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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1992 Oct 1;89(19):8990–8994. doi: 10.1073/pnas.89.19.8990

Proposed acquisition of an animal protein domain by bacteria.

P Bork 1, R F Doolittle 1
PMCID: PMC50050  PMID: 1409594

Abstract

A systematic screen of a protein sequence data base confirms that the fibronectin type III (Fn3) domain is widely distributed among animal proteins and occurs also in several bacterial carbohydrate-splitting enzymes. The motif has yet to be identified in proteins from plants or fungi. All indications are that the bacterial sequences are much too similar to the animal type to be the result of conventional vertical descent. Rather, it is likely that the bacterial units were initially acquired from an animal source and are being spread further by horizontal transfers between distantly related bacteria.

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Selected References

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  1. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2247–2249. doi: 10.1093/nar/19.suppl.2247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baron M., Main A. L., Driscoll P. C., Mardon H. J., Boyd J., Campbell I. D. 1H NMR assignment and secondary structure of the cell adhesion type III module of fibronectin. Biochemistry. 1992 Feb 25;31(7):2068–2073. doi: 10.1021/bi00122a025. [DOI] [PubMed] [Google Scholar]
  3. Bazan J. F. Structural design and molecular evolution of a cytokine receptor superfamily. Proc Natl Acad Sci U S A. 1990 Sep;87(18):6934–6938. doi: 10.1073/pnas.87.18.6934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bork P., Grunwald C. Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach. Eur J Biochem. 1990 Jul 31;191(2):347–358. doi: 10.1111/j.1432-1033.1990.tb19129.x. [DOI] [PubMed] [Google Scholar]
  5. Bork P., Sander C., Valencia A. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7290–7294. doi: 10.1073/pnas.89.16.7290. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bork P. Shuffled domains in extracellular proteins. FEBS Lett. 1991 Jul 29;286(1-2):47–54. doi: 10.1016/0014-5793(91)80937-x. [DOI] [PubMed] [Google Scholar]
  7. Candussio A., Schmid G., Böck A. Biochemical and genetic analysis of a maltopentaose-producing amylase from an alkaliphilic gram-positive bacterium. Eur J Biochem. 1990 Jul 20;191(1):177–185. doi: 10.1111/j.1432-1033.1990.tb19108.x. [DOI] [PubMed] [Google Scholar]
  8. Doolittle R. F., Feng D. F. Nearest neighbor procedure for relating progressively aligned amino acid sequences. Methods Enzymol. 1990;183:659–669. doi: 10.1016/0076-6879(90)83043-9. [DOI] [PubMed] [Google Scholar]
  9. Doolittle R. F. Stein and Moore Award address. Reconstructing history with amino acid sequences. Protein Sci. 1992 Feb;1(2):191–200. doi: 10.1002/pro.5560010201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Feng D. F., Doolittle R. F. Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzymol. 1990;183:375–387. doi: 10.1016/0076-6879(90)83025-5. [DOI] [PubMed] [Google Scholar]
  11. Feng D. F., Doolittle R. F. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987;25(4):351–360. doi: 10.1007/BF02603120. [DOI] [PubMed] [Google Scholar]
  12. Fitch W. M. Distinguishing homologous from analogous proteins. Syst Zool. 1970 Jun;19(2):99–113. [PubMed] [Google Scholar]
  13. Gilkes N. R., Henrissat B., Kilburn D. G., Miller R. C., Jr, Warren R. A. Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families. Microbiol Rev. 1991 Jun;55(2):303–315. doi: 10.1128/mr.55.2.303-315.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gribskov M., McLachlan A. D., Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355–4358. doi: 10.1073/pnas.84.13.4355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Guiseppi A., Aymeric J. L., Cami B., Barras F., Creuzet N. Sequence analysis of the cellulase-encoding celY gene of Erwinia chrysanthemi: a possible case of interspecies gene transfer. Gene. 1991 Sep 30;106(1):109–114. doi: 10.1016/0378-1119(91)90573-t. [DOI] [PubMed] [Google Scholar]
  16. He S. Y., Collmer A. Molecular cloning, nucleotide sequence, and marker exchange mutagenesis of the exo-poly-alpha-D-galacturonosidase-encoding pehX gene of Erwinia chrysanthemi EC16. J Bacteriol. 1990 Sep;172(9):4988–4995. doi: 10.1128/jb.172.9.4988-4995.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Holmgren A., Bränden C. I. Crystal structure of chaperone protein PapD reveals an immunoglobulin fold. Nature. 1989 Nov 16;342(6247):248–251. doi: 10.1038/342248a0. [DOI] [PubMed] [Google Scholar]
  18. Lasters I., Wodak S. J., Alard P., van Cutsem E. Structural principles of parallel beta-barrels in proteins. Proc Natl Acad Sci U S A. 1988 May;85(10):3338–3342. doi: 10.1073/pnas.85.10.3338. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Meinke A., Braun C., Gilkes N. R., Kilburn D. G., Miller R. C., Jr, Warren R. A. Unusual sequence organization in CenB, an inverting endoglucanase from Cellulomonas fimi. J Bacteriol. 1991 Jan;173(1):308–314. doi: 10.1128/jb.173.1.308-314.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Melasniemi H., Paloheimo M., Hemiö L. Nucleotide sequence of the alpha-amylase-pullulanase gene from Clostridium thermohydrosulfuricum. J Gen Microbiol. 1990 Mar;136(3):447–454. doi: 10.1099/00221287-136-3-447. [DOI] [PubMed] [Google Scholar]
  21. Médigue C., Rouxel T., Vigier P., Hénaut A., Danchin A. Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol. 1991 Dec 20;222(4):851–856. doi: 10.1016/0022-2836(91)90575-q. [DOI] [PubMed] [Google Scholar]
  22. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
  23. Patthy L. Homology of a domain of the growth hormone/prolactin receptor family with type III modules of fibronectin. Cell. 1990 Apr 6;61(1):13–14. doi: 10.1016/0092-8674(90)90208-v. [DOI] [PubMed] [Google Scholar]
  24. Pereira M. E., Mejia J. S., Ortega-Barria E., Matzilevich D., Prioli R. P. The Trypanosoma cruzi neuraminidase contains sequences similar to bacterial neuraminidases, YWTD repeats of the low density lipoprotein receptor, and type III modules of fibronectin. J Exp Med. 1991 Jul 1;174(1):179–191. doi: 10.1084/jem.174.1.179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ryu S. E., Kwong P. D., Truneh A., Porter T. G., Arthos J., Rosenberg M., Dai X. P., Xuong N. H., Axel R., Sweet R. W. Crystal structure of an HIV-binding recombinant fragment of human CD4. Nature. 1990 Nov 29;348(6300):419–426. doi: 10.1038/348419a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Saito T., Suzuki K., Yamamoto J., Fukui T., Miwa K., Tomita K., Nakanishi S., Odani S., Suzuki J., Ishikawa K. Cloning, nucleotide sequence, and expression in Escherichia coli of the gene for poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis. J Bacteriol. 1989 Jan;171(1):184–189. doi: 10.1128/jb.171.1.184-189.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sander C., Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. doi: 10.1002/prot.340090107. [DOI] [PubMed] [Google Scholar]
  28. Watanabe T., Suzuki K., Oyanagi W., Ohnishi K., Tanaka H. Gene cloning of chitinase A1 from Bacillus circulans WL-12 revealed its evolutionary relationship to Serratia chitinase and to the type III homology units of fibronectin. J Biol Chem. 1990 Sep 15;265(26):15659–15665. [PubMed] [Google Scholar]
  29. de Vos A. M., Ultsch M., Kossiakoff A. A. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science. 1992 Jan 17;255(5042):306–312. doi: 10.1126/science.1549776. [DOI] [PubMed] [Google Scholar]

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