Biochemical comparison of two glucose 6-phosphate dehydrogenase isozymes from a cold-adapted Pseudomonas mandelii

DangThu, Quynh; Jang, Sei‐Heon; Lee, ChangWoo

doi:10.1007/s00792-020-01171-3

Cited by 10 publications

(7 citation statements)

References 34 publications

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“…5 ). A full Entner-Doudoroff pathway and glyoxylate shunt are also present, cycles that typically act as alternatives to glycolysis and the citric acid cycle, respectively 58 , 59 . The glyoxylate shunt may also allow Hybrid_5 to accumulate C4 compounds alongside the TCA cycle 60 .…”

Section: Resultsmentioning

confidence: 99%

“…Hybrid_5 also possesses adaptations within its central carbon metabolism that can contribute to oxidative stress tolerance. The glyoxylate shunt is up-regulated under oxidative stress, as it lacks the TCA cycle’s decarboxylation steps that produce NADH 58 , 103 , and glucose 6-phosphate dehydrogenase ( G6PD / zwf ) in the Entner-Doudoroff pathway converts NADP + to NADPH to protect cells from oxidative stress 59 . The pyruvate dehydrogenases aceE and aceF are involved in both oxidative and cold stress responses 72 .…”

Section: Discussionmentioning

confidence: 99%

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MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes

Maggiori

Raymond-Bouchard

Brennan

et al. 2021

Sci Rep

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Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes

Maggiori

Raymond-Bouchard

Brennan

et al. 2021

Sci Rep

View full text Add to dashboard Cite

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“…Approximately 100 types of cold-adapted enzymes have been reported over the last few years ( Santiago et al, 2016 ; Pereira et al, 2017 ; DangThu et al, 2020 ). According to International Commission of Enzymes nomenclature, these enzymes can be classified into six primary categories: hydrolase, oxidoreductases, ransferases, lyases, isomerases, and synthetases.…”

Section: Principal Types Of Cold-adapted Enzymes From Microorganismsmentioning

confidence: 99%

Advances in cold-adapted enzymes derived from microorganisms

Liu

Zhang

et al. 2023

Front. Microbiol.

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Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.

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“…The use of the ED pathway is widespread in Pseudomonas and other bacteria ( 18 , 19 ), and previous studies reported on the presence of several copies of G6PDH-encoding genes in this genus ( 20 – 23 ). Pseudomonas putida KT2440 and other members of this genus display a cyclic glycolysis ( Fig.…”

Section: Introductionmentioning

confidence: 99%

Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria

2021

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Glucose-6-phosphate dehydrogenase (G6PDH) is widely distributed in nature and catalyzes the first committing step in the oxidative branch of the pentose phosphate (PP) pathway, feeding either the reductive PP or the Entner-Doudoroff pathway. Besides its role in central carbon metabolism, this dehydrogenase provides reduced cofactors, thereby affecting redox balance. Although G6PDH is typically considered to display specificity toward NADP+, some variants accept NAD+ similarly or even preferentially. Furthermore, the number of G6PDH isozymes encoded in bacterial genomes varies from none to more than four orthologues. On this background, we systematically analyzed the interplay of the three G6PDH isoforms of the soil bacterium Pseudomonas putida KT2440 from genomic, genetic, and biochemical perspectives. P. putida represents an ideal model to tackle this endeavor, as its genome harbors gene orthologues for most dehydrogenases in central carbon metabolism. We show that the three G6PDHs of strain KT2440 have different cofactor specificities and that the isoforms encoded by zwfA and zwfB carry most of the activity, acting as metabolic “gatekeepers” for carbon sources that enter at different nodes of the biochemical network. Moreover, we demonstrate how multiplication of G6PDH isoforms is a widespread strategy in bacteria, correlating with the presence of an incomplete Embden-Meyerhof-Parnas pathway. The abundance of G6PDH isoforms in these species goes hand in hand with low NADP+ affinity, at least in one isozyme. We propose that gene duplication and relaxation in cofactor specificity is an evolutionary strategy toward balancing the relative production of NADPH and NADH. IMPORTANCE Protein families have likely arisen during evolution by gene duplication and divergence followed by neofunctionalization. While this phenomenon is well documented for catabolic activities (typical of environmental bacteria that colonize highly polluted niches), the coexistence of multiple isozymes in central carbon catabolism remains relatively unexplored. We have adopted the metabolically versatile soil bacterium Pseudomonas putida KT2440 as a model to interrogate the physiological and evolutionary significance of coexisting glucose-6-phosphate dehydrogenase (G6PDH) isozymes. Our results show that each of the three G6PDHs in this bacterium display distinct biochemical properties, especially at the level of cofactor preference, impacting bacterial physiology in a carbon source-dependent fashion. Furthermore, the presence of multiple G6PDHs differing in NAD+ or NADP+ specificity in bacterial species strongly correlates with their predominant metabolic lifestyle. Our findings support the notion that multiplication of genes encoding cofactor-dependent dehydrogenases is a general evolutionary strategy toward achieving redox balance according to the growth conditions.

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Biochemical comparison of two glucose 6-phosphate dehydrogenase isozymes from a cold-adapted Pseudomonas mandelii

Cited by 10 publications

References 34 publications

MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes

MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes

Advances in cold-adapted enzymes derived from microorganisms

Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria

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