Phylogenetic Study of the Evolution of PEP-Carboxykinase

Aich, Sanjukta; Delbaere, L. T. J.

doi:10.1177/117693430700300012

Cited by 25 publications

(15 citation statements)

References 16 publications

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“…Figure 1 shows the phylogenetic tree based on the amino acid sequences of ATP-PEPCK, which has two clades; one contains the Candidatus Kuenenia stuttgartiensis PEPCK and the other clade contains all other PEPCKs. This result is similar to other reports (Fukuda et al 2004;Aich & Delbaere 2007). The Candidatus Kuenenia stuttgartiensis PEPCK might be the ancestor of ATP and GTP dependent PEPCKs (Aich & Delbaere 2007).…”

Section: Sequence Analysis Revealed That Phpepck Is Atp-dependentsupporting

confidence: 92%

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Expression analysis of phosphoenolpyruvate carboxykinase in Porphyra haitanensis (Rhodophyta) sporophytes and gametophytes

Zhang

Wang

2013

Phycological Research

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Summary Phosphoenolpyruvate carboxykinase (PEPCK) catalyzes carboxylation of phosphoenolpyruvate or decarboxylation of oxaloacetate, which plays an important role in some C4 plants and algae. The full‐length cDNA of the PEPCK gene cloned from Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta), was denoted Phpepck. It had a nucleotide sequence of 2300 bp, including a 5′‐untranslated region (UTR) of 147 bp, a 3′‐UTR of 329 bp and an open reading frame of 1824 bp. The expression of PEPCK in P. haitanensis sporophytes and gametophytes was examined at the levels of transcription, translation and enzyme activity. Both PEPCK abundance and activity were higher in sporophytes than those in gametophytes, suggesting that a C4‐like carbon‐fixation mechanism might be functional in P. haitanensis sporophytes.

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Section: Sequence Analysis Revealed That Phpepck Is Atp-dependentsupporting

confidence: 92%

“…This result is similar to other reports (Fukuda et al . ; Aich & Delbaere ). The Candidatus Kuenenia stuttgartiensis PEPCK might be the ancestor of ATP and GTP dependent PEPCKs (Aich & Delbaere ).…”

Section: Discussionmentioning

confidence: 99%

Expression analysis of phosphoenolpyruvate carboxykinase in Porphyra haitanensis (Rhodophyta) sporophytes and gametophytes

Zhang

Wang

2013

Phycological Research

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“…According to its annotation, both Clade 1 and Clade 3 genomes also encode an ATP-linked (in contrast to GTP-linked) PEP carboxykinase based on the enzyme commission number assigned to the annotated sequences (EC: 4.1.1.49) [110]. This bidirectional enzyme could either carboxylate PEP yielding 1 ATP+oxaloacetate or decarboxylate oxaloacetate at the expense of ATP.…”

Section: Resultsmentioning

confidence: 99%

Genomic Evaluation of Thermoanaerobacter spp. for the Construction of Designer Co-Cultures to Improve Lignocellulosic Biofuel Production

et al. 2013

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The microbial production of ethanol from lignocellulosic biomass is a multi-component process that involves biomass hydrolysis, carbohydrate transport and utilization, and finally, the production of ethanol. Strains of the genus Thermoanaerobacter have been studied for decades due to their innate abilities to produce comparatively high ethanol yields from hemicellulose constituent sugars. However, their inability to hydrolyze cellulose, limits their usefulness in lignocellulosic biofuel production. As such, co-culturing Thermoanaerobacter spp. with cellulolytic organisms is a plausible approach to improving lignocellulose conversion efficiencies and yields of biofuels. To evaluate native lignocellulosic ethanol production capacities relative to competing fermentative end-products, comparative genomic analysis of 11 sequenced Thermoanaerobacter strains, including a de novo genome, Thermoanaerobacter thermohydrosulfuricus WC1, was conducted. Analysis was specifically focused on the genomic potential for each strain to address all aspects of ethanol production mentioned through a consolidated bioprocessing approach. Whole genome functional annotation analysis identified three distinct clades within the genus. The genomes of Clade 1 strains encode the fewest extracellular carbohydrate active enzymes and also show the least diversity in terms of lignocellulose relevant carbohydrate utilization pathways. However, these same strains reportedly are capable of directing a higher proportion of their total carbon flux towards ethanol, rather than non-biofuel end-products, than other Thermoanaerobacter strains. Strains in Clade 2 show the greatest diversity in terms of lignocellulose hydrolysis and utilization, but proportionately produce more non-ethanol end-products than Clade 1 strains. Strains in Clade 3, in which T. thermohydrosulfuricus WC1 is included, show mid-range potential for lignocellulose hydrolysis and utilization, but also exhibit extensive divergence from both Clade 1 and Clade 2 strains in terms of cellular energetics. The potential implications regarding strain selection and suitability for industrial ethanol production through a consolidated bioprocessing co-culturing approach are examined throughout the manuscript.

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“…4.1.1.32) and ATP-using (E.C. 4.1.1.49) PEPCK enzymes [21]. It focused on distribution of these co-substrate types among domains Bacteria, Archaea, and Eukarya, but did not address the eukaryotic cell-compartment-specific forms.…”

Section: Resultsmentioning

confidence: 99%

A genetic polymorphism evolving in parallel in two cell compartments and in two clades

et al. 2013

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BackgroundThe enzyme phosphoenolpyruvate carboxykinase, PEPCK, occurs in its guanosine-nucleotide-using form in animals and a few prokaryotes. We study its natural genetic variation in Colias (Lepidoptera, Pieridae). PEPCK offers a route, alternative to pyruvate kinase, for carbon skeletons to move between cytosolic glycolysis and mitochondrial Krebs cycle reactions.ResultsPEPCK is expressed in both cytosol and mitochondrion, but differently in diverse animal clades. In vertebrates and independently in Drosophila, compartment-specific paralogous genes occur. In a contrasting expression strategy, compartment-specific PEPCKs of Colias and of the silkmoth, Bombyx, differ only in their first, 5′, exons; these are alternatively spliced onto a common series of following exons. In two Colias species from distinct clades, PEPCK sequence is highly variable at nonsynonymous and synonymous sites, mainly in its common exons. Three major amino acid polymorphisms, Gly 335 ↔ Ser, Asp 503 ↔ Glu, and Ile 629 ↔ Val occur in both species, and in the first two cases are similar in frequency between species. Homology-based structural modelling shows that the variants can alter hydrogen bonding, salt bridging, or van der Waals interactions of amino acid side chains, locally or at one another′s sites which are distant in PEPCK′s structure, and thus may affect its enzyme function. We ask, using coalescent simulations, if these polymorphisms′ cross-species similarities are compatible with neutral evolution by genetic drift, but find the probability of this null hypothesis is 0.001 ≤ P ≤ 0.006 under differing scenarios.ConclusionOur results make the null hypothesis of neutrality of these PEPCK polymorphisms quite unlikely, but support an alternative hypothesis that they are maintained by natural selection in parallel in the two species. This alternative can now be justifiably tested further via studies of PEPCK genotypes′ effects on function, organismal performance, and fitness. This case emphasizes the importance, for evolutionary insight, of studying gene-specific mechanisms affected by natural genetic variation as an essential complement to surveys of such variation.

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Phylogenetic Study of the Evolution of PEP-Carboxykinase

Cited by 25 publications

References 16 publications

Expression analysis of phosphoenolpyruvate carboxykinase in Porphyra haitanensis (Rhodophyta) sporophytes and gametophytes

Expression analysis of phosphoenolpyruvate carboxykinase in Porphyra haitanensis (Rhodophyta) sporophytes and gametophytes

Genomic Evaluation of Thermoanaerobacter spp. for the Construction of Designer Co-Cultures to Improve Lignocellulosic Biofuel Production

A genetic polymorphism evolving in parallel in two cell compartments and in two clades

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