Molecular Biology Reports

, Volume 45, Issue 5, pp 1527–1532 | Cite as

Positive selection adaptation of two-domain arginine kinase (AK) from cold seep Vesicomyidae clams

  • Xue Kong
  • Helu Liu
  • Haibin ZhangEmail author
Short Communication


Arginine kinase (AK) is an important member of Phosphagen kinases which engage in energy metabolism process, and AKs from cold seep clams may develop an effective mechanism to adapt a special habitat (e.g. low temperature). Three Vesicomyidae clams and seven Veneridae clams (belong to the same Order Veneroida) were chosen to analyze the evolution of two-domain AKs. In the present study, ten two-domain AKs were identified and Neighbor-joining tree showed that AKs were divided into two groups. Branch-site model indicated that two-domain AKs were subjected to strong positive selection (ω2a = 17.5058). 16 positively selective sites were detected and five of them showed posterior probabilities of 0.95 or more. Comparative analysis found that domain 2 might be suffered from more evolutionary selection pressure than domain 1, as most positively sites were located at domain 2. Residue Pro (positively selective site) (587P in ApAK) in domain 2 from all Vesicomyidae AKs might participate in change of the synergism and in the function of its cold-adapted characteristics. In conclusion, our studies provide evidence of positive Darwinian selection in the two-domain AKs family of Vesicomyidae clams, and may contribute to a better understanding of its adaptation mechanisms to cold seep habitats.


Two-domain arginine kinases Cold seep Positive selection Vesicomyidae Veneridae 



The authors thank Dr. Robert C. Vrijenhoek and Shannon B. Johnson for their help in sample collection. The authors thank Yanan Li and Jiawei Chen for their helpful comments. This work was supported by Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB06010104), The National Key Research and Development Program of China (2017YFC0306600), Knowledge Innovation Program of CAS (SIDSSE–201401), Hundred Talents Program of CAS (SIDSSE–BR–201401), National Natural Science Foundation of China (41576127), and Major scientific and technological projects of Hainan Province (ZDKJ2016009).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were not followed.

Supplementary material

11033_2018_4227_MOESM1_ESM.pdf (240 kb)
Fig. S1 Schematic diagrams of two-domain AKs. ATP-gua Ptrans refer to ATP-guanido phosphotransferase catalytic domain. Sequences information was the same as Fig. 2 (PDF 240 KB)
11033_2018_4227_MOESM2_ESM.pdf (41 kb)
Fig. S2 Neighbor-joining tree of two-domain AKs. Sequences information was the same as Fig. 1 (PDF 41 KB)
11033_2018_4227_MOESM3_ESM.docx (14 kb)
Supplementary material 3 (DOCX 14 KB)


  1. 1.
    Uda K, Yamamoto K, Iwasaki N, Iwai M, Fujikura K, Ellington WR, Suzuki T (2008) Two-domain arginine kinase from the deep-sea clam Calyptogena kaikoi—evidence of two active domains. Comp Biochem Physiol B Biochem Mol Biol 151:176–182CrossRefPubMedGoogle Scholar
  2. 2.
    France RM, Sellers DS, Grossman SH (1997) Purification, characterization, and hydrodynamic properties of arginine kinase from gulf shrimp (Penaeus aztecus). Arch Biochem Biophys 345:73–78CrossRefPubMedGoogle Scholar
  3. 3.
    Suzuki T, Yamamoto Y, Umekawa M (2000) Stichopus japonicus arginine kinase: gene structure and unique substrate recognition system. Biochem J 3:579–585CrossRefGoogle Scholar
  4. 4.
    Robin Y, Klotz C, Thoai NV (1969) A new form of adenosine triphosphate-arginine phosphotransferase with a molecular weight of 160000. Biochim Biophys Acta 171:357–359. CrossRefPubMedGoogle Scholar
  5. 5.
    Miranda MR, Canepa GE, Bouvier LA, Pereira CA (2006) Trypanosoma cruzi: oxidative stress induces arginine kinase expression. Exp Parasitol 114:341–344CrossRefPubMedGoogle Scholar
  6. 6.
    Holt SM, Kinsey ST (2002) Osmotic effects on arginine kinase function in living muscle of the blue crab Callinectes sapidus. J Exp Biol 205:1775–1785PubMedGoogle Scholar
  7. 7.
    Yao CL, Wu CG, Xiang JH, Dong B (2005) Molecular cloning and response to laminarin stimulation of arginine kinase in haemolymph in Chinese shrimp, Fenneropenaeus chinensis. Fish Shellfish Immunol 19:317–329CrossRefPubMedGoogle Scholar
  8. 8.
    Astrofsky KM, Roux MM, Klimpel KR, Fox JG, Dhar AK (2002) Isolation of differentially expressed genes from white spot virus (WSV) infected Pacific blue shrimp (Penaeus stylirostris). Arch Virol 147:1799–1812CrossRefPubMedGoogle Scholar
  9. 9.
    Anosike EO, Moreland BH, Watts DC (1975) Evolutionary variation between a monomer and a dimer arginine kinase. Purification of the enzyme from Holothuria forskali and a comparison of some properties with that from Homarus vulgaris. Biochem J 145:535–543CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Seals JD, Grossman SH (1988) Purification and characterization of arginine kinase from the sea cucumber Caudina arenicola. Comp Biochem Physiol Part B 89:701–707. CrossRefGoogle Scholar
  11. 11.
    Suzuki T, Yamamoto K, Tada H, Uda K (2012) Cold-adapted features of arginine kinase from the deep-sea clam Calyptogena kaikoi. Mar Biotechnol 14:294–303CrossRefPubMedGoogle Scholar
  12. 12.
    Letunic I, Bork P (2018) 20 years of the SMART protein domain annotation resource. Nucleic Acids Res 46:D493–D496. CrossRefPubMedGoogle Scholar
  13. 13.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591CrossRefPubMedGoogle Scholar
  16. 16.
    Merceron R, Awama AM, Montserret R, Marcillat O, Gouet P (2015) The substrate-free and -bound crystal structures of the duplicated taurocyamine kinase from the human parasite Schistosoma mansoni. J Biol Chem 290:12951–12963CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Zhou G, Somasundaram T, Blanc E, Parthasarathy G, Ellington WR, Chapman MS (1998) Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions. Proc Natl Acad Sci USA 95:8449–8454CrossRefPubMedGoogle Scholar
  18. 18.
    Suzuki T, Fukuta H, Nagato H, Umekawa M (2000) Arginine kinase from Nautilus pompilius, a living fossil. Site-directed mutagenesis studies on the role of amino acid residues in the Guanidino specificity region. J Biol Chem 275:23884–23890CrossRefPubMedGoogle Scholar
  19. 19.
    Fujimoto N, Tanaka K, Suzuki T (2005) Amino acid residues 62 and 193 play the key role in regulating the synergism of substrate binding in oyster arginine kinase. FEBS Lett 579:1688–1692CrossRefPubMedGoogle Scholar
  20. 20.
    Ellington WR (2001) Evolution and physiological roles of phosphagen systems. Annu Rev Physiol 63:289–325CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Institute of Deep-Sea Science and EngineeringChinese Academy of SciencesSanyaChina
  2. 2.University of Chinese Academy of SciencesBeijingChina

Personalised recommendations