Proteins of unknown biochemical function: A persistent problem and a roadmap to help overcome it

Plant Physiology

Volumn 169, Issue 3, 2015, Pages 1436-1442

  Niehaus, Thomas D ^a   Thamm, Antje M K ^a   De Crécy Lagard, Valérie ^a   Hanson, Andrew D ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT PROTEIN; TRANSCRIPTOME;

BIOLOGY; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; GENOMICS; METABOLISM; PHYSIOLOGY; PLANT; PLANT GENOME; PROCEDURES; PROTEIN TRANSPORT; SYSTEMS BIOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; GENOMICS; METABOLIC NETWORKS AND PATHWAYS; PLANT PROTEINS; PLANTS; PROTEIN TRANSPORT; SYSTEMS BIOLOGY; TRANSCRIPTOME;

EID: 84946216240     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.15.00959     Document Type: Article

References (31)

1. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815
2. Barchi L, Lanteri S, Portis E, Valè G, Volante A, Pulcini L, Ciriaci T, Acciarri N, Barbierato V, Toppino L, et al (2012) A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. PLoS One 7: e43740
3. Bessman MJ, Frick DN, O’Handley SF (1996) The MutT proteins or “Nudix” hydrolases, a family of versatile, widely distributed, “housecleaning” enzymes. J Biol Chem 271: 25059–25062
4. Bradbury LM, Niehaus TD, Hanson AD (2013) Comparative genomics approaches to understanding and manipulating plant metabolism. Curr Opin Biotechnol 24: 278–284
5. Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, et al (2014) MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol 164: 513–524
6. Chory J, Ecker JR, Briggs S, Caboche M, Coruzzi GM, Cook D, Dangl J, Grant S, Guerinot ML, Henikoff S, et al (2000) National Science Foundation-Sponsored Workshop Report: “The 2010 Project” functional genomics and the virtual plant: a blueprint for understanding how plants are built and how to improve them. Plant Physiol 123: 423–426
7. de Crécy-Lagard V, Hanson AD (2007) Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol 15: 563–570
8. Earnshaw WC (2013) Deducing protein function by forensic integrative cell biology. PLoS Biol 11: e1001742
9. Ferro M, Brugière S, Salvi D, Seigneurin-Berny D, Court M, Moyet L, Ramus C, Miras S, Mellal M, Le Gall S, et al (2010) ATCHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics 9: 1063–1084
10. Fischer M, Römisch W, Saller S, Illarionov B, Richter G, Rohdich F, Eisenreich W, Bacher A (2004) Evolution of vitamin B2 biosynthesis: structural and functional similarity between pyrimidine deaminases of eubacterial and plant origin. J Biol Chem 279: 36299–36308
11. Foor F, Brown GM (1975) Purification and properties of guanosine triphosphate cyclohydrolase II from Escherichia coli. J Biol Chem 250: 3545–3551
12. Frelin O, Huang L, Hasnain G, Jeffryes JG, Ziemak MJ, Rocca JR, Wang B, Rice J, Roje S, Yurgel SN, et al (2015) A directed-overflow and damagecontrol N-glycosidase in riboflavin biosynthesis. Biochem J 466: 137–145
13. Frishman D (2007) Protein annotation at genomic scale: the current status. Chem Rev 107: 3448–3466
14. Gerdes S, Lerma-Ortiz C, Frelin O, Seaver SM, Henry CS, de Crécy- Lagard V, Hanson AD (2012) Plant B vitamin pathways and their compartmentation: a guide for the perplexed. J Exp Bot 63: 5379–5395
15. Goyer A, Hasnain G, Frelin O, Ralat MA, Gregory III JF, Hanson AD (2013) A cross-kingdom Nudix enzyme that pre-empts damage in thiamin metabolism. Biochem J 454: 533–542
16. Hanson AD, Pribat A, Waller JC, de Crécy-Lagard V (2010) ‘Unknown’ proteins and ‘orphan’ enzymes: the missing half of the engineering parts list–and how to find it. Biochem J 425: 1–11
17. Isbell HS, Frush HL (1958) Mutarotation, hydrolysis, and rearrangement reactions of glycosylamines. J Org Chem 23: 1309–1319
18. Ischebeck T, Zbierzak AM, Kanwischer M, Dörmann P (2006) A salvage pathway for phytol metabolism in Arabidopsis. J Biol Chem 281: 2470–2477
19. Munanairi A, O’Banion SK, Gamble R, Breuer E, Harris AW, Sandwick RK (2007) The multiple Maillard reactions of ribose and deoxyribose sugars and sugar phosphates. Carbohydr Res 342: 2575–2592
20. Naponelli V, Noiriel A, Ziemak MJ, Beverley SM, Lye LF, Plume AM, Botella JR, Loizeau K, Ravanel S, Rébeillé F, et al (2008) Phylogenomic and functional analysis of pterin-4a-carbinolamine dehydratase family (COG2154) proteins in plants and microorganisms. Plant Physiol 146: 1515–1527
21. Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7: 238–251
22. Ouyang M, Ma J, Zou M, Guo J, Wang L, Lu C, Zhang L (2010) The photosensitive phs1 mutant is impaired in the riboflavin biogenesis pathway. J Plant Physiol 167: 1466–1476
23. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, et al (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691–5702
24. Politis DN, Romano JP, Wolf M (1999) Subsampling, Ed 1. Springer Science & Business Media, New York
25. Rhee SY, Mutwil M (2014) Towards revealing the functions of all genes in plants. Trends Plant Sci 19: 212–221
26. Schnoes AM, Brown SD, Dodevski I, Babbitt PC (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5: e1000605
27. Seaver SMD, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain G, Niehaus TD, El Yacoubi B, Pasternak S, et al (2014) Highthroughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci USA 111: 9645–9650
28. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta- Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43: D447–D452
29. Tylicki A, Czerniecki J, Dobrzyn P, Matanowska A, Olechno A, Strumilo S (2005) Modification of thiamine pyrophosphate dependent enzyme activity by oxythiamine in Saccharomyces cerevisiae cells. Can J Microbiol 51: 833–839
30. Wheatley NM, Sundberg CD, Gidaniyan SD, Cascio D, Yeates TO (2014) Structure and identification of a pterin dehydratase-like protein as a ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) assembly factor in the a-carboxysome. J Biol Chem 289: 7973–7981
31. Woebken D, Teeling H, Wecker P, Dumitriu A, Kostadinov I, Delong EF, Amann R, Glöckner FO (2007) Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their crosscomparison with planctomycete genomes. ISME J 1: 419–435