Skip to main content
SpringerLink
Log in

Evolution of Sulfur Binding by Hemoglobin in Siboglinidae (Annelida) with Special Reference to Bone-Eating Worms, Osedax

  • Original Article
  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

Most members of Siboglinidae (Annelida) harbor endosymbiotic bacteria that allow them to thrive in extreme environments such as hydrothermal vents, methane seeps, and whale bones. These symbioses are enabled by specialized hemoglobins (Hbs) that are able to bind hydrogen sulfide for transportation to their chemosynthetic endosymbionts. Sulfur-binding capabilities are hypothesized to be due to cysteine residues at key positions in both vascular and coelomic Hbs, especially in the A2 and B2 chains. Members of the genus Osedax, which live on whale bones, do not have chemosynthetic endosymbionts, but instead harbor heterotrophic bacteria capable of breaking down complex organic compounds. Although sulfur-binding capabilities are important in other siboglinids, we questioned whether Osedax retained these cysteine residues and the potential ability to bind hydrogen sulfide. To answer these questions, we used high-throughput DNA sequencing to isolate and analyze Hb sequences from 8 siboglinid lineages. For Osedax mucofloris, we recovered three (A1, A2, and B1) Hb chains, but the B2 chain was not identified. Hb sequences from gene subfamilies A2 and B2 were translated and aligned to determine conservation of cysteine residues at previously identified key positions. Hb linker sequences were also compared to determine similarity between Osedax and siboglinids/sulfur-tolerant annelids. For O. mucofloris, our results found conserved cysteines within the Hb A2 chain. This finding suggests that Hb in O. mucofloris has retained some capacity to bind hydrogen sulfide, likely due to the need to detoxify this chemical compound that is abundantly produced within whale bones.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. doi:10.1016/S0022-2836(05)80360-2

    Article  CAS  PubMed  Google Scholar 

  • Arp AJ, Childress JJ (1981) Blood function in the hydrothermal vent vestimentiferan tube worm. Science 213:342–344. doi:10.1126/science.213.4505.342

    Article  CAS  PubMed  Google Scholar 

  • Bailly X, Leroy R, Carney S et al (2003) The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection. PNAS 100:5885–5890. doi:10.1073/pnas.1037686100

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bright M, Eichinger I, Salvini-Plawen L (2012) The metatrochophore of a deep-sea hydrothermal vent vestimentiferan (Polychaeta:Siboglinidae). Org Divers Evol 13:163–188. doi:10.1007/s13127-012-0117-z

    Article  PubMed  PubMed Central  Google Scholar 

  • Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    Article  CAS  PubMed  Google Scholar 

  • Cavanaugh CM, Gardiner SL (1981) Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts. Science (New York) 213:340–342. doi:10.1126/science.213.4505.340

    Article  CAS  Google Scholar 

  • Danise S, Higgs ND (2015) Bone-eating Osedax worms lived on Mesozoic marine reptile deadfalls. Biol Lett 11:20150072. doi:10.1098/rsbl.2015.0072

    Article  PubMed  PubMed Central  Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165

    Article  CAS  PubMed  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. doi:10.1093/nar/gkh340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eichinger I, Schmitz-Esser S, Schmid M et al (2014) Symbiont-driven sulfur crystal formation in a thiotrophic symbiosis from deep-sea hydrocarbon seeps. Environ Microbiol Rep 6:364–372. doi:10.1111/1758-2229.12149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Flores JF, Fisher CR, Carney SL et al (2005) Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin. Proc Natl Acad Sci USA 102:2713–2718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Glover AG, Källström B, Smith CR, Dahlgren TG (2005) World-wide whale worms? A new species of Osedax from the shallow north Atlantic. Proc R Soc Lond B 272:2587–2592. doi:10.1098/rspb.2005.3275

    Article  Google Scholar 

  • Glover AG, Wiklund H, Taboada S et al (2013) Bone-eating worms from the Antarctic: the contrasting fate of whale and wood remains on the Southern Ocean seafloor. Proc R Soc B 280:20131390. doi:10.1098/rspb.2013.1390

    Article  PubMed  PubMed Central  Google Scholar 

  • Goffredi SK, Orphan VJ, Rouse GW et al (2005) Evolutionary innovation: a bone-eating marine symbiosis. Environ Microbiol 7:1369–1378. doi:10.1111/j.1462-2920.2005.00824.x

    Article  CAS  PubMed  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29:644–652. doi:10.1038/nbt.1883

    Article  CAS  Google Scholar 

  • Halanych KM (2005) Molecular phylogeny of siboglinid annelids (a.k.a. pogonophorans): a review. Hydrobiologia 535–536:297–307. doi:10.1007/s10750-004-1437-6

    Google Scholar 

  • Halanych KM, Feldman RA, Vrijenhoek RC (2001) Molecular evidence that Sclerolinum brattstromi is closely related to vestimentiferans, not to frenulate pogonophorans (Siboglinidae, Annelida). Biol Bull 201:65–75

    Article  CAS  PubMed  Google Scholar 

  • Higgs ND, Glover AG, Dahlgren TG, Little CTS (2011) Bone-boring worms: Characterizing the morphology, rate, and method of bioerosion by Osedax mucofloris (Annelida, Siboglinidae). Biol Bull 221:307–316

    PubMed  Google Scholar 

  • Hilário A, Johnson SB, Cunha MR, Vrijenhoek RC (2010) High diversity of frenulates (Polychaeta: Siboglinidae) in the Gulf of Cadiz mud volcanoes: a DNA taxonomy analysis. Deep Sea Res Part I 57:143–150. doi:10.1016/j.dsr.2009.10.004

    Article  Google Scholar 

  • Hilário A, Capa M, Dahlgren TG et al (2011) New perspectives on the ecology and evolution of siboglinid tubeworms. PLoS ONE 6:e16309. doi:10.1371/journal.pone.0016309

    Article  PubMed  PubMed Central  Google Scholar 

  • Huusgaard RS, Vismann B, Kühl M et al (2012) The potent respiratory system of Osedax mucofloris (Siboglinidae, Annelida)—a prerequisite for the origin of bone-eating Osedax? PLoS ONE 7:e35975. doi:10.1371/journal.pone.0035975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. ISMB. pp 138–148

  • Julian D, Gaill F, Wood E et al (1999) Roots as a site of hydrogen sulfide uptake in the hydrocarbon seep vestimentiferan Lamellibrachia sp. J Exp Biol 202:2245–2257

    CAS  PubMed  Google Scholar 

  • Katz S, Klepal W, Bright M (2010) The skin of Osedax (Siboglinidae, Annelida): an ultrastructural investigation of its epidermis. J Morphol 271:1272–1280. doi:10.1002/jmor.10873

    Article  PubMed  Google Scholar 

  • Katz S, Klepal W, Bright M (2011) The Osedax trophosome: Organization and ultrastructure. Biol Bull 220:128–139

    PubMed  Google Scholar 

  • Kocot KM, Cannon JT, Todt C et al (2011) Phylogenomics reveals deep molluscan relationships. Nature 477:452–456. doi:10.1038/nature10382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. doi:10.1186/gb-2009-10-3-r25

    Article  PubMed  PubMed Central  Google Scholar 

  • Li Y, Kocot KM, Schander C et al (2015) Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida). Mol Phylogenet Evol 85:221–229. doi:10.1016/j.ympev.2015.02.008

    Article  CAS  PubMed  Google Scholar 

  • Maiti R, Van Domselaar GH, Zhang H, Wishart DS (2004) SuperPose: a simple server for sophisticated structural superposition. Nucleic Acids Res 32:W590–W594

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McDonald E, Brown CT (2013) Khmer: working with big data in bioinformatics. CoRR, abs/1303.2223, 2013

  • McMullin ER, Hourdez S, Schaeffer SW, Fisher CR (2003) Phylogeny and biogeography of deep sea vestimentiferan tubeworms and their bacterial symbionts. Symbiosis 34:1–41

    Google Scholar 

  • Meunier C, Andersen AC, Bruneaux M et al (2010) Structural characterization of hemoglobins from Monilifera and Frenulata tubeworms (Siboglinids): first discovery of giant hexagonal-bilayer hemoglobin in the former “Pogonophora” group. Comp Biochem Physiol A 155:41–48. doi:10.1016/j.cbpa.2009.09.010

    Article  Google Scholar 

  • National Research Council, Division of Medical Science, subcommittee on Hydrogen Sulfide (1979) Hydrogen sulfide. University Park Press, Baltimore

  • Numoto N, Nakagawa T, Kita A et al (2005) Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi. Proc Natl Acad Sci USA 102:14521–14526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Numoto N, Nakagawa T, Kita A et al (2008) Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin. Biochemistry 47:11231–11238. doi:10.1021/bi8012609

    Article  CAS  PubMed  Google Scholar 

  • Okonechnikov K, Golosova O, Fursov M, Team the U (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167. doi:10.1093/bioinformatics/bts091

    Article  CAS  PubMed  Google Scholar 

  • Rouse GW, Goffredi SK, Vrijenhoek RC (2004) Osedax: bone-eating marine worms with dwarf males. Science 305:668–671. doi:10.1126/science.1098650

    Article  CAS  PubMed  Google Scholar 

  • Rouse GW, Wilson NG, Worsaae K, Vrijenhoek RC (2015) A dwarf male reversal in bone-eating worms. Curr Biol 25:236–241. doi:10.1016/j.cub.2014.11.032

    Article  CAS  PubMed  Google Scholar 

  • Schulze A, Halanych KM (2003) Siboglinid evolution shaped by habitat preference and sulfide tolerance. Hydrobiologia 496:199–205. doi:10.1023/A:1026192715095

    Article  Google Scholar 

  • Smith CR, Glover AG, Treude T et al (2015) Whale-fall ecosystems: recent insights into ecology, paleoecology, and evolution. Annu Rev Mar Sci 7:571–596. doi:10.1146/annurev-marine-010213-135144

    Article  Google Scholar 

  • Southward EC (1978) A new species of Lamellisabella (Pogonophora) from the north Atlantic. J Mar Biol Assoc UK 58:713–718. doi:10.1017/S0025315400041357

    Article  Google Scholar 

  • Southward EC (1988) Development of the gut and segmentation of newly settled stages of Ridgeia (Vestimentifera): implications for relationship between Vestimentifera and Pogonophora. J Mar Biol Assoc UK 68:465–487. doi:10.1017/S0025315400043344

    Article  Google Scholar 

  • Southward AJ, Southward EC (1981) Dissolved organic matter and the nutrition of the Pogonophora: a reassessment based on recent studies of their morphology and biology. Kiel Meeresf 5:445–453

    CAS  Google Scholar 

  • Southward EC, Schulze A, Gardiner SL (2005) Pogonophora (Annelida): form and function. In: Bartolomaeus T, Purschke G (eds) Morphology, molecules, evolution and phylogeny in Polychaeta and related taxa. Springer, Netherlands, pp 227–251

    Chapter  Google Scholar 

  • Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. doi:10.1093/bioinformatics/btu033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suzuki T, Takagi T, Ohta S (1990) Primary structure of a constituent polypeptide chain (AIII) of the giant haemoglobin from the deep-sea tube worm Lamellibrachia. A possible H2S-binding site. http://www.biochemj.org/bj/266/bj2660221.htm

  • Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thornhill DJ, Wiley AA, Campbell AL et al (2008) Endosymbionts of Siboglinum fiordicum and the phylogeny of bacterial endosymbionts in Siboglinidae (Annelida). Biol Bull 214:135–144

    Article  CAS  PubMed  Google Scholar 

  • Treude T, Smith C, Wenzhöfer F et al (2009) Biogeochemistry of a deep-sea whale fall: sulfate reduction, sulfide efflux and methanogenesis. Mar Ecol Prog Ser 382:1–21. doi:10.3354/meps07972

    Article  CAS  Google Scholar 

  • Verna C, Ramette A, Wiklund H, Dahlgren TG, Glover AG, Gaill F, Dubilier N (2010) High symbiont diversity in the bone-eating worm Osedax mucofloris from shallow whale-falls in the North Atlantic. Environ Microbiol 12:2355–2370

    Article  CAS  PubMed  Google Scholar 

  • Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2015) The I-TASSER Suite: protein structure and function prediction. Nat Methods 12:7–8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yuasa HJ, Green BN, Takagi T et al (1996) Electrospray ionization mass spectrometric composition of the 400 kDa hemoglobin from the pogonophoran Oligobrachia mashikoi and the primary structures of three major globin chains. Biochimica et Biophysica Acta (BBA) 1296:235–244. doi:10.1016/0167-4838(96)00081-7

    Article  Google Scholar 

  • Zal F, Lallier FH, Green BN et al (1996a) The multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila II. Complete polypeptide chain composition investigated by maximum entropy analysis of mass spectra. J Biol Chem 271:8875–8881. doi:10.1074/jbc.271.15.8875

    Article  CAS  PubMed  Google Scholar 

  • Zal F, Lallier FH, Wall JS et al (1996b) The multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila I. Reexamination of the number and masses of its constituents. J Biol Chem 271:8869–8874. doi:10.1074/jbc.271.15.8869

    Article  CAS  PubMed  Google Scholar 

  • Zal F, Suzuki T, Kawasaki Y et al (1997) Primary structure of the common polypeptide chain b from the multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila: an insight on the sulfide binding-site. Proteins: Structure. Funct Bioinform 29:562–574

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We are indebted to the late Christopher Schander for his contribution of Osedax mucofloris tissue for sequencing. We would like to thank the crews of the R/V Seward Johnson, R/V Aurelia, and R/V Håkons-Mosby for their assistance in procuring samples. We would also like to thank Amanda Shaver and Franziska Franke for preparation of cDNA for samples used in this study. Pamela M. Brannock, Kevin M. Kocot, and Nathan V. Whelan provided guidance and input on procedures used in this study and the writing of versions of this manuscript. This work was funded by National Science Foundation grants IOS-0843473 to K. M. H, S. R. S., and D. J. T., OCE-1155188 to K. M. H., DEB-1036537 to K. M. H. and S. R. S. It represents contributions #141 and #49 to the Auburn University (AU) Marine Biology Program and Molette Biology Laboratory for Environmental and Climate Change Studies, respectively.

Author information

Authors and Affiliations

  1. Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA

    Damien S. Waits, Scott R. Santos, Daniel J. Thornhill, Yuanning Li & Kenneth M. Halanych

Authors
  1. Damien S. Waits
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Scott R. Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Daniel J. Thornhill
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuanning Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kenneth M. Halanych
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Damien S. Waits or Kenneth M. Halanych.

Additional information

Genbank Accession Numbers KT166952–KT166980.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 12 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Waits, D.S., Santos, S.R., Thornhill, D.J. et al. Evolution of Sulfur Binding by Hemoglobin in Siboglinidae (Annelida) with Special Reference to Bone-Eating Worms, Osedax . J Mol Evol 82, 219–229 (2016). https://doi.org/10.1007/s00239-016-9739-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-016-9739-7

Keywords

Search

Navigation