Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi
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Islam-2015-Experimental validat.pdf
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Author(s)
Islam, M. Ahsanul
Tchigvintsev, Anatoli
Yim, Veronica
Savchenko, Alexei
Yakunin, Alexander F.
Mahadevan, Radhakrishnan
Edwards, Elizabeth A.
Date Issued
September 2015
Journal
Microbial Biotechnology
Publisher
Wiley Blackwell
Citation
Islam, M. Ahsanul, Anatoli Tchigvintsev, Veronica Yim, Alexei Savchenko, Alexander F. Yakunin, Radhakrishnan Mahadevan, and Elizabeth A. Edwards. “Experimental Validation of in Silico Model-Predicted Isocitrate Dehydrogenase and Phosphomannose Isomerase from Dehalococcoides Mccartyi.” Microbial Biotechnology (September 16, 2015): n/a–n/a.
Version
Final published version
Abstract
Gene sequences annotated as proteins of unknown or non-specific function and hypothetical proteins account for a large fraction of most genomes. In the strictly anaerobic and organohalide respiring Dehalococcoides mccartyi, this lack of annotation plagues almost half the genome. Using a combination of bioinformatics analyses and genome-wide metabolic modelling, new or more specific annotations were proposed for about 80 of these poorly annotated genes in previous investigations of D. mccartyi metabolism. Herein, we report the experimental validation of the proposed reannotations for two such genes (KB1_0495 and KB1_0553) from D. mccartyi strains in the KB-1 community. KB1_0495 or DmIDH was originally annotated as an NAD[superscript +]-dependent isocitrate dehydrogenase, but biochemical assays revealed its activity primarily with NADP[superscript +] as a cofactor. KB1_0553, also denoted as DmPMI, was originally annotated as a hypothetical protein/sugar isomerase domain protein. We previously proposed that it was a bifunctional phosphoglucose isomerase/phosphomannose isomerase, but only phosphomannose isomerase activity was identified and confirmed experimentally. Further bioinformatics analyses of these two protein sequences suggest their affiliation to potentially novel enzyme families within their respective larger enzyme super families.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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DOI of Published Version
https://doi.org/10.1111/1751-7915.12315
