Análisis bioinformático de la presencia de bacteriocinas en el genoma de Lactobacillus plantarum
Palabras clave:
Bacteriocina, Bioinformática, Genoma, Lactobacillus plan tarumResumen
Los organismos tienen la capacidad de producir sustancias con el fin de sobrevivir a su entorno, estas sustancias son muy variadas, pero en este caso nuestro interés se ve en las bacteriocinas, péptidos antimicrobianos sintetizados ribosomalmente. Existe una gran variedad de estas bacteriocinas, pero muy pocas son usadas en la actualidad a pesar de sus diversas ventajas biotecnológicas. En este caso, se analizó el genoma de Lactobacillus plantarum, una bacteria ácido-láctica con gran potencial en producción de estas sustancias antimicrobianas, por medio de herramientas bioinformáticas para hallar posibles genes relacionados con la producción de bacteriocinas. De acuerdo con los análisis realizados, y comparando con genes con secuencias conocidas de bacteriocinas, se encontró que esta bacteria produce y/o tiene genes relacionados con 3 bacteriocinas principalmente, Plantaricina K, Plantaricina A y Glycocin.
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Donia MS, Fischbach MA. Small molecules from the human microbiota. Science (80- ). 2015 Jul;349(6246):1254766.
Newstead LL, Varjonen K, Nuttall T, Paterson GK. Staphylococcal-Produced Bacteriocins and Antimicrobial Peptides: Their Potential as Alternative Treatments for Staphylococcus aureus Infections. Antibiotics. 2020;9(2):40.
Salwan R, Sharma V. Molecular and biotechnological aspects of secondary metabolites in actinobacteria. Microbiol Res. 2020;231:126374. 4. Simons A, Alhanout K, Duval RE. Bacteriocins, Antimicrobial Peptides from Bacterial Origin: Overview of Their Biology and Their Impact against Multidrug-Resistant Bacteria. Microorganisms. 2020 Apr;8(5):639.
Scholl D. Phage Tail–Like Bacteriocins. Annu Rev Virol. 2017 Sep;4(1):453–67.
Alvarez-Sieiro P, Montalbán-López M, Mu D, Kuipers OP. Bacteriocins of lactic acid bacteria: extending the family. Appl Microbiol Biotechnol. 2016 Apr;100(7):2939–51.
Radaic A, de Jesus MB, Kapila YL. Bacterial anti-microbial peptides and nano-sized drug delivery systems: The state of the art toward improved bacteriocins. J Control Release. 2020 May;321:100–18.
Seddik HA, Bendali F, Gancel F, Fliss I, Spano G, Drider D. Lactobacillus plantarum and Its Probiotic and Food Potentialities. Probiotics Antimicrob Proteins. 2017 Jun;9(2):111–22.
Russo P, Arena MP, Fiocco D, Capozzi V, Drider D, Spano G. Lactobacillus plantarum with broad antifungal activity: A promising approach to increase safety and shelflife of cereal-based products. Int J Food Microbiol. 2017;247:48–54.
Huang Y, Wang X, Wang J, Wu F, Sui Y, Yang L, et al. Lactobacillus plantarum strains as potential probiotic cultures with cholesterol-lowering activity. J Dairy Sci. 2013 May;96(5):2746–53.
Yang KM, Jiang ZY, Zheng CT, Wang L, Yang XF. Effect of Lactobacillus plantarum on diarrhea and intestinal barrier function of young piglets challenged with enterotoxigenic Escherichia coli K881. J Anim Sci. 2014;92(4):1496–503.
Le B, Yang SH. Efficacy of Lactobacillus plantarum in prevention of inflammatory bowel disease. Toxicol Reports. 2018;5:314–7.
Chen Y, Wang Y, Chow Y, Yanagida F, Liao C, Chiu C. Purification and characterization of plantaricin Y, a novel bacteriocin produced by Lactobacillus plantarum 510. Arch Microbiol. 2014 Mar;196(3):193–9. 14.Hu M, Zhao H, Zhang C, Yu J, Lu Z. Purification and Characterization of Plantaricin 163, a Novel Bacteriocin Produced by Lactobacillus plantarum 163 Isolated from Traditional Chinese Fermented Vegetables. J Agric Food Chem. 2013 Nov;61(47):11676–82.
Zhao S, Han J, Bie X, Lu Z, Zhang C, Lv F. Purification and Characterization of Plantaricin JLA-9: A Novel Bacteriocin against Bacillus spp. Produced by Lactobacillus plantarum JLA-9 from Suan-Tsai, a Traditional Chinese Fermented Cabbage. J Agric Food Chem. 2016;64(13):2754–64.
Czaplewski L, Bax R, Clokie M, Dawson M, Fairhead H, Fischetti VA, et al. Alternatives to antibiotics—a pipeline portfolio review. Lancet Infect Dis. 2016 Feb;16(2):239–51.
Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res [Internet]. 2019 Jul 2;47(W1):W81–7. Available from: https://academic.oup.com/nar/ article/47/W1/W81/5481154
Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I. BACTIBASE second release: a database and tool platform for bacteriocin characterization. BMC Microbiol [Internet]. 2010;10(1):22. Available from: http:// bmcmicrobiol.biomedcentral.com/ articles/10.1186/1471-2180-10-22
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics [Internet]. 2014 May 1;30(9):1236–40. Available from: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/ bioinformatics/btu031
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, et al. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015 Jan;43(D1):D447–52.
Jolley KA, Maiden MC. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010 Dec;11(1):595. 22.Rezaei Javan R, van Tonder AJ, King JP, Harrold CL, Brueggemann AB. Genome Sequencing Reveals a Large and Diverse Repertoire of Antimicrobial Peptides. Front Microbiol. 2018;9.
Bogaardt C, van Tonder AJ, Brueggemann AB. Genomic analyses of pneumococci reveal a wide diversity of bacteriocins – including pneumocyclicin, a novel circular bacteriocin. BMC Genomics. 2015 Dec;16(1):554.
Letzel A-C, Pidot SJ, Hertweck C. Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics. 2014;15(1):983.
Collins FWJ, O’Connor PM, O’Sullivan O, Gómez-Sala B, Rea MC, Hill C, et al. Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome. Sci Rep. 2017 Dec;7(1):3481.
Russell AH, Truman AW. Genome mining strategies for ribosomally synthesised and post-translationally modified peptides. Comput Struct Biotechnol J. 2020;18:1838–51.
Merwin NJ, Mousa WK, Dejong CA, Skinnider MA, Cannon MJ, Li H, et al. DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products. Proc Natl Acad Sci. 2020 Jan;117(1):371–80.
Diep DB, Straume D, Kjos M, Torres C, Nes IF. An overview of the mosaic bacteriocin pln loci from Lactobacillus plantarum. Peptides. 2009 Aug;30(8):1562–74.
Biswas S, Garcia De Gonzalo C V., Repka LM, van der Donk WA. Structure–Activity Relationships of the S-Linked Glycocin Sublancin. ACS Chem Biol. 2017 Dec;12(12):2965–9.
Hu D, Chen Y, Sun C, Jin T, Fan G, Liao Q, et al. Genome guided investigation of antibiotics producing actinomycetales strain isolated from a Macau mangrove ecosystem. Sci Rep [Internet]. 2018 Dec 24;8(1):14271. Available from: http://www.nature. com/articles/s41598-018-32076-z
Franke CM, Tiemersma J, Venema G, Kok J. Membrane Topology of the Lactococcal Bacteriocin ATP-binding Cassette Transporter Protein LcnC. J Biol Chem. 1999 Mar;274(13):8484–90.
Rogne P, Haugen C, Fimland G, Nissen-Meyer J, Kristiansen PE. Three-dimensional structure of the two-peptide bacteriocin plantaricin JK. Peptides. 2009 Sep;30(9):1613–21.
Kristiansen PE, Fimland G, Mantzilas D, Nissen-Meyer J. Structure and Mode of Action of the Membrane-permeabilizing Antimicrobial Peptide Pheromone Plantaricin A. J Biol Chem. 2005 Jun;280(24):22945–50.
Venugopal H, Edwards PJB, Schwalbe M, Claridge JK, Libich DS, Stepper J, et al. Structural, Dynamic, and Chemical Characterization of a Novel S-Glycosylated Bacteriocin. Biochemistry. 2011 Apr;50(14):2748–55.
