bioRxiv preprint doi: https://doi.org/10.1101/205583; this version posted November 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Oxidative pathways of deoxyribose and deoxyribonate catabolism 1* 1 2 1 Morgan N. Price, Jayashree Ray, Anthony T. Iavarone, Hans K. Carlson, Elizabeth M. 3 3 1,4,* 1,5,* Ryan, Rex R. Malmstrom, Adam P. Arkin, and Adam M. Deutschbauer 1 Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley CA, USA 2 QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley CA, USA 3 DOE Joint Genome Institute, Walnut Creek CA, USA 4 Department of Bioengineering, University of California, Berkeley CA, USA 5 Department of Plant and Microbial Biology, University of California, Berkeley CA, USA *
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[email protected] Abstract Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-D-ribose and 2-deoxy-D-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl-CoA and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway.