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Moriya Y, Yamada T, Okuda S, Nakagawa Z, Kotera M, Tokimatsu T, Kanehisa M, Goto S. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. J Chem Inf Model 2016; 56:510-6. [PMID: 26822930 DOI: 10.1021/acs.jcim.5b00216] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.
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Affiliation(s)
- Yuki Moriya
- Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Takuji Yamada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University , 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan
| | - Zenichi Nakagawa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Masaaki Kotera
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Toshiaki Tokimatsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Minoru Kanehisa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan
| | - Susumu Goto
- Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan
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Kotera M, Nishimura Y, Nakagawa ZI, Muto A, Moriya Y, Okamoto S, Kawashima S, Katayama T, Tokimatsu T, Kanehisa M, Goto S. PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list. J Bioinform Comput Biol 2015; 12:1442001. [PMID: 25385078 DOI: 10.1142/s0219720014420013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genomics is faced with the issue of many partially annotated putative enzyme-encoding genes for which activities have not yet been verified, while metabolomics is faced with the issue of many putative enzyme reactions for which full equations have not been verified. Knowledge of enzymes has been collected by IUBMB, and has been made public as the Enzyme List. To date, however, the terminology of the Enzyme List has not been assessed comprehensively by bioinformatics studies. Instead, most of the bioinformatics studies simply use the identifiers of the enzymes, i.e. the Enzyme Commission (EC) numbers. We investigated the actual usage of terminology throughout the Enzyme List, and demonstrated that the partial characteristics of reactions cannot be retrieved by simply using EC numbers. Thus, we developed a novel ontology, named PIERO, for annotating biochemical transformations as follows. First, the terminology describing enzymatic reactions was retrieved from the Enzyme List, and was grouped into those related to overall reactions and biochemical transformations. Consequently, these terms were mapped onto the actual transformations taken from enzymatic reaction equations. This ontology was linked to Gene Ontology (GO) and EC numbers, allowing the extraction of common partial reaction characteristics from given sets of orthologous genes and the elucidation of possible enzymes from the given transformations. Further future development of the PIERO ontology should enhance the Enzyme List to promote the integration of genomics and metabolomics.
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Affiliation(s)
- Masaaki Kotera
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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Muto A, Kotera M, Tokimatsu T, Nakagawa Z, Goto S, Kanehisa M. Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J Chem Inf Model 2013; 53:613-22. [PMID: 23384306 PMCID: PMC3632090 DOI: 10.1021/ci3005379] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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The
metabolic network is both a network of chemical reactions and
a network of enzymes that catalyze reactions. Toward better understanding
of this duality in the evolution of the metabolic network, we developed
a method to extract conserved sequences of reactions called reaction
modules from the analysis of chemical compound structure transformation
patterns in all known metabolic pathways stored in the KEGG PATHWAY
database. The extracted reaction modules are repeatedly used as if
they are building blocks of the metabolic network and contain chemical
logic of organic reactions. Furthermore, the reaction modules often
correspond to traditional pathway modules defined as sets of enzymes
in the KEGG MODULE database and sometimes to operon-like gene clusters
in prokaryotic genomes. We identified well-conserved, possibly ancient,
reaction modules involving 2-oxocarboxylic acids. The chain extension
module that appears as the tricarboxylic acid (TCA) reaction sequence
in the TCA cycle is now shown to be used in other pathways together
with different types of modification modules. We also identified reaction
modules and their connection patterns for aromatic ring cleavages
in microbial biodegradation pathways, which are most characteristic
in terms of both distinct reaction sequences and distinct gene clusters.
The modular architecture of biodegradation modules will have a potential
for predicting degradation pathways of xenobiotic compounds. The collection
of these and many other reaction modules is made available as part
of the KEGG database.
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Affiliation(s)
- Ai Muto
- Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan
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