The Entner–Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants

Abstract

Glucose degradation pathways are central for energy and carbon metabolism throughout all domains of life. They provide ATP, NAD(P)H, and biosynthetic precursors for amino acids, nucleotides, and fatty acids. It is general knowledge that cyanobacteria and plants oxidize carbohydrates via glycolysis [the Embden-Meyerhof-Parnas (EMP) pathway] and the oxidative pentose phosphate (OPP) pathway. However, we found that both possess a third, previously overlooked pathway of glucose breakdown: the Entner-Doudoroff (ED) pathway. Its key enzyme, 2-keto-3-deoxygluconate-6-phosphate (KDPG) aldolase, is widespread in cyanobacteria, moss, fern, algae, and plants and is even more common among cyanobacteria than phosphofructokinase (PFK), the key enzyme of the EMP pathway. Active KDPG aldolases from the cyanobacterium Synechocystis and the plant barley (Hordeum vulgare) were biochemically characterized in vitro. KDPG, a metabolite unique to the ED pathway, was detected in both in vivo, indicating an active ED pathway. Phylogenetic analyses revealed that photosynthetic eukaryotes acquired KDPG aldolase from the cyanobacterial ancestors of plastids via endosymbiotic gene transfer. Several Synechocystis mutants in which key enzymes of all three glucose degradation pathways were knocked out indicate that the ED pathway is physiologically significant, especially under mixotrophic conditions (light and glucose) and under autotrophic conditions in a day/ night cycle, which is probably the most common condition encountered in nature. The ED pathway has lower protein costs and ATP yields than the EMP pathway, in line with the observation that oxygenic photosynthesizers are nutrient-limited, rather than ATP-limited. Furthermore, the ED pathway does not generate futile cycles in organisms that fix CO 2 via the Calvin-Benson cycle. T he breakdown of glucose is central for energy and biosynthetic metabolism throughout all domains of life. The Embden-Meyerhof-Parnas (EMP) pathway (glycolysis) and the oxidative pentose phosphate (OPP) pathway are the backbones of eukaryotic carbon and energy metabolism (1, 2). They generate ATP, NAD(P)H, and biosynthetic precursors for amino acids, nucleotides, and fatty acids. Prokaryotes, in contrast, exhibit a broad diversity in sugar oxidation pathways (3-5). These routes differ in ATP yield, in the enzymes and cofactors involved, and in the chemical intermediates of the pathways. The most common glycolytic routes in prokaryotes are the EMP, ED, and OPP pathways (Fig. 1). The key enzyme unique to the ED pathway is 2-keto-3-deoxygluconate-6-phosphate (KDPG) aldolase (Eda), whereas phosphofructokinase (PFK) is unique to the EMP pathway in the catabolic direction (3, 6). KDPG as a metabolite is exclusively found in the ED pathway (Fig. 1). The first two steps of the OPP pathway are catalyzed by glucose 6-phosphate-dehydrogenase (Zwf) and 6-phosphogluconate dehydrogenase (Gnd). As the pentose phosphate pathway can either run in its oxidative mode (OPP pathway) to oxidize carbohydrates or in its reductive mode ...

Role of Type 2 NAD(P)H Dehydrogenase NdbC in Redox Regulation of Carbon Allocation in Synechocystis

“…These results are in agreement with earlier studies showing that the mRNA amount of ndbC follows circadian rhythm peaking in the dark together with genes involved in sugar catabolism (Kucho et al, 2005;Layana and Diambra, 2011) as well as in the beginning of heterotrophy (Lee et al, 2007). Conversely, 6-PG hydratase (IlvD), which belongs to the recently discovered Entner-Doudoroff pathway in cyanobacteria (Chen et al, 2016), was up-regulated in DndbC in LC (Table III) and might partially compensate for the down-regulation of EMP and OPP.…”

“…6C). The up-regulated Entner-Doudoroff pathway in DndbC (in LC), which is physiologically significant under mixotrophy (Chen et al, 2016), also could contribute to carbon flux distribution in the cells. Nevertheless, similar problems were present in cell division, as demonstrated in autotrophic conditions (Supplemental Fig.…”

Metabolic evolution and the self-organization of ecosystems

“…Previous studies identified some unique presence/absence patterns for core metabolic genes in both Prochlorococcus and Synechococcus and relative to other cyanobacteria. For example, both have replaced the cyanobacterial RuBisCO and related proteins of the CO2-concentrating mechanism with proteobacterial variants (17)(18)(19), lost key genes in the cyanobacterial TCA cycle (20) and glycolysis (21), and acquired a menaquinone-based malate dehydrogenase (22). Photorespiration proteins are, in turn, universally preserved in Synechococcus, but unevenly distributed across Prochlorococcus ecotypes (9,23).…”

Interaction of the Nitrogen Regulatory Protein GlnB (PII) with Biotin Carboxyl Carrier Protein (BCCP) Controls Acetyl-CoA Levels in the Cyanobacterium Synechocystis sp. PCC 6803

“…The two main metabolic routes which provide the cell with acetyl-CoA are CO 2 fixation through the Calvin-Benson-Bessham cycle (CBB) or degradation of glycogen through various pathways (Xiong et al, 2015; Chen et al, 2016). The biggest differences in acetyl-CoA pools were visible in the first 48 h of growth.…”