Coevolution of aah: A Dps -like gene with the host bacterium revealed by comparative genomic analysis

The Scientific World Journal

Volumn 2012, Issue , 2012, Pages

  Ping, Liyan ^a   Platzer, Matthias ^b   Wen, Gaiping ^b   Delaroque, Nicolas ^a  

^a MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

^b FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DNA BINDING PROTEIN; PROTEIN AAH; UNCLASSIFIED DRUG; DPS PROTEIN, BACTERIA;

ACTINOBACTERIA; ARTICLE; BACTERIAL GENOME; CODON; COEVOLUTION; COMPARATIVE GENOMIC HYBRIDIZATION; CORRELATION ANALYSIS; NONHUMAN; PHYLOGENY; PROTEIN FUNCTION; PROTEIN ISOLATION; STOP CODON; BACTERIUM; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); MICROBACTERIUM ARBORESCENS; MICROCOCCINEAE;

BACTERIA; BACTERIAL PROTEINS; BASE COMPOSITION; BASE SEQUENCE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION;

EID: 84858110364     PISSN: None     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1100/2012/504905     Document Type: Article

References (52)

1. Almiron M., Link A. J., Furlong D., Kolter R., A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli Genes Development 1992 6 2646 2654 (Pubitemid 23052891)
2. Radolf J. D., Borenstein L. A., Kim J. Y., Role of disulfide bonds in the oligomeric structure and protease resistance of recombinant and native Treponema pallidum surface antigen 4D Journal of Bacteriology 1987 169 4 1365 1371 (Pubitemid 17063456)
3. Noordhoek G. T., Hermans P. W. M., Paul A. N., Schouls L. M., van der Sluis J. J., van Embden J. D. A., Treponema pallidum subspecies pallidum (Nichols) and Treponema pallidum subspecies pertenue (CDC 2575) differ in at least one nucleotide: comparison of two homologous antigens Microbial Pathogenesis 1989 6 1 29 42 (Pubitemid 19091589)
4. Walfield A. M., Roche E. S., Zounes M. C., Kirkpatrick H., Wild M. A., Textor G., Tsai P. K., Richardson C., Primary structure of an oligomeric antigen of Treponema pallidum Infection and Immunity 1989 57 2 633 635 (Pubitemid 19046393)
5. Norris S. J., Polypeptides of Treponema pallidum: progress toward understanding their structural, functional, and immunologic roles. Treponema Pallidum Polypeptide Research Group Microbiological Reviews 1993 57 3 750 779 (Pubitemid 23262517)
6. Ceci P., Ilari A., Falvo E., Chiancone E., The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: x-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties The Journal of Biological Chemistry 2003 278 22 20319 20326 (Pubitemid 36799231)
7. Roy S., Saraswathi R., Gupta S., Sekar K., Chatterji D., Vijayan M., Role of N and C-terminal tails in DNA binding and assembly in Dps: structural studies of Mycobacterium smegmatis Dps deletion mutants Journal of Molecular Biology 2007 370 4 752 767 (Pubitemid 46879776)
8. Grant R. A., Filman D. J., Finkel S. E., Kolter R., Hogle J. M., The crystal structure of Dps, a ferritin homolog that binds and protects DNA Nature Structural Biology 1998 5 4 294 303 (Pubitemid 28164882)
9. Ilari A., Stefanini S., Chiancone E., Tsernoglou D., The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site Nature Structural Biology 2000 7 1 38 43 (Pubitemid 30043246)
10. Papinutto E., Dundon W. G., Pitulis N., Battistutta R., Montecucco C., Zanotti G., Structure of two iron-binding proteins from Bacillus anthracis The Journal of Biological Chemistry 2002 277 17 15093 15098 (Pubitemid 34952587)
11. Ren B., Tibbelin G., Kajino T., Asami O., Ladenstein R., The multi-layered structure of Dps with a novel di-nuclear ferroxidase center Journal of Molecular Biology 2003 329 3 467 477 (Pubitemid 36593206)
12. Zhao G., Ceci P., Ilari A., Giangiacomo L., Laue T. M., Chiancone E., Dennis Chasteen N., Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells. A ferritin-like DNA-binding protein of Escherichia coli The Journal of Biological Chemistry 2002 277 31 27689 27696 (Pubitemid 34966712)
13. Ferguson G. P., Creighton R. I., Nikolaev Y., Booth I. R., Importance of RpoS and Dps in survival of exposure of both exponential- and stationary-phase Escherichia coli cells to the electrophile N- ethylmaleimide Journal of Bacteriology 1998 180 5 1030 1036 (Pubitemid 28119458)
14. Choi S. H., Baumler D. J., Kaspar C. W., Contribution of dps to acid stress tolerance and oxidative stress tolerance in Escherichia coli O157:H7 Applied and Environmental Microbiology 2000 66 9 3911 3916
15. Ilari A., Ceci P., Ferrari D., Rossi G. L., Chiancone E., Iron incorporation into Escherichia coli Dps gives rise to a ferritin-like microcrystalline core The Journal of Biological Chemistry 2002 277 40 37619 37623
16. Chen L., James L. P., Helmann J. D., Metalloregulation in Bacillus subtilis: isolation and characterization of two genes differentially repressed by metal ions Journal of Bacteriology 1993 175 17 5428 5437 (Pubitemid 23264438)
17. Chen L., Helmann J. D., Bacillus subtilis MrgA is a Dps(PexB) homologue: evidence for metalloregulation of an oxidative-stress gene Molecular Microbiology 1995 18 2 295 300
18. Bozzi M., Mignogna G., Stefanini S., Barra D., Longhi C., Valenti P., Chiancone E., A novel non-heme iron-binding ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua The Journal of Biological Chemistry 1997 272 6 3259 3265
19. Polidoro M., de Biase D., Montagnini B., Guarrera L., Cavallo S., Valenti P., Stefanini S., Chiancone E., The expression of the dodecameric ferritin in Listeria spp. is induced by iron limitation and stationary growth phase Gene 2002 296 1-2 121 128 (Pubitemid 35287330)
20. Hebraud M., Guzzo J., The main cold shock protein of Listeria monocytogenes belongs to the family of ferritin-like proteins FEMS Microbiology Letters 2000 190 1 29 34 (Pubitemid 30645830)
21. Evans D. J. Jr., Evans D. G., Takemura T., Nakano H., Lampert H. C., Graham D. Y., Granger D. N., Kvietys P. R., Characterization of a Helicobacter pylori neutrophil-activating protein Infection and Immunity 1995 63 6 2213 2220
22. Namavar F., Sparrius M., Veerman E. C. I., Appelmelk B. J., Vandenbroucke-Grauls C. M. J. E., Neutrophil-activating protein mediates adhesion of Helicobacter pylori to sulfated carbohydrates on high-molecular-weight salivary mucin Infection and Immunity 1998 66 2 444 447 (Pubitemid 28074179)
23. Teneberg S., Miller-Podraza H., Lampert H. C., Evans D. J., Evans D. G., Danielsson D., Karlsson K. A., Carbohydrate binding specificity of the neutrophil-activating protein of Helicobacter pylori The Journal of Biological Chemistry 1997 272 30 19067 19071 (Pubitemid 27318264)
24. Ceci P., Mangiarotti L., Rivetti C., Chiancone E., The neutrophil-activating Dps protein of Helicobacter pylori, HP-NAP, adopts a mechanism different from Escherichia coli Dps to bind and condense DNA Nucleic Acids Research 2007 35 7 2247 2256 (Pubitemid 47073712)
25. Brentjens R. J., Ketterer M., Apicella M. A., Spinola S. M., Fine tangled pili expressed by Haemophilus ducreyi are a novel class of pili Journal of Bacteriology 1996 178 3 808 816 (Pubitemid 26036654)
26. Pena M. M. O., Bullerjahn G. S., The DpsA protein of Synechococcus sp. strain PCC7942 is a DNA-binding hemoprotein: linkage of the Dps and bacterioferritin protein families The Journal of Biological Chemistry 1995 270 38 22478 22482
27. Tonello F., Dundon W. G., Satin B., Molinari M., Tognon G., Grandi G., Del Giudice G., Rappuoli R., Montecucco C., The Helicobacter pylori neutrophil-activating protein is an iron-binding protein with dodecameric structure Molecular Microbiology 1999 34 2 238 246 (Pubitemid 29486242)
28. Yamamoto Y., Higuchi M., Poole L. B., Kamio Y., Role of the dpr product in oxygen tolerance in Streptococcus mutans Journal of Bacteriology 2000 182 13 3740 3747 (Pubitemid 30413025)
29. Yamamoto Y., Poole L. B., Hantgan R. R., Kamio Y., An iron-binding protein, Dpr, from Streptococcus mutans prevents iron-dependent hydroxyl radical formation in vitro Journal of Bacteriology 2002 184 11 2931 2939 (Pubitemid 34517815)
30. Pulliainen A. T., Haataja S., Khknen S., Finne J., Molecular basis of H 2 O 2 resistance mediated by streptococcal Dpr: demonstration of the functional involvement of the putative ferroxidase center by site-directed mutagenesis in Streptococcus suis The Journal of Biological Chemistry 2003 278 10 7996 8005 (Pubitemid 36800538)
31. Rocha E. R., Owens G. Jr., Smith C. J., The redox-sensitive transcriptional activator OxyR regulates the peroxide response regulon in the obligate anaerobe Bacteroides fragilis Journal of Bacteriology 2000 182 18 5059 5069
32. Horsburgh M. J., Clements M. O., Crossley H., Ingham E., Foster S. J., PerR controls oxidative stress resistance and iron storage proteins and is required for virulence in Staphylococcus aureus Infection and Immunity 2001 69 6 3744 3754 (Pubitemid 32493293)
33. Ishikawa T., Mizunoe Y., Kawabata S. I., Takade A., Harada M., Wai S. N., Yoshida S. I., The iron-binding protein Dps confers hydrogen peroxide stress resistance to Campylobacter jejuni Journal of Bacteriology 2003 185 3 1010 1017 (Pubitemid 36139460)
34. Gupta S., Pandit S. B., Srinivasan N., Chatterji D., Proteomics analysis of carbon-starved Mycobacterium smegmatis: induction of Dps-like protein Protein Engineering 2002 15 6 503 511 (Pubitemid 34742258)
35. Gupta S., Chatterji D., Bimodal protection of DNA by Mycobacterium smegmatis DNA-binding protein from stationary phase cells The Journal of Biological Chemistry 2003 278 7 5235 5241 (Pubitemid 36801036)
36. Roy S., Saraswathi R., Chatterji D., Vijayan M., Structural studies on the second Mycobacterium smegmatis Dps: invariant and variable features of structure, assembly and function Journal of Molecular Biology 2008 375 4 948 959 (Pubitemid 350309389)
37. Ueshima J., Shoji M., Ratnayake D. B., Abe K., Yoshida S., Yamamoto K., Nakayama K., Purification, gene cloning, gene expression, and mutants of Dps from the obligate anaerobe Porphyromonas gingivalis Infection and Immunity 2003 71 3 1170 1178 (Pubitemid 36254298)
38. Chen H., Ponniah G., Salonen N., Blum P., Culture-independent analysis of fecal enterobacteria in environmental samples by single-cell mRNA profiling Applied and Environmental Microbiology 2004 70 8 4432 4439 (Pubitemid 39095460)
39. Ping L., Bchler R., Mithfer A., Svato A., Spiteller D., Dettner K., Gmeiner S., Piel J., Schlott B., Boland W., A novel Dps-type protein from insect gut bacteria catalyses hydrolysis and synthesis of N-acyl amino acids Environmental Microbiology 2007 9 6 1572 1583 (Pubitemid 46763538)
40. Bhattacharyya G., Grove A., The N-terminal extensions of Deinococcus radiodurans Dps-1 mediate DNA major groove interactions as well as assembly of the dodecamer The Journal of Biological Chemistry 2007 282 16 11921 11930 (Pubitemid 47100660)
41. Cuypers M. G., Mitchell E. P., Romo C. V., McSweeney S. M., The crystal structure of the Dps2 from Deinococcus radiodurans reveals an unusual pore profile with a non-specific metal binding site Journal of Molecular Biology 2007 371 3 787 799 (Pubitemid 47090184)
42. Wei X., Mingjia H., Xiufeng L., Yang G., Qingyu W., Identification and biochemical properties of Dps (starvation-induced DNA binding protein) from cyanobacterium Anabaena sp. PCC 7120 IUBMB Life 2007 59 10 675 681 (Pubitemid 47463912)
43. Ishikawa J., Hotta K., FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G + C content FEMS Microbiology Letters 1999 174 2 251 253 (Pubitemid 29217014)
44. Sueoka N., Directional mutation pressure and neutral molecular evolution Proceedings of the National Academy of Sciences of the United States of America 1988 85 8 2653 2657
45. Lobry J. R., Chessel D., Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria Journal of Applied Genetics 2003 44 2 235 261 (Pubitemid 37123440)
46. Bentley S. D., Maiwald M., Murphy L. D., Pallen M. J., Yeats C. A., Dover L. G., Norbertczak H. T., Besra G. S., Quail M. A., Harris D. E., Von Herbay A., Goble A., Rutter S., Squares R., Squares S., Barrell B. G., Parkhill J., Relman D. A., Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei The Lancet 2003 361 9358 637 644 (Pubitemid 36246545)
47. Casjens S., Palmer N., van Vugt R., Huang W. M., Stevenson B., Rosa P., Lathigra R., Sutton G., Peterson J., Dodson R. J., Haft D., Hickey E., Gwinn M., White O., Fraser C. M., A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi Molecular Microbiology 2000 35 3 490 516 (Pubitemid 30085269)
48. Evans D. J. Jr., Evans D. G., Lampert H. C., Nakano H., Identification of four new prokaryotic bacterioferritins, from Helicobacter pylori, Anabaena variabilis, Bacillus subtilis and Treponema pallidum, by analysis of gene sequences Gene 1995 153 1 123 127
49. Weisburg W. G., Oyaizu Y., Oyaizu H., Woese C. R., Natural relationship between bacteroides and flavobacteria Journal of Bacteriology 1985 164 1 230 236 (Pubitemid 16223513)
50. Fitzgerald J. R., Musser J. M., Evolutionary genomics of pathogenic bacteria Trends in Microbiology 2001 9 11 547 553 (Pubitemid 34121941)
51. Lowe T. M., Eddy S. R., tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Research 1997 25 5 955 964 (Pubitemid 27298263)
52. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G., The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Research 1997 25 24 4876 4882 (Pubitemid 28022245)