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Torrance EL, Diop A, Bobay LM. Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596828. [PMID: 38895235 PMCID: PMC11185547 DOI: 10.1101/2024.05.31.596828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotpots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.
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Affiliation(s)
- Ellis L Torrance
- Dept. of Biology, University of North Carolina Greensboro, Greensboro, NC 27412
- Systems Biology Dept., Sandia National Laboratories, Livermore, CA 94551
| | - Awa Diop
- Dept. of Biological Sciences, North Carolina State University, Raleigh, NC 27695
| | - Louis-Marie Bobay
- Dept. of Biology, University of North Carolina Greensboro, Greensboro, NC 27412
- Dept. of Biological Sciences, North Carolina State University, Raleigh, NC 27695
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Daza-Prieto B, Raicevic N, Cabal A, Hyden P, Mösenbacher T, Ladstätter J, Richter S, Stöger A, Joao Cardoso M, Chakeri A, Hasenberger P, Stadlbauer S, Mach RL, Martinovic A, Ruppitsch W. Enterococcus montenegrensis sp. nov., isolated from artisanal Montenegrin dry sausage. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240650 DOI: 10.1099/ijsem.0.006206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
A novel, Gram-positive, facultative anaerobe, coccoid and non-motile bacterium, designated as CoE-012-22T was isolated from dried beef sausage (the original name in Montenegro is Govedji Kulen) manufactured in the municipality of Rozaje (Montenegro) in 2021. Cells of this strain were oxidase- and catalase-negative. Growth occurred at 4-50 °C, at pH 5.0-8.0 and with 0-6.5 % (w/v) NaCl in diverse growth media. MALDI-TOF analysis identified the strain as Enterococcus canintestini (log score 2). Phylogenetic analysis of the 16S rRNA gene and whole genome sequences assigned the strain to the genus Enterococcus. The closest relatives were E. canintestini DSM 21207T and E. dispar ATCC 51266T with 16S rRNA gene sequence pairwise similarities of 99.34 and 98.59 %, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolate CoE-012-22T and other enterococci species were below the thresholds for species delineation thresholds (95.0 % ANI; 70.0 % dDDH) with maximum identities of 84.13 % (ANIb), 86.43 % (ANIm) and 28.4 % (dDDH) to E. saigonensis JCM 31193T and 70.97 % (ANIb), 88.99 % (ANIm) and 32.4 % (dDDH) to E. malodoratus ATCC 43197T. Two unknown Enterococcus isolates, Enterococcus sp. MJM12 and Enterococcus SMC-9, showed identities of 99.87 and 99.94 % (16S rRNA), 98.57 and 98.65 % (ANIb), 98.93 and 99.02 % (ANIm), and 89.8 and 90.0 % (dDDH) to strain CoE-012-22T and can therefore be regarded as the same species. Based on the characterization results, strain CoE-012-22T was considered to represent a novel species, for which the name Enterococcus montenegrensis sp. nov. is proposed. The type strain is CoE-012-22T (=DSM 115843T=NCIMB 15468T).
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Affiliation(s)
- Beatriz Daza-Prieto
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area of Biochemical Technology, Technical University Vienna, Vienna, Austria
| | - Nadja Raicevic
- FoodHub - Centre of Excellence for Digitalisationof Microbial Food Safety Risk Assessment and Quality Parameters for Accurate Food Authenticity Certification, University of Donja Gorica, Podgorica, Montenegro
| | - Adriana Cabal
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Patrick Hyden
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Tobias Mösenbacher
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Johann Ladstätter
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Susanne Richter
- Institute of Veterinary Disease Control, Austrian Agency for Health and Food Safety, Mödling, Austria
| | - Anna Stöger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Maria Joao Cardoso
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- ECDC Fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Ali Chakeri
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Center for Public Health, Medical University Vienna, Vienna, Austria
| | - Petra Hasenberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Silke Stadlbauer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, Research Area of Biochemical Technology, Technical University Vienna, Vienna, Austria
| | - Aleksandra Martinovic
- FoodHub - Centre of Excellence for Digitalisationof Microbial Food Safety Risk Assessment and Quality Parameters for Accurate Food Authenticity Certification, University of Donja Gorica, Podgorica, Montenegro
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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Xue Y, Zhang L, Liu F, Dai F, Kong L, Ma D, Han Y. Alkaline "Nanoswords" Coordinate Ferroptosis-like Bacterial Death for Antibiosis and Osseointegration. ACS NANO 2023; 17:2711-2724. [PMID: 36662033 DOI: 10.1021/acsnano.2c10960] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ferroptosis is an iron-dependent cell death and is associated with cancer therapy. Can it play a role in resistance of postoperative infection of implants, especially with an extracellular supplement of Fe ions in a non-cytotoxic dose? To answer this, "nanoswords" of Fe-doped titanite are fabricated on a Ti implant surface to resist bacterial invasion by a synergistic action of ferroptosis-like bacteria killing, proton disturbance, and physical puncture. The related antibiosis mechanism is explored by atomic force microscopy and genome sequencing. The nanoswords induce an increased local pH value, which not only weakens the proton motive force, reducing adenosine triphosphate synthesis of Staphylococcus aureus, but also decreases the membrane modulus, making the nanoswords distort and even puncture a bacterial membrane easily. Simultaneously, more Fe ions are taken by bacteria due to increased bacterial membrane permeability, resulting in ferroptosis-like death of bacteria, and this is demonstrated by intracellular iron enrichment, lipid peroxidation, and glutathione depletion. Interestingly, a microenvironment constructed by these nanoswords improves osteoblast behavior in vitro and bone regeneration in vivo. Overall, the nanoswords can induce ferroptosis-like bacterial death without cytotoxicity and have great promise in applications with clinical implants for outstanding antibiosis and biointegration performance.
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Affiliation(s)
- Yang Xue
- State-key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lan Zhang
- State-key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710049, China
| | - Fuwei Liu
- Fourth Military Medical University, Xi'an 710038, China
| | - Fang Dai
- State-key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710049, China
| | - Liang Kong
- Fourth Military Medical University, Xi'an 710038, China
| | - Dayan Ma
- State-key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yong Han
- State-key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, Xi'an 710049, China
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Subramaniam S, Smith GR. RecBCD enzyme and Chi recombination hotspots as determinants of self vs. non-self: Myths and mechanisms. ADVANCES IN GENETICS 2022; 109:1-37. [PMID: 36334915 PMCID: PMC10047805 DOI: 10.1016/bs.adgen.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacteria face a challenge when DNA enters their cells by transformation, mating, or phage infection. Should they treat this DNA as an invasive foreigner and destroy it, or consider it one of their own and potentially benefit from incorporating new genes or alleles to gain useful functions? It is frequently stated that the short nucleotide sequence Chi (5' GCTGGTGG 3'), a hotspot of homologous genetic recombination recognized by Escherichia coli's RecBCD helicase-nuclease, allows E. coli to distinguish its DNA (self) from any other DNA (non-self) and to destroy non-self DNA, and that Chi is "over-represented" in the E. coli genome. We show here that these latter statements (dogmas) are not supported by available evidence. We note Chi's wide-spread occurrence and activity in distantly related bacterial species and phages. We illustrate multiple, highly non-random features of the genomes of E. coli and coliphage P1 that account for Chi's high frequency and genomic position, leading us to propose that P1 selects for Chi's enhancement of recombination, whereas E. coli selects for the preferred codons in Chi. We discuss other, previously described mechanisms for self vs. non-self determination involving RecBCD and for RecBCD's destruction of DNA that cannot recombine, whether foreign or domestic, with or without Chi.
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Affiliation(s)
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, United States.
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