Crystal Structure of GH49 Dextranase from <i>Arthrobacter oxidans</i> KQ11: Identification of Catalytic Base and Improvement of Thermostability Using Semirational Design Based on <i>B</i>-Factors

Ren, Wei; Liu, Le; Gu, Lide; Yan, Wanli; Ye, Feng; Dong, Dongxue; Wang, Shujun; Lyu, Mingsheng; Wang, Changhai

doi:10.1021/acs.jafc.9b01290

Cited by 31 publications

(34 citation statements)

References 53 publications

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“…Another SNP (S20_15783417) was also found to be significantly associated with both germination rates at two stages (Table 4, Figure 3). This SNP is located on a gene encoding dextranase, which is a marine enzyme usually secreted by bacteria, showing high salt tolerance [42]. In plants, dextranase enzyme function could be related to the breakdown of dextran (a long chain sugar molecule) in sugar manufacture [43].…”

Section: Gwas Analysis Of Seedling Germination Traits Under Salt Stressmentioning

confidence: 99%

Genome-Wide Association Study (GWAS) Analysis of Camelina Seedling Germination under Salt Stress Condition

2020

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Camelina sativa is an important renewable oilseed crop for biofuel and feedstock that can relieve the reliance on petroleum-derived oils and reduce greenhouse gases and waste solids resulting from petroleum-derived oils consumption. C. sativa has recently seen revived attention due to its high oil content, high omega-3 unsaturated fatty acids, short life cycle, broader regional adaptation, and low-input agronomic requirements. However, abiotic stress such as salinity stress has imposed threatens on plant photosynthesis and growth by reducing water availability or osmotic stress, ion (Na+ and Cl−) toxicity, nutritional disorders and oxidative stress yield. There still remains much to know for the molecular mechanisms underlying these effects. In this study, a preliminary study applying 10 C. sativa cultivars to be treated under a gradient NaCl concentrations ranging from 0–250 mM and found that 100 mM was the optimal NaCl concentration to effectively differentiate phenotypic performance among different genotypes. Then, a spring panel consisting of 211 C. sativa accessions were germinated under 100 mM NaCl concentration. Six seedling germination traits, including germination rate at two stages (5-day and 9-day seedling stages), germination index, dry and fresh weight, and dry/fresh ratio, were measured. Significant correlations were found between the germination rate at two stages as well as plant biomass traits. Combining the phenotypic data and previously obtained genotypic data, a total of 17 significant trait-associated single nucleotide polymorphisms (SNPs) for the germination rate at the two stages and dry weight were identified from genome-wide association analysis (GWAS). These SNPs are located on putative candidate genes controlling plant root development by synergistically mediating phosphate metabolism, signal transduction and cell membrane activities. These identified SNPs could provide a foundation for future molecular breeding efforts aimed at improved salt tolerance in C. sativa.

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Section: Gwas Analysis Of Seedling Germination Traits Under Salt Stressmentioning

confidence: 99%

Genome-Wide Association Study (GWAS) Analysis of Camelina Seedling Germination under Salt Stress Condition

2020

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“…In addition, the oceans, which covers more than three quarters of the Earth's surface, is an open ecosystem. It has been estimated that at least 50%, and potentially more than 90%, of all marine species are undescribed [33][34][35][36]. Marine microorganisms have been recognized as potential sources of novel enzymes with better biocatalytic properties than their terrestrial counterparts.…”

Section: Introductionmentioning

confidence: 99%

“…Marine microorganisms have been recognized as potential sources of novel enzymes with better biocatalytic properties than their terrestrial counterparts. These properties, such as salt tolerance, hyperthermostability, barophilicity, alkali-resistance, and low optimum temperatures, are necessary for e cient bioprocesses exploitation [33][34][35][36]. Hainan is a big maritime province in China and rich in marine resources, but the knowledge of cellulolytic microbes isolated from this area is limited.…”

Section: Introductionmentioning

confidence: 99%

Isolation and Characterization of Cellulolytic Marine Bacteria for Litopenaeus Vannamei Aquaculture Using Sugarcane Bagasse as Carbon Source

Wei¹,

Xu²,

Long³

et al. 2020

Preprint

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Background: In aquaculture system, it is essential to adjust the inherent disadvantage of C/N ratio by adding a lot of additional carbon sources, such as sugarcane molasses, organic acids, and organic acid salts, which will greatly increase the cost of shrimp aquaculture. Herein, we aimed to isolate cellulolytic marine bacteria to hydrolyze sugarcane bagasse (SB) for reducing the cost of addition of external carbon sources in industrial Litopenaeus vannamei aquaculture.Results: A total of 97 cellulolytic marine bacterial strains belonged to 6 genera were isolated from 2,585 indigenous bacteria, indicating that seagrass bed can be used as an important place for screening the cellulolytic bacteria. The hydrolysis capacity (HC) of 58 cellulolytic marine bacterial strains was ranged from 1.1–4.0. MW-M5 displayed the largest HC value, followed by MW-M10 and MW-M14. The cellulase contents of 30 strains were more than 3 U/g in the supernatant of fermentation broth after 24 h, which was significantly higher than that of commercial cellulose. 26 cellulolytic marine bacteria with HC greater than 2 were safe for L. vannamei. MW-M19 with the lowest multiple antibiotic resistance index, 0.1, had a highest SB enzyme activity, 4.14 U/mL. The SB decomposition rates of CFW-C18 and MW-M15 were up to about 63.81% and 48.57% after fifteen days, respectively. Conclusions: These results provide valuable information for further construction of a shrimp aquaculture system based on low-cost external carbon sources using cellulolytic bacteria, and even for other biotechnological applications.

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“…Dextranases have drawn considerable attention due to their high potential for application in various fields, including in medical, dental, and sugar industries [30–36]. Dextranases (α-1,6-D-glucan 6-glucanohydrolase; EC 3.2.1.11) hydrolyze dextran to oligosaccharides at the α-1,6 glucosidic bond and are members of the glycoside hydrolase families (GH) 49 and 66 based on amino acid sequence homology [32, 37–39].…”

Section: Introductionmentioning

confidence: 99%

“…Dextranases (α-1,6-D-glucan 6-glucanohydrolase; EC 3.2.1.11) hydrolyze dextran to oligosaccharides at the α-1,6 glucosidic bond and are members of the glycoside hydrolase families (GH) 49 and 66 based on amino acid sequence homology [32, 37–39]. A. oxidans KQ11 was previously isolated by our research group from the Yellow Sea in the Lianyungang coastal region of China and produces dextranase (Aodex, Protein Data Bank code 6NZS) [36]. Here, we present a systematic study of the effects of repetitive dosing of various concentrations of Mg–Fe-LDH NPs on the marine bacterium A. oxidans KQ11 and its ability to produce Aodex.…”

Section: Introductionmentioning

confidence: 99%

Characterization and mechanism of the effects of Mg–Fe layered double hydroxide nanoparticles on a marine bacterium: new insights from genomic and transcriptional analyses

Ren

Ding²,

Gu³

et al. 2019

Biotechnol Biofuels

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Background Layered double hydroxides (LDHs) have received widespread attention for their potential applications in catalysis, polymer nanocomposites, pharmaceuticals, and sensors. Here, the mechanism underlying the physiological effects of Mg–Fe layered double hydroxide nanoparticles on the marine bacterial species Arthrobacter oxidans KQ11 was investigated. Results Increased yields of marine dextranase (Aodex) were obtained by exposing A. oxidans KQ11 to Mg–Fe layered double hydroxide nanoparticles (Mg–Fe-LDH NPs). Furthermore, the potential effects of Mg–Fe-LDH NPs on bacterial growth and Aodex production were preliminarily investigated. A. oxidans KQ11 growth was not affected by exposure to the Mg–Fe-LDH NPs. In contrast, a U-shaped trend of Aodex production was observed after exposure to NPs at a concentration of 10 μg/L–100 mg/L, which was due to competition between Mg–Fe-LDH NP adsorption on Aodex and the promotion of Aodex expression by the NPs. The mechanism underling the effects of Mg–Fe-LDH NPs on A. oxidans KQ11 was investigated using a combination of physiological characterization, genomics, and transcriptomics. Exposure to 100 mg/L of Mg–Fe-LDH NPs led to NP adsorption onto Aodex, increased expression of Aodex , and generation of a new Shine-Dalgarno sequence (GGGAG) and sRNAs that both influenced the expression of Aodex . Moreover, the expressions of transcripts related to ferric iron metabolic functions were significantly influenced by treatment. Conclusions These results provide valuable information for further investigation of the A. oxidans KQ11 response to Mg–Fe-LDH NPs and will aid in achieving improved marine dextranase production, and even improve such activities in other marine microorganisms. Electronic supplementary material The online version of this article (10.1186/s13068-019-1528-2) contains supplementary material, which is available to authorized users.

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Crystal Structure of GH49 Dextranase from Arthrobacter oxidans KQ11: Identification of Catalytic Base and Improvement of Thermostability Using Semirational Design Based on B-Factors

Cited by 31 publications

References 53 publications

Genome-Wide Association Study (GWAS) Analysis of Camelina Seedling Germination under Salt Stress Condition

Genome-Wide Association Study (GWAS) Analysis of Camelina Seedling Germination under Salt Stress Condition

Isolation and Characterization of Cellulolytic Marine Bacteria for Litopenaeus Vannamei Aquaculture Using Sugarcane Bagasse as Carbon Source

Characterization and mechanism of the effects of Mg–Fe layered double hydroxide nanoparticles on a marine bacterium: new insights from genomic and transcriptional analyses

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