Genetic analysis of the gene in halophilic archaea isolated from Xinjiang region, China

Abstract

Some novel members of extremely halophilic archaea, strains AJ11, AJ12 and AJ13, were isolated from the Aularz Lake located in the Altun Mountain National Nature Reserve of Xinjiang, Uygur Autonomous Region in China. Partial DNA fragments encoding a bacteriorhodopsin (BR), as well as for 16S rRNA of isolated strains, were amplified by PCR and their DNA sequences were determined subsequently. On the basis of homology and phylogenetic analysis of the 16S rDNA, we thought that the isolated strains forming a microbiological population are the members of the genus Natrinema. The results of genetic analysis, such as GC content, transition/transversion (Ti/Tv) rate ratios and synonymous substitution rates (Ks) indicate that the br fragments, with a high level of genetic divergence, are faced with both purifying selection and bias mutation pressure. The study provides the basis for use of species and BR proteins resources.

References

1. Comeron J M (1999). K-estimator: calculation of the number of nucleotidesubstitutions per site and the confidence intervals. Bioinformatics, 15(9): 763–764. doi:10.1093/bioinformatics/15.9.763
2. Dunn R, McCoy J, Simsek M, Majumdar A, Chang S H, Rajbhandary U L, Khorana H G (1981). The bacteriorhodopsin gene. Proc Natl Acad Sci USA, 78(11): 6744–6748. doi:10.1073/pnas.78.11.6744
3. Gupta R, Lanter J M, Woese C R (1983). Sequence of the ribosomal RNA from Halobacterium volcanii, an archaebacte-rium. Science, 221: 656–659. doi:10.1126/science.221.4611.656
4. Ihara K, Umemura T, Katagiri I, Kitajima-Ihara T, Sugiyama Y, Kimura Y, Mukohata Y (1999). Evolution of the archaeal rhodopsins: evolution ratechanges by gene duplication and functional differentiation. J Mol Biol, 285(1): 163–174. doi:10.1006/jmbi.1998.2286
5. Kitajima T, Hirayama J, Ihara K, Sugiyama Y, Kamo N, Mukohata Y (1996). Novel bacterial rhodopsins from Haloarcula vallismortis. Biochem Biophys Res Commun, 220(2): 341–345. doi:10.1006/bbrc.1996.0407
6. Li L, Wu M, Qiao S Y, Chen K S (2001). Cloning and expression of the bacteriorhodopsin gene. Journal of Zhejiang University (Engineering Science), 35(3): 324–327 (in Chinese)
7. Luecke H, Schobert B, Richter H T, Cartailler J P, Lanyi J K (1999). Structuralchanges in bacteriorhodopsin during ion transport at 2 angstrom resolution. Science, 286(5438): 255–260. doi:10.1126/science.286.5438.255
8. McGenity T J, Gemmell R T, Grant W D (1998). Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov. Int J Syst Bacteriol, 48(4): 1187–1196
9. Mukohata Y, Ihara K, Tamura T, Sugiyama Y (1999). Halobacterial rhodopsin. J Biochem, 125(4): 649–657
10. Mukohata Y, Sugiyama Y, Ihara K, Yoshida M (1998). An Australian Halobacteria contains a novel proton pump retinal protein: archaerhodopsin. Biochem Biophys Res Commun, 151(3): 1339–1345. doi:10.1016/S0006-291X(88)80509-6
12. Oesterhelt D, Stoeckenius W (1971). Rhodopsin-likeprotein from the purple membrane of Halobacteriumhalobium. Nature, 233(39): 149–152
13. Oesterhelt D, Stoeckenius W (1974). Isolationof the cell membrane of Halobacterium halobium and its fraction into red and purple membrane. Methods Enzymol, 31: 667–678. doi:10.1016/0076-6879(74)31072-5
14. Otomo J, Urabe Y, Tomioka H, Sasabe H (1992). The primary structures of helices A to G of three new bacteriorhodopsin-likeretinal proteins. J Gen Microbiol, 138(11): 2389–2396
15. Radax C, Gruber C, Stan-Lotter H (2001). Novel haloarchaeal 16S rRNA genesequences from Alpine Permo-Triassic rock salt. Extremophiles, 5(4): 221–228. doi:10.1007/s007920100192
16. Stackebrandt E, Goebel B M (1994). Taxonomicnote: a place for DNA-DNA reassociation and 16S rRNA sequence analysisin the present species definition in bacteriology. Int J Syst Bacteriol, 44(4): 846–849
17. Sugiyama Y, Yamada N, Mukohata Y (1994). The light-driven proton pump, cruxrhodopsin-2in Haloarcula sp.arg-2 (bR⁺, hR^-), and its coupledATP formation. Arch Biochem Biophys, 1188(3): 287–292. doi:10.1016/0005-2728(94)90047-7
18. Tateno M, Ihara K, Mukohata Y (1994). The novel ion pump rhodopsins from Haloarcula form a family independent fromboth the bacteriorhodopsin and archaerhodopsin families/tribes. Arch Biochem Biophys, 315(1): 127–132. doi:10.1006/abbi.1994.1480
19. Uegaki K, Sugiyama Y, Mukohata Y (1991). Archaerhodopsin-2, from Halobacterium sp. aus-2 further reveals essentialamino acid residues for light-driven proton pumps. Arch Biochem Biophys, 286(1): 107–110. doi:10.1016/0003-9861(91)90014-A
20. Wang H, Zhan S X, SunN Q A, Xu D Q, Zhao W, Huang W D, Li Q G (2000). Primarystructure of helix C to helix G of a new retinal protein in H. sp. xz515. Chin Sci Bull, 45(12): 1108–1112. doi:10.1007/BF02887184
21. Xin H, Itoh T, Zhou P, Suzuki K, Kamekura M, Nakase T (2000). Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake,Xinjiang, China. Int J Syst Evol Microbiol, 50(3): 1297–1303
22. Xu X H, Wu M (2004). Spectralanalysis and application of photoelectric characteristics in bacteriorhodopsin. Journal of Zhejiang University (Science Edition), 31(5): 570–574 (in Chinese)
23. Xu X H, Wu M, Cao Y, Wu Y H (2005). Isolation and phylogenetic analysis of halophilic archaea AJ6. Journal of Zhejiang University (Science Edition), 32(1): 83–88 (in Chinese)
24. Xu X W, Ren P G, Liu S J, Wu M, Zhou P J (2005). Natrinema altunense sp. nov., an extremely halophilicarchaeon isolated from a salt lake in Altun Mountain in Xinjiang,China. Int J Syst Evol Microbiol, 55: 1311–1314. doi:10.1099/ijs.0.63622-0
25. Xu X W, Wu M, Huang W D (2004). Isolation and 16S rDNA sequence analysisof extremely halophilic archaea from saline in Altun region. Journal of Zhejiang University (Engineering Science), 38(4): 508–512 (in Chinese)
26. Xu X W, Wu M, Ruan H, Hong J, Huang W D (2004). Partial Sequenceof the gene for a new BR protein, and nucleotide sequence of 16S rRNAencoding gene from a halophilic archaeum AJ4. Chinese Journal of Biochemistry and Molecular Biology, 20(1): 55–60 (in Chinese)
27. Xu X W, Wu M, Ruan H, Huang W D, Dilbar Tohty (2004). Sequencing and analysispartial sequence of the gene for a novel Br protein. Hereditas (Beijing), 26(3): 343–348 (in Chinese)
28. Yang Z, Yoder A D (1999). Estimationof the transition/transversion rate bias and species sampling. J Mol Evol, 48(3): 274–283. doi:10.1007/PL00006470
29. Yatsunami R, Kawakami T, Ohtani H, Nakamura S (2000). A novel bacteriorhodopsin-like protein from Haloarcula japonica strain TR-1: gene cloning,sequencing, and transcript analysis. Extremophiles, 4(2): 109–114
30. Yu X W, Dilbar Tohty, Wu Y H, Wu M (2005). Bacteriorhodopsin gene and phylogenetic analysis on halophilic archaeaAB3. Journal of Zhejiang University (EngineeringScience), 39(3): 418–422 (in Chinese)