A look behind the screens: Characterization of the HSP70 family during osmotic stress in a non-model crop

Journal of Proteomics

Volumn 119, Issue , 2015, Pages 10-20

  Vanhove, Anne Catherine ^a   Vermaelen, Wesley ^b   Swennen, Rony ^a,c,d   Carpentier, Sebastien Christian ^a,b  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b KU LEUVEN   (Belgium)

^c BIOVERSITY INTERNATIONAL   (Italy)

^d International Institute of Tropical Agriculture   (Tanzania)

Author keywords

HSP70; Non model plant; Protein family; Proteogenomics; Stress

Indexed keywords

CYTOPLASM PROTEIN; HEAT SHOCK PROTEIN 70; ISOPROTEIN; VEGETABLE PROTEIN;

ALLOPOLYPLOIDY; AMINO ACID SEQUENCE; ARABIDOPSIS THALIANA; ARTICLE; BANANA; CHROMOSOME 1; CHROMOSOME 2; CHROMOSOME 6; CHROMOSOME 7; CHROMOSOME 8; CONTROLLED STUDY; CROP; DNA POLYMORPHISM; FAMILY STRESS; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENETIC VARIABILITY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; KARYOTYPE; MERISTEM; MULTIGENE FAMILY; NONHUMAN; OSMOTIC STRESS; PARALOGY; PHYLOGENETIC TREE; PLANT CELL; PLANT CHROMOSOME; PLANT GENOME; PLANT STRESS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FAMILY; PROTEIN SYNTHESIS; PROTEOMICS; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL DIFFERENCE GEL ELECTROPHORESIS; UBIQUITINATION; METABOLISM; MUSA; OSMOTIC PRESSURE;

HSP70 HEAT-SHOCK PROTEINS; MUSA; OSMOTIC PRESSURE; PLANT PROTEINS; PROTEOMICS;

EID: 84922614655     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.01.014     Document Type: Article

References (53)

1. Boston R.S., Viitanen P.V., Vierling E. Molecular chaperones and protein folding in plants. Plant Mol Biol 1996, 32:191-222.
2. Miernyk J.A. The 70kDa stress-related proteins as molecular chaperones. Trends Plant Sci 1997, 2:180-187.
3. Wang W., Vinocur B., Shoseyov O., Altman A. Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 2004, 9:244-252.
4. Swindell W.R., Huebner M., Weber A.P. Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways. BMC Genomics 2007, 8.
5. Jung K.-H., Gho H.-J., Nguyen M., Kim S.-R., An G. Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress. Funct Integr Genomics 2013, 13:391-402.
6. Anderson J.V., Li Q.B., Haskell D.W., Guy C.L. Structural organization of the spinach endoplasmic reticulum-luminal 70-kiloDalton heat-shock cognate gene and expression of 70-kiloDalton heat-shock genes during cold acclimation. Plant Physiol 1994, 104:1359-1370.
7. Liska A.J., Shevchenko A. Expanding the organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications. Proteomics 2003, 3:19-28.
8. Carpentier S.C., Panis B., Vertommen A., Swennen R., Sergeant K., Renaut J., et al. Proteome analysis of non-model plants: a challenging but powerful approach. Mass Spectrom Rev 2008, 27:354-377.
9. Carpentier S.C., Coemans B., Podevin N., Laukens K., Witters E., Matsumura H., et al. Functional genomics in a non-model crop: transcriptomics or proteomics?. Physiol Plant 2008, 133:117-130.
10. Taylor N.L., Heazlewood J.L., Day D.A., Millar A.H. Differential impact of environmental stresses on the pea mitochondrial proteome. Mol Cell Proteomics 2005, 4:1122-1133.
11. Carpentier S.C., Witters E., Laukens K., Van Onckelen H., Swennen R., Panis B. Banana (Musa spp.) as a model to study the meristem proteome: acclimation to osmotic stress. Proteomics 2007, 7:92-105.
12. Vincent D., Ergül A., Bohlman M.C., Tattersall E.A.R., Tillett R.L., Wheatley M.D., et al. Proteomic analysis reveals differences between Vitis vinifera L. cv. Chardonnay and cv. Cabernet Sauvignon and their responses to water deficit and salinity. J Exp Bot 2007, 58:1873-1892.
13. Carpentier S.C., Vertommen A., Swennen R., Witters E., Fortes C., Souza M.T., et al. Sugar-mediated acclimation: the importance of sucrose metabolism in meristems. J Proteome Res 2010, 9:5038-5046.
14. Kjellsen T.D., Shiryaeva L., Schroder W.P., Strimbeck G.R. Proteomics of extreme freezing tolerance in Siberian spruce (Picea obovata). J Proteomics 2010, 73:965-975.
15. Abreu I.A., Farinha A.P., Negrao S., Goncalves N., Fonseca C., Rodrigues M., et al. Coping with abiotic stress: proteome changes for crop improvement. J Proteomics 2013, 93:145-168.
16. FAO 2012.
17. Simmonds N.W. Bananas 1966, Longmans, London.
18. Carpentier S.C., Panis B., Renaut J., Samyn B., Vertommen A., Vanhove A.-C., et al. The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop. Phytochemistry 2011, 72:1243-1250.
19. D'Hont A., Denoeud F., Aury J.-M., Baurens F.-C., Carreel F., Garsmeur O., et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 2012, 488:213-217.
20. Davey M.W., Gudimella R., Harikrishna J.A., Sin L.W., Khalid N., Keulemans J. A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids. BMC Genomics 2013, 14.
21. Droc G., Larivière D., Guignon V., Yahiaoui N., This D., Garsmeur O., et al. The Banana Genome Hub. Database 2013, 2013.
22. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
23. Perrière G., Gouy M. WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 1996, 78:364-369.
24. Tung C.-W., Ho S.-Y. Computational identification of ubiquitylation sites from protein sequences. BMC Bioinforma 2008, 9.
25. Radivojac P., Vacic V., Haynes C., Cocklin R.R., Mohan A., Heyen J.W., et al. Identification, analysis, and prediction of protein ubiquitination sites. Proteins: Struct Funct Bioinf 2010, 78:365-380.
26. Lescot M., Dehais P., Thijs G., Marchal K., Moreau Y., Van de Peer Y., et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 2002, 30:325-327.
27. Higo K., Ugawa Y., Iwamoto M., Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 1999, 27:297-300.
28. Strosse H., Schoofs H., Panis B., Andre E., Reyniers K., Swennen R. Development of embryogenic cell suspensions from shoot meristematic tissue in bananas and plantains (Musa spp.). Plant Sci 2006, 170:104-112.
29. Voets L., Dupré de Boulois H., Renard L., Strullu D.-G., Declerck S. Development of an autotrophic culture system for the in vitro mycorrhization of potato plantlets. FEMS Microbiol Lett 2005, 248:111-118.
30. Carpentier S., Witters E., Laukens K., Swennen R., Panis B. Two-dimensional gel electrophoresis and subsequent protein identification via MALDI-MS/MS; a successful approach to unravel the abiotic stress responses in a non-model organism (Musa spp.). Mol Cell Proteomics 2005, 4:S257.
31. Carpentier S.C., Swennen R., Panis B. Plant protein sample preparation for 2DE. The protein protocols handbook 2009, 107-117. Humana Press, Totowa. J.M. Walker (Ed.).
32. Shevchenko A., Tomas H., Havlis J., Olsen J.V., Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 2006, 1:2856-2860.
33. Li W., Jaroszewski L., Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 2001, 17:282-283.
34. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
35. Vertommen A., Moller A.L.B., Cordewener J.H.G., Swennen R., Panis B., Finnie C., et al. A workflow for peptide-based proteomics in a poorly sequenced plant: a case study on the plasma membrane proteome of banana. J Proteomics 2011, 74:1218-1229.
36. Carpentier S., America T. Proteome analysis of orphan plant species, fact or fiction?. Plant proteomics 2014, 333-346. Humana Press. J.V. Jorrin-Novo, S. Komatsu, W. Weckwerth, S. Wienkoop (Eds.).
37. Rouard M., Guignon V., Aluome C., Laporte M.-A., Droc G., Walde C., et al. GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 2011, 39:D1095-D1102.
38. Renuse S., Chaerkady R., Pandey A. Proteogenomics. Proteomics 2011, 11:620-630.
39. Guy C.L., Li Q.B. The organization and evolution of the spinach stress 70 molecular chaperone gene family. Plant Cell 1998, 10:539-556.
40. Sung D.Y., Kaplan F., Guy C.L. Plant Hsp70 molecular chaperones: protein structure, gene family, expression and function. Physiol Plant 2001, 113:443-451.
41. Schmidt F., Schimd M., Jungblut P.R., Mattowb J., Faciusc A., Pleissner K. Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis. J Am Soc Mass Spectrom 2003, 14:943-995.
42. Yoshimura K., Masuda A., Kuwano M., Yokota A., Akashi K. Programmed proteome response for drought avoidance/tolerance in the root of a C(3) xerophyte (wild watermelon) under water deficits. Plant Cell Physiol 2008, 49:226-241.
43. Lin B.L., Wang J.S., Liu H.C., Chen R.W., Meyer Y., Barakat A., et al. Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana. Cell Stress Chaperones 2001, 6:201-208.
44. Sarkar N.K., Kundnani P., Grover A. Functional analysis of Hsp70 superfamily proteins of rice (Oryza sativa). Cell Stress Chaperones 2013, 18:427-437.
45. Hartl F.U., Bracher A., Hayer-Hartl M. Molecular chaperones in protein folding and proteostasis. Nature 2011, 475:324-332.
46. Thomas D.S., Turner D., Eamus D. Independent effects of the environment on the leaf gas exchange of three banana (Musa spp.) cultivars of different genomic constitution. Sci Hortic 1998, 75:41-57.
47. Robinson J.C., Sauco V.G. Bananas and plantains. Wallingford OX10 8DE 2010, CABI Publishing-CAB International, Oxon, UK. 2nd ed.
48. Vanhove A., Vermaelen W., Panis B., Swennen R., Carpentier S. Screening the banana biodiversity for drought tolerance: can an in vitro growth model and proteomics be used as a tool to discover tolerant varieties and understand homeostasis. Front Plant Sci 2012, 3. [art.nr. 176].
49. Adams K.L., Cronn R., Percifield R., Wendel J.F. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci U S A 2003, 100:4649-4654.
50. Adams K.L., Wendel J.F. Polyploidy and genome evolution in plants. Curr Opin Plant Biol 2005, 8:135-141.
51. De Langhe E., Hribova E., Carpentier S., Dolezel J., Swennen R. Did backcrossing contribute to the origin of hybrid edible bananas?. Ann Bot 2010, 106:849-857.
52. Henry I.M., Carpentier S.C., Pampurova S., Van Hoylandt A., Panis B., Swennen R., et al. Structure and regulation of the Asr gene family in banana. Planta 2011, 234:785-798.
53. Sung D.Y., Vierling E., Guy C.L. Comprehensive expression profile analysis of the Arabidopsis Hsp70 gene family. Plant Physiol 2001, 126:789-800.