Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes.
Avidin
Biotin-binding
Defense protein
Phylogeny
Plant invasiveness
Journal
BMC ecology and evolution
ISSN: 2730-7182
Titre abrégé: BMC Ecol Evol
Pays: England
ID NLM: 101775613
Informations de publication
Date de publication:
09 04 2021
09 04 2021
Historique:
received:
15
11
2020
accepted:
30
03
2021
entrez:
10
4
2021
pubmed:
11
4
2021
medline:
24
4
2021
Statut:
epublish
Résumé
Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria. Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal pathogens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria. Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.
Sections du résumé
BACKGROUND
Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria.
RESULTS
Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal pathogens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria.
CONCLUSIONS
Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.
Identifiants
pubmed: 33836663
doi: 10.1186/s12862-021-01784-y
pii: 10.1186/s12862-021-01784-y
pmc: PMC8033661
doi:
Substances chimiques
Avidin
1405-69-2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
53Références
Protein Sci. 2013 Jul;22(7):980-94
pubmed: 23661323
Dev Comp Immunol. 2017 May;70:106-118
pubmed: 28069430
Syst Appl Microbiol. 2013 May;36(3):155-9
pubmed: 23337028
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7
pubmed: 21558174
J Mol Biol. 1990 Jul 5;214(1):143-70
pubmed: 2115087
Biochem Biophys Res Commun. 1964;14:205-9
pubmed: 5319841
Cell Mol Life Sci. 2006 Dec;63(24):2992-3017
pubmed: 17086379
Int J Syst Evol Microbiol. 2009 Nov;59(Pt 11):2830-3
pubmed: 19628608
Antonie Van Leeuwenhoek. 2020 Mar;113(3):349-355
pubmed: 31628625
Int J Cancer. 1982 Oct 15;30(4):461-4
pubmed: 6292118
Cell Chem Biol. 2018 Mar 15;25(3):318-329.e4
pubmed: 29396291
BMC Struct Biol. 2007 Mar 07;7:8
pubmed: 17343730
Bioinformatics. 2014 Nov 15;30(22):3276-8
pubmed: 25095880
J Nutr. 2003 Aug;133(8):2519-25
pubmed: 12888630
J Mol Biol. 1993 Dec 5;234(3):779-815
pubmed: 8254673
Front Microbiol. 2016 Dec 20;7:2003
pubmed: 28066339
J Struct Biol. 2015 Aug;191(2):139-48
pubmed: 26126731
Int J Dev Biol. 1989 Mar;33(1):125-34
pubmed: 2485692
Protein Sci. 2005 Feb;14(2):417-23
pubmed: 15659374
Nucleic Acids Res. 2017 Jan 4;45(D1):D25-D31
pubmed: 27924010
FEBS Lett. 2003 Dec 18;555(3):449-54
pubmed: 14675754
Bioinformatics. 2017 Nov 15;33(22):3645-3647
pubmed: 29036507
Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5
pubmed: 18940856
Biochim Biophys Acta. 1995 Jul 25;1263(1):60-6
pubmed: 7632734
J Mol Biol. 2000 Sep 8;302(1):205-17
pubmed: 10964570
Proc Natl Acad Sci U S A. 1987 Oct;84(20):7009-13
pubmed: 3313384
Nat Methods. 2011 Sep 29;8(10):785-6
pubmed: 21959131
J Biol Chem. 2003 Feb 7;278(6):4010-4
pubmed: 12458212
J Mol Biol. 2009 Feb 20;386(2):379-90
pubmed: 19111749
Biochim Biophys Acta. 1993 Dec 14;1216(3):441-5
pubmed: 8268225
BMC Genomics. 2005 Mar 18;6:41
pubmed: 15777476
Science. 1940 Sep 6;92(2384):224-5
pubmed: 17743857
Bioinformatics. 2008 Sep 15;24(18):1987-93
pubmed: 18678588
Syst Appl Microbiol. 2020 Sep;43(5):126122
pubmed: 32847788
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169
pubmed: 27899622
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8
pubmed: 16845081
Biosci Biotechnol Biochem. 2005 May;69(5):966-71
pubmed: 15914917
Annu Rev Microbiol. 1981;35:405-52
pubmed: 6271040
Int J Syst Evol Microbiol. 2005 Jan;55(Pt 1):225-229
pubmed: 15653878
FEBS Lett. 1999 Nov 12;461(1-2):52-8
pubmed: 10561495
J Insect Physiol. 2005 Oct;51(10):1117-26
pubmed: 16039663
Chem Biol. 2006 Oct;13(10):1029-39
pubmed: 17052607
Nucleic Acids Res. 2014 Jan;42(Database issue):D32-7
pubmed: 24217914
FEBS J. 2009 Mar;276(5):1383-97
pubmed: 19187241
Mol Biol Evol. 2013 Dec;30(12):2725-9
pubmed: 24132122
Biochem J. 2003 Jan 15;369(Pt 2):249-54
pubmed: 12358604
Int J Syst Evol Microbiol. 2006 May;56(Pt 5):1059-1065
pubmed: 16627655
J Appl Microbiol. 2006 Jun;100(6):1228-38
pubmed: 16696670
Int J Syst Evol Microbiol. 2007 May;57(Pt 5):1050-1054
pubmed: 17473257
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D29-33
pubmed: 15608199
Appl Environ Microbiol. 2006 Feb;72(2):1198-206
pubmed: 16461667
PLoS One. 2013 Oct 24;8(10):e77207
pubmed: 24204770
FEBS Lett. 1997 Jun 16;409(3):357-60
pubmed: 9224689
Gen Comp Endocrinol. 1981 Jun;44(2):230-2
pubmed: 7250686
BMC Bioinformatics. 2003 Jul 10;4:29
pubmed: 12854978
J Mol Biol. 1998 May 29;279(1):211-21
pubmed: 9636711
Front Microbiol. 2018 Jan 05;8:2614
pubmed: 29354105
Int J Syst Evol Microbiol. 2016 Oct;66(10):4243-4249
pubmed: 27470589
PLoS One. 2018 Jul 6;13(7):e0200393
pubmed: 29979771
Appl Environ Microbiol. 2007 May;73(10):3254-64
pubmed: 17400786
Int J Syst Evol Microbiol. 2011 Apr;61(Pt 4):864-869
pubmed: 20495038
Biochem J. 2007 Aug 1;405(3):397-405
pubmed: 17447892
Int J Syst Evol Microbiol. 2019 Sep;69(9):2750-2754
pubmed: 31241445
Biochem J. 1963 Dec;89:609-20
pubmed: 14101982
Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1754-8
pubmed: 7878054
Appl Environ Microbiol. 2005 Nov;71(11):7041-52
pubmed: 16269740
J Endocrinol. 1977 Jun;73(3):535-6
pubmed: 874405
Biochem J. 2003 May 15;372(Pt 1):219-25
pubmed: 12558501
Int J Syst Evol Microbiol. 2010 Dec;60(Pt 12):2972-2978
pubmed: 20118290
Nat Methods. 2006 Apr;3(4):267-73
pubmed: 16554831
Trends Biotechnol. 2007 Jun;25(6):269-77
pubmed: 17433846
PLoS One. 2017 Apr 20;12(4):e0176086
pubmed: 28426764
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):813-21
pubmed: 21904034
Biochem J. 2002 May 1;363(Pt 3):609-17
pubmed: 11964162
Science. 1942 Sep 11;96(2489):257
pubmed: 17770530
Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):901-13
pubmed: 23633601
Appl Environ Microbiol. 2004 Oct;70(10):5980-7
pubmed: 15466541
Biochem Biophys Res Commun. 2001 Jul 20;285(3):734-41
pubmed: 11453655