Heterologous Expression of Thermogutta terrifontis Endo-Xanthanase in Penicillium verruculosum, Isolation and Primary Characterization of the Enzyme

Denisenko, Yury A.; Короткова, О. Г.; Зоров, И. Н.; Рожкова, А. М.; Семенова, М. В.; Elcheninov, Alexandr G.; Kublanov, Ilya V.; Sinitsyn, A. P.

doi:10.1134/s000629792104009x

Cited by 6 publications

(9 citation statements)

References 12 publications

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“…CCNA_01705 is encoded near the lactose 3-dehydrogenase ( Fig 6B ) and contains a single DUF1080 domain (PF06439). The only characterized proteins with this domain architecture that we are aware of are the 3-ketotrehalose hydrolase BT2157 [ 8 ] and the endo-xanthanase/lichenase THTE_1561 [ 33 ]. Since 3-ketotrehalose and 3’-ketolactose are similar compounds, we propose that CCNA_01705 is the 3’-ketolactose hydrolase of C .…”

Section: Resultsmentioning

confidence: 99%

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

2022

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To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29 bacteria, we systematically examined the gaps in GapMind’s predicted pathways, and we used the mutant fitness data to find additional genes that were involved in their utilization. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server (http://papers.genomics.lbl.gov/carbon) and takes just 30 seconds for the typical genome.

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Section: Resultsmentioning

confidence: 99%

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

2022

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“…We found that in C. crescentus NA1000, CCNA_01705 is important for lactose utilization (Figure 6A) and is encoded near the lactose 3-dehydrogenase (Figure 6B). CCNA_01705 contains a single DUF1080 domain (PF06439), and the only characterized proteins with this domain architecture that we are aware of are the 3-ketotrehalose hydrolase BT2157 (Liu et al 2021) and the endo-xanthanase/lichenase THTE_1561 (Denisenko et al 2021). Since 3-ketotrehalose and 3'-ketolactose are similar compounds, we propose that CCNA_01705 is the 3'-ketolactose hydrolase of C. crescentus.…”

Section: Lactose Utilization Via a Putative Periplasmic 3'-ketolactose Hydrolasementioning

confidence: 96%

GapMind for Carbon Sources: Automated annotations of catabolic pathways

Price

Deutschbauer

Arkin

2021

Preprint

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GapMind for carbon sources is an automated tool for annotating catabolic pathways in bacterial and archaeal genomes. GapMind includes 62 compounds and identifies potential transporters and enzymes by their similarity to experimentally-characterized proteins. To improve GapMind’s coverage, we used high-throughput genetic data from 29 bacteria and systematically examined the gaps. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server (http://papers.genomics.lbl.gov/carbon) and takes just 30 seconds for the typical genome.

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“…terrifontis R1(T); heterologous host Penicillium verruculosum 537 (ΔniaD) 23.7 kDa Activity (U/mg) on native xanthan (0.12), CMC (0.58), β-glucan (0.56), curdlan (0.12), lichenan (1.48), laminarin (0.17), galactomannan (0.12), xyloglucan (0.18). Xanthan lyase increased the efficiency of xanthan hydrolysis pH 4.0, 55 °C; 90% of activity retained at 50–60 °C, pH 3–5; 30% of activity retained at pH 2 and 6, and at 80 °C Denisenko et al 2021 Xanthan-specific endo-(1,4)-β- d -glucanase Mi GH (WP_067195711, GH5, EC 3.2.1.-) Microbacterium sp. XT11 47 kDa Cleaved endo-β-(1,4)-glycosidic linkages of the native xanthan was not active on the lyase-treated xanthan pH 6.0, 35–40 °C.…”

Section: Bacterial Xanthan-specific Enzymesmentioning

confidence: 99%

“…Furthermore, apart from xanthan, this enzyme hydrolyzed CMC, β-glucan, curdlan, lichenan, laminarin, galactomannan, and xyloglucan. The advantageous combination of thermostability at 60 °C, broad substrate specificity, and small size (23.7 kDa) positions DUF1080 as a promising candidate for various technical applications (Denisenko et al 2021 ).…”

Section: Bacterial Xanthan-specific Enzymesmentioning

confidence: 99%

Xanthan: enzymatic degradation and novel perspectives of applications

Berezina,

Rykov,

Schwarz

et al. 2024

Appl Microbiol Biotechnol

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The extracellular heteropolysaccharide xanthan, synthesized by bacteria of the genus Xanthomonas, is widely used as a thickening and stabilizing agent across the food, cosmetic, and pharmaceutical sectors. Expanding the scope of its application, current efforts target the use of xanthan to develop innovative functional materials and products, such as edible films, eco-friendly oil surfactants, and biocompatible composites for tissue engineering. Xanthan-derived oligosaccharides are useful as nutritional supplements and plant defense elicitors. Development and processing of such new functional materials and products often necessitate tuning of xanthan properties through targeted structural modification. This task can be effectively carried out with the help of xanthan-specific enzymes. However, the complex molecular structure and intricate conformational behavior of xanthan create problems with its enzymatic hydrolysis or modification. This review summarizes and analyzes data concerning xanthan-degrading enzymes originating from microorganisms and microbial consortia, with a particular focus on the dependence of enzymatic activity on the structure and conformation of xanthan. Through a comparative study of xanthan-degrading pathways found within various bacterial classes, different microbial enzyme systems for xanthan utilization have been identified. The characterization of these new enzymes opens new perspectives for modifying xanthan structure and developing innovative xanthan-based applications. Key points • The structure and conformation of xanthan affect enzymatic degradation. • Microorganisms use diverse multienzyme systems for xanthan degradation. • Xanthan-specific enzymes can be used to develop xanthan variants for novel applications.

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Heterologous Expression of Thermogutta terrifontis Endo-Xanthanase in Penicillium verruculosum, Isolation and Primary Characterization of the Enzyme

Cited by 6 publications

References 12 publications

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

GapMind for Carbon Sources: Automated annotations of catabolic pathways

Xanthan: enzymatic degradation and novel perspectives of applications

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