Genomic Analysis of Aminotransferases in Arabidopsis thaliana

Abstract

Aminotransferases are an important and diverse group of proteins. Of the approximately 25,000 predicted proteins in the Arabidopsis proteome, it is estimated that 4,000 are involved in cellular metabolism. Sequence analyses predict that roughly one percent of the “metabolism” sequences of Arabidopsis encode aminotransferases. Many plant aminotransferase genes have been identified, and their corresponding gene products have been localized and characterized. These studies have implicated aminotransferase reactions in a diverse variety of pathways in plants, including such primary metabolic pathways as amino acid biosynthesis and catabolism, photorespiration, and vitamin biosynthesis, as well as carbon and nitrogen shuttles, and plant stress responses. Thus, these enzymes may be reasonable targets for metabolic engineering to produce crop varieties with enhanced stress resistance and nutrient content. In addition, several aminotransferases that are absent from animals may be excellent targets for herbicides. The first part of this review focuses on recent progress on the identification and characterization of aminotransferases from Arabidopsis and other plants. There is still much to learn about plant aminotransferases; in Arabidopsis more than 40% of the aminotransferase-like sequences remain uncharacterized. The second part of this review discusses uncharacterized aminotransferase-like sequences in the Arabidopsis genome. Although it is not yet possible to predict the reactions catalyzed by these uncharacterized aminotransferases based on sequence alone, potential functions of these putative aminotransferases are discussed in light of sequence motifs, publicly available transcript expression data, and sequence similarity to characterized homologs from other organisms.

Keywords:

• Arabidopsis genome
• 2-oxoacid
• plant aminotransferase
• pyridoxal-5′-phosphate
• transaminase.

ACKNOWLEDGEMENTS

We thank Dr. Eran Pichersky for his continued encouragement and interest in this work. We also thank Drs. Jeff Landgraf and Curtis Wilkerson for helpful tips and suggestions for the microarray analysis. A. H. Liepman was supported in part by a fellowship from the University of Michigan Cellular Biotechnology Training Program (NIH-GM08353).

Notes

¹These sequences are exact duplicates.

²This uncharacterized gene encodes a protein with 85% identity/96% similarity to PSAT1.

∗Putative ortholog characterized in another plant.

∗∗PSORT/TargetP predicted localization.

∗Truncated signature (less than 50%).

∗∗(+) indicates presence of EST in NCBI database (www.ncbi.nlm.nih.gov/), MPSS signal (dbixs001.dbi.udel.edu/MPSS4/java.html), or microarray signal (genome-www5.stanford.edu/MicroArray/SMD/ or pfgweb.gsc.riken.go.jp/pub_data/seki002.html); (−) indicates no transcript detected in these datasets.

¹Aromatic amino acid aminotransferase from Pyrococcus horikoshii (PDB ID: 1DJU).

²Aspartate aminotransferase from Thermus thermophilus (PDB ID: 1BKG).

³Tyrosine aminotransferase from Trypanosoma cruzi (PDB ID: 1BW0).

⁴Dialkylglycine decarboxylase from Burkholderia cepacia (PDB ID: 1D7U).

⁵Diaminopelargonate aminotransferase from Escherichia coli (PDB ID: 1DTY).

⁶Human mitochondrial branched chain amino acid aminotransferase (PDB ID: 1EKF).

⁷Branched chain amino acid aminotransferase from Escherichia coli (PDB ID: 1I1K).

⁸D-amino acid aminotransferase from thermophilic Bacillus sp. (PDB ID: 3DAA).

^aAminotransferase I/II (PFAM 00155).

^bCys/Met metabolism PLP-dependent enzyme (PFAM 01053).

^cDegT/DnrJ/EryC1/StrS family (PFAM 01041).

^dOrn/Lys/Arg decarboxylase (PFAM 01276).

^eAminotransferase III (PFAM 00202).

^fAminotransferase IV (PFAM 01063).