1
|
Dorman CJ. Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations. Mol Microbiol 2023; 119:19-28. [PMID: 36565252 PMCID: PMC10108321 DOI: 10.1111/mmi.15014] [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: 10/28/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/25/2022]
Abstract
Transcription is a noisy and stochastic process that produces sibling-to-sibling variations in physiology across a population of genetically identical cells. This pattern of diversity reflects, in part, the burst-like nature of transcription. Transcription bursting has many causes and a failure to remove the supercoils that accumulate in DNA during transcription elongation is an important contributor. Positive supercoiling of the DNA ahead of the transcription elongation complex can result in RNA polymerase stalling if this DNA topological roadblock is not removed. The relaxation of these positive supercoils is performed by the ATP-dependent type II topoisomerases DNA gyrase and topoisomerase IV. Interference with the action of these topoisomerases involving, inter alia, topoisomerase poisons, fluctuations in the [ATP]/[ADP] ratio, and/or the intervention of nucleoid-associated proteins with GapR-like or YejK-like activities, may have consequences for the smooth operation of the transcriptional machinery. Antibiotic-tolerant (but not resistant) persister cells are among the phenotypic outliers that may emerge. However, interference with type II topoisomerase activity can have much broader consequences, making it an important epigenetic driver of physiological diversity in the bacterial population.
Collapse
Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|
2
|
Evolutionary Instability of Collateral Susceptibility Networks in Ciprofloxacin-Resistant Clinical Escherichia coli Strains. mBio 2022; 13:e0044122. [PMID: 35862779 PMCID: PMC9426462 DOI: 10.1128/mbio.00441-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Collateral sensitivity and resistance occur when resistance development toward one antimicrobial either potentiates or deteriorates the effect of others. Previous reports on collateral effects on susceptibility focus on newly acquired resistance determinants and propose that novel treatment guidelines informed by collateral networks may reduce the evolution, selection, and spread of antimicrobial resistance. In this study, we investigate the evolutionary stability of collateral networks in five ciprofloxacin-resistant, clinical Escherichia coli strains. After 300 generations of experimental evolution without antimicrobials, we show complete fitness restoration in four of five genetic backgrounds and demonstrate evolutionary instability in collateral networks of newly acquired resistance determinants. We show that compensatory mutations reducing efflux expression are the main drivers destabilizing initial collateral networks and identify rpoS as a putative target for compensatory evolution. Our results add another layer of complexity to future predictions and clinical application of collateral networks.
Collapse
|
3
|
Forquet R, Nasser W, Reverchon S, Meyer S. Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters. Nucleic Acids Res 2022; 50:7287-7297. [PMID: 35776118 PMCID: PMC9303308 DOI: 10.1093/nar/gkac579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
DNA supercoiling acts as a global transcriptional regulator in bacteria, but the promoter sequence or structural determinants controlling its effect remain unclear. It was previously proposed to modulate the torsional angle between the −10 and −35 hexamers, and thereby regulate the formation of the closed-complex depending on the length of the ‘spacer’ between them. Here, we develop a thermodynamic model of this notion based on DNA elasticity, providing quantitative and parameter-free predictions of the relative activation of promoters containing a short versus long spacer when the DNA supercoiling level is varied. The model is tested through an analysis of in vitro and in vivo expression assays of mutant promoters with variable spacer lengths, confirming its accuracy for spacers ranging from 15 to 19 nucleotides, except those of 16 nucleotides where other regulatory mechanisms likely overcome the effect of this specific step. An analysis at the whole-genome scale in Escherichia coli then demonstrates a significant effect of the spacer length on the genomic expression after transient or inheritable superhelical variations, validating the model’s predictions. Altogether, this study shows an example of mechanical constraints associated to promoter binding by RNA Polymerase underpinning a basal and global regulatory mechanism.
Collapse
Affiliation(s)
- Raphaël Forquet
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
| | - Sam Meyer
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240 MAP, F-69622, France
| |
Collapse
|
4
|
Duprey A, Groisman EA. The regulation of DNA supercoiling across evolution. Protein Sci 2021; 30:2042-2056. [PMID: 34398513 PMCID: PMC8442966 DOI: 10.1002/pro.4171] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 11/11/2022]
Abstract
DNA supercoiling controls a variety of cellular processes, including transcription, recombination, chromosome replication, and segregation, across all domains of life. As a physical property, DNA supercoiling alters the double helix structure by under- or over-winding it. Intriguingly, the evolution of DNA supercoiling reveals both similarities and differences in its properties and regulation across the three domains of life. Whereas all organisms exhibit local, constrained DNA supercoiling, only bacteria and archaea exhibit unconstrained global supercoiling. DNA supercoiling emerges naturally from certain cellular processes and can also be changed by enzymes called topoisomerases. While structurally and mechanistically distinct, topoisomerases that dissipate excessive supercoils exist in all domains of life. By contrast, topoisomerases that introduce positive or negative supercoils exist only in bacteria and archaea. The abundance of topoisomerases is also transcriptionally and post-transcriptionally regulated in domain-specific ways. Nucleoid-associated proteins, metabolites, and physicochemical factors influence DNA supercoiling by acting on the DNA itself or by impacting the activity of topoisomerases. Overall, the unique strategies that organisms have evolved to regulate DNA supercoiling hold significant therapeutic potential, such as bactericidal agents that target bacteria-specific processes or anticancer drugs that hinder abnormal DNA replication by acting on eukaryotic topoisomerases specialized in this process. The investigation of DNA supercoiling therefore reveals general principles, conserved mechanisms, and kingdom-specific variations relevant to a wide range of biological questions.
Collapse
Affiliation(s)
- Alexandre Duprey
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
| | - Eduardo A. Groisman
- Department of Microbial PathogenesisYale School of MedicineNew HavenConnecticutUSA
- Yale Microbial Sciences InstituteWest HavenConnecticutUSA
| |
Collapse
|
5
|
Forquet R, Pineau M, Nasser W, Reverchon S, Meyer S. Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters. mSystems 2021; 6:e0097821. [PMID: 34427530 PMCID: PMC8422995 DOI: 10.1128/msystems.00978-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
DNA supercoiling acts as a global transcriptional regulator that contributes to the rapid transcriptional response of bacteria to many environmental changes. Although a large fraction of promoters from phylogenetically distant species respond to superhelical variations, the sequence or structural determinants of this behavior remain elusive. Here, we focus on the sequence of the "discriminator" element that was shown to modulate this response in several promoters. We develop a quantitative thermodynamic model of this regulatory effect, focusing on open complex formation during transcription initiation independently from promoter-specific regulatory proteins. We analyze previous and new expression data and show that the model predictions quantitatively match the in vitro and in vivo supercoiling response of selected promoters with mutated discriminator sequences. We then test the universality of this mechanism by a statistical analysis of promoter sequences from transcriptomes of phylogenetically distant bacteria under conditions of supercoiling variations (i) by gyrase inhibitors, (ii) by environmental stresses, or (iii) inherited in the longest-running evolution experiment. In all cases, we identify a robust and significant sequence signature in the discriminator region, suggesting that supercoiling-modulated promoter opening underpins a ubiquitous regulatory mechanism in the prokaryotic kingdom based on the fundamental mechanical properties of DNA and its basal interaction with RNA polymerase. IMPORTANCE In this study, we highlight the role of the discriminator as a global sensor of supercoiling variations and propose the first quantitative regulatory model of this principle, based on the specific step of promoter opening during transcription initiation. It defines the predictive rule by which DNA supercoiling quantitatively modulates the expression rate of bacterial promoters, depending on the G/C content of their discriminator and independently from promoter-specific regulatory proteins. This basal mechanism affects a wide range of species, which is tested by an extensive analysis of global high-throughput expression data. Altogether, ours results confirm and provide a quantitative framework for the long-proposed notion that the discriminator sequence is a significant determinant of promoter supercoiling sensitivity, underpinning the ubiquitous regulatory action of DNA supercoiling on the core transcriptional machinery, in particular in response to quick environmental changes.
Collapse
Affiliation(s)
- Raphaël Forquet
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - Maïwenn Pineau
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - William Nasser
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - Sylvie Reverchon
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - Sam Meyer
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| |
Collapse
|
6
|
Lara AR, Jaén KE, Folarin O, Keshavarz-Moore E, Büchs J. Effect of the oxygen transfer rate on oxygen-limited production of plasmid DNA by Escherichia coli. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
7
|
Dorman CJ, Ní Bhriain N. CRISPR-Cas, DNA Supercoiling, and Nucleoid-Associated Proteins. Trends Microbiol 2019; 28:19-27. [PMID: 31519332 DOI: 10.1016/j.tim.2019.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 12/11/2022]
Abstract
In this opinion article we highlight links between the H-NS nucleoid-associated protein, variable DNA topology, the regulation of CRISPR-cas locus expression, CRISPR-Cas activity, and the recruitment of novel genetic information by the CRISPR array. We propose that the requirement that the invading mobile genetic element be negatively supercoiled limits effective CRISPR action to a window in the bacterial growth cycle when DNA topology is optimal, and that this same window is used for the efficient integration of new spacer sequences at the CRISPR array. H-NS silences CRISPR promoters, and we propose that antagonists of H-NS, such as the LeuO transcription factor, provide a basis for a stochastic genetic switch that acts at random in each cell in the bacterial population. In addition, we wish to propose a mechanism by which mobile genetic elements can suppress CRISPR-cas transcription using H-NS homologues. Although the individual components of this network are known, we propose a new model in which they are integrated and linked to the physiological state of the bacterium. The model provides a basis for cell-to-cell variation in the expression and performance of CRISPR systems in bacterial populations.
Collapse
Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Trinity College Dublin, Dublin 2, Ireland.
| | - Niamh Ní Bhriain
- Department of Microbiology, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|
8
|
Dorman CJ. DNA supercoiling and transcription in bacteria: a two-way street. BMC Mol Cell Biol 2019; 20:26. [PMID: 31319794 PMCID: PMC6639932 DOI: 10.1186/s12860-019-0211-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/09/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The processes of DNA supercoiling and transcription are interdependent because the movement of a transcription elongation complex simultaneously induces under- and overwinding of the DNA duplex and because the initiation, elongation and termination steps of transcription are all sensitive to the topological state of the DNA. RESULTS Policing of the local and global supercoiling of DNA by topoisomerases helps to sustain the major DNA-based transactions by eliminating barriers to the movement of transcription complexes and replisomes. Recent data from whole-genome and single-molecule studies have provided new insights into how interactions between transcription and the supercoiling of DNA influence the architecture of the chromosome and how they create cell-to-cell diversity at the level of gene expression through transcription bursting. CONCLUSIONS These insights into fundamental molecular processes reveal mechanisms by which bacteria can prevail in unpredictable and often hostile environments by becoming unpredictable themselves.
Collapse
Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| |
Collapse
|
9
|
Our Evolving Understanding of the Mechanism of Quinolones. Antibiotics (Basel) 2018; 7:antibiotics7020032. [PMID: 29642475 PMCID: PMC6023003 DOI: 10.3390/antibiotics7020032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 12/16/2022] Open
Abstract
The maintenance of DNA supercoiling is essential for the proper regulation of a plethora of biological processes. As a consequence of this mode of regulation, ahead of the replication fork, DNA replication machinery is prone to introducing supercoiled regions into the DNA double helix. Resolution of DNA supercoiling is essential to maintain DNA replication rates that are amenable to life. This resolution is handled by evolutionarily conserved enzymes known as topoisomerases. The activity of topoisomerases is essential, and therefore constitutes a prime candidate for targeting by antibiotics. In this review, we present hallmark investigations describing the mode of action of quinolones, one of the antibacterial classes targeting the function of topoisomerases in bacteria. By chronologically analyzing data gathered on the mode of action of this imperative antibiotic class, we highlight the necessity to look beyond primary drug-target interactions towards thoroughly understanding the mechanism of quinolones at the level of the cell.
Collapse
|
10
|
Bacterial pathogen gene regulation: a DNA-structure-centred view of a protein-dominated domain. Clin Sci (Lond) 2017; 130:1165-77. [PMID: 27252403 DOI: 10.1042/cs20160024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/15/2016] [Indexed: 02/03/2023]
Abstract
The mechanisms used by bacterial pathogens to regulate the expression of their genes, especially their virulence genes, have been the subject of intense investigation for several decades. Whole genome sequencing projects, together with more targeted studies, have identified hundreds of DNA-binding proteins that contribute to the patterns of gene expression observed during infection as well as providing important insights into the nature of the gene products whose expression is being controlled by these proteins. Themes that have emerged include the importance of horizontal gene transfer to the evolution of pathogens, the need to impose regulatory discipline upon these imported genes and the important roles played by factors normally associated with the organization of genome architecture as regulatory principles in the control of virulence gene expression. Among these architectural elements is the structure of DNA itself, its variable nature at a topological rather than just at a base-sequence level and its ability to play an active (as well as a passive) part in the gene regulation process.
Collapse
|
11
|
Dorman CJ, Bogue MM. The interplay between DNA topology and accessory factors in site-specific recombination in bacteria and their bacteriophages. Sci Prog 2016; 99:420-437. [PMID: 28742481 PMCID: PMC10365484 DOI: 10.3184/003685016x14811202974921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Site-specific recombination is employed widely in bacteria and bacteriophage as a basis for genetic switching events that control phenotypic variation. It plays a vital role in the life cycles of phages and in the replication cycles of chromosomes and plasmids in bacteria. Site-specific recombinases drive these processes using very short segments of identical (or nearly identical) DNA sequences. In some cases, the efficiencies of the recombination reactions are modulated by the topological state of the participating DNA sequences and by the availability of accessory proteins that shape the DNA. These dependencies link the molecular machines that conduct the recombination reactions to the physiological state of the cell. This is because the topological state of bacterial DNA varies constantly during the growth cycle and so does the availability of the accessory factors. In addition, some accessory factors are under allosteric control by metabolic products or second messengers that report the physiological status of the cell. The interplay between DNA topology, accessory factors and site-specific recombination provides a powerful illustration of the connectedness and integration of molecular events in bacterial cells and in viruses that parasitise bacterial cells.
Collapse
Affiliation(s)
| | - Marina M. Bogue
- Natural Science (Microbiology) from Trinity College Dublin, Ireland
| |
Collapse
|
12
|
Dorman CJ, Dorman MJ. DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression. Biophys Rev 2016; 8:89-100. [PMID: 28510216 DOI: 10.1007/s12551-016-0238-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/01/2016] [Indexed: 11/28/2022] Open
Abstract
Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.
Collapse
Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | - Matthew J Dorman
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| |
Collapse
|
13
|
DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression. Biophys Rev 2016; 8:209-220. [PMID: 28510224 DOI: 10.1007/s12551-016-0205-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/01/2016] [Indexed: 12/27/2022] Open
Abstract
Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination. The topological state of DNA also influences its affinity for some DNA binding proteins, especially in DNA sequences that have a high A + T base content. The underwinding of DNA by the ATP-dependent topoisomerase DNA gyrase creates a continuum between metabolic flux, DNA topology and gene expression that underpins the global response of the genome to changes in the intracellular and external environments. These connections describe a fundamental and generalised mechanism affecting global gene expression that underlies the specific control of transcription operating through conventional transcription factors. This mechanism also provides a basal level of control for genes acquired by horizontal DNA transfer, assisting microbial evolution, including the evolution of pathogenic bacteria.
Collapse
|
14
|
Higgins NP, Vologodskii AV. Topological Behavior of Plasmid DNA. Microbiol Spectr 2015; 3:10.1128/microbiolspec.PLAS-0036-2014. [PMID: 26104708 PMCID: PMC4480603 DOI: 10.1128/microbiolspec.plas-0036-2014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 11/20/2022] Open
Abstract
The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.
Collapse
Affiliation(s)
- N Patrick Higgins
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | | |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Redgrave LS, Sutton SB, Webber MA, Piddock LJV. Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success. Trends Microbiol 2014; 22:438-45. [PMID: 24842194 DOI: 10.1016/j.tim.2014.04.007] [Citation(s) in RCA: 573] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/11/2014] [Accepted: 04/16/2014] [Indexed: 12/12/2022]
Abstract
Quinolone and fluoroquinolone antibiotics are potent, broad-spectrum agents commonly used to treat a range of infections. Resistance to these agents is multifactorial and can be via one or a combination of target-site gene mutations, increased production of multidrug-resistance (MDR) efflux pumps, modifying enzymes, and/or target-protection proteins. Fluoroquinolone-resistant clinical isolates of bacteria have emerged readily and recent data have shown that resistance to this class of antibiotics can have diverse, species-dependent impacts on host-strain fitness. Here we outline the impacts of quinolone-resistance mutations in relation to the fitness and evolutionary success of mutant strains.
Collapse
Affiliation(s)
- Liam S Redgrave
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Sam B Sutton
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark A Webber
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Laura J V Piddock
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK.
| |
Collapse
|
17
|
Donczew R, Zakrzewska-Czerwińska J, Zawilak-Pawlik A. Beyond DnaA: the role of DNA topology and DNA methylation in bacterial replication initiation. J Mol Biol 2014; 426:2269-82. [PMID: 24747048 DOI: 10.1016/j.jmb.2014.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 12/31/2022]
Abstract
The replication of chromosomal DNA is a fundamental event in the life cycle of every cell. The first step of replication, initiation, is controlled by multiple factors to ensure only one round of replication per cell cycle. The process of initiation has been described most thoroughly for bacteria, especially Escherichia coli, and involves many regulatory proteins that vary considerably between different species. These proteins control the activity of the two key players of initiation in bacteria: the initiator protein DnaA and the origin of chromosome replication (oriC). Factors involved in the control of the availability, activity, or oligomerization of DnaA during initiation are generally regarded as the most important and thus have been thoroughly characterized. Other aspects of the initiation process, such as origin accessibility and susceptibility to unwinding, have been less explored. However, recent findings indicate that these factors have a significant role. This review focuses on DNA topology, conformation, and methylation as important factors that regulate the initiation process in bacteria. We present a comprehensive summary of the factors involved in the modulation of DNA topology, both locally at oriC and more globally at the level of the entire chromosome. We show clearly that the conformation of oriC dynamically changes, and control of this conformation constitutes another, important factor in the regulation of bacterial replication initiation. Furthermore, the process of initiation appears to be associated with the dynamics of the entire chromosome and this association is an important but largely unexplored phenomenon.
Collapse
Affiliation(s)
- Rafał Donczew
- Institute of Immunology and Experimental Therapy, Department of Microbiology, Polish Academy of Sciences, Weigla 12, 53-114 Wrocław, Poland.
| | - Jolanta Zakrzewska-Czerwińska
- Institute of Immunology and Experimental Therapy, Department of Microbiology, Polish Academy of Sciences, Weigla 12, 53-114 Wrocław, Poland; Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-138 Wrocław, Poland.
| | - Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy, Department of Microbiology, Polish Academy of Sciences, Weigla 12, 53-114 Wrocław, Poland.
| |
Collapse
|
18
|
Amato SM, Brynildsen MP. Nutrient transitions are a source of persisters in Escherichia coli biofilms. PLoS One 2014; 9:e93110. [PMID: 24667358 PMCID: PMC3965526 DOI: 10.1371/journal.pone.0093110] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 03/03/2014] [Indexed: 11/18/2022] Open
Abstract
Chronic and recurrent infections have been attributed to persisters in biofilms, and despite this importance, the mechanisms of persister formation in biofilms remain unclear. The plethora of biofilm characteristics that could give rise to persisters, including slower growth, quorum signaling, oxidative stress, and nutrient heterogeneity, have complicated efforts to delineate formation pathways that generate persisters during biofilm development. Here we sought to specifically determine whether nutrient transitions, which are a common metabolic stress encountered within surface-attached communities, stimulate persister formation in biofilms and if so, to then identify the pathway. To accomplish this, we established an experimental methodology where nutrient availability to biofilm cells could be controlled exogenously, and then used that method to discover that diauxic carbon source transitions stimulated persister formation in Escherichia coli biofilms. Previously, we found that carbon source transitions stimulate persister formation in planktonic E. coli cultures, through a pathway that involved ppGpp and nucleoid-associated proteins, and therefore, tested the functionality of that pathway in biofilms. Biofilm persister formation was also found to be dependent on ppGpp and nucleoid-associated proteins, but the importance of specific proteins and enzymes between biofilm and planktonic lifestyles was significantly different. Data presented here support the increasingly appreciated role of ppGpp as a central mediator of bacterial persistence and demonstrate that nutrient transitions can be a source of persisters in biofilms.
Collapse
Affiliation(s)
- Stephanie M. Amato
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Mark P. Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
| |
Collapse
|
19
|
Quinn HJ, Cameron ADS, Dorman CJ. Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response. PLoS Genet 2014; 10:e1004215. [PMID: 24603618 PMCID: PMC3945435 DOI: 10.1371/journal.pgen.1004215] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 01/16/2014] [Indexed: 12/26/2022] Open
Abstract
The evolution of new gene networks is a primary source of genetic innovation that allows bacteria to explore and exploit new niches, including pathogenic interactions with host organisms. For example, the archetypal DNA binding protein, OmpR, is identical between Salmonella Typhimurium serovar Typhimurium and Escherichia coli, but regulatory specialization has resulted in different environmental triggers of OmpR expression and largely divergent OmpR regulons. Specifically, ompR mRNA and OmpR protein levels are elevated by acid pH in S. Typhimurium but not in E. coli. This differential expression pattern is due to differences in the promoter regions of the ompR genes and the E. coli ompR orthologue can be made acid-inducible by introduction of the appropriate sequences from S. Typhimurium. The OmpR regulon in S. Typhimurium overlaps that of E. coli at only 15 genes and includes many horizontally acquired genes (including virulence genes) that E. coli does not have. We found that OmpR binds to its genomic targets in higher abundance when the DNA is relaxed, something that occurs in S. Typhimurium as a result of acid stress and which is a requirement for optimal expression of its virulence genes. The genomic targets of OmpR do not share a strong nucleotide sequence consensus: we propose that the ability of OmpR to recruit additional genes to its regulon arises from its modest requirements for specificity in its DNA targets with its preference for relaxed DNA allowing it to cooperate with DNA-topology-based allostery to modulate transcription in response to acid stress.
Collapse
Affiliation(s)
- Heather J. Quinn
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Andrew D. S. Cameron
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Charles J. Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
- * E-mail:
| |
Collapse
|
20
|
Leuschner C, Antranikian G. Heat-stable enzymes from extremely thermophilic and hyperthermophilic microorganisms. World J Microbiol Biotechnol 2014; 11:95-114. [PMID: 24414414 DOI: 10.1007/bf00339139] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Only in the last decade have microorganisms been discovered which grow near or above 100°C. The enzymes that are formed by these extremely thermophilic (growth temperature 65 to 85°C) and hyperthermophilic (growth temperature 85 to 110°C) microorganisms are of great interest. This review covers the extracellular and intracellular enzymes of these exotic microorganisms that have recently been described. Polymer-hydrolysing enzymes, such as amylolytic, cellulolytic, hemicellulolytic and proteolytic enzymes, will be discussed. In addition, the properties of the intracellular enzymes involved in carbohydrate and amino-acid metabolism and DNA-binding and chaperones and chaperone-like proteins from hyperthermophiles are described. Due to the unusual properties of these heat-stable enzymes, they are expected to fill the gap between biological and chemical processes.
Collapse
|
21
|
Cameron ADS, Kröger C, Quinn HJ, Scally IK, Daly AJ, Kary SC, Dorman CJ. Transmission of an oxygen availability signal at the Salmonella enterica serovar Typhimurium fis promoter. PLoS One 2013; 8:e84382. [PMID: 24358360 PMCID: PMC3865300 DOI: 10.1371/journal.pone.0084382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022] Open
Abstract
The nucleoid-associated protein FIS is a global regulator of gene expression and chromosome structure in Escherichia coli and Salmonella enterica. Despite the importance of FIS for infection and intracellular invasion, very little is known about the regulation of S. enterica fis expression. Under standard laboratory growth conditions, fis is highly expressed during rapid growth but is then silenced as growth slows. However, if cells are cultured in non-aerated conditions, fis expression is sustained during stationary phase. This led us to test whether the redox-sensing transcription factors ArcA and FNR regulate S. enterica fis. Deletion of FNR had no detectable effect, whereas deletion of ArcA had the unexpected effect of further elevating fis expression in stationary phase. ArcA required RpoS for induction of fis expression, suggesting that ArcA indirectly affects fis expression. Other putative regulators were found to play diverse roles: FIS acted directly as an auto-repressor (as expected), whereas CRP had little direct effect on fis expression. Deleting regions of the fis promoter led to the discovery of a novel anaerobically-induced transcription start site (Pfis-2) upstream of the primary transcription start site (Pfis-1). Promoter truncation also revealed that the shortest functional fis promoter was incapable of sustained expression. Moreover, fis expression was observed to correlate directly with DNA supercoiling in non-aerated conditions. Thus, the full-length S. enterica fis promoter region may act as a topological switch that is sensitive to stress-induced duplex destabilisation and up-regulates expression in non-aerated conditions.
Collapse
Affiliation(s)
- Andrew D. S. Cameron
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
- Department of Biology, University of Regina, Regina, SK, Canada
| | - Carsten Kröger
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Heather J. Quinn
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Isobel K. Scally
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Anne J. Daly
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Stefani C. Kary
- Department of Biology, University of Regina, Regina, SK, Canada
| | - Charles J. Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
- * E-mail:
| |
Collapse
|
22
|
Mlc is a transcriptional activator with a key role in integrating cyclic AMP receptor protein and integration host factor regulation of leukotoxin RNA synthesis in Aggregatibacter actinomycetemcomitans. J Bacteriol 2013; 195:2284-97. [PMID: 23475968 DOI: 10.1128/jb.02144-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aggregatibacter actinomycetemcomitans, a periodontal pathogen, synthesizes leukotoxin (LtxA), a protein that helps the bacterium evade the host immune response. Transcription of the ltxA operon is induced during anaerobic growth. The cyclic AMP (cAMP) receptor protein (CRP) indirectly increases ltxA expression, but the intermediary regulator is unknown. Integration host factor (IHF) binds to and represses the leukotoxin promoter, but neither CRP nor IHF is responsible for the anaerobic induction of ltxA RNA synthesis. Thus, we have undertaken studies to identify other regulators of leukotoxin transcription and to demonstrate how these proteins work together to modulate leukotoxin synthesis. First, analyses of ltxA RNA expression from defined leukotoxin promoter mutations in the chromosome identify positions -69 to -35 as the key control region and indicate that an activator protein modulates leukotoxin transcription. We show that Mlc, which is a repressor in Escherichia coli, functions as a direct transcriptional activator in A. actinomycetemcomitans; an mlc deletion mutant reduces leukotoxin RNA synthesis, and recombinant Mlc protein binds specifically at the -68 to -40 region of the leukotoxin promoter. Furthermore, we show that CRP activates ltxA expression indirectly by increasing the levels of Mlc. Analyses of Δmlc, Δihf, and Δihf Δmlc strains demonstrate that Mlc can increase RNA polymerase (RNAP) activity directly and that IHF represses ltxA RNA synthesis mainly by blocking Mlc binding. Finally, a Δihf Δmlc mutant still induces ltxA during anaerobic growth, indicating that there are additional factors involved in leukotoxin transcriptional regulation. A model for the coordinated regulation of leukotoxin transcription is presented.
Collapse
|
23
|
Symbiotic characterization of Vibrio fischeri ES114 mutants that display enhanced luminescence in culture. Appl Environ Microbiol 2013; 79:2480-3. [PMID: 23377934 DOI: 10.1128/aem.03111-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio fischeri ES114 is a bioluminescent symbiont of the squid Euprymna scolopes. Like most isolates from E. scolopes, ES114 produces only dim luminescence outside the host, even in dense cultures. We previously identified mutants with brighter luminescence, and here we report their symbiotic phenotypes, providing insights into the host environment.
Collapse
|
24
|
Chintakayala K, Singh SS, Rossiter AE, Shahapure R, Dame RT, Grainger DC. E. coli Fis protein insulates the cbpA gene from uncontrolled transcription. PLoS Genet 2013; 9:e1003152. [PMID: 23341772 PMCID: PMC3547828 DOI: 10.1371/journal.pgen.1003152] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/24/2012] [Indexed: 12/20/2022] Open
Abstract
The Escherichia coli curved DNA binding protein A (CbpA) is a poorly characterised nucleoid associated factor and co-chaperone. It is expressed at high levels as cells enter stationary phase. Using genetics, biochemistry, and genomics, we have examined regulation of, and DNA binding by, CbpA. We show that Fis, the dominant growth-phase nucleoid protein, prevents CbpA expression in growing cells. Regulation by Fis involves an unusual “insulation” mechanism. Thus, Fis protects cbpA from the effects of a distal promoter, located in an adjacent gene. In stationary phase, when Fis levels are low, CbpA binds the E. coli chromosome with a preference for the intrinsically curved Ter macrodomain. Disruption of the cbpA gene prompts dramatic changes in DNA topology. Thus, our work identifies a novel role for Fis and incorporates CbpA into the growing network of factors that mediate bacterial chromosome structure. Compaction of chromosomal DNA is a fundamental process that impacts on all aspects of cellular biology. However, our understanding of chromosome organisation in bacteria is poorly developed. Since bacteria are amongst the most abundant living organisms on the planet, this represents a startling gap in our knowledge. Despite our lack of understanding, it has long been known that Escherichia coli, and other bacteria, radically re-model their chromosomes in response to environmental stress. This is most notable during periods of starvation, when the E. coli chromosome is super compacted. In dissecting the molecular mechanisms that control this phenomenon, we have found that regulatory cross-talk between DNA–organising proteins plays an essential role. Thus, the major DNA folding protein from growing E. coli inhibits production of the major chromosome organisers in starved cells. Our findings illustrate the highly dynamic nature of bacterial chromosomes. Thus, DNA topology, gene transcription, and chromosome folding proteins entwine to create a web of interactions that define the properties of the chromosome.
Collapse
Affiliation(s)
- Kiran Chintakayala
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Shivani S. Singh
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Amanda E. Rossiter
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rajesh Shahapure
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University, Leiden, The Netherlands
| | - Remus T. Dame
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University, Leiden, The Netherlands
| | - David C. Grainger
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
| |
Collapse
|
25
|
Dron A, Rabouille S, Claquin P, Le Roy B, Talec A, Sciandra A. Light-dark (12:12) cycle of carbon and nitrogen metabolism in Crocosphaera watsonii WH8501: relation to the cell cycle. Environ Microbiol 2011; 14:967-81. [DOI: 10.1111/j.1462-2920.2011.02675.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
26
|
Stefanopoulou M, Kokoschka M, Sheldrick WS, Wolters DA. Cell response of Escherichia coli
to cisplatin-induced stress. Proteomics 2011; 11:4174-88. [DOI: 10.1002/pmic.201100203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/19/2011] [Accepted: 08/04/2011] [Indexed: 11/08/2022]
|
27
|
Cameron ADS, Stoebel DM, Dorman CJ. DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica. Mol Microbiol 2011; 80:85-101. [DOI: 10.1111/j.1365-2958.2011.07560.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
28
|
Bright mutants of Vibrio fischeri ES114 reveal conditions and regulators that control bioluminescence and expression of the lux operon. J Bacteriol 2010; 192:5103-14. [PMID: 20693328 DOI: 10.1128/jb.00524-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio fischeri ES114, an isolate from the Euprymna scolopes light organ, produces little bioluminescence in culture but is ∼1,000-fold brighter when colonizing the host. Cell-density-dependent regulation alone cannot explain this phenomenon, because cells within colonies on solid medium are much dimmer than symbiotic cells despite their similar cell densities. To better understand this low luminescence in culture, we screened ∼20,000 mini-Tn5 mutants of ES114 for increased luminescence and identified 28 independent "luminescence-up" mutants with insertions in 14 loci. Mutations affecting the Pst phosphate uptake system led to the discovery that luminescence is upregulated under low-phosphate conditions by PhoB, and we also found that ainS, which encodes an autoinducer synthase, mediates repression of luminescence during growth on plates. Other novel luminescence-up mutants had insertions in acnB, topA, tfoY, phoQ, guaB, and two specific tRNA genes. Two loci, hns and lonA, were previously described as repressors of bioluminescence in transgenic Escherichia coli carrying the light-generating lux genes, and mutations in arcA and arcB were consistent with our report that Arc represses lux. Our results reveal a complex regulatory web governing luminescence and show how certain environmental conditions are integrated into regulation of the pheromone-dependent lux system.
Collapse
|
29
|
Gober JW, Kashket ER. Role of DNA Superhelicity in Regulation of Bacteroid-Associated Functions of Bradyrhizobium sp. Strain 32H1. Appl Environ Microbiol 2010; 55:1420-5. [PMID: 16347935 PMCID: PMC202881 DOI: 10.1128/aem.55.6.1420-1425.1989] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium sp. strain 32H1 cells express a number of bacteroid-associated functions and repress some functions related to the free-living state when grown ex planta under conditions of low (0.2%) oxygen tension and relatively high levels (>8 mM) of medium K. Expression of the bacteroid-associated phenotype was blocked by the DNA gyrase inhibitor novobiocin. Because the degree of negative supercoiling of DNA is the result of the activities of both DNA gyrase and topoisomerase I, we measured these enzymes in cells grown under nitrogen-fixing (low O(2), high K) and non-nitrogen-fixing conditions (low O(2), low [50 muM] K or high O(2), high K). Lower topoisomerase I activities were seen in extracts from nitrogen-fixing cells than in those from non-nitrogen-fixing cells. In contrast, DNA gyrase levels were lower in high-O(2)-grown cells than under the other conditions tested. These differences are consistent with an increase in DNA superhelicity associated with growth under low-O(2), high-K conditions. A spontaneous mutant resistant to the DNA gyrase inhibitor ciprofloxacin was found to be constitutive with respect to the K requirement, because it expressed the bacteroid-associated phenotype when grown under low-O(2), low-K conditions. The mutant cells gave rise to effective nodules on Macroptilium atropurpureum and possessed the low topoisomerase I activities and high DNA gyrase levels of low-O(2)-, high-K-grown wild-type cells. Our data suggest that changes in DNA supercoiling resulting from low O(2) tension and a high K concentration exert a major influence on the expression of the bacteroid-associated phenotype.
Collapse
Affiliation(s)
- J W Gober
- Department of Microbiology, Boston University School of Medicine, 80 E. Concord St., Boston, Massachusetts 02118-2394
| | | |
Collapse
|
30
|
Pennebaker K, Mackey KRM, Smith RM, Williams SB, Zehr JP. Diel cycling of DNA staining and nifH gene regulation in the unicellular cyanobacterium Crocosphaera watsonii strain WH 8501 (Cyanophyta). Environ Microbiol 2010; 12:1001-10. [PMID: 20105217 DOI: 10.1111/j.1462-2920.2010.02144.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Crocosphaera watsonii WH 8501 is a marine unicellular cyanobacterium that fixes nitrogen primarily during the dark phase of a light-dark (LD) cycle. Circadian clocks modulate gene transcription and cellular activity in many, if not all, cyanobacteria. A model for circadian control has been proposed in cyanobacteria, called the oscilloid model, which is based on topological changes of nucleoid DNA which in turn regulates gene transcription. In this study, the marine unicellular diazotrophic cyanobacteria C. watsonii WH 8501 and Cyanothece sp. ATCC 51142 were found to have daily fluctuations in DNA staining using Hoechst 33342 and SYBR I Green fluorescent dyes. Up to 20-fold decreases in DNA fluorescence of Hoechst-stained cells were observed during the dark phase when cultures were grown with a 12:12 LD cycle or under continuous light (LL). The variation in DNA staining was consistent with changes in DNA topology proposed in the oscilloid model. The abundance of nifH transcripts in C. watsonii WH 8501 was rhythmic under LD and LL cycles, consistent with a circadian rhythm. Cycles of DNA fluorescence and photosynthetic efficiency were disrupted when cultures were shifted into an early dark phase; however, nifH transcripts predictably increased in abundance following the premature transition from light to darkness. Thus, nifH gene expression in C. watsonii WH 8501 appears to be influenced by both circadian and environmental factors.
Collapse
Affiliation(s)
- Kory Pennebaker
- Ocean Sciences Department, University of California, Santa Cruz, CA 95064, USA
| | | | | | | | | |
Collapse
|
31
|
Corcoran CP, Dorman CJ. DNA relaxation-dependent phase biasing of the fim genetic switch in Escherichia coli depends on the interplay of H-NS, IHF and LRP. Mol Microbiol 2009; 74:1071-82. [PMID: 19889099 DOI: 10.1111/j.1365-2958.2009.06919.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reversible inversion of the DNA element fimS is responsible for the phase variable expression of type 1 fimbriae in Escherichia coli. The FimB tyrosine integrase site-specific recombinase inverts fimS in the on-to-off and off-to-on directions with approximately equal efficiencies. However, when DNA supercoiling is relaxed, fimS adopts predominantly the on orientation. This orientational bias is known to require binding of the nucleoid-associated protein LRP within fimS. Here we show that binding of the IHF protein to a site immediately adjacent to fimS is also required for phase-on orientational bias. In the absence of both LRP and IHF binding, fimS adopts the off orientation and the H-NS protein is required to maintain this alternative orientational bias. Thus, fimS has three Recombination Directionality Factors, H-NS, IHF and LRP. The relevant H-NS binding site straddles the left inverted repeat in phase-off fimS and this site is disrupted when fimS inverts to the on orientation. The inversion of fimS with the associated creation and removal of an H-NS binding site required for DNA inversion biasing represents a novel mechanism for modulating the interaction of H-NS with a DNA target and for influencing a site-specific recombination reaction.
Collapse
Affiliation(s)
- Colin P Corcoran
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | | |
Collapse
|
32
|
Kim M, Lim S, Kim D, Choy HE, Ryu S. A tdcA mutation reduces the invasive ability of Salmonella enterica serovar typhimurium. Mol Cells 2009; 28:389-95. [PMID: 19812899 DOI: 10.1007/s10059-009-0133-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/25/2009] [Accepted: 08/26/2009] [Indexed: 10/20/2022] Open
Abstract
We previously observed that the transcription of some flagellar genes decreased in Salmonella Typhimurium tdcA mutant, which is a gene encoding the transcriptional activator of the tdc operon. Since flagella-mediated bacterial motility accelerates the invasion of Salmonella, we have examined the effect of tdcA mutation on the invasive ability as well as the flagellar biosynthesis in S. Typhimurium. A tdcA mutation caused defects in motility and formation of flagellin protein, FliC in S. Typhimurium. Invasion assays in the presence of a centrifugal force confirmed that the defect of flagellum synthesis decreases the ability of Salmonella to invade into cultured epithelial cells. In addition, we also found that the expression of Salmonella pathogenicity island 1 (SPI1) genes required for Salmonella invasion was down-regulated in the tdcA mutant because of the decreased expression of fliZ, a positive regulator of SPI1 transcriptional activator, hilA. Finally, the virulence of a S. Typhimurium tdcA mutant was attenuated compared to a wild type when administered orally. This study implies the role of tdcA in the invasion process of S. Typhimurium.
Collapse
Affiliation(s)
- Minjeong Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | | | | | | | | |
Collapse
|
33
|
Trigueros S, Tran T, Sorto N, Newmark J, Colloms SD, Sherratt DJ, Tolmasky ME. mwr Xer site-specific recombination is hypersensitive to DNA supercoiling. Nucleic Acids Res 2009; 37:3580-7. [PMID: 19359357 PMCID: PMC2699498 DOI: 10.1093/nar/gkp208] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The multiresistance plasmid pJHCMW1, first identified in a Klebsiella pneumoniae strain isolated from a neonate with meningitis, includes a Xer recombination site, mwr, with unique characteristics. Efficiency of resolution of mwr-containing plasmid dimers is strongly dependent on the osmotic pressure of the growth medium. An increase in supercoiling density of plasmid DNA was observed as the osmotic pressure of the growth culture decreased. Reporter plasmids containing directly repeated mwr, or the related cer sites were used to test if DNA topological changes were correlated with significant changes in efficiency of Xer recombination. Quantification of Holliday junctions showed that while recombination at cer was efficient at all levels of negative supercoiling, recombination at mwr became markedly less efficient as the level of supercoiling was reduced. These results support a model in which modifications at the level of supercoiling density caused by changes in the osmotic pressure of the culture medium affects resolution of mwr-containing plasmid dimers, a property that separates mwr from other Xer recombination target sites.
Collapse
Affiliation(s)
- Sonia Trigueros
- Bionanotechnology IRC Department of Physics, University of Oxford, Oxford OX1 3QU, UK.
| | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
The Gram-negative bacterium Escherichia coli and its close relative Salmonella enterica have made important contributions historically to our understanding of how bacteria control DNA supercoiling and of how supercoiling influences gene expression and vice versa. Now they are contributing again by providing examples where changes in DNA supercoiling affect the expression of virulence traits that are important for infectious disease. Available examples encompass both the earliest stages of pathogen–host interactions and the more intimate relationships in which the bacteria invade and proliferate within host cells. A key insight concerns the link between the physiological state of the bacterium and the activity of DNA gyrase, with downstream effects on the expression of genes with promoters that sense changes in DNA supercoiling. Thus the expression of virulence traits by a pathogen can be interpreted partly as a response to its own changing physiology. Knowledge of the molecular connections between physiology, DNA topology and gene expression offers new opportunities to fight infection.
Collapse
Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland.
| | | |
Collapse
|
35
|
Known Bioactive Small Molecules Probe the Function of a Widely Conserved but Enigmatic Bacterial ATPase, YjeE. ACTA ACUST UNITED AC 2008; 15:1287-95. [DOI: 10.1016/j.chembiol.2008.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 09/30/2008] [Accepted: 10/14/2008] [Indexed: 11/22/2022]
|
36
|
Hadjifrangiskou M, Koehler TM. Intrinsic curvature associated with the coordinately regulated anthrax toxin gene promoters. MICROBIOLOGY-SGM 2008; 154:2501-2512. [PMID: 18667583 DOI: 10.1099/mic.0.2007/016162-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The current model for virulence gene regulation in Bacillus anthracis involves several trans-acting factors, the most important of which appears to be the anthrax toxin activator encoded by the atxA gene. AtxA is a positive regulator of the toxin genes pagA, cya and lef, and of a number of other plasmid- and chromosome-encoded genes. The AtxA protein (56 kDa) possesses a predicted winged-helix DNA-binding domain and phosphotransferase system-regulated domains, but the mechanism for positive regulation of AtxA target genes is not known. Sequence similarities in the promoter regions of AtxA-regulated genes are not apparent, and recombinant AtxA binds DNA with a high affinity in a non-specific manner. We hypothesized that the toxin genes possess common structural features or cis-acting elements that are required for positive regulation. We employed deletion analyses to determine the minimal sequences required for atxA-mediated toxin gene expression. In silico modelling and in vitro experiments using double-stranded DNA corresponding to the toxin gene promoter regions indicated significant curvature associated with these regions. These findings suggest that the structural topology of the DNA plays an important role in the control of anthrax toxin gene expression.
Collapse
Affiliation(s)
- Maria Hadjifrangiskou
- Department of Microbiology and Molecular Genetics, University of Texas - Houston Health Science Center, 6431 Fannin St, Houston, TX 77030, USA
| | - Theresa M Koehler
- Department of Microbiology and Molecular Genetics, University of Texas - Houston Health Science Center, 6431 Fannin St, Houston, TX 77030, USA
| |
Collapse
|
37
|
Normanno D, Vanzi F, Pavone FS. Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping. Nucleic Acids Res 2008; 36:2505-13. [PMID: 18310101 PMCID: PMC2377426 DOI: 10.1093/nar/gkn071] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 01/07/2008] [Accepted: 02/05/2008] [Indexed: 11/12/2022] Open
Abstract
Gene expression regulation is a fundamental biological process which deploys specific sets of genomic information depending on physiological or environmental conditions. Several transcription factors (including lac repressor, LacI) are present in the cell at very low copy number and increase their local concentration by binding to multiple sites on DNA and looping the intervening sequence. In this work, we employ single-molecule manipulation to experimentally address the role of DNA supercoiling in the dynamics and stability of LacI-mediated DNA looping. We performed measurements over a range of degrees of supercoiling between -0.026 and +0.026, in the absence of axial stretching forces. A supercoiling-dependent modulation of the lifetimes of both the looped and unlooped states was observed. Our experiments also provide evidence for multiple structural conformations of the LacI-DNA complex, depending on torsional constraints. The supercoiling-dependent modulation demonstrated here adds an important element to the model of the lac operon. In fact, the complex network of proteins acting on the DNA in a living cell constantly modifies its topological and mechanical properties: our observations demonstrate the possibility of establishing a signaling pathway from factors affecting DNA supercoiling to transcription factors responsible for the regulation of specific sets of genes.
Collapse
Affiliation(s)
- Davide Normanno
- LENS, European Laboratory for Non-linear Spectroscopy, Università degli Studi di Firenze, Via N. Carrara 1, I-50019 Sesto Fiorentino (FI), Italy.
| | | | | |
Collapse
|
38
|
Burkala E, Reimers JM, Schmidt KH, Davis N, Wei P, Wright BE. Secondary structures as predictors of mutation potential in the lacZ gene of Escherichia coli. MICROBIOLOGY-SGM 2007; 153:2180-2189. [PMID: 17600062 DOI: 10.1099/mic.0.2007/005470-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Four independent nonsense mutations were engineered into the Escherichia coli chromosomal lacZ gene, and reversion rates back to LacZ(+) phenotypes were determined. The mutation potential of bases within putative DNA secondary structures formed during transcription was predicted by a sliding-window analysis that simulates successive folding of the ssDNA creating these structures. The relative base mutabilities predicted by the mfg computer program correlated with experimentally determined reversion rates in three of the four mutants analysed. The nucleotide changes in revertants at one nonsense codon site consisted of a triple mutation, presumed to occur by a templated repair mechanism. Additionally, the effect of supercoiling on mutation was investigated and, in general, reversion rates increased with higher levels of negative supercoiling. Evidence indicates that predicted secondary structures are in fact formed in vivo and that directed mutation in response to starvation stress is dependent upon the exposure of particular bases, the stability of the structures in which these bases are unpaired and the level of DNA supercoiling within the cell.
Collapse
Affiliation(s)
- Evan Burkala
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | - Karen H Schmidt
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Nick Davis
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Ping Wei
- University of Massachusetts, Worcester, MA 01605, USA
| | - Barbara E Wright
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| |
Collapse
|
39
|
Abstract
In the absence of oxygen, Escherichia coli can use alternative exogenous electron acceptors, including trimethylamine oxide (TMAO), to generate energy. In this study, we showed that in contrast to the other anaerobic respiratory systems, the TMAO reductase (Tor) system was expressed during both aerobiosis and anaerobiosis. By using a torA-lacZ fusion and quantitative reverse transcription polymerase chain reaction, we established that the torCAD operon encoding the Tor system was induced in the presence of TMAO mainly during exponential phase, and that optimal induction required a certain level of DNA supercoiling. We also showed that the presence of oxygen prevented neither the biogenesis of the Tor system nor the reduction of TMAO. The physiological role of TMAO reduction during aerobiosis has not been yet established, but our experiments suggest that alkaline TMA production could enhance the growth conditions by increasing the pH of the culture.
Collapse
Affiliation(s)
- Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, Institut de Biologie Structurale et Microbiologie, Centre National de la Recherche Scientifique, 31, chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | | | | | | | | |
Collapse
|
40
|
O Cróinín T, Dorman CJ. Expression of the Fis protein is sustained in late-exponential- and stationary-phase cultures of Salmonella enterica serovar Typhimurium grown in the absence of aeration. Mol Microbiol 2007; 66:237-51. [PMID: 17784910 DOI: 10.1111/j.1365-2958.2007.05916.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The classic expression pattern of the Fis global regulatory protein during batch culture consists of a high peak in the early logarithmic phase of growth, followed by a sharp decrease through mid-exponential growth phase until Fis is almost undetectable at the end of the exponential phase. We discovered that this pattern is contingent on the growth regime. In Salmonella enterica serovar Typhimurium cultures grown in non-aerated SPI1-inducing conditions, Fis can be detected readily in stationary phase. On the other hand, cultures grown with standard aeration showed the classic Fis expression pattern. Sustained Fis expression in non-aerated cultures was also detected in some Escherichia coli strains, but not in others. This novel pattern of Fis expression was independent of sequence differences in the fis promoter regions of Salmonella and E. coli. Instead, a clear negative correlation between the expression of the Fis protein and of the stress-and-stationary-phase sigma factor RpoS was observed in a variety of strains. An rpoS mutant displayed elevated levels of Fis and had a higher frequency of epithelial cell invasion under these growth conditions. We discuss a model whereby Fis and RpoS levels vary in response to environmental signals allowing the expression and repression of SPI1 invasion genes.
Collapse
Affiliation(s)
- Tadhg O Cróinín
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Ireland
| | | |
Collapse
|
41
|
Partridge JD, Scott C, Tang Y, Poole RK, Green J. Escherichia coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions. J Biol Chem 2006; 281:27806-15. [PMID: 16857675 DOI: 10.1074/jbc.m603450200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. Several previous transcript-profiling experiments have compared separate anaerobic and aerobic cultures. Here the process of adaptation was investigated by determining changes in transcript profiles when anaerobic steady-state cultures were perturbed by the introduction of air. Within 5 min of culture aeration the abundances of transcripts associated with anaerobic metabolism were decreased, whereas transcripts associated with aerobic metabolism were increased. In addition to the rapid switch to aerobic central metabolism, transcript profiling, supported by experiments with relevant mutants, revealed transient changes suggesting that the peroxide stress response, methionine biosynthesis, and degradation of putrescine play important roles during the adaptation to aerobic conditions.
Collapse
Affiliation(s)
- Jonathan D Partridge
- Department of Molecular Biology and Biotechnology, the University of Sheffield, Sheffield S10 2TN, United Kingdom
| | | | | | | | | |
Collapse
|
42
|
Jeong KS, Xie Y, Hiasa H, Khodursky AB. Analysis of pleiotropic transcriptional profiles: a case study of DNA gyrase inhibition. PLoS Genet 2006; 2:e152. [PMID: 17009874 PMCID: PMC1584274 DOI: 10.1371/journal.pgen.0020152] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Accepted: 08/02/2006] [Indexed: 01/05/2023] Open
Abstract
Genetic and environmental perturbations often result in complex transcriptional responses involving multiple genes and regulons. In order to understand the nature of a response, one has to account for the contribution of the downstream effects to the formation of a response. Such analysis can be carried out within a statistical framework in which the individual effects are independently collected and then combined within a linear model. Here, we modeled the contribution of DNA replication, supercoiling, and repair to the transcriptional response of inhibition of the Escherichia coli gyrase. By representing the gyrase inhibition as a true pleiotropic phenomenon, we were able to demonstrate that: (1) DNA replication is required for the formation of spatial transcriptional domains; (2) the transcriptional response to the gyrase inhibition is coordinated between at least two modules involved in DNA maintenance, relaxation and damage response; (3) the genes whose transcriptional response to the gyrase inhibition does not depend on the main relaxation activity of the cell can be classified on the basis of a GC excess in their upstream and coding sequences; and (4) relaxation by topoisomerase I dominates the transcriptional response, followed by the effects of replication and RecA. We functionally tested the effect of the interaction between relaxation and repair activities, and found support for the model derived from the microarray data. We conclude that modeling compound transcriptional profiles as a combination of downstream transcriptional effects allows for a more realistic, accurate, and meaningful representation of the transcriptional activity of a genome. Pleiotropism—a movement, or reaction, in multiple directions: although it was initially used specifically to describe the effect of a single genetic mutation on multiple characters in the offspring, the transcriptional responses of cells are often best described in terms of pleiotropy, when a single input affects multiple components inside the cell. This, in turn, presents a dilemma with the analysis and interpretation of the observed effects: which effects are directly due to the input itself and which are not? How are the effects related to each other and which are more important? And finally, can the overall transcriptional response be summarized as a combination of the effects? There is, however, a problem with recording the effects when they occur almost simultaneously in the same organism. The authors approached this by recording the effects independently, using mutants that could generate all of the effects of interest but one, and then estimating the effects and their interactions from a multivariate linear model. The authors applied this method to explain the transcriptional response of Escherichia coli to a quinolone antibacterial, a relative of Cipro (ciprofloxacin hydrochloride), and discovered unexpected interactions between DNA maintenance modules in the cell.
Collapse
Affiliation(s)
- Kyeong Soo Jeong
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Yang Xie
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Arkady B Khodursky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
43
|
Zeller T, Klug G. Thioredoxins in bacteria: functions in oxidative stress response and regulation of thioredoxin genes. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2006; 93:259-66. [PMID: 16555095 DOI: 10.1007/s00114-006-0106-1] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thioredoxins fulfill a number of different important cellular functions in all living organisms. In bacteria, thioredoxin genes are often regulated by external factors. In turn, thioredoxins influence the expression of many other genes. The multiple and important functions of thioredoxins in cells necessitate to appropriately adjust their level. This review outlines different strategies that have evolved for the regulation of bacterial thioredoxin genes. It also summarizes effects of thioredoxins on gene regulation and presents a recent model for a redox-dependent gene regulation that is mediated by thioredoxins.
Collapse
Affiliation(s)
- Tanja Zeller
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | | |
Collapse
|
44
|
Weigl D, Molloy MJ, Clayton TM, Griffith J, Smith CR, Steward T, Merrill BM, Deprince RB, Jone CS, Persmark M. Characterization of a topologically aberrant plasmid population from pilot-scale production of clinical-grade DNA. J Biotechnol 2006; 121:1-12. [PMID: 16150507 DOI: 10.1016/j.jbiotec.2005.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Revised: 06/17/2005] [Accepted: 06/27/2005] [Indexed: 11/15/2022]
Abstract
As part of a program to develop DNA vaccines for pharmaceutical applications, we recently established a manufacturing process for the production of clinical grade plasmid DNA. In an evaluation of two cell separation methods, the cell culture experienced a temperature spike in a new tangential flow filtration rig, resulting in an aberrant plasmid HPLC peak. Analysis by agarose gel electrophoresis and HPLC demonstrated that the aberrant plasmid material's overall primary structure, methylation pattern and topological integrity was indistinguishable from that of reference material. Transmission electron microscopy and high-resolution agarose gel electrophoresis revealed that the unknown plasmid form exhibited a very low level of supercoiling, whereas the normal supercoiled fraction contained highly twisted DNA. We hypothesized that an enzymatic process, induced by stress during the temperature spike, caused the distinct plasmid topology. This idea was supported by a lab-scale fermentation experiment, where plasmid topology was shown to be similarly altered by conditions designed to induce metabolic stress.
Collapse
Affiliation(s)
- Debra Weigl
- BioPharmaceutical Product Development-US, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
DNA in bacterial cells is maintained in a negatively supercoiled state. This contributes to the organization of the bacterial nucleoid and also influences the global gene expression pattern in the cell through modulatory effects on transcription. Supercoiling arises as a result of changes to the linking number of the relaxed double-stranded DNA molecule and is set and reset by the action of DNA topoisomerases. This process is subject to a multitude of influences that are usually summarized as environmental stress. Responsiveness of linking number change to stress offers the promise of a mechanism for the wholesale adjustment of the transcription programme of the cell as the bacterium experiences different environments. Recent data from DNA microarray experiments support this proposition. The emerging picture is one of DNA supercoiling acting at or near the apex of a regulatory hierarchy where it collaborates with nucleoid-associated proteins and transcription factors to determine the gene expression profile of the cell.
Collapse
|
46
|
Zheng J, Tung SL, Leung KY. Regulation of a type III and a putative secretion system in Edwardsiella tarda by EsrC is under the control of a two-component system, EsrA-EsrB. Infect Immun 2005; 73:4127-37. [PMID: 15972502 PMCID: PMC1168592 DOI: 10.1128/iai.73.7.4127-4137.2005] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Edwardsiella tarda is a gram-negative enteric pathogen that causes hemorrhagic septicemia in fish and gastro- and extraintestinal infections in humans. A type III secretion system (TTSS) and a putative secretion system (EVP) have been found to play important roles in E. tarda pathogenesis. Our previous studies suggested that the TTSS and EVP gene clusters were regulated by a two-component system of EsrA-EsrB. In the present study, we characterized another regulator, EsrC, which showed significant sequence similarity to the AraC family of transcriptional regulators. Mutants with in-frame deletions of esrC increased the 50% lethal doses in blue gourami fish, reduced extracellular protein production, and failed to aggregate. Complementation of esrC restored these three phenotypes. Two-dimensional gel electrophoresis showed that EsrC regulated the expression of secreted proteins encoded by the TTSS (such as EseB and EseD) and EVP (EvpC) gene clusters. The expression of esrC required a functional two-component system of EsrA-EsrB. EsrC in turn regulated the expression of selected genes encoded in TTSS (such as the transcriptional unit of orf29and orf30, but not esaC) and genes encoded in the EVP gene cluster. The present study sheds light on the regulation of these two key virulence-associated secretion systems and provides greater insight into the pathogenic mechanisms of this bacterium.
Collapse
Affiliation(s)
- J Zheng
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Science Dr. 4, Singapore 117543, Republic of Singapore
| | | | | |
Collapse
|
47
|
Kwack MS, Park JE, Park JK, Lee JS. Purification and characterization of a novel ATP-independent type I DNA topoisomerase from a marine methylotroph. Arch Biochem Biophys 2005; 437:168-77. [PMID: 15850556 DOI: 10.1016/j.abb.2005.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 03/12/2005] [Accepted: 03/14/2005] [Indexed: 10/25/2022]
Abstract
DNA topoisomerase is involved in DNA repair and replication. In this study, a novel ATP-independent 30-kDa type I DNA topoisomerase was purified and characterized from a marine methylotroph, Methylophaga sp. strain 3. The purified enzyme composed of a single polypeptide was active over a broad range of temperature and pH. The enzyme was able to relax only negatively supercoiled DNA. Mg(2+) was required for its relaxation activity, while ATP gave no effect. The enzyme was clearly inhibited by camptothecin, ethidium bromide, and single-stranded DNA, but not by nalidixic acid and etoposide. Interestingly, the purified enzyme showed Mn(2+)-activated endonuclease activity on supercoiled DNA. The N-terminal sequence of the purified enzyme showed no homology with those of other type I enzymes. These results suggest that the purified enzyme is an ATP-independent type I DNA topoisomerase that has, for the first time, been characterized from a marine methylotroph.
Collapse
Affiliation(s)
- Man Sup Kwack
- Department of Biotechnology and Research Center for Proteineous Materials, Chosun University, Gwangju 501-759, Republic of Korea
| | | | | | | |
Collapse
|
48
|
Liu YJ, Hu B, Zhu JB, Shen SJ, Yu GQ. nifH promoter activity is regulated by DNA supercoiling in Sinorhizobium meliloti. Acta Biochim Biophys Sin (Shanghai) 2005; 37:221-6. [PMID: 15806287 DOI: 10.1111/j.1745-7270.2005.00037.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In prokaryotes, DNA supercoiling regulates the expression of many genes; for example, the expression of Klebsiella pneumoniae nifLA operon depends on DNA negative supercoiling in anaerobically grown cells, which indicates that DNA supercoiling might play a role in gene regulation of the anaerobic response. Since the expression of the nifH promoter in Sinorhizobium meliloti is not repressed by oxygen, it is proposed that the status of DNA supercoiling may not affect the expression of the nifH promoter. We tested this hypothesis by analyzing nifH promoter activity in wild-type and gyr- Escherichia coli in the presence and absence of DNA gyrase inhibitors. Our results show that gene expression driven by the S. meliloti nifH promoter requires the presence of active DNA gyrase. Because DNA gyrase increases the number of negative superhelical turns in DNA in the presence of ATP, our data indicate that negative supercoiling is also important for nifH promoter activity. Our study also shows that the DNA supercoiling-dependent S. meliloti nifH promoter activity is related to the trans-acting factors NtrC and NifA that activate it. DNA supercoiling appeared to have a stronger effect on NtrC-activated nifH promoter activity than on NifA-activated promoter activity. Collectively, these results from the S. meliloti nifH promoter model system seem to indicate that, in addition to regulating gene expression during anaerobic signaling, DNA supercoiling may also provide a favorable topology for trans-acting factor binding and promoter activation regardless of oxygen status.
Collapse
Affiliation(s)
- Yan-Jie Liu
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | | | | | | | | |
Collapse
|
49
|
Travers A, Muskhelishvili G. DNA supercoiling — a global transcriptional regulator for enterobacterial growth? Nat Rev Microbiol 2005; 3:157-69. [PMID: 15685225 DOI: 10.1038/nrmicro1088] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A fundamental principle of exponential bacterial growth is that no more ribosomes are produced than are necessary to support the balance between nutrient availability and protein synthesis. Although this conclusion was first expressed more than 40 years ago, a full understanding of the molecular mechanisms involved remains elusive and the issue is still controversial. There is currently agreement that, although many different systems are undoubtedly involved in fine-tuning this balance, an important control, and in our opinion perhaps the main control, is regulation of the rate of transcription initiation of the stable (ribosomal and transfer) RNA transcriptons. In this review, we argue that regulation of DNA supercoiling provides a coherent explanation for the main modes of transcriptional control - stringent control, growth-rate control and growth-phase control - during the normal growth of Escherichia coli.
Collapse
Affiliation(s)
- Andrew Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
| | | |
Collapse
|
50
|
McKinlay JB, Zeikus JG. Extracellular iron reduction is mediated in part by neutral red and hydrogenase in Escherichia coli. Appl Environ Microbiol 2004; 70:3467-74. [PMID: 15184145 PMCID: PMC427799 DOI: 10.1128/aem.70.6.3467-3474.2004] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Both microbial iron reduction and microbial reduction of anodes in fuel cells can occur by way of soluble electron mediators. To test whether neutral red (NR) mediates iron reduction, as it does anode reduction, by Escherichia coli, ferrous iron levels were monitored in anaerobic cultures grown with amorphous iron oxide. Ferrous iron levels were 19.4 times higher in cultures fermenting pyruvate in the presence of NR than in the absence of NR. NR did not stimulate iron reduction in cultures respiring with nitrate. To explore the mechanism of NR-mediated iron reduction, cell extracts of E. coli were used. Cell extract-NADH-NR mixtures had an enzymatic iron reduction rate almost 15-fold higher than the chemical NR-mediated iron reduction rate observed in controls with no cell extract. Hydrogen was consumed during stationary phase (in which iron reduction was detectable) especially in cultures containing both NR and iron oxide. An E. coli hypE mutant, with no hydrogenase activity, was also impaired in NR-mediated iron reduction activity. NR-mediated iron reduction rates by cell extracts were 1.5 to 2 times higher with hydrogen or formate as the electron source than with NADH. Our findings suggest that hydrogenase donates electrons to NR for extracellular iron reduction. This process appears to be analogous to those of iron reduction by bacteria that use soluble electron mediators (e.g., humic acids and 2,6-anthraquinone disulfonate) and of anode reduction by bacteria using soluble mediators (e.g., NR and thionin) in microbial fuel cells.
Collapse
Affiliation(s)
- James B McKinlay
- Department of Biochemistry and Microbiology, Michigan State University, East Lansing, MI 48824, USA
| | | |
Collapse
|