Evolutionary Analysis of the TPP-Dependent Enzyme Family

Costelloe, Seán; Ward, John M.; Dalby, Paul A.

doi:10.1007/s00239-007-9056-2

Cited by 70 publications

(90 citation statements)

References 35 publications

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“…Previous phylogenetic analyses have suggested a common origin for XFPs, transketolases, 2-oxoisovalerate dehydrogenases and dihydroxyacetone synthases [Costelloe et al, 2008]. Although not shown in this study, our preliminary phylogenetic analyses confirmed that XFPs constitute a cluster clearly distinguishable from the other three enzymes.…”

Section: Phylogenetic Reconstructionssupporting

confidence: 68%

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Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

et al. 2010

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Phosphoketolases (XFPs) are glycolytic enzymes present in several organisms belonging to the Eukarya and Bacteria domains. A total of 151 putative xfp genes were detected in 650 complete genomes available in public databases. Elimination of redundant sequences and pseudogenes rendered a final data set of 128 phosphoketolases, which was analyzed by phylogenetic methods. The distribution of xfp genes was uneven in most taxonomic groups, with the exception of the taxonomical division Lactobacillaceae, in which all the species studied harbored a putative xfp gene. Putative xfp genes were also present predominantly in Rhizobiales and Actinobacteria divisions, in which 23 out of 28 genomes and 23 out of 41 genomes contained at least one putative xfp homolog, respectively. Phylogenetic analyses showed clear discordance with the expected order of organismal descent even in groups where xfp is prevalent, such as Lactobacillaceae. The presence of putative paralogs in some organisms cannot account for these discrepancies; instead, these paralogs are most possibly xenologs. The results of the phylogenetic analyses, the distribution of xfp genes and the location of some xfp genes in plasmids are independent pieces of evidence that point to horizontal gene transfer as a major driving force in the evolution of phosphoketolases.

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Section: Phylogenetic Reconstructionssupporting

confidence: 68%

“…Previous structural [Duggleby, 2006] and phylogenetic analyses [Costelloe et al, 2008] of proteins belonging to the TPP-dependent family have shown that XFPs share the same domain structure and are evolutionarily related to transketolases. However, no detailed phylogenetic study of XFPs has been carried out so far.…”

Section: Introductionmentioning

confidence: 99%

Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

et al. 2010

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“…Other organisms, such as Cupriavidus oxalaticus, also use oxalyl-CoA decarboxylase to metabolize oxalate but use formate dehydrogenase to generate NADH with the electrons derived from oxalate (8,9). Oxalyl-CoA decarboxylase is a TPP-dependent enzyme with distant homology to yeast pyruvate decarboxylases (10). The M. thermoacetica genome has sequences with low homology to oxalyl-CoA decarboxylase but no homolog of formyl-CoA transferase.…”

mentioning

confidence: 99%

Identification and Characterization of Oxalate Oxidoreductase, a Novel Thiamine Pyrophosphate-dependent 2-Oxoacid Oxidoreductase That Enables Anaerobic Growth on Oxalate

Pierce

Becker

Ragsdale

2010

Journal of Biological Chemistry

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Moorella thermoacetica is an anaerobic acetogen, a class of bacteria that is found in the soil, the animal gastrointestinal tract, and the rumen. This organism engages the Wood-Ljungdahl pathway of anaerobic CO 2 fixation for heterotrophic or autotrophic growth. This paper describes a novel enzyme, oxalate oxidoreductase (OOR), that enables M. thermoacetica to grow on oxalate, which is produced in soil and is a common component of kidney stones. Exposure to oxalate leads to the induction of three proteins that are subunits of OOR, which oxidizes oxalate coupled to the production of two electrons and CO 2 or bicarbonate. Like other members of the 2-oxoacid: ferredoxin oxidoreductase family, OOR contains thiamine pyrophosphate and three [Fe 4 S 4 ] clusters. However, unlike previously characterized members of this family, OOR does not use coenzyme A as a substrate. Oxalate is oxidized with a k cat of 0.09 s ؊1 and a K m of 58 M at pH 8. OOR also oxidizes a few other 2-oxoacids (which do not induce OOR) also without any requirement for CoA. The enzyme transfers its reducing equivalents to a broad range of electron acceptors, including ferredoxin and the nickel-dependent carbon monoxide dehydrogenase. In conjunction with the well characterized WoodLjungdahl pathway, OOR should be sufficient for oxalate metabolism by M. thermoacetica, and it constitutes a novel pathway for oxalate metabolism.Moorella thermoacetica is a strictly anaerobic Gram-positive acetogenic bacterium. Acetogens are commonly found in the soil, animal gastrointestinal tract, and the rumen and grow heterotrophically or autotrophically on many different electron donors. Electrons from these substrates are used to reduce CO 2 to acetate by the Wood-Ljungdahl pathway. During growth by this pathway, acetate and cell mass are the only growth products, and electron-rich growth substrates like glucose are converted stoichiometrically to acetate; therefore, M. thermoacetica is called a homoacetogen. M. thermoacetica can use other electron acceptors (e.g. nitrate, nitrite, thiosulfate, and dimethyl sulfoxide). Under most conditions, nitrate reduction occurs preferentially to CO 2 reduction, and nitrate has been shown to repress autotrophic growth (1, 2). However, oxalate is unique in its properties as an electron donor by M. thermoacetica for acetogenic growth. When both nitrate and CO 2 are provided to cells growing on oxalate, CO 2 is reduced to acetate during exponential growth phase, and nitrate is only used as the electron acceptor during stationary phase (3). Oxalate is the only substrate with which M. thermoacetica has been shown to reduce CO 2 instead of nitrate when both are present.Oxalate (C 2 O 4 2Ϫ ) is the most oxidized two-carbon compound. It is made in high concentrations by some plants and fungi and can reach high micromolar concentrations in soil (4). Oxalate is toxic to mammals but is metabolized by many bacteria and plants by various pathways. In Oxalobacter formigenes, oxalate is first activated to oxalylCoA and then decarboxylated, giv...

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“…Obwohl beide Domänen auf der Sequenzebene sehr unterschiedlich sind, ergaben Vergleiche der PP-und Pyr-Domänen aus allen Familien eine hohe strukturelle Ähnlichkeit (Tab. 1, [3]). Man spricht in diesem Zusammenhang auch vom ThDP-binding fold [4].…”

Section: Enzymfamilienunclassified

Diversität asymmetrischer Thiamin-Katalyse

Müller

2011

Biospektrum

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Evolutionary Analysis of the TPP-Dependent Enzyme Family

Cited by 70 publications

References 35 publications

Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

Bacterial and Eukaryotic Phosphoketolases: Phylogeny, Distribution and Evolution

Identification and Characterization of Oxalate Oxidoreductase, a Novel Thiamine Pyrophosphate-dependent 2-Oxoacid Oxidoreductase That Enables Anaerobic Growth on Oxalate

Diversität asymmetrischer Thiamin-Katalyse

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