Publication Cover
Biofouling
The Journal of Bioadhesion and Biofilm Research
Volume 30, 2014 - Issue 2
748
Views
40
CrossRef citations to date
0
Altmetric
Articles

First study on gene expression of cement proteins and potential adhesion-related genes of a membranous-based barnacle as revealed from Next-Generation Sequencing technology

, , , , &
Pages 169-181 | Received 21 Feb 2012, Accepted 04 Oct 2013, Published online: 12 Dec 2013

References

  • Aldred N, Clare AS. 2008. The adhesive strategies of cyprids and development of barnacle-resistant marine coatings. Biofouling. 24:351–363.
  • Ansorge WJ. 2009. Next-generation DNA sequencing techniques. New Biotechnol. 25:195–203.
  • Bacchetti De Gregoris T, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS. 2011. Deep sequencing of naupliar-, cyprid- and adult-specific normalised expressed sequence tag (EST) libraries of the acorn barnacle Balanus amphitrite. Biofouling. 27:367–374.
  • Bartlett TC, Cuthbertson BJ, Shepard EF, Chapman RW, Gross PS, Warr GW. 2002. Crustins, homologues of an 11.5 kDa antibacterial peptide, from two species of Penaeid shrimp, Litopenaeus vannamei and Litopenaeus setiferus. Mar Biotechnol. 4:278–293.
  • Bourget E. 1987. Barnacle shells: composition, structure and growth. In: Southward AJ, editor. Barnacle biology, crustacean issues. Rotterdam: Balkema; p. 267–285.
  • Briand J-F. 2009. Marine antifouling laboratory bioassays: an overview of their diversity. Biofouling. 25:297–311.
  • Burden DK, Barlow DE, Spillmann CM, Orihuela B, Rittschof D, Everett RK, Wahl KJ. 2012. Barnacle Balanus amphitrite adheres by a stepwise cementing process. Langmuir. 28:13364–13372.
  • Chen Z-F, Matsumura K, Wang H, Arellano SM, Yan X, Alam I, Archer JAC, Bajic VB, Qian P-Y. 2011. Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach. PLoS ONE. 6:e22913.
  • Clare AS, Matsumura K. 2000. Nature and perception of barnacle settlement pheromones. Biofouling. 15:57–71.
  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 21:3674–3676.
  • Dickinson GH. 2008. Barnacle cement: a polymerization model based on evolutionary concepts [doctoral thesis]. Durham (NC): Duke University.
  • Dickinson GH, Vega IE, Wahl KJ, Orihuela B, Beyley V, Rodriguez EN, Everett RK, Bonaventura J, Rittschof D. 2009. Barnacle cement: a polymerization model based on evolutionary concepts. J Exp Biol. 212:3499–3510.
  • Donpudsa S, Rimphanitchayakit V, Tassanakajon A, Söderhäll I, Söderhäll K. 2010. Characterization of two crustin antimicrobial peptides from the freshwater crayfish Pacifastacus leniusculus. J Invert Path. 104:234–238.
  • Dreanno C, Kirby RR, Clare AS. 2006. Locating the barnacle settlement pheromone: spatial and ontogenetic expression of the settlement-inducing protein complex of Balanus amphitrite. Proc R Soc B Biol Sci. 273:2721–2728.
  • Elbourne PD, Clare AS. 2010. Ecological relevance of a conspecific, waterborne settlement cue in Balanus amphitrite (Cirripedia). J Exp Mar Biol Ecol. 392:99–106.
  • Elbourne PD, Veater RA, Clare AS. 2008. Interaction of conspecific cues in Balanus amphitrite Darwin (Cirripedia) settlement assays: continued argument for the single-larva assay. Biofouling. 24:87–96.
  • Endo N, Nogata Y, Yoshimura E, Matsumura K. 2009. Purification and partial amino acid sequence analysis of the larval settlement-inducing pheromone from adult extracts of the barnacle, Balanus amphitrite (=Amphibalanus amphitrite). Biofouling. 25:429–434.
  • Feldmeyer B, Wheat C, Krezdorn N, Rotter B, Pfenninger M. 2011. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics. 12:317.
  • Fernandez JG, Ingber DE. 2012. Unexpected strength and toughness in chitosan-fibroin laminates inspired by insect cuticle. Adv Mater. 24:480–484.
  • Gamo T, Inokuchi T, Laufer H. 1977. Polypeptides of fibroin and sericin secreted from the different sections of the silk gland in Bombyx mori. Insect Biochem. 7:285–295.
  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 29:644–652.
  • Hadfield MG. 1998. The D P Wilson Lecture. Research on settlement and metamorphosis of marine invertebrate larvae: past, present and future. Biofouling. 12:9–29.
  • He L-S, Zhang G, Qian P-Y. 2013. Characterization of two 20 kDa-cement protein (cp20k) homologues in Amphibalanus amphitrite. PLoS ONE. 8:e64130.
  • Henrissat B, Davies G. 1997. Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol. 7:637–644.
  • Herrera-Estrella A, Chet I. 1999. Chitinases in biological control. EXS. 87:171–184.
  • Hiro F. 1939. Studies on the cirripedian fauna of Japan IV. Cirripeds of Formosa (Taiwan), with some geographical and ecological remarks on the littoral forms. Mem Coll Sci, Kyoto Imp Univ, Ser B. 15:245–284.
  • Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. 2009. Exploring the human genome with functional maps. Genome Res. 19:1093–1106.
  • Iseli C, Jongeneel CV, Bucher P. 1999. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Paper presented at: Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology; Heidelberg, Germany. Palo Alto (CA): AAAI Press; p. 138–158.
  • Jiravanichpaisal P, Lee SY, Kim Y-A, Andrén T, Söderhälla I. 2007. Antibacterial peptides in hemocytes and hematopoietic tissue from freshwater crayfish Pacifastacus leniusculus: characterization and expression pattern. Dev Comp Immunol. 31:441–455.
  • Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comp Appl Biosci. 8:275–282.
  • Kamino K. 2001. Novel barnacle underwater adhesive protein is a charged amino acid-rich protein constituted by a Cys-rich repetitive sequence. Biochem J. 356:503–507.
  • Kamino K. 2008. Underwater adhesive of marine organisms as the vital link between biological science and material science. Mar Biotechnol. 10:111–121.
  • Kamino K. 2010. Absence of cross-linking via trans-glutaminase in barnacle cement and redefinition of the cement. Biofouling. 26:755–760.
  • Kamino K. 2013. Mini-review: barnacle adhesives and adhesion. Biofouling. 29:735–749.
  • Kamino K, Inoue K, Maruyama T, Takamatsu N, Harayama S, Shizuri Y. 2000. Barnacle cement proteins. J Biol Chem. 275:27360–27365.
  • Kamino K, Nakano M, Kanai S. 2012. Significance of the conformation of building blocks in curing of barnacle underwater adhesive. FEBS J. 279:1750–1760.
  • Kamino K, Odo S, Maruyama T. 1996. Cement proteins of the acorn-barnacle, Megabalanus rosa. Biol Bull. 190:403–409.
  • Karande AA, Gaonkar SN. 1977. Histology and histochemistry of cement glands of Balanus kondakovi. Proc Indian Acad Sci. 86:409–416.
  • Khandeparker L, Anil AC. 2007. Underwater adhesion: the barnacle way. Int J Adhes Adhes. 27:165–172.
  • Lacombe D. 1970. A comparative study of the cement glands in some balanid barnacles (Cirripedia, Balanidae). Biol Bull. 139:164–179.
  • Lacombe D, Liguori VR. 1969. Comparative histological studies of the cement apparatus of Lepas anatifera and Balanus tintinnabulum. Biol Bull. 137:170–180.
  • Lottaz C, Iseli C, Jongeneel CV, Bucher P. 2003. Modeling sequencing errors by combining Hidden Markov models. Bioinformatics. 19:ii103–ii112.
  • Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. 2012. Direct comparisons of Illumina vs Roche 454 Sequencing Technologies on the same microbial community DNA sample. PLoS ONE. 7:e30087.
  • Maki JS, Yule AB, Rittschof D, Mitchell R. 1994. The effect of bacterial films on the temporary adhesion and permanent fixation of cypris larvae, Balanus amphitrite Darwin. Biofouling. 8:121–131.
  • Mardis ER. 2008. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 9:387–402.
  • Marone M, Mozzetti S, De Ritis D, Pierelli L, Scambia G. 2001. Semiquantitative RT-PCR analysis to assess the expression levels of multiple transcripts from the same sample. Biol Proced Online. 3:19–25.
  • Matsumura K, Nagano M, Fusetani N. 1998. Purification of a larval settlement-inducing protein complex (SIPC) of the barnacle, Balanus amphitrite. J Exp Zool. 281:12–20.
  • Metzker ML. 2010. Sequencing technologies – the next generation. Nat Rev Genet. 11:31–46.
  • Mizrachi E, Hefer C, Ranik M, Joubert F, Myburg A. 2010. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics. 11:681.
  • Mori Y, Urushida Y, Nakano M, Uchiyama S, Kamino K. 2007. Calcite-specific coupling protein in barnacle underwater cement. FEBS J. 274:6436–6446.
  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 5:621–628.
  • Naldrett MJ, Kaplan DL. 1997. Characterization of barnacle (Balanus eburneus and B. cenatus) adhesive proteins. Mar Biol. 127:629–635.
  • Okano K, Shimizu K, Satuito C, Fusetani N. 1996. Visualization of cement exocytosis in the cypris cement gland of the barnacle Megabalanus rosa. J Exp Biol. 199:2131–2137.
  • Otani M, Oumi T, Uwai S, Hanyuda T, Prabowo RE, Yamaguchi T, Kawai H. 2007. Occurrence and diversity of barnacles on international ships visiting Osaka Bay, Japan, and the risk of their introduction. Biofouling. 23:277–286.
  • Otness JS, Medcalf DG. 1972. Chemical and physical characterization of barnacle cement. Comp Biochem Phys B. 43:443–449.
  • Passano L. 1960. Molting and its control. In: Waterman TH, editor. The physiology of Crustacea. New York (NY): Academic Press; p. 473–536.
  • Power AM, Klepal W, Zheden V, Jonker J, McEvilly P, Byern J. 2010. Mechanisms of adhesion in adult barnacles. In: Byern J, Grunwald I, editors. Biological adhesive systems. Vienna: Springer; p. 153–168.
  • Relf JM, Chisholm JRS, Kemp GD, Smith VJ. 1999. Purification and characterization of a cysteine-rich 11.5 kDa antibacterial protein from the granular haemocytes of the shore crab, Carcinus maenas. Eur J Biochem. 264:350–357.
  • Roer R, Dillman R. 1984. The structure and calcification of the crustacean cuticle. Am Zool. 24:893–909.
  • Ronaghi M, Uhlén M, Nyrén P. 1998. A sequencing method based on real-time pyrophosphate. Science. 281:363–365.
  • Saroyan JR, Lindner E, Dooley CA, Bleile HR. 1970. Barmacle cement – key to second generation antifouling coatings. Ind Eng Chem Prod Res Dev. 9:122–133.
  • Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol. 26:1135–1145.
  • Sullan RMA, Gunari N, Tanur AE, Chan Y, Dickinson GH, Orihuela B, Rittschof D, Walker GC. 2009. Nanoscale structures and mechanics of barnacle cement. Biofouling. 25:263–275.
  • Sun Y, Du L, Jiang Z, Ding X, Xu H, Yu Y, Zhang Q. 2011. Expression of functional recombinant barnacle cement protein Bacp-20k in Escherichia coli. Paper presented at: Bioinformatics and Biomedical Engineering, (iCBBE); 2011 5th International Conference; Wuhan, China. New York (NY): IEEE; p. 1–4.
  • Sutherland TD, Young JH, Weisman S, Hayashi CY, Merritt DJ. 2010. Insect silk: one name, many materials. Annu Rev Entomol. 55:171–188.
  • Suzuki R, Mori Y, Kamino K, Yamazaki T. 2006. 3D-structure of barnacle cement protein, Mrcp-20k. Pept Sci. 2005:257–258.
  • Townsin RL. 2003. The ship hull fouling penalty. Biofouling. 19:9–15.
  • Urushida Y, Nakano M, Matsuda S, Inoue N, Kanai S, Kitamura N, Nishino T, Kamino K. 2007. Identification and functional characterization of a novel barnacle cement protein. FEBS J. 274:4336–4346.
  • Valluzzi R, Gido SP, Muller W, Kaplan DL. 1999. Orientation of silk III at the air–water interface. Int J Biol Macromol. 24:237–242.
  • Walker G. 1970. The histology, histochemistry and ultrastructure of the cement apparatus of three adult sessile barnacles, Elminius modestus, Balanus balanoides and Balanus hameri. Mar Biol. 7:239–248.
  • Walker G. 1972. The biochemical composition of the cement of two barnacle species, Balanus hameri and Balanus crenatus. J Mar Biol Assoc UK. 52:429–435.
  • Yan X-C, Chen Z-F, Sun J, Matsumura K, Wu RSS, Qian P-Y. 2012. Transcriptomic analysis of neuropeptides and peptide hormones in the barnacle Balanus amphitrite: evidence of roles in larval settlement. PLoS ONE. 7:e46513.
  • Zhang J, Li F, Wang Z, Xiang J. 2007. Cloning and recombinant expression of a crustin-like gene from Chinese shrimp, Fenneropenaeus chinensis. J Biotechnol. 127:605–614.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.