Dias, Oscar

Ferreira, E. C.

Rocha, I.

Rocha, Miguel

Ferreira, Eugénio C.

Universidade do Minho: RepositoriUM

Metabolic Reconstruction of Less Characterized Microorganisms: A NewMethodology for Reaction Identification from Genome Sequencing DataOscar Dias,1, ∗ Miguel Rocha,2 Isabel Rocha,1 and Eugénio Campos Ferreira11 IBB - Institute for Biotechnology and Bioengineering2 CCTC - Computer Science Technology CenterMOTIVATION:The Genome-Scale Reconstruction of Metabolic Networks encompasses several steps, suchas genome annotation, reactions identification and stoichiometry determination, compart-mentation, determination of the biomass composition, energy requirements and additionalconstraints.According to the IMG system [4] [a] there are currently more than 4.000 genomes (4.355as of July 2009) fully sequenced with more than 500 (535 as of July 2009) being draftedright now. Sequence similarities between genes and genomes can be established using wellestablished algorithms such as BLAST [1] or FASTA [3].The yeast Kluyveromyces lactis, for which the complete genome sequence is available [2],is attracting increasing attention due to its ability to grow on lactose as a sole carbon source.Whereas the reconstruction of the metabolic network of a given organism is becoming awidespread procedure, starting with the fully sequenced and (partially) annotated genomesequence, there are still many improvements needed in the current methodologies and a clearlack of computational tools for many of the steps.In this work, a method which is able to collect online similarity information from genomesequencing data, using the BLAST algorithm, and store it on a relational database forlater manual curation is proposed. Also, a computational tool implementing the proposedapproach was developed. The genome of the yeast K. lactis will be used as a case study forthis method, providing information for the first stage of the reconstruction of this eukaryote.CONCLUSIONS:The outcome of the alignment of K. lactis genes sequences to the NCBI database, demon-strated that the developed method provides valuable information for the reconstruction of apreliminary metabolic network.The identification of several protein coding sequences and subsequent functions assign-ment, allowed to conclude that the developed framework can be useful for the reconstructionof genome-scale metabolic networks, especially for those organisms that lack informationabout the proteins encoded in its genome, such as the case study.[1] S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman. BASIC LOCAL ALIGNMENT SEARCHTOOL. JOURNAL OF MOLECULAR BIOLOGY, 215(3):403–410, OCT 5 1990.[2] B. Dujon et al. Genome evolution in yeasts. NATURE, 430(6995):35–44, JUL 1 2004.[3] D. Lipman and W. Pearson. RAPID AND SENSITIVE PROTEIN SIMILARITY SEARCHES. SCI-ENCE, 227(4693):1435–1441, 1985.[4] V. M. Markowitz, E. Szeto, K. Palaniappan, Y. Grechkin, K. Chu, I.-M. A. Chen, I. Dubchak, I. Ander-son, A. Lykidis, K. Mavromatis, N. N. Ivanova, and N. C. Kyrpides. The integrated microbial genomes(IMG) system in 2007: data content and analysis tool extensions. NUCLEIC ACIDS RESEARCH, 36(Sp. Iss. SI):D528–D533, JAN 2008.[a] Integrated Microbial GenomesKeywords: Metabolic Model, Kluyveromyces lactis, Genome-Scale Models Reconstruction, BLAST57

Metabolic reconstruction of less characterized microorganisms : a new methodology for reaction identification from genome sequencing data

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Metabolic reconstruction of less characterized microorganisms : a new methodology for reaction identification from genome sequencing data

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Universidade do Minho: RepositoriUM