Phylogenetic analysis of methionine synthesis genes from Thalassiosira pseudonana

Abstract

Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. The sulfate assimilation and methionine synthesis pathways provide S-containing amino acids for the synthesis of proteins and a range of metabolites such as dimethylsulfoniopropionate. To obtain an insight into the localization and organization of the sulfur metabolism pathways we surveyed the genome of Thalassiosira pseudonana-a model organism for diatom research. We have identified and annotated genes for enzymes involved in respective pathways. Protein localization was predicted using similarities to known signal peptide motifs. We performed detailed phylogenetic analyses of enzymes involved in sulfate uptake/reduction and methionine metabolism. Moreover, we have found in up-stream sequences of studied diatoms methionine biosynthesis genes a conserved motif, which shows similarity to the Met31, a cis-motif regulating expression of methionine biosynthesis genes in yeast.

Keywords: Diatoms; Methionine synthesis; Phylogenetics.

Fig. 1

Phylogenetic tree of homoserine acetyltransferase proteins. T. pseudonana protein is marked with an asterisk. The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program (curated alignment with 105 characters was used). The T. pseudonana protein is marked with an asterisk. Reliability for internal branch was assessed using the aLRT. The number next to species name represents entry code of given protein in a databank.

Fig. 2

Phylogenetic tree of homoserine kinase proteins (HSK). The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program (curated alignment with 99 characters was used). The T. pseudonana protein is marked with an asterisk. Reliability for internal branch was assessed using the aLRT. The number next to species name represents entry code of given protein in a databank. Collapsed branches contain sequences of the same species or genus.

Fig. 3

Phylogenetic tree of PLP-dependent enzymes. The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program (curated alignment with 149 characters was used). T. pseudonana proteins are marked with asterisks. Reliability for internal branch was assessed using the aLRT test. The number next to species’ name represents entry code of given protein in a databank.

Fig. 4

Phylogenetic tree of methionine synthase proteins. The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program (curated alignment with 811 characters was used). The T. pseudonana protein is marked with an asterisk. Reliability for internal branch was assessed using the aLRT. The number next to species’ name represents entry code of given protein in a databank.

Fig. 5

Phylogenetic tree of S-adenosylmethionine proteins. The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program (curated alignment with 315 characters was used). T. pseudonana proteins are marked with asterisks. Reliability for internal branch was assessed using the aLRT test. The number next to species’ name represents entry code of given protein in a respective databank.

Fig. 6

The sequence-logo comparison of conserved motifs between a yeast MET31 binding site and b the motif found in putative promoters of T. pseudonana methionine metabolism genes.