Skip to main content
Log in

Defense responses of sulfur dioxygenase to sulfide stress in the razor clam Sinonovacula constricta

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

Background

Sulfide is a well-known toxicant widely distributed in the culture environment. As a representative burrowing benthic bivalve, the razor clam Sinonovacula constricta is highly sulfide tolerant. Mitochondrial sulfide oxidation is an important way for sulfide detoxification, where sulfur dioxygenase (SDO) is the second key enzyme.

Objective

To investigate the mechanism of sulfide tolerance in S. constricta, the molecular characterization of its SDO (designated as ScSDO) was studied.

Methods

The cDNA sequence of ScSDO was cloned by RACE technique. The response of ScSDO in gills and livers of S. constricta was investigated during sulfide exposure (50, 150, and 300 μM sulfide) for 0, 3, 6, 12, 24, 48, 72, and 96 h by qRT-PCR. Moreover, the temporal expression of ScSDO protein in S. constricta gills after exposure to 150 μM sulfide was detected by Western blot. The subcellular location of ScSDO was identified by TargetP 1.1 prediction and Western Blot analysis.

Results

The full-length cDNA of ScSDO was 2914 bp, encoding a protein of 304 amino acids. The deduced ScSDO protein was highly conserved, containing the signature HXHXDH motif of the metallo-β-lactamase superfamily and two metal-binding sites, of which metal-binding site I is known to be the catalytically active center. Subcellular localization confirmed that ScSDO was located only in the mitochondria. Responding to the sulfide exposure, distinct time-dependent increases in ScSDO expression were detected at both mRNA and protein levels. Moreover, the gills exhibited a higher ScSDO expression level than the livers.

Conclusions

All of our results suggest that ScSDO plays an important role in mitochondrial sulfide oxidation during sulfide stress, making S. constricta highly sulfide tolerant. In addition, as a respiratory tissue, the gills play a more critical role in sulfide detoxification.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Affonso EG, Polez VL, Corrêa CF, Mazon AF, Araújo MR, Moraes G, Rantin FT (2002) Blood parameters and metabolites in the teleost fish Colossoma macropomum exposed to sulfide or hypoxia. Comp Biochem Physiol C 133:375–382

    CAS  Google Scholar 

  • Affonso EG, Polez VL, Corrêa CF, Mazon AF, Araújo MR, Moraes G, Rantin FT (2004) Physiological responses to sulfide toxicity by the air-breathing catfish, hoplosternum littorale (siluriformes, callichthyidae). Comp Biochem Physiol C 139:251–257

    CAS  Google Scholar 

  • Arp AJ, Hansen BM, Julian D (1992) Burrow environment and coelomic fluid characteristics of the echiurian worm Urechis caupo from populations at three sites in northern California. Mar Biol 113:613–623

    Article  Google Scholar 

  • Bagarinao T (1992) Sulfide as an environmental factor and toxicant: tolerance and adaptations in aquatic organisms. Aquat Toxicol 24:21–62

    Article  CAS  Google Scholar 

  • Bagarinao T, Vetter RD (1990) Oxidative detoxification of sulfide by mitochondria of the California killifish Fundulus parvipinnis and the speckled sanddab Citharichthys sitgmaeus. J Comp Physiol B 160:519–527

    Article  CAS  Google Scholar 

  • Bebrone C (2007) Metallo-beta-lactamases (classification, activity, genetic organization, structure, zinc coordination) and their superfamily. Biochem Pharmacol 74:1686–1701

    Article  CAS  PubMed  Google Scholar 

  • Bourgeois RP, Felder DL (2001) Postexposure metabolic effects of sulfide and evidence of sulfide-based ATP production in callianassid ghost shrimp (Crustacea: Decapoda: Thalassinidea). J Exp Mar Biol Ecol 263:105–121

    Article  CAS  Google Scholar 

  • Chen AH, Yao GX, Sun GM (2005) Studies on the relationship between the sulphuret concentration in the substeatum and mortality of the hard clam (Meretrix meretrix) in Jiangsu sea area. J Aquacult 26:8–11

    Google Scholar 

  • Daiyasu H, Osaka K, Ishino Y, Toh H (2001) Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold. FEBS Lett 503:1–6

    Article  CAS  PubMed  Google Scholar 

  • Forgan LG, Forster ME (2010) Oxygen consumption, ventilation frequency and cytochrome c oxidase activity in blue cod (Parapercis colias) exposed to hydrogen sulphide or isoeugenol. Comp Biochem Physiol C 151:57–65

    Google Scholar 

  • Goubern M, Andriamihaja M, Nubel T, Blachier F, Bouillaud F (2007) Sulfide, the first inorganic substrate for human cells. FASEB J 21:1699–1706

    Article  CAS  PubMed  Google Scholar 

  • Grieshaber MK, Völkel S (1998) Animal adaptations for tolerance and exploitation of poisonous sulfide. Annu Rev Physiol 60:33–53

    Article  CAS  PubMed  Google Scholar 

  • Guan YQ, Wang HC (2009) Effects of sulphide on the enzyme of respiratory metabolism and energy metabolism of macrobrachium nipponense. Ecol Environ Sci 18:2017–2022

    Google Scholar 

  • Guan YQ, Pei SR, Li ZJ (2011) Effects of acute sulfide stress on immune responses and antioxidant system of macrobrachium nipponense. J Hydroecol 32:89–94

    Google Scholar 

  • Hance JM, Andrzejewski  JE, Predmore  BL, Dunlap KJ, Misiak KL, Julian  D (2008) Cytotoxicity from sulfide exposure in a sulfide-tolerant marine invertebrate. J Exp Mar Biol Ecol 359:102–109

  • Hildebrandt TM, Grieshaber MK (2008) Three enzymatic activities catalyze the oxidation of sulfide to thiosulfate in mammalian and invertebrate mitochondria. FEBS J 275:3352–3361

    Article  CAS  PubMed  Google Scholar 

  • Hildebrandt T, Meo  ID, Zeviani  M, Viscomi  C, Braun HP (2013) Proteome adaptations in ETHE1 deficient mice indicate a role of sulfide signaling in lipid catabolism and cytoskeleton organization via post-translational protein modifications. Biosci Rep 33:e00052

  • Holdorf MM, Bennett B, Crowder MW, Makaroff CA (2008) Spectroscopic studies on Arabidopsis ETHE1, a glyoxalase II-like protein. J Inorg Biochem 102:1825–1830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holdorf MM, Owen HA, Lieber SR, Yuan L, Adams N, Dabney-Smith C, Makaroff CA (2012) Arabidopsis ETHE1 encodes a sulfur dioxygenase that is essential for embryo and endosperm development. Plant Physiol 160:226–236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jackson MR, Melideo SL, Jorns MS (2012) Human sulfide:quinone oxidoreductase catalyzes the first step in hydrogen sulfide metabolism and produces a sulfane sulfur metabolite. Biochemistry 51:6804–6815

    Article  CAS  PubMed  Google Scholar 

  • Jørgensen BB, Fenchel T (1974) The sulfur cycle of a marine sediment model system. Mar Biol 24:189–201

    Article  Google Scholar 

  • Julian D, April KL, Patel S, Stein JR, Wohlgemuth SE (2005) Mitochondrial depolarization following hydrogen sulfide exposure in erythrocytes from a sulfide-tolerant marine invertebrate. J Exp Biol 208:4109–4122

  • Julian D, Passman WE, Arp AJ (1996) Water lung and body wall contributions to respiration in an echiuran worm. Resp Physiol 106:187–198

    Article  CAS  Google Scholar 

  • Kabil O, Banerjee R (2012) Characterization of patient mutations in human persulfide dioxygenase (ETHE1) involved in H2S catabolism. J Biol Chem 287:44561–44567

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Konishi M, Watsuji TO, Nakagawa S, Hatada Y, Takai K, Toyofuku T (2013) Effects of hydrogen sulfide on bacterial communities on the surface of galatheid crab, Shinkaia crosnieri, and in a bacterial mat cultured in rearing tanks. Microbes Environ 28:25–32

    Article  PubMed  Google Scholar 

  • Lagoutte E, Mimoun S, Andriamihaja M, Chaumontet C, Blachier F, Bouillaud F (2010) Oxidation of hydrogen sulfide remains a priority in mammalian cells and causes reverse electron transfer in colonocytes. Biochim Biophys Acta 1797:1500–1511

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Xin Y, Xun L (2014) Distribution, diversity, and activities of sulfur dioxygenases in heterotrophic bacteria. Appl Environ Microbiol 80:1799–1806

    Article  PubMed  PubMed Central  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408

    Article  CAS  Google Scholar 

  • Ma ZJ (2003) A study on the tolerating mechanism for sulfide in Urechis unicinctus (Echiura: Urechidae). Master Thesis, Ocean University, China, Qingdao, Shandong, China

  • McCoy JG, Bingman CA, Bitto E, Holdorf MM, Makaroff CA, Phillips GN Jr (2006) Structure of an ETHE1-like protein from Arabidopsis thaliana. Acta Crystallogr D 62:964–970

    Article  PubMed  Google Scholar 

  • Mineri R, Rimoldi M, Burlina AB, Koskull S, Perletti C, Heese B, Dobeln UV, Mereghetti  P, Meo  ID, Invernizzi F, Zeviani  M, Uziel  G, Tiranti V (2008) Identification of new mutations in the ETHE1 gene in a cohort of 14 patients presenting with ethylmalonic encephalopathy. J Med Gen 45:473–478

  • Peng C, Zhao XG, Liu SX, Shi W, Han Y, Guo C, Jiang JG, Wan HB, Shen TD, Liu GX (2016) Effects of anthropogenic sound on digging behavior, metabolism, Ca2+/Mg2+ ATPase activity, and metabolism-related gene expression of the bivalve Sinonovacula constricta. Sci Rep 6:24266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng C, Zhao XG, Liu SX, Shi W, Han Y, Guo C, Peng X, Chai XL, Liu GX (2017) Ocean acidification alters the burrowing behaviour, Ca2+/Mg2+-ATPase activity, metabolism, and gene expression of a bivalve species, Sinonovacula constricta. MEPS 575:107–117

    Article  CAS  Google Scholar 

  • Pettinati I, Brem  J, McDonough  MA, Schofield CJ (2015) Crystal structure of human persulfide dioxygenase: structural basis of ethylmalonic encephalopathy. Human Mol Genet 24:2458–2469

  • Powell MA, Somero GN (1986) Hydrogen sulfide oxidation is coupled to oxidative phosphorylation in mitochondria of Solemya reidi. Science 233:563–566

    Article  CAS  PubMed  Google Scholar 

  • Shahak Y, Hauska G (2008) Sulfide oxidation from cyanobacteria to humans: sulfide-quinone oxidoreductase (SQR). In: Hell R, Dahl C, Knaff D, Leustek T (eds) Sulfur metabolism in phototrophic organisms. Advances in Photosynthesis and Respiration, vol 27. Springer, Dordrecht, pp 320–335

  • Shen YY, Chen JQ, Shen WL, Chen CF, Lin ZH, Li CH (2020) Molecular characterization of a novel sulfde:quinone oxidoreductase from the razor clam Sinonovacula constricta and its expression response to sulfde stress. Comp Biochem Physiol B 239:110367

    Article  PubMed  Google Scholar 

  • Theissen U, Martin W (2008) Sulfide:quinone oxidoreductase (SQR) from the lugworm Arenicola marina shows cyanide- and thioredoxin-dependent activity. FEBS J 275:1131–1139

    Article  CAS  PubMed  Google Scholar 

  • Tiranti V, D’Adamo P, Briem E, Ferrari G, Mineri R, Lamantea E, Mandel H, Balestri P, Garcia-Silva MT, Vollmer B, Rinaldo P, Hahn SH, Leonard J, Rahman S, Dionisi-Vici C, Garavaglia B, Gasparini P, Zeviani M (2004) Ethylmalonic encephalopathy is caused by mutations in ETHE1, a gene encoding a mitochondrial matrix protein. Am J Hum Genet 74:239–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tiranti V, Viscomi C, Hildebrandt T, Di MI, Mineri R, Tiveron C, Levitt MD, Prelle A, Fagiolari G, Rimoldi M, Zeviani M (2009) Loss of ethe1, a mitochondrial dioxygenase, causes fatal sulfide toxicity in ethylmalonic encephalopathy. Nat Med 15:200–205

    Article  CAS  PubMed  Google Scholar 

  • Tiranti V, Zeviani M (2013) Altered sulfide (H2S) metabolism in ethyl malonic encephalopathy. Cold Spring Harb Perspect Biol 5:a011437

  • Vismann B (1996) Sulfide species and total sulfide toxicity in the shrimp Crangon crangon. J Exp Mar Biol Ecol 204:141–154

    Article  CAS  Google Scholar 

  • Völkel S, Grieshaber MK (1992) Mechanisms of sulfide tolerance in the peanut worm Sipunculus nudus (Sipunculida) and in the lugworm Arenicola marina (Polychaeta). J Comp Physiol B 162:469–477

    Article  Google Scholar 

  • Völkel S, Grieshaber MK (1997) Sulphide oxidation and oxidative phosphorylation in the mitochondria of the lugworm Arenicola marina. J Exp Biol 200:83–92

    Article  Google Scholar 

  • Völkel S, Hauschild  K, Grieshaber MK (1995) Sulfide stress and tolerance in the lugworm Arenicola marina during low tide. Mar Ecol Prog Ser 122:205–215

  • Wang H, Liu S, Liu X, Li X, Wen Q, Lin J (2014) Identification and characterization of an ETHE1-like sulfur dioxygenase in extremely acidophilic Acidithiobacillus spp. Appl Microbiol Biotechnol 98:7511–7522

    Article  CAS  PubMed  Google Scholar 

  • Wu W, Pang X, Lin J, Liu X, Wang R, Lin J, Chen L (2017) Discovery of a new subgroup of sulfur dioxygenases and characterization of sulfur dioxygenases in the sulfur metabolic network of Acidithiobacillus caldus. PLoS ONE 12:e0183668

    Article  PubMed  PubMed Central  Google Scholar 

  • Yin H, Zhang X, Li X, He Z, Liang Y, Guo X, Hu Q, Xiao Y, Cong J, Ma L, Niu J, Liu X (2014) Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans. BMC Microbiol 14:179

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Liu XL, Liu JG, Zhang ZF (2013) Characteristics and function of sulfur dioxygenase in echiuran worm Urechis unicinctus. PLoS ONE 8:e81885

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Liu X, Qin Z, Liu J, Zhang Z (2016) Expression characteristics of sulfur dioxygenase and its function adaption to sulfide in echiuran worm Urechis unicinctus. Gene 593:334–341

    Article  CAS  PubMed  Google Scholar 

  • Zhao XL, Fu JP, Jiang LT, Zhang WW, Shao YN, Jin CH, Xiong JB, Li CH (2018) Transcriptome-based identification of the optimal reference genes as internal controls for quantitative RT-PCR in razor clam (Sinonovacula constricta). Genes Genom 40:603–613

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Key Research and Development Program of China (2018YFD0901405-5), the National Natural Science Foundation of China (31702317), Modern Agro-industry Technology Research System (CARS-49), Zhejiang Major Program of Science and Technology (2016C02055-9) and Key Research and Development project of Zhejiang Province(2019C02054).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Zhihua Lin or Yinghui Dong.

Ethics declarations

Conflict of interest

All of the authors declare that they have no conflict of interest.

Research involving human and animal rights

All animal experiments were performed in accordance with the ethical guidelines of Zhejiang Wanli University.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, C., Shen, Y., Shen, W. et al. Defense responses of sulfur dioxygenase to sulfide stress in the razor clam Sinonovacula constricta. Genes Genom 43, 513–522 (2021). https://doi.org/10.1007/s13258-021-01077-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-021-01077-0

Keywords

Navigation