IUBMB Life, 49: 121 – 123, 2000 Copyright c ° 2000 IUBMB 1521-6543/00 $12.00 + .00 Original Research Article Lessons From Sequenced Genomes. Overlapping Genes in Methanococcus jannaschii ? Maciej Szymanski and Jan Barciszewski Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland Summary This paper describes our nding on overlapping genes in Metha- nococcus jannaschii genome. We found that one of the open reading frames (ORFs) within the M. jannaschii genome contains the nu- cleotide sequence of tRNA Ser , which raises a serious question of the correctness of the initiation codon assignment for that ORF. We suggest that there are two other possible AUG initiation codons downstream from the TTG triplet, which was initially considered as a translation start site. Only one of the AUG triplets is preceded by the Shine – Dalgarno sequence that seems to be required for binding the ribosome and initiation of translation. IUBMB Life, 49: 121 – 123, 2000 Keywords Genome analysis; initiation codons; Methanococcus jannaschii ; tRNA Ser . INTRODUCTION Advances in DNA sequencing technology have enabled the determination of several complete microbial genomes within past few years. Thus far » 30 are already known, and > 50 are in the process of being completed (1). The high-throughpu t se- quencing and analysis of the collected data will provide informa- tion on context and evolutionary distance of organisms as well as plausible hypotheses on the functioning of particular genes, ranging from certain to possible (2, 3). Generally, that approach illustrates to what extent an automated computational sequence analysis can be rapid, exhaustive, and in many cases accurate, to the extent that can be reached through intensive work by sequence analysis experts (4). However, that is not always the case. Analysis of the genomes of several microbes has led to the conclusion that some of them are lacking important housekeep- ing genes, e.g., aminoacyl-tRNA synthetases (5, 6). The most Received 14 July 1999; accepted 17 December 1999. Address correspondence to Prof. dr hab. Jan Barciszewski. Fax: (48 61) 852 0532; E-mail: jbarcisz@ibch.poznan.pl striking nding was that the genome of Methanococcus jan- naschi is missing ve aminoacyl-tRNA synthetases, those spe- cic for glutamine, asparagine, methionine, cysteine, and ly- sine (7 ). Whereas Gln-tRNA and Asn-tRNA might possibly be formed by amidation of the glutamate and aspartate attached to tRNA by GluRS and AspRS, respectively (5, 6), no such mech- anism is available for MetRS, CysRS, and LysRS. Recently, lysine-tRNA synthetase has been identied in the closely re- lated species, M. maripaludis. It does not, however, show any similarity to other lysine-tRNA synthetases, which belong to class I, but instead seems to be a class II synthetase (8, 9). EXPERIMENTAL PROCEDURE The M. jannaschi genome sequence was taken from The Insti- tute of Genomic Research (TIGR) data (1). The other accession number to GENBANK nucleotide sequences are shown in the legend to Fig. 2. RESULTS AND DISCUSSION We were interested to check whether other M. jannaschii genes involved in protein synthesis showed differences in com- parison with other organisms. As an example, we chose the genes for transfer RNAs. Detailed inspection of the M. jan- naschii genome revealed that one of the predicted coding re- gions described in TIGR database as MJ1364, encoding a 487 – amino acid protein contains in-frame a gene for tRNA Ser (GCU) (Fig. 1). According to the accompanying description of the MJ1364, a putative open reading frame (ORF) was identied on the basis of sequence similarity (> 50%) at the protein level to the conserved hypothetical protein from Methanobacterium thermoautotroph- icum. However, that region of homology involves amino acids 121 –345 and does not contain the sequence for the tRNA gene. The tRNA gene nucleotide sequence starts at position 12 downstream of the initiation codon (TTG) of MJ1364 and spans 121