In Silico Characterization of Heavy Metal Binding Protein Predicted In the Genome Sequence of Lactobacillus pentosus KCA1
Barre latérale de l'article
Contenu principal de l'article
Résumé
Heavy metals, such as lead, cadmium, arsenic and mercury can contaminate the food chain and pose serious health problems.
We characterized the heavy metal binding protein predicted in the genome sequence of Lactobacillus pentosus KCA1.
Bioinformatic tools such as BLASTp, ClustalW and iterative threading assembly refinement (I-TASSER) server were used for
protein sequence similarity, secondary structure and 3-D model prediction for potential active binding sites. Two cysteine
residues were identified at position 12 and 15 (Cys12 and Cys15), separated by proline (P) and serine (S). The secondary
structure prediction revealed 2 alpha helices and 5 beta-strands. The 3-D model structure of KCA1_2798 has a confidence scoreof 1.26 that reflects a model of good quality with binding site residues predicted to occur at five positions (Thr11, Cys12, Ser14, Cys15, Gly63) of the KCA1_2798 sequence based on a protein (3iwlA) template. The heavy metal binding protein encoded in the genome sequence of L. pentosus KCA1 has laid a foundation for further investigation into its potential health applications.
Téléchargements
Renseignements sur l'article
Cette œuvre est sous licence Creative Commons Attribution - Pas d'Utilisation Commerciale - Pas de Modification 4.0 International.
Références
Abriouel H, Benomar N, Perez Pulido R, Canamero MM, Galvez A. (2011). Annotated genome sequence of Lactobacillus pentosus MP-10, which has probiotic potential, from naturally fermented Alorena green table olives. Journal of Bacteriology. 193: 4559–4560.
Adebamowo EO, Agbede OA, Sridhar MKC, Adebamowo CA. (2006).An evaluation of lead levels in residential paints sold in Nigeria markets. Indoor Built Environment.15:551–4.
Andersen O, Nielsen JB, Nordberg GF. (2004). Nutritional interactions in intestinal cadmium uptake-possibilities for risk reduction. Biometals. 17:543-547.
Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J, Renckens B, van Hijum SA, Siezen RJ. (2013). Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman. PLoS One. 8:e59239.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ. (2004). PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Research. 32: W400-W404.
Banci L, Bertini I, Ciofi-Baffoni S, Finney LA, Outten CE, O'Halloran TV. (2002). A new zinc-protein coordination site in intracellular metal trafficking: solution structure of the Apo and Zn(II) forms of ZntA(46-118). Journal of Molecular Biology. 8;323(5):883-97.
Boal AK, Rosenzweig AC. (2009). Crystal structures of cisplatin bound to a human copper chaperone. Journal of American Chemical Society.14;131:14196-7.
Bull PC, Cox DW. (1994). Wilson disease and Menkes disease: new handles on heavy-metal transport. Trends in Genetics. 10 (7): 246–52.
Cole C, Barber JD, Barton GJ. (2008). The Jpred 3 secondary structure prediction server. Nucleic Acids Research. 36: W197-W201.
Dauwe T, Janssens E, Bervoets L, Blust R, Eens M. (2004). Relationships between metal concentration in great tit nestling and their environment and food. Environmental Pollution. 131:373-380.
Fahmy K, Merroun M, Pollmann K, Raff J, Savchuk O, Hennig C, Selenska- Pobell S. (2006). Secondary Structure and Pd(II) Coordination in S-Layer Proteins from Bacillus sphaericus Studied by Infrared and X-Ray Absorption Spectroscopy. Biophysics Journal. 91: 996.
-
Zavaglia A. (2011). FTIR spectroscopy structural analysis of the interaction between Lactobacillus kefir S-layers and metal ions. Journal of Molecular Structure. 987: 186–192.
Gitschier J, Moffat B, Reilly D, Wood WI, Fairbrother WJ. (1998). Solution structure of the fourth metal-binding domain from the Menkes copper-transporting ATPase.B Nature Structural Biology. 5 (1): 47–54
Gonzalez-Soto E, Gonzalez-Rodriguez V, Lopez-Suarez C, Castro-Romero JM, Perez-Iglesias J, Fernandez-Solis JM. (2000). Migration of lead and cadmium from ceramic materials used in food preparation. Bulletin of Environmental Contamination and Toxicology. 65:598-603.
Halttunen T, Kankaanpaa P, Ouwehand A, Tahvonen R, Salminen S. (2003). Cadmium decontamination by lactic acid bacteria. Bioscience and Microflora. 22: 93–97.
Halttunen T, Collado MC, El-Nezami H, Meriluoto J, Salminen S. (2008). Combining strains of lactic acid bacteria may reduce their toxin and heavy metal removal efficiency from aqueous solution. Letter of Applied Microbiology. 46:160–165.
Hanson RM (2010). Jmol – a paradigm shift in crystallographic visualization. Journal of Applied Crystallography. 43(5): 1250-1260.
Hirokawa T, Boon-Chieng S, Mitaku S. (1998). SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics. 14: 378–379.
Hsu PC, Guo YL (2002). Antioxidant nutrients and lead toxicity. Toxicology. 180:33-44.
Ibrahim F, Halttunen T, Tahvonen R, Salminen S (2006). Probiotic bacteria as potential detoxification tools: assessing their heavy metal binding isotherms. Canadian Journal of Microbiology. 52:877-885.
IARC (2012). International Agency for Research on Cancer-IARC Monographs on the evaluation of carcinogenic risks to humans, vol. 100C.
JECFA (2004). Evaluation of certain food additives and contaminants. Sixty-first report of the Joint FAO/WHO Expert Committee on food Additives. WHO Tech. Rep. Ser. 922: 139-144.
Jones DT. (1999). Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology. 292: 195-202.
Monachese M, Burton JP, Reid G. (2012). Bioremediation and Tolerance of Humans to Heavy Metals through Microbial Processes: a Potential Role for Probiotics? Applied and Environmental Microbiology. 78;18: 6397-6404.
Mrvcic J, Stanzer D, Bacun-Druzina V, Stehlik-Tomas V. (2009). Copper binding by lactic acid bacteria (LAB). Bioscience and Microflora. 28:1–6.
Muller M, Anke M (1994). Distribution of cadmium in the food chain (soil-plant-human) of a cadmium exposed area and the health risk of the general population. Science of Total Environment. 156:151-158.
Passerini A, Lippi M, Frasconi P (2011). Metal Detector v2.0: Predicting the Geometry of Metal Binding Sites from Protein Sequence. Nucleic Acids Research. 39; 2:W288-W292.
Rosen JF (1995). Adverse health effects of lead at low exposure levels. Trends in the management of childhood lead poisoning. Toxicology, 97:11-17.
Roy A, Kucukural A, Zhang Y (2010). I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols. 5: 725-738.
Satarug S, Moore MR (2004). Adverse health effects of chronic exposure to low-level cadmium in foodstuffs and cigarette smoke. Envrionmental Health Perspective. 112:1099-1103.
Struzynska L, Walski M, Gadamski R, Dabrowska-Bouta B, Rafalowska U (1997). Lead-induced abnormalities in blood-brain permeability in experimental chronic toxicity. Molecular Chemistry and Neuropathology. 31:207-224.
Sussell A, Hart C, Wild D, Ashley K (1999). An evaluation of worker lead exposures and cleaning effectiveness during removal of deteriorated lead-based paint. Applied Occupational and Environmental Hygiene. 14(3):177-85.
Tillet T (2009). The price of progress: modern environmental health hazards in Africa. Environmental Health Perspective. 117:A257.
Wernimont AK, Huffman DL, Lamb AL, O'Halloran TV, Rosenzweig AC. (2000). Structural basis for copper transfer by the metallochaperone for the Menkes/Wilson disease proteins. Nature Structural Biology. 7(9):766-71.
Yang Zhang. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 9:40
Zimmermann M, Clarke O, Gulbis JM, Keizer DW, Jarvis RS, Cobbett CS, Hinds MG, Xiao Z, Wedd AG (2009). Metal binding affinities of Arabidopsis zinc and copper transporters: selectivities match the relative, but not the absolute, affinities of their amino-terminal domains. Biochemistry. 48(49):11640-11654.
Zhai Q, Wang G, Zhao J, Liu X, Tian F, Zhang H, Chen W (2013). Protective Effects of Lactobacillus plantarum CCFM8610 against Acute
Cadmium Toxicity in Mice. Applied