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Patakova P, Vasylkivska M, Sedlar K, Jureckova K, Bezdicek M, Lovecka P, Branska B, Kastanek P, Krofta K. Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop ( Humulus lupulus L.). Front Microbiol 2024; 15:1305338. [PMID: 38389535 PMCID: PMC10882544 DOI: 10.3389/fmicb.2024.1305338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Background This paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth. Methods P. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out. Results and discussion The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.
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Affiliation(s)
- Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
- Department of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Matej Bezdicek
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Brno, Czechia
- Department of Internal Medicine-Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Petra Lovecka
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | | | - Karel Krofta
- Hop Research Institute, Co. Ltd., Zatec, Czechia
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Pelliciari S, Bodet-Lefèvre S, Fenyk S, Stevens D, Winterhalter C, Schramm FD, Pintar S, Burnham DR, Merces G, Richardson TT, Tashiro Y, Hubbard J, Yardimci H, Ilangovan A, Murray H. The bacterial replication origin BUS promotes nucleobase capture. Nat Commun 2023; 14:8339. [PMID: 38097584 PMCID: PMC10721633 DOI: 10.1038/s41467-023-43823-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Genome duplication is essential for the proliferation of cellular life and this process is generally initiated by dedicated replication proteins at chromosome origins. In bacteria, DNA replication is initiated by the ubiquitous DnaA protein, which assembles into an oligomeric complex at the chromosome origin (oriC) that engages both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) to promote DNA duplex opening. However, the mechanism of DnaA specifically opening a replication origin was unknown. Here we show that Bacillus subtilis DnaAATP assembles into a continuous oligomer at the site of DNA melting, extending from a dsDNA anchor to engage a single DNA strand. Within this complex, two nucleobases of each ssDNA binding motif (DnaA-trio) are captured within a dinucleotide binding pocket created by adjacent DnaA proteins. These results provide a molecular basis for DnaA specifically engaging the conserved sequence elements within the bacterial chromosome origin basal unwinding system (BUS).
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Affiliation(s)
- Simone Pelliciari
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Salomé Bodet-Lefèvre
- Centre for Molecular Cell Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, Newark Street, London, E1 2AT, UK
| | - Stepan Fenyk
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Daniel Stevens
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Charles Winterhalter
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Frederic D Schramm
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Sara Pintar
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Daniel R Burnham
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - George Merces
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Tomas T Richardson
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Yumiko Tashiro
- Centre for Molecular Cell Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, Newark Street, London, E1 2AT, UK
| | - Julia Hubbard
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Hasan Yardimci
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Aravindan Ilangovan
- Centre for Molecular Cell Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, Newark Street, London, E1 2AT, UK.
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK.
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Yin ZN, Lai FL, Gao F. Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis. Brief Bioinform 2023; 25:bbad432. [PMID: 38008420 PMCID: PMC10676776 DOI: 10.1093/bib/bbad432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/11/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023] Open
Abstract
Accurate identification of replication origins (ORIs) is crucial for a comprehensive investigation into the progression of human cell growth and cancer therapy. Here, we proposed a computational approach Ori-FinderH, which can efficiently and precisely predict the human ORIs of various lengths by combining the Z-curve method with deep learning approach. Compared with existing methods, Ori-FinderH exhibits superior performance, achieving an area under the receiver operating characteristic curve (AUC) of 0.9616 for K562 cell line in 10-fold cross-validation. In addition, we also established a cross-cell-line predictive model, which yielded a further improved AUC of 0.9706. The model was subsequently employed as a fitness function to support genetic algorithm for generating artificial ORIs. Sequence analysis through iORI-Euk revealed that a vast majority of the created sequences, specifically 98% or more, incorporate at least one ORI for three cell lines (Hela, MCF7 and K562). This innovative approach could provide more efficient, accurate and comprehensive information for experimental investigation, thereby further advancing the development of this field.
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Affiliation(s)
- Zhen-Ning Yin
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Fei-Liao Lai
- 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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4
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Aroh O, Liles MR, Halanych KM. Genomic characterization of a novel, widely distributed Mycoplasma species "Candidatus Mycoplasma mahonii" associated with the brittlestar Gorgonocephalus chilensis. PLoS One 2023; 18:e0290305. [PMID: 37616244 PMCID: PMC10449156 DOI: 10.1371/journal.pone.0290305] [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: 02/07/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023] Open
Abstract
Symbiotic relationships are ubiquitous throughout the world's oceans, yet for many marine organisms, including those in the high latitudes, little is understood about symbiotic associations and functional relationships. From a recently determined genome sequence of a filter-feeding basket star from Argentina, Gorgonocephalus chilensis, we discovered a novel Mycoplasma species with a 796Kb genome (CheckM completeness of 97.9%, G+C content = 30.1%). Similar to other Mycoplasma spp. within Mycoplasmatota, genomic analysis of the novel organism revealed reduced metabolic pathways including incomplete biosynthetic pathways, suggesting an obligate association with their basket star host. Results of 16S rRNA and multi-locus phylogenetic analyses revealed that this organism belonged to a recently characterized non-free-living lineage of Mycoplasma spp. specifically associated with marine invertebrate animals. Thus, the name "Candidatus Mycoplasma mahonii" is proposed for this novel species. Based on 16S rRNA PCR-screening, we found that Ca. M. mahonii also occurs in Gorgonocephalus eucnemis from the Northwest Pacific and other Gorgonocephalus chilensis from Argentinian waters. The level of sequence conservation within Ca. M. mahonii is considerable between widely disparate high-latitude Gorgonocephalus species, suggesting that oceanic dispersal of this microbe may be greater than excepted.
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Affiliation(s)
- Oluchi Aroh
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Kenneth M. Halanych
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
- Centre for Marine Science, University of North Carolina Wilmington, Wilmington, NC, United States of America
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5
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Felice AG, Santos LNQ, Kolossowski I, Zen FL, Alves LG, Rodrigues TCV, Prado LCS, Jaiswal AK, Tiwari S, Miranda FM, Ramos RTJ, Azevedo V, Oliveira CJF, Benevides LJ, Soares SC. Comparative genomics of Bordetella pertussis and prediction of new vaccines and drug targets. J Biomol Struct Dyn 2022; 40:10136-10152. [PMID: 34155952 DOI: 10.1080/07391102.2021.1940279] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pertussis is a highly contagious respiratory disease caused by Bordetella pertussis, a Gram-negative bacterium described over a century ago. Despite broad vaccine coverage and treatment options, the disease is remerging as a public health problem especially in infants and older children. Recent data indicate re-emergence of the disease is related to bacterial resistance to immune defences and decreased vaccine effectiveness, which obviously suggests the need of new effective vaccines and drugs. In an attempt to contribute with solutions to this great challenge, bioinformatics tools were used to genetically comprehend the species of these bacteria and predict new vaccines and drug targets. In fact, approaches were used to analysis genomic plasticity, gene synteny and species similarities between the 20 genomes of Bordetella pertussis already available. Furthermore, it was conducted reverse vaccinology and docking analysis to identify proteins with potential to become vaccine and drug targets, respectively. The analyses showed the 20 genomes belongs to a homogeneous group that has preserved most of the genes over time. Besides that, were found genomics islands and good proteins to be candidates for vaccine and drugs. Taken together, these results suggests new possibilities that may be useful to develop new vaccines and drugs that will help the prevention and treatment strategies of pertussis disease caused by these Bordetella strains. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Andrei G Felice
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Leonardo N Q Santos
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Ian Kolossowski
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Felipe L Zen
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Leandro G Alves
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thaís C V Rodrigues
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ligia C S Prado
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Arun K Jaiswal
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fábio M Miranda
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - Rommel T J Ramos
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.,Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Carlo J F Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Leandro J Benevides
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Siomar C Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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6
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Martinez-Vaz BM, Dodge AG, Lucero RM, Stockbridge RB, Robinson AA, Tassoulas LJ, Wackett LP. Wastewater bacteria remediating the pharmaceutical metformin: Genomes, plasmids and products. Front Bioeng Biotechnol 2022; 10:1086261. [PMID: 36588930 PMCID: PMC9800807 DOI: 10.3389/fbioe.2022.1086261] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be bioremediated by wastewater treatment plants (WWTPs). Metformin is not adsorbed well by activated carbon and toxic N-chloro derivatives can form in chlorinated water. Most earlier studies on metformin biodegradation have used wastewater consortia and details of the genomes, relevant genes, metabolic products, and potential for horizontal gene transfer are lacking. Here, two metformin-biodegrading bacteria from a WWTP were isolated and their biodegradation characterized. Aminobacter sp. MET metabolized metformin stoichiometrically to guanylurea, an intermediate known to accumulate in some environments including WWTPs. Pseudomonas mendocina MET completely metabolized metformin and utilized all the nitrogen atoms for growth. Pseudomonas mendocina MET also metabolized metformin breakdown products sometimes observed in WWTPs: 1-N-methylbiguanide, biguanide, guanylurea, and guanidine. The genome of each bacterium was obtained. Genes involved in the transport of guanylurea in Aminobacter sp. MET were expressed heterologously and shown to serve as an antiporter to expel the toxic guanidinium compound. A novel guanylurea hydrolase enzyme was identified in Pseudomonas mendocina MET, purified, and characterized. The Aminobacter and Pseudomonas each contained one plasmid of 160 kb and 90 kb, respectively. In total, these studies are significant for the bioremediation of a major pollutant in WWTPs today.
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Affiliation(s)
- Betsy M. Martinez-Vaz
- Department of Biology and Biochemistry Program, Hamline University, St. Paul, MN, United States
| | - Anthony G. Dodge
- Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Rachael M. Lucero
- Program in Chemical Biology and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Randy B. Stockbridge
- Program in Chemical Biology and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Ashley A. Robinson
- Department of Biology and Biochemistry Program, Hamline University, St. Paul, MN, United States
| | - Lambros J. Tassoulas
- Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
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7
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Koppenhöfer S, Lang AS. Patterns of abundance, chromosomal localization, and domain organization among c-di-GMP-metabolizing genes revealed by comparative genomics of five alphaproteobacterial orders. BMC Genomics 2022; 23:834. [PMID: 36522693 PMCID: PMC9756655 DOI: 10.1186/s12864-022-09072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/17/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a bacterial second messenger that affects diverse processes in different bacteria, including the cell cycle, motility, and biofilm formation. Its cellular levels are controlled by the opposing activities of two types of enzymes, with synthesis by diguanylate cyclases containing a GGDEF domain and degradation by phosphodiesterases containing either an HD-GYP or an EAL domain. These enzymes are ubiquitous in bacteria with up to 50 encoded in some genomes, the specific functions of which are mostly unknown. RESULTS We used comparative analyses to identify genomic patterns among genes encoding proteins with GGDEF, EAL, and HD-GYP domains in five orders of the class Alphaproteobacteria. GGDEF-containing sequences and GGDEF-EAL hybrids were the most abundant and had the highest diversity of co-occurring auxiliary domains while EAL and HD-GYP containing sequences were less abundant and less diverse with respect to auxiliary domains. There were striking patterns in the chromosomal localizations of the genes found in two of the orders. The Rhodobacterales' EAL-encoding genes and Rhizobiales' GGDEF-EAL-encoding genes showed opposing patterns of distribution compared to the GGDEF-encoding genes. In the Rhodobacterales, the GGDEF-encoding genes showed a tri-modal distribution with peaks mid-way between the origin (ori) and terminus (ter) of replication and at ter while the EAL-encoding genes peaked near ori. The patterns were more complex in the Rhizobiales, but the GGDEF-encoding genes were biased for localization near ter. CONCLUSIONS The observed patterns in the chromosomal localizations of these genes suggest a coupling of synthesis and hydrolysis of c-di-GMP with the cell cycle. Moreover, the higher proportions and diversities of auxiliary domains associated with GGDEF domains and GGDEF-EAL hybrids compared to EAL or HD-GYP domains could indicate that more stimuli affect synthesis compared to hydrolysis of c-di-GMP.
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Affiliation(s)
- Sonja Koppenhöfer
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
| | - Andrew S. Lang
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
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Abstract
The technology of recombineering, in vivo genetic engineering, was initially developed in Escherichia coli and uses bacteriophage-encoded homologous recombination proteins to efficiently recombine DNA at short homologies (35 to 50 nt). Because the technology is homology driven, genomic DNA can be modified precisely and independently of restriction site location. Recombineering uses linear DNA substrates that are introduced into the cell by electroporation; these can be PCR products, synthetic double-strand DNA (dsDNA), or single-strand DNA (ssDNA). Here we describe the applications, challenges, and factors affecting ssDNA and dsDNA recombineering in a variety of non-model bacteria, both Gram-negative and -positive, and recent breakthroughs in the field. We list different microbes in which the widely used phage λ Red and Rac RecET recombination systems have been used for in vivo genetic engineering. New homologous ssDNA and dsDNA recombineering systems isolated from non-model bacteria are also described. The Basic Protocol outlines a method for ssDNA recombineering in the non-model species of Shewanella. The Alternate Protocol describes the use of CRISPR/Cas as a counter-selection system in conjunction with recombineering to enhance recovery of recombinants. We provide additional background information, pertinent considerations for experimental design, and parameters critical for success. The design of ssDNA oligonucleotides (oligos) and various internet-based tools for oligo selection from genome sequences are also described, as is the use of oligo-mediated recombination. This simple form of genome editing uses only ssDNA oligo(s) and does not require an exogenous recombination system. The information presented here should help researchers identify a recombineering system suitable for their microbe(s) of interest. If no system has been characterized for a specific microbe, researchers can find guidance in developing a recombineering system from scratch. We provide a flowchart of decision-making paths for strategically applying annealase-dependent or oligo-mediated recombination in non-model and undomesticated bacteria. © 2022 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: ssDNA recombineering in Shewanella species Alternate Protocol: ssDNA recombineering coupled to CRISPR/Cas9 in Shewanella species.
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Affiliation(s)
- Anna Corts
- Cultivarium, 490 Arsenal Way, Ste 110, Watertown, Massachusetts 02472
| | - Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nina Costantino
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
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Lorenzi JN, Thibessard A, Lioy VS, Boccard F, Leblond P, Pernodet JL, Bury-Moné S. Ribosomal RNA operons define a central functional compartment in the Streptomyces chromosome. Nucleic Acids Res 2022; 50:11654-11669. [PMID: 36408918 PMCID: PMC9723626 DOI: 10.1093/nar/gkac1076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/27/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. These bacteria possess a large linear chromosome genetically compartmentalized: core genes are grouped in the central part, while terminal regions are populated by poorly conserved genes. In exponentially growing cells, chromosome conformation capture unveiled sharp boundaries formed by ribosomal RNA (rrn) operons that segment the chromosome into multiple domains. Here we further explore the link between the genetic distribution of rrn operons and Streptomyces genetic compartmentalization. A large panel of genomes of species representative of the genus diversity revealed that rrn operons and core genes form a central skeleton, the former being identifiable from their core gene environment. We implemented a new nomenclature for Streptomyces genomes and trace their rrn-based evolutionary history. Remarkably, rrn operons are close to pericentric inversions. Moreover, the central compartment delimited by rrn operons has a very dense, nearly invariant core gene content. Finally, this compartment harbors genes with the highest expression levels, regardless of gene persistence and distance to the origin of replication. Our results highlight that rrn operons are structural boundaries of a central functional compartment prone to transcription in Streptomyces.
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Affiliation(s)
- Jean-Noël Lorenzi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | | | - Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Jean-Luc Pernodet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
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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: 7] [Impact Index Per Article: 3.5] [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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11
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Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants. BMC Microbiol 2022; 22:258. [PMID: 36271336 DOI: 10.1186/s12866-022-02670-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Moraxella bovis and Moraxella bovoculi both associate with infectious bovine keratoconjunctivitis (IBK), an economically significant and painful ocular disease that affects cattle worldwide. There are two genotypes of M. bovoculi (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. M. bovis is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of M. bovis genomic diversity, and to compare core and accessory genes and predicted outer membrane protein profiles both within and between M. bovis and M. bovoculi. RESULTS Phylogenetic trees and bioinformatic analyses of 36 M. bovis chromosomes sequenced in this study and additional available chromosomes of M. bovis and both genotype 1 and 2 M. bovoculi, showed there are two genotypes (1 and 2) of M. bovis. The two M. bovis genotypes share a core of 2015 genes, with 121 and 186 genes specific to genotype 1 and 2, respectively. The two genotypes differ by their chromosome size and prophage content, encoded protein variants of the virulence factor hemolysin, and by their affiliation with different plasmids. Eight plasmid types were identified in this study, with types 1 and 6 observed in 88 and 56% of genotype 2 strains, respectively, and absent from genotype 1 strains. Only type 1 plasmids contained one or two gene copies encoding filamentous haemagglutinin-like proteins potentially involved with adhesion. A core of 1403 genes was shared between the genotype 1 and 2 strains of both M. bovis and M. bovoculi, which encoded a total of nine predicted outer membrane proteins. CONCLUSIONS There are two genotypes of M. bovis that differ in both chromosome content and plasmid profiles and thus may not equally associate with IBK. Immunological reagents specifically targeting select genotypes of M. bovis, or all genotypes of M. bovis and M. bovoculi together could be designed from the outer membrane proteins identified in this study.
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12
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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: 12] [Impact Index Per Article: 6.0] [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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13
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Musilova J, Kourilova X, Pernicova I, Bezdicek M, Lengerova M, Obruca S, Sedlar K. Novel thermophilic polyhydroxyalkanoates producing strain Aneurinibacillus thermoaerophilus CCM 8960. Appl Microbiol Biotechnol 2022; 106:4669-4681. [PMID: 35759037 DOI: 10.1007/s00253-022-12039-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/26/2022]
Abstract
Aneurinibacillus thermoaerophilus CCM 8960 is a thermophilic bacterium isolated from compost in Brno. The bacterium accumulates polyhydroxyalkanoates (PHAs), a biodegradable and renewable alternative to petrochemical polymers. The bacterium reveals several features that make it a very interesting candidate for the industrial production of PHA. At first, due to its thermophilic character, the bacterium can be utilized in agreement with the concept of next-generation industrial biotechnology (NGIB), which relies on extremophiles. Second, the bacterium is capable of producing PHA copolymers containing a very high portion of 4-hydroxybutyrate (4HB). Such materials possess unique properties and can be advantageously used in multiple applications, including but not limited to medicine and healthcare. Therefore, this work focuses on the in-depth characterization of A. thermoaerophilus CCM 8960. In particular, we sequenced and assembled the genome of the bacterium and identified its most important genetic features, such as the presence of plasmids, prophages, CRISPR arrays, antibiotic-resistant genes, and restriction-modification (R-M) systems, which might be crucial for the development of genome editing tools. Furthermore, we focused on genes directly involved in PHA metabolism. We also experimentally studied the kinetics of glycerol and 1,4-butanediol (1,4BD) utilization as well as biomass growth and PHA production during cultivation. Based on these data, we constructed a metabolic model to reveal metabolic fluxes and nodes of glycerol and 1,4BD concerning their incorporation into the poly(3-hydroxybutyrate-co-4-hydroxybutyrate (P(3HB-co-4HB)) structure. KEY POINTS: • Aneurinibacillus sp. H1 was identified as Aneurinibacillus thermoaerophilus. • PHA metabolism pathway with associated genes was presented. • Unique monomer composition of produced PHAs was reported.
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Affiliation(s)
- Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Xenie Kourilova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Iva Pernicova
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Matej Bezdicek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Martina Lengerova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Stanislav Obruca
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic.
- Department of Informatics, Institute of Bioinformatics, Ludwig-Maximilians-Universität München, Munich, Germany.
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14
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Convergent evolution in two bacterial replicative helicase loaders. Trends Biochem Sci 2022; 47:620-630. [DOI: 10.1016/j.tibs.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
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15
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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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16
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Dineen RL, Penno C, Kelleher P, Bourin MJB, O'Connell‐Motherway M, van Sinderen D. Molecular analysis of the replication functions of the bifidobacterial conjugative megaplasmid pMP7017. Microb Biotechnol 2021; 14:1494-1511. [PMID: 33939264 PMCID: PMC8313286 DOI: 10.1111/1751-7915.13810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
pMP7017 is a conjugative megaplasmid isolated from the gut commensal Bifidobacterium breve JCM7017 and was shown to encode two putative replicases, designated here as RepA and RepB. In the current work, RepB was identified as the pMP7017 replicative initiator, as the repB gene, and its surrounding region was shown to be sufficient to allow autonomous replication in two bifidobacterial species, B. breve and Bifidobacterium longum subsp. longum. RepB was shown to bind to repeat sequence downstream of its coding sequence and this region was determined to be essential for efficient replication. Based on our results, we hypothesize that pMP7017 is an iteron-regulated plasmid (IRP) under strict auto-regulatory control. Recombinantly produced and purified RepB was determined to exist as a dimer in solution, differing from replicases of other IRPs, which exist as a mix of dimers and monomers. Furthermore, a stable low-copy Bifidobacterium-E. coli shuttle vector, pRD1.3, was created which can be employed for cloning and expression of large genes, as was demonstrated by the cloning and heterologous expression of the 5.1 kb apuB gene encoding the extracellular amylopullulanase from B. breve UCC2003 into B. longum subsp. longum NCIMB8809.
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Affiliation(s)
- Rebecca L. Dineen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Christophe Penno
- CNRS UMR 6553 EcoBioUniversite de Rennes 1Campus de Beaulieu, Bat. 14ARennes cedex35042France
| | - Philip Kelleher
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Maxence J. B. Bourin
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | | | - Douwe van Sinderen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
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17
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Hrab P,
Rückert
C, Busche T, Ostash I, Kalinowski J, Fedorenko V, Yushchuk O, Ostash B. Complete genome sequence of Streptomyces cyanogenus S136, producer of anticancer angucycline landomycin A. 3 Biotech 2021; 11:282. [PMID: 34094801 PMCID: PMC8137763 DOI: 10.1007/s13205-021-02834-4] [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: 04/03/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022] Open
Abstract
Streptomyces cyanogenus S136 is the only known producer of landomycin A (LaA), one of the founding members of angucycline family of aromatic polyketides. LaA displays potent anticancer activities which has made this natural product a target of numerous chemical and cell biological studies. Little is known about the potential of S136 strain to produce other secondary metabolites. Here we report complete genome sequence of LaA producer and how we used this sequence to evaluate for this species its phylogenetic position and diversity of gene clusters for natural product biosynthesis. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02834-4.
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Affiliation(s)
- Pavlo Hrab
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm 102, Lviv, 79005 Ukraine
| | - Christian
Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University,
Sequenz 1
, 33615 Bielefeld, Germany
| | - Tobias Busche
- Technology Platform Genomics, CeBiTec, Bielefeld University,
Sequenz 1
, 33615 Bielefeld, Germany
| | - Iryna Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm 102, Lviv, 79005 Ukraine
| | -
Jörn
Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University,
Sequenz 1
, 33615 Bielefeld, Germany
| | - Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm 102, Lviv, 79005 Ukraine
| | - Oleksandr Yushchuk
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm 102, Lviv, 79005 Ukraine
| | - Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, 4 Hrushevskoho st., Rm 102, Lviv, 79005 Ukraine
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18
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Repar J, Zahradka D, Sović I, Zahradka K. Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Sci Rep 2021; 11:10939. [PMID: 34035321 PMCID: PMC8149714 DOI: 10.1038/s41598-021-89173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4-11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli. Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.
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Affiliation(s)
- Jelena Repar
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Davor Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Sović
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Ksenija Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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19
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Musilova J, Kourilova X, Bezdicek M, Lengerova M, Obruca S, Skutkova H, Sedlar K. First Complete Genome of the Thermophilic Polyhydroxyalkanoates-Producing Bacterium Schlegelella thermodepolymerans DSM 15344. Genome Biol Evol 2021; 13:6081016. [PMID: 33432323 PMCID: PMC8023429 DOI: 10.1093/gbe/evab007] [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: 01/06/2021] [Indexed: 11/13/2022] Open
Abstract
Schlegelella thermodepolymerans is a moderately thermophilic bacterium capable of producing polyhydroxyalkanoates-biodegradable polymers representing an alternative to conventional plastics. Here, we present the first complete genome of the type strain S. thermodepolymerans DSM 15344 that was assembled by hybrid approach using both long (Oxford Nanopore) and short (Illumina) reads. The genome consists of a single 3,858,501-bp-long circular chromosome with GC content of 70.3%. Genome annotation identified 3,650 genes in total, whereas 3,598 open reading frames belonged to protein-coding genes. Functional annotation of the genome and division of genes into clusters of orthologous groups revealed a relatively high number of 1,013 genes with unknown function or unknown clusters of orthologous groups, which reflects the fact that only a little is known about thermophilic polyhydroxyalkanoates-producing bacteria on a genome level. On the other hand, 270 genes involved in energy conversion and production were detected. This group covers genes involved in catabolic processes, which suggests capability of S. thermodepolymerans DSM 15344 to utilize and biotechnologically convert various substrates such as lignocellulose-based saccharides, glycerol, or lipids. Based on the knowledge of its genome, it can be stated that S. thermodepolymerans DSM 15344 is a very interesting, metabolically versatile bacterium with great biotechnological potential.
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Affiliation(s)
- Jana Musilova
- 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
| | - 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
| | - Helena Skutkova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Czech Republic
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20
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Aulestia M, Flores A, Mangas EL, Pérez-Pulido AJ, Santero E, Camacho EM. Isolation and genomic characterization of the ibuprofen-degrading bacterium Sphingomonas strain MPO218. Environ Microbiol 2020; 23:267-280. [PMID: 33169907 DOI: 10.1111/1462-2920.15309] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/06/2020] [Indexed: 11/28/2022]
Abstract
The presence of pharmaceutical compounds in waters and soils is of particular concern because these compounds can be biologically active, even at environmental concentrations. Most pharmaceutical contaminants result from inefficient removal of these compounds during wastewater treatment. Although microorganisms able to biodegrade pharmaceuticals compounds have been described, the isolation and characterization of new bacterial strains capable of degrading drugs remain important to improve the removal of this pollutant. In this work, we describe the Sphingomonas wittichii strain MPO218 as able to use ibuprofen as the sole carbon and energy source. The genome of MPO218 consists of a circular chromosome and two circular plasmids. Our analysis shows that the largest plasmid, named pIBU218, is conjugative and can horizontally transfer the capability of growing on ibuprofen after conjugation with another related bacterium, Sphingopyxis granuli TFA. This plasmid appears to be unstable since it undergoes different deletions in absence of selection when growth on ibuprofen is not selected. This is the first described example of a natural and conjugative plasmid that enables growth on ibuprofen and is another example of how horizontal gene transfer plays a crucial role in the evolution of bacteria.
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Affiliation(s)
- Magaly Aulestia
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Amando Flores
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Eugenio L Mangas
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Antonio J Pérez-Pulido
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
| | - Eva M Camacho
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo/CSIC/Universidad Pablo de Olavide/Junta de Andalucía, Seville, Spain
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21
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Wang D, Lai FL, Gao F. Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae. Brief Bioinform 2020; 22:6278693. [PMID: 34020544 DOI: 10.1093/bib/bbaa182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/29/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
DNA replication is a fundamental process in all organisms; this event initiates at sites termed origins of replication. The characteristics of eukaryotic replication origins are best understood in Saccharomyces cerevisiae. For this species, origin prediction algorithms or web servers have been developed based on the sequence features of autonomously replicating sequences (ARSs). However, their performances are far from satisfactory. By utilizing the Z-curve methodology, we present a novel pipeline, Ori-Finder 3, for the computational prediction of replication origins in S. cerevisiae at the genome-wide level based solely on DNA sequences. The ARS exhibiting both an AT-rich stretch and ARS consensus sequence element can be predicted at the single-nucleotide level. For the identified ARSs in the S. cerevisiae reference genome, 83 and 60% of the top 100 and top 300 predictions matched the known ARS records, respectively. Based on Ori-Finder 3, we subsequently built a database of the predicted ARSs identified in more than a hundred S. cerevisiae genomes. Consequently, we developed a user-friendly web server including the ARS prediction pipeline and the predicted ARSs database, which can be freely accessed at http://tubic.tju.edu.cn/Ori-Finder3.
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Affiliation(s)
- Dan Wang
- Department of Physics, School of Science, Tianjin University
| | - Fei-Liao Lai
- Department of Physics, School of Science, Tianjin University
| | - Feng Gao
- Department of Physics, School of Science, and the Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University
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22
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Whole-Genome Comparative and Pathogenicity Analysis of Salmonella enterica subsp. enterica Serovar Rissen. G3-GENES GENOMES GENETICS 2020; 10:2159-2170. [PMID: 32358017 PMCID: PMC7341144 DOI: 10.1534/g3.120.401201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Salmonella are a type of bacteria known to cause food-borne illness. Their host range varies widely, and their susceptibility to the host determines its pathogenicity. Salmonella enterica serovar Rissen (S. Rissen) is a widely distributed serotype; however, its virulence and pathogenicity are poorly understood. In this study, the pathogenicity and antibiotic resistance of a representative S. Rissen isolate were investigated. The cell model results showed that S. Rissen preferred to replicate in human macrophage cells U937 compared to murine macrophage cells RAW264.7, suggesting that it has a level of host adaptability. Genome sequencing and comparison analysis revealed that the distribution and nonsynonymous single nucleotide polymorphisms of virulence factors in S. Rissen were similar to those in S. Typhi rather than to those in S. Typhimurium. Taken together, our results suggest that although S. Rissen is a common serotype distributed in swine herds, pork and chicken products, it has strong ability to infect humans.
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23
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Yan F, Gao F. A systematic strategy for the investigation of vaccines and drugs targeting bacteria. Comput Struct Biotechnol J 2020; 18:1525-1538. [PMID: 32637049 PMCID: PMC7327267 DOI: 10.1016/j.csbj.2020.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Infectious and epidemic diseases induced by bacteria have historically caused great distress to people, and have even resulted in a large number of deaths worldwide. At present, many researchers are working on the discovery of viable drug and vaccine targets for bacteria through multiple methods, including the analyses of comparative subtractive genome, core genome, replication-related proteins, transcriptomics and riboswitches, which plays a significant part in the treatment of infectious and pandemic diseases. The 3D structures of the desired target proteins, drugs and epitopes can be predicted and modeled through target analysis. Meanwhile, molecular dynamics (MD) analysis of the constructed drug/epitope-protein complexes is an important standard for testing the suitability of these screened drugs and vaccines. Currently, target discovery, target analysis and MD analysis are integrated into a systematic set of drug and vaccine analysis strategy for bacteria. We hope that this comprehensive strategy will help in the design of high-performance vaccines and drugs.
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Affiliation(s)
- Fangfang Yan
- 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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24
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Hornung BVH, Kuijper EJ, Smits WK. An in silico survey of Clostridioides difficile extrachromosomal elements . Microb Genom 2020; 5. [PMID: 31526450 PMCID: PMC6807378 DOI: 10.1099/mgen.0.000296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Gram-positive enteropathogen Clostridioides difficile (Clostridium difficile) is the major cause of healthcare-associated diarrhoea and is also an important cause of community-acquired infectious diarrhoea. Considering the burden of the disease, many studies have employed whole-genome sequencing of bacterial isolates to identify factors that contribute to virulence and pathogenesis. Though extrachromosomal elements (ECEs) such as plasmids are important for these processes in other bacteria, the few characterized plasmids of C. difficile have no relevant functions assigned and no systematic identification of plasmids has been carried out to date. Here, we perform an in silico analysis of publicly available sequence data to show that ~13 % of all C. difficile strains contain ECEs, with 1–6 elements per strain. Our approach identifies known plasmids (e.g. pCD6, pCD630 and cloning plasmids) and six novel putative plasmid families. Our study shows that plasmids are abundant and may encode functions that are relevant for C. difficile physiology. The newly identified plasmids may also form the basis for the construction of novel cloning plasmids for C. difficile that are compatible with existing tools.
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Affiliation(s)
- Bastian V H Hornung
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Ed J Kuijper
- Netherlands Centre for One Health, The Netherlands.,Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Netherlands Centre for One Health, The Netherlands.,Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden, The Netherlands
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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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Nyong EC, Zaia SR, Allué-Guardia A, Rodriguez AL, Irion-Byrd Z, Koenig SSK, Feng P, Bono JL, Eppinger M. Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes. Front Microbiol 2020; 11:619. [PMID: 32351476 PMCID: PMC7175801 DOI: 10.3389/fmicb.2020.00619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
The toxigenic conversion of Escherichia coli strains by Shiga toxin-converting (Stx) bacteriophages were prominent and recurring events in the stepwise evolution of enterohemorrhagic E. coli (EHEC) O157:H7 from an enteropathogenic (EPEC) O55:H7 ancestor. Atypical, attenuated isolates have been described for both non-sorbitol fermenting (NSF) O157:H7 and SF O157:NM serotypes, which are distinguished by the absence of Stx, the characteristic virulence hallmark of Stx-producing E. coli (STEC). Such atypical isolates either never acquired Stx-phages or may have secondarily lost stx during the course of infection, isolation, or routine subculture; the latter are commonly referred to as LST (Lost Shiga Toxin)-isolates. In this study we analyzed the genomes of 15 NSF O157:H7 and SF O157:NM strains from North America, Europe, and Asia that are characterized by the absence of stx, the virulence hallmark of STEC. The individual genomic basis of the Stx (-) phenotype has remained largely undetermined as the majority of STEC genomes in public genome repositories were generated using short read technology and are in draft stage, posing a major obstacle for the high-resolution whole genome sequence typing (WGST). The application of LRT (long-read technology) sequencing provided us with closed genomes, which proved critical to put the atypical non-shigatoxigenic NSF O157:H7 and SF O157:NM strains into the phylogenomic context of the stepwise evolutionary model. Availability of closed chromosomes for representative Stx (-) NSF O157:H7 and SF O157:NM strains allowed to describe the genomic basis and individual evolutionary trajectories underlying the absence of Stx at high accuracy and resolution. The ability of LRT to recover and accurately assemble plasmids revealed a strong correlation between the strains' featured plasmid genotype and chromosomally inferred clade, which suggests the coevolution of the chromosome and accessory plasmids. The identified ancestral traits in the pSFO157 plasmid of NSF O157:H7 strain LSU-61 provided additional evidence for its intermediate status. Taken together, these observations highlight the utility of LRTs for advancing our understanding of EHEC O157:H7/NM pathogenome evolution. Insights into the genomic and phenotypic plasticity of STEC on a lineage- and genome-wide scale are foundational to improve and inform risk assessment, biosurveillance, and prevention strategies.
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Affiliation(s)
- Emmanuel C. Nyong
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sam R. Zaia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Anna Allué-Guardia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Armando L. Rodriguez
- Research Computing Support Group, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Zaina Irion-Byrd
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | | | - James L. Bono
- United States Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture (ARS-USDA), Clay Center, NE, United States
| | - Mark Eppinger
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
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28
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Kopejtka K, Lin Y, Jakubovičová M, Koblížek M, Tomasch J. Clustered Core- and Pan-Genome Content on Rhodobacteraceae Chromosomes. Genome Biol Evol 2020; 11:2208-2217. [PMID: 31273387 PMCID: PMC6699656 DOI: 10.1093/gbe/evz138] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2019] [Indexed: 12/18/2022] Open
Abstract
In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate, and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular, Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.
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Affiliation(s)
- Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Yan Lin
- Department of Physics, School of Science, Tianjin University, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Markéta Jakubovičová
- Faculty of Information Technology, Czech Technical University in Prague, Czech Republic
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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29
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Gao F. Recent developments of software and database in microbial genomics and functional genomics. Brief Bioinform 2020; 20:732-734. [PMID: 29481602 DOI: 10.1093/bib/bby013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- 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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30
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Gao F, Leonard AC. Editorial: DNA Replication Origins in Microbial Genomes, Volume 2. Front Microbiol 2019; 10:2416. [PMID: 31708893 PMCID: PMC6819313 DOI: 10.3389/fmicb.2019.02416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/07/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin, China
- Frontier Science Center of Synthetic Biology (MOE), Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Alan C. Leonard
- Laboratory of Microbial Genetics, Department of Biomedical and Chemical Engineering and Science, Florida Institute of Technology, Melbourne, FL, United States
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31
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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: 10] [Impact Index Per Article: 2.0] [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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32
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Podosokorskaya OA, Teplyuk AV, Zayulina KS, Kopitsyn DS, Dominova IN, Elcheninov AG, Toshchakov SV, Kublanov IV. The Metabolism of Thermophilic Hydrolytic Bacterium Thauera hydrothermalis Strain par-f-2 Isolated from the West Siberian Subsurface Biosphere. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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33
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Richardson TT, Stevens D, Pelliciari S, Harran O, Sperlea T, Murray H. Identification of a basal system for unwinding a bacterial chromosome origin. EMBO J 2019; 38:e101649. [PMID: 31267560 PMCID: PMC6669920 DOI: 10.15252/embj.2019101649] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/03/2023] Open
Abstract
Genome duplication is essential for cell proliferation, and DNA synthesis is generally initiated by dedicated replication proteins at specific loci termed origins. In bacteria, the master initiator DnaA binds the chromosome origin (oriC) and unwinds the DNA duplex to permit helicase loading. However, despite decades of research it remained unclear how the information encoded within oriC guides DnaA-dependent strand separation. To address this fundamental question, we took a systematic genetic approach in vivo and identified the core set of essential sequence elements within the Bacillus subtilis chromosome origin unwinding region. Using this information, we then show in vitro that the minimal replication origin sequence elements are necessary and sufficient to promote the mechanical functions of DNA duplex unwinding by DnaA. Because the basal DNA unwinding system characterized here appears to be conserved throughout the bacterial domain, this discovery provides a framework for understanding oriC architecture, activity, regulation and diversity.
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Affiliation(s)
- Tomas T Richardson
- Centre for Bacterial Cell BiologyInstitute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Daniel Stevens
- Centre for Bacterial Cell BiologyInstitute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Simone Pelliciari
- Centre for Bacterial Cell BiologyInstitute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Omar Harran
- Centre for Bacterial Cell BiologyInstitute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Theodor Sperlea
- Chromosome Biology GroupLOEWE Center for Synthetic MicrobiologySYNMIKROPhilipps‐Universität MarburgMarburgGermany
| | - Heath Murray
- Centre for Bacterial Cell BiologyInstitute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle Upon TyneUK
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34
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Quan CL, Gao F. Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes. FEBS Lett 2019; 593:918-925. [PMID: 30941752 DOI: 10.1002/1873-3468.13374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/28/2019] [Accepted: 03/31/2019] [Indexed: 11/10/2022]
Abstract
Base composition asymmetry and gene orientation bias are two common genomic structures in bacterial genomes. Here, correlation coefficients between nucleotide disparities and coding sequence (CDS) skew have been calculated, which provides insights into their relationship from an individual genome perspective. Consequently, we find GC and RY disparities correlate significantly with CDS skew, since around 60% of the bacterial genomes under study have correlation coefficients > 0.9. Then, we present a model for quantitative assessment of nucleotide disparity and CDS skew in which a numerical index R2 is used for evaluation. We find that skew curves with higher R2 perform better on the prediction of replication origins in bacteria.
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Affiliation(s)
- Chun-Lan Quan
- Department of Physics, School of Science, Tianjin University, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), China
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