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Sousa J, Santos-Pereira C, Gomes JS, Costa ÂMA, Santos AO, Franco-Duarte R, Linhares JMM, Sousa SF, Silvério SC, Rodrigues LR. Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library. Appl Microbiol Biotechnol 2024; 108:329. [PMID: 38727750 PMCID: PMC11087322 DOI: 10.1007/s00253-024-13169-4] [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: 01/10/2024] [Revised: 04/22/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Xylanases are key biocatalysts in the degradation of the β-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-β-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-β-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.
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Affiliation(s)
- Joana Sousa
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cátia Santos-Pereira
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana S Gomes
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ângela M A Costa
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andréia O Santos
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S - Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - João M M Linhares
- Physics Center of Minho and Porto Universities (CF-UM-UP), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sérgio F Sousa
- LAQV/REQUIMTE BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sara C Silvério
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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Liew KJ, Shahar S, Shamsir MS, Shaharuddin NB, Liang CH, Chan KG, Pointing SB, Sani RK, Goh KM. Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation. ENVIRONMENTAL MICROBIOME 2024; 19:29. [PMID: 38706006 PMCID: PMC11071339 DOI: 10.1186/s40793-024-00572-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism. RESULTS Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures. CONCLUSIONS This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.
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Grants
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- 4J549 UTM QuickWin grant
- 4J549 UTM QuickWin grant
- T2EP30123-0028 Singapore Ministry of Education ARC Tier 2 fund
- 1736255, 1849206, and 1920954 National Science Foundation
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Affiliation(s)
- Kok Jun Liew
- Codon Genomics, 42300 Seri Kembangan, Selangor, Malaysia
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Nawal Binti Shaharuddin
- School of Professional and Continuing Education, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Chee Hung Liang
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Stephen Brian Pointing
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
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Zhu L, Li W, Huang C, Tian Y, Xi B. Functional redundancy is the key mechanism used by microorganisms for nitrogen and sulfur metabolism during manure composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169389. [PMID: 38104842 DOI: 10.1016/j.scitotenv.2023.169389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
The microbial ecological functions associated with the nitrogen and sulfur cycles during composting have not been thoroughly elucidated. Using metagenomic sequencing, the microbial mechanisms underlying the nitrogen and sulfur metabolism during livestock and poultry manure composting were investigated in this study. The findings demonstrate that functional redundancy among microorganisms is a crucial factor for the nitrogen and sulfur cycling during livestock and poultry manure composting. Processes such as organic sulfur synthesis, assimilatory sulfate reduction, ammonia assimilation, and denitrification were found to be prevalent. Additionally, there was a certain degree of conservation in nitrogen and sulfur conversion functions among microorganisms at the phylum level. All high-quality metagenomic assembly genomes (MAGs) possessed carbon fixation potential, with 86.3 % of MAGs containing both nitrogen and sulfur conversion genes. Except for bin30, other MAGs encoding sulfur oxidation enzymes were found to be associated with at least one denitrification gene. This suggests a potential interplay between nitrogen and sulfur metabolism among microorganisms. 45, 19, 1, 31, 1, and 2 MAGs could completely regulate organic sulfur synthesis, assimilatory sulfate reduction, thiosulfate oxidation to sulfate, glutamine synthase-glutamate synthase pathway (GS-GOGAT), denitrification, and dissimilatory nitrate reduction, respectively by encoding the required enzymes. TN and pH were the key factors driving the functional redundancy in nitrogen and sulfur microbial community.
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Affiliation(s)
- Lin Zhu
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Li
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Caihong Huang
- State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Yu Tian
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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Chopra A, Franco-Duarte R, Rajagopal A, Choowong P, Soares P, Rito T, Eberhard J, Jayasinghe TN. Exploring the presence of oral bacteria in non-oral sites of patients with cardiovascular diseases using whole metagenomic data. Sci Rep 2024; 14:1476. [PMID: 38233502 PMCID: PMC10794416 DOI: 10.1038/s41598-023-50891-x] [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: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024] Open
Abstract
Cardiovascular diseases (CVDs) encompass various conditions affecting the heart and its blood vessels and are often linked with oral microbes. Our data analysis aimed to identify oral bacteria from other non-oral sites (i.e., gut, arterial plaque and cultured blood) that could be linked with CVDs. Taxonomic profiling identified bacteria to the species level and compared with the Human Oral Microbiome Database (HOMD). The oral bacteria in the gut, cultured blood and arterial plaque samples were catalogued, with their average frequency calculated for each sample. Additionally, data were filtered by comparison with the Human Microbiome Project (HMP) database. We identified 17,243 microbial species, of which 410 were present in the HOMD database and further denominated as "oral", and were found in at least one gut sample, but only 221 and 169 species were identified in the cultured blood and plaque samples, respectively. Of the 410 species, 153 were present solely in oral-associated environments after comparison with the HMP database, irrespective of their presence in other body sites. Our results suggest a potential connection between the presence of specific species of oral bacterial and occurrence of CVDs. Detecting these oral bacterial species in non-oral sites of patients with CVDs could help uncover the link between oral health and general health, including cardiovascular conditions via bacterial translocation.
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Affiliation(s)
- Aditi Chopra
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ricardo Franco-Duarte
- Department of Biology, CBMA (Center of Molecular and Environmental Biology), University of Minho, Braga, Portugal
- Institute of Science and Innovation for Biosustainability (IB-S), University of Minho, Braga, Portugal
| | - Anjale Rajagopal
- Department of Periodontology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Phannaphat Choowong
- School of Dentistry, Faculty of Medicine and Health, The University of Sydney, University of Sydney, Sydney, Australia
| | - Pedro Soares
- Department of Biology, CBMA (Center of Molecular and Environmental Biology), University of Minho, Braga, Portugal
- Institute of Science and Innovation for Biosustainability (IB-S), University of Minho, Braga, Portugal
| | - Teresa Rito
- Department of Biology, CBMA (Center of Molecular and Environmental Biology), University of Minho, Braga, Portugal
- Institute of Science and Innovation for Biosustainability (IB-S), University of Minho, Braga, Portugal
| | - Joerg Eberhard
- School of Dentistry, Faculty of Medicine and Health, The University of Sydney, University of Sydney, Sydney, Australia
| | - Thilini N Jayasinghe
- School of Dentistry, Faculty of Medicine and Health, The University of Sydney, University of Sydney, Sydney, Australia.
- The Charles Perkins Centre, The University of Sydney, University of Sydney, Sydney, Australia.
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