Photorespiration pathways in a chemolithoautotroph

Abstract

Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of 2-phosphoglycolate, an essential process termed photorespiration, was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, but remains uncharacterized in chemolithoautotrophic bacteria. Here, we study photorespiration in the model chemolithoautotroph Cupriavidus necator (Ralstonia eutropha) by characterizing the proxy-process of glycolate metabolism, performing comparative transcriptomics of autotrophic growth under low and high CO 2 concentrations, and testing autotrophic growth phenotypes of gene deletion strains at ambient CO 2 . We find that the canonical plant-like C 2 cycle does not operate in this bacterium and instead the bacterial-like glycerate pathway is the main photorespiratory pathway. Upon disruption of the glycerate pathway, we find that an oxidative pathway, which we term the malate cycle, supports photorespiration. In this cycle, glyoxylate is condensed with acetyl-CoA to give malate, which undergoes two oxidative decarboxylation steps to regenerate acetyl-CoA. When both pathways are disrupted, autotrophic growth is abolished at ambient CO 2 . We present bioinformatic data suggesting that the malate cycle may support photorespiration in diverse chemolithoautotrophic bacteria. This study thus demonstrates a so-far unknown photorespiration pathway, highlighting important diversity in microbial carbon fixation metabolism.

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle

“…Transcriptomic data are available in the Gene Expression Omnibus (accession no. GSE141999 ) ( 58 ) and are available in Dataset S1 . Bioinformatic genome analysis of Rubisco and malate synthase are available in Dataset S2 and at GitHub ( https://github.com/flamholz/malate_synthase/tree/master/pipeline ) ( 59 ).…”