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Gomaa B, Lu J, Abdelhamed H, Banes M, Pechanova O, Pechan T, Arick MA, Karsi A, Lawrence ML. Identification of Protein Biomarkers for Differentiating Listeria monocytogenes Genetic Lineage III. Foods 2024; 13:1302. [PMID: 38731673 PMCID: PMC11083783 DOI: 10.3390/foods13091302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Listeria monocytogenes is the causative agent of listeriosis, a severe foodborne illness characterized by septicemia, meningitis, encephalitis, abortions, and occasional death in infants and immunocompromised individuals. L. monocytogenes is composed of four genetic lineages (I, II, III, and IV) and fourteen serotypes. The aim of the current study was to identify proteins that can serve as biomarkers for detection of genetic lineage III strains based on simple antibody-based methods. Liquid chromatography (LC) with electrospray ionization tandem mass spectrometry (ESI MS/MS) followed by bioinformatics and computational analysis were performed on three L. monocytogenes strains (NRRL B-33007, NRRL B-33014, and NRRL B-33077), which were used as reference strains for lineages I, II, and III, respectively. Results from ESI MS/MS revealed 42 unique proteins present in NRRL B-33077 and absent in NRRL B-33007 and NRRL B-33014 strains. BLAST analysis of the 42 proteins against a broader panel of >80 sequenced strains from lineages I and II revealed four proteins [TM2 domain-containing protein (NRRL B-33077_2770), DUF3916 domain-containing protein (NRRL B-33077_1897), DNA adenine methylase (NRRL B-33077_1926), and protein RhsA (NRRL B-33077_1129)] that have no homology with any sequenced strains in lineages I and II. The four genes that encode these proteins were expressed in Escherichia coli strain DE3 and purified. Polyclonal antibodies were prepared against purified recombinant proteins. ELISA using the polyclonal antibodies against 12 L. monocytogenes lineage I, II, and III isolates indicated that TM2 protein and DNA adenine methylase (Dam) detected all lineage III strains with no reaction to lineage I and II strains. In conclusion, two proteins including TM2 protein and Dam are potentially useful biomarkers for detection and differentiation of L. monocytogenes lineage III strains in clinical, environmental, and food processing facilities. Furthermore, these results validate the approach of using a combination of proteomics and bioinformatics to identify useful protein biomarkers.
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Affiliation(s)
- Basant Gomaa
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA; (B.G.); (J.L.); (H.A.); (M.B.); (A.K.)
| | - Jingjun Lu
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA; (B.G.); (J.L.); (H.A.); (M.B.); (A.K.)
| | - Hossam Abdelhamed
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA; (B.G.); (J.L.); (H.A.); (M.B.); (A.K.)
| | - Michelle Banes
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA; (B.G.); (J.L.); (H.A.); (M.B.); (A.K.)
| | - Olga Pechanova
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA; (O.P.); (T.P.); (M.A.A.II)
| | - Tibor Pechan
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA; (O.P.); (T.P.); (M.A.A.II)
| | - Mark A. Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA; (O.P.); (T.P.); (M.A.A.II)
| | - Attila Karsi
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA; (B.G.); (J.L.); (H.A.); (M.B.); (A.K.)
| | - Mark L. Lawrence
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA; (B.G.); (J.L.); (H.A.); (M.B.); (A.K.)
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Zhang W, Lyu L, Xu Z, Ni J, Wang D, Lu J, Yao YF. Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress. Microbiol Spectr 2023; 11:e0247923. [PMID: 37882553 PMCID: PMC10715015 DOI: 10.1128/spectrum.02479-23] [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: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The intracellular pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) comes across a wide variety of stresses from entry to dissemination, such as reactive oxygen species. To adapt itself to oxidative stress, Salmonella must adopt various and complex strategies. In this study, we revealed that DNA adenine methyltransferase was essential for S. Typhimurium to survive in hydrogen peroxide. We then screened out oxidative stress-responsive genes that were potentially regulated by DNA methylation in S. Typhimurium. Our results show that the DNA methylome is highly stable throughout the genome, and the coupled change of m6A GATC with gene expression is identified in only a few positions, which suggests the complexity of the DNA methylation and gene expression regulation networks. The results may shed light on our understanding of m6A-mediated gene expression regulation in bacteria.
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Affiliation(s)
- Wenting Zhang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Lyu
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihiong Xu
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinjing Ni
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Lu
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
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3
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Stone CJ, Boyer GF, Behringer MG. Differential adenine methylation analysis reveals increased variability in 6mA in the absence of methyl-directed mismatch repair. mBio 2023; 14:e0128923. [PMID: 37796009 PMCID: PMC10653831 DOI: 10.1128/mbio.01289-23] [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: 05/30/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Methylation greatly influences the bacterial genome by guiding DNA repair and regulating pathogenic and stress-response phenotypes. But, the rate of epigenetic changes and their consequences on molecular phenotypes are underexplored. Through a detailed characterization of genome-wide adenine methylation in a commonly used laboratory strain of Escherichia coli, we reveal that mismatch repair deficient populations experience an increase in epimutations resulting in a genome-wide reduction of 6mA methylation in a manner consistent with genetic drift. Our findings highlight how methylation patterns evolve and the constraints on epigenetic evolution due to post-replicative DNA repair, contributing to a deeper understanding of bacterial genome evolution and how epimutations may introduce semi-permanent variation that can influence adaptation.
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Affiliation(s)
- Carl J. Stone
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Gwyneth F. Boyer
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Megan G. Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Zhao Y, Liu G, Yang F, Liang Y, Gao Q, Xiang C, Li X, Yang R, Zhang G, Jiang H, Yu L, Yang S. Multilayered regulation of secondary metabolism in medicinal plants. MOLECULAR HORTICULTURE 2023; 3:11. [PMID: 37789448 PMCID: PMC10514987 DOI: 10.1186/s43897-023-00059-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/27/2023] [Indexed: 10/05/2023]
Abstract
Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants; moreover, these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps. The first regulatory layer involves a complex network of transcription factors; a second, more recently discovered layer of complexity in the regulation of SMs is epigenetic modification, such as DNA methylation, histone modification and small RNA-based mechanisms, which can jointly or separately influence secondary metabolites by regulating gene expression. Here, we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants, providing a new perspective on the multiple layers of regulation of gene expression.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanze Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
| | - Feng Yang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Liang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Run Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huifeng Jiang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China.
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, 650201, Kunming, China.
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5
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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CRISPR-Cas9-Mediated Mutation of Methyltransferase METTL4 Results in Embryonic Defects in Silkworm Bombyx mori. Int J Mol Sci 2023; 24:ijms24043468. [PMID: 36834878 PMCID: PMC9965800 DOI: 10.3390/ijms24043468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
DNA N6-methyladenine (6mA) has recently been found to play regulatory roles in gene expression that links to various biological processes in eukaryotic species. The functional identification of 6mA methyltransferase will be important for understanding the underlying molecular mechanism of epigenetic 6mA methylation. It has been reported that the methyltransferase METTL4 can catalyze the methylation of 6mA; however, the function of METTL4 remains largely unknown. In this study, we aim to investigate the role of the Bombyx mori homolog METTL4 (BmMETTL4) in silkworm, a lepidopteran model insect. By using CRISPR-Cas9 system, we somatically mutated BmMETTL4 in silkworm individuates and found that disruption of BmMETTL4 caused the developmental defect of late silkworm embryo and subsequent lethality. We performed RNA-Seq and identified that there were 3192 differentially expressed genes in BmMETTL4 mutant including 1743 up-regulated and 1449 down-regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes involved in molecular structure, chitin binding, and serine hydrolase activity were significantly affected by BmMETTL4 mutation. We further found that the expression of cuticular protein genes and collagens were clearly decreased while collagenases were highly increased, which had great contributions to the abnormal embryo and decreased hatchability of silkworm. Taken together, these results demonstrated a critical role of 6mA methyltransferase BmMETTL4 in regulating embryonic development of silkworm.
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Keçeli Oğuz S, Has EG, Akçelik N, Akçelik M. Phenotypic impacts and genetic regulation characteristics of the DNA adenine methylase gene (dam) in Salmonella Typhimurium biofilm forms. Res Microbiol 2023; 174:103991. [PMID: 36113833 DOI: 10.1016/j.resmic.2022.103991] [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: 05/25/2022] [Revised: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
In this study, transcriptional level gene expression changes in biofilm forms of Salmonella Typhimurium ATCC 14028 and its dam mutant were investigated by performing RNAseq analysis. As a result of these analyzes, a total of 233 differentially expressed genes (DEGs) were identified in the dam mutant, of which 145 genes were downregulated and 88 genes were upregulated compared to the wild type. According to data from miRNA sequence analysis, of 13 miRNAs differentially expressed in dam mutant, 9 miRNAs were downregulated and 4 miRNAs were upregulated. These data provide the first evidence that the dam gene is a global regulator of biofilm formation in Salmonella. In addition, phenotypic analyses revealed that bacterial swimming and swarming motility and cellulose production were highly inhibited in the dam mutant. It was determined that bacterial adhesion in Caco-2 and HEp-2 cell lines was significantly reduced in dam mutant. At the end of 90 min, the adhesion rate of wild type strain was 43.3% in Caco-2 cell line, while this rate was 14.9% in dam mutant. In the HEp-2 cell line, while 45.5% adherence was observed in the wild-type strain, this rate decreased to 15.3% in the dam mutant.
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Affiliation(s)
- Selma Keçeli Oğuz
- Department of Biology, Ankara University, Yenimahalle, 06100, Ankara, Turkey.
| | - Elif Gamze Has
- Department of Biology, Ankara University, Yenimahalle, 06100, Ankara, Turkey.
| | - Nefise Akçelik
- Biotechnology Institute, Ankara University, Keçiören, 06135, Ankara, Turkey.
| | - Mustafa Akçelik
- Department of Biology, Ankara University, Yenimahalle, 06100, Ankara, Turkey.
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8
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Chen Y. Recent Advances in Excimer-Based Fluorescence Probes for Biological Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238628. [PMID: 36500722 PMCID: PMC9741103 DOI: 10.3390/molecules27238628] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
The fluorescent probe is a powerful tool for biological sensing and optical imaging, which can directly display analytes at the molecular level. It provides not only direct visualization of biological structures and processes, but also the capability of drug delivery systems regarding the target therapy. Conventional fluorescent probes are mainly based on monomer emission which has two distinguishing shortcomings in practice: small Stokes shifts and short lifetimes. Compared with monomer-based emission, excimer-based fluorescent probes have large Stokes shifts and long lifetimes which benefit biological applications. Recent progress in excimer-based fluorescent sensors (organic small molecules only) for biological applications are highlighted in this review, including materials and mechanisms as well as their representative applications. The progress suggests that excimer-based fluorescent probes have advantages and potential for bioanalytical applications.
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Affiliation(s)
- Yi Chen
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, TIPC, CAS, Beijing 100190, China;
- University of Chinese Academy of Sciences, Beijing 100190, China
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9
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Ratiometric Electrochemical Biosensing of Methyltransferase Activity. Catalysts 2022. [DOI: 10.3390/catal12111362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).
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10
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Ginibre N, Legrand L, Bientz V, Ogier JC, Lanois A, Pages S, Brillard J. Diverse Roles for a Conserved DNA-Methyltransferase in the Entomopathogenic Bacterium Xenorhabdus. Int J Mol Sci 2022; 23:ijms231911981. [PMID: 36233296 PMCID: PMC9570324 DOI: 10.3390/ijms231911981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022] Open
Abstract
In bacteria, DNA-methyltransferase are responsible for DNA methylation of specific motifs in the genome. This methylation usually occurs at a very high rate. In the present study, we studied the MTases encoding genes found in the entomopathogenic bacteria Xenorhabdus. Only one persistent MTase was identified in the various species of this genus. This MTase, also broadly conserved in numerous Gram-negative bacteria, is called Dam: DNA-adenine MTase. Methylome analysis confirmed that the GATC motifs recognized by Dam were methylated at a rate of >99% in the studied strains. The observed enrichment of unmethylated motifs in putative promoter regions of the X. nematophila F1 strain suggests the possibility of epigenetic regulations. The overexpression of the Dam MTase responsible for additional motifs to be methylated was associated with impairment of two major phenotypes: motility, caused by a downregulation of flagellar genes, and hemolysis. However, our results suggest that dam overexpression did not modify the virulence properties of X. nematophila. This study increases the knowledge on the diverse roles played by MTases in bacteria.
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Affiliation(s)
- Nadège Ginibre
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Ludovic Legrand
- LIPME, Université de Toulouse, INRAE, CNRS, 31320 Castanet-Tolosan, France
| | - Victoria Bientz
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | | | - Anne Lanois
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Sylvie Pages
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Julien Brillard
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
- Correspondence: ; Tel.: +33-467144711
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Yi H, Lin F, Wang X, Su J, Zhao L, Lv S, Deng R, Zhou C, Dai J, Xiao D. Determination of Endonuclease Activity by an Enzyme-Free Fluorescent Biosensor Using the Hybridization Chain Reaction (HCR). ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2102180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Huaichao Yi
- College of Chemical Engineering, Sichuan University, Chengdu, China
| | - Fengyi Lin
- College of Chemistry, Sichuan University, Chengdu, China
| | - Xiaokun Wang
- College of Chemical Engineering, Sichuan University, Chengdu, China
| | - Jiaqi Su
- College of Chemistry, Sichuan University, Chengdu, China
| | - Lijun Zhao
- Ministry of Agriculture and Rural Affairs, Laboratory of Quality and Safety Risk Assessment for Livestock and Poultry Products, Chengdu, China
| | - Sitong Lv
- College of Chemistry, Sichuan University, Chengdu, China
| | - Ru Deng
- College of Chemistry, Sichuan University, Chengdu, China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu, China
| | - Jianyuan Dai
- College of Chemistry, Sichuan University, Chengdu, China
| | - Dan Xiao
- College of Chemical Engineering, Sichuan University, Chengdu, China
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12
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6-Amino-3-(prop-2-en-1-yl)-9H-purin-3-ium Tetracopper(I) Hexabromide: Synthesis and X-ray Structure Determination. MOLBANK 2022. [DOI: 10.3390/m1401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
6-Amino-3-(prop-2-en-1-yl)-9H-purin-3-ium tetracopper(I) hexabromide [(C5H5N5(C3H5))2Cu4Br6] (1) is synthesized in this paper. The title compound is characterized by Raman spectroscopy and single crystal X-ray diffraction: monoclinic, Sp.gr. P21/c, Z = 2, unit cell dimensions: a = 8.6870(3), b = 9.7447(2), c = 16.4418(4) Å, β = 100.681(3)°, V = 1367.72(7) Å3 at 150 K. The peculiarities of the metal coordination and distribution of weak interactions are analyzed. The significant role of hydrogen bonds in the construction of 1 crystal structure is shown.
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Integration of the Salmonella Typhimurium Methylome and Transcriptome Reveals That DNA Methylation and Transcriptional Regulation Are Largely Decoupled under Virulence-Related Conditions. mBio 2022; 13:e0346421. [PMID: 35658533 PMCID: PMC9239280 DOI: 10.1128/mbio.03464-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Despite being in a golden age of bacterial epigenomics, little work has systematically examined the plasticity and functional impacts of the bacterial DNA methylome. Here, we leveraged single-molecule, real-time sequencing (SMRT-seq) to examine the m6A DNA methylome of two Salmonella enterica serovar Typhimurium strains: 14028s and a ΔmetJ mutant with derepressed methionine metabolism, grown in Luria broth or medium that simulates the intracellular environment. We found that the methylome is remarkably static: >95% of adenosine bases retain their methylation status across conditions. Integration of methylation with transcriptomic data revealed limited correlation between changes in methylation and gene expression. Further, examination of the transcriptome in ΔyhdJ bacteria lacking the m6A methylase with the most dynamic methylation pattern in our data set revealed little evidence of YhdJ-mediated gene regulation. Curiously, despite G(m6A)TC motifs being particularly resistant to change across conditions, incorporating dam mutants into our analyses revealed two examples where changes in methylation and transcription may be linked across conditions. This includes the novel finding that the ΔmetJ motility defect may be partially driven by hypermethylation of the chemotaxis gene tsr. Together, these data redefine the S. Typhimurium epigenome as a highly stable system that has rare but important roles in transcriptional regulation. Incorporating these lessons into future studies will be critical as we progress through the epigenomic era.
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Yu J, Xu X, Wang Y, Zhai X, Pan Z, Jiao X, Zhang Y. Prophage-mediated genome differentiation of the Salmonella Derby ST71 population. Microb Genom 2022; 8. [PMID: 35451954 PMCID: PMC9453062 DOI: 10.1099/mgen.0.000817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although Salmonella Derby ST71 strains have been recognized as poultry-specific by previous studies, multiple swine-associated S. Derby ST71 strains were identified in this long-term, multi-site epidemic study. Here, 15 representative swine-associated S. Derby ST71 strains were sequenced and compared with 65 (one swine-associated and 64 poultry-associated) S. Derby ST71 strains available in the NCBI database at a pangenomic level through comparative genomics analysis to identify genomic features related to the differentiation of swine-associated strains and previously reported poultry-associated strains. The distribution patterns of known Salmonella pathogenicity islands (SPIs) and virulence factor (VF) encoding genes were not capable of differentiating between the two strain groups. The results demonstrated that the S. Derby ST71 population harbours an open pan-genome, and swine-associated ST71 strains contain many more genes than the poultry-associated strains, mainly attributed to the prophage sequence contents in the genomes. The numbers of prophage sequences identified in the swine-associated strains were higher than those in the poultry-associated strains. Prophages specifically harboured by the swine-associated strains were found to contain genes that facilitate niche adaptation for the bacterial hosts. Gene deletion experiments revealed that the dam gene specifically present in the prophage of the swine-associated strains is important for S. Derby to adhere onto the host cells. This study provides novel insights into the roles of prophages during the genome differentiation of Salmonella.
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Affiliation(s)
- Jinyan Yu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xiaomeng Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xianyue Zhai
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Zhiming Pan
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xinan Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
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15
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Lee KA, Thomas AM, Bolte LA, Björk JR, de Ruijter LK, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Leeming ER, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Vijay A, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Bataille V, Hospers GAP, Spector TD, Weersma RK, Segata N. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat Med 2022; 28:535-544. [PMID: 35228751 PMCID: PMC8938272 DOI: 10.1038/s41591-022-01695-5] [Citation(s) in RCA: 163] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022]
Abstract
The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linked to the clinical benefits of ICIs. We performed shotgun metagenomic sequencing of stool samples collected before ICI initiation from five observational cohorts recruiting ICI-naive patients with advanced cutaneous melanoma (n = 165). Integrating the dataset with 147 metagenomic samples from previously published studies, we found that the gut microbiome has a relevant, but cohort-dependent, association with the response to ICIs. A machine learning analysis confirmed the link between the microbiome and overall response rates (ORRs) and progression-free survival (PFS) with ICIs but also revealed limited reproducibility of microbiome-based signatures across cohorts. Accordingly, a panel of species, including Bifidobacterium pseudocatenulatum, Roseburia spp. and Akkermansia muciniphila, associated with responders was identified, but no single species could be regarded as a fully consistent biomarker across studies. Overall, the role of the human gut microbiome in ICI response appears more complex than previously thought, extending beyond differing microbial species simply present or absent in responders and nonresponders. Future studies should adopt larger sample sizes and take into account the complex interplay of clinical factors with the gut microbiome over the treatment course.
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Affiliation(s)
- Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Laura Kist de Ruijter
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | | | | | | | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Neus Calbet-Llopart
- Dermatology Department, Hospital Clínic Barcelona, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Lisa Derosa
- U1015 INSERM, University Paris Saclay, Gustave Roussy Cancer Center and Oncobiome Network, Villejuif-Grand-Paris, France
| | - Nathalie Dhomen
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Kelly Brooks
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Mark Harries
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
- Department of Medical Oncology, Guys Cancer Centre, Guys and St Thomas's NHS Trust, London, UK
| | - Emily R Leeming
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Richard Marais
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Luigi Nezi
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy
| | | | - Miriam Potrony
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Susana Puig
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | | | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Sabrina Tamburini
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy
| | - Sara Valpione
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Amrita Vijay
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Rheumatology & Orthopaedics Division, School of Medicine, University of Nottingham, Nottingham, UK
| | - Levi Waldron
- Department CIBIO, University of Trento, Trento, Italy
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Laurence Zitvogel
- U1015 INSERM, University Paris Saclay, Gustave Roussy Cancer Center and Oncobiome Network, Villejuif-Grand-Paris, France
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Paul Nathan
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Véronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, Mount Vernon Cancer Centre, Northwood, UK
| | - Geke A P Hospers
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy.
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16
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DNA Methylation in Prokaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:21-43. [DOI: 10.1007/978-3-031-11454-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci. mSphere 2021; 6:e0079921. [PMID: 34787444 PMCID: PMC8597746 DOI: 10.1128/msphere.00799-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although prokaryotic DNA methylation investigations have long focused on immunity against exogenous DNA, it has been recently recognized that DNA methylation impacts gene expression and phase variation in Streptococcus pneumoniae and Streptococcus suis. A comprehensive analysis of DNA methylation is lacking for beta-hemolytic streptococci, and thus we sought to examine DNA methylation in the major human pathogen group A Streptococcus (GAS). Using a database of 224 GAS genomes encompassing 80 emm types, we found that nearly all GAS strains encode a type I restriction modification (RM) system that lacks the hsdS′ alleles responsible for impacting gene expression in S. pneumoniae and S. suis. The GAS type I system is located on the core chromosome, while sporadically present type II orphan methyltransferases were identified on prophages. By combining single-molecule real-time (SMRT) analyses of 10 distinct emm types along with phylogenomics of 224 strains, we were able to assign 13 methylation patterns to the GAS population. Inactivation of the type I RM system, occurring either naturally through phage insertion or through laboratory-induced gene deletion, abrogated DNA methylation detectable via either SMRT or MinION sequencing. Contrary to a previous report, inactivation of the type I system did not impact transcript levels of the gene (mga) encoding the key multigene activator protein (Mga) or Mga-regulated genes. Inactivation of the type I system significantly increased plasmid transformation rates. These data delineate the breadth of the core chromosomal type I RM system in the GAS population and clarify its role in immunity rather than impacting Mga regulon expression. IMPORTANCE The advent of whole-genome approaches capable of detecting DNA methylation has markedly expanded appreciation of the diverse roles of epigenetic modification in prokaryotic physiology. For example, recent studies have suggested that DNA methylation impacts gene expression in some streptococci. The data described herein are from the first systematic analysis of DNA methylation in a beta-hemolytic streptococcus and one of the few analyses to comprehensively characterize DNA methylation across hundreds of strains of the same bacterial species. We clarify that DNA methylation in group A Streptococcus (GAS) is primarily due to a type I restriction modification (RM) system present in the core genome and does not impact mga-regulated virulence gene expression, but does impact immunity against exogenous DNA. The identification of the DNA motifs recognized by each type I RM system may assist with optimizing methods for GAS genetic manipulation and help us understand how bacterial pathogens acquire exogenous DNA elements.
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18
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Zheng Q, Wang T, Li X, Qian H, Bian X, Li X, Bai H, Ding S, Yan Y. Femtomolar and locus-specific detection of N 6-methyladenine in DNA by integrating double-hindered replication and nucleic acid-functionalized MB@Zr-MOF. J Nanobiotechnology 2021; 19:408. [PMID: 34876148 PMCID: PMC8650346 DOI: 10.1186/s12951-021-01156-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022] Open
Abstract
In this study, a novel electrochemical biosensor was constructed for ultrasensitive and locus-specific detection of N6-Methyladenine (m6A) in DNA using double-hindered replication and nucleic acid-coated methylene blue (MB)@Zr-MOF. Based on the combination of m6A-impeded replication and AgI-mediated mismatch replication, this mode could effectively stop the extension of the strand once DNA polymerase encountered m6A site, which specifically distinguish the m6A site from natural A site in DNA. Also, Zr-MOF with high porosity and negative surface potential features was carefully chose to load cationic MB, resulting a stable and robust MB@Zr-MOF electrochemical tag. As a result, the developed biosensor exhibited a wide linear range from 1 fM to 1 nM with detection limit down to 0.89 fM. Profiting from the high sensitivity and selectivity, the biosensing strategy revealed good applicability, which had been demonstrated by quantitating m6A DNA at specific site in biological matrix. Thus, the biosensor provides a promising platform for locus-specific m6A DNA analysis. ![]()
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Affiliation(s)
- Qingyuan Zheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Tong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xinmin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.,Department of Laboratory Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400016, China
| | - Husun Qian
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xintong Bian
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xingrong Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Huijie Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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19
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20
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Gao C, Che B, Dai H. A new G-triplex-based strategy for sensitivity enhancement of the detection of endonuclease activity and inhibition. RSC Adv 2021; 11:28008-28013. [PMID: 35480740 PMCID: PMC9037997 DOI: 10.1039/d1ra04203c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/14/2021] [Indexed: 01/09/2023] Open
Abstract
EcoRI is an important biomacromolecule in live cells and protects bacterial cells against foreign DNA. In this work, we developed a simple and convenient G-triplex (G3) (5′-TGGGAAGGGAGGGAATTCCCT-3′)-based colorimetric assay for the rapid and selective detection of EcoRI activity and inhibition. The sequence specifically responds to EcoRI in the presence of K+ and hemin to form a G-triplex/hemin complex. Taking advantage of G-triplex, EcoRI activity was investigated under the optimized conditions. The absorption intensity ratio displayed a linear relationship against the concentration of EcoRI in the range 0 to 100 U mL−1, and the detection limit was 5.7 U mL−1. Furthermore, G3 showed good selectivity, and the ability to be used to screen for EcoRI inhibitors, indicating its potential in detection and analysis applications. A new G-triplex-based probe was developed for detecting EcoRI activity and inhibition. The probe showed good selectivity towards EcoRI. The assay was colorimetric and can be monitored by the naked eye.![]()
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Affiliation(s)
- Congcong Gao
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
| | - Baoquan Che
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
| | - Hong Dai
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
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21
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Mehershahi KS, Chen SL. DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium. Nucleic Acids Res 2021; 49:7375-7388. [PMID: 34181709 PMCID: PMC8287963 DOI: 10.1093/nar/gkab530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. In particular, both orphan methyltransferases and those from phasevariable restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. We now show that three distinct non-phasevariable Type I RMSs in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes. We demonstrated this using both Type I RMS knockout mutants as well as heterologous installation of Type I RMSs into two E. coli strains. These data provide three clear and currently rare examples of restriction modification systems that have no impact on their host organism’s gene regulation. This leads to the possibility that other such nonregulatory methylation systems may exist, broadening our view of the potential role that RMSs may play in bacterial evolution.
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Affiliation(s)
- Kurosh S Mehershahi
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228
| | - Swaine L Chen
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228.,Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore 138672
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22
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Chen ZP, Zhang HM, Yang P, Yuan R, Li Y, Liang WB. No-nonspecific recognition-based amplification strategy for endonuclease activity screening with dual-color DNA nano-clew. Biosens Bioelectron 2021; 190:113446. [PMID: 34166945 DOI: 10.1016/j.bios.2021.113446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
The inevitable nonspecific recognition severely restricted widely used nucleic acid amplification strategies, which has become an urgent problem in current scientific research. Herein, we developed a novel no-nonspecific recognition-based amplification strategy to construct dual-color dye loaded nano-clew as ultrabright illuminant for screening endonuclease activity with Escherichia coliRY13 I (EcoR I) as a model, which overcame some major drawbacks such as nonspecific recognition and photobleaching. Typically, the target endonuclease induces cleavage of the customized dumbbell-shape substrate (DSS) to generate two same triggers that can initiate the rolling circle amplification (RCA) to prepare long single-strand DNA (lssDNA), which could self-assemble into irregular DNA nano-clew based on the electrostatic interactions with Mg2+ to furtherly capture the donor and accepter fluorophore proximately, constructing the dye loaded nano-clew with dual-color fluorescence (FL) emission to resist photobleaching. Importantly, in absence of EcoR I, even if the DSS could combine with circular template a little, the reaction system performed hardly RCA reaction due to no cohesive terminus, resulting an extremely low background fluorescence signal because of the prevention of nonspecific RCA reaction. As expected, the proposed sensing platform with a low limit of detection (LOD) of 3.4 × 10-7 U/μL was demonstrated to work well for endonuclease inhibitors screening also. Furthermore, the proposed no-nonspecific recognition strategy could be readily extended to various DNA or RNA enzymes such as DNA methyltransferase, DNA repair-related enzymes and polynucleotide kinase just by simply changing the recognition sequence in the DNA substrate, performing great potential of endonucleases-related clinical diagnosis and drugs discovery.
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Affiliation(s)
- Zhao-Peng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Hao-Min Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Peng Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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23
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Payelleville A, Brillard J. Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data. Front Microbiol 2021; 12:685670. [PMID: 34054792 PMCID: PMC8160106 DOI: 10.3389/fmicb.2021.685670] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/22/2021] [Indexed: 12/21/2022] Open
Abstract
DNA methylation can be part of epigenetic mechanisms, leading to cellular subpopulations with heterogeneous phenotypes. While prokaryotic phenotypic heterogeneity is of critical importance for a successful infection by several major pathogens, the exact mechanisms involved in this phenomenon remain unknown in many cases. Powerful sequencing tools have been developed to allow the detection of the DNA methylated bases at the genome level, and they have recently been extensively applied on numerous bacterial species. Some of these tools are increasingly used for metagenomics analysis but only a limited amount of the available methylomic data is currently being exploited. Because newly developed tools now allow the detection of subpopulations differing in their genome methylation patterns, it is time to emphasize future strategies based on a more extensive use of methylomic data. This will ultimately help to discover new epigenetic gene regulations involved in bacterial phenotypic heterogeneity, including during host-pathogen interactions.
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Affiliation(s)
- Amaury Payelleville
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France.,Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
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24
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Shi Z, Yu Z, Chen W. 4-Methylcytosine distribution follows the power function in Geobacter sulfurreducens genome. Biochem Biophys Res Commun 2021; 547:65-68. [PMID: 33596482 DOI: 10.1016/j.bbrc.2021.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/07/2021] [Indexed: 10/22/2022]
Abstract
Single-molecule real-time DNA sequencing revealed that 4-methylcytosine (m4C) commonly exists in bacterial genomes. In this work, samples with different m4C methylation patterns were studied. Results reveal that m4C modification is a biochemical reaction with distance effect, and its distribution follows the power function in the positive, negative, and double strands of genomic DNA sequences of Geobacter sulfurreducens. Furthermore, the value of regression coefficient in the fitting formula for double strands was the sum of those in the fitting formulae for positive and negative strands. Meanwhile, the value of exponent coefficient was the average, implicating an interesting mathematical phenomenon about power function. Considering the potent role of m4C in gene expression and the present results being obtained from the same genomic DNA sequence, this work suggests that the patterns of m4C distribution may be served as a signal for G. sulfurreducens to rapidly identify the genes to respond to environmental stresses or signals. This study opens a new avenue to extend our knowledge about the modification mechanisms and the epigenetic information of m4C modification in prokaryotes.
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Affiliation(s)
- Zhenhua Shi
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, No.15 Shangxiadian Road, Cangshan District, Fuzhou, Fujian, 350002, China.
| | - Zhen Yu
- Fujian Provincial Key Laboratory of Medical Texting, Fujian Academy of Medical Sciences, Fuzhou, 350001, China
| | - Wanqiu Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, No.15 Shangxiadian Road, Cangshan District, Fuzhou, Fujian, 350002, China
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25
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Sibbald SJ, Lawton M, Archibald JM. Mitochondrial Genome Evolution in Pelagophyte Algae. Genome Biol Evol 2021; 13:6126422. [PMID: 33675661 PMCID: PMC7936722 DOI: 10.1093/gbe/evab018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2021] [Indexed: 11/19/2022] Open
Abstract
The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756), and five strains of Aureoc. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984, and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 bp (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five Aureoc. anophagefferens strains varied slightly in length (42,401–42,621 bp) and were 99.4–100.0% identical. Gene content and order were highly conserved between the Aureoc. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in Aureoc. anophagefferens containingDNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. Although the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five Aureoc. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to nonbloom-forming species.
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Affiliation(s)
- Shannon J Sibbald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Maggie Lawton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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Kolenda R, Burdukiewicz M, Wimonć M, Aleksandrowicz A, Ali A, Szabo I, Tedin K, Bartholdson Scott J, Pickard D, Schierack P. Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens. Appl Environ Microbiol 2021; 87:e02177-20. [PMID: 33127819 PMCID: PMC7783345 DOI: 10.1128/aem.02177-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/22/2020] [Indexed: 12/18/2022] Open
Abstract
The initial steps of Salmonella pathogenesis involve adhesion to and invasion into host epithelial cells. While well-studied for Salmonella enterica serovar Typhimurium, the factors contributing to this process in other, host-adapted serovars remains unexplored. Here, we screened clinical isolates of serovars Gallinarum, Dublin, Choleraesuis, Typhimurium, and Enteritidis for adhesion to and invasion into intestinal epithelial cell lines of human, porcine, and chicken origins. Thirty isolates with altered infectivity were used for genomic analyses, and 14 genes and novel mutations associated with high or low infectivity were identified. The functions of candidate genes included virulence gene expression regulation and cell wall or membrane synthesis and components. The role of several of these genes in Salmonella adhesion to and invasion into cells has not previously been investigated. The genes dksA (encoding a stringent response regulator) and sanA (encoding a vancomycin high-temperature exclusion protein) were selected for further analyses, and we confirmed their roles in adhesion to and invasion into host cells. Furthermore, transcriptomic analyses were performed for S Enteritidis and S Typhimurium, with two highly infective and two marginally infective isolates for each serovar. Expression profiles for the isolates with altered infection phenotypes revealed the importance of type 3 secretion system expression levels in the determination of an isolate's infection phenotype. Taken together, these data indicate a new role in cell host infection for genes or gene variants previously not associated with adhesion to and invasion into the epithelial cells.IMPORTANCESalmonella is a foodborne pathogen affecting over 200 million people and resulting in over 200,000 fatal cases per year. Its adhesion to and invasion into intestinal epithelial cells represent one of the first and key steps in the pathogenesis of salmonellosis. Still, around 35 to 40% of bacterial genes have no experimentally validated function, and their contribution to bacterial virulence, including adhesion and invasion, remains largely unknown. Therefore, the significance of this study is in the identification of new genes or gene allelic variants previously not associated with adhesion and invasion. It is well established that blocking adhesion and/or invasion would stop or hamper bacterial infection; therefore, the new findings from this study could be used in future developments of anti-Salmonella therapy targeting genes involved in these key processes. Such treatment could be a valuable alternative, as the prevalence of antibiotic-resistant bacteria is increasing very rapidly.
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Affiliation(s)
- Rafał Kolenda
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Institute of Biotechnology, Faculty Environment and Natural Sciences, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | | | - Marcjanna Wimonć
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Adrianna Aleksandrowicz
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Istvan Szabo
- National Salmonella Reference Laboratory, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Josefin Bartholdson Scott
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge Department of Medicine, Cambridge, United Kingdom
| | - Derek Pickard
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge Department of Medicine, Cambridge, United Kingdom
| | - Peter Schierack
- Institute of Biotechnology, Faculty Environment and Natural Sciences, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Public Health Campus, Brandenburg, Germany
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27
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Park HJ, Seong HJ, Lee J, Heo L, Sul WJ, Han SW. Two DNA Methyltransferases for Site-Specific 6mA and 5mC DNA Modification in Xanthomonas euvesicatoria. FRONTIERS IN PLANT SCIENCE 2021; 12:621466. [PMID: 33841456 PMCID: PMC8025778 DOI: 10.3389/fpls.2021.621466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/25/2021] [Indexed: 05/08/2023]
Abstract
Xanthomonas euvesicatoria (Xe) is a gram-negative phytopathogenic bacterium that causes bacterial spot disease in tomato/pepper leading to economic losses in plantations. DNA methyltransferases (MTases) are critical for the survival of prokaryotes; however, their functions in phytopathogenic bacteria remain unclear. In this study, we characterized the functions of two putative DNA MTases, XvDMT1 and XvDMT2, in Xe by generating XvDMT1- and XvDMT2-overexpressing strains, Xe(XvDMT1) and Xe(XvDMT2), respectively. Virulence of Xe(XvDMT2), but not Xe(XvDMT1), on tomato was dramatically reduced. To postulate the biological processes involving XvDMTs, we performed a label-free shotgun comparative proteomic analysis, and results suggest that XvDMT1 and XvDMT2 have distinct roles in Xe. We further characterized the functions of XvDMTs using diverse phenotypic assays. Notably, both Xe(XvDMT1) and Xe(XvDMT2) showed growth retardation in the presence of sucrose and fructose as the sole carbon source, with Xe(XvDMT2) being the most severely affected. In addition, biofilm formation and production of exopolysaccharides were declined in Xe(XvDMT2), but not Xe(XvDMT1). Xe(XvDMT2) was more tolerant to EtOH than Xe(XvDMT1), which had enhanced tolerance to sorbitol but decreased tolerance to polymyxin B. Using single-molecule real-time sequencing and methylation-sensitive restriction enzymes, we successfully predicted putative motifs methylated by XvDMT1 and XvDMT2, which are previously uncharacterized 6mA and 5mC DNA MTases, respectively. This study provided new insights into the biological functions of DNA MTases in prokaryotic organisms.
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Affiliation(s)
- Hye-Jee Park
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
- R and D Innovation Center, Seoul Clinical Laboratories, Yongin, South Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Jongchan Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Lynn Heo
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Sang-Wook Han
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
- *Correspondence: Sang-Wook Han
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28
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Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe 2020; 29:94-106.e4. [PMID: 33217332 DOI: 10.1016/j.chom.2020.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/28/2020] [Accepted: 10/26/2020] [Indexed: 01/13/2023]
Abstract
Many bacteria resist invasive DNA by incorporating sequences into CRISPR loci, which enable sequence-specific degradation. CRISPR systems have been well studied from isolate genomes, but culture-independent metagenomics provide a new window into their diversity. We profiled CRISPR loci and cas genes in the body-wide human microbiome using 2,355 metagenomes, yielding functional and taxonomic profiles for 2.9 million spacers by aligning the spacer content to each sample's metagenome and corresponding gene families. Spacer and repeat profiles agree qualitatively with those from isolate genomes but expand their diversity by approximately 13-fold, with the highest spacer load present in the oral microbiome. The taxonomy of spacer sequences parallels that of their source community, with functional targets enriched for viral elements. When coupled with cas gene systems, CRISPR-Cas subtypes are highly site and taxon specific. Our analysis provides a comprehensive collection of natural CRISPR-cas loci and targets in the human microbiome.
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29
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Guo Y, Gu D, Huang T, Cao L, Zhu X, Zhou Y, Wang K, Kang X, Meng C, Jiao X, Pan Z. Essential role of Salmonella Enteritidis DNA adenine methylase in modulating inflammasome activation. BMC Microbiol 2020; 20:226. [PMID: 32723297 PMCID: PMC7389876 DOI: 10.1186/s12866-020-01919-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/21/2020] [Indexed: 01/08/2023] Open
Abstract
Background Salmonella Enteritidis (SE) is one of the major foodborne zoonotic pathogens of worldwide importance which can induce activation of NLRC4 and NLRP3 inflammasomes during infection. Given that the inflammasomes play an essential role in resisting bacterial infection, Salmonella has evolved various strategies to regulate activation of the inflammasome, most of which largely remain unclear. Results A transposon mutant library in SE strain C50336 was screened for the identification of the potential factors that regulate inflammasome activation. We found that T3SS-associated genes invC, prgH, and spaN were required for inflammasome activation in vitro. Interestingly, C50336 strains with deletion or overexpression of Dam were both defective in activation of caspase-1, secretion of IL-1β and phosphorylation of c-Jun N-terminal kinase (Jnk). Transcriptome sequencing (RNA-seq) results showed that most of the differentially expressed genes and enriched KEGG pathways between the C50336-VS-C50336Δdam and C50336-VS-C50336::dam groups overlapped, which includes multiple signaling pathways related to the inflammasome. C50336Δdam and C50336::dam were both found to be defective in suppressing the expression of several anti-inflammasome factors. Moreover, overexpression of Dam in macrophages by lentiviral infection could specifically enhance the activation of NLRP3 inflammasome independently via promoting the Jnk pathway. Conclusions These data indicated that Dam was essential for modulating inflammasome activation during SE infection, there were complex and dynamic interplays between Dam and the inflammasome under different conditions. New insights were provided about the battle between SE and host innate immunological mechanisms.
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Affiliation(s)
- Yaxin Guo
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Dan Gu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tingting Huang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Liyan Cao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinyu Zhu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yi Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Kangru Wang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xilong Kang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Chuang Meng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China. .,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China. .,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, Jiangsu, China. .,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China. .,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China.
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30
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Oliveira PH, Fang G. Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria. Trends Microbiol 2020; 29:28-40. [PMID: 32417228 DOI: 10.1016/j.tim.2020.04.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/19/2020] [Accepted: 04/10/2020] [Indexed: 12/14/2022]
Abstract
An increasing number of studies have reported that bacterial DNA methylation has important functions beyond the roles in restriction-modification systems, including the ability of affecting clinically relevant phenotypes such as virulence, host colonization, sporulation, biofilm formation, among others. Although insightful, such studies have a largely ad hoc nature and would benefit from a systematic strategy enabling a joint functional characterization of bacterial methylomes by the microbiology community. In this opinion article, we propose that highly conserved DNA methyltransferases (MTases) represent a unique opportunity for bacterial epigenomic studies. These MTases are rather common in bacteria, span various taxonomic scales, and are present in multiple human pathogens. Apart from well-characterized core DNA MTases, like those from Vibrio cholerae, Salmonella enterica, Clostridioides difficile, or Streptococcus pyogenes, multiple highly conserved DNA MTases are also found in numerous human pathogens, including those belonging to the genera Burkholderia and Acinetobacter. We discuss why and how these MTases can be prioritized to enable a community-wide, integrative approach for functional epigenomic studies. Ultimately, we discuss how some highly conserved DNA MTases may emerge as promising targets for the development of novel epigenetic inhibitors for biomedical applications.
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Affiliation(s)
- Pedro H Oliveira
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA.
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine, New York, NY, USA.
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31
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The complex phylogenetic relationships of a 4mC/6mA DNA methyltransferase in prokaryotes. Mol Phylogenet Evol 2020; 149:106837. [PMID: 32304827 DOI: 10.1016/j.ympev.2020.106837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
Abstract
DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the complexity of its evolutionary history, we inferred that only one significant shift in molecular evolutionary rate characterizes the diversification of this protein family.
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32
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Ma F, Zhang Q, Zhang CY. Nanomaterial-based biosensors for DNA methyltransferase assay. J Mater Chem B 2020; 8:3488-3501. [DOI: 10.1039/c9tb02458a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We review the recent advances in the development of nanomaterial-based biosensors for DNA methyltransferase assay.
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Affiliation(s)
- Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Qian Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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33
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Li Y, Sun S, Tian X, Qiu JG, Jiang B, Zhang CY. A dumbbell probe-based dual signal amplification strategy for sensitive detection of multiple DNA methyltransferases. Chem Commun (Camb) 2020; 56:13627-13630. [DOI: 10.1039/d0cc05991a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Integration of a dumbbell probe with dual signal amplification enables simultaneously sensitive detection of multiple DNA methyltransferases.
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Affiliation(s)
- Yueying Li
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
| | - Shuli Sun
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
| | - Jian-Ge Qiu
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - BingHua Jiang
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
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34
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Goodhead I, Blow F, Brownridge P, Hughes M, Kenny J, Krishna R, McLean L, Pongchaikul P, Beynon R, Darby AC. Large-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microb Genom 2020; 6:e000285. [PMID: 31922467 PMCID: PMC7067036 DOI: 10.1099/mgen.0.000285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 07/10/2019] [Indexed: 01/30/2023] Open
Abstract
The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple 'omic' strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.
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Affiliation(s)
- Ian Goodhead
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- School of Science, Engineering and Environment, Peel Building, University of Salford, M5 4WT, UK
| | - Frances Blow
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA
| | - Philip Brownridge
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Margaret Hughes
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Ritesh Krishna
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- IBM Research UK, STFC Daresbury Laboratory, Warrington, WA4 4AD, UK
| | - Lynn McLean
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Pisut Pongchaikul
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Rob Beynon
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Alistair C. Darby
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
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Wen J, Liu Y, Li J, Lin H, Zheng Y, Chen Y, Fu X, Chen L. A label-free protamine-assisted colorimetric sensor for highly sensitive detection of S1 nuclease activity. Analyst 2020; 145:2774-2778. [DOI: 10.1039/d0an00060d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free, simple and rapid colorimetric method for the sensitive detection of S1 nuclease activity based on protamine-assisted aggregation of gold nanoparticles.
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Affiliation(s)
- Jiahui Wen
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Yongming Liu
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Jingwen Li
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Hao Lin
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Yiran Zheng
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Yan Chen
- School of Resources and Environmental Engineering
- Shandong Agriculture and Engineering University
- Jinan 250100
- China
| | - Xiuli Fu
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Lingxin Chen
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation
- The Research Center for Coastal Environmental Engineering and Technology
- Yantai Institute of Coastal Zone Research
- Chinese Academy of Sciences
- Yantai 264003
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Park HJ, Lee J, Kim M, Han SW. Profiling Differentially Abundant Proteins by Overexpression of Three Putative Methyltransferases in Xanthomonas axonopodis pv. glycines. Proteomics 2020; 20:e1900125. [PMID: 31693783 DOI: 10.1002/pmic.201900125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 10/10/2019] [Indexed: 11/07/2022]
Abstract
Methyltransferases (MTases) are enzymes that modify specific substrates by adding a methyl group using S-adenosyl-l-methionine. Functions of MTases have been extensively studied in eukaryotic organisms and animal pathogenic bacteria. Despite their importance, mechanisms underlying MTase function in plant pathogenic bacteria have not been studied in depth, as is the case of Xanthomonas axonopodis pv. glycines (Xag) that causes bacterial pustule disease in soybean crops worldwide. Here, the association between Xag proteome alterations and three MTase-overexpressing strains, Xag(XgMT1), Xag(XgMT2), and Xag(XgMT3), compared to Xag carrying an empty vector, Xag(EV) is reported. Using label-free shotgun comparative proteomic analysis, proteins are identified in all three biological replicates of the four strains and ranged from 1004 to 1082. In comparative analyses, 124, 135, and 134 proteins are differentially changed (over twofold) by overexpression of XgMT1, XgMT2, and XgMT3, respectively. These proteins are also categorized using cluster of orthologous group (COG) analyses, allowing postulation of biological mechanisms associated with three MTases in Xag. COGs reveal that the three MTases may play distinct roles, although some functions may overlap. These results are expected to allow new insight into understanding and predicting the biological functions of MTases in plant pathogenic bacteria. Data are available via ProteomeXchange (Identifier PXD012590).
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Affiliation(s)
- Hye-Jee Park
- Department of Plant Science and Technology , Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Jongchan Lee
- Department of Plant Science and Technology , Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Minyoung Kim
- Department of Plant Science and Technology , Chung-Ang University, Anseong, 17456, Republic of Korea
| | - Sang-Wook Han
- Department of Plant Science and Technology , Chung-Ang University, Anseong, 17456, Republic of Korea
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Abstract
In all domains of life, genomes contain epigenetic information superimposed over the nucleotide sequence. Epigenetic signals control DNA-protein interactions and can cause phenotypic change in the absence of mutation. A nearly universal mechanism of epigenetic signalling is DNA methylation. In bacteria, DNA methylation has roles in genome defence, chromosome replication and segregation, nucleoid organization, cell cycle control, DNA repair and regulation of transcription. In many bacterial species, DNA methylation controls reversible switching (phase variation) of gene expression, a phenomenon that generates phenotypic cell variants. The formation of epigenetic lineages enables the adaptation of bacterial populations to harsh or changing environments and modulates the interaction of pathogens with their eukaryotic hosts.
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Payelleville A, Blackburn D, Lanois A, Pagès S, Cambon MC, Ginibre N, Clarke DJ, Givaudan A, Brillard J. Role of the Photorhabdus Dam methyltransferase during interactions with its invertebrate hosts. PLoS One 2019; 14:e0212655. [PMID: 31596856 PMCID: PMC6785176 DOI: 10.1371/journal.pone.0212655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/20/2019] [Indexed: 11/19/2022] Open
Abstract
Photorhabdus luminescens is an entomopathogenic bacterium found in symbiosis with the nematode Heterorhabditis. Dam DNA methylation is involved in the pathogenicity of many bacteria, including P. luminescens, whereas studies about the role of bacterial DNA methylation during symbiosis are scarce. The aim of this study was to determine the role of Dam DNA methylation in P. luminescens during the whole bacterial life cycle including during symbiosis with H. bacteriophora. We constructed a strain overexpressing dam by inserting an additional copy of the dam gene under the control of a constitutive promoter in the chromosome of P. luminescens and then achieved association between this recombinant strain and nematodes. The dam overexpressing strain was able to feed the nematode in vitro and in vivo similarly as a control strain, and to re-associate with Infective Juvenile (IJ) stages in the insect. No difference in the amount of emerging IJs from the cadaver was observed between the two strains. Compared to the nematode in symbiosis with the control strain, a significant increase in LT50 was observed during insect infestation with the nematode associated with the dam overexpressing strain. These results suggest that during the life cycle of P. luminescens, Dam is not involved the bacterial symbiosis with the nematode H. bacteriophora, but it contributes to the pathogenicity of the nemato-bacterial complex.
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Affiliation(s)
| | - Dana Blackburn
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Anne Lanois
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
| | - Sylvie Pagès
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
| | - Marine C. Cambon
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
- Évolution et Diversité Biologique, CNRS, UPS Université Paul Sabatier, Toulouse, France
| | | | - David J. Clarke
- Department of Microbiology, University College Cork, Cork, Ireland
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Li Y, Wang L, Ding C, Luo X. Highly selective ratiometric electrogenerated chemiluminescence assay of DNA methyltransferase activity via polyaniline and anti-fouling peptide modified electrode. Biosens Bioelectron 2019; 142:111553. [DOI: 10.1016/j.bios.2019.111553] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
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40
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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Quantitative Proteomic Analyses of a Pathogenic Strain and Its Highly Passaged Attenuated Strain of Mycoplasma hyopneumoniae. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4165735. [PMID: 31355261 PMCID: PMC6634062 DOI: 10.1155/2019/4165735] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/14/2019] [Accepted: 05/27/2019] [Indexed: 12/21/2022]
Abstract
Mycoplasma hyopneumoniae is the causative agent of porcine enzootic pneumonia, a chronic respiratory disease in swine resulting in enormous economic losses. To identify the components that contribute to virulence and unveil those biological processes potentially related to attenuation, we used isobaric tags for relative and absolute quantification technology (iTRAQ) to compare the protein profiles of the virulent M. hyopneumoniae strain 168 and its attenuated highly passaged strain 168L. We identified 489 proteins in total, 70 of which showing significant differences in level of expression between the two strains. Remarkably, proteins participating in inositol phosphate metabolism were significantly downregulated in the virulent strain, while some proteins involved in nucleoside metabolism were upregulated. We also mined a series of novel promising virulence-associated factors in our study compared with those in previous reports, such as some moonlighting adhesins, transporters, lipoate-protein ligase, and ribonuclease and several hypothetical proteins with conserved functional domains, deserving further research. Our survey constitutes an iTRAQ-based comparative proteomic analysis of a virulent M. hyopneumoniae strain and its attenuated strain originating from a single parent with a well-characterized genetic background and lays the groundwork for future work to mine for potential virulence factors and identify candidate vaccine proteins.
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Forde BM, McAllister LJ, Paton JC, Paton AW, Beatson SA. SMRT sequencing reveals differential patterns of methylation in two O111:H- STEC isolates from a hemolytic uremic syndrome outbreak in Australia. Sci Rep 2019; 9:9436. [PMID: 31263188 PMCID: PMC6602927 DOI: 10.1038/s41598-019-45760-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 05/23/2019] [Indexed: 11/21/2022] Open
Abstract
In 1995 a severe haemolytic-uremic syndrome (HUS) outbreak in Adelaide occurred. A recent genomic analysis of Shiga toxigenic Escherichia coli (STEC) O111:H- strains 95JB1 and 95NR1 from this outbreak found that the more virulent isolate, 95NR1, harboured two additional copies of the Shiga toxin 2 (Stx2) genes encoded within prophage regions. The structure of the Stx2-converting prophages could not be fully resolved using short-read sequence data alone and it was not clear if there were other genomic differences between 95JB1 and 95NR1. In this study we have used Pacific Biosciences (PacBio) single molecule real-time (SMRT) sequencing to characterise the genome and methylome of 95JB1 and 95NR1. We completely resolved the structure of all prophages including two, tandemly inserted, Stx2-converting prophages in 95NR1 that were absent from 95JB1. Furthermore we defined all insertion sequences and found an additional IS1203 element in the chromosome of 95JB1. Our analysis of the methylome of 95NR1 and 95JB1 identified hemi-methylation of a novel motif (5′-CTGCm6AG-3′) in more than 4000 sites in the 95NR1 genome. These sites were entirely unmethylated in the 95JB1 genome, and included at least 177 potential promoter regions that could contribute to regulatory differences between the strains. IS1203 mediated deactivation of a novel type IIG methyltransferase in 95JB1 is the likely cause of the observed differential patterns of methylation between 95NR1 and 95JB1. This study demonstrates the capability of PacBio SMRT sequencing to resolve complex prophage regions and reveal the genetic and epigenetic heterogeneity within a clonal population of bacteria.
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Affiliation(s)
- Brian M Forde
- Australian Infectious Diseases Centre, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lauren J McAllister
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Centre, The University of Queensland, Brisbane, QLD, Australia. .,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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The Leucine-Responsive Regulatory Protein Lrp Participates in Virulence Regulation Downstream of Small RNA ArcZ in Erwinia amylovora. mBio 2019; 10:mBio.00757-19. [PMID: 31138749 PMCID: PMC6538786 DOI: 10.1128/mbio.00757-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Fire blight disease continues to plague the commercial production of apples and pears despite more than a century of research into disease epidemiology and disease control. The causative agent of fire blight, Erwinia amylovora coordinates turning on or off specific virulence-associated traits at the appropriate time during disease development. The development of novel control strategies requires an in-depth understanding of E. amylovora regulatory mechanisms, including regulatory control of virulence-associated traits. This study investigates how the small RNA ArcZ regulates motility at the transcriptional level and identifies the transcription factor Lrp as a novel participant in the regulation of several virulence-associated traits. We report that ArcZ and Lrp together affect key virulence-associated traits through integration of transcriptional and posttranscriptional mechanisms. Further understanding of the topology of virulence regulatory networks can uncover weak points that can subsequently be exploited to control E. amylovora. Erwinia amylovora causes the devastating fire blight disease of apple and pear trees. During systemic infection of host trees, pathogen cells must rapidly respond to changes in their environment as they move through different host tissues that present distinct challenges and sources of nutrition. Growing evidence indicates that small RNAs (sRNAs) play an important role in disease progression as posttranscriptional regulators. The sRNA ArcZ positively regulates the motility phenotype and transcription of flagellar genes in E. amylovora Ea1189 yet is a direct repressor of translation of the flagellar master regulator, FlhD. We utilized transposon mutagenesis to conduct a forward genetic screen and identified suppressor mutations that increase motility in the Ea1189ΔarcZ mutant background. This enabled us to determine that the mechanism of transcriptional activation of the flhDC mRNA by ArcZ is mediated by the leucine-responsive regulatory protein, Lrp. We show that Lrp contributes to expression of virulence and several virulence-associated traits, including production of the exopolysaccharide amylovoran, levansucrase activity, and biofilm formation. We further show that Lrp is regulated posttranscriptionally by ArcZ through destabilization of lrp mRNA. Thus, ArcZ regulation of FlhDC directly and indirectly through Lrp forms an incoherent feed-forward loop that regulates levansucrase activity and motility as outputs. This work identifies Lrp as a novel participant in virulence regulation in E. amylovora and places it in the context of a virulence-associated regulatory network.
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44
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Beaulaurier J, Schadt EE, Fang G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat Rev Genet 2019; 20:157-172. [PMID: 30546107 PMCID: PMC6555402 DOI: 10.1038/s41576-018-0081-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Indeed, as the number of mapped bacterial methylomes approaches 2,000, increasing evidence supports roles for methylation in regulation of gene expression, virulence and pathogen-host interactions.
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Affiliation(s)
- John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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45
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Cui YX, Feng XN, Wang YX, Pan HY, Pan H, Kong DM. An integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity. Chem Sci 2019; 10:2290-2297. [PMID: 30881654 PMCID: PMC6385671 DOI: 10.1039/c8sc05102j] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
DNA methylation is a significant epigenetic mechanism involving processes of transferring a methyl group onto cytosine or adenine. Such DNA modification catalyzed by methyltransferase (MTase) plays important roles in the modulation of gene expression and other cellular activities. Herein, we develop a simple and sensitive biosensing platform for the detection of DNA MTase activity by using only two oligonucleotides. The fluorophore labeled molecular beacon (MB) can be methylated by MTase and subsequently cleaved by endonuclease DpnI at the stem, giving a shortened MB. The shortened MB can then hybridize with a primer DNA, initiating a cycle of strand displacement amplification (SDA) reactions. The obtained SDA products can unfold new MB and initiate another cycle of SDA reaction. Therefore, continuous enlargement of SDA and exponential amplification of the fluorescence signal are achieved. Because the triple functions of substrate, template and probe are elegantly integrated in one oligonucleotide, only two oligonucleotides are necessary for multiple amplification cycles, which not only reduces the complexity of the system, but also overcomes the laborious and cumbersome operation that is always a challenge in conventional methods. This platform exhibits an extremely low limit of detection of 3.3 × 10-6 U mL-1, which is the lowest to our knowledge. The proposed MTase-sensing platform was also demonstrated to perform well in a real-time monitoring mode, which can achieve a further simplified and high-throughput detection. The sensing strategy might be extended to the activity detection of other enzymes, thus showing great application potential in bioanalysis and clinical diagnosis.
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Affiliation(s)
- Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
| | - Xue-Nan Feng
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
| | - Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
| | - Hui-Yu Pan
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Hua Pan
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
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Genome-Wide Analysis of Mycoplasma dispar Provides Insights into Putative Virulence Factors and Phylogenetic Relationships. G3-GENES GENOMES GENETICS 2019; 9:317-325. [PMID: 30573467 PMCID: PMC6385981 DOI: 10.1534/g3.118.200941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mycoplasma dispar is an important pathogen involved in bovine respiratory disease, which causes huge economic losses worldwide. Our knowledge regarding the genomics, pathogenic mechanisms, and genetics of M. dispar is rather limited. In this study, the complete genome of M. dispar GS01 strain was sequenced using PacBio SMRT technology and first genome-wide analyzed. M. dispar GS01 has a single circular chromosome of 1,065,810 bp encoding 825 predicted proteins. Twenty-three potential virulence genes and two pathogenicity islands were identified in M. dispar This pathogen was cytopathogenic, could form prolific biofilms, and could produce a large amount of H2O2 Methylation analysis revealed adenine and cytosine methylation across the genome and 13 distinct nucleotide motifs. Comparative analysis showed a high collinearity relationship between M. dispar GS01 and type strain ATCC 27140. Phylogenetic analysis demonstrated that M. dispar is genetically close to M. flocculare and M. hyopneumoniae The data presented in this study will aid further study on the pathogenic mechanisms and evolution of M. dispar.
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47
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Zhao H, Ma C, Yan Y, Chen M. A sensitive cyclic signal amplification fluorescence strategy for determination of methyltransferase activity based on graphene oxide and RNase H. J Mater Chem B 2019. [DOI: 10.1039/c9tb00743a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A sensitive fluorometric method for DNA methyltransferase activity detection based on graphene oxide and RNase H-assisted signal amplification.
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Affiliation(s)
- Han Zhao
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Changbei Ma
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Ying Yan
- School of Life Sciences
- Central South University
- Changsha 410013
- China
| | - Mingjian Chen
- School of Life Sciences
- Central South University
- Changsha 410013
- China
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Comparative genomic and methylome analysis of non-virulent D74 and virulent Nagasaki Haemophilus parasuis isolates. PLoS One 2018; 13:e0205700. [PMID: 30383795 PMCID: PMC6211672 DOI: 10.1371/journal.pone.0205700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Haemophilus parasuis is a respiratory pathogen of swine and the etiological agent of Glässer's disease. H. parasuis isolates can exhibit different virulence capabilities ranging from lethal systemic disease to subclinical carriage. To identify genomic differences between phenotypically distinct strains, we obtained the closed whole-genome sequence annotation and genome-wide methylation patterns for the highly virulent Nagasaki strain and for the non-virulent D74 strain. Evaluation of the virulence-associated genes contained within the genomes of D74 and Nagasaki led to the discovery of a large number of toxin-antitoxin (TA) systems within both genomes. Five predicted hemolysins were identified as unique to Nagasaki and seven putative contact-dependent growth inhibition toxin proteins were identified only in strain D74. Assessment of all potential vtaA genes revealed thirteen present in the Nagasaki genome and three in the D74 genome. Subsequent evaluation of the predicted protein structure revealed that none of the D74 VtaA proteins contain a collagen triple helix repeat domain. Additionally, the predicted protein sequence for two D74 VtaA proteins is substantially longer than any predicted Nagasaki VtaA proteins. Fifteen methylation sequence motifs were identified in D74 and fourteen methylation sequence motifs were identified in Nagasaki using SMRT sequencing analysis. Only one of the methylation sequence motifs was observed in both strains indicative of the diversity between D74 and Nagasaki. Subsequent analysis also revealed diversity in the restriction-modification systems harbored by D74 and Nagasaki. The collective information reported in this study will aid in the development of vaccines and intervention strategies to decrease the prevalence and disease burden caused by H. parasuis.
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Xu X, Wang L, Li X, Cui W, Jiang W. Multiple sealed primers-mediated rolling circle amplification strategy for sensitive and specific detection of DNA methyltransferase activity. Talanta 2018; 194:282-288. [PMID: 30609532 DOI: 10.1016/j.talanta.2018.09.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/20/2018] [Accepted: 09/30/2018] [Indexed: 01/19/2023]
Abstract
DNA methyltransferase (MTase) aberrant expression has a close relationship to tumorigenesis. DNA MTase activity detection is of great importance to its biomedical research and theranostics study. Here, multiple sealed primers-mediated rolling circle amplification (RCA) strategy is developed for sensitively and specifically detecting DNA MTase activity. The DNA probe has a folded, double-loop structure that seals multiple primers. First, in the presence of DNA MTase, the DNA probe is methylated, which then gets cleaved by the restriction endonuclease and breaks into multiple DNA oligonucleotide fragments. Second, each DNA oligonucleotide fragment acts as an independent primer for triggering RCA reaction respectively, producing long DNA strands that contain several interval G-quadruplexes. Finally, copious of G-quadruplexes are obtained, which bind N-methylmesoporphyrin IX (NMM) to generate significantly enhanced fluorescence. When DNA MTase is absent or inactive, the DNA probe is stable and cannot release the primers for RCA reaction. In the proposed strategy, the action of DNA MTase on one DNA probe is converted to the multiple amplifications triggered by multiple released primers. The detection limit for Dam MTase is down to 0.0085 U/mL, and the target MTase can be well discriminated from its MTases analogues. The method is utilized in screening of Dam MTase inhibitors and analyzing of spiked Dam MTase in biological samples. The results suggest that the strategy may provide a promising tool for DNA MTase activity detection in biomedical research and cancer theranostics.
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Affiliation(s)
- Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China
| | - Lei Wang
- School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng 252059, PR China
| | - Wanling Cui
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China.
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Payelleville A, Legrand L, Ogier JC, Roques C, Roulet A, Bouchez O, Mouammine A, Givaudan A, Brillard J. The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines. Sci Rep 2018; 8:12091. [PMID: 30108278 PMCID: PMC6092372 DOI: 10.1038/s41598-018-30620-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/03/2018] [Indexed: 01/01/2023] Open
Abstract
DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (>94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium's lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.
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Affiliation(s)
| | - Ludovic Legrand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Céline Roques
- GeT-PlaGe, INRA, US 1426, Genotoul, Castanet-Tolosan, France
| | - Alain Roulet
- GeT-PlaGe, INRA, US 1426, Genotoul, Castanet-Tolosan, France
| | - Olivier Bouchez
- GeT-PlaGe, INRA, US 1426, Genotoul, Castanet-Tolosan, France
| | - Annabelle Mouammine
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH1015, Switzerland
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