Abstract
To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system ‘Search similar carotenoids’ using our original chemical fingerprint ‘Carotenoid DB Chemical Fingerprints’. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool ‘Search similar profiled organisms’. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. Database URL: http://carotenoiddb.jp
Highlights
Carotenoids have been investigated due to the importance of their diverse biological functions, since the beginning of the 19th century [1]
Aiming to extract organisms closely related through the biosynthesis of carotenoids, we developed a precise similarity search system exploiting the ‘Carotenoid DB Chemical Fingerprints’ from the International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names
The numbers of organisms we could compile are not evenly distributed in the three domains of life (Archaea: 8, Bacteria: 170 and Eukaryotes: 505), and not all the carotenoid entries could be linked to source organisms in the time so far available, our statistics on distribution in organisms show some insights into natural history
Summary
Carotenoids have been investigated due to the importance of their diverse biological functions, since the beginning of the 19th century [1]. For deeper understanding of the world of carotenoids— how organisms are related via carotenoids, either evolutionarily, or symbiotically, or in food chains through natural histories, and how carotenoids have been evolved with biological functions, we compiled 1117 structures and their distribution among organisms using the latest available original papers. We made these data accessible via the Internet at ‘http://carotenoiddb.jp’.
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