Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism

Takase, Ryuichi; Mikami, Bunzo; Kawai, Shigeyuki; Murata, Kousaku; Hashimoto, Wataru

doi:10.1074/jbc.m114.585661

Cited by 43 publications

(67 citation statements)

References 67 publications

(33 reference statements)

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“…UMI-0128 and Sphingomonas sp. A12930 are 40.08% and 33.08% respectively. The catalytic tetrad Asn-Tyr-Lys-Ser and the cofactor-binding sequence motif Thr-Gly-X-X-X-Gly-X-Gly were also found in Bw805 (Fig.…”

Section: Resultsmentioning

confidence: 95%

Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation

Zhu

Chen

Bao

et al. 2016

Sci Rep

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A novel marine strain representing efficient degradation ability toward brown algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The alga-associated marine bacteria promote the nutrient cycle and perform important functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis Alg07 genome was carried out. Results of gene annotation and carbohydrate-active enzyme analysis showed that the strain harbored enzymes that can completely degrade alginate and laminarin, which are the specific polysaccharides of brown algae. We also found genes for the utilization of mannitol, the major storage monosaccharide in the cell of brown algae. To understand the process of brown algae decomposition by B. weihaiensis Alg07, RNA-seq transcriptome analysis and qRT-PCR were performed. The genes involved in alginate metabolism were all up-regulated in the initial stage of kelp degradation, suggesting that the strain Alg07 first degrades alginate to destruct the cell wall so that the laminarin and mannitol are released and subsequently decomposed. The key genes involved in alginate and laminarin degradation were expressed in Escherichia coli and characterized. Overall, the model of brown algae degradation by the marine strain Alg07 was established, and novel alginate lyases and laminarinase were discovered.

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Section: Resultsmentioning

confidence: 95%

Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation

Zhu

Chen

Bao

et al. 2016

Sci Rep

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“…A1 NAD(P)H-dependent DEH reductase (A1-R’) 19 , E. coli KdgK 28 , and E. coli KDPG aldolase (Eda) 29 (Fig. 1).…”

Section: Resultsmentioning

confidence: 99%

Crucial role of 4-deoxy-L-erythro-5-hexoseulose uronate reductase for alginate utilization revealed by adaptive evolution in engineered Saccharomyces cerevisiae

Matsuoka

Hirayama

Kashihara

et al. 2017

Sci Rep

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In brown macroalgae, alginate and D-mannitol are promising carbohydrates for biorefinery. Saccharomyces cerevisiae is widely used as a microbial cell factory, but this budding yeast is unable to utilize either alginate or D-mannitol. Alginate can be depolymerized by both endo-type and exo-type alginate lyases, yielding a monouronate, 4-deoxy-L-erythro-5-hexoseulose uronate (DEH), a key intermediate in the metabolism of alginate. Here, we constructed engineered two S. cerevisiae strains that are able to utilize both DEH and D-mannitol on two different strain backgrounds, and we also improved their aerobic growth in a DEH liquid medium through adaptive evolution. In both evolved strains, one of the causal mutations was surprisingly identical, a c.50A > G mutation in the codon-optimized NAD(P)H-dependent DEH reductase gene, one of the 4 genes introduced to confer the capacity to utilize DEH. This mutation resulted in an E17G substitution at a loop structure near the coenzyme-binding site of this reductase, and enhanced the reductase activity and aerobic growth in both evolved strains. Thus, the crucial role for this reductase reaction in the metabolism of DEH in the engineered S. cerevisiae is demonstrated, and this finding provides significant information for synthetic construction of a S. cerevisiae strain as a platform for alginate utilization.

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“…-4.2 (Liang et al 2007) P. stipitis XR 1K8C (h) K270R, N272D 2.9 9.3 -1.2 (Maddock et al 2015) E. coli CaADH 1KEV (h) G198D, S199V, P201E, Y218A >1 ? -4.6 (Maurer et al 2005) B Log Relative Activity c (Medina et al 2001) A. PCC7119 FDNR 2BSA S223D 0.12 8.1x10 3 -5.4 (Nakanishi et al 1997) M. musculus CR 1CYD T38D 31 1.3x10 3 -0.51 (Paladini et al 2009 (Schepens et al 2000) S. bicolor MDH 7MDH (1CIV) G84D, S85I, R87Q, S88A 12 2.1x10 4 -0.96 (Scrutton et al 1990) E. coli GTR 1GET A179G, A183G, V197E, R198M, K199F, H200D, R204P 8.1 1.8x10 4 -1.5 (Shiraishi et al 1998) N. crassa CbR S920D, R932S 65 7.2x10 4 -2.6 (Takase et al 2014) S. sp. A1-R 3AFN H37N, G38S, R39H, K40V, A41D >1 ?…”

mentioning

confidence: 99%

A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases

et al. 2016

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Structure-based Conversion of the Coenzyme Requirement of a Short-chain Dehydrogenase/Reductase Involved in Bacterial Alginate Metabolism

Cited by 43 publications

References 67 publications

Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation

Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation

Crucial role of 4-deoxy-L-erythro-5-hexoseulose uronate reductase for alginate utilization revealed by adaptive evolution in engineered Saccharomyces cerevisiae

A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases

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