composition, evolution, and expression of virulence determinants in bacterial plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:111-132. [PMID: 22559066 DOI: 10.1146/annurev-phyto-081211-173022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genome sequence analyses of bacterial plant pathogens are revealing important insights into the molecular determinants of pathogenicity and, through transcript characterization, responses to environmental conditions, evidence for small RNAs, and validation of uncharacterized genes. Genome comparison sheds further light on the processes impacting pathogen evolution and differences in gene repertoire among isolates contributing to niche specialization. Information derived from pathogen genome analysis is providing tools for use in diagnosis and interference with host-pathogen interactions for the purpose of disease control. However, the existing information infrastructure fails to adequately integrate the increasing numbers of sequence data sets, bioinformatic analyses, and experimental characterization, as required for effective systems-level analysis. Enhanced standardization of data formats at the point of publication is proposed as a possible solution.
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Affiliation(s)
- Magdalen Lindeberg
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, USA.
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Pellegrini M, Renda ME, Vecchio A. Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases. BMC Bioinformatics 2012; 13 Suppl 4:S3. [PMID: 22536970 PMCID: PMC3303744 DOI: 10.1186/1471-2105-13-s4-s3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters. Results In this paper we present TReaDS - Tandem Repeats Discovery Service, a tandem repeat meta search engine. TReaDS forwards user requests to several state of the art tools for finding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, TReaDS allows the user to (i) simultaneously run different algorithms on the same data set, (ii) choose for each algorithm a different setting of parameters, and (iii) obtain a report that can be downloaded for further, off-line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases. Conclusions By using the tool TReaDS we discover that, for 27 repeat expansion diseases out of a currently known set of 29, long fuzzy tandem repeats are covering the expansion loci. Tests with control sets confirm the specificity of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability. We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our capabilities in detecting important phenomena related to tandem repeats.
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Affiliation(s)
- Marco Pellegrini
- Istituto di Informatica e Telematica, Consiglio Nazionale delle Ricerche, Pisa I-56124, Italy
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Liu G, Leffak M. Instability of (CTG)n•(CAG)n trinucleotide repeats and DNA synthesis. Cell Biosci 2012; 2:7. [PMID: 22369689 PMCID: PMC3310812 DOI: 10.1186/2045-3701-2-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/27/2012] [Indexed: 12/21/2022] Open
Abstract
Expansion of (CTG)n•(CAG)n trinucleotide repeat (TNR) microsatellite sequences is the cause of more than a dozen human neurodegenerative diseases. (CTG)n and (CAG)n repeats form imperfectly base paired hairpins that tend to expand in vivo in a length-dependent manner. Yeast, mouse and human models confirm that (CTG)n•(CAG)n instability increases with repeat number, and implicate both DNA replication and DNA damage response mechanisms in (CTG)n•(CAG)n TNR expansion and contraction. Mutation and knockdown models that abrogate the expression of individual genes might also mask more subtle, cumulative effects of multiple additional pathways on (CTG)n•(CAG)n instability in whole animals. The identification of second site genetic modifiers may help to explain the variability of (CTG)n•(CAG)n TNR instability patterns between tissues and individuals, and offer opportunities for prognosis and treatment.
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Affiliation(s)
- Guoqi Liu
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA.
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A high-frequency mutation in Bacillus subtilis: requirements for the decryptification of the gudB glutamate dehydrogenase gene. J Bacteriol 2011; 194:1036-44. [PMID: 22178973 DOI: 10.1128/jb.06470-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Common laboratory strains of Bacillus subtilis encode two glutamate dehydrogenases: the enzymatically active protein RocG and the cryptic enzyme GudB that is inactive due to a duplication of three amino acids in its active center. The inactivation of the rocG gene results in poor growth of the bacteria on complex media due to the accumulation of toxic intermediates. Therefore, rocG mutants readily acquire suppressor mutations that decryptify the gudB gene. This decryptification occurs by a precise deletion of one part of the 9-bp direct repeat that causes the amino acid duplication. This mutation occurs at the extremely high frequency of 10(-4). Mutations affecting the integrity of the direct repeat result in a strong reduction of the mutation frequency; however, the actual sequence of the repeat is not essential. The mutation frequency of gudB was not affected by the position of the gene on the chromosome. When the direct repeat was placed in the completely different context of an artificial promoter, the precise deletion of one part of the repeat was also observed, but the mutation frequency was reduced by 3 orders of magnitude. Thus, transcription of the gudB gene seems to be essential for the high frequency of the appearance of the gudB1 mutation. This idea is supported by the finding that the transcription-repair coupling factor Mfd is required for the decryptification of gudB. The Mfd-mediated coupling of transcription to mutagenesis might be a built-in precaution that facilitates the accumulation of mutations preferentially in transcribed genes.
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Abstract
Minimum spanning trees (MSTs) are frequently used in molecular epidemiology research to estimate relationships among individual strains or isolates. Nevertheless, there are significant caveats to MST algorithms that have been largely ignored in molecular epidemiology studies and that have the potential to confound or alter the interpretation of the results of those analyses. Specifically, (i) presenting a single, arbitrarily selected MST illustrates only one of potentially many equally optimal solutions, and (ii) statistical metrics are not used to assess the credibility of MST estimations. Here, we survey published MSTs previously used to infer microbial population structure in order to determine the effect of these factors. We propose a technique to estimate the number of alternative MSTs for a data set and find that multiple MSTs exist for each case in our survey. By implementing a bootstrapping metric to evaluate the reliability of alternative MST solutions, we discover that they encompass a wide range of credibility values. On the basis of these observations, we conclude that current approaches to studying population structure using MSTs are inadequate. We instead propose a systematic approach to MST estimation that bases analyses on the optimal computation of an input distance matrix, provides information about the number and configurations of alternative MSTs, and allows identification of the most credible MST or MSTs by using a bootstrapping metric. It is our hope this algorithm will become the new "gold standard" approach for analyzing MSTs for molecular epidemiology so that this generally useful computational approach can be used informatively and to its full potential.
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45
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Strain Typing Using Multiple “Variable Number of Tandem Repeat” Analysis and Genetic Element CRISPR. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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46
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Lin S, Haas S, Zemojtel T, Xiao P, Vingron M, Li R. Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators. Gene 2011; 473:139-49. [DOI: 10.1016/j.gene.2010.11.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/13/2010] [Accepted: 11/26/2010] [Indexed: 01/27/2023]
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Brevik ØJ, Ottem KF, Nylund A. Multiple-locus, variable number of tandem repeat analysis (MLVA) of the fish-pathogen Francisella noatunensis. BMC Vet Res 2011; 7:5. [PMID: 21261955 PMCID: PMC3037875 DOI: 10.1186/1746-6148-7-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 01/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since Francisella noatunensis was first isolated from cultured Atlantic cod in 2004, it has emerged as a global fish pathogen causing disease in both warm and cold water species. Outbreaks of francisellosis occur in several important cultured fish species making a correct management of this disease a matter of major importance. Currently there are no vaccines or treatments available. A strain typing system for use in studies of F. noatunensis epizootics would be an important tool for disease management. However, the high genetic similarity within the Francisella spp. makes strain typing difficult, but such typing of the related human pathogen Francisella tullarensis has been performed successfully by targeting loci with higher genetic variation than the traditional signature sequences. These loci are known as Variable Numbers of Tandem Repeat (VNTR). The aim of this study is to identify possible useful VNTRs in the genome of F. noatunensis. RESULTS Seven polymorphic VNTR loci were identified in the preliminary genome sequence of F. noatunensis ssp. noatunensis GM2212 isolate. These VNTR-loci were sequenced in F. noatunensis isolates collected from Atlantic cod (Gadus morhua) from Norway (n = 21), Three-line grunt (Parapristipoma trilineatum) from Japan (n = 1), Tilapia (Oreochromis spp.) from Indonesia (n = 3) and Atlantic salmon (Salmo salar) from Chile (n = 1). The Norwegian isolates presented in this study show both nine allelic profiles and clades, and that the majority of the farmed isolates belong in two clades only, while the allelic profiles from wild cod are unique. CONCLUSIONS VNTRs can be used to separate isolates belonging to both subspecies of F. noatunensis. Low allelic diversity in F. noatunensis isolates from outbreaks in cod culture compared to isolates wild cod, indicate that transmission of these isolates may be a result of human activity. The sequence based MLVA system presented in this study should provide a good starting point for further development of a genotyping system that can be used in studies of epizootics and disease management of francisellosis.
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Affiliation(s)
- Øyvind J Brevik
- Department of Biology, University of Bergen, Post box 7800, N-5020 Bergen, Norway
| | - Karl F Ottem
- Department of Biology, University of Bergen, Post box 7800, N-5020 Bergen, Norway
| | - Are Nylund
- Department of Biology, University of Bergen, Post box 7800, N-5020 Bergen, Norway
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Herrmann D, Rose E, Müller U, Wagner R. Microarray-based STR genotyping using RecA-mediated ligation. Nucleic Acids Res 2010; 38:e172. [PMID: 20682559 PMCID: PMC2943619 DOI: 10.1093/nar/gkq657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We describe a novel assay capable of accurately determining the length of short tandem repeat (STR) alleles. STR genotyping is achieved utilizing RecA-mediated ligation (RML), which combines the high fidelity of RecA-mediated homology searching with allele-specific ligation. RecA catalyzes the pairing of synthetic oligonucleotides with one strand of a double-stranded DNA target, in this case a PCR amplicon. Ligation occurs only when two adjacent oligonucleotides are base paired to the STR region without any overlap or gap. RecA activity is required to overcome the inherent difficulty of annealing repeated sequences in register. This assay is capable of determining STR genotypes of human samples, is easily adapted to high throughput or automated systems and can have widespread utility in diagnostic and forensic applications.
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Affiliation(s)
- David Herrmann
- Gene Check Inc., Greeley, CO 80634 and UWILA International Consulting, Alachua, FL 32615, USA
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49
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Chen J, Deng X, Sun X, Jones D, Irey M, Civerolo E. Guangdong and Florida populations of 'Candidatus Liberibacter asiaticus' distinguished by a genomic locus with short tandem repeats. PHYTOPATHOLOGY 2010; 100:567-572. [PMID: 20465412 DOI: 10.1094/phyto-100-6-0567] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Huanglongbing (HLB) (yellow shoot disease) is a highly destructive disease that threatens citrus production worldwide. The disease was first observed in Guangdong, P.R. China, over 100 years ago, and was found in Florida, United States, in 2005. 'Candidatus Liberibacter asiaticus' has been associated with HLB in many citrus-growing regions around the world, including Guangdong and Florida. The global epidemiology of HLB, as well as management of the disease, relies on knowledge of 'Ca. L. asiaticus' populations in different geographical regions around the world. In this study, we identified a genetic marker containing small tandem repeats in the genome of 'Ca. L. asiaticus' and comparatively analyzed the tandem repeat numbers (TRNs) in 'Ca. L. asiaticus' populations from Guangdong and Florida. Analyses of TRNs showed that the bacterial population in Guangdong was different from that in Florida. The Guangdong population consisted predominately of strains with a TRN of 7 (TRN(7)) at a frequency of 47.6%. The Florida population consisted predominately of strains with a TRN of 5 (TRN(5)) at a frequency of 84.4%. TRNs ranged from 3 to 16. The apparent absence of TRNs of 9, 10, 11, and 12 separated the bacterial strains into two groups: TRNs < 10 (TRN(<10)) and TRNs > 10 (TRN(>10)). In Florida, TRN(<10) strains (103/109, or 94.5%) were widely distributed in all HLB-affected counties. TRN(>10) strains (6/109, or 5.5%) were found in central Florida. This is the first report documenting the differentiation of 'Ca. L. asiaticus' populations between Asia and North America and the possible presence of two differentially distributed genotypes of 'Ca. L. asiaticus' in Florida.
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Affiliation(s)
- J Chen
- U.S. Department of Agriculture-Agricultural Research Services, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA.
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50
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Mil-Homens D, Rocha EPC, Fialho AM. Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage. Microbiology (Reading) 2010; 156:1084-1096. [DOI: 10.1099/mic.0.032623-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the Burkholderia cepacia complex (Bcc) are respiratory pathogens in patients with cystic fibrosis (CF). Close repetitive DNA sequences often associate with surface antigens to promote genetic variability in pathogenic bacteria. The genome of Burkholderia cenocepacia J2315, a CF isolate belonging to the epidemic lineage Edinburgh–Toronto (ET-12), was analysed for the presence of close repetitive DNA sequences. Among the 422 DNA close repeats, 45 genes potentially involved in virulence were identified and grouped into 12 classes; of these, 13 genes were included in the antigens class. Two trimeric autotransporter adhesins (TAA) among the 13 putative antigens are absent from the other Burkholderia genomes and are clustered downstream of the cci island that is a marker for transmissible B. cenocepacia strains. This cluster contains four adhesins, one outer-membrane protein, one sensor histidine kinase and two transcriptional regulators. By using PCR, we analysed three genes among 47 Bcc isolates to determine whether the cluster was conserved. These three genes were present in the isolates of the ET-12 lineage but absent in all the other members. Furthermore, the BCAM0224 gene was exclusively detected in this epidemic lineage and may serve as a valuable new addition to the field of Bcc diagnostics. The BCAM0224 gene encodes a putative TAA that demonstrates adhesive properties to the extracellular matrix protein collagen type I. Quantitative real-time PCR analysis indicated that BCAM0224 gene expression occurred preferentially for cells grown under high osmolarity, oxygen-limited conditions and oxidative stress. Inactivation of BCAM0224 in B. cenocepacia attenuates the ability of the mutant to promote cell adherence in vitro and impairs the overall bacterial virulence against Galleria mellonella as a model of infection. Together, our data show that BCAM0224 from B. cenocepacia J2315 represents a new collagen-binding TAA with no bacterial orthologues which has an important role in cellular adhesion and virulence.
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Affiliation(s)
- Dalila Mil-Homens
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Lisbon 1049-001, Portugal
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics Group, CNRS URA2171, Institute Pasteur, F-75015 Paris, France
- Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris 6, Paris, F-75005 France
| | - Arsenio M. Fialho
- IBB-Institute for Biotechnology and Bioengineering, Center for Biological and Chemical Engineering, Instituto Superior Técnico, Lisbon 1049-001, Portugal
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