Bioinformatics As a Tool for Assessing the Quality of Sub-cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics As a Test Case

Overview

Journal Bioinform Biol Insights

Publisher Sage Publications

Specialty Biology

Date 2010 Feb 9

PMID 20140071

Citations 19

Authors

Helene San Clemente

Rafael Pont-Lezica

Elisabeth Jamet

Affiliations

Soon will be listed here.

Abstract

Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB (http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).

Citing Articles

Plant Cell Wall Proteomes: The Core of Conserved Protein Families and the Case of Non-Canonical Proteins.

San Clemente H, Kolkas H, Canut H, Jamet E Int J Mol Sci. 2022; 23(8).

PMID: 35457091 PMC: 9029284. DOI: 10.3390/ijms23084273.

Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives.

Taylor D, Bishop D Int J Mol Sci. 2022; 23(3).

PMID: 35163441 PMC: 8836245. DOI: 10.3390/ijms23031517.

The Cell Wall Proteome of Reveals Specificities Compared to Those of Flowering Plants.

Kolkas H, Balliau T, Chourre J, Zivy M, Canut H, Jamet E Front Plant Sci. 2022; 12:765846.

PMID: 35095945 PMC: 8792609. DOI: 10.3389/fpls.2021.765846.

Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Infection.

Petrova N, Mokshina N Plants (Basel). 2022; 11(2).

PMID: 35050051 PMC: 8779086. DOI: 10.3390/plants11020163.

Sorghum's Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review.

Ngara R, Goche T, Swanevelder D, Chivasa S Life (Basel). 2021; 11(7).

PMID: 34357076 PMC: 8305457. DOI: 10.3390/life11070704.

References

Boudart G, Jamet E, Rossignol M, Lafitte C, Borderies G, Jauneau A . Cell wall proteins in apoplastic fluids of Arabidopsis thaliana rosettes: identification by mass spectrometry and bioinformatics. Proteomics. 2004; 5(1):212-21. DOI: 10.1002/pmic.200400882. View

Hadlington J, Denecke J . Sorting of soluble proteins in the secretory pathway of plants. Curr Opin Plant Biol. 2000; 3(6):461-8. DOI: 10.1016/s1369-5266(00)00114-x. View

Oh I, Park A, Bae M, Kwon S, Kim Y, Lee J . Secretome analysis reveals an Arabidopsis lipase involved in defense against Alternaria brassicicola. Plant Cell. 2005; 17(10):2832-47. PMC: 1242276. DOI: 10.1105/tpc.105.034819. View

Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R . InterProScan: protein domains identifier. Nucleic Acids Res. 2005; 33(Web Server issue):W116-20. PMC: 1160203. DOI: 10.1093/nar/gki442. View

Roudier F, Fernandez A, Fujita M, Himmelspach R, Borner G, Schindelman G . COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. Plant Cell. 2005; 17(6):1749-63. PMC: 1143074. DOI: 10.1105/tpc.105.031732. View

Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M . ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol. 2003; 131(1):16-26. PMC: 166783. DOI: 10.1104/pp.011577. View

Shiu S, Bleecker A . Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci U S A. 2001; 98(19):10763-8. PMC: 58549. DOI: 10.1073/pnas.181141598. View

Lee S, Saravanan R, Damasceno C, Yamane H, Kim B, Rose J . Digging deeper into the plant cell wall proteome. Plant Physiol Biochem. 2005; 42(12):979-88. DOI: 10.1016/j.plaphy.2004.10.014. View

Jamet E, Albenne C, Boudart G, Irshad M, Canut H, Pont-Lezica R . Recent advances in plant cell wall proteomics. Proteomics. 2008; 8(4):893-908. DOI: 10.1002/pmic.200700938. View

10.

Watson B, Lei Z, Dixon R, Sumner L . Proteomics of Medicago sativa cell walls. Phytochemistry. 2004; 65(12):1709-20. DOI: 10.1016/j.phytochem.2004.04.026. View

11.

Liu C, Mehdy M . A nonclassical arabinogalactan protein gene highly expressed in vascular tissues, AGP31, is transcriptionally repressed by methyl jasmonic acid in Arabidopsis. Plant Physiol. 2007; 145(3):863-74. PMC: 2048811. DOI: 10.1104/pp.107.102657. View

12.

van Hengel A, Roberts K . AtAGP30, an arabinogalactan-protein in the cell walls of the primary root, plays a role in root regeneration and seed germination. Plant J. 2003; 36(2):256-70. DOI: 10.1046/j.1365-313x.2003.01874.x. View

13.

Chivasa S, Ndimba B, Simon W, Robertson D, Yu X, Knox J . Proteomic analysis of the Arabidopsis thaliana cell wall. Electrophoresis. 2002; 23(11):1754-65. DOI: 10.1002/1522-2683(200206)23:11<1754::AID-ELPS1754>3.0.CO;2-E. View

14.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

15.

Schultz C, Rumsewicz M, Johnson K, Jones B, Gaspar Y, Bacic A . Using genomic resources to guide research directions. The arabinogalactan protein gene family as a test case. Plant Physiol. 2002; 129(4):1448-63. PMC: 166734. DOI: 10.1104/pp.003459. View

16.

McCaig B, Meagher R, Dean J . Gene structure and molecular analysis of the laccase-like multicopper oxidase (LMCO) gene family in Arabidopsis thaliana. Planta. 2005; 221(5):619-36. DOI: 10.1007/s00425-004-1472-6. View

17.

Pourcel L, Routaboul J, Kerhoas L, Caboche M, Lepiniec L, Debeaujon I . TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat. Plant Cell. 2005; 17(11):2966-80. PMC: 1276023. DOI: 10.1105/tpc.105.035154. View

18.

Irshad M, Canut H, Borderies G, Pont-Lezica R, Jamet E . A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: confirmed actors and newcomers. BMC Plant Biol. 2008; 8:94. PMC: 2551616. DOI: 10.1186/1471-2229-8-94. View

19.

Jacobs J, Roe J . SKS6, a multicopper oxidase-like gene, participates in cotyledon vascular patterning during Arabidopsis thaliana development. Planta. 2005; 222(4):652-66. DOI: 10.1007/s00425-005-0012-3. View

20.

Fowler T, Bernhardt C, Tierney M . Characterization and expression of four proline-rich cell wall protein genes in Arabidopsis encoding two distinct subsets of multiple domain proteins. Plant Physiol. 1999; 121(4):1081-92. PMC: 59476. DOI: 10.1104/pp.121.4.1081. View