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Carbone V, Reilly K, Sang C, Schofield LR, Ronimus RS, Kelly WJ, Attwood GT, Palevich N. Crystal Structures of Bacterial Pectin Methylesterases Pme8A and PmeC2 from Rumen Butyrivibrio. Int J Mol Sci 2023; 24:13738. [PMID: 37762041 PMCID: PMC10530356 DOI: 10.3390/ijms241813738] [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: 08/14/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Pectin is a complex polysaccharide that forms a substantial proportion of the plant's middle lamella of forage ingested by grazing ruminants. Methanol in the rumen is derived mainly from methoxy groups released from pectin by the action of pectin methylesterase (PME) and is subsequently used by rumen methylotrophic methanogens that reduce methanol to produce methane (CH4). Members of the genus Butyrivibrio are key pectin-degrading rumen bacteria that contribute to methanol formation and have important roles in fibre breakdown, protein digestion, and the biohydrogenation of fatty acids. Therefore, methanol release from pectin degradation in the rumen is a potential target for CH4 mitigation technologies. Here, we present the crystal structures of PMEs belonging to the carbohydrate esterase family 8 (CE8) from Butyrivibrio proteoclasticus and Butyrivibrio fibrisolvens, determined to a resolution of 2.30 Å. These enzymes, like other PMEs, are right-handed β-helical proteins with a well-defined catalytic site and reaction mechanisms previously defined in insect, plant, and other bacterial pectin methylesterases. Potential substrate binding domains are also defined for the enzymes.
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Affiliation(s)
| | | | | | | | | | | | | | - Nikola Palevich
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand; (V.C.); (K.R.); (C.S.); (L.R.S.); (R.S.R.); (W.J.K.); (G.T.A.)
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Sechovcová H, Rudl Kulhavá L, Fliegerová K, Killer J, Kopečný J. Advantages of label free method in comparison with 2DE proteomic analysis of Butyrivibrio fibrisolvens 3071 grown on different carbon sources. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2129477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hana Sechovcová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | | | - Kateřina Fliegerová
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
| | - Jiří Killer
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, CAS, Laboratory of Anaerobic Microbiology, Prague, Czech Republic
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Sechovcová H, Kulhavá L, Fliegerová K, Trundová M, Morais D, Mrázek J, Kopečný J. Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources. Proteome Sci 2019; 17:2. [PMID: 31168299 PMCID: PMC6545216 DOI: 10.1186/s12953-019-0150-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/15/2019] [Indexed: 01/12/2023] Open
Abstract
Background The rumen microbiota is one of the most complex consortia of anaerobes, involving archaea, bacteria, protozoa, fungi and phages. They are very effective at utilizing plant polysaccharides, especially cellulose and hemicelluloses. The most important hemicellulose decomposers are clustered with the genus Butyrivibrio. As the related species differ in their range of hydrolytic activities and substrate preferences, Butyrivibrio fibrisolvens was selected as one of the most effective isolates and thus suitable for proteomic studies on substrate comparisons in the extracellular fraction. The B. fibrisolvens genome is the biggest in the butyrivibria cluster and is focused on “environmental information processing” and “carbohydrate metabolism”. Methods The study of the effect of carbon source on B. fibrisolvens 3071 was based on cultures grown on four substrates: xylose, glucose, xylan, xylan with 25% glucose. The enzymatic activities were studied by spectrophotometric and zymogram methods. Proteomic study was based on genomics, 2D electrophoresis and nLC/MS (Bruker Daltonics) analysis. Results Extracellular β-endoxylanase as well as xylan β-xylosidase activities were induced with xylan. The presence of the xylan polymer induced hemicellulolytic enzymes and increased the protein fraction in the interval from 40 to 80 kDa. 2D electrophoresis with nLC/MS analysis of extracellular B. fibrisolvens 3071 proteins found 14 diverse proteins with significantly different expression on the tested substrates. Conclusion The comparison of four carbon sources resulted in the main significant changes in B. fibrisolvens proteome occurring outside the fibrolytic cluster of proteins. The affected proteins mainly belonged to the glycolysis and protein synthesis cluster. Electronic supplementary material The online version of this article (10.1186/s12953-019-0150-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hana Sechovcová
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic.,5Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 166 286 Prague, Czech Republic
| | - Lucie Kulhavá
- 2Institute of Physiology, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic.,4Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Kateřina Fliegerová
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Mária Trundová
- 3Institute of Biotechnology, CAS, v.v.i., Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Daniel Morais
- 6Institute of Microbiology, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jakub Mrázek
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Jan Kopečný
- 1Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, 142 20 Prague, Czech Republic
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Butyrivibrio hungatei MB2003 Competes Effectively for Soluble Sugars Released by Butyrivibrio proteoclasticus B316 T during Growth on Xylan or Pectin. Appl Environ Microbiol 2019; 85:AEM.02056-18. [PMID: 30478228 PMCID: PMC6344614 DOI: 10.1128/aem.02056-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/29/2018] [Indexed: 11/25/2022] Open
Abstract
Feeding a future global population of 9 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Butyrivibrio species are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings suggest that closely related species of Butyrivibrio have developed unique strategies for the degradation of plant fiber and the subsequent assimilation of carbohydrates in order to coexist in the competitive rumen environment. The identification of genes expressed during these competitive interactions gives further insight into the enzymatic machinery used by these bacteria as they degrade the xylan and pectin components of plant fiber. Rumen bacterial species belonging to the genus Butyrivibrio are important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four species are recognized; they have very similar substrate utilization profiles, but little is known about how these microorganisms are able to coexist in the rumen. To investigate this question, Butyrivibrio hungatei MB2003 and Butyrivibrio proteoclasticus B316T were grown alone or in coculture on xylan or pectin, and their growth, release of sugars, fermentation end products, and transcriptomes were examined. In monocultures, B316T was able to grow well on xylan and pectin, while MB2003 was unable to utilize either of these insoluble substrates to support significant growth. Cocultures of B316T grown with MB2003 revealed that MB2003 showed growth almost equivalent to that of B316T when either xylan or pectin was supplied as the substrate. The effect of coculture on the transcriptomes of B316T and MB2003 was assessed; B316T transcription was largely unaffected by the presence of MB2003, but MB2003 expressed a wide range of genes encoding proteins for carbohydrate degradation, central metabolism, oligosaccharide transport, and substrate assimilation, in order to compete with B316T for the released sugars. These results suggest that B316T has a role as an initiator of primary solubilization of xylan and pectin, while MB2003 competes effectively for the released soluble sugars to enable its growth and maintenance in the rumen. IMPORTANCE Feeding a future global population of 9 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Butyrivibrio species are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings suggest that closely related species of Butyrivibrio have developed unique strategies for the degradation of plant fiber and the subsequent assimilation of carbohydrates in order to coexist in the competitive rumen environment. The identification of genes expressed during these competitive interactions gives further insight into the enzymatic machinery used by these bacteria as they degrade the xylan and pectin components of plant fiber.
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Su M, Nie Y, Shao R, Duan S, Jiang Y, Wang M, Xing Z, Sun Q, Liu X, Xu W. Diversified gut microbiota in newborns of mothers with gestational diabetes mellitus. PLoS One 2018; 13:e0205695. [PMID: 30332459 PMCID: PMC6192631 DOI: 10.1371/journal.pone.0205695] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
Gestational diabetes mellitus (GDM), a high-risk pregnancy complication of great effect on the perinatal health of women and newborns, may cause changes of gut microbiota in mothers and further affect gut microbiota in newborns. This study aimed to investigate the potential effect of mother GDM on newborns’ gut microbiota. Meconium DNA was extracted from a total of 34 full-term and C-sectioned newborns, in which 20 newborns had mothers diagnosed with GDM, while 14 had unaffected mothers. Sequencing and bioinformatics analysis of 16S rRNA indicated that the gut microbiota of GDM newborns showed differences compared to control newborns. The taxonomy analyses suggested that the overall bacterial content significantly differed by maternal diabetes status, with the microbiome of the GDM group showing lower alpha-diversity than that of control group. The phyla of Proteobacteria and Actinobacteria in GDM newborns increased, while that of Bacteroidetes significantly reduced (P<0.05). Moreover, several unique gut microbiota in phylum of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Planctomycetes found in control newborns were absent in GDM ones. At genus level, the relative abundance of Prevotella and Lactobacillus significantly decreased (P<0.05) in GDM newborns. Correlation analysis indicated that maternal fasting glucose levels were positively correlated with the relative abundance of phylum Actinobacteria and genus Acinetobacter, while negatively correlated with that of phylum Bacteroidetes and genus Prevotella. However, bacteria in GDM grade A2 (GDM_A2) newborns did not show any statistical variation compared to those from control newborns, which might be attributed to the additional intervention by insulin. The results of this study have important implications for understanding the potential effects of GDM on the gut microbiota of newborns and thus possibly their metabolism at later stages in their lives.
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Affiliation(s)
- Minglian Su
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- Department of Obstetric and Gynecologic Diseases, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- West China School of Clinical Medicine, Sichuan University, Chengdu, P. R. China
| | - Yuanyang Nie
- Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, P. R. China
| | - Ruocheng Shao
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- West China School of Clinical Medicine, Sichuan University, Chengdu, P. R. China
| | - Shihao Duan
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- West China School of Clinical Medicine, Sichuan University, Chengdu, P. R. China
| | - Youhui Jiang
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- West China School of Clinical Medicine, Sichuan University, Chengdu, P. R. China
| | - Mingyue Wang
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- West China School of Clinical Medicine, Sichuan University, Chengdu, P. R. China
| | - Zhichao Xing
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- West China School of Clinical Medicine, Sichuan University, Chengdu, P. R. China
| | - Qun Sun
- College of Life Sciences, Sichuan University, Chengdu, P. R. China
| | - Xinghui Liu
- Department of Obstetric and Gynecologic Diseases, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- * E-mail: (XW); (LX)
| | - Wenming Xu
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- Department of Obstetric and Gynecologic Diseases, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
- * E-mail: (XW); (LX)
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Li Z, Bai H, Zheng L, Jiang H, Cui H, Cao Y, Yao J. Bioactive polysaccharides and oligosaccharides as possible feed additives to manipulate rumen fermentation in Rusitec fermenters. Int J Biol Macromol 2018; 109:1088-1094. [DOI: 10.1016/j.ijbiomac.2017.11.098] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
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