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Forsdyke DR. Homostability. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Abstract
Recent advancements in fluorescence imaging have shown that the bacterial nucleoid is surprisingly dynamic in terms of both behavior (movement and organization) and structure (density and supercoiling). Links between chromosome structure and replication initiation have been made in a number of species, and it is universally accepted that favorable chromosome structure is required for initiation in all cells. However, almost nothing is known about whether cells use changes in chromosome structure as a regulatory mechanism for initiation. Such changes could occur during natural cell cycle or growth phase transitions, or they could be manufactured through genetic switches of topoisomerase and nucleoid structure genes. In this review, we explore the relationship between chromosome structure and replication initiation and highlight recent work implicating structure as a regulatory mechanism. A three-component origin activation model is proposed in which thermal and topological structural elements are balanced with trans-acting control elements (DnaA) to allow efficient initiation control under a variety of nutritional and environmental conditions. Selective imbalances in these components allow cells to block replication in response to cell cycle impasse, override once-per-cell-cycle programming during growth phase transitions, and promote reinitiation when replication forks fail to complete.
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Chattopadhyay S, Sahoo S, Kanner WA, Chakrabarti J. Pressures in archaeal protein coding genes: a comparative study. Comp Funct Genomics 2010; 4:56-65. [PMID: 18629113 PMCID: PMC2447400 DOI: 10.1002/cfg.246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2002] [Accepted: 11/25/2002] [Indexed: 11/06/2022] Open
Abstract
Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC-rich to AT-rich protein-coding gene-containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons. These findings suggest that the deviations from the second parity rule (through the increasing differences between complementary base contents) and the increasing purine load hinder the chance of formation of the intra-strand Watson-Crick base-paired secondary structures in mRNAs (synonymous with the protein-coding genes we dealt with), thereby increasing the translational efficiency. We hypothesize that the ATrich protein-coding gene-containing archaeal species might have better translational efficiency than their GC-rich counterparts.
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Affiliation(s)
- Sujay Chattopadhyay
- Department of Theoretical Physics, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India.
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Prakash JSS, Sinetova M, Zorina A, Kupriyanova E, Suzuki I, Murata N, Los DA. DNA supercoiling regulates the stress-inducible expression of genes in the cyanobacterium Synechocystis. MOLECULAR BIOSYSTEMS 2009; 5:1904-12. [PMID: 19763333 DOI: 10.1039/b903022k] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Changes in the supercoiling of genomic DNA play an important role in the regulation of gene expression. We compared the genome-wide expression of genes in cells of the cyanobacterium Synechocystis sp. PCC 6803 when they were subjected to salt, cold, and heat stress, in the presence of novobiocin, an inhibitor of DNA gyrase, and in its absence. The analysis revealed that the expression of a large number of stress-inducible genes depends on the extent of genomic DNA supercoiling. The function of the two-component regulatory systems, which are known as sensors and transducers of salt, cold, and heat stress, depends on, and might be controlled by, the degree of supercoiling of the genomic DNA. These results suggest that stress-induced changes in superhelicity of genomic DNA provide an important permissive background for successful acclimatization of cyanobacterial cells to stress conditions.
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Affiliation(s)
- Jogadhenu S S Prakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Gachibowli, Hyderbad 500 046, Andhra Pradesh, India
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Friedman SM, Hossain M, Hasson TH, Kawamura A. Gene Expression Profiling of Intrinsic Thermotolerance in Escherichia coli. Curr Microbiol 2006; 52:50-4. [PMID: 16392005 DOI: 10.1007/s00284-005-4578-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Accepted: 08/22/2005] [Indexed: 10/25/2022]
Abstract
DNA microarrays were employed to compare gene expression in a thermotolerant, nalidixic acid-resistant mutant of Escherichia coli with that of the parental strain. When grown at 37 degrees C, up-regulated genes in the mutant included those coding for multiple antibiotic resistance proteins and enzymes for the degradation of small molecules, whereas among the down-regulated genes were those coding for fimbrial, flagellar, and outer membrane proteins as well as sigma 38. When the mutant grown at 42 degrees C was compared to the mutant grown at 37 degrees C, enhanced expression of several genes coding for flagellar proteins was detected. Reverse transcriptase-polymerase chain reaction analysis of selected genes confirmed results obtained with microarrays.
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Affiliation(s)
- S Marvin Friedman
- Department of Biological Sciences, Hunter College of The City University of New York, 695 Park Avenue, New York, NY 10021, USA.
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6
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Chargaff’s GC rule. Evol Bioinform Online 2006. [DOI: 10.1007/978-0-387-33419-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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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.
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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
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Abstract
The hypothesis that genomic regions rich in non-protein-coding RNAs (ncRNAs) can be identified using local variations in single-base and dinucleotide statistics has been investigated. (G+C)%, (G-C)% difference, (A-T)% difference and dinucleotide-frequency statistics were compared among seven classes of ncRNAs and three genomes. Significant variations were observed in (G+C)% and, in Methanococcus jannaschii, in the frequency of the dinucleotide 'CG'. Screening programs based on these two base-composition statistics were developed. With (G+C)% screening alone, a 1% fraction of the M.jannaschii genome containing all 44 known transfer RNAs, ribosomal RNAs and signal recognition particle RNAs could be identified. When (G+C)% combined with CG dinucleotide-frequency screening was used, 43 of the 44 known M.jannaschii structural ncRNAs were again identified, while the number of presumably false hits overlapping a known or putative protein-coding gene was reduced from 15 to 6. In addition, 19 candidate ncRNAs were identified including one with significant homology to several known archaeal RNaseP RNAs.
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Affiliation(s)
- Peter Schattner
- Center for Biomolecular Science and Engineering, 227 Sinsheimer Laboratories, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.
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Friedman SM, Lu T, Drlica K. Mutation in the DNA gyrase A Gene of Escherichia coli that expands the quinolone resistance-determining region. Antimicrob Agents Chemother 2001; 45:2378-80. [PMID: 11451702 PMCID: PMC90659 DOI: 10.1128/aac.45.8.2378-2380.2001] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In three Escherichia coli mutants, a change (Ala-51 to Val) in the gyrase A protein outside the standard quinolone resistance-determining region (QRDR) lowered the level of quinolone susceptibility more than changes at amino acids 67, 82, 84, and 106 did. Revision of the QRDR to include amino acid 51 is indicated.
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Affiliation(s)
- S M Friedman
- Department of Biological Sciences, Hunter College of The City University of New York, New York, New York 10021, USA.
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10
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Abstract
Of Chargaff's four rules on DNA base composition, only his first parity rule was incorporated into mainstream biology as the DNA double helix. Now, the cluster rule, the second parity rule, and the GC rule, reveal the multiple levels of information in our genomes and potential conflicts between them. In these terms we can understand how double-stranded RNA became an intracellular alarm signal, how potentially recombining nucleic acids can distinguish between 'self' and 'not-self' so leading to the origin of species, how isochores evolved to facilitate gene duplication, and how unlikely it is that any mutation can ever remain truly neutral.
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Affiliation(s)
- D R Forsdyke
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L3N6, Canada.
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11
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Tse-Dinh YC. Increased sensitivity to oxidative challenges associated with topA deletion in Escherichia coli. J Bacteriol 2000; 182:829-32. [PMID: 10633122 PMCID: PMC94351 DOI: 10.1128/jb.182.3.829-832.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deletion of topA in Escherichia coli was found to result in a higher level of killing after treatment with either hydrogen peroxide or N-ethylmaleimide. This effect on oxidative challenge response represents a new role for E. coli DNA topoisomerase I in addition to prevention of excessive negative supercoiling of DNA.
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Affiliation(s)
- Y C Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA.
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Lu T, Zhao X, Drlica K. Gatifloxacin activity against quinolone-resistant gyrase: allele-specific enhancement of bacteriostatic and bactericidal activities by the C-8-methoxy group. Antimicrob Agents Chemother 1999; 43:2969-74. [PMID: 10582891 PMCID: PMC89596 DOI: 10.1128/aac.43.12.2969] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibacterial activities of gatifloxacin (AM1155), a new C-8-methoxy fluoroquinolone, and two structurally related compounds, AM1121 and ciprofloxacin, were studied with an isogenic set of ten quinolone-resistant, gyrA (gyrase) mutants of Escherichia coli. To compare the effect of each mutation on resistance, the mutant responses were normalized to those of wild-type cells. Alleles exhibiting the most resistance to growth inhibition mapped in alpha-helix 4, which is thought to lie on a GyrA dimer surface that interacts with DNA. The C-8-methoxy group lowered the resistance due to these mutations more than it lowered resistance arising from several gyrA alleles located outside alpha-helix 4. These data are consistent with alpha-helix 4 being a distinct portion of the quinolone-binding site of GyrA. A helix change to proline behaved more like nonhelix alleles, indicating that helix perturbation differs from the other changes at helix residues. Addition of a parC (topoisomerase IV) resistance allele revealed that the C-8-methoxy group also facilitated attack of topoisomerase IV. When lethal effects were measured at a constant multiple of the minimum inhibitory concentration for each fluoroquinolone to normalize for differences in bacteriostatic action, gatifloxacin was more potent than the C-8-H compounds, both in the presence and absence of protein synthesis (an exception was observed when alanine was substituted for aspartic acid at position 82). Collectively, these data show that the C-8-methoxy group contributes to the enhanced activity of gatifloxacin against resistant gyrase and wild-type topoisomerase IV.
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Affiliation(s)
- T Lu
- Public Health Research Institute, New York, New York 10016, USA
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Qi H, Menzel R, Tse-Dinh YC. Increased thermosensitivity associated with topoisomerase I deletion and promoter mutations in Escherichia coli. FEMS Microbiol Lett 1999; 178:141-6. [PMID: 10483733 DOI: 10.1111/j.1574-6968.1999.tb13770.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
An Escherichia coli mutant with three of the promoters for the topoisomerase I gene (topA) deleted, such that only the sigma 32-dependent promoter (P1) remained, had a decreased level of topoisomerase I at 30 degrees C and showed increased thermosensitivity at 52 degrees C. However, it could still develop thermotolerance and had a wild-type level of resistance to 52 degrees C treatment if exposed first to 42 degrees C. This indicated that newly synthesized topoisomerase I from transcription initiated at P1 was important for development of thermotolerance. Two other E. coli mutants lacking topA were > 100 times more sensitive to high temperature than their wild-type isogenic strains.
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Affiliation(s)
- H Qi
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla 10595, USA
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Chadsey MS, Karlinsey JE, Hughes KT. The flagellar anti-sigma factor FlgM actively dissociates Salmonella typhimurium sigma28 RNA polymerase holoenzyme. Genes Dev 1998; 12:3123-36. [PMID: 9765212 PMCID: PMC317189 DOI: 10.1101/gad.12.19.3123] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/1998] [Accepted: 08/05/1998] [Indexed: 11/25/2022]
Abstract
The anti-sigma factor FlgM of Salmonella typhimurium inhibits transcription of class 3 flagellar genes through a direct interaction with the flagellar-specific sigma factor, sigma28. FlgM is believed to prevent RNA polymerase (RNAP) holoenzyme formation by sequestering free sigma28. We have analyzed FlgM-mediated inhibition of sigma28 activity in vitro. FlgM is able to inhibit sigma28 activity even when sigma28 is first allowed to associate with core RNAP. Surface plasmon resonance (SPR) was used to evaluate the interaction between FlgM and both sigma28 and sigma28 holoenzyme (Esigma28). The Kd of the sigma28-FlgM complex is approximately 2 x 10(-10) M; missense mutations in FlgM that cause a defect in sigma28 inhibition in vivo increase the Kd of this interaction by 4- to 10-fold. SPR measurements of Esigma28 dissociation in the presence of FlgM indicate that FlgM destabilizes Esigma28, presumably via an interaction with the sigma subunit. Our data provide the first direct evidence of an interaction between FlgM and Esigma28. We propose that this secondary activity of FlgM, which we term holoenzyme destabilization, enhances the sensitivity of the cell to changes in FlgM levels during flagellar biogenesis.
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Affiliation(s)
- M S Chadsey
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
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15
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Abstract
Bacterial and archeal type I topoisomerases, including topoisomerase I, topoisomerase III and reverse gyrase, have different potential roles in the control of DNA topology including regulation of supercoiling and maintenance of genetic stability. Analysis of their coding sequences in different organisms shows that they belong to the type IA family of DNA topoisomerases, but there is variability in organization of various enzymatic domains necessary for topoisomerase activity. The torus-like structure of the conserved transesterification domain with the active site tyrosine for DNA cleavage/rejoining suggests steps of enzyme conformational change driven by DNA substrate and Mg(II) cofactor binding, that are required for catalysis of change in DNA linking number.
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Affiliation(s)
- Y C Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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16
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Abstract
For many years, DNA gyrase was thought to be responsible both for unlinking replicated daughter chromosomes and for controlling negative superhelical tension in bacterial DNA. However, in 1990 a homolog of gyrase, topoisomerase IV, that had a potent decatenating activity was discovered. It is now clear that topoisomerase IV, rather than gyrase, is responsible for decatenation of interlinked chromosomes. Moreover, topoisomerase IV is a target of the 4-quinolones, antibacterial agents that had previously been thought to target only gyrase. The key event in quinolone action is reversible trapping of gyrase-DNA and topoisomerase IV-DNA complexes. Complex formation with gyrase is followed by a rapid, reversible inhibition of DNA synthesis, cessation of growth, and induction of the SOS response. At higher drug concentrations, cell death occurs as double-strand DNA breaks are released from trapped gyrase and/or topoisomerase IV complexes. Repair of quinolone-induced DNA damage occurs largely via recombination pathways. In many gram-negative bacteria, resistance to moderate levels of quinolone arises from mutation of the gyrase A protein and resistance to high levels of quinolone arises from mutation of a second gyrase and/or topoisomerase IV site. For some gram-positive bacteria, the situation is reversed: primary resistance occurs through changes in topoisomerase IV while gyrase changes give additional resistance. Gyrase is also trapped on DNA by lethal gene products of certain large, low-copy-number plasmids. Thus, quinolone-topoisomerase biology is providing a model for understanding aspects of host-parasite interactions and providing ways to investigate manipulation of the bacterial chromosome by topoisomerases.
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Affiliation(s)
- K Drlica
- Public Health Research Institute, New York, New York 10016, USA.
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Tse-Dinh YC, Qi H, Menzel R. DNA supercoiling and bacterial adaptation: thermotolerance and thermoresistance. Trends Microbiol 1997; 5:323-6. [PMID: 9263411 DOI: 10.1016/s0966-842x(97)01080-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
When bacterial cells are shifted to higher temperatures their degree of DNA supercoiling changes. Topoisomerases are involved in bacterial adaptation to environmental changes requiring rapid shifts in gene expression. This role in heat shock has been elucidated by genetic studies on the Escherichia coli topA gene and its sigma 32-dependent promoter, P1. Other studies have shown that certain gyrA mutants have increased thermoresistance.
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Affiliation(s)
- Y C Tse-Dinh
- Dept of Biochemistry and Molecular Biology, New York Medical College, Valhalla 10595, USA.
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