Tryptophan is an essential amino acid that, in eukaryotes, is synthesized either in the plastids of photoautotrophs or in the cytosol of fungi and oomycetes. Here we present an in silico analysis of the tryptophan biosynthetic pathway in stramenopiles, based on analysis of the genomes of the oomycetes Phytophthora sojae and P. ramorum and the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. Although the complete pathway is putatively located in the complex chloroplast of diatoms, only one of the involved enzymes, indole-3-glycerol phosphate synthase (InGPS), displays a possible cyanobacterial origin. On the other hand, in P. tricornutum this gene is fused with the cyanobacteria-derived hypothetical protein COG4398. Anthranilate synthase is also fused in diatoms. This fusion gene is almost certainly of bacterial origin, although the particular source of the gene cannot be resolved. All other diatom enzymes originate from the nucleus of the primary host (red alga) or secondary host (ancestor of chromalveolates). The entire pathway is of eukaryotic origin and cytosolic localization in oomycetes; however, one of the enzymes, anthranilate phosphoribosyl transferase, was likely transferred to the oomycete nucleus from the red algal nucleus during secondary endosymbiosis. This suggests possible retention of the complex plastid in the ancestor of stramenopiles and later loss of this organelle in oomycetes.
- MeSH
- aldosa-ketosaisomerasy genetika metabolismus MeSH
- anthranilátfosforibosyltransferasa genetika metabolismus MeSH
- anthranilátsynthasa genetika metabolismus MeSH
- chloroplasty metabolismus MeSH
- fylogeneze MeSH
- indol-3-glycerolfosfátsynthasa genetika metabolismus MeSH
- molekulární evoluce MeSH
- molekulární sekvence - údaje MeSH
- molekulární struktura MeSH
- Phytophthora metabolismus MeSH
- rozsivky cytologie genetika metabolismus MeSH
- sekvence aminokyselin MeSH
- tryptofan biosyntéza chemie MeSH
- tryptofansynthasa genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- aldosa-ketosaisomerasy MeSH
- anthranilátfosforibosyltransferasa MeSH
- anthranilátsynthasa MeSH
- indol-3-glycerolfosfátsynthasa MeSH
- phosphoribosylanthranilate isomerase MeSH Prohlížeč
- tryptofan MeSH
- tryptofansynthasa MeSH
Quantitative structure-function relationships (QSFR) and quantitative structure-stability relationships (QSSR) analyses are described here. The objective of these analyses is to investigate and quantitatively describe the effect of the changes in structure of protein on its function or stability. During the analysis, the structural and physico-chemical properties of the amino acid residues are related to activity or stability data derived for the group of proteins containing systematic substitutions at certain positions. Four examples of the application of these analyses on the data obtained with proteins modified by site-directed mutagenesis experiments are provided. Structure-function relationships were studied for 15 mutants in position 172 of the haloalkane dehalogenase and 19 mutants in position 222 of the subtilisin, while the structure-stability relationships were investigated for 13 mutants in position 157 of phage T4 lysozyme and 18 mutants in position 49 of alpha-subunits tryptophan synthase. A total of 402 molecular descriptors derived from AAindex database were used to quantify amino acid properties and the multivariate statistical technique--partial least squares projections to latent structures--was used to identify those of them which are important for explanation of the activity and stability data. Quantitative models were developed and internally validated for every data set. The possibilities for further development of both analyses and their application for predictive and analytical purposes in protein engineering research are discussed.
The submerged culture of the Claviceps purpurea strain studied was polymorphous. In the process of alkaloid synthesis, cytodifferentiation preceded biochemical differentiation. The onset of the alkaloid phase was characterized by: predominance of chlamydospores in the culture, the presence of vegetative cells with reduced or arrested proliferation, maximum acetylCoA carboxylase activity, the maximum amount of total fatty acids, an over-average cell pool tryptophan level and minimum tryptophan synthetase activity. Intracellular ricinoleic acid was an indicator of differentiation of the culture towards alkaloid formation and also of alkaloid synthesis. The cytodifferentiation period in the initial phases of fermentation, when the cell has several alternative possibilities of development, is regarded as the most sensitive sector of the regulatory mechanisms of alkaloid formation.
- MeSH
- acetyl-CoA-karboxylasa metabolismus MeSH
- Claviceps enzymologie růst a vývoj metabolismus MeSH
- fermentace MeSH
- kyseliny ricinolejové biosyntéza MeSH
- mastné kyseliny biosyntéza MeSH
- námelové alkaloidy biosyntéza MeSH
- spory hub enzymologie růst a vývoj metabolismus MeSH
- tryptofan biosyntéza MeSH
- tryptofansynthasa metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- acetyl-CoA-karboxylasa MeSH
- kyseliny ricinolejové MeSH
- mastné kyseliny MeSH
- námelové alkaloidy MeSH
- tryptofan MeSH
- tryptofansynthasa MeSH
