Proteins of Unknown Biochemical Function: A Persistent Problem and a Roadmap to Help Overcome It.
The number of sequenced genomes is rapidly increasing, but functional annotation of the genes in these genomes lags far behind. Even in Arabidopsis (Arabidopsis thaliana), only approximately 40% of enzyme- and transporter-encoding genes have credible functional annotations, and this number is even lower in nonmodel plants. Functional characterization of unknown genes is a challenge, but various databases (e.g. for protein localization and coexpression) can be mined to provide clues. If homologous microbial genes exist-and about one-half the genes encoding unknown enzymes and transporters in Arabidopsis have microbial homologs-cross-kingdom comparative genomics can powerfully complement plant-based data. Multiple lines of evidence can strengthen predictions and warrant experimental characterization. In some cases, relatively quick tests in genetically tractable microbes can determine whether a prediction merits biochemical validation, which is costly and demands specialized skills.
Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611.
Thomas D
TD
Niehaus
Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611.
Antje M K
AM
Thamm
Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611.
Valérie
V
de Crécy-Lagard
Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611 adha@ufl.edu.
Andrew D
http://orcid.org/0000-0003-2585-9340
AD
Hanson
D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D010944:Plants / Q000235:genetics / Q000378:metabolism*; D021381:Protein Transport; D049490:Systems Biology / Q000379:methods; D059467:Transcriptome
D010940:Plant Proteins