Abstract
BackgroundEven before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the proteins encoded in the Kluyveromyces lactis genome.ResultsIn this work, a new metabolic genome-wide functional re-annotation of the proteins encoded in the Kluyveromyces lactis genome was performed, resulting in the annotation of 1759 genes with metabolic functions, and the development of a methodology supported by merlin (software developed in-house). The new annotation includes novelties, such as the assignment of transporter superfamily numbers to genes identified as transporter proteins. Thus, the genes annotated with metabolic functions could be exclusively enzymatic (1410 genes), transporter proteins encoding genes (301 genes) or have both metabolic activities (48 genes). The new annotation produced by this work largely surpassed the Kluyveromyces lactis currently available annotations. A comparison with KEGG’s annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations. Moreover, there are 32 genes with annotations different from KEGG.ConclusionsThe methodology developed throughout this work can be used to re-annotate any yeast or, with a little tweak of the reference organism, the proteins encoded in any sequenced genome. The new annotation provided by this study offers basic knowledge which might be useful for the scientific community working on this model yeast, because new functions have been identified for the so-called metabolic genes. Furthermore, it served as the basis for the reconstruction of a compartmentalized, genome-scale metabolic model of Kluyveromyces lactis, which is currently being finished.
Highlights
Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology
Since the genome sequence of K. lactis was published in 2004, the proteins encoded in the Kluyveromyces lactis genome had never been thoroughly reviewed and annotated; or at least this information was not published, to our knowledge
2000 genes with potential to be assigned with metabolic functions within the proteins encoded in the Kluyveromyces lactis genome were studied
Summary
Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. While the Crabtreepositive yeast S. cerevisiae has a strong tendency to ferment, even under aerobic conditions, K. lactis is considered Crabtree-negative and preferably uses respiration for energy generation, unless oxygen becomes limiting [6,7]. Another crucial difference between the two yeasts is that K. lactis, in contrast to S. cerevisiae, is not capable of growing under complete anaerobiosis [8]
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