Book of Abstracts: Albany 2005
Identification of Missing tRNA Modification Genes by Comparative Genomics
Genome sequencing efforts of the last decade have revealed how little is known about the relationship between DNA sequences and biological functions. In the best genetically characterized organisms, a third of the genes have no assigned function. Systematic approaches such as functional and structural genomics can lead to elucidation of some functions, especially if they are functions similar to currently understood activities. However, analysis of the literature reveals many known enzymatic activities or pathways for which the cognate genes remain unknown. Identification of "missing" genes by comparative genomics is a powerful way to link genes to function. The development of bioinformatic platforms that are freely available such as SEED, STRING, or COG have now allowed such strategies to become more efficient.
Post-transcriptional modification of the four canonical nucleosides is characteristic of both tRNA and rRNA. Some modifications are specific to one kingdom while others are universal and roughly 50% of the RNA modification genes are still to be identified. By combining occurrence-profiling, chromosome-clustering and homology searches, candidates for missing functions can be proposed. These predictions are then tested experimentally. Using such methods we identified several new families such as the tRNA 5,6-dihydrouridine synthase family (J. Biol. Chem 277, 25090-25095 (2002)) involved in a very common modification found in all kingdoms of life. More recently the whole pathway for synthesis of the queuine precursor, 7-aminoethyl 7-deazaguanine (preq1) from GTP was discovered (J. Biol. Chem 279, 6280-6285 (2004)). The presence of orthologs of these genes in Archaea suggest the biosynthesis pathway for the common precursor of queuosine and archaeosine, 7-cyano-7-deazaguanine (preQ0) was discovered. This pathway might have also been utilized by Streptomyces sp. to synthesize the structurally related antibiotics toyacamycin and tubercidin. Gene candidates for other tRNA modifications enzymes involved in the synthesis of Wyeosine, and N6-threonylcarbamoyladenosine will be discussed. The comparative genomic strategies presented in these studies can be used to find missing genes in other pathways.
Valerie de Crecy-Lagard
Department of Microbiology