LysY: the best marker of prokaryotic lysine biosynthesis through the aminoadipate pathway


Phylogenetic study is a powerful approach for interpreting genomic sequences as well as showing evolutionary relationships. The extremely thermophilic bacterium Thermus thermophilus performs lysine biosynthesis in a unique way. However, the genes involved in this lysine biosynthetic pathway are distributed among many organisms. Which gene is characteristic of this pathway? In this paper, the phylogenetic study reveals that LysY is a key enzyme to the evolution of prokaryotic lysine biosynthesis through the aminoadipate pathway, and is the most useful marker of this pathway. Introduction The extremely thermophilic bacterium Thermus thermophilus synthesizes lysine through the aminoadipate pathway, although all bacteria and plants were believed to synthesize lysine through the diaminopimelate. The first half of the biosynthesis (from 2-oxogultarate to 2-aminoadipate) proceeds in the same manner as that of fungi (Nishida et al. 1999; Nishida and Nishiyama 2000). The reactions were also suggested to be similar to those of leucine biosynthesis and a part of the tricarboxylic acid cycle (Irvin and Bhattacharjee 1998; Nishida et al. 1999; Velasco et al. 2002). The second half of the biosynthesis from 2-aminoadipate to lysine is similar to the conversion of glutamate to ornithine in arginine biosynthesis (Miyazaki et al. 2002). This second half pathway is typical of the lysine biosynthetic pathway of T. thermophilus. The enzymes related to this pathway are LysX, LysY, LysZ, LysJ, and LysK (Nishida et al. 1999; Miyazaki et al. 2001; Miyazaki et al. 2002). Materials and Methods We performed a homology search for each of the five proteins using the BLAST program (Altschul et al. 1990) with the given parameter values on the Kyoto Encyclopedia Genes and Genomes ( or the National Center for Biotechnology Information ( The multiple-alignment of LysY and the 24 extensive homologous sequences was created using the CLUSTAL W (Thompson et al. 1994) on the DNA Data Bank of Japan. The phylogenetic tree by the neighbor-joining method with 1,000 bootstrap analyses was constructed based on the alignment using MEGA version 2.1 (Kumar et al. 2001). Results and Discussion The result of the homology search showed that some prokaryotes had more than two extensive homologous sequences (a value of E < 10) to each of LysX, LysZ, LysJ, or LysK. On the other hand, all organisms that we used in this study, except for Deinococcus radiodurans and T. thermophilus, had a single or no extensive homologous sequence to LysY. The extremely radioresistant bacterium D. radiodurans has two extensive homologous sequences to LysY. Therefore, LysY and the extensive homologous sequences are suggested to be orthologous. We assume that LysY catalyzes the conversion of N-acetylaminoadipate 5-phosphate to N-acetylaminoadipate 5-semialdehyde in lysine biosynthesis of T. thermophilus (Nishida et al. 1999). On the other hand, ArgC catalyzes the conversion of N-acetylglutamate 5-phosphate to N-acetylglutamate 5-semialdehyde in argine biosynthesis. These enzymes share structural and functional similarities and are therefore thought to have diverged from a common ancestor (Nishida et al. 1999). In this study, no organism was found, which had both ArgC and LysY separately, except for D. radiodurans and T. thermophilus. The phylogenetic tree (Fig. 1) showed that LysY clustered together with the gene<lb>products from Aeropyrum pernix, D. radiodurans, Ferroplasma acidarmanus,<lb>Pyrococcus abyssi, P. furiosus, P. horikoshii, Sulfolobus solfataricus, and S. tokodaii.<lb>The bootstrap analysis indicated 98% support values for monophyletic lineage of this<lb>cluster. Deinococcus radiodurans has homologues of the genes involved in the lysine<lb>biosynthetic pathway of T. thermophilus, but these genes are not clustered (Nishida<lb>2001; Nishida and Narumi 2002). However, Aeropyrum, Ferroplasma, Pyrococcus, and<lb>Sulfolobus have a similar gene cluster to that of T. thermophilus (Brinkman et al. 2002).<lb>This suggests that the proteins from these archaea are involved in both arginine and<lb>lysine biosyntheses. On the other hand, the other proteins are suggested to be ArgCs in<lb>arginine biosynthesis. In any case, we conclude that LysY is a key enzyme to the<lb>evolution of prokaryotic lysine biosynthesis through the aminoadipate pathway.<lb>Therefore, LysY is the best marker of prokaryotic lysine biosynthesis through the<lb>aminoadipate pathway. References<lb>Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment<lb>search tool. J Mol Biol 215:403-410 Brinkman AB, Bell SD, Jan Lebbink R, de Vos WM, van der Oost J (2002) The<lb>Sulfolobus solfataricus Lrp-like protein LysM regulates lysine biosynthesis in response<lb>to lysine availability. J Biol Chem 277:29537-29549 Irvin SD, Bhattacharjee JK (1998) A unique fungal lysine biosynthesis enzyme shares a<lb>common ancestor with tricarboxylic acid cycle and leucine biosynthetic enzymes found<lb>in diverse organisms. J Mol Evol 46:401-408 Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary<lb>genetics analysis software. Bioinformatics 17:1244-1245 Miyazaki J, Kobashi N, Fujii T, Nishiyama M, Yamane H (2002) Characterization of a<lb>lysK gene as an argE homolog in Thermus thermophilus HB27. FEBS Lett 512:269-274 Miyazaki J, Kobashi N, Nishiyama M, Yamane H (2001) Functional and evolutionary<lb>relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through<lb>α-aminoadipate. J Bacteriol 183:5067-5073 Nishida H (2001) Distribution of genes for lysine biosynthesis through the aminoadipate<lb>pathway among prokaryotic genomes. Bioinformatics 17:189-191 Nishida H, Narumi I (2002) Disruption analysis of DR1420 and/or DR1758 in the<lb>extremely radioresistant bacterium Deinococcus radiodurans. Microbiology<lb>148:2911-2914 Nishida H, Nishiyama M (2000) What is characteristic of fungal lysine synthesis<lb>through the α-aminoadipate pathway? J Mol Evol 51:299-302 Nishida H, Nishiyama M, Kobashi N, Kosuge T, Hoshino T, Yamane H (1999) A<lb>prokaryotic gene cluster involved in synthesis of lysine through the amino adipate<lb>pathway: a key to the evolution of amino acid biosynthesis. Genome Res 9:1175-1183 Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity<lb>of progressive multiple sequence alignment through sequence weighting,<lb>position-specific gap penalties and weight matrix choice. Nucleic Acids Res<lb>22:4673-4680 Velasco AM, Leguina JI, Lazcano A (2002) Molecular evolution of the lysine<lb>biosynthetic pathways. J Mol Evol 55:445-459

Cite this paper

@inproceedings{Nishida2003LysYTB, title={LysY: the best marker of prokaryotic lysine biosynthesis through the aminoadipate pathway}, author={Hiromi Nishida and Makoto Nishiyama}, year={2003} }