101
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Peter BJ, Arsuaga J, Breier AM, Khodursky AB, Brown PO, Cozzarelli NR. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol 2004; 5:R87. [PMID: 15535863 PMCID: PMC545778 DOI: 10.1186/gb-2004-5-11-r87] [Citation(s) in RCA: 245] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 10/01/2004] [Accepted: 10/11/2004] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In turn, supercoiling influences local DNA structure and can affect gene expression. We used microarrays representing nearly the entire genome of Escherichia coli MG1655 to examine the dynamics of chromosome structure. RESULTS We measured the transcriptional response to a loss of supercoiling caused either by genetic impairment of a topoisomerase or addition of specific topoisomerase inhibitors during log-phase growth and identified genes whose changes are statistically significant. Transcription of 7% of the genome (306 genes) was rapidly and reproducibly affected by changes in the level of supercoiling; the expression of 106 genes increased upon chromosome relaxation and the expression of 200 decreased. These changes are most likely to be direct effects, as the kinetics of their induction or repression closely follow the kinetics of DNA relaxation in the cells. Unexpectedly, the genes induced by relaxation have a significantly enriched AT content in both upstream and coding regions. CONCLUSIONS The 306 supercoiling-sensitive genes are functionally diverse and widely dispersed throughout the chromosome. We propose that supercoiling acts as a second messenger that transmits information about the environment to many regulatory networks in the cell.
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Affiliation(s)
- Brian J Peter
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA
- Current address: Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
| | - Javier Arsuaga
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA
- Mathematics Department, University of California, Berkeley, CA 94720, USA
| | - Adam M Breier
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
| | - Arkady B Khodursky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Patrick O Brown
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5307, USA
| | - Nicholas R Cozzarelli
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA
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102
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Jeong KS, Ahn J, Khodursky AB. Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biol 2004; 5:R86. [PMID: 15535862 PMCID: PMC545777 DOI: 10.1186/gb-2004-5-11-r86] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Revised: 09/13/2004] [Accepted: 09/29/2004] [Indexed: 12/16/2022] Open
Abstract
Analysis of the transcriptional activity in Escherichia coli K12 revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome and showed that spatial patterns of transcription could be modulated pharmacologically and genetically. Background Although genes on the chromosome are organized in a fixed order, the spatial correlations in transcription have not been systematically evaluated. We used a combination of genomic and signal processing techniques to investigate the properties of transcription in the genome of Escherichia coli K12 as a function of the position of genes on the chromosome. Results Spectral analysis of transcriptional series revealed the existence of statistically significant patterns in the spatial series of transcriptional activity. These patterns could be classified into three categories: short-range, of up to 16 kilobases (kb); medium-range, over 100-125 kb; and long-range, over 600-800 kb. We show that the significant similarities in gene activities extend beyond the length of an operon and that local patterns of coexpression are dependent on DNA supercoiling. Unlike short-range patterns, the formation of medium and long-range transcriptional patterns does not strictly depend on the level of DNA supercoiling. The long-range patterns appear to correlate with the patterns of distribution of DNA gyrase on the bacterial chromosome. Conclusions Localization of structural components in the transcriptional signal revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome. The demonstration that spatial patterns of transcription could be modulated pharmacologically and genetically, along with the identification of molecular correlates of transcriptional patterns, offer for the first time strong evidence of physiologically determined higher-order organization of transcription in the bacterial chromosome.
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Affiliation(s)
- Kyeong Soo Jeong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Jaeyong Ahn
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Arkady B Khodursky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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103
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Rabus R, Ruepp A, Frickey T, Rattei T, Fartmann B, Stark M, Bauer M, Zibat A, Lombardot T, Becker I, Amann J, Gellner K, Teeling H, Leuschner WD, Glöckner FO, Lupas AN, Amann R, Klenk HP. The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments. Environ Microbiol 2004; 6:887-902. [PMID: 15305914 DOI: 10.1111/j.1462-2920.2004.00665.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C(4)-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a beta-oxidation complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and ncc. D. psychrophila encodes more than 30 two-component regulatory systems, including a new Ntr subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.
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Affiliation(s)
- R Rabus
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
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104
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Burden S, Lin YX, Zhang R. Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences. Bioinformatics 2004; 21:601-7. [PMID: 15454410 DOI: 10.1093/bioinformatics/bti047] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Although a great deal of research has been undertaken in the area of promoter prediction, prediction techniques are still not fully developed. Many algorithms tend to exhibit poor specificity, generating many false positives, or poor sensitivity. The neural network prediction program NNPP2.2 is one such example. RESULTS To improve the NNPP2.2 prediction technique, the distance between the transcription start site (TSS) associated with the promoter and the translation start site (TLS) of the subsequent gene coding region has been studied for Escherichia coli K12 bacteria. An empirical probability distribution that is consistent for all E.coli promoters has been established. This information is combined with the results from NNPP2.2 to create a new technique called TLS-NNPP, which improves the specificity of promoter prediction. The technique is shown to be effective using E.coli DNA sequences, however, it is applicable to any organism for which a set of promoters has been experimentally defined. AVAILABILITY The data used in this project and the prediction results for the tested sequences can be obtained from http://www.uow.edu.au/~yanxia/E_Coli_paper/SBurden_Results.xls CONTACT alh98@uow.edu.au.
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Affiliation(s)
- S Burden
- Department of Mathematics and Applied Statistics, University of Wollongong Wollongong, NSW 2522, Australia.
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105
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Affiliation(s)
- David W Ussery
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Nikolaj Tindbæk
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Peter F Hallin
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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106
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Hosid S, Trifonov EN, Bolshoy A. Sequence periodicity of Escherichia coli is concentrated in intergenic regions. BMC Mol Biol 2004; 5:14. [PMID: 15333140 PMCID: PMC516772 DOI: 10.1186/1471-2199-5-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 08/26/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequence periodicity with a period close to the DNA helical repeat is a very basic genomic property. This genomic feature was demonstrated for many prokaryotic genomes. The Escherichia coli sequences display the period close to 11 base pairs. RESULTS Here we demonstrate that practically only ApA/TpT dinucleotides contribute to overall dinucleotide periodicity in Escherichia coli. The noncoding sequences reveal this periodicity much more prominently compared to protein-coding sequences. The sequence periodicity of ApC/GpT, ApT and GpC dinucleotides along the Escherichia coli K-12 is found to be located as well mainly within the intergenic regions. CONCLUSIONS The observed concentration of the dinucleotide sequence periodicity in the intergenic regions of E. coli suggests that the periodicity is a typical property of prokaryotic intergenic regions. We suppose that this preferential distribution of dinucleotide periodicity serves many biological functions; first of all, the regulation of transcription.
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Affiliation(s)
- Sergey Hosid
- Genome Diversity Center, Institute of Evolution, University of Haifa, Mt. Carmel 31905 ISRAEL
| | - Edward N Trifonov
- Genome Diversity Center, Institute of Evolution, University of Haifa, Mt. Carmel 31905 ISRAEL
| | - Alexander Bolshoy
- Genome Diversity Center, Institute of Evolution, University of Haifa, Mt. Carmel 31905 ISRAEL
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107
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Travers AA. The structural basis of DNA flexibility. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:1423-1438. [PMID: 15306459 DOI: 10.1098/rsta.2004.1390] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Although the average physico-chemical properties of a long DNA molecule may approximate to those of a thin isotropic homogeneous rod, DNA behaves more locally as an anisotropic heterogeneous rod. This bending anisotropy is sequence dependent and to a first approximation reflects both the geometry and stability of individual base steps. The biological manipulation and packaging of the molecule often depend crucially on local variations in both bending and torsional flexibility. However, whereas the probability of DNA untwisting can be strongly correlated with a high bending flexibility, DNA bending, especially when the molecule is tightly wrapped on a protein surface, may be energetically favoured by a less flexible sequence whose preferred configuration conforms more closely to that of the complementary protein surface. In the latter situation the lower bending flexibility may be more than compensated for on binding by a reduced required deformation energy relative to a fully isotropic DNA molecule.
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Affiliation(s)
- A A Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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108
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Ussery DW, Hallin PF. Genome Update: AT content in sequenced prokaryotic genomes. MICROBIOLOGY-SGM 2004; 150:749-752. [PMID: 15073284 DOI: 10.1099/mic.0.27103-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- David W Ussery
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK-2800, Denmark
| | - Peter F Hallin
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK-2800, Denmark
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109
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College, University of Dublin, Dublin 2, Ireland.
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110
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Norris V, Woldringh C, Mileykovskaya E. A hypothesis to explain division site selection in Escherichia coli by combining nucleoid occlusion and Min. FEBS Lett 2004; 561:3-10. [PMID: 15013745 DOI: 10.1016/s0014-5793(04)00135-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Revised: 01/21/2004] [Accepted: 01/29/2004] [Indexed: 10/26/2022]
Abstract
The positioning of the site of cell division in Escherichia coli results, it is generally believed, from the operation of nucleoid occlusion in combination with the Min system. Nucleoid occlusion prevents division over the nucleoids and directs it by default to the mid-cell region between segregating nucleoids or to polar regions while the Min system prevents division in polar regions. Unresolved questions include how these systems interact to control the earliest known event in division, the assembly at the membrane of the tubulin-like protein, FtsZ, and, more importantly, what exactly constitutes a division site. Evidence exists that (1) the coupled transcription, translation and insertion of proteins into membrane (transertion), can structure the cytoplasmic membrane into phospholipid domains, (2) the MinD protein can convert vesicles into tubes and (3) a variety of membranous structures can be observed at mid-cell. These data support a model in which transertion from the segregating daughter chromosomes leads to the formation of a distinct proteolipid domain between them at mid-cell; the composition of this domain allows phospholipid tubes to extend like fingers into the cytoplasm; these tubes then become the substrate for the dynamic assembly and disassembly of FtsZ which converts them into the invaginating fold responsible for division; the Min system inhibits division at unwanted sites and times by removing these tubes especially at the cell poles.
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Affiliation(s)
- Vic Norris
- Assemblages Moléculaires: Modélisation et Imagerie SIMS, FRE CNRS 2829, Faculté des Sciences and Techniques, Université de Rouen, 76821 Mont-Saint-Aignan, France.
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111
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Ussery DW, Hallin PF. Genome Update: length distributions of sequenced prokaryotic genomes. Microbiology (Reading) 2004; 150:513-516. [PMID: 14993295 DOI: 10.1099/mic.0.27032-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- David W Ussery
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK-2800, Denmark
| | - Peter F Hallin
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK-2800, Denmark
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112
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Pridmore RD, Berger B, Desiere F, Vilanova D, Barretto C, Pittet AC, Zwahlen MC, Rouvet M, Altermann E, Barrangou R, Mollet B, Mercenier A, Klaenhammer T, Arigoni F, Schell MA. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci U S A 2004; 101:2512-7. [PMID: 14983040 PMCID: PMC356981 DOI: 10.1073/pnas.0307327101] [Citation(s) in RCA: 338] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus johnsonii NCC 533 is a member of the acidophilus group of intestinal lactobacilli that has been extensively studied for their "probiotic" activities that include, pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into its physiology and identify genes potentially involved in interactions with the host, we sequenced and analyzed the 1.99-Mb genome of L. johnsonii NCC 533. Strikingly, the organism completely lacked genes encoding biosynthetic pathways for amino acids, purine nucleotides, and most cofactors. In apparent compensation, a remarkable number of uncommon and often duplicated amino acid permeases, peptidases, and phosphotransferase-type transporters were discovered, suggesting a strong dependency of NCC 533 on the host or other intestinal microbes to provide simple monomeric nutrients. Genome analysis also predicted an abundance (>12) of large and unusual cell-surface proteins, including fimbrial subunits, which may be involved in adhesion to glycoproteins or other components of mucin, a characteristic expected to affect persistence in the gastrointestinal tract (GIT). Three bile salt hydrolases and two bile acid transporters, proteins apparently critical for GIT survival, were also detected. In silico genome comparisons with the >95% complete genome sequence of the closely related Lactobacillus gasseri revealed extensive synteny punctuated by clear-cut insertions or deletions of single genes or operons. Many of these regions of difference appear to encode metabolic or structural components that could affect the organisms competitiveness or interactions with the GIT ecosystem.
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Affiliation(s)
- R David Pridmore
- Department of Nutrition and Health, Nestlé Research Center, PO Box 44, Vers-chez-les-Blanc, 1000 Lausanne 26, Switzerland.
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113
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Gerstel U, Römling U. The csgD promoter, a control unit for biofilm formation in Salmonella typhimurium. Res Microbiol 2004; 154:659-67. [PMID: 14643403 DOI: 10.1016/j.resmic.2003.08.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Expression of cellulose and curli fimbriae in Salmonella typhimurium is dependent on the transcriptional regulator CsgD. Transcription of csgD itself is influenced by a variety of regulatory stimuli. Complex nucleoprotein arrangements modulate the transcriptional activity of csgD and trigger the transition between the planktonic status and biofilm formation.
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Affiliation(s)
- Ulrich Gerstel
- Microbiology and Tumorbiology Center (MTC), Karolinska Institute, Stockholm, Sweden
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114
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Kaji M, Matsushita O, Tamai E, Miyata S, Taniguchi Y, Shimamoto S, Katayama S, Morita S, Okabe A. A novel type of DNA curvature present in a Clostridium perfringens ferredoxin gene: characterization and role in gene expression. MICROBIOLOGY-SGM 2004; 149:3083-3091. [PMID: 14600220 DOI: 10.1099/mic.0.26503-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This study has revealed that a Clostridium perfringens ferredoxin gene (per-fdx) possesses a novel type of DNA curvature, which is formed by five phased A-tracts extending from upstream to downstream of the -35 region. The three A-tracts upstream of the promoter and the two within the promoter are located at the positions corresponding to A-tracts present in a C. perfringens phospholipase C gene (plc) and a Clostridium pasteurianum ferredoxin gene (pas-fdx), respectively. DNA fragments of the per-fdx, pas-fdx and plc genes (nucleotide positions -69 to +1 relative to the transcription initiation site) were fused to a chloramphenicol acetyltransferase reporter gene on a plasmid, pPSV, and their in vivo promoter activities were examined by assaying the chloramphenicol acetyltransferase activity of each C. perfringens transformant. Comparison of the three constructs showed that the order of promoter activity is, in descending order, per-fdx, pas-fdx and plc. Deletion of the three upstream A-tracts of the per-fdx gene drastically decreased the promoter activity, as demonstrated previously for the plc promoter. Substitution of the most downstream A-tract decreased the promoter activities of the per-fdx and pas-fdx genes. These results indicate that not only the phased A-tracts upstream of the promoter but also those within the promoter stimulate the promoter activity, and suggest that the high activity of the per-fdx promoter is due to the combined effects of these two types of A-tracts.
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Affiliation(s)
- Masato Kaji
- Department of Hospital Pharmacy, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Osamu Matsushita
- Department of Microbiology, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Eiji Tamai
- Department of Microbiology, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Shigeru Miyata
- Department of Microbiology, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Yuki Taniguchi
- Department of Microbiology, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Seiko Shimamoto
- Department of Microbiology, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Seiichi Katayama
- Department of Biochemistry, Faculty of Science, Okayama University of Science, 1-1, Ridai-cho, Okayama 700-0005, Japan
| | - Shushi Morita
- Department of Hospital Pharmacy, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Akinobu Okabe
- Department of Microbiology, Kagawa Medical University, 1750-1, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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115
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Allen TE, Herrgård MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ. Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. J Bacteriol 2003; 185:6392-9. [PMID: 14563874 PMCID: PMC219383 DOI: 10.1128/jb.185.21.6392-6399.2003] [Citation(s) in RCA: 65] [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
The recent availability of heterogeneous high-throughput data types has increased the need for scalable in silico methods with which to integrate data related to the processes of regulation, protein synthesis, and metabolism. A sequence-based framework for modeling transcription and translation in prokaryotes has been established and has been extended to study the expression state of the entire Escherichia coli genome. The resulting in silico analysis of the expression state highlighted three facets of gene expression in E. coli: (i) the metabolic resources required for genome expression and protein synthesis were found to be relatively invariant under the conditions tested; (ii) effective promoter strengths were estimated at the genome scale by using global mRNA abundance and half-life data, revealing genes subject to regulation under the experimental conditions tested; and (iii) large-scale genome location-dependent expression patterns with approximately 600-kb periodicity were detected in the E. coli genome based on the 49 expression data sets analyzed. These results support the notion that a structured model-driven analysis of expression data yields additional information that can be subjected to commonly used statistical analyses. The integration of heterogeneous genome-scale data (i.e., sequence, expression data, and mRNA half-life data) is readily achieved in the context of an in silico model.
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Affiliation(s)
- Timothy E Allen
- Department of Bioengineering, University of California-San Diego, La Jolla, California 92093-0412, USA
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116
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Mølbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D. The Plasmid Genome Database. Microbiology (Reading) 2003; 149:3043-3045. [PMID: 14600215 DOI: 10.1099/mic.0.c0123-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lars Mølbak
- CEH-Oxford, Mansfield Road, Oxford, OX1 3SR, UK
- Danish Veterinary Institute, Bülowsvej 27, DK-1790 Copenhagen V, Denmark
| | - Adrian Tett
- CEH-Oxford, Mansfield Road, Oxford, OX1 3SR, UK
| | - David W Ussery
- Center for Biological Sequence Analysis, Institute of BioZentrum-DTU, Technical University of Denmark, Building 208, DK-2800, Lyngby, Denmark
| | - Kerr Wall
- Pennsylvania State University, Department of Biology, 208 Mueller Lab., University Park, PA 16802, USA
| | | | - Mark Bailey
- CEH-Oxford, Mansfield Road, Oxford, OX1 3SR, UK
| | - Dawn Field
- CEH-Oxford, Mansfield Road, Oxford, OX1 3SR, UK
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117
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Abstract
Aeromonas spp. have been related to food and waterborne diseases. The pore forming toxin aerolysin is regarded as the most important virulence factor in Aeromonas food poisoning. In this work the aerolysin promoters from several Aeromonas spp. strains have been sequenced, and divided into two sequence groups. Further analyses of the promoters were carried out in a reporter-plasmid, pSTINA-II. This plasmid was constructed as a hybrid of pUC4K, pACYC184 and pKK232-8. We could conclude that our constructed reporter-gene plasmid was functional and was used to compare different promoters in an aerolysin negative Aeromonas spp. This construct made it possible to study the expression of the reporter gene using different aerolysin promoters under several conditions. We were able to show that the two obtained sequence groups of aerolysin promoters gave different expression of the reporter gene, and that this expression was dependent of temperature and osmolarity. Reducing the size of one promoter sequence from 254 to 148 bp and 102 bp gave a gradual reduction of the reporter gene expression under all conditions. According to our assay there seems to be more than one functional promoter upstream of the aerolysin gene, although the RT-PCR indicated one transcription starting point, under all test conditions.
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Affiliation(s)
- Øyvind Ørmen
- Departament de Microbiologia i Parasitologia Sanitaries, Facultat de Farmacia, Universitat de, Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
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118
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Baar C, Eppinger M, Raddatz G, Simon J, Lanz C, Klimmek O, Nandakumar R, Gross R, Rosinus A, Keller H, Jagtap P, Linke B, Meyer F, Lederer H, Schuster SC. Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci U S A 2003; 100:11690-5. [PMID: 14500908 PMCID: PMC208819 DOI: 10.1073/pnas.1932838100] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
To understand the origin and emergence of pathogenic bacteria, knowledge of the genetic inventory from their nonpathogenic relatives is a prerequisite. Therefore, the 2.11-megabase genome sequence of Wolinella succinogenes, which is closely related to the pathogenic bacteria Helicobacter pylori and Campylobacter jejuni, was determined. Despite being considered nonpathogenic to its bovine host, W. succinogenes holds an extensive repertoire of genes homologous to known bacterial virulence factors. Many of these genes have been acquired by lateral gene transfer, because part of the virulence plasmid pVir and an N-linked glycosylation gene cluster were found to be syntenic between C. jejuni and genomic islands of W. succinogenes. In contrast to other host-adapted bacteria, W. succinogenes does harbor the highest density of bacterial sensor kinases found in any bacterial genome to date, together with an elaborate signaling circuitry of the GGDEF family of proteins. Because the analysis of the W. succinogenes genome also revealed genes related to soil- and plant-associated bacteria such as the nif genes, W. succinogenes may represent a member of the epsilon proteobacteria with a life cycle outside its host.
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Affiliation(s)
- Claudia Baar
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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119
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Zaritsky A, Woldringh CL. Localizing cell division in sphericalEscherichia coliby nucleoid occlusion. FEMS Microbiol Lett 2003; 226:209-14. [PMID: 14553913 DOI: 10.1016/s0378-1097(03)00580-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The spatial relationship between FtsZ localization and nucleoid segregation was followed in Escherichia coli thyA cells, made spheroidal by brief exposure to mecillinam and after manipulating chromosome replication time using changes ('steps') in thymine concentration [Zaritsky et al., Microbiology 145 (1999) 1015-1022]. In such cells, fluorescent FtsZ-GFP arcs did not overlap the DAPI-stained nucleoids. It is concluded that FtsZ rings are deposited between segregating nucleoids, consistent with the nucleoid occlusion model [Woldringh et al., J. Bacteriol. 176 (1994) 6030-6038].
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Affiliation(s)
- Arieh Zaritsky
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Be'er-Sheva 84105, Israel.
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120
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van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR. Strand misalignments lead to quasipalindrome correction. Trends Genet 2003; 19:365-9. [PMID: 12850440 DOI: 10.1016/s0168-9525(03)00136-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Vera van Noort
- Nijmegen Center for Molecular Life Sciences, P/A Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands
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121
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Langkjaer RB, Casaregola S, Ussery DW, Gaillardin C, Piskur J. Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts. Nucleic Acids Res 2003; 31:3081-91. [PMID: 12799436 PMCID: PMC162263 DOI: 10.1093/nar/gkg423] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2003] [Revised: 04/11/2003] [Accepted: 04/11/2003] [Indexed: 11/13/2022] Open
Abstract
The complete sequences of mitochondrial DNA (mtDNA) from the two budding yeasts Saccharomyces castellii and Saccharomyces servazzii, consisting of 25 753 and 30 782 bp, respectively, were analysed and compared to Saccharomyces cerevisiae mtDNA. While some of the traits are very similar among Saccharomyces yeasts, others have highly diverged. The two mtDNAs are much more compact than that of S.cerevisiae and contain fewer introns and intergenic sequences, although they have almost the same coding potential. A few genes contain group I introns, but group II introns, otherwise found in S.cerevisiae mtDNA, are not present. Surprisingly, four genes (ATP6, COX2, COX3 and COB) in the mtDNA of S.servazzii contain, in total, five +1 frameshifts. mtDNAs of S.castellii, S.servazzii and S.cerevisiae contain all genes on the same strand, except for one tRNA gene. On the other hand, the gene order is very different. Several gene rearrangements have taken place upon separation of the Saccharomyces lineages, and even a part of the transcription units have not been preserved. It seems that the mechanism(s) involved in the generation of the rearrangements has had to ensure that all genes stayed encoded by the same DNA strand.
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MESH Headings
- Base Sequence
- DNA, Intergenic
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- Endodeoxyribonucleases/metabolism
- Endoribonucleases/genetics
- Gene Order
- Genes, rRNA
- Introns
- Mitochondrial Proteins/genetics
- Molecular Sequence Data
- Open Reading Frames
- RNA/chemistry
- RNA/metabolism
- RNA, Catalytic/genetics
- RNA, Mitochondrial
- RNA, Transfer/genetics
- Repetitive Sequences, Nucleic Acid
- Ribonuclease P
- Saccharomyces/genetics
- Saccharomyces cerevisiae/genetics
- Sequence Analysis, DNA
- Species Specificity
- Transcription Initiation Site
- Transcription, Genetic
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Affiliation(s)
- R B Langkjaer
- BioCentrum-DTU, Technical University of Denmark, Building 301, DK-2800 Kgl. Lyngby, Denmark
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122
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Jensen LJ, Skovgaard M, Sicheritz-Pontén T, Jørgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D. Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome. BMC Genomics 2003; 4:12. [PMID: 12697059 PMCID: PMC156604 DOI: 10.1186/1471-2164-4-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2002] [Accepted: 04/02/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short and randomly scattered throughout the genome. This trend is seen for most of the bacterial and archaeal genomes published to date. RESULTS In contrast we have found that a large fraction of the genes coding for such orphan proteins in the Methanopyrus kandleri AV19 genome occur within two large regions. These genes have no known homologs except from other M. kandleri genes. However, analysis of their lengths, codon usage, and Ribosomal Binding Site (RBS) sequences shows that they are most likely true protein coding genes and not random open reading frames. CONCLUSIONS Although these regions can be considered as candidates for massive lateral gene transfer, our bioinformatics analysis suggests that this is not the case. We predict many of the organism specific proteins to be transmembrane and belong to protein families that are non-randomly distributed between the regions. Consistent with this, we suggest that the two regions are most likely unrelated, and that they may be integrated plasmids.
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Affiliation(s)
- Lars Juhl Jensen
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Marie Skovgaard
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark
| | | | - Christiane Lundegaard
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Corinna Cavan Pedersen
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Nanna Petersen
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - David Ussery
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark
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123
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Zhang Y, Crothers DM. High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc Natl Acad Sci U S A 2003; 100:3161-6. [PMID: 12629220 PMCID: PMC152263 DOI: 10.1073/pnas.0530189100] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2003] [Indexed: 11/18/2022] Open
Abstract
We have developed a high-throughput approach to the labor-intensive problems of DNA cyclization, which we use to characterize DNA curvature and mechanical properties. The method includes a combinatorial approach to make the DNA constructs needed and automated real-time measurement of the kinetics using fluorescence. We validated the approach and investigated the flexibility of two kinds of nicked DNA and AT dinucleotide repeats. We found that, although the nicks hardly alter the bending flexibility, they significantly increase the torsional flexibility, and that the AT repeat has 28% (+/-12%) lower bending rigidity than a generic DNA sequence.
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Affiliation(s)
- Yongli Zhang
- Departments of Molecular Biophysics and Biochemistry and Chemistry, Yale University, New Haven, CT 06511, USA
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124
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Coenye T, Vandamme P. Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome. BMC Genomics 2003; 4:10. [PMID: 12697060 PMCID: PMC153513 DOI: 10.1186/1471-2164-4-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2002] [Accepted: 03/17/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid) and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired via recent horizontal gene transfer or is part of an ancestral single chromosome, we compared the abundance, distribution and composition of simple sequence repeats (SSRs) between both replicons and also compared the respective compositional biases. RESULTS Our data show that both replicons are very similar in respect to distribution and composition of SSRs and presence of compositional biases. Minor variations in SSR and compositional biases observed may be attributable to minor differences in gene expression and regulation of gene expression or can be attributed to the small sample numbers observed. CONCLUSIONS The observed similarities indicate that both replicons have shared a similar evolutionary history and thus suggest that the megaplasmid was not recently acquired from other organisms by lateral gene transfer but is a part of an ancestral R. solanacearum chromosome.
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Affiliation(s)
- Tom Coenye
- Laboratorium voor Microbiologie, Ghent University,K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Peter Vandamme
- Laboratorium voor Microbiologie, Ghent University,K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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125
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Petersen L, Larsen TS, Ussery DW, On SLW, Krogh A. RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. J Mol Biol 2003; 326:1361-72. [PMID: 12595250 DOI: 10.1016/s0022-2836(03)00034-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with a period of 10-11 nucleotides. The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended -10 promoter. We predicted a total of 764 presumed RpoD promoters in the C.jejuni genome, of which 654 were located upstream of annotated genes. A similar promoter was identified in Helicobacter pylori, a close phylogenetic relative of Campylobacter, but not in Escherichia coli, Vibrio cholerae, or six other Proteobacterial genomes, or in Staphylococcus aureus. We used upstream regions of high confidence genes as training data (n=529, for the C.jejuni genome). We found it necessary to limit the training set to genes that are preceded by an intergenic region of >100bp or by a gene oriented in the opposite direction to be able to identify a conserved sequence motif, and ended up with a training set of 175 genes. This leads to the conclusion that the remaining genes (354) are more rarely preceded by a (RpoD) promoter, and consequently that operon structure may be more widespread in C.jejuni than has been assumed by others. Structural predictions of the regions upstream of the TATA-box indicates a region of highly curved DNA, and we assume that this facilitates the wrapping of the DNA around the RNA polymerase holoenzyme, and offsets the absence of a conserved -35 binding motif.
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Affiliation(s)
- Lise Petersen
- Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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126
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Abstract
It is probable that, increasingly, genome investigations are going to be based on statistical formalization. This review summarizes the state of art and potentiality of using statistics in microbial genome analysis. First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites. Then I describe how to use phylogenetic methods in genome analysis and methods for genome-wide scanning for positively selected amino acids. I conclude with speculations on the future course of genome statistical modeling.
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Affiliation(s)
- Pietro Liò
- Department of Zoology, University of Cambridge, UK.
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127
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Zhang Y, Crothers DM. Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophys J 2003; 84:136-53. [PMID: 12524271 PMCID: PMC1302599 DOI: 10.1016/s0006-3495(03)74838-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2002] [Accepted: 09/23/2002] [Indexed: 10/21/2022] Open
Abstract
DNA cyclization is potentially the most powerful approach for systematic quantitation of sequence-dependent DNA bending and flexibility. We extend the statistical mechanics of the homogeneous DNA circle to a model that considers discrete basepairs, thus allowing for inhomogeneity, and apply the model to analysis of DNA cyclization. The theory starts from an iterative search for the minimum energy configuration of circular DNA. Thermodynamic quantities such as the J factor, which is essentially the ratio of the partition functions of circular and linear forms, are evaluated by integrating the thermal fluctuations around the configuration under harmonic approximation. Accurate analytic expressions are obtained for equilibrium configurations of homogeneous circular DNA with and without bending anisotropy. J factors for both homogeneous and inhomogeneous DNA are evaluated. Effects of curvature, helical repeat, and bending and torsional flexibility in DNA cyclization are analyzed in detail, revealing that DNA cyclization can detect as little as one degree of curvature and a few percent change in flexibility. J factors calculated by our new approach are well consistent with Monte Carlo simulations, whereas the new theory has much greater efficiency in computations. Simulation of experimental results has been demonstrated.
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Affiliation(s)
- Yongli Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
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128
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Abstract
Marine phages are the most abundant biological entities in the oceans. They play important roles in carbon cycling through marine food webs, gene transfer by transduction and conversion of hosts by lysogeny. The handful of marine phage genomes that have been sequenced to date, along with prophages in marine bacterial genomes, and partial sequencing of uncultivated phages are yielding glimpses of the tremendous diversity and physiological potential of the marine phage community. Common gene modules in diverse phages are providing the information necessary to make evolutionary comparisons. Finally, deciphering phage genomes is providing clues about the adaptive response of phages and their hosts to environmental cues.
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Affiliation(s)
- John H Paul
- College of Marine Sciences, University of South Florida, 140 Seventh Ave S, St Petersburg, FL 33701, USA.
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129
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Abstract
The non-neighbor interactions between base-pairs were taken into account to calculate the angular parameters (Omega, rho and tau) describing the orientation of successive base-pair planes and the translation parameters (D(y)) along the long axis of base-pair steps for 36 independent tetramers. A statistical mechanical model was proposed to predict the DNA flexibility that is mainly related to the thermal fluctuations at individual base-pair steps. The DNA flexibility can be described by the root-mean-square deviation of the end-to-end distance of DNA helical structure. The present model was then used to investigate the extreme flexible pattern in prokaryotic and eukaryotic promoter sequences. The results demonstrated several extreme flexible regions related to functionally important elements exist both in prokaryotic promoters and in eukaryotic promoters, DNA flexibility and AT content are highly correlated. The probabilities finding flexibility pattern in promoter sequences were also estimated statistically. The biological implications were discussed briefly.
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Affiliation(s)
- Lu Tsai
- Department of Biological Science and Biotechnology, Tsinghua University, Beijing, 100084, PR China
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130
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Ussery D, Soumpasis DM, Brunak S, Staerfeldt HH, Worning P, Krogh A. Bias of purine stretches in sequenced chromosomes. COMPUTERS & CHEMISTRY 2002; 26:531-41. [PMID: 12144181 DOI: 10.1016/s0097-8485(02)00013-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 bp or longer (hereafter referred to as 'purine tracts'), as well as stretches of alternating pyrimidines/purine (pyr/pur tracts') of the same length. Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.
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Affiliation(s)
- David Ussery
- Department of Biotechnology, Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby.
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131
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Woldringh CL. The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation. Mol Microbiol 2002; 45:17-29. [PMID: 12100545 DOI: 10.1046/j.1365-2958.2002.02993.x] [Citation(s) in RCA: 182] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many recent reviews in the field of bacterial chromosome segregation propose that newly replicated DNA is actively separated by the functioning of specific proteins. This view is primarily based on an interpretation of the position of fluorescently labelled DNA regions and proteins in analogy to the active segregation mechanism in eukaryotic cells, i.e. to mitosis. So far, physical aspects of DNA organization such as the diffusional movement of DNA supercoil segments and their interaction with soluble proteins, leading to a phase separation between cytoplasm and nucleoid, have received relatively little attention. Here, a quite different view is described taking into account DNA-protein interactions, the large variation in the cellular position of fluorescent foci and the compaction and fusion of segregated nucleoids upon inhibition of RNA or protein synthesis. It is proposed that the random diffusion of DNA supercoil segments is transiently constrained by the process of co- transcriptional translation and translocation (transertion) of membrane proteins. After initiation of DNA replication, a bias in the positioning of transertion areas creates a bidirectionality in chromosome segregation that becomes self-enhanced when neighbouring genes on the same daughter chromosome are expressed. This transertion-mediated segregation model is applicable to multifork replication during rapid growth and to multiple chromosomes and plasmids that occur in many bacteria.
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Affiliation(s)
- Conrad L Woldringh
- Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, The Netherlands.
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132
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Thayer KM, Beveridge DL. Hidden Markov models from molecular dynamics simulations on DNA. Proc Natl Acad Sci U S A 2002; 99:8642-7. [PMID: 12072566 PMCID: PMC124344 DOI: 10.1073/pnas.132148699] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An enhanced bioinformatics tool incorporating the participation of molecular structure as well as sequence in protein DNA recognition is proposed and tested. Boltzmann probability models of sequence-dependent DNA structure from all-atom molecular dynamics simulations were obtained and incorporated into hidden Markov models (HMMs) that can recognize molecular structural signals as well as sequence in protein-DNA binding sites on a genome. The binding of catabolite activator protein (CAP) to cognate DNA sequences was used as a prototype case for implementation and testing of the method. The results indicate that even HMMs based on probabilistic roll/tilt dinucleotide models of sequence-dependent DNA structure have some capability to discriminate between known CAP binding and nonbinding sites and to predict putative CAP binding sites in unknowns. Restricting HMMs to sequence only in regions of strong consensus in which the protein makes base specific contacts with the cognate DNA further improved the discriminatory capabilities of the HMMs. Comparison of results with controls based on sequence only indicates that extending the definition of consensus from sequence to structure improves the transferability of the HMMs, and provides further supportive evidence of a role for dynamical molecular structure as well as sequence in genomic regulatory mechanisms.
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Affiliation(s)
- Kelly M Thayer
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457, USA.
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133
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Abstract
Our thesis is that the DNA composition and structure of genomes are selected in part by mutation bias (GC pressure) and in part by ecology. To illustrate this point, we compare and contrast the oligonucleotide composition and the mosaic structure in 36 complete genomes and in 27 long genomic sequences from archaea and eubacteria. We report the following findings (1) High-GC-content genomes show a large underrepresentation of short distances between G(n) and C(n) homopolymers with respect to distances between A(n) and T(n) homopolymers; we discuss selection versus mutation bias hypotheses. (2) The oligonucleotide compositions of the genomes of Neisseria (meningitidis and gonorrhoea), Helicobacter pylori and Rhodobacter capsulatus are more biased than the other sequenced genomes. (3) The genomes of free-living species or nonchronic pathogens show more mosaic-like structure than genomes of chronic pathogens or intracellular symbionts. (4) Genome mosaicity of intracellular parasites has a maximum corresponding to the average gene length; in the genomes of free-living and nonchronic pathogens the maximum occurs at larger length scales. This suggests that free-living species can incorporate large pieces of DNA from the environment, whereas for intracellular parasites there are recombination events between homologous genes. We discuss the consequences in terms of evolution of genome size. (5) Intracellular symbionts and obligate pathogens show small, but not zero, amount of chromosome mosaicity, suggesting that recombination events occur in these species.
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Affiliation(s)
- Pietro Liò
- Department of Zoology, University of Cambridge, United Kingdom.
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134
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Petersen RF, Langkjaer RB, Hvidtfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J. Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts. J Mol Biol 2002; 318:627-36. [PMID: 12054811 DOI: 10.1016/s0022-2836(02)00037-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Petite-positive Saccharomyces yeasts can be roughly divided into the sensu stricto, including Saccharomyces cerevisiae, and sensu lato group, including Saccharomyces castellii; the latter was recently studied for transmission and the organisation of its mitochondrial genome. S. castellii mitochondrial molecules (mtDNA) carrying point mutations, which confer antibiotic resistance, behaved in genetic crosses as the corresponding point mutants of S. cerevisiae. While S. castellii generated spontaneous petite mutants in a similar way as S. cerevisiae, the petites exhibited a different inheritance pattern. In crosses with the wild type strains a majority of S. castellii petites was neutral, and the suppressivity in suppressive petites was never over 50%. The two yeasts also differ in organisation of their mtDNA molecules. The 25,753 bp sequence of S. castellii mtDNA was determined and the coding potential of both yeasts is similar. However, the S. castellii intergenic sequences are much shorter and do not contain sequences homologous to the S. cerevisiae biologically active intergenic sequences, as ori/rep/tra, which are responsible for the hyper-suppressive petite phenotype found in S. cerevisiae. The structure of one suppressive S. castellii mutant, CA38, was also determined. Apparently, a short direct intergenic repeat was involved in the generation of this petite mtDNA molecule.
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Affiliation(s)
- Randi F Petersen
- BioCentrum-DTU, Technical University of Denmark, Building 301, DK-2800 Kgl. Lyngby, Denmark
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135
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Masulis IS, Buckin VA, Ozoline ON. Flexible elements in the structure of promoter DNA as probed by cationic surfactant binding. J Biomol Struct Dyn 2002; 19:919-27. [PMID: 11922845 DOI: 10.1080/07391102.2002.10506794] [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] [Indexed: 10/28/2022]
Abstract
A susceptibility of promoter DNA for adaptive conformational transitions has been studied using a cationic surfactant dodecyltrimethylammonium bromide (C(12)TAB) as a model DNA-binding ligand. DNAse 1 and KMnO(4) were utilized as structure-specific reagents. Both reagents revealed ligand-induced perturbations in the double helix of promoters T7A1 and T7D. These conformational transitions appeared to be strongly associated with pyrimidine-purine steps, which have non-random distribution within RNA polymerase contact region of the promoter DNA and are present in the binding sites for a majority of transcription regulation proteins. Potential flexibility of these elements creates therefore a specific media for transcription complex formation. Molecular mechanism of DNA interaction with C(12)TAB is discussed.
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Affiliation(s)
- I S Masulis
- Institute of Cell Biophysics, Russian Academy of Sciences Pushchino, Moscow Region, 142290 Russia
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136
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Abstract
We describe an original approach to determining sequence-structure relationships for DNA. This approach, termed ADAPT, combines all-atom molecular mechanics with a multicopy algorithm to build nucleotides that contain all four standard bases in variable proportions. These nucleotides enable us to search very rapidly for base sequences that energetically favor chosen types of DNA deformation or chosen DNA-protein or DNA-ligand interactions. Sequences satisfying the chosen criteria can be found by energy minimization, combinatorial sequence searching, or genome scanning, in a manner similar to the threading approaches developed for protein structure prediction. In the latter case, we are able to analyze roughly 2000 base pairs per second. Applications of the method to DNA allomorphic transitions, DNA deformation, and specific DNA interactions are presented.
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Affiliation(s)
- I Lafontaine
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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137
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Abstract
We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural model for a DNA decamer containing the EcoRI restriction site. Our findings agree well with recent crystal and NMR structures of the EcoRI dodecamer, where an overall bend of seven degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that the sequence has a higher flexibility, assumed to be isotropic, compared to that of a "generic" DNA sequence. This model was used as a starting point for the investigation of the effect of cytosine methylation on DNA bending and flexibility. While methylation did not affect bend magnitude or direction, it resulted in a reduction in bending flexibility and under-winding of the methylated nucleotides. We demonstrate that our approach can augment the understanding of DNA structure and dynamics by adding information about the global structure and flexibility of the sequence. We also show that cyclization kinetics can be used to study the properties of modified nucleotides.
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Affiliation(s)
- Dafna Nathan
- Departments of Chemistry, Yale University, New Haven, CT 06520, USA
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138
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139
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Phylactides M, Rowntree R, Nuthall H, Ussery D, Wheeler A, Harris A. Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:553-9. [PMID: 11856314 DOI: 10.1046/j.0014-2956.2001.02679.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene shows a complex pattern of expression, with temporal and spatial regulation that is not accounted for by elements in the promoter. One approach to identifying the regulatory elements for CFTR is the mapping of DNase I hypersensitive sites (DHS) within the locus. We previously identified at least 12 clusters of DHS across the CFTR gene and here further evaluate DHS in introns 2, 3, 10, 16, 17a, 18, 20 and 21 to assess their functional importance in regulation of CFTR gene expression. Transient transfections of enhan- cer/reporter constructs containing the DHS regions showed that those in introns 20 and 21 augmented the activity of the CFTR promoter. Structural analysis of the DNA sequence at the DHS suggested that only the one intron 21 might be caused by inherent DNA structures. Cell specificity of the DHS suggested a role for the DHS in introns 2 and 18 in CFTR expression in some pancreatic duct cells. Finally, regulatory elements at the DHS in introns 10 and 18 may contribute to upregulation of CFTR gene transcription by forskolin and mitomycin C, respectively. These data support a model of regulation of expression of the CFTR gene in which multiple elements contribute to tightly co-ordinated expression in vivo.
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Affiliation(s)
- Marios Phylactides
- Paediatric Molecular Genetics, Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, UK
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140
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Abstract
Empirical rules based on tetranucleotide parameters were presented to predict the structural parameters twist (Omega), roll (rho), tilt (tau) and slide (D(y)). A statistical mechanical model was used to analyze the flexibility of the Escherichia coli genome. The replication terminus region displayed a low level of flexibility. A strong correlation can be seen between G+C content and flexibility. Average flexibilities in the coding regions were found to be significantly larger than those in non-coding regions. The flexible characteristics in the 5'-neighborhood of the coding regions and in three class sigma promoter sequences in the E. coli genome were also analyzed.
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Affiliation(s)
- L Tsai
- Department of Biological Science and Technology, Tsinghua University, Beijing, PR China
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141
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Abstract
DNA with a curved trajectory of its helix axis is called bent DNA, or curved DNA. Interestingly, biologically important DNA regions often contain this structure, irrespective of the origin of DNA. In the last decade, considerable progress has been made in clarifying one role of bent DNA in prokaryotic transcription and its mechanism of action. However, the role of bent DNA in eukaryotic transcription remains unclear. Our recent study raises the possibility that bent DNA is implicated in the "functional packaging" of transcriptional regulatory regions into chromatin. In this article, I review recent progress in bent DNA research in eukaryotic transcription, and summarize the history of bent DNA research and several subjects relevant to this theme. Finally, I propose a hypothesis that bent DNA structures that mimic a negative supercoil, or have a right-handed superhelical writhe, organize local chromatin infrastructure to help the very first interaction between cis-acting DNA elements and activators that trigger transcription.
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Affiliation(s)
- T Ohyama
- Department of Biology, Faculty of Science and High Technology Research Center, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
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142
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Guijo MI, Patte J, del Mar Campos M, Louarn JM, Rebollo JE. Localized remodeling of the Escherichia coli chromosome: the patchwork of segments refractory and tolerant to inversion near the replication terminus. Genetics 2001; 157:1413-23. [PMID: 11290700 PMCID: PMC1461588 DOI: 10.1093/genetics/157.4.1413] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The behavior of chromosomal inversions in Escherichia coli depends upon the region they affect. Regions flanking the replication terminus have been termed nondivisible zones (NDZ) because inversions ending in the region were either deleterious or not feasible. This regional phenomenon is further analyzed here. Thirty segments distributed between 23 and 29 min on the chromosome map have been submitted to an inversion test. Twenty-five segments either became deleterious when inverted or were noninvertible, but five segments tolerated inversion. The involvement of polar replication pause sites in this distribution was investigated. The results suggest that the Tus/pause site system may forbid some inversion events, but that other constraints to inversion, unrelated to this system, exist. Our current model for deleterious inversions is that the segments involved carry polar sequences acting in concert with other polar sequences located outside the segments. The observed patchwork of refractory and tolerant segments supports the existence of several NDZs in the 23- to 29-min region. Microscopic observations revealed that deleterious inversions are associated with high frequencies of abnormal nucleoid structure and distribution. Combined with other information, the data suggest that NDZs participate in the organization of the terminal domain of the nucleoid.
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Affiliation(s)
- M I Guijo
- Departamento de Bioquimica y Biologia Molecular y Genética, Facultad de Ciencias, Universidad de Extremadura, 06080 Badajoz, Spain
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143
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Miyano M, Kawashima T, Ohyama T. A common feature shared by bent DNA structures locating in the eukaryotic promoter region. Mol Biol Rep 2001; 28:53-61. [PMID: 11710566 DOI: 10.1023/a:1011999730828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Eukaryotic promoters often contain a bent DNA structure, suggesting that this structure plays some role in transcription. To reveal the role, we need more information on the promoters that contain or flank a bent DNA structure. In this study, we collected such promoters by the following approach: we first isolated human genomic DNA fragments that contained at least one bent DNA structure, then shotgun cloned them into a promoter trap vector, screened DNA fragments that functioned as a promoter, and finally found the promoters of interest by determining the bent DNA locus and the region expressing promoter activity. From 1,187 recombinant plasmids, we isolated 51 that showed promoter activity. Structural and functional analyses of randomly selected 10 clones with inserts of 548-913 bp demonstrated 11 sequences that could drive transcription. Unexpectedly, all of these clones met our purpose: i.e., each segment that showed a promoter activity (67-179 bp) was very close to the bent DNA structure (spanning about 150 bp in all clones), and in some cases overlapped it. More interestingly, these bent DNA structures all had a superhelical writhe. We propose a hypothesis that in the bent-DNA-containing eukaryotic promoters. bent DNA organizes local chromatin infrastructure appropriately for transcription initiation.
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Affiliation(s)
- M Miyano
- Department of Biology, Faculty of Science, Konan University, Kobe, Japan
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144
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Ussery D, Larsen TS, Wilkes KT, Friis C, Worning P, Krogh A, Brunak S. Genome organisation and chromatin structure in Escherichia coli. Biochimie 2001; 83:201-12. [PMID: 11278070 DOI: 10.1016/s0300-9084(00)01225-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have analysed the complete sequence of the Escherichia coli K12 isolate MG1655 genome for chromatin-associated protein binding sites, and compared the predicted location of predicted sites with experimental expression data from 'DNA chip' experiments. Of the dozen proteins associated with chromatin in E. coli, only three have been shown to have significant binding preferences: integration host factor (IHF) has the strongest binding site preference, and FIS sites show a weak consensus, and there is no clear consensus site for binding of the H-NS protein. Using hidden Markov models (HMMs), we predict the location of 608 IHF sites, scattered throughout the genome. A subset of the IHF sites associated with repeats tends to be clustered around the origin of replication. We estimate there could be roughly 6000 FIS sites in E. coli, and the sites tend to be localised in two regions flanking the replication termini. We also show that the regions upstream of genes regulated by H-NS are more curved and have a higher AT content than regions upstream of other genes. These regions in general would also be localised near the replication terminus.
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Affiliation(s)
- D Ussery
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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145
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Capiaux H, Cornet F, Corre J, Guijo MI, Pérals K, Rebollo JE, Louarn JM. Polarization of the Escherichia coli chromosome. A view from the terminus. Biochimie 2001; 83:161-70. [PMID: 11278065 DOI: 10.1016/s0300-9084(00)01202-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The E. coli chromosome replication arms are polarized by motifs such as RRNAGGGS oligomers, found preferentially on leading strands. Their skew increases regularly from the origin to dif (the site in the center of the terminus where chromosome dimer resolution occurs), to reach a value of 90% near dif. Convergent information indicates that polarization in opposite directions from the dif region controls tightly the activity of dif, probably by orienting mobilization of the terminus at cell division. Another example of polarization is the presence, in the region peripheral to the terminus, of small non-divisible zones whose inversion interferes with spatial separation of sister nucleoids. The two phenomena may contribute to the organization of the Ter macrodomain.
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Affiliation(s)
- H Capiaux
- Laboratoire de Microbiologie et de Génétique moléculaires du CNRS, 118, route de Narbonne, 31320 Toulouse cedex, France
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146
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Roychoudhury M, Sitlani A, Lapham J, Crothers DM. Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proc Natl Acad Sci U S A 2000; 97:13608-13. [PMID: 11095739 PMCID: PMC17623 DOI: 10.1073/pnas.250476297] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The method of DNA cyclization kinetics reveals special properties of the TATAAACGCC sequence motif found in DNA sequences that have high affinity for core histones. Replacement of 30 bp of generic DNA by three 10-bp repeats of the motif in small cyclization constructs increases cyclization rates by two orders of magnitude. We document a 13 degrees bend in the motif and characterize the direction of curvature. The bending force constant is smaller by nearly 2-fold and there is a 35% decrease in the twist modulus, relative to generic DNA. These features are the likely source of the high affinity for bending around core histones to form nucleosomes. Our results establish a protocol for determination of the ensemble-averaged global solution structure and mechanical properties of any approximately 10-bp DNA sequence element of interest, providing information complementary to that from NMR and crystallographic structural studies.
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Affiliation(s)
- M Roychoudhury
- Department of Chemistry, P.O. Box 208107, Yale University, New Haven, CT 06520, USA
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147
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Brem R. Identifying structured regions in E. coliDNA. Genome Biol 2000. [DOI: 10.1186/gb-2000-1-2-reports0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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