1
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Clark C, Jonušas J, Mitchell JD, Francis A. An algebraic model for inversion and deletion in bacterial genome rearrangement. J Math Biol 2023; 87:34. [PMID: 37517046 PMCID: PMC10387463 DOI: 10.1007/s00285-023-01965-x] [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: 09/18/2022] [Revised: 07/03/2023] [Accepted: 07/08/2023] [Indexed: 08/01/2023]
Abstract
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in bacterial genomes through the same biological mechanism as inversions, and hence a model that incorporates both is desirable. However, while inversion distances between genomes have been well studied, there has yet to be a model which accounts for the combination of both deletions and inversions. To account for both of these operations, we introduce an algebraic model that utilises partial permutations. This leads to an algorithm for calculating the minimum distance to the most recent common ancestor of two bacterial genomes evolving by inversions (of adjacent regions) and deletions. The algebraic model makes the existing short inversion models more complete and realistic by including deletions, and also introduces new algebraic tools into evolutionary distance problems.
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Affiliation(s)
- Chad Clark
- Centre for Research in Mathematics and Data Science, Western Sydney University, Penrith, NSW, Australia.
| | - Julius Jonušas
- Mathematical Institute, School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - James D Mitchell
- Mathematical Institute, School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - Andrew Francis
- Centre for Research in Mathematics and Data Science, Western Sydney University, Penrith, NSW, Australia
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2
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Aswal M, Singhal N, Kumar M. Comprehensive genomic analysis of hypocholesterolemic probiotic Enterococcus faecium LR13 reveals unique proteins involved in cholesterol-assimilation. Front Nutr 2023; 10:1082566. [PMID: 37081914 PMCID: PMC10110904 DOI: 10.3389/fnut.2023.1082566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Hypercholesterolemia is a major risk factor for cardiovascular diseases (CVDs). Chemotherapeutic agents for CVDs exhibit several side effects. Specific probiotics with hypocholesterolemic effects can be safe and effective alternatives to chemotherapeutics. Here, we have analyzed and compared the genome of a novel rhizospheric Enterococcus faecium LR13 cholesterol-assimilating probiotic with other probiotic/pathogenic E. faecium strains to discern genetic factors underlying probiotic efficacy and cholesterol-assimilation. Genomic analyses of E. faecium probiotic strains revealed that LR13 and WEFA23 (cholesterol-assimilating probiotics) harbored 21 unique proteins absent in non-cholesterol-assimilating probiotics. Of these, 14 proteins could directly help in cholesterol-assimilation by producing short chain fatty acids, lipid (sterol) transport and membrane stabilization, and bile salt hydrolase activity. This suggests that cholesterol-assimilation is an intrinsic, strain-specific trait exhibited by probiotics with a specific genetic constitution. Moreover, the unique proteins identified in this study can serve as biomarkers for discerning/characterizing cholesterol-assimilating probiotics as novel biotherapeutics against CVDs.
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3
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Sen I, Kavšek A, Riedel CG. Chromatin Immunoprecipitation and Sequencing (ChIP-seq) Optimized for Application in Caenorhabditis elegans. Curr Protoc 2021; 1:e187. [PMID: 34242493 DOI: 10.1002/cpz1.187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has become one of the most popular methods to study protein-DNA interactions and can be used, for instance, to identify the binding sites of transcription factors or to determine the distributions of histones with specific post-translational modifications throughout the genome. Although standard ChIP-seq protocols work well in most experimental systems, there are exceptions, and one of these is the popular model organism Caenorhabditis elegans. Even though this system is very amenable to genetic and cytological methods, biochemical approaches are challenging. This is due to both the animals' cuticle, which impairs lysis as well as penetration by cross-linkers, and the rather low protein and chromatin content per body weight. These issues have rendered standard ChIP-seq protocols inefficient in C. elegans and raised a need for their improvement. Here, we describe improved protocols, with the most important advances being the efficient breakage of the C. elegans cuticle by freeze-grinding and the use of a very sensitive sequencing library construction procedure, optimized for the relatively low DNA content per body weight of C. elegans. The protocols should therefore improve the reproducibility, sensitivity, and uniformity across tissues of ChIP-seq in this organism. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth and harvesting of synchronized Caenorhabditis elegans Basic Protocol 2: Chromatin immunoprecipitation (ChIP) Basic Protocol 3: Library construction for Illumina sequencing.
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Affiliation(s)
- Ilke Sen
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
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4
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Abstract
The universal triple-nucleotide genetic code is often viewed as a given, randomly selected through evolution. However, as summarized in this article, many observations and deductions within structural and thermodynamic frameworks help to explain the forces that must have shaped the code during the early evolution of life on Earth.
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5
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Irrgang A, Falgenhauer L, Fischer J, Ghosh H, Guiral E, Guerra B, Schmoger S, Imirzalioglu C, Chakraborty T, Hammerl JA, Käsbohrer A. CTX-M-15-Producing E. coli Isolates from Food Products in Germany Are Mainly Associated with an IncF-Type Plasmid and Belong to Two Predominant Clonal E. coli Lineages. Front Microbiol 2017; 8:2318. [PMID: 29209306 PMCID: PMC5702323 DOI: 10.3389/fmicb.2017.02318] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 11/09/2017] [Indexed: 01/06/2023] Open
Abstract
Extended-spectrum beta-lactamases (ESBL) mediating resistance to 3rd generation cephalosporins are a major public health issue. As food may be a vehicle in the spread of ESLB-producing bacteria, a study on the occurrence of cephalosporin-resistantu Escherichia coli in food was initiated. A total of 404 ESBL-producing isolates were obtained from animal-derived food samples (e.g., poultry products, pork, beef and raw milk) between 2011 and 2013. As CTX-M-15 is the most abundant enzyme in ESBL-producing E. coli causing human infections, this study focusses on E. coli isolates from food samples harboring the blaCTX-M-15 gene. The blaCTX-M-15 gene was detected in 5.2% (n = 21) of all isolates. Molecular analyses revealed a phylogenetic group A ST167 clone that was repeatedly isolated from raw milk and beef samples over a period of 6 months. The analyses indicate that spread of CTX-M-15-producing E. coli in German food samples were associated with a multireplicon IncF (FIA FIB FII) plasmid and additional antimicrobial resistance genes such as aac(6)-Ib-cr, blaOXA-1, catB3, different tet-variants as well as a class 1 integron with an aadA5/dfrA17 gene cassette. In addition, four phylogenetic group A ST410 isolates were detected. Three of them carried a chromosomal copy of the blaCTX-M-15 gene and a single isolate with the gene on a 90 kb IncF plasmid. The blaCTX-M-15 gene was always associated with the ISEcp1 element. In conclusion, CTX-M-15-producing E. coli were detected in German food samples. Among isolates of different matrices, two prominent clonal lineages, namely A-ST167 and A-ST410, were identified. These lineages may be important for the foodborne dissemination of CTX-M-15-producing E. coli in Germany. Interestingly, these clonal lineages were reported to be widely distributed and especially prevalent in isolates from humans and livestock. Transmission of CTX-M-15-harboring isolates from food-producing animals to food appears probable, as isolates obtained from livestock and food samples within the same time period exhibit comparable characteristics as compared to isolates detected from human. However, the routes and direction of transmission need further investigation.
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Affiliation(s)
- Alexandra Irrgang
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Elisabet Guiral
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Beatriz Guerra
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,European Food Safety Authority, Parma, Italy
| | - Silvia Schmoger
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jens A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Institute of Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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6
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Tsai MY, Zhang B, Zheng W, Wolynes PG. Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA. J Am Chem Soc 2016; 138:13497-13500. [PMID: 27685351 DOI: 10.1021/jacs.6b08416] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fis protein is a nucleoid-associated protein that plays many roles in transcriptional regulation and DNA site-specific recombination. In contrast to the naïve expectation based on stoichiometry, recent single-molecule studies have shown that the dissociation of Fis protein from DNA is accelerated by increasing the concentration of the Fis protein. Because the detailed molecular mechanism of facilitated dissociation is still not clear, in this study, we employ computational methods to explore the binding landscapes of Fis:DNA complexes with various stoichiometries. When two Fis molecules are present, simulations uncover a ternary complex, where the originally bound Fis protein is partially dissociated from DNA. The simulations support a three-state sequential kinetic model (N ⇄ I → D) for facilitated dissociation, thus explaining the concentration-dependent dissociation.
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Affiliation(s)
- Min-Yeh Tsai
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Weihua Zheng
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Peter G Wolynes
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
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7
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Falgenhauer L, Imirzalioglu C, Ghosh H, Gwozdzinski K, Schmiedel J, Gentil K, Bauerfeind R, Kämpfer P, Seifert H, Michael GB, Schwarz S, Pfeifer Y, Werner G, Pietsch M, Roesler U, Guerra B, Fischer J, Sharp H, Käsbohrer A, Goesmann A, Hille K, Kreienbrock L, Chakraborty T. Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. Int J Antimicrob Agents 2016; 47:457-65. [PMID: 27208899 DOI: 10.1016/j.ijantimicag.2016.03.019] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/23/2016] [Accepted: 03/28/2016] [Indexed: 12/14/2022]
Abstract
Multidrug-resistant Escherichia coli encoding CTX-M-type extended-spectrum β-lactamases (ESBLs) are isolated in increasing numbers from humans, companion animals and livestock, raising concern regarding the exchange and spread of isolates in these populations. In this study, whole-genome sequencing of CTX-M-15-producing E. coli isolates recently sampled from humans, companion animals, livestock and farm environments was performed. In total, 26 different sequence types (STs) were detected, of which ST410 was the most frequent and was the only ST present in all populations studied. Five clades (designated A-E) were detected within the ST410 isolates. In particular, isolates of clade B were present in all four populations and had core genomes that differed by less than 70 single nucleotide polymorphisms (SNPs). Isolates of clades B and C were also clonally marked, exhibiting identical chromosomal insertions of blaCTX-M-15 at distinct loci. These data provide strong evidence for the clonal dissemination of specific clades of CTX-M-15-producing E. coli ST410 in human and animal populations.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Katrin Gentil
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Rolf Bauerfeind
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus Liebig University Giessen, Giessen, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, Germany
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Yvonne Pfeifer
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Michael Pietsch
- Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Free University Berlin, Berlin, Germany
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Hannah Sharp
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Annemarie Käsbohrer
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Alexander Goesmann
- Institute of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Katja Hille
- Institute for Biometry, Epidemiology, and Information Processing, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Lothar Kreienbrock
- Institute for Biometry, Epidemiology, and Information Processing, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany; German Center for Infection Research (DZIF), Braunschweig, Germany.
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8
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Wang B, Shao Y, Chen T, Chen W, Chen F. Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics. Sci Rep 2015; 5:18330. [PMID: 26691589 PMCID: PMC4686929 DOI: 10.1038/srep18330] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/16/2015] [Indexed: 12/11/2022] Open
Abstract
Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.
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Affiliation(s)
- Bin Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Tao Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Wanping Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
| | - Fusheng Chen
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China.,Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068, Hubei Province, P. R. China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, P. R. China
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9
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Ahmed W, Menon S, Karthik PV, Nagaraja V. Reduction in DNA topoisomerase I level affects growth, phenotype and nucleoid architecture of Mycobacterium smegmatis. MICROBIOLOGY-SGM 2014; 161:341-353. [PMID: 25516959 DOI: 10.1099/mic.0.000014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The steady-state negative supercoiling of eubacterial genomes is maintained by the action of DNA topoisomerases. Topoisomerase distribution varies in different species of mycobacteria. While Mycobacterium tuberculosis (Mtb) contains a single type I (TopoI) and a single type II (Gyrase) enzyme, Mycobacterium smegmatis (Msm) and other members harbour additional relaxases. TopoI is essential for Mtb survival. However, the necessity of TopoI or other relaxases in Msm has not been investigated. To recognize the importance of TopoI for growth, physiology and gene expression of Msm, we have developed a conditional knock-down strain of TopoI in Msm. The TopoI-depleted strain exhibited extremely slow growth and drastic changes in phenotypic characteristics. The cessation of growth indicates the essential requirement of the enzyme for the organism in spite of having additional DNA relaxation enzymes in the cell. Notably, the imbalance in TopoI level led to the altered expression of topology modulatory proteins, resulting in a diffused nucleoid architecture. Proteomic and transcript analysis of the mutant indicated reduced expression of the genes involved in central metabolic pathways and core DNA transaction processes. RNA polymerase (RNAP) distribution on the transcription units was affected in the TopoI-depleted cells, suggesting global alteration in transcription. The study thus highlights the essential requirement of TopoI in the maintenance of cellular phenotype, growth characteristics and gene expression in mycobacteria. A decrease in TopoI level led to altered RNAP occupancy and impaired transcription elongation, causing severe downstream effects.
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Affiliation(s)
- Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Shruti Menon
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Pullela V Karthik
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Valakunja Nagaraja
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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10
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Holins in bacteria, eukaryotes, and archaea: multifunctional xenologues with potential biotechnological and biomedical applications. J Bacteriol 2014; 197:7-17. [PMID: 25157079 DOI: 10.1128/jb.02046-14] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Holins form pores in the cytoplasmic membranes of bacteria for the primary purpose of releasing endolysins that hydrolyze the cell wall and induce cell death. Holins are encoded within bacteriophage genomes, where they promote cell lysis for virion release, and within bacterial genomes, where they serve a diversity of potential or established functions. These include (i) release of gene transfer agents, (ii) facilitation of programs of differentiation such as those that allow sporulation and spore germination, (iii) contribution to biofilm formation, (iv) promotion of responses to stress conditions, and (v) release of toxins and other proteins. There are currently 58 recognized families of holins and putative holins with members exhibiting between 1 and 4 transmembrane α-helical spanners, but many more families have yet to be discovered. Programmed cell death in animals involves holin-like proteins such as Bax and Bak that may have evolved from bacterial holins. Holin homologues have also been identified in archaea, suggesting that these proteins are ubiquitous throughout the three domains of life. Phage-mediated cell lysis of dual-membrane Gram-negative bacteria also depends on outer membrane-disrupting "spanins" that function independently of, but in conjunction with, holins and endolysins. In this minireview, we provide an overview of their modes of action and the first comprehensive summary of the many currently recognized and postulated functions and uses of these cell lysis systems. It is anticipated that future studies will result in the elucidation of many more such functions and the development of additional applications.
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11
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Structural change of DNA induced by nucleoid proteins: growth phase-specific Fis and stationary phase-specific Dps. Biophys J 2014; 105:1037-44. [PMID: 23972855 DOI: 10.1016/j.bpj.2013.07.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 12/29/2022] Open
Abstract
The effects of nucleoid proteins Fis and Dps of Escherichia coli on the higher order structure of a giant DNA were studied, in which Fis and Dps are known to be expressed mainly in the exponential growth phase and stationary phase, respectively. Fis causes loose shrinking of the higher order structure of a genome-sized DNA, T4 DNA (166 kbp), in a cooperative manner, that is, the DNA conformational transition proceeds through the appearance of a bimodal size distribution or the coexistence of elongated coil and shrunken globular states. The effective volume of the loosely shrunken state induced by Fis is 30-60 times larger than that of the compact state induced by spermidine, suggesting that cellular enzymes can access for DNA with the shrunken state but cannot for the compact state. Interestingly, Dps tends to inhibit the Fis-induced shrinkage of DNA, but promotes DNA compaction in the presence of spermidine. These characteristic effects of nucleotide proteins on a giant DNA are discussed by adopting a simple theoretical model with a mean-field approximation.
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12
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Abstract
Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.
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13
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Joyeux M, Vreede J. A model of H-NS mediated compaction of bacterial DNA. Biophys J 2013; 104:1615-22. [PMID: 23561538 DOI: 10.1016/j.bpj.2013.02.043] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/24/2013] [Accepted: 02/12/2013] [Indexed: 12/26/2022] Open
Abstract
The histone-like nucleoid structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. H-NS can bind to DNA in two different ways: in trans, by binding to two separate DNA duplexes, or in cis, by binding to different sites on the same duplex. Based on scanning force microscopy imaging and optical trap-driven unzipping assays, it has recently been suggested that DNA compaction may result from the antagonistic effects of H-NS binding to DNA in trans and cis configurations. To get more insight into the compaction mechanism, we constructed a coarse-grained model description of the compaction of bacterial DNA by H-NS. These simulations highlight the fact that DNA compaction indeed results from the subtle equilibrium between several competing factors, which include the deformation dynamics of the plasmid and the several binding modes of protein dimers to DNA, i.e., dangling configurations, cis- and trans-binding. In particular, the degree of compaction is extremely sensitive to the difference in binding energies of the cis and trans configurations. Our simulations also point out that the conformations of the DNA-protein complexes are significantly different in bulk and in planar conditions, suggesting that conformations observed on mica surfaces may differ significantly from those that prevail in living cells.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, Centre National de la Recherche Scientifique UMR5588, Université Joseph Fourier Grenoble 1, St. Martin d'Hères, France.
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14
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Kundukad B, Cong P, van der Maarel JRC, Doyle PS. Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein. Nucleic Acids Res 2013; 41:8280-8. [PMID: 23828037 PMCID: PMC3783175 DOI: 10.1093/nar/gkt593] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HU is a protein that plays a role in various bacterial processes including compaction, transcription and replication of the genome. Here, we use atomic force microscopy to study the effect of HU on the stiffness and supercoiling of double-stranded DNA. First, we measured the persistence length, height profile, contour length and bending angle distribution of the DNA-HU complex after different incubation times of HU with linear DNA. We found that the persistence and contour length depend on the incubation time. At high concentrations of HU, DNA molecules first become stiff with a larger value of the persistence length. The persistence length then decreases over time and the molecules regain the flexibility of bare DNA after ∼2 h. Concurrently, the contour length shows a slight increase. Second, we measured the change in topology of closed circular relaxed DNA following binding of HU. Here, we observed that HU induces supercoiling over a similar time span as the measured change in persistence length. Our observations can be rationalized in terms of the formation of a nucleoprotein filament followed by a structural rearrangement of the bound HU on DNA. The rearrangement results in a change in topology, an increase in bending flexibility and an increase in contour length through a decrease in helical pitch of the duplex.
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Affiliation(s)
- Binu Kundukad
- BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore-Massachusetts Institute of Technology Alliance, National University of Singapore, Singapore 117576, Department of Physics, National University of Singapore, Singapore 117542 and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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15
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Drecktrah D, Hall LS, Hoon-Hanks LL, Samuels DS. An inverted repeat in the ospC operator is required for induction in Borrelia burgdorferi. PLoS One 2013; 8:e68799. [PMID: 23844242 PMCID: PMC3700930 DOI: 10.1371/journal.pone.0068799] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 06/03/2013] [Indexed: 01/27/2023] Open
Abstract
Borrelia burgdorferi, the spirochete that causes Lyme disease, differentially regulates synthesis of the outer membrane lipoprotein OspC to infect its host. OspC is required to establish infection but then repressed in the mammal to avoid clearance by the adaptive immune response. Inverted repeats (IR) upstream of the promoter have been implicated as an operator to regulate ospC expression. We molecularly dissected the distal inverted repeat (dIR) of the ospC operator by site-directed mutagenesis at its endogenous location on the circular plasmid cp26. We found that disrupting the dIR but maintaining the proximal IR prevented induction of OspC synthesis by DNA supercoiling, temperature, and pH. Moreover, the base-pairing potential of the two halves of the dIR was more important than the nucleotide sequence in controlling OspC levels. These results describe a cis-acting element essential for the expression of the virulence factor OspC.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, The University of Montana, Missoula, Montana, United States of America
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16
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Zhang Z, Saier MH. Transposon-mediated adaptive and directed mutations and their potential evolutionary benefits. J Mol Microbiol Biotechnol 2012; 21:59-70. [PMID: 22248543 DOI: 10.1159/000333108] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Transposons, mobile genetic elements that can hop from one chromosomal location to another, are known to be both beneficial and deleterious to the cell that bears them. Their value in accelerating evolutionary adaptation is well recognized. We herein summarize published research dealing with these elements and then move on to review our own research efforts which focus on a small transposon that can induce mutations under the control of host factors in a process that phenotypically and mechanistically conforms to the definition of 'directed mutation'. Directed mutations occur at higher frequencies when they are beneficial, being induced by the stress condition that they relieve. Here, we review evidence for transposon-mediated directed mutation in Escherichia coli. Deletion mutants in the crp gene can not grow on glycerol (Glp(-)); however, these cells mutate specifically to efficient glycerol utilization (Glp(+)) at rates that are greatly enhanced by the presence of glycerol or the loss of the glycerol repressor (GlpR). These rates are greatly depressed by glucose or by glpR overexpression. Of the four tandem GlpR-binding sites (O1-O4) in the control region of the glpFK operon, O4 (downstream) specifically controls glpFK expression while O1 (upstream) controls mutation rate. Mutation is due to insertion of the small transposon IS5 into a specific site just upstream of the glpFK promoter. Mutational control by the glycerol regulon repressor GlpR is independent of the selection and assay procedures, and IS5 insertion into other gene activation sites is unaffected by the presence of glycerol or the loss of GlpR. The results establish the principle of transposon-mediated directed mutation, identify a protein responsible for its regulation, and define essential aspects of the mechanism.
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Affiliation(s)
- Zhongge Zhang
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, USA.
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17
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The challenge of merging food safety diagnostic needs with quantitative PCR platforms. Trends Food Sci Technol 2011. [DOI: 10.1016/j.tifs.2011.02.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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18
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Saier, Jr. MH. Did Adaptive and Directed Mutation Evolve to Accelerate Stress-Induced Evolutionary Change? J Mol Microbiol Biotechnol 2011; 21:5-7. [DOI: 10.1159/000332746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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19
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Condensed DNA: condensing the concepts. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 105:208-22. [PMID: 20638406 DOI: 10.1016/j.pbiomolbio.2010.07.002] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 07/11/2010] [Indexed: 01/09/2023]
Abstract
DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.
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20
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Cook PR. A model for all genomes: the role of transcription factories. J Mol Biol 2010; 395:1-10. [PMID: 19852969 DOI: 10.1016/j.jmb.2009.10.031] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2009] [Revised: 09/30/2009] [Accepted: 10/14/2009] [Indexed: 12/26/2022]
Abstract
A model for all genomes involving one major architectural motif is presented: DNA or chromatin loops are tethered to "factories" through the transcription machinery-a polymerase (active or inactive) or its transcription factors (activators or repressors). These loops appear and disappear as polymerases initiate and terminate (and as factors bind and dissociate), so the structure is ever-changing and self-organizing. This model is parsimonious, detailed (and so easily tested), and incorporates elements found in various other models.
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Affiliation(s)
- Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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21
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Weiner A, Zauberman N, Minsky A. Recombinational DNA repair in a cellular context: a search for the homology search. Nat Rev Microbiol 2009; 7:748-55. [PMID: 19756013 DOI: 10.1038/nrmicro2206] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Double-strand DNA breaks (DSBs) are the most detrimental lesion that can be sustained by the genetic complement, and their inaccurate mending can be just as damaging. According to the consensual view, precise DSB repair relies on homologous recombination. Here, we review studies on DNA repair, chromatin diffusion and chromosome confinement, which collectively imply that a genome-wide search for a homologous template, generally thought to be a pivotal stage in all homologous DSB repair pathways, is improbable. The implications of this assertion for the scope and constraints of DSB repair pathways and for the ability of diverse organisms to cope with DNA damage are discussed.
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Affiliation(s)
- Allon Weiner
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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22
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On mapping the genetic code. J Theor Biol 2009; 259:860-2. [DOI: 10.1016/j.jtbi.2009.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2009] [Revised: 04/27/2009] [Accepted: 05/05/2009] [Indexed: 01/04/2023]
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23
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Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: examining the effect of transcription on nucleoid structure in the absence of transertion. J Bacteriol 2009; 191:4180-5. [PMID: 19395497 DOI: 10.1128/jb.01707-08] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In Escherichia coli the genome must be compacted approximately 1,000-fold to be contained in a cellular structure termed the nucleoid. It is proposed that the structure of the nucleoid is determined by a balance of multiple compaction forces and one major expansion force. The latter is mediated by transertion, a coupling of transcription, translation, and translocation of nascent membrane proteins and/or exported proteins. In supporting this notion, it has been shown consistently that inhibition of transertion by the translation inhibitor chloramphenicol results in nucleoid condensation due to the compaction forces that remain active in the cell. Our previous study showed that during optimal growth, RNA polymerase is concentrated into transcription foci or "factories," analogous to the eukaryotic nucleolus, indicating that transcription and RNA polymerase distribution affect the nucleoid structure. However, the interpretation of the role of transcription in the structure of the nucleoid is complicated by the fact that transcription is implicated in both compacting forces and the expansion force. In this work, we used a new approach to further examine the effect of transcription, specifically from rRNA operons, on the structure of the nucleoid, when the major expansion force was eliminated. Our results showed that transcription is necessary for the chloramphenicol-induced nucleoid compaction. Further, an active transcription from multiple rRNA operons in chromosome is critical for the compaction of nucleoid induced by inhibition of translation. All together, our data demonstrated that transcription of rRNA operons is a key mechanism affecting genome compaction and nucleoid structure.
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