D-galactose catabolism in archaea: operation of the DeLey–Doudoroff pathway in <i>Haloferax volcanii</i>

Tästensen, Julia-Beate; Johnsen, Ulrike; Reinhardt, Andreas; Ortjohann, Marius; Schönheit, Peter

doi:10.1093/femsle/fnaa029

Cited by 11 publications

(16 citation statements)

References 48 publications

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“…Novel versions, as well as previously unknown carbohydrate pathways, are continuing to be discovered via the promiscuity of enzymes, especially aldolases. A recent paper by Tästensen et al [69] has shown that H. volcanii can utilize D-galactose as an energy source, and a cluster of genes for the putative enzymes of the DeLey-Doudoroff pathway were identified such as D-galactose dehydrogenase, D-galactonate dehydratase, KDGal kinase and a 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase, which was demonstrated to be promiscuous in utilizing both KDPGal and KDPG, the C4 epimer. A gene cluster for an ABC transporter was identified and a knock-out mutant showed its involvement in D-galactose uptake.…”

Section: Aldolasesmentioning

confidence: 99%

Enzymology of Alternative Carbohydrate Catabolic Pathways

2020

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The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria.

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Section: Aldolasesmentioning

confidence: 99%

Enzymology of Alternative Carbohydrate Catabolic Pathways

2020

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“…In halophilic archaea, sugar metabolism has been studied in particular in Haloferax and Haloarcula species (5)(6)(7)(8)(9)(10). Haloferax volcanii, which represents a model organism of haloarchaea (11), exhibits a high metabolic versatility in utilizing various sugars, hexoses, pentoses and deoxysugars, and other carbon compounds, e.g., acetate, as growth substrates (12).…”

Section: Importancementioning

confidence: 99%

Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii

et al. 2021

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The halophilic archaeon Haloferax volcanii has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. Following our previous studies on key enzymes of this pathway, we now focus on the characterization of enzymes involved in 3-phosphoglycerate conversion to pyruvate, in anaplerosis and in acetyl-CoA formation from pyruvate. These enzymes include phosphoglycerate mutase, enolase, pyruvate kinase, phosphoenolpyruvate carboxylase and pyruvate: ferredoxin oxidoreductase. The essential function of these enzymes were shown by transcript analyses and growth experiments with respective deletion mutants. Further, it is shown that H. volcanii - during aerobic growth on glucose - excreted significant amounts of acetate, which was consumed in the stationary phase (acetate switch). The enzyme catalyzing the conversion of acetyl-CoA to acetate as part of the acetate overflow mechanism, an ADP-forming acetyl-CoA synthetase (ACD), was characterized. The functional involvement of ACD in acetate formation and of AMP-forming acetyl-CoA synthetases (ACSs) in activation of excreted acetate was proven by using respective deletion mutants. Together, the data provide a comprehensive analysis of enzymes of the spED pathway, of anaplerosis, and report first genetic evidence of the functional involvement of enzymes of the acetate switch in archaea. Importance: In this work we provide a comprehensive analysis of glucose degradation via the semiphosphorylative Entner-Doudoroff pathway in the haloarchaeal model organism Haloferax volcanii. The study includes transcriptional analyses, growth experiments with deletion mutants and characterization of all enzymes involved in the conversion of 3-phosphoglycerate to acetyl-CoA and in anaplerosis. Phylogenetic analyses of several enzymes indicate various lateral gene transfer events from bacteria to haloarchaea. Further, we analyzed the key players involved in the acetate switch, i.e in the formation (overflow) and subsequent consumption of acetate during aerobic growth on glucose. Together, the data provide novel aspects on glucose degradation, anaplerosis and acetate switch in H. volcanii and thus expand our understanding of the unusual sugar metabolism in archaea.

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“…Its genome has been sequenced and carefully annotated [ 1 , 10 , 11 ]. A plethora of biological aspects have been successfully tackled in this species, with examples including DNA replication [ 4 ]; cell division and cell shape [ 12 , 13 , 14 , 15 , 16 ]; metabolism [ 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 ]; protein secretion [ 26 , 27 , 28 , 29 ]; motility and biofilms [ 30 , 31 , 32 , 33 , 34 , 35 ]; mating [ 36 ]; signaling [ 37 ]; virus defense [ 38 ]; proteolysis [ 39 , 40 , 41 , 42 , 43 , 44 ]; posttranslational modification (N-glycosylation; SAMPylation) [ 45 , 46 , 47 , 48 , 49 , 50 ]; gene regulation [ 21 , 25 , 51 , 52 , 53 , 54 , 55 ]; microproteins [ 56 , 57 , 58 ] and small noncoding RNAs (sRNAs) […”

Section: Introductionmentioning

confidence: 99%

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Pfeiffer

Dyall‐Smith

2021

Genes

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Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

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D-galactose catabolism in archaea: operation of the DeLey–Doudoroff pathway in Haloferax volcanii

Cited by 11 publications

References 48 publications

Enzymology of Alternative Carbohydrate Catabolic Pathways

Enzymology of Alternative Carbohydrate Catabolic Pathways

Glucose Metabolism and Acetate Switch in Archaea: the Enzymes in Haloferax volcanii

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

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