OpenLB
Open Library of Bioscience
Advanced Search
Nucleic acids research
01 08, 2020;48 (D1): D590-D598.

PADS Arsenal: a database of prokaryotic defense systems related genes.

Yadong Zhang, Zhewen Zhang, Hao Zhang, Yongbing Zhao, Zaichao Zhang, Jingfa Xiao
Author Information
  1. Yadong Zhang: National Genomics Data Center, Beijing 100101, China.
  2. Zhewen Zhang: National Genomics Data Center, Beijing 100101, China.
  3. Hao Zhang: National Genomics Data Center, Beijing 100101, China.
  4. Yongbing Zhao: Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA.
  5. Zaichao Zhang: Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada.
  6. Jingfa Xiao: National Genomics Data Center, Beijing 100101, China.
PMID: 31620779 DOI: 10.1093/nar/gkz916

Abstract

Defense systems are vital weapons for prokaryotes to resist heterologous DNA and survive from the constant invasion of viruses, and they are widely used in biochemistry investigation and antimicrobial drug research. So far, numerous types of defense systems have been discovered, but there is no comprehensive defense systems database to organize prokaryotic defense gene datasets. To fill this gap, we unveil the prokaryotic antiviral defense system (PADS) Arsenal (https://bigd.big.ac.cn/padsarsenal), a public database dedicated to gathering, storing, analyzing and visualizing prokaryotic defense gene datasets. The initial version of PADS Arsenal integrates 18 distinctive categories of defense system with the annotation of 6 600 264 genes retrieved from 63,701 genomes across 33 390 species of archaea and bacteria. PADS Arsenal provides various ways to retrieve defense systems related genes information and visualize them with multifarious function modes. Moreover, an online analysis pipeline is integrated into PADS Arsenal to facilitate annotation and evolutionary analysis of defense genes. PADS Arsenal can also visualize the dynamic variation information of defense genes from pan-genome analysis. Overall, PADS Arsenal is a state-of-the-art open comprehensive resource to accelerate the research of prokaryotic defense systems.

References

  1. Annu Rev Biochem. 1969;38:467-500 [PMID: 4897066]
  2. Nucleic Acids Res. 2002 Jul 15;30(14):3059-66 [PMID: 12136088]
  3. Bioessays. 2011 Jan;33(1):43-51 [PMID: 20979102]
  4. Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2963-8 [PMID: 21285367]
  5. Nat Rev Microbiol. 2005 May;3(5):371-82 [PMID: 15864262]
  6. Science. 2018 Mar 2;359(6379): [PMID: 29371424]
  7. Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251 [PMID: 29790974]
  8. J Bacteriol. 2011 Nov;193(21):6039-56 [PMID: 21908672]
  9. Nat Chem Biol. 2016 Apr;12(4):208-14 [PMID: 26991085]
  10. Nat Rev Microbiol. 2018 Jan;16(1):5-11 [PMID: 28736447]
  11. Curr Opin Microbiol. 2005 Aug;8(4):473-9 [PMID: 15979388]
  12. Nucleic Acids Res. 2015 Jan;43(Database issue):D298-9 [PMID: 25378308]
  13. Nucleic Acids Res. 1988 May 25;16(10):4341-52 [PMID: 2837731]
  14. Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432 [PMID: 30357350]
  15. Trends Genet. 2008 Nov;24(11):539-51 [PMID: 18819722]
  16. Nat Biotechnol. 2013 Mar;31(3):227-9 [PMID: 23360964]
  17. Nat Chem Biol. 2007 Nov;3(11):709-10 [PMID: 17934475]
  18. Nucleic Acids Res. 2018 Jan 4;46(D1):D749-D753 [PMID: 29106666]
  19. BMC Bioinformatics. 2007 May 23;8:172 [PMID: 17521438]
  20. Biochemistry (Mosc). 2015 Oct;80(10):1373-86 [PMID: 26567582]
  21. Bioinformatics. 2015 Nov 15;31(22):3691-3 [PMID: 26198102]
  22. Nucleic Acids Res. 2001 Jan 1;29(1):41-3 [PMID: 11125044]
  23. Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9 [PMID: 25428365]
  24. BMC Evol Biol. 2017 Apr 4;17(1):94 [PMID: 28376755]
  25. Nucleic Acids Res. 2013 Apr;41(8):4360-77 [PMID: 23470997]
  26. Nucleic Acids Res. 2015 May 26;43(10):5120-9 [PMID: 25925567]
  27. Science. 2010 Jan 8;327(5962):167-70 [PMID: 20056882]
  28. Bioinformatics. 2016 Sep 15;32(18):2847-9 [PMID: 27207943]
  29. Annu Rev Genet. 2011;45:61-79 [PMID: 22060041]
  30. Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28 [PMID: 30395293]
  31. Nucleic Acids Res. 2019 Jan 8;47(D1):D8-D14 [PMID: 30365034]
  32. CRC Crit Rev Biochem. 1976 Nov;4(2):123-64 [PMID: 795607]
  33. BMC Bioinformatics. 2018 Jul 25;19(1):276 [PMID: 30045713]
  34. Nat Microbiol. 2018 Jan;3(1):90-98 [PMID: 29085076]
  35. BMC Biol. 2014 Aug 21;12:66 [PMID: 25141959]
  36. EMBO J. 2015 Jan 13;34(2):169-83 [PMID: 25452498]
  37. Mob Genet Elements. 2013 Sep 1;3(5):e26219 [PMID: 24251069]
  38. Bioinformatics. 2016 Nov 15;32(22):3501-3503 [PMID: 27412096]
  39. Mol Biotechnol. 2003 Mar;23(3):225-43 [PMID: 12665693]
  40. Extremophiles. 2014 Sep;18(5):877-93 [PMID: 25113822]
  41. Microbiol Mol Biol Rev. 2013 Mar;77(1):53-72 [PMID: 23471617]
  42. Nature. 2010 Nov 4;468(7320):67-71 [PMID: 21048762]
  43. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 [PMID: 9254694]
  44. Trends Biochem Sci. 2009 Aug;34(8):401-7 [PMID: 19646880]
  45. BMC Bioinformatics. 2017 Feb 6;18(1):92 [PMID: 28166719]
  46. Nat Struct Mol Biol. 2014 Sep;21(9):743-53 [PMID: 25192263]
  47. Int J Food Microbiol. 2002 Sep 15;78(1-2):119-31 [PMID: 12222629]
  48. Nat Rev Microbiol. 2011 Jun;9(6):467-77 [PMID: 21552286]
  49. Science. 2013 Feb 15;339(6121):819-23 [PMID: 23287718]
  50. Trends Biochem Sci. 2014 Jun;39(6):257-9 [PMID: 24836995]
  51. Annu Rev Microbiol. 2017 Sep 8;71:233-261 [PMID: 28657885]
  52. Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4057-62 [PMID: 27035975]
  53. Nature. 2014 Mar 13;507(7491):258-261 [PMID: 24531762]
  54. Front Cell Infect Microbiol. 2012 Sep 13;2:119 [PMID: 22993722]
  55. Mol Cell. 2005 Aug 5;19(3):405-19 [PMID: 16061186]
  56. Syst Biol. 2010 May;59(3):307-21 [PMID: 20525638]
  57. Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12 [PMID: 22096229]

MeSH Term

Archaea
Archaeal Viruses
Bacteria
Bacteriophages
CRISPR-Cas Systems
DNA Restriction-Modification Enzymes
Databases, Genetic
Host-Pathogen Interactions
Software

Chemicals

DNA Restriction-Modification Enzymes
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC007121 (PADS Arsenal)

Word Cloud

Similar Articles

Cited By