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Mengkrog Holen M, Tuveng TR, Kent MP, Vaaje‐Kolstad G. The gastric mucosa of Atlantic salmon (Salmo salar) is abundant in highly active chitinases. FEBS Open Bio 2024; 14:23-36. [PMID: 37581908 PMCID: PMC10761930 DOI: 10.1002/2211-5463.13694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/19/2023] [Accepted: 08/14/2023] [Indexed: 08/16/2023] Open
Abstract
Atlantic salmon (Salmo salar) possesses a genome containing 10 genes encoding chitinases, yet their functional roles remain poorly understood. In other fish species, chitinases have been primarily linked to digestion, but also to other functions, as chitinase-encoding genes are transcribed in a variety of non-digestive organs. In this study, we investigated the properties of two chitinases belonging to the family 18 glycoside hydrolase group, namely Chia.3 and Chia.4, both isolated from the stomach mucosa. Chia.3 and Chia.4, exhibiting 95% sequence identity, proved inseparable using conventional chromatographic methods, necessitating their purification as a chitinase pair. Biochemical analysis revealed sustained chitinolytic activity against β-chitin for up to 24 h, spanning a pH range of 2 to 6. Moreover, subsequent in vitro investigations established that this chitinase pair efficiently degrades diverse chitin-containing substrates into chitobiose, highlighting the potential of Atlantic salmon to utilize novel chitin-containing feed sources. Analysis of the gastric matrix proteome demonstrates that the chitinases are secreted and rank among the most abundant proteins in the gastric matrix. This finding correlates well with the previously observed high transcription of the corresponding chitinase genes in Atlantic salmon stomach tissue. By shedding light on the secreted chitinases in the Atlantic salmon's stomach mucosa and elucidating their functional characteristics, this study enhances our understanding of chitinase biology in this species. Moreover, the observed capacity to effectively degrade chitin-containing materials implies the potential utilization of alternative feed sources rich in chitin, offering promising prospects for sustainable aquaculture practices.
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Affiliation(s)
- Matilde Mengkrog Holen
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of BiosciencesNorwegian University of Life SciencesÅsNorway
| | - Tina Rise Tuveng
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
| | - Matthew Peter Kent
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of BiosciencesNorwegian University of Life SciencesÅsNorway
| | - Gustav Vaaje‐Kolstad
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
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2
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Enuh BM, Nural Yaman B, Tarzi C, Aytar Çelik P, Mutlu MB, Angione C. Whole-genome sequencing and genome-scale metabolic modeling of Chromohalobacter canadensis 85B to explore its salt tolerance and biotechnological use. Microbiologyopen 2022; 11:e1328. [PMID: 36314754 PMCID: PMC9597258 DOI: 10.1002/mbo3.1328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022] Open
Abstract
Salt tolerant organisms are increasingly being used for the industrial production of high-value biomolecules due to their better adaptability compared to mesophiles. Chromohalobacter canadensis is one of the early halophiles to show promising biotechnology potential, which has not been explored to date. Advanced high throughput technologies such as whole-genome sequencing allow in-depth insight into the potential of organisms while at the frontiers of systems biology. At the same time, genome-scale metabolic models (GEMs) enable phenotype predictions through a mechanistic representation of metabolism. Here, we sequence and analyze the genome of C. canadensis 85B, and we use it to reconstruct a GEM. We then analyze the GEM using flux balance analysis and validate it against literature data on C. canadensis. We show that C. canadensis 85B is a metabolically versatile organism with many features for stress and osmotic adaptation. Pathways to produce ectoine and polyhydroxybutyrates were also predicted. The GEM reveals the ability to grow on several carbon sources in a minimal medium and reproduce osmoadaptation phenotypes. Overall, this study reveals insights from the genome of C. canadensis 85B, providing genomic data and a draft GEM that will serve as the first steps towards a better understanding of its metabolism, for novel applications in industrial biotechnology.
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Affiliation(s)
- Blaise Manga Enuh
- Biotechnology and Biosafety Department, Graduate and Natural Applied ScienceEskişehir Osmangazi UniversityEskişehirTurkey
| | - Belma Nural Yaman
- Biotechnology and Biosafety Department, Graduate and Natural Applied ScienceEskişehir Osmangazi UniversityEskişehirTurkey,Department of Biomedical Engineering, Faculty of Engineering and ArchitectureEskişehir Osmangazi UniversityEskişehirTurkey
| | - Chaimaa Tarzi
- School of Computing, Engineering & Digital TechnologiesTeesside UniversityMiddlesbroughUK
| | - Pınar Aytar Çelik
- Biotechnology and Biosafety Department, Graduate and Natural Applied ScienceEskişehir Osmangazi UniversityEskişehirTurkey,Environmental Protection and Control ProgramEskişehir Osmangazi UniversityEskişehirTurkey
| | - Mehmet Burçin Mutlu
- Department of Biology, Faculty of ScienceEskisehir Technical UniversityEskisehirTurkey
| | - Claudio Angione
- School of Computing, Engineering & Digital TechnologiesTeesside UniversityMiddlesbroughUK,Centre for Digital InnovationTeesside UniversityMiddlesbroughUK,National Horizons CentreTeesside UniversityDarlingtonUK
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Johan UUM, Rahman RNZRA, Kamarudin NHA, Latip W, Ali MSM. A new hyper-thermostable carboxylesterase from Anoxybacillus geothermalis D9. Int J Biol Macromol 2022; 222:2486-2497. [DOI: 10.1016/j.ijbiomac.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
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Draft Genome Sequence of
Virgibacillus
sp. Strain AGTR, Isolated from Hypersaline Lake Acıgöl in Turkey. Microbiol Resour Announc 2022; 11:e0055522. [PMID: 36043865 PMCID: PMC9584221 DOI: 10.1128/mra.00555-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virgibacillus sp. strain AGTR, which is a haloalkaliphilic microorganism, was isolated from a sediment sample collected in hypersaline Lake Acıgöl in Turkey. It has the potential to produce biotechnologically essential proteases. Here, the whole-genome sequence and its annotations are reported.
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Ding Y, Nie L, Yang XC, Li Y, Huo YY, Li Z, Gao Y, Cui HL, Li J, Xu XW. Mechanism and Structural Insights Into a Novel Esterase, E53, Isolated From Erythrobacter longus. Front Microbiol 2022; 12:798194. [PMID: 35069500 PMCID: PMC8767022 DOI: 10.3389/fmicb.2021.798194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Esterases are a class of enzymes that split esters into an acid and an alcohol in a chemical reaction with water, having high potential in pharmaceutical, food and biofuel industrial applications. To advance the understanding of esterases, we have identified and characterized E53, an alkalophilic esterase from a marine bacterium Erythrobacter longus. The crystal structures of wild type E53 and three variants were solved successfully using the X-ray diffraction method. Phylogenetic analysis classified E53 as a member of the family IV esterase. The enzyme showed highest activity against p-nitrophenyl butyrate substrate at pH 8.5-9.5 and 40°C. Based on the structural feature, the catalytic pocket was defined as R1 (catalytic center), R2 (pocket entrance), and R3 (end area of pocket) regions. Nine variants were generated spanning R1-R3 and thorough functional studies were performed. Detailed structural analysis and the results obtained from the mutagenesis study revealed that mutations in the R1 region could regulate the catalytic reaction in both positive and negative directions; expanding the bottleneck in R2 region has improved the enzymatic activity; and R3 region was associated with the determination of the pH pattern of E53. N166A in R3 region showed reduced activity only under alkaline conditions, and structural analysis indicated the role of N166 in stabilizing the loop by forming a hydrogen bond with L193 and G233. In summary, the systematic studies on E53 performed in this work provide structural and functional insights into alkaliphilic esterases and further our knowledge of these enzymes.
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Affiliation(s)
- Yi Ding
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | | | - Xiao-Chen Yang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Yang Li
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ying-Yi Huo
- Teaching Center of Biological Experiments, Zhejiang University, Hangzhou, China
| | - Zhengyang Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Gao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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Microbiota profiling and screening of the lipase active halotolerant yeasts of the olive brine. World J Microbiol Biotechnol 2021; 37:23. [PMID: 33428003 DOI: 10.1007/s11274-020-02976-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022]
Abstract
Searching for novel enzymes that could be active in organic solvents has become an area of interest in recent years. Olive brine naturally provides a suitable environment for the survival of halophilic and acidophilic microorganisms and the resulting genome is thought to be a gene source for determining the halophilic and acidophilic proteins that are active in a non-aqueous organic solvent medium, and so it has been used in several biotechnological and industrial applications. In this study, microbial analysis of natural, cracked green olive brine from the southern region of Turkey has been made by next-generation sequencing of the brine metagenome for the first time in the literature. The number of reads assigned to fungal operational taxonomic units was the highest percentage (73.04%) with the dominant representation of Ascomycota phylum (99% of fungi). Bacterial OTU was 3.56% of the reads and Proteobacteria phylum was 65% of the reads. The lipase production capacity of the yeasts that were grown on the media containing elevated concentrations of NaCl (1-3 M) was determined on a Rhodamine B-including medium. Molecular identification of the selected yeasts was performed and 90% of sequenced yeasts had a high level of similarity with Candida diddensiae, whereas 10% showed similarity to Candida boidinii. The hydrolytic lipase activities using olive oil were analyzed and both yeasts showed cell-bound lipase activity at pH 3.0.
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