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Gruninger RJ, Kevorkova M, Low KE, Jones DR, Worrall L, McAllister TA, Abbott DW. Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen. Protein J 2024:10.1007/s10930-024-10221-0. [PMID: 39153129 DOI: 10.1007/s10930-024-10221-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2024] [Indexed: 08/19/2024]
Abstract
Glucuronoyl esterases (GEs) are carbohydrate active enzymes in carbohydrate esterase family 15 which are involved in the hydrolysis of lignin-carbohydrate complexes. They are encoded by a wide range of aerobic and anaerobic fungi and bacteria inhabiting diverse environments. The rumen microbiome is a complex microbial community with a wide array of enzymes that specialize in deconstructing plant cell wall carbohydrates. Enzymes from the rumen tend to show low similarity to homologues found in other environments, making the rumen microbiome a promising source for the discovery of novel enzymes. Using a combination of phylogenetic and structural analysis, we investigated the structure-function relationship of GEs from the rumen bacteria Fibrobacter succinogenes and Ruminococcus flavefaciens, and from the rumen fungus, Piromyces rhizinflata. All adopt a canonical α/β hydrolase fold and possess a structurally conserved Ser-His-Glu/Asp catalytic triad. Structural variations in the enzymes are localized to loops surrounding the active site. Analysis of the active site structures in these enzymes emphasized the importance of structural plasticity in GEs with non-canonical active site conformations. We hypothesize that interkingdom HGT events may have contributed to the diversity of GEs in the rumen, and this is demonstrated by the phylogenetic and structural similarity observed between rumen bacterial and fungal GEs. This study advances our understanding of the structure-function relationship in glucuronoyl esterases and illuminates the evolutionary dynamics that contribute to enzyme diversity in the rumen microbiome.
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Affiliation(s)
- Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
| | - Maya Kevorkova
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Liam Worrall
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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Singh BN, Tabatabaei M, Pandit A, Elling L, Gupta VK. Emerging advances in glycoengineering of carbohydrates/glycans and their industrial applications. Biotechnol Adv 2024; 72:108324. [PMID: 38360155 DOI: 10.1016/j.biotechadv.2024.108324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Affiliation(s)
- Brahma N Singh
- Herbal Nanobiotechnology Lab, Pharmacology Division, CSIR-National Botanical Research Institute, Lucknow 226001, India
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Ireland
| | - Lothar Elling
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstraße 20, D-52074 Aachen, Germany
| | - Vijai Kumar Gupta
- School of Biotechnology, Dublin City University, Glasnevin, Dublin D09 K20V, Ireland; Biodesign Europe, Dublin City University, Glasnevin, Dublin D09 K20V, Ireland.
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Shi J, Zhang G, Ke W, Pan Y, Hou M, Chang C, Sa D, Lv M, Liu Y, Lu Q. Effect of endogenous sodium and potassium ions in plants on the quality of alfalfa silage and bacterial community stability during fermentation. FRONTIERS IN PLANT SCIENCE 2023; 14:1295114. [PMID: 38205017 PMCID: PMC10777314 DOI: 10.3389/fpls.2023.1295114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
This study investigated the impact of endogenous sodium and potassium ions in plants on the quality of alfalfa silage, as well as the stability of bacterial communities during fermentation. Silage was produced from the fermented alfalfa, and the chemical composition, fermentation characteristics, and microbiome were analyzed to understand their interplay and impact on silage fermentation quality. The alfalfa was cultivated under salt stress with the following: (a) soil content of <1‰ (CK); (b) 1‰-2‰ (LP); (c) 2‰-3‰ (MP); (d) 3‰-4‰ (HP). The results revealed that the pH of silage was negatively correlated with the lactic acid content. With the increase of lactic acid (LA) content increased (26.3-51.0 g/kg DM), the pH value decreased (4.9-5.3). With the increase of salt stress, the content of Na+ in silage increased (2.2-5.4 g/kg DM). The presence of endogenous Na+ and K+ ions in plants significantly affected the quality of alfalfa silage and the dynamics of bacterial communities during fermentation. Increased salt stress led to changes in microbial composition, with Lactococcus and Pantoea showing a gradual increase in abundance, especially under high salt stress. Low pH inhibited the growth of certain bacterial genera, such as Pantoea and Pediococcus. The abundance of Escherichia-Shigella and Comamonas negatively correlated with crude protein (CP) content, while Enterococcus and Lactococcus exhibited a positive correlation. Furthermore, the accumulation of endogenous Na+ in alfalfa under salt stress suppressed bacterial proliferation, thereby reducing protein degradation during fermentation. The pH of the silage was high, and the LA content was also high. Silages from alfalfa under higher salt stress had higher Na+ content. The alpha diversity of bacterial communities in alfalfa silages showed distinct patterns. Desirable genera like Lactococcus and Lactobacillus predominated in silages produced from alfalfa under salt stress, resulting in better fermentation quality.
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Affiliation(s)
- Jinhong Shi
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Guijie Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Wencan Ke
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Yongxiang Pan
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
| | - Meiling Hou
- College of Life Science, Baicheng Normal University, Baicheng, China
| | - Chun Chang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Duowen Sa
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Mingju Lv
- Inner Mongolia Agriculture and Animal Husbandry Extension Center, Hohhot, China
| | - Yinghao Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Qiang Lu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China
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