DMRP: construction and bioinformatics analysis of databases for metal - related proteins in Acidithiobacillus ferrooxidans
DOI: 359 Downloads 7753 Views
Author(s)
Abstract
A.ferrooxidan as one of the main biological leaching ore bacteria,has great application value in industrial leaching ore,has been the research hotspot in recent years. Studies on the existing A.ferrooxidan is associated with a variety of metal ions: arsenic, aluminum, cobalt, strontium, chromium, copper, mercury, lead, lithium,etc. So far, A.ferrooxidan leading research has formed a lot of experimental data,including A.ferrooxidan the basic information of the nucleic acid,protein and enzyme, genome,transcriptome and proteomics data and dynamic data,etc. Therefore, the existing A.ferrooxidan metal-related protein data collection and mining, constructing special A.ferrooxidan metal-related protein database, set up a corresponding biological leaching mining research platform is the problem to be solved, in order to facilitate A.ferrooxidan biological leaching to provide better support for the further development of research.
Keywords
Acidithiobacillus ferrooxidan;metal - related proteins; databases
Cite this paper
Yan Wei, Peng Chen, Shiqiang Ge, Zhengrong Wu, Ruixiang Xu, Wenbin Zhao, Hongyu Li, Qinjian Xie, Xin Wang, Jianping Zhou,
DMRP: construction and bioinformatics analysis of databases for metal - related proteins in Acidithiobacillus ferrooxidans
, SCIREA Journal of Biology.
Volume 1, Issue 2, December 2016 | PP. 79-92.
References
[ 1 ] | Barbosa, L.C., Garrido, S.S., Marchetto, R. 2015. BtoxDB: A comprehensive database of protein structural data on toxin-antitoxin systems. Computers in Biology and Medicine, 58, 146-153. |
[ 2 ] | Binkley, J., Arnaud, M.B., Inglis, D.O., Skrzypek, M.S., Shah, P., Wymore, F., Binkley, G., Miyasato, S.R., Simison, M., Sherlock, G. 2014. The Candida Genome Database: The new homology information page highlights protein similarity and phylogeny. Nucleic Acids Research, 42(D1), D711-D716. |
[ 3 ] | Chen, P., Yan, L., Leng, F.F., Nan, W.B., Yue, X.X., Zheng, Y.N., Feng, N., Li, H.Y. 2011. Bioleaching of realgar by Acidithiobacillus ferrooxidans using ferrous iron and elemental sulfur as the sole and mixed energy sources. Bioresource Technology, 102(3), 3260-3267. |
[ 4 ] | Cheng, H., Deng, W.K., Wang, Y.B., Ren, J., Liu, Z.X., Xue, Y. 2014. dbPPT: a comprehensive database of protein phosphorylation in plants. Database-the Journal of Biological Databases and Curation. |
[ 5 ] | He, Z.G., Zhong, H., Hu, Y.H., Mao, S.M., Xu, J. 2006. Analysis of differential protein expression in Acidithiobacillus ferrooxidans grown under different energy resources respectively using SELDI-ProteinChip technologies. Journal of Microbiological Methods, 65(1), 10-20. |
[ 6 ] | Hu, Q., Ma, T., Wang, K., Xu, T., Liu, J., Qiu, Q. 2012. The Yak genome database: an integrative database for studying yak biology and high-altitude adaption. BMC Genomics. |
[ 7 ] | Kucera, J., Bouchal, P., Lochman, J., Potesil, D., Janiczek, O., Zdrahal, Z., Mandl, M. 2013. Ferrous iron oxidation by sulfur-oxidizing Acidithiobacillus ferrooxidans and analysis of the process at the levels of transcription and protein synthesis. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 103(4), 905-919. |
[ 8 ] | Levicán, G., Ugalde, J.A., Ehrenfeld, N., Maass, A., Parada, P. 2008. Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics. |
[ 9 ] | Lombardi, A.T., Garcia, O., Jr. 2002. Biological leaching of Mn, Al, Zn, Cu and Ti in an anaerobic sewage sludge effectuated by Thiobacillus ferrooxidans and its effect on metal partitioning. Water Res, 36(13), 3193-202. |
[ 10 ] | Olivieri, A., Degenhardt, O.S., McDonald, G.R., Narang, D., Paulsen, I.M., Kozuska, J.L., Holt, A. 2012. On the disruption of biochemical and biological assays by chemicals leaching from disposable laboratory plasticware. Can J Physiol Pharmacol, 90(6), 697-703. |
[ 11 ] | Quatrini, R., Jedlicki, E., Holmes, D.S. 2005. Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans. J Ind Microbiol Biotechnol (2005) 32: 606–614. |
[ 12 ] | Raquel Quatrini, Jorge Valdés, Eugenia Jedlicki, Holmes, D.S. 2007. The Use of Bioinformatics and Genome Biology to Advance Our Understanding of Bioleaching Microorganisms. Laboratory of Bioinformatics and Genome Biology, Av. Zanartu 1482, 1-19. |
[ 13 ] | Song, W.J., Sontz, P.A., Ambroggio, X.I., Tezcan1, F.A. 2014. Metals in Protein–Protein Interfaces. The Annual Review of Biophysics. |
[ 14 ] | Zhang, Y., Wu, X., Liu, D., Duan, H., Fan, H. 2013. Sequencing and bioinformatics analysis of the metal-related genes in Acidithiobacillus ferrooxidans strain DC. Folia Microbiol (Praha), 58(6), 551-60. |