Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Identification of Novel Phytase Genes from an Agricultural Soil-Derived Metagenome

  • Tan, Hao (BIOMERIT Research Centre, Microbiology Department, University College Cork, National University of Ireland) ;
  • Mooij, Marlies J. (BIOMERIT Research Centre, Microbiology Department, University College Cork, National University of Ireland) ;
  • Barret, Matthieu (BIOMERIT Research Centre, Microbiology Department, University College Cork, National University of Ireland) ;
  • Hegarty, Pardraig M. (BIOMERIT Research Centre, Microbiology Department, University College Cork, National University of Ireland) ;
  • Harrington, Catriona (BIOMERIT Research Centre, Microbiology Department, University College Cork, National University of Ireland) ;
  • Dobson, Alan D.W. (Environmental Research Institute, University College Cork, National University of Ireland) ;
  • O'Gara, Fergal (BIOMERIT Research Centre, Microbiology Department, University College Cork, National University of Ireland)
  • Received : 2013.07.08
  • Accepted : 2013.10.10
  • Published : 2014.01.28
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Abstract

Environmental microorganisms are emerging as an important source of new enzymes for wide-scale industrial application. In this study, novel phytase genes were identified from a soil microbial community. For this, a function-based screening approach was utilized for the identification of phytase activity in a metagenomic library derived from an agricultural soil. Two novel phytases were identified. Interestingly, one of these phytases is an unusual histidine acid phosphatase family phytase, as the conserved motif of the active site of PhyX possesses an additional amino acid residue. The second phytase belongs to a new type, which is encoded by multiple open reading frames (ORFs) and is different to all phytases known to date, which are encoded by a single ORF.

Keywords

References

  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75. https://doi.org/10.1186/1471-2164-9-75
  2. Chu HM, Guo RT, Lin TW, Chou CC, Shr HL, Lai HL, et al. 2004. Structures of Selenomonas ruminantium phytase in complex with persulfated phytate: DSP phytase fold and mechanism for sequential substrate hydrolysis. Structure 12: 2015-2024. https://doi.org/10.1016/j.str.2004.08.010
  3. Conry MJ, Hogan JJ. 2001. Comparison of cereals grown under high (conventional) and low (reduced) input systems. Teagasc, Crops Research Centre, Oak Park, Carlow.
  4. Dvoráková J. 1998. Phytase: sources, preparation and exploitation. Folia Microbiol. 43: 323-338. https://doi.org/10.1007/BF02818571
  5. Fu D, Huang H, Meng K, Wang Y, Luo H, Yang P, et al. 2009. Improvement of Yersinia frederiksenii phytase performance by a single amino acid substitution. Biotechnol. Bioeng. 103: 857-864. https://doi.org/10.1002/bit.22315
  6. Greiner R, Konietzny U, Jany K-D. 1993. Purification and characterization of two phytases from Escherichia coli. Arch. Biochem. Biophys. 303: 107-113. https://doi.org/10.1006/abbi.1993.1261
  7. Guyetant S, Giraud M, L'Hours L, Derrien S, Rubini S, Lavenier D, Raimbault F. 2005. Cluster of reconfigurable nodes for scanning large genomic banks. Parallel Comput. 31: 7396.
  8. Ha NC, Oh BC, Shin S, Kim HJ, Oh TK, Kim YO, et al. 2000. Crystal structures of a novel, thermostable phytase in partially and fully calcium-loaded states. Nat. Struct. Biol. 7: 147-153. https://doi.org/10.1038/72421
  9. Hegeman CE, Grabau EA. 2001. A novel phytase with sequence similarity to purple acid phosphatases is expressed in cotyledons of germinating soybean seedlings. Plant Physiol. 126: 1598-1608. https://doi.org/10.1104/pp.126.4.1598
  10. Huang H, Luo H, Wang Y, Fu D, Shao N, Yang P, et al. 2009. Novel low-temperature-active phytase from Erwinia carotovora v ar. carotovota ACCC 10276. J. Microbiol. Biotechnol. 19: 1085-1091.
  11. Huang H, Shi P, Wang Y, Luo H, Shao N, Wang G, et al. 2009. Diversity of beta-propeller phytase genes in the intestinal contents of grass carp provides insight into the release of major phosphorus from phytate in nature. Appl. Environ. Microbiol. 75: 1508-1516. https://doi.org/10.1128/AEM.02188-08
  12. Huang H, Zhang R, Fu D, Luo J, Li Z, Luo H, et al. 2011. Diversity, abundance and characterization of ruminal cysteine phytases suggest their important role in phytate degradation. Environ. Microbiol. 13: 747-757. https://doi.org/10.1111/j.1462-2920.2010.02379.x
  13. Jorquera M, Martínez O, Maruyama F, Marschner P, de la Luz Mora M. 2008. Current and future biotechnological applications of bacterial phytases and phytase-producing bacteria. Microb. Environ. 23: 182-191. https://doi.org/10.1264/jsme2.23.182
  14. Knowlton KF, McKinney JM, Wilson KF, Cobb C. 2003. Effect of an exogenous phytase enzyme blend and dietary phosphorus content on P excretion in lactating cows. J. Dairy Sci. 86: 224.
  15. Konietzny U, Greiner R. 2004. Bacterial phytase: potential application, in vivo function and regulation of its synthesis. Braz. J. Biol. 35: 11-18.
  16. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM, Peterson KM. 1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166: 175-176. https://doi.org/10.1016/0378-1119(95)00584-1
  17. Kuang R, Chan KH, Yeung E, Lim BL. 2009. Molecular and biochemical characterization of AtPAP15, a purple acid phosphatase with phytase activity, in Arabidopsis. Plant Physiol. 151: 199-209. https://doi.org/10.1104/pp.109.143180
  18. Lee DY, Schroeder J, Gordon DT. 1988. Enhancement of Cu bioavailability in the rat by phytic acid. J. Nutr. 118: 712-717. https://doi.org/10.1093/jn/118.6.712
  19. Lei X, Stahl CH. 2001. Biotechnological development of effective phytases for mineral nutrition and environmental protection. Appl. Microbiol. Biotechnol. 57: 474-481. https://doi.org/10.1007/s002530100795
  20. Martínez A, Bradley AS, Waldbauer JR, Summons RE, Delong EF. 2007. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc. Natl. Acad. Sci. USA 104: 5590-5595. https://doi.org/10.1073/pnas.0611470104
  21. Mukhametzyanova AD, Akhmetova AI, Sharipova MR. 2012. Microorganisms as phytase producers. Microbiology 81: 267-275. https://doi.org/10.1134/S0026261712030095
  22. Mullaney EJ, Ullah AH. 2003. The term phytase comprises several different classes of enzymes. Biochem. Biophys. Res. Commun. 312: 179-184. https://doi.org/10.1016/j.bbrc.2003.09.176
  23. Patel KJ, Vig S, Kumar GN, Archana G. 2010. Effect of transgenic rhizobacteria over-expressing Citrobacter braakii appA on phytate-P availability to mung bean plants. J. Microbiol. Biotechnol. 20: 1491-1499. https://doi.org/10.4014/jmb.1006.06016
  24. Selle PH, Cowieson AJ, Ravindran V. 2009. Consequences of calcium interactions with phytate and phytase for poultry and pigs. Livestock Sci. 124: 126-141. https://doi.org/10.1016/j.livsci.2009.01.006
  25. Selle PH, Ravindran V. 2008. Phytate-degrading enzymes in pig nutrition. Livestock Sci. 113: 99-122. https://doi.org/10.1016/j.livsci.2007.05.014
  26. Seo M-J, Kim J-N, Cho E-A, Park H, Choi H-J, Pyun Y-R. 2005. Purification and characterization of a novel extracellular alkaline phytase from Aeromonas sp. J. Microbiol. Biotechnol. 15: 745-748.
  27. Shin S, Ha NC, Oh BC, Oh TK, Oh BH. 2001. Enzyme mechanism and catalytic property of $\beta$ propeller phytase. Structure 9: 851-858. https://doi.org/10.1016/S0969-2126(01)00637-2
  28. Thacker PA, Rossnagel BG, Raboy V. 2004. Effect of phytase supplementation on phosphorus digestibility in low-phytate barley fed to finishing pigs. Arch. Anim. Nutr. 58: 61-68. https://doi.org/10.1080/00039420310001656686
  29. Unno Y, Okubo K, Wasaki J, Shinano T, Osaki M. 2005. Plant growth promotion abilities and microscale bacterial dynamics in the rhizosphere of Lupin analysed by phytate utilization ability. Environ. Microbiol. 7: 396-404. https://doi.org/10.1111/j.1462-2920.2004.00701.x
  30. Van Etten RL, Davidson R, Stevis PE, MacArthur H, Moore DL. 1991. Covalent structure, disulfide bonding, and identification of reactive surface and active site residues of human prostatic acid phosphatase. J. Biol. Chem. 266: 2313- 2319.
  31. Vats P, Banerjee UC. 2004. Production studies and catalytic properties of phytases: an overview. Enzyme Microb. Technol. 35: 3-14. https://doi.org/10.1016/j.enzmictec.2004.03.010
  32. Yanke LJ, Bae HD, Selinger LB, Cheng KJ. 1998. Phytase activity of anaerobic ruminal bacteria. Microbiology 144: 1565-1573. https://doi.org/10.1099/00221287-144-6-1565
  33. Yao B, Shao N, Huang H, Meng K, Luo H, Wang Y, Yang P. 2008. Cloning, expression, and characterization of a new phytase from the phytopathogenic bacterium Pectobacterium wasabiae DSMZ 18074. J. Microbiol. Biotechnol. 18: 1221-1226.
  34. Yao MZ, Zhang YH, Lu WL, Hu MQ, Wang W, Liang AH. 2012. Phytases: crystal structures, protein engineering and potential biotechnological applications. J. Appl. Microbiol. 112: 1-14. https://doi.org/10.1111/j.1365-2672.2011.05181.x

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