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Weinroth MD, Clawson ML, Harhay GP, Eppinger M, Harhay DM, Smith TPL, Bono JL. Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition. Front Microbiol 2023; 14:1303387. [PMID: 38169669 PMCID: PMC10758439 DOI: 10.3389/fmicb.2023.1303387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.
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Affiliation(s)
- Margaret D. Weinroth
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Michael L. Clawson
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Gregory P. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Dayna M. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Timothy P. L. Smith
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - James L. Bono
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
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2
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Carter MQ, Quiñones B, He X, Pham A, Carychao D, Cooley MB, Lo CC, Chain PSG, Lindsey RL, Bono JL. Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California. Microorganisms 2023; 11:2803. [PMID: 38004814 PMCID: PMC10673567 DOI: 10.3390/microorganisms11112803] [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: 09/16/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains isolated from wild birds in a major agricultural region in California. Shiga toxin genes stx2f were present in all avian strains. Pangenome analyses of 20 complete genomes revealed a total of 11,249 genes, of which nearly 80% were accessory genes. Both core gene-based phylogenetic and accessory gene-based relatedness analyses consistently grouped the three stx2f-positive clinical strains with the five avian strains carrying ST7971. Among the three Stx2f-converting prophage integration sites identified, ssrA was the most common one. Besides the locus of enterocyte effacement and type three secretion system, the high pathogenicity island, OI-122, and type six secretion systems were identified. Substantial strain variation in virulence gene repertoire, Shiga toxin production, and cytotoxicity were revealed. Six avian strains exhibited significantly higher cytotoxicity than that of stx2f-positive E. coli, and three of them exhibited a comparable level of cytotoxicity with that of enterohemorrhagic E. coli outbreak strains, suggesting that wild birds could serve as a reservoir of E. albertii strains with great potential to cause severe diseases in humans.
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Affiliation(s)
- Michelle Qiu Carter
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Xiaohua He
- Foodborne Toxin Detection and Prevention Research Unit, U.S. Department of Agriculture, Western Regional Research Center, Albany, CA 94710, USA;
| | - Antares Pham
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Diana Carychao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Michael B. Cooley
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (B.Q.); (A.P.); (D.C.); (M.B.C.)
| | - Chien-Chi Lo
- Biosecurity and Public Health Group, U.S. Department of Energy, Los Alamos National Laboratory, Santa Fe, NM 87545, USA; (C.-C.L.); (P.S.G.C.)
| | - Patrick S. G. Chain
- Biosecurity and Public Health Group, U.S. Department of Energy, Los Alamos National Laboratory, Santa Fe, NM 87545, USA; (C.-C.L.); (P.S.G.C.)
| | - Rebecca L. Lindsey
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;
| | - James L. Bono
- Meat Safety and Quality Research Unit, U.S. Department of Agriculture, U.S. Meat Animal Research Center, Clay Center, NE 68933, USA;
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3
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Abbas Z, Rehman MU, Tayara H, Chong KT. ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion. Bioinformatics 2023; 39:btad664. [PMID: 37929975 PMCID: PMC10639035 DOI: 10.1093/bioinformatics/btad664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/20/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
MOTIVATION The origins of replication sites (ORIs) are precise regions inside the DNA sequence where the replication process begins. These locations are critical for preserving the genome's integrity during cell division and guaranteeing the faithful transfer of genetic data from generation to generation. The advent of experimental techniques has aided in the discovery of ORIs in many species. Experimentation, on the other hand, is often more time-consuming and pricey than computational approaches, and it necessitates specific equipment and knowledge. Recently, ORI sites have been predicted using computational techniques like motif-based searches and artificial intelligence algorithms based on sequence characteristics and chromatin states. RESULTS In this article, we developed ORI-Explorer, a unique artificial intelligence-based technique that combines multiple feature engineering techniques to train CatBoost Classifier for recognizing ORIs from four distinct eukaryotic species. ORI-Explorer was created by utilizing a unique combination of three traditional feature-encoding techniques and a feature set obtained from a deep-learning neural network model. The ORI-Explorer has significantly outperformed current predictors on the testing dataset. Furthermore, by employing the sophisticated SHapley Additive exPlanation method, we give crucial insights that aid in comprehending model success, highlighting the most relevant features vital for forecasting cell-specific ORIs. ORI-Explorer is also intended to aid community-wide attempts in discovering potential ORIs and developing innovative verifiable biological hypotheses. AVAILABILITY AND IMPLEMENTATION The used datasets along with the source code are made available through https://github.com/Z-Abbas/ORI-Explorer and https://zenodo.org/record/8358679.
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Affiliation(s)
- Zeeshan Abbas
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Mobeen Ur Rehman
- Khalifa University Center for Autonomous Robotic Systems (KUCARS), Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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Dong MJ, Luo H, Gao F. DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes. Nucleic Acids Res 2022; 51:D117-D120. [PMID: 36305822 PMCID: PMC9825612 DOI: 10.1093/nar/gkac964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 01/29/2023] Open
Abstract
DoriC was first launched in 2007 as a database of replication origins (oriCs) in bacterial genomes and has since been constantly updated to integrate the latest research progress in this field. The database was subsequently extended to include the oriCs in archaeal genomes as well as those in plasmids. This latest release, DoriC 12.0, includes the oriCs in both draft and complete prokaryotic genomes. At the same time, the number of oriCs in the database has also increased significantly and currently contains over 200 000 bacterial entries distributed in more than 40 phyla. Among them, a large number are from bacteria in new phyla whose oriCs were not explored before. Additionally, new oriC features and improvements have been introduced, especially in the visualization and analysis of oriCs. Currently, DoriC is considered as an important database in the fields of bioinformatics, microbial genomics, and even synthetic biology, providing a valuable resource as well as a comprehensive platform for the research on oriCs. DoriC 12.0 can be accessed at https://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/.
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Affiliation(s)
| | | | - Feng Gao
- To whom correspondence should be addressed. Tel: +86 22 27404118; Fax: +86 22 27404118;
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Dong MJ, Luo H, Gao F. Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1207-1213. [PMID: 36257484 DOI: 10.1016/j.gpb.2022.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 12/26/2022]
Abstract
The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated at genomic loci referred to as replication origins (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriCs in 2008 called Ori-Finder, which contributes to clarify the characteristics of bacterial oriCs. The oriCs of hundreds of sequenced bacterial genomes have been annotated in the genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of oriCs. This has facilitated large-scale data mining of functional elements in oriCs and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of oriCs are integrated into the updated framework, which has also been redesigned to predict oriCs in draft genomes. The interactive visualization module displays more genomic information related to oriCs and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses. The redesigned interface provides additional customization options for oriC prediction. Ori-Finder 2022 is freely available at http://tubic.tju.edu.cn/Ori-Finder/ and https://tubic.org/Ori-Finder/.
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Affiliation(s)
- Mei-Jing Dong
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.
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6
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Comparative Genomics of Escherichia coli Serotype O55:H7 Using Complete Closed Genomes. Microorganisms 2022; 10:microorganisms10081545. [PMID: 36013963 PMCID: PMC9413875 DOI: 10.3390/microorganisms10081545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 12/01/2022] Open
Abstract
Escherichia coli O55:H7 is a human foodborne pathogen and is recognized as the progenitor strain of E. coli O157:H7. While this strain is important from a food safety and genomic evolution standpoint, much of the genomic diversity of E. coli O55:H7 has been demonstrated using draft genomes. Here, we combine the four publicly available E. coli O55:H7 closed genomes with six newly sequenced closed genomes to provide context to this strain’s genomic diversity. We found significant diversity within the 10 E. coli O55:H7 strains that belonged to three different sequence types. The prophage content was about 10% of the genome, with three prophages common to all strains and seven unique to one strain. Overall, there were 492 insertion sequences identified within the six new sequence strains, with each strain on average containing 75 insertions (range 55 to 114). A total of 31 plasmids were identified between all isolates (range 1 to 6), with one plasmid (pO55) having an identical phylogenetic tree as the chromosome. The release and comparison of these closed genomes provides new insight into E. coli O55:H7 diversity and its ability to cause disease in humans.
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7
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Yao Y, Zhang S, Xue T. Integrating LASSO Feature Selection and Soft Voting Classifier to Identify Origins of Replication Sites. Curr Genomics 2022; 23:83-93. [PMID: 36778978 PMCID: PMC9878833 DOI: 10.2174/1389202923666220214122506] [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] [Received: 09/30/2021] [Revised: 12/11/2021] [Accepted: 01/18/2022] [Indexed: 11/22/2022] Open
Abstract
Background: DNA replication plays an indispensable role in the transmission of genetic information. It is considered to be the basis of biological inheritance and the most fundamental process in all biological life. Considering that DNA replication initiates with a special location, namely the origin of replication, a better and accurate prediction of the origins of replication sites (ORIs) is essential to gain insight into the relationship with gene expression. Objective: In this study, we have developed an efficient predictor called iORI-LAVT for ORIs identification. Methods: This work focuses on extracting feature information from three aspects, including mono-nucleotide encoding, k-mer and ring-function-hydrogen-chemical properties. Subsequently, least absolute shrinkage and selection operator (LASSO) as a feature selection is applied to select the optimal features. Comparing the different combined soft voting classifiers results, the soft voting classifier based on GaussianNB and Logistic Regression is employed as the final classifier. Results: Based on 10-fold cross-validation test, the prediction accuracies of two benchmark datasets are 90.39% and 95.96%, respectively. As for the independent dataset, our method achieves high accuracy of 91.3%. Conclusion: Compared with previous predictors, iORI-LAVT outperforms the existing methods. It is believed that iORI-LAVT predictor is a promising alternative for further research on identifying ORIs.
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Affiliation(s)
- Yingying Yao
- School of Mathematics and Statistics, Xidian University, Xi’an 710071, P.R. China
| | - Shengli Zhang
- School of Mathematics and Statistics, Xidian University, Xi’an 710071, P.R. China,Address correspondence to this author at the School of Mathematics and Statistics, Xidian University, Xi’an 710071, P.R. China; Tel/Fax: +86-29- 88202860; E-mail:
| | - Tian Xue
- School of Mathematics and Statistics, Xidian University, Xi’an 710071, P.R. China
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8
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Hertel R, Schöne K, Mittelstädt C, Meißner J, Zschoche N, Collignon M, Kohler C, Friedrich I, Schneider D, Hoppert M, Kuhn R, Schwedt I, Scholz P, Poehlein A, Martienssen M, Ischebeck T, Daniel R, Commichau FM. Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:70-84. [PMID: 34786867 DOI: 10.1111/1758-2229.13022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate-resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate-sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia.
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Affiliation(s)
- Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Kerstin Schöne
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Carolin Mittelstädt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Janek Meißner
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Nick Zschoche
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Madeline Collignon
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Christian Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ines Friedrich
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Michael Hoppert
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Ramona Kuhn
- Chair of Biotechnology of Water Treatment, Institute of Environmental Technology, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Inge Schwedt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Patricia Scholz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, Göttingen, 37077, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Marion Martienssen
- Chair of Biotechnology of Water Treatment, Institute of Environmental Technology, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, Göttingen, 37077, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
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9
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Shahid M, Ilyas M, Hussain W, Khan YD. ORI-Deep: improving the accuracy for predicting origin of replication sites by using a blend of features and long short-term memory network. Brief Bioinform 2022; 23:6511972. [PMID: 35048955 DOI: 10.1093/bib/bbac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 11/14/2022] Open
Abstract
Replication of DNA is an important process for the cell division cycle, gene expression regulation and other biological evolution processes. It also has a crucial role in a living organism's physical growth and structure. Replication of DNA comprises of three stages known as initiation, elongation and termination, whereas the origin of replication sites (ORI) is the location of initiation of the DNA replication process. There exist various methodologies to identify ORIs in the genomic sequences, however, these methods have used either extensive computations for execution, or have limited optimization for the large datasets. Herein, a model called ORI-Deep is proposed to identify ORIs from the multiple cell type genomic sequence benchmark data. An efficient method is proposed using a deep neural network to identify ORIs for four different eukaryotic species. For better representation of data, a feature vector is constructed using statistical moments for the training and testing of data and is further fed to a long short-term memory (LSTM) network. To prove the effectiveness of the proposed model, we applied several validation techniques at different levels to obtain seven accuracy metrics, and the accuracy score for self-consistency, 10-fold cross-validation, jackknife and the independent set test is observed to be 0.977, 0.948, 0.976 and 0.977, respectively. Based on the results, it can be concluded that ORI-Deep can efficiently predict the sites of origin replication in DNA sequence with high accuracy. Webserver for ORI-Deep is available at (https://share.streamlit.io/waqarhusain/orideep/main/app.py), whereas source code is available at (https://github.com/WaqarHusain/OriDeep).
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Affiliation(s)
- Mahwish Shahid
- School of Systems and Technologies, University of Management and Technology, Lahore, Pakistan
| | - Maham Ilyas
- University of Management and Technology, Lahore, Pakistan
| | - Waqar Hussain
- University of Management and Technology, Lahore, Pakistan
| | - Yaser Daanial Khan
- Department of Computer Science, University of Management and Technology, Lahore, Pakistan
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10
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Hermankova K, Kourilova X, Pernicova I, Bezdicek M, Lengerova M, Obruca S, Sedlar K. Complete Genome Sequence of the Type Strain Tepidimonas taiwanensis LMG 22826T, a Thermophilic Alkaline Protease and Polyhydroxyalkanoate Producer. Genome Biol Evol 2021; 13:6462190. [PMID: 34908127 PMCID: PMC8715522 DOI: 10.1093/gbe/evab280] [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] [Accepted: 12/09/2021] [Indexed: 11/20/2022] Open
Abstract
Tepidimonas taiwanensis is a moderately thermophilic, Gram-negative, rod-shaped, chemoorganoheterotrophic, motile bacterium. The alkaline protease producing type strain T. taiwanensis LMG 22826T was recently reported to also be a promising producer of polyhydroxyalkanoates (PHAs)—renewable and biodegradable polymers representing an alternative to conventional plastics. Here, we present its first complete genome sequence which is also the first complete genome sequence of the whole species. The genome consists of a single 2,915,587-bp-long circular chromosome with GC content of 68.75%. Genome annotation identified 2,764 genes in total while 2,634 open reading frames belonged to protein-coding genes. Although functional annotation of the genome and division of genes into Clusters of Orthologous Groups (COGs) revealed a relatively high number of 694 genes with unknown function or unknown COG, the majority of genes were assigned a function. Most of the genes, 406 in total, were involved in energy production and conversion, and amino acid transport and metabolism. Moreover, particular key genes involved in the metabolism of PHA were identified. Knowledge of the genome in connection with the recently reported ability to produce bioplastics from the waste stream of wine production makes T. taiwanensis LMG 22826T, an ideal candidate for further genome engineering as a bacterium with high biotechnological potential.
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Affiliation(s)
- Kristyna Hermankova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Czech Republic
| | - Xenie Kourilova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Czech Republic
| | - Iva Pernicova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Martina Lengerova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Czech Republic
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Czech Republic.,Department of Informatics, Institute of Bioinformatics, Ludwig-Maximilians-Universität München, Germany
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11
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Fitzgerald SF, Lupolova N, Shaaban S, Dallman TJ, Greig D, Allison L, Tongue SC, Evans J, Henry MK, McNeilly TN, Bono JL, Gally DL. Genome structural variation in Escherichia coli O157:H7. Microb Genom 2021; 7. [PMID: 34751643 PMCID: PMC8743559 DOI: 10.1099/mgen.0.000682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.
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Affiliation(s)
- Stephen F Fitzgerald
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Nadejda Lupolova
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David Greig
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Sue C Tongue
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Madeleine K Henry
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 OPZ, UK
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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12
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Amadio A, Bono JL, Irazoqui M, Larzábal M, Marques da Silva W, Eberhardt MF, Riviere NA, Gally D, Manning SD, Cataldi A. Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle. PLoS One 2021; 16:e0258753. [PMID: 34710106 PMCID: PMC8553066 DOI: 10.1371/journal.pone.0258753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cattle are the main reservoir of Enterohemorrhagic Escherichia coli (EHEC), with O157:H7 the distinctive serotype. EHEC is the main causative agent of a severe systemic disease, Hemolytic Uremic Syndrome (HUS). Argentina has the highest pediatric HUS incidence worldwide with 12–14 cases per 100,000 children. Herein, we assessed the genomes of EHEC O157:H7 isolates recovered from cattle in the humid Pampas of Argentina. According to phylogenetic studies, EHEC O157 can be divided into clades. Clade 8 strains that were classified as hypervirulent. Most of the strains of this clade have a Shiga toxin stx2a-stx2c genotype. To better understand the molecular bases related to virulence, pathogenicity and evolution of EHEC O157:H7, we performed a comparative genomic analysis of these isolates through whole genome sequencing. The isolates classified as clade 8 (four strains) and clade 6 (four strains) contained 13 to 16 lambdoid prophages per genome, and the observed variability of prophages was analysed. An inter strain comparison show that while some prophages are highly related and can be grouped into families, other are unique. Prophages encoding for stx2a were highly diverse, while those encoding for stx2c were conserved. A cluster of genes exclusively found in clade 8 contained 13 genes that mostly encoded for DNA binding proteins. In the studied strains, polymorphisms in Q antiterminator, the Q-stx2A intergenic region and the O and P γ alleles of prophage replication proteins are associated with different levels of Stx2a production. As expected, all strains had the pO157 plasmid that was highly conserved, although one strain displayed a transposon interruption in the protease EspP gene. This genomic analysis may contribute to the understanding of the genetic basis of the hypervirulence of EHEC O157:H7 strains circulating in Argentine cattle. This work aligns with other studies of O157 strain variation in other populations that shows key differences in Stx2a-encoding prophages.
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Affiliation(s)
- Ariel Amadio
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - James L. Bono
- U.S Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, United States of America
| | - Matías Irazoqui
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - Mariano Larzábal
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - Wanderson Marques da Silva
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | | | - Nahuel A. Riviere
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - David Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Shannon D. Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Angel Cataldi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
- * E-mail:
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13
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Wu K, Cheng ZH, Williams E, Turner NT, Ran D, Li H, Zhou X, Guo H, Sung W, Liu DF, Lynch M, Long H. Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains. Genome Biol Evol 2021; 13:evab148. [PMID: 34180992 PMCID: PMC8350357 DOI: 10.1093/gbe/evab148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Microbial strains with high genomic stability are particularly sought after for testing the quality of commercial microbiological products, such as biological media and antibiotics. Yet, using mutation-accumulation experiments and de novo assembled complete genomes based on Nanopore long-read sequencing, we find that the widely used quality-control strain Shewanella putrefaciens ATCC-8071, also a facultative pathogen, is a hypermutator, with a base-pair substitution mutation rate of 2.42 × 10-8 per nucleotide site per cell division, ∼146-fold greater than that of the wild-type strain CGMCC-1.6515. Using complementation experiments, we confirm that mutL dysfunction, which was a recent evolutionary event, is the cause for the high mutation rate of ATCC-8071. Further analyses also give insight into possible relationships between mutation and genome evolution in this important bacterium. This discovery of a well-known strain being a hypermutator necessitates screening the mutation rate of bacterial strains before any quality control or experiments.
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Affiliation(s)
- Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhou-Hua Cheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Emily Williams
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Nathan T Turner
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Dapeng Ran
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Haichao Li
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Xia Zhou
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Huilin Guo
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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14
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Complete Closed Genome Sequence of the Extremely Heat-Resistant Strain Escherichia coli AW1.7. Microbiol Resour Announc 2021; 10:e0050221. [PMID: 34292065 PMCID: PMC8297447 DOI: 10.1128/mra.00502-21] [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] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli isolate AW1.7 is an extremely heat-resistant bacterium and has been widely used as a reference strain in extreme heat resistance studies for almost a decade. Here, we report its complete closed genome sequence.
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15
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Zayulina KS, Elcheninov AG, Toshchakov SV, Kochetkova TV, Novikov AA, Blamey JM, Kublanov IV. Novel hyperthermophilic crenarchaeon Infirmifilum lucidum gen. nov. sp. nov., reclassification of Thermofilum uzonense as Infirmifilum uzonense comb. nov. and assignment of the family Thermofilaceae to the order Thermofilales ord. nov. Syst Appl Microbiol 2021; 44:126230. [PMID: 34293647 DOI: 10.1016/j.syapm.2021.126230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 02/01/2023]
Abstract
A novel hyperthermophilic crenarchaeon, strain 3507LTT, was isolated from a terrestrial hot spring near Tinguiririca volcano, Chile. Cells were non-motile thin, slightly curved filamentous rods. It grew at 73-93 °C and pH range of 5 to 7.5 with an optimum at 85 °C and pH 6.0-6.7. The presence of culture broth filtrate of another hyperthemophilic archaeon as well as yeast extract was obligatory for growth of the novel isolate. Strain 3507LTT is an anaerobic chemoorganoheterotroph, fermenting monosaccharides, disaccharides and polysaccharides (lichenan, starch, xanthan gum, xyloglucan, alpha-cellulose and amorphous cellulose). No growth stimulation was detected when nitrate, thiosulfate, selenate or elemental sulfur were added as the electron acceptors. The complete genome of strain 3507LTT consisted of a single circular chromosome with size of 1.63 Mbp. The DNA G+C content was 53.9%. According to the 16S rRNA gene sequence as well as conserved protein sequences phylogenetic analyses, strain 3507LTT together with Thermofilum uzonense formed a separate cluster within a Thermofilaceae family (Thermoproteales/Thermoprotei/Crenarchaeota). Based on phenotypic characteristics, phylogeny as well as AAI comparisons, a novel genus and species Infirmifilum lucidum strain 3507LTT (=VKM B-3376T = KCTC 15797T) gen. nov. sp. nov. was proposed. Its closest relative, Thermofilum uzonense strain 1807-2T should be reclassified as Infirmifilum uzonense strain 1807-2T comb. nov. Finally, based on phylogenomic and comparative genome analyses of representatives of Thermofilaceae family and other representatives of Thermoproteales order, a proposal of transfer of the family Thermofilaceae into a separate order Thermofilales ord. nov. was made.
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Affiliation(s)
- Kseniya S Zayulina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Andrei A Novikov
- Gubkin University, 65-1, Leninsky prospect, 119991 Moscow, Russia
| | - Jenny M Blamey
- Fundacion Biociencia, Jose Domingo Cañas, 2280 Ñuñoa, Santiago, Chile; Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Estación Central, Santiago, Chile
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
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16
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Tan X, Wu X, Han M, Wang L, Xu L, Li B, Yuan Y. Yeast autonomously replicating sequence (ARS): Identification, function, and modification. Eng Life Sci 2021. [DOI: 10.1002/elsc.202000085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xiao‐Yu Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Xiao‐Le Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Ming‐Zhe Han
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Li Xu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Bing‐Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Ying‐Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
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17
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Chashchina GV, Shchyolkina AK, Kolosov SV, Beniaminov AD, Kaluzhny DN. Recurrent Potential G-Quadruplex Sequences in Archaeal Genomes. Front Microbiol 2021; 12:647851. [PMID: 33868206 PMCID: PMC8044849 DOI: 10.3389/fmicb.2021.647851] [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] [Received: 12/30/2020] [Accepted: 03/03/2021] [Indexed: 11/23/2022] Open
Abstract
Evolutionary conservation or over-representation of the potential G-quadruplex sequences (PQS) in genomes are usually considered as a sign of the functional relevance of these sequences. However, uneven base distribution (GC-content) along the genome may along the genome may result in seeming abundance of PQSs over average in the genome. Apart from this, a number of other conserved functional signals that are encoded in the GC-rich genomic regions may inadvertently result in emergence of G-quadruplex compatible sequences. Here, we analyze the genomes of archaea focusing our search to repetitive PQS (rPQS) motifs within each organism. The probability of occurrence of several identical PQSs within a relatively short archaeal genome is low and, thus, the structure and genomic location of such rPQSs may become a direct indication of their functionality. We have found that the majority of the genomes of Methanomicrobiaceae family of archaea contained multiple copies of the interspersed highly similar PQSs. Short oligonucleotides corresponding to the rPQS formed the G-quadruplex (G4) structure in presence of potassium ions as demonstrated by circular dichroism (CD) and enzymatic probing. However, further analysis of the genomic context for the rPQS revealed a 10–12 nt cytosine-rich track adjacent to 3'-end of each rPQS. Synthetic DNA fragments that included the C-rich track tended to fold into alternative structures such as hairpin structure and antiparallel triplex that were in equilibrium with G4 structure depending on the presence of potassium ions in solution. Structural properties of the found repetitive sequences, their location in the genomes of archaea, and possible functions are discussed.
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Affiliation(s)
- Galina V Chashchina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna K Shchyolkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Simon V Kolosov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Artemy D Beniaminov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry N Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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18
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Locus of Heat Resistance (LHR) in Meat-Borne Escherichia coli: Screening and Genetic Characterization. Appl Environ Microbiol 2021; 87:AEM.02343-20. [PMID: 33483306 DOI: 10.1128/aem.02343-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022] Open
Abstract
Microbial resistance to processing treatments poses a food safety concern, as treatment tolerant pathogens can emerge. Occasional foodborne outbreaks caused by pathogenic Escherichia coli have led to human and economic losses. Therefore, this study screened for the extreme heat resistance (XHR) phenotype as well as one known genetic marker, the locus of heat resistance (LHR), in 4,123 E. coli isolates from diverse meat animals at different processing stages. The prevalences of XHR and LHR among the meat-borne E. coli were found to be 10.3% and 11.4%, respectively, with 19% agreement between the two. Finished meat products showed the highest LHR prevalence (24.3%) compared to other processing stages (0 to 0.6%). None of the LHR+ E. coli in this study would be considered pathogens based on screening for virulence genes. Four high-quality genomes were generated by whole-genome sequencing of representative LHR+ isolates. Nine horizontally acquired LHRs were identified and characterized, four plasmid-borne and five chromosomal. Nine newly identified LHRs belong to ClpK1 LHR or ClpK2 LHR variants sharing 61 to 68% nucleotide sequence identity, while one LHR appears to be a hybrid. Our observations suggest positive correlation between the number of LHR regions present in isolates and the extent of heat resistance. The isolate exhibiting the highest degree of heat resistance possessed four LHRs belonging to three different variant groups. Maintenance of as many as four LHRs in a single genome emphasizes the benefits of the LHR in bacterial physiology and stress response.IMPORTANCE Currently, a "multiple-hurdle" approach based on a combination of different antimicrobial interventions, including heat, is being utilized during meat processing to control the burden of spoilage and pathogenic bacteria. Our recent study (M. Guragain, G. E. Smith, D. A. King, and J. M. Bosilevac, J Food Prot 83:1438-1443, 2020, https://doi.org/10.4315/JFP-20-103) suggests that U.S. beef cattle harbor Escherichia coli that possess the locus of heat resistance (LHR). LHR seemingly contributes to the global stress tolerance in bacteria and hence poses a food safety concern. Therefore, it is important to understand the distribution of the LHRs among meat-borne bacteria identified at different stages of different meat processing systems. Complete genome sequencing and comparative analysis of selected heat-resistant bacteria provide a clearer understanding of stress and heat resistance mechanisms. Further, sequencing data may offer a platform to gain further insights into the genetic background that provides optimal bacterial tolerance against heat and other processing treatments.
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19
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Wu F, Yang R, Zhang C, Zhang L. A deep learning framework combined with word embedding to identify DNA replication origins. Sci Rep 2021; 11:844. [PMID: 33436981 PMCID: PMC7804333 DOI: 10.1038/s41598-020-80670-x] [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: 10/23/2020] [Accepted: 12/24/2020] [Indexed: 01/29/2023] Open
Abstract
The DNA replication influences the inheritance of genetic information in the DNA life cycle. As the distribution of replication origins (ORIs) is the major determinant to precisely regulate the replication process, the correct identification of ORIs is significant in giving an insightful understanding of DNA replication mechanisms and the regulatory mechanisms of genetic expressions. For eukaryotes in particular, multiple ORIs exist in each of their gene sequences to complete the replication in a reasonable period of time. To simplify the identification process of eukaryote's ORIs, most of existing methods are developed by traditional machine learning algorithms, and target to the gene sequences with a fixed length. Consequently, the identification results are not satisfying, i.e. there is still great room for improvement. To break through the limitations in previous studies, this paper develops sequence segmentation methods, and employs the word embedding technique, 'Word2vec', to convert gene sequences into word vectors, thereby grasping the inner correlations of gene sequences with different lengths. Then, a deep learning framework to perform the ORI identification task is constructed by a convolutional neural network with an embedding layer. On the basis of the analysis of similarity reduction dimensionality diagram, Word2vec can effectively transform the inner relationship among words into numerical feature. For four species in this study, the best models are obtained with the overall accuracy of 0.975, 0.765, 0.885, 0.967, the Matthew's correlation coefficient of 0.940, 0.530, 0.771, 0.934, and the AUC of 0.975, 0.800, 0.888, 0.981, which indicate that the proposed predictor has a stable ability and provide a high confidence coefficient to classify both of ORIs and non-ORIs. Compared with state-of-the-art methods, the proposed predictor can achieve ORI identification with significant improvement. It is therefore reasonable to anticipate that the proposed method will make a useful high throughput tool for genome analysis.
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Affiliation(s)
- Feng Wu
- School of Mechanical, Electrical and Information Engineering, Shandong University at Weihai, Weihai, 264200, China
| | - Runtao Yang
- School of Mechanical, Electrical and Information Engineering, Shandong University at Weihai, Weihai, 264200, China.
| | - Chengjin Zhang
- School of Mechanical, Electrical and Information Engineering, Shandong University at Weihai, Weihai, 264200, China
| | - Lina Zhang
- School of Mechanical, Electrical and Information Engineering, Shandong University at Weihai, Weihai, 264200, China
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20
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Complete Genome Sequence of a Hyperthermophilic Archaeon, Thermosphaera sp. Strain 3507, Isolated from a Chilean Hot Spring. Microbiol Resour Announc 2020; 9:9/50/e01262-20. [PMID: 33303673 PMCID: PMC7729421 DOI: 10.1128/mra.01262-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A complete genome sequence of a hyperthermophilic archaeon, Thermosphaera sp. strain 3507, which was isolated from a Chilean hot spring, is presented. The genome is 1,305,106 bp with a G+C content of 47.6%. Twenty-seven carbohydrate-active enzyme genes were identified, which is in accordance with the ability of the strain to grow on various polysaccharides. A complete genome sequence of a hyperthermophilic archaeon, Thermosphaera sp. strain 3507, which was isolated from a Chilean hot spring, is presented. The genome is 1,305,106 bp with a G+C content of 47.6%. Twenty-seven carbohydrate-active enzyme genes were identified, which is in accordance with the ability of the strain to grow on various polysaccharides.
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21
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Manavalan B, Basith S, Shin TH, Lee G. Computational prediction of species-specific yeast DNA replication origin via iterative feature representation. Brief Bioinform 2020; 22:6000361. [PMID: 33232970 PMCID: PMC8294535 DOI: 10.1093/bib/bbaa304] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/13/2022] Open
Abstract
Deoxyribonucleic acid replication is one of the most crucial tasks taking place in the cell, and it has to be precisely regulated. This process is initiated in the replication origins (ORIs), and thus it is essential to identify such sites for a deeper understanding of the cellular processes and functions related to the regulation of gene expression. Considering the important tasks performed by ORIs, several experimental and computational approaches have been developed in the prediction of such sites. However, existing computational predictors for ORIs have certain curbs, such as building only single-feature encoding models, limited systematic feature engineering efforts and failure to validate model robustness. Hence, we developed a novel species-specific yeast predictor called yORIpred that accurately identify ORIs in the yeast genomes. To develop yORIpred, we first constructed optimal 40 baseline models by exploring eight different sequence-based encodings and five different machine learning classifiers. Subsequently, the predicted probability of 40 models was considered as the novel feature vector and carried out iterative feature learning approach independently using five different classifiers. Our systematic analysis revealed that the feature representation learned by the support vector machine algorithm (yORIpred) could well discriminate the distribution characteristics between ORIs and non-ORIs when compared with the other four algorithms. Comprehensive benchmarking experiments showed that yORIpred achieved superior and stable performance when compared with the existing predictors on the same training datasets. Furthermore, independent evaluation showcased the best and accurate performance of yORIpred thus underscoring the significance of iterative feature representation. To facilitate the users in obtaining their desired results without undergoing any mathematical, statistical or computational hassles, we developed a web server for the yORIpred predictor, which is available at: http://thegleelab.org/yORIpred.
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Affiliation(s)
| | - Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Republic of Korea
| | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Republic of Korea
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Republic of Korea
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22
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Microbiota of the Therapeutic Euganean Thermal Muds with a Focus on the Main Cyanobacteria Species. Microorganisms 2020; 8:microorganisms8101590. [PMID: 33076380 PMCID: PMC7650686 DOI: 10.3390/microorganisms8101590] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/17/2022] Open
Abstract
The Euganean Thermal District has been known since Roman times for the therapeutic properties of peloids, obtained from natural clays that have undergone a traditional maturation process. This leads to the growth of a green microbial biofilm with Cyanobacteria and the target species Phormidium sp. ETS-05 as fundamental components for their ability to synthetize anti-inflammatory molecules. Currently, in-depth studies on the microbiota colonizing Euganean peloids, as in general on peloids utilized worldwide, are missing. This is the first characterization of the microbial community of Euganean thermal muds, also investigating the effects of environmental factors on its composition. We analysed 53 muds from 29 sites (Spas) using a polyphasic approach, finding a stable microbiota peculiar to the area. Differences among mud samples mainly depended on two parameters: water temperature and shading of mud maturation plants. In the range 37-47 °C and in the case of irradiance attenuation due to the presence of protective roofs, a statistically significant higher mud Chl a content was detected. Moreover, in these conditions, a characteristic microbial and Cyanobacteria population composition dominated by Phormidium sp. ETS-05 was observed. We also obtained the complete genome sequence of this target species using a mixed sequencing approach based on Illumina and Nanopore sequencing.
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Prathiviraj R, Chellapandi P. Comparative genomic analysis reveals starvation survival systems in Methanothermobacter thermautotrophicus ΔH. Anaerobe 2020; 64:102216. [PMID: 32504807 DOI: 10.1016/j.anaerobe.2020.102216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Methanothermobacter thermautotrophicus ΔH (MTH) is a thermophilic hydrogenotrophic methanogenic archaeon capable of reducing CO2 with H2 to produce methane gas. It is the potential candidate in the biomethanation of CO2 and CO in anaerobic reactors and biogas upgrading process. However, systematic studies addressing its genome conservation and function remain scant in this genome. In this study, we have evaluated its evolutionary resemblance and metabolic discrepancy, particularly in starvation survival systems by comparing the genomic contexts with Methanothermobacter marburgensis str. Marburg (MMG) and Methanobacterium formicicum DSM 1535 (MFO). The phylogenomic analysis of this study indicated that there was a strong phylogenomic signal among MTH, MMG, and MFO in the whole-genome tree. DNA replication machinery was conserved in the MTH genome and might have evolved at different evolution rates. Genome synteny analysis observed collinearity of either gene orders or gene families has to be maintained with syntenic blocks located in the syntenic out-paralogs. A genome-wide metabolic analysis identified some unique putative metabolic subsystems in MTH, which are proposed to determine its growth characteristics in diverse environments. MTH genome comprised of 93 unique genes-coding for starvation survival and stress-response proteins. These proteins confer its adaptation to nutritional deprivation and other abiotic stresses. MTH has a typical system to withstand its growth and cell viability during stable operation and recovery after prolonged starvation. Thus, the present work will provide an insight to improve the genome refinement and metabolic reconstruction in parallel to other closely related species.
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Affiliation(s)
- R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India.
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Beta-Lactam Sensitive Bacteria Can Acquire ESBL-Resistance via Conjugation after Long-Term Exposure to Lethal Antibiotic Concentration. Antibiotics (Basel) 2020; 9:antibiotics9060296. [PMID: 32498393 PMCID: PMC7345503 DOI: 10.3390/antibiotics9060296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/05/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
Beta-lactams are commonly used antibiotics that prevent cell-wall biosynthesis. Beta-lactam sensitive bacteria can acquire conjugative resistance elements and hence become resistant even after being exposed to lethal (above minimum inhibitory) antibiotic concentrations. Here we show that neither the length of antibiotic exposure (1 to 16 h) nor the beta-lactam type (penam or cephem) have a major impact on the rescue of sensitive bacteria. We demonstrate that an evolutionary rescue can occur between different clinically relevant bacterial species (Klebsiella pneumoniae and Escherichia coli) by plasmids that are commonly associated with extended-spectrum beta-lactamase (ESBL) positive hospital isolates. As such, it is possible that this resistance dynamic may play a role in failing antibiotic therapies in those cases where resistant bacteria may readily migrate into the proximity of sensitive pathogens. Furthermore, we engineered a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-plasmid to encode a guiding CRISPR-RNA against the migrating ESBL-plasmid. By introducing this plasmid into the sensitive bacterium, the frequency of the evolutionarily rescued bacteria decreased by several orders of magnitude. As such, engineering pathogens during antibiotic treatment may provide ways to prevent ESBL-plasmid dispersal and hence resistance evolution.
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25
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Luo H, Gao F. DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Res 2020; 47:D74-D77. [PMID: 30364951 PMCID: PMC6323995 DOI: 10.1093/nar/gky1014] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007. DoriC 5.0, an updated database of oriC regions in both bacterial and archaeal genomes, was published in the 2013 Nucleic Acids Research database issue. Now, the latest release DoriC 10, a large-scale update of replication origins in prokaryotic genomes including chromosomes and plasmids, has been presented with a completely redesigned user interface, which is freely available at http://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/. In the current release, the database of DoriC has made significant improvements compared with version 5.0 as follows: (i) inclusion of oriCs on more bacterial chromosomes increased from 1633 to 7580; (ii) inclusion of oriCs on more archaeal chromosomes increased from 86 to 226; (iii) inclusion of 1209 plasmid replication origins retrieved from NCBI annotations or predicted by in silico analysis; (iv) inclusion of more replication origin elements on bacterial chromosomes including DnaA-trio motifs. Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication origin predictions.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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26
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Sperlea T, Muth L, Martin R, Weigel C, Waldminghaus T, Heider D. gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning. Sci Rep 2020; 10:6727. [PMID: 32317695 PMCID: PMC7174414 DOI: 10.1038/s41598-020-63424-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/31/2020] [Indexed: 01/23/2023] Open
Abstract
The biology of bacterial cells is, in general, based on information encoded on circular chromosomes. Regulation of chromosome replication is an essential process that mostly takes place at the origin of replication (oriC), a locus unique per chromosome. Identification of high numbers of oriC is a prerequisite for systematic studies that could lead to insights into oriC functioning as well as the identification of novel drug targets for antibiotic development. Current methods for identifying oriC sequences rely on chromosome-wide nucleotide disparities and are therefore limited to fully sequenced genomes, leaving a large number of genomic fragments unstudied. Here, we present gammaBOriS (Gammaproteobacterial oriC Searcher), which identifies oriC sequences on gammaproteobacterial chromosomal fragments. It does so by employing motif-based machine learning methods. Using gammaBOriS, we created BOriS DB, which currently contains 25,827 gammaproteobacterial oriC sequences from 1,217 species, thus making it the largest available database for oriC sequences to date. Furthermore, we present gammaBOriTax, a machine-learning based approach for taxonomic classification of oriC sequences, which was trained on the sequences in BOriS DB. Finally, we extracted the motifs relevant for identification and classification decisions of the models. Our results suggest that machine learning sequence classification approaches can offer great support in functional motif identification.
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Affiliation(s)
- Theodor Sperlea
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany
| | - Lea Muth
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany
| | - Roman Martin
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany
| | - Christoph Weigel
- Institute of Biotechnology, Faculty III, Technische Universität Berlin (TUB), Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Torsten Waldminghaus
- Chromosome Biology Group, LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35043, Marburg, Lahn, Germany
| | - Dominik Heider
- Faculty of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, D-35032, Marburg, Lahn, Germany.
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27
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Dao FY, Lv H, Zulfiqar H, Yang H, Su W, Gao H, Ding H, Lin H. A computational platform to identify origins of replication sites in eukaryotes. Brief Bioinform 2020; 22:1940-1950. [PMID: 32065211 DOI: 10.1093/bib/bbaa017] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
The locations of the initiation of genomic DNA replication are defined as origins of replication sites (ORIs), which regulate the onset of DNA replication and play significant roles in the DNA replication process. The study of ORIs is essential for understanding the cell-division cycle and gene expression regulation. Accurate identification of ORIs will provide important clues for DNA replication research and drug development by developing computational methods. In this paper, the first integrated predictor named iORI-Euk was built to identify ORIs in multiple eukaryotes and multiple cell types. In the predictor, seven eukaryotic (Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, Pichia pastoris, Schizosaccharomyces pombe and Kluyveromyces lactis) ORI data was collected from public database to construct benchmark datasets. Subsequently, three feature extraction strategies which are k-mer, binary encoding and combination of k-mer and binary were used to formulate DNA sequence samples. We also compared the different classification algorithms' performance. As a result, the best results were obtained by using support vector machine in 5-fold cross-validation test and independent dataset test. Based on the optimal model, an online web server called iORI-Euk (http://lin-group.cn/server/iORI-Euk/) was established for the novel ORI identification.
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Affiliation(s)
- Fu-Ying Dao
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Hao Lv
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Hasan Zulfiqar
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Hui Yang
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Wei Su
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Hui Gao
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Hui Ding
- Center for Informational Biology at University of Electronic Science and Technology of China
| | - Hao Lin
- Center for Informational Biology at University of Electronic Science and Technology of China
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28
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Campanaro S, Treu L, Rodriguez-R LM, Kovalovszki A, Ziels RM, Maus I, Zhu X, Kougias PG, Basile A, Luo G, Schlüter A, Konstantinidis KT, Angelidaki I. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:25. [PMID: 32123542 PMCID: PMC7038595 DOI: 10.1186/s13068-020-01679-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/08/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository. RESULTS Here, 134 publicly available metagenomes derived from different biogas reactors were used to recover 1635 metagenome-assembled genomes (MAGs) representing different biogas bacterial and archaeal species. All genomes were estimated to be > 50% complete and nearly half ≥ 90% complete with ≤ 5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth dynamics for microbes involved in different steps of the food chain. CONCLUSIONS The outcome of this study highlights a high flexibility of the biogas microbiome, allowing it to modify its composition and to adapt to the environmental conditions, including temperatures and a wide range of substrates. Our findings enhance our mechanistic understanding of the AD microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.
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Affiliation(s)
- Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padua, Italy
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Luis M. Rodriguez-R
- School of Civil & Environmental Engineering and School of Biological Sciences (Adjunct), Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512 USA
| | - Adam Kovalovszki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ryan M. Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, BC Canada
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Xinyu Zhu
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Panagiotis G. Kougias
- Hellenic Agricultural Organization DEMETER, Soil and Water Resources Institute, Thermi-Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padua, Italy
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Andreas Schlüter
- Hellenic Agricultural Organization DEMETER, Soil and Water Resources Institute, Thermi-Thessaloniki, Greece
| | - Konstantinos T. Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences (Adjunct), Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332-0512 USA
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Liu B, Chen S, Yan K, Weng F. iRO-PsekGCC: Identify DNA Replication Origins Based on Pseudo k-Tuple GC Composition. Front Genet 2019; 10:842. [PMID: 31620165 PMCID: PMC6759546 DOI: 10.3389/fgene.2019.00842] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/13/2019] [Indexed: 11/22/2022] Open
Abstract
Identification of replication origins is playing a key role in understanding the mechanism of DNA replication. This task is of great significance in DNA sequence analysis. Because of its importance, some computational approaches have been introduced. Among these predictors, the iRO-3wPseKNC predictor is the first discriminative method that is able to correctly identify the entire replication origins. For further improving its predictive performance, we proposed the Pseudo k-tuple GC Composition (PsekGCC) approach to capture the "GC asymmetry bias" of yeast species by considering both the GC skew and the sequence order effects of k-tuple GC Composition (k-GCC) in this study. Based on PseKGCC, we proposed a new predictor called iRO-PsekGCC to identify the DNA replication origins. Rigorous jackknife test on two yeast species benchmark datasets (Saccharomyces cerevisiae, Pichia pastoris) indicated that iRO-PsekGCC outperformed iRO-3wPseKNC. It can be anticipated that iRO-PsekGCC will be a useful tool for DNA replication origin identification. Availability and implementation: The web-server for the iRO-PsekGCC predictor was established, and it can be accessed at http://bliulab.net/iRO-PsekGCC/.
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Affiliation(s)
- Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China
| | - Shengyu Chen
- School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, United States
| | - Ke Yan
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China
| | - Fan Weng
- School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, China
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30
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Wang D, Gao F. Comprehensive Analysis of Replication Origins in Saccharomyces cerevisiae Genomes. Front Microbiol 2019; 10:2122. [PMID: 31572328 PMCID: PMC6753640 DOI: 10.3389/fmicb.2019.02122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 08/29/2019] [Indexed: 12/15/2022] Open
Abstract
DNA replication initiates from multiple replication origins (ORIs) in eukaryotes. Discovery and characterization of replication origins are essential for a better understanding of the molecular mechanism of DNA replication. In this study, the features of autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae have been comprehensively analyzed as follows. Firstly, we carried out the analysis of the ARSs available in S. cerevisiae S288C. By evaluating the sequence similarity of experimentally established ARSs, we found that 94.32% of ARSs are unique across the whole genome of S. cerevisiae S288C and those with high sequence similarity are prone to locate in subtelomeres. Subsequently, we built a non-redundant dataset with a total of 520 ARSs, which are based on ARSs annotation of S. cerevisiae S288C from SGD and then supplemented with those from OriDB and DeOri databases. We conducted a large-scale comparison of ORIs among the diverse budding yeast strains from a population genomics perspective. We found that 82.7% of ARSs are not only conserved in genomic sequence but also relatively conserved in chromosomal position. The non-conserved ARSs tend to distribute in the subtelomeric regions. We also conducted a pan-genome analysis of ARSs among the S. cerevisiae strains, and a total of 183 core ARSs existing in all yeast strains were determined. We extracted the genes adjacent to replication origins among the 104 yeast strains to examine whether there are differences in their gene functions. The result showed that the genes involved in the initiation of DNA replication, such as orc3, mcm2, mcm4, mcm6, and cdc45, are conservatively located adjacent to the replication origins. Furthermore, we found the genes adjacent to conserved ARSs are significantly enriched in DNA binding, enzyme activity, transportation, and energy, whereas for the genes adjacent to non-conserved ARSs are significantly enriched in response to environmental stress, metabolites biosynthetic process and biosynthesis of antibiotics. In general, we characterized the replication origins from the genome-wide and population genomics perspectives, which would provide new insights into the replication mechanism of S. cerevisiae and facilitate the design of algorithms to identify genome-wide replication origins in yeast.
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Affiliation(s)
- Dan Wang
- Department of Physics, School of Science, Tianjin University, Tianjin, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
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31
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Sakai HD, Kurosawa N. Complete genome sequence of the Sulfodiicoccus acidiphilus strain HS-1 T, the first crenarchaeon that lacks polB3, isolated from an acidic hot spring in Ohwaku-dani, Hakone, Japan. BMC Res Notes 2019; 12:444. [PMID: 31331368 PMCID: PMC6647314 DOI: 10.1186/s13104-019-4488-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/17/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Sulfodiicoccus acidiphilus HS-1T is the type species of the genus Sulfodiicoccus, a thermoacidophilic archaeon belonging to the order Sulfolobales (class Thermoprotei; phylum Crenarchaeota). While S. acidiphilus HS-1T shares many common physiological and phenotypic features with other Sulfolobales species, the similarities in their 16S rRNA gene sequences are less than 89%. In order to know the genomic features of S. acidiphilus HS-1T in the order Sulfolobales, we determined and characterized the genome of this strain. RESULTS The circular genome of S. acidiphilus HS-1T is comprised of 2353,189 bp with a G+C content of 51.15 mol%. A total of 2459 genes were predicted, including 2411 protein coding and 48 RNA genes. The notable genomic features of S. acidiphilus HS-1T in Sulfolobales species are the absence of genes for polB3 and the autotrophic carbon fixation pathway, and the distribution pattern of essential genes and sequences related to genomic replication initiation. These insights contribute to an understanding of archaeal genomic diversity and evolution.
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Affiliation(s)
- Hiroyuki D Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan.,Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, 102-8471, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan.
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32
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Lou C, Zhao J, Shi R, Wang Q, Zhou W, Wang Y, Wang G, Huang L, Feng X, Zhou F. sefOri: selecting the best-engineered sequence features to predict DNA replication origins. Bioinformatics 2019; 36:49-55. [DOI: 10.1093/bioinformatics/btz506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/25/2019] [Accepted: 06/13/2019] [Indexed: 01/08/2023] Open
Abstract
AbstractMotivationCell divisions start from replicating the double-stranded DNA, and the DNA replication process needs to be precisely regulated both spatially and temporally. The DNA is replicated starting from the DNA replication origins. A few successful prediction models were generated based on the assumption that the DNA replication origin regions have sequence level features like physicochemical properties significantly different from the other DNA regions.ResultsThis study proposed a feature selection procedure to further refine the classification model of the DNA replication origins. The experimental data demonstrated that as large as 26% improvement in the prediction accuracy may be achieved on the yeast Saccharomyces cerevisiae. Moreover, the prediction accuracies of the DNA replication origins were improved for all the four yeast genomes investigated in this study.Availability and implementationThe software sefOri version 1.0 was available at http://www.healthinformaticslab.org/supp/resources.php. An online server was also provided for the convenience of the users, and its web link may be found in the above-mentioned web page.Supplementary informationSupplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chenwei Lou
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Jian Zhao
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Ruoyao Shi
- BioKnow Health Informatics Lab, College of Life Sciences, Jilin University, Changchun 130012, China
| | - Qian Wang
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Wenyang Zhou
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Yubo Wang
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun 130012, China
| | - Lan Huang
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Xin Feng
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Fengfeng Zhou
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
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33
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Li XM, Kang YX, Lin L, Jia EH, Piao DR, Jiang H, Zhang CC, He J, Chang YF, Guo XK, Zhu Y. Genomic Characterization Provides New Insights for Detailed Phage- Resistant Mechanism for Brucella abortus. Front Microbiol 2019; 10:917. [PMID: 31130926 PMCID: PMC6510165 DOI: 10.3389/fmicb.2019.00917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/11/2019] [Indexed: 01/18/2023] Open
Abstract
As the causative agent of cattle brucellosis, Brucella abortus commonly exhibits smooth phenotype (by virtue of colony morphology) that is characteristically sensitive to specific Brucella phages, playing until recently a major role in taxonomical classification of the Brucella species by the phage typing approach. We previously reported the discrepancy between traditional phenotypic typing and MLVA results of a smooth phage-resistant (SPR) strain Bab8416 isolated from a 45-year-old custodial worker with brucellosis in a cattle farm. Here, we performed whole genome sequencing and further obtained a complete genome sequence of strain Bab8416 by a combination of multiple NGS technologies and routine PCR sequencing. The detailed genetic differences between B. abortus SPR Bab8416 and large smooth phage-sensitive (SPS) strains were investigated in a comprehensively comparative genomic study. The large indels between B. abortus SPS strains and Bab8416 showed possible divergence between two evolutionary branches at a far phylogenetic node. Compared to B. abortus SPS strain 9-941 (Bab9-941), the specific re-arrangement event in Bab8416 displaying a closer linear relationship with B. melitensis 16M than other B. abortus strains resulted in the truncation of c-di-GMP synthesis, and 3 c-di-GMP-metabolizing genes, were present in Bab8416 and B. melitensis 16M, but absent in Bab9-941 and other B. abortus strains, indicating potential SPR-associated key determinants and novel molecular mechanisms. Moreover, despite almost completely intact smooth LPS related genes, only one mutated OmpA family protein of Bab8416, functionally related to flagellar and efflux pump, was newly identified. Several point mutations were identified to be Bab8416 specific while a majority of them were verified to be B. abortus ST2 characteristic. In conclusion, our study therefore identifies new SPR-associated factors that could play a role in refining and updating Brucella taxonomic schemes and provides resources for further detailed analysis of mechanism for Brucella phage resistance.
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Affiliation(s)
- Xu-Ming Li
- Stake Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yao-Xia Kang
- Baotou Municipal Center for Disease Control and Prevention, Baotou, China
| | - Liang Lin
- Baotou Municipal Center for Disease Control and Prevention, Baotou, China
| | - En-Hou Jia
- Baotou Municipal Center for Disease Control and Prevention, Baotou, China
| | - Dong-Ri Piao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Hai Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Cui-Cai Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China
| | - Jin He
- Stake Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Xiao-Kui Guo
- Department of Immunology and Microbiology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - YongZhang Zhu
- Department of Immunology and Microbiology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Dao FY, Lv H, Wang F, Feng CQ, Ding H, Chen W, Lin H. Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique. Bioinformatics 2018; 35:2075-2083. [DOI: 10.1093/bioinformatics/bty943] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Fu-Ying Dao
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lv
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fang Wang
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Chao-Qin Feng
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hui Ding
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wei Chen
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hao Lin
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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35
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Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1. 3 Biotech 2018; 8:472. [PMID: 30456006 DOI: 10.1007/s13205-018-1498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/01/2018] [Indexed: 12/27/2022] Open
Abstract
Mobile genetic elements involved in mediating horizontal transfer events contribute to bacterial evolution, and bacterial genomic plasticity and instability result in variation in functional genetic information in Streptomyces secondary metabolism. In a previous study, we reported the complete genome sequence of the industrial Streptomyces strain F613-1, which produces high yields of clavulanic acid. In this study, we used comparative genomics and bioinformatics to investigate the unique genomic features of this strain. Taken together, comparative genomics were used to systematically investigate secondary metabolism capabilities and indicated that frequent exchange of genetic materials between Streptomyces replicons may shape the remarkable diversities in their secondary metabolite repertoires. Moreover, a 136.9-kb giant region of plasticity (RGP) was found in the F613-1 chromosome, and the chromosome and plasmid pSCL4 are densely packed with an exceptionally large variety of potential secondary metabolic gene clusters, involving several determinants putatively accounting for antibiotic production. In addition, the differences in the architecture and size of plasmid pSCL4 between F613-1 and ATCC 27064 suggest that the pSCL4 plasmid could evolve from pSCL4-like and pSCL2-like extrachromosomal replicons. Furthermore, the genomic analyses revealed that strain F613-1 has developed specific genomic architectures and genetic patterns that are well suited to meet the requirements of industrial innovation processes.
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Wang X, Xie Y, Li G, Liu J, Li X, Tian L, Sun J, Ou HY, Qu H. Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374. Virulence 2018; 9:510-521. [PMID: 29338592 PMCID: PMC5955473 DOI: 10.1080/21505594.2017.1421894] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hypervirulent K. pneumoniae variants (hvKP) have been increasingly reported worldwide, causing metastasis of severe infections such as liver abscesses and bacteremia. The capsular serotype K2 hvKP strains show diverse multi-locus sequence types (MLSTs), but with limited genetics and virulence information. In this study, we report a hypermucoviscous K. pneumoniae strain, RJF293, isolated from a human bloodstream sample in a Chinese hospital. It caused a metastatic infection and fatal septic shock in a critical patient. The microbiological features and genetic background were investigated with multiple approaches. The Strain RJF293 was determined to be multilocis sequence type (ST) 374 and serotype K2, displayed a median lethal dose (LD50) of 1.5 × 102 CFU in BALB/c mice and was as virulent as the ST23 K1 serotype hvKP strain NTUH-K2044 in a mouse lethality assay. Whole genome sequencing revealed that the RJF293 genome codes for 32 putative virulence factors and exhibits a unique presence/absence pattern in comparison to the other 105 completely sequenced K. pneumoniae genomes. Whole genome SNP-based phylogenetic analysis revealed that strain RJF293 formed a single clade, distant from those containing either ST66 or ST86 hvKP. Compared to the other sequenced hvKP chromosomes, RJF293 contains several strain-variable regions, including one prophage, one ICEKp1 family integrative and conjugative element and six large genomic islands. The sequencing of the first complete genome of an ST374 K2 hvKP clinical strain should reinforce our understanding of the epidemiology and virulence mechanisms of this bloodstream infection-causing hvKP with clinical significance.
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Affiliation(s)
- Xiaoli Wang
- a Department of Critical Care Medicine , Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Yingzhou Xie
- b State Key Laboratory of Microbial Metabolism , Joint International Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai , China
| | - Gang Li
- c Department of Laboratory Medicine , Jinshan Hospital, Shanghai Medical College, Fudan University , Shanghai , China.,d Department of Laboratory Medicine , Huashan Hospital, Shanghai Medical College, Fudan University , Shanghai , China
| | - Jialin Liu
- a Department of Critical Care Medicine , Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Xiaobin Li
- b State Key Laboratory of Microbial Metabolism , Joint International Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai , China
| | - Lijun Tian
- a Department of Critical Care Medicine , Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Jingyong Sun
- e Department of Clinical Microbiology , Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Hong-Yu Ou
- b State Key Laboratory of Microbial Metabolism , Joint International Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai , China
| | - Hongping Qu
- a Department of Critical Care Medicine , Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai , China
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Liu B, Weng F, Huang DS, Chou KC. iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC. Bioinformatics 2018; 34:3086-3093. [DOI: 10.1093/bioinformatics/bty312] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/18/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China
- Gordon Life Science Institute, Belmont, MA, USA
| | - Fan Weng
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Belmont, MA, USA
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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38
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Genomic and physiological analyses of an indigenous strain, Enterococcus faecium 17OM39. Funct Integr Genomics 2018; 18:385-399. [PMID: 29556852 DOI: 10.1007/s10142-018-0596-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 02/16/2018] [Accepted: 02/26/2018] [Indexed: 12/30/2022]
Abstract
The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity. The strain was able to tolerate bile salts and showed bile salt hydrolytic (BSH) activity, exopolysaccharide production and adherence to human HT-29 cell line. Importantly, partial haemolytic activity was detected and the strain was susceptible to the human serum. Genomics investigation of strain 17OM39 revealed the presence of diverse genes encoding for proteolytic enzymes, stress response systems and the ability to produce essential amino acids, vitamins and antimicrobial compound Bacteriocin-A. No virulence factors and plasmids were found in this genome of the strain 17OM39. Collectively, these physiological and genomic features of 17OM39 confirm the potential of this strain as a candidate probiotic.
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39
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Atanasova NS, Heiniö CH, Demina TA, Bamford DH, Oksanen HM. The Unexplored Diversity of Pleolipoviruses: The Surprising Case of Two Viruses with Identical Major Structural Modules. Genes (Basel) 2018; 9:genes9030131. [PMID: 29495629 PMCID: PMC5867852 DOI: 10.3390/genes9030131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 01/01/2023] Open
Abstract
Extremely halophilic Archaea are the only known hosts for pleolipoviruses which are pleomorphic non-lytic viruses resembling cellular membrane vesicles. Recently, pleolipoviruses have been acknowledged by the International Committee on Taxonomy of Viruses (ICTV) as the first virus family that contains related viruses with different DNA genomes. Genomic diversity of pleolipoviruses includes single-stranded and double-stranded DNA molecules and their combinations as linear or circular molecules. To date, only eight viruses belong to the family Pleolipoviridae. In order to obtain more information about the diversity of pleolipoviruses, further isolates are needed. Here we describe the characterization of a new halophilic virus isolate, Haloarcula hispanica pleomorphic virus 4 (HHPV4). All pleolipoviruses and related proviruses contain a conserved core of approximately five genes designating this virus family, but the sequence similarity among different isolates is low. We demonstrate that over half of HHPV4 genome is identical to the genome of pleomorphic virus HHPV3. The genomic regions encoding known virion components are identical between the two viruses, but HHPV4 includes unique genetic elements, e.g., a putative integrase gene. The co-evolution of these two viruses demonstrates the presence of high recombination frequency in halophilic microbiota and can provide new insights considering links between viruses, membrane vesicles, and plasmids.
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Affiliation(s)
- Nina S Atanasova
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
- Finnish Meteorological Institute; Erik Palménin aukio 1, FI-00101 Helsinki, Finland.
| | - Camilla H Heiniö
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Tatiana A Demina
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Dennis H Bamford
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Hanna M Oksanen
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
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40
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Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M, Rossel C, Pfeifer K, Schleper C. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome. Front Microbiol 2018; 9:28. [PMID: 29434576 PMCID: PMC5797428 DOI: 10.3389/fmicb.2018.00028] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.
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Affiliation(s)
- Sophie S Abby
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Laboratoire Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Centre National de la Recherche Scientifique, Université Grenoble Alpes, Grenoble, France
| | - Michael Melcher
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Melina Kerou
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Michaela Stieglmeier
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Claudia Rossel
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kevin Pfeifer
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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42
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Li J, Qian S, Xiong L, Zhu C, Shu M, Wang J, Jiao Y, He H, Zhang F, Linhardt RJ, Zhong W. Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY-Q. Front Microbiol 2017; 8:2085. [PMID: 29163390 PMCID: PMC5674928 DOI: 10.3389/fmicb.2017.02085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/11/2017] [Indexed: 12/21/2022] Open
Abstract
Microbial degradation of nicotine is an important process to control nicotine residues in the aqueous environment. In this study, a high active nicotine degradation strain named Pseudomonas sp. JY-Q was isolated from tobacco waste extract (TWE). This strain could completely degrade 5.0 g l−1 nicotine in 24 h under optimal culture conditions, and it showed some tolerance even at higher concentrations (10.0 g l−1) of nicotine. The complete genome of JY-Q was sequenced to understand the mechanism by which JY-Q could degrade nicotine and tolerate such high nicotine concentrations. Comparative genomic analysis indicated that JY-Q degrades nicotine through putative novel mechanisms. Two candidate gene cluster duplications located separately at distant loci were predicted to be responsible for nicotine degradation. These two nicotine (Nic) degradation-related loci (AA098_21325—AA098_21340, AA098_03885—AA098_03900) exhibit nearly completely consistent gene organization and component synteny. The nicotinic acid (NA) degradation gene cluster (AA098_17770–AA098_17790) and Nic-like clusters were both predicted to be flanked by mobile genetic elements (MGE). Furthermore, we analyzed the regions of genomic plasticity (RGP) in the JY-Q strain and found a dynamic genome carrying a type VI secretion system (T6SS) that promotes nicotine metabolism and tolerance based on transcriptomics and used in silico methods to identify the T6SS effector protein. Thus, a novel nicotine degradation mechanism was elucidated for Pseudomonas sp. JY-Q, suggesting its potential application in the bioremediation of nicotine-contaminated environments, such as TWEs.
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Affiliation(s)
- Jun Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Shulan Qian
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Lie Xiong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Chengyun Zhu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Ming Shu
- Technology Center, China Tobacco Zhejiang Industrial Co., Ltd., Hangzhou, China
| | - Jie Wang
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yang Jiao
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Houlong He
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Fuming Zhang
- Departments of Chemical and Biological Engineering, Biological Science, Chemistry and Chemical Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Robert J Linhardt
- Departments of Chemical and Biological Engineering, Biological Science, Chemistry and Chemical Biology and Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Weihong Zhong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Wagner S, Lupolova N, Gally DL, Argyle SA. Convergence of plasmid architectures drives emergence of multi-drug resistance in a clonally diverse Escherichia coli population from a veterinary clinical care setting. Vet Microbiol 2017; 211:6-14. [PMID: 29102123 PMCID: PMC5680696 DOI: 10.1016/j.vetmic.2017.09.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/17/2017] [Accepted: 09/20/2017] [Indexed: 12/27/2022]
Abstract
Multi-drug resistant E. coli associated with urinary tract infections in dogs have a commensal strain background. Beta-lactam resistance is associated with blaCMY-2 located exclusively on a highly clonal IncI1 plasmid. IncI1 plasmids carried no other identifiable resistance genes. Isolates in some cases carried up to 5 plasmids, responsible for carriage of the additional resistances.
The purpose of this study was to determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs. Illumina and single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible. This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype. Plasmid-mediated AmpC (CMY-2) beta-lactamase resistance was associated with a clonal group of IncI1 plasmids that has remained stable in isolates collected up to a decade apart. Other plasmids, in particular those with an IncF replicon type, contained other resistance gene markers, so that the emergence of these MDR strains was driven by the accumulation of multiple plasmids, up to 5 replicons in specific cases. This study indicates that vulnerable patients, often with complex clinical histories provide a setting leading to the emergence of MDR E. coli strains in clonally distinct commensal backgrounds. While it is known that horizontally-transferred resistance supplements uropathogenic strains of E. coli such as ST131, our study demonstrates that the selection of an MDR phenotype in commensal E. coli strains can result in opportunistic infections in vulnerable patient populations. These strains provide a reservoir for the onward transfer of resistance alleles into more typically pathogenic strains and provide opportunities for the coalition of resistance and virulence determinants on plasmids as evidenced by the IncF replicons characterised in this study.
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Affiliation(s)
- Sam Wagner
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Roslin, Midlothian, United Kingdom
| | - Nadejda Lupolova
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Roslin, Midlothian, United Kingdom
| | - David L Gally
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Roslin, Midlothian, United Kingdom
| | - Sally A Argyle
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Roslin, Midlothian, United Kingdom.
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44
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Complete Genome Sequences of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311, Isolated from Fermented Meat Products. GENOME ANNOUNCEMENTS 2017; 5:5/38/e00915-17. [PMID: 28935727 PMCID: PMC5609406 DOI: 10.1128/genomea.00915-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311 were sequenced and assembled using PacBio single-molecule real-time (SMRT) technology. The strains were isolated from Swiss fermented meat products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95 Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.
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Yu Z, Ma Y, Zhong W, Qiu J, Li J. Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles. Front Microbiol 2017; 8:1278. [PMID: 28744269 PMCID: PMC5504354 DOI: 10.3389/fmicb.2017.01278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 12/22/2022] Open
Abstract
Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.
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Affiliation(s)
- Zhiliang Yu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Yunting Ma
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Weihong Zhong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Juanping Qiu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Jun Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong UniversityShanghai, China
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Wang Q, Sun J, Li J, Ding Y, Li XP, Lin J, Hassan B, Feng Y. Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs. MICROBIOME 2017; 5:70. [PMID: 28683827 PMCID: PMC5500976 DOI: 10.1186/s40168-017-0288-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Polymyxin is a cationic polypeptide antibiotic that can disrupt bacterial cell membrane by interacting with its lipopolysaccharide molecules and is used as a last resort drug against lethal infections by the carbapenem-resistant superbugs (like NDM-1). However, global discovery of the MCR-1 colistin resistance dramatically challenges the newly renewed interest in colistin for clinical use. METHODS The mcr-1-harboring plasmids were acquired from swine and human Escherichia coli isolated in China, from 2015 to 2016, and subjected to Illumina PacBio RSII and Hi-Seq2000 for full genome sequencing. PCR was applied to close the gap of the assembled contigs. Ori-Finder was employed to predict the replication origin (oriC) in plasmids. The phenotype of MCR-1-producing isolates was evaluated on the LBA plates with various level of colistin. Genetic deletion was used to test the requirement of the initial "ATG" codon for the MCR-1 function. RESULTS Here, we report full genomes of over 10 mcr-1-harboring plasmids with diversified replication incompatibilities. A novel hybrid IncI2/IncFIB plasmid pGD17-2 was discovered and characterized from a swine isolate with colistin resistance. Intriguingly, co-occurrence of two unique mcr-1-bearing plasmids (pGD65-3, IncI2, and pGD65-5, IncX4) was detected in a single isolate GD65, which might accelerate dissemination of the mcr-1 under environmental selection pressure. Genetic analyses of these plasmids mapped mobile elements in the context of antibiotic resistance and determined two insertion sequences (ISEcp1 and ISApl1) that are responsible for the mobilization of mcr-1. Gene deletion also proved that the first ATG codon is redundant in the mcr-1 gene. CONCLUSIONS Collectively, our results extend landscapes of the diversified mcr-1-bearing plasmid reservoirs.
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Affiliation(s)
- Qingjing Wang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jun Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Youfa Ding
- Lishui People's Hospital, Lishui, 323000, Zhejiang, China
| | - Xing-Ping Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jingxia Lin
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | | | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
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Phylogenomic proximity and metabolic discrepancy of Methanosarcina mazei Go1 across methanosarcinal genomes. Biosystems 2017; 155:20-28. [DOI: 10.1016/j.biosystems.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 02/04/2023]
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Construction of Expression Shuttle Vectors for the Haloarchaeon Natrinema sp. J7 Based on Its Chromosomal Origins of Replication. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:4237079. [PMID: 28348508 PMCID: PMC5350488 DOI: 10.1155/2017/4237079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/28/2016] [Accepted: 12/26/2016] [Indexed: 12/11/2022]
Abstract
Haloarchaeon Natrinema sp. J7, the first reported archaeon harboring both plasmid and chromosome-based temperate viruses, is a useful model for investigating archaeal virus-host and virus-virus interactions. However, the lack of genetic tools has limited such studies. On the basis of the automatically replicating sequences of the J7 chromosome and the pyrF marker, we constructed seven vectors, six of which were confirmed to possess replication ability in a pyrF-deletion derivative of J7 (J7-F). Among these vectors, pFJ1, pFJ4, and pFJ6 could be transformed into the host strain with relatively high efficiency (approximately 103 colony-forming units/μg DNA) and were present at about one copy per chromosome. These three vectors could be stably maintained in J7-F without selection and were used for heterologous protein expression. Only pFJ6 was found to be present in the transformed cells in an exclusively episomal, nonintegrated state (one copy per chromosome). In contrast, some pFJ1 and pFJ4 DNA was probably integrated into the J7-F chromosome. In addition, pFJ6 was found to be compatible with pYCJ in J7 cells, suggesting that these two vectors could be used for further studies of virus-virus and virus-host interactions.
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Demina TA, Atanasova NS, Pietilä MK, Oksanen HM, Bamford DH. Vesicle-like virion of Haloarcula hispanica pleomorphic virus 3 preserves high infectivity in saturated salt. Virology 2016; 499:40-51. [DOI: 10.1016/j.virol.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 12/26/2022]
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Shaaban S, Cowley LA, McAteer SP, Jenkins C, Dallman TJ, Bono JL, Gally DL. Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing. Microb Genom 2016; 2:e000096. [PMID: 28348836 PMCID: PMC5359411 DOI: 10.1099/mgen.0.000096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 11/18/2022] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans is associated with multiple horizontally acquired genes, the majority present in active or cryptic prophages. Our understanding of the evolution and phylogeny of EHEC O157 continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value for the analysis of prophage content and its chromosomal location. In this study, we applied Single Molecule Real Time (SMRT) sequencing, using the Pacific Biosciences long-read sequencing platform, to isolates selected from the main sub-clusters of this clonal group. Prophage regions were extracted from these sequences and from published reference strains. Genome position and prophage diversity were analysed along with genetic content. Prophages could be assigned to clusters, with smaller prophages generally exhibiting less diversity and preferential loss of structural genes. Prophages encoding Shiga toxin (Stx) 2a and Stx1a were the most diverse, and more variable compared to prophages encoding Stx2c, further supporting the hypothesis that Stx2c-prophage integration was ancestral to acquisition of other Stx types. The concept that phage type (PT) 21/28 (Stx2a+, Stx2c+) strains evolved from PT32 (Stx2c+) was supported by analysis of strains with excised Stx-encoding prophages. Insertion sequence elements were over-represented in prophage sequences compared to the rest of the genome, showing integration in key genes such as stx and an excisionase, the latter potentially acting to capture the bacteriophage into the genome. Prophage profiling should allow more accurate prediction of the pathogenic potential of isolates.
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Affiliation(s)
- Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Lauren A. Cowley
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - Sean P. McAteer
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - Timothy J. Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, London NW9 5EQ, UK
| | - James L. Bono
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, NE 68933-0166, USA
| | - David L. Gally
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
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