Fine-tuned method to extract high purified proteins from the seagrass Halophila stipulacea to be used for proteome analyses

References

• Boudouresque CF, Bernard G, Pergent G, Shimabukuro H, Verlaque M. 2009. Regression of Mediterranean seagrasses caused by natural processes and anthropogenic disturbances and stress: a critical review. Bot Mar. 52:395–418.
   Web of Science ®Google Scholar
• Brahim MB, Mabrouk L, Hamza A, Jribi J. 2020. Comparison of spatial scale variability of shoot density and epiphytic leaf assemblages of Halophila stipulacea and Cymodocea nodosa on the Eastern Coast of Tunisia. Plant Biosystems. 154 (3):413–426.
   Web of Science ®Google Scholar
• Carbone M, Gavagnin M, Mollo E, Bidello M, Roussis V, Cimino G. 2008. Further syphonosides from the sea hare Syphonota geographica and the sea-grass Halophila stipulacea. Tetrahedron. 64(1):191–196.
   Web of Science ®Google Scholar
• Carvalho PC, Lima DB, Leprevost FV, Santos MDM, Fischer JSG, Aquino PF, Moresco JJ, Yates JR, Barbosa VC. 2016. Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0. Nat Protoc. 11(1):102–117.
   PubMed Web of Science ®Google Scholar
• Dattolo E, Gu J, Bayer PE, Mazzuca S, Serra IA, Spadafora A, Bernardo L, Natali L, Cavallini A, Procaccini G. 2013. Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles. Front Plant Sci. 4:195
   PubMed Web of Science ®Google Scholar
• Eriksson J, Chait BT, Fenyö D. 2000. A statistical basis for testing the significance of mass spectrometric protein identification results. Anal Chem. 72(5):999–1005.
   PubMed Web of Science ®Google Scholar
• Galasso G, Conti F, Peruzzi L, Ardenghi NMG, Banfi E, Celesti-Grapow L, Albano A, Alessandrini A, Bacchetta G, Ballelli S, et al. 2018. An updated checklist of the vascular flora alien to Italy. Plant Biosyst. 152(3):556–592.
   Web of Science ®Google Scholar
• Gavagnin M, Carbone M, Amodeo P, Mollo E, Vitale RM, Roussis V, Cimino G. 2007. Structure and absolute stereochemistry of syphonoside, a unique macrocyclic glycoterpenoid from marine organisms. J Org Chem. 72(15):5625–5630.
   PubMed Web of Science ®Google Scholar
• Georgiou D, Alexandre A, Luis J, Santos R. 2016. Temperature is not a limiting factor for the expansion of Halophila stipulacea throughout the Mediterranean Sea. Mar Ecol Prog Ser. 544:159–167.
   Web of Science ®Google Scholar
• Jiang Z, Kumar M, Padula MP, Pernice M, Kahlke T, Kim M, Ralph PJ. 2017. Development of an efficient protein extraction method compatible with LC-MS/MS for proteome mapping in two Australian seagrasses Zostera muelleri and Posidonia australis. Front Plant Sci. 8:1416
   PubMed Web of Science ®Google Scholar
• Keller A, Nesvizhskii AI, Kolker E, Aebersold R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 74(20):5383–5392. PMID: 12403597.
   PubMed Web of Science ®Google Scholar
• Kohn T, Rast P, Kallscheuer N, Wiegand S, Boedeker C, Jetten MSM, Jeske O, Vollmers J, Kaster AK, Rohde M, et al. 2020. The microbiome of Posidonia oceanica seagrass leaves can be dominated by Planctomycetes. Front Microbiol. 11:1458
   PubMed Web of Science ®Google Scholar
• Kruse CPS, Basu P, Luesse DR, Wyatt SE. 2017. Transcriptome and proteome responses in RNAlater preserved tissue of Arabidopsis thaliana. PLoS One. 12(4):e0175943
   PubMed Web of Science ®Google Scholar
• Kumar M, Padula MP, Davey P, Pernice M, Jiang Z, Sablok G, Contreras-Porcia L, Ralph PJ. 2017. Proteome analysis reveals extensive light stress-response reprogramming in the seagrass Zostera muelleri (Alismatales, Zosteraceae) Metabolism. Front Plant Sci. 7:2023
   PubMed Web of Science ®Google Scholar
• Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227(5259):680–685.
   PubMed Web of Science ®Google Scholar
• Lucas-Elío P, Goodwin L, Woyke T, Pitluck S, Nolan M, Kyrpides NC, Detter JC, Copeland A, Lu M, Bruce D, et al. 2012. Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)). Stand Genomic Sci. 7(1):31–43.
   PubMed Web of Science ®Google Scholar
• Mazzuca S, Bjork M, Beer S, Felisberto P, Gobert S, Procaccini G, Runcie J, Silva J, Borges A, Brunet C, et al. 2013. Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism, and ecosystem carbon fluxes. Front Plant Sci. 4:38
   PubMed Web of Science ®Google Scholar
• Mazzuca S, Spadafora A, Filadoro D, Vannini C, Marsoni M, Cozza R, Bracale M, Pangaro T, Innocenti AM. 2009. Seagrass light acclimation: 2-DE protein analysis in Posidonia leaves grown in chronic low light conditions. J Exp Mar Biol Ecol . 374(2):113–122.
   Web of Science ®Google Scholar
• Migliore L, Rotini A, Randazzo D, Albanese NN, Giallongo A. 2007. Phenols content and 2-D electrophoresis protein pattern: a promising tool to monitor Posidonia meadows health state. BMC Ecol. 7:6.
   PubMedGoogle Scholar
• Mollo E, Cimino G, Ghiselin MT. 2015. Alien biomolecules: a new challenge for natural product chemists. Biol Invasions. 17(3):941–950.
   Web of Science ®Google Scholar
• Mollo E, Gavagnin M, Carbone M, Castelluccio F, Pozone F, Roussis V, Templado J, Ghiselin M, Cimino G. 2008. Factors promoting marine invasions: a chemoecological approach. Proc Natl Acad Sci U S A. 105(12):4582–4586.
   PubMed Web of Science ®Google Scholar
• Nesvizhskii AI, Keller A, Kolker E, Aebersold R. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem. 75(17):4646–4658.
   PubMed Web of Science ®Google Scholar
• Nguyen HM, Savva I, Kleitou P, Kletou D, Lima F, Sapir Y, Winters G. 2020a. Seasonal dynamics of native and invasive Halophila stipulacea populations. Aquat. Bot. 162:103205.
   Web of Science ®Google Scholar
• Nguyen HM, Yadav NS, Barak S, Lima FP, Sapir Y, Winters G. 2020b. Responses of invasive and native populations of the seagrass Halophila stipulacea to simulated climate change. Front Mar Sci. 6:812.
   Web of Science ®Google Scholar
• Piro A, Marín-Guirao L, Serra IA, Spadafora A, Sandoval-Gil JM, Bernardeau-Esteller J, Fernandez JM, Mazzuca S. 2015. The modulation of leaf metabolism plays a role in salt tolerance of Cymodocea nodosa exposed to hypersaline stress in mesocosms. Front Plant Sci. 6:464.
   PubMed Web of Science ®Google Scholar
• Piro A, Bernardo L, Serra IA, Barrote I, Olivé I, Costa MM, Lucini L, Santos R, Mazzuca S, Silva J. 2020. Leaf proteome modulation and cytological features of seagrass Cymodocea nodosa in response to long-term high CO2 exposure in volcanic vents. Sci Rep. 10:22332. https://doi.org/10.1038/s41598-020-78764-7
   Google Scholar
• Procaccini G, Acunto S, Famà P, Maltagliati F. 1999. Structural; morphological and genetic variability in Halophila stipulacea (Hydrocharitaceae) populations in the western Mediterranean. Mar. Biol. 135(1):181–189.
   Web of Science ®Google Scholar
• Procaccini G, Ruocco M, Marín-Guirao L, Dattolo E, Brunet C, D’Esposito D, Lauritano C, Mazzuca S, Serra IA, Bernardo L, et al. 2017. Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica. Sci Rep. 7:42890.,
   PubMed Web of Science ®Google Scholar
• Sablok G, Hayward R, Davey PA, Santos RP, Schliep M, Larkum A, Pernice M, Dolferus R, Ralph PJ. 2018. SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants. Sci Rep. 8(1):2749.
   PubMedGoogle Scholar
• Saito MA, Bulygin VV, Moran DM, Taylor C, Scholin C. 2011. Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Front Microbiol. 2:215.
   PubMed Web of Science ®Google Scholar
• Serra IA, Mazzuca S. 2011. Posidonia oceanica: from ecological status to genetic and proteomic resources. In: Pirog RS, editor. Seagrass: ecology, uses and threats. New York (NY): Nova Sciences Publisher, Inc; p. 71–116. Chapter 2.
   Google Scholar
• Shevchenko A, Tomas H, Havli J, Olsen JV, Mann M. 2006. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc. 1(6):2856–2860.
   PubMed Web of Science ®Google Scholar
• Spadafora A, Filadoro D, Mazzuca S, Bracale M, Marsoni M, Cardilio M, Innocenti AM. 2008. 2-DE polypeptide mapping of Posidonia oceanica leaves; a molecular tool for marine environment studies. Plant Biosyst. 142(2):213–218.
   Web of Science ®Google Scholar
• Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. 2003. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13(9):2129–2141.
   PubMed Web of Science ®Google Scholar
• Tsakogiannis A, Manousaki T, Anagnostopoulou V, Stavroulaki M, Apostolaki ET. 2020. The importance of genomics for deciphering the invasion success of the seagrass Halophila stipulacea in the changing Mediterranean Sea. Diversity. 12(7):263.
   Google Scholar
• Weidner S, Arnold W, Stackebrandt E, Pühler A. 2000. Phylogenetic analysis of bacterial communities associated with leaves of the seagrass Halophila stipulacea by a culture-independent small subunit rRNA gene approach. Microb Ecol. 39(1):22–31.
   PubMed Web of Science ®Google Scholar
• Winters G, Beer S, Willette DA, Viana IG, Chiquillo KL, Beca-Carretero P, Villamayor B, Azcárate-García T, Shem-Tov R, Mwabvu B, et al. 2020. The tropical seagrass Halophila stipulacea: reviewing what we know from its native and invasive habitats; alongside identifying knowledge gaps. Front Mar Sci. 7:300.
   Web of Science ®Google Scholar