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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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Béchade B, Hu Y, Sanders JG, Cabuslay CS, Łukasik P, Williams BR, Fiers VJ, Lu R, Wertz JT, Russell JA. Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny. FEMS Microbiol Ecol 2022; 98:6602351. [PMID: 35660864 DOI: 10.1093/femsec/fiac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.
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Affiliation(s)
- Benoît Béchade
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Yi Hu
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America.,State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Christian S Cabuslay
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Piotr Łukasik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Bethany R Williams
- Department of Biology, Calvin College, Grand Rapids, Michigan, United States of America
| | - Valerie J Fiers
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Richard Lu
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - John T Wertz
- Department of Biology, Calvin College, Grand Rapids, Michigan, United States of America
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
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3
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Abstract
Carbohydrate esterases are a group of enzymes which release acyl or alkyl groups attached by ester linkage to carbohydrates. The CAZy database, which classifies enzymes that assemble, modify, and break down carbohydrates and glycoconjugates, classifies all carbohydrate esterases into 16 families. This chapter is an overview of the research for nearly 50 years around the main groups of carbohydrate esterases dealing with the degradation of polysaccharides, their main biochemical and molecular traits, as well as its application for the synthesis of high added value esters.
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Fan D, Liu L, Zhu L, Peng F, Zhou Q, Liu C. Global Analysis of the Impact of Deleting Trigger Factor on the Transcriptome Profile of Escherichia coli. J Cell Biochem 2016; 118:141-153. [PMID: 27279076 DOI: 10.1002/jcb.25620] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/07/2016] [Indexed: 11/12/2022]
Abstract
Trigger factor (TF) is a key component of prokaryotic chaperone network, which is involved various basic cellular processes such as nascent peptide folding, protein trafficking, ribosome assembly. To better understanding the physiological roles of TF, global transcriptome profiles of a variety of TF deletion mutant strains of Escherichia coli were determined. We found that deletion of the tig gene, encoding TF, led to a dramatic alteration of transcriptome profile, not only affecting the gene expression of members of the chaperone network, but also changing the levels of quite a few RNAs related to metabolism and other cellular processes. Further studies showed that this alteration was only partially recovered by knockin of TF domain-deletion mutants into the endogenous tig locus, indicating that structural integrity is crucial for the biological function of TF. Finally, by combining the transcriptome and phenotype results, a physiological mechanism underlying the impact of TF deletion on the transcriptome profile was proposed. J. Cell. Biochem. 118: 141-153, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Dongjie Fan
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin, 150080, China.,State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lushan Liu
- Department of Emergency, Beijing Bo'ai Hospital, 10 Jiaomen North Road, Fengtai District, Beijing 100068, China.,China Rehabilitation Research Center, Capital Medical University, Beijing 100068, China
| | - Lingxiang Zhu
- National Research Institute for Family Planning (NRIFP), Beijing 100081, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China.,Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan 430072, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin, 150080, China.,Beijing CapitalBio MedLab, 88 D2, Branch Six Street, Economic and Technological Development Zone, Beijing 101111, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin, 150080, China
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Kirsch R, Heckel DG, Pauchet Y. How the rice weevil breaks down the pectin network: Enzymatic synergism and sub-functionalization. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 71:72-82. [PMID: 26899322 DOI: 10.1016/j.ibmb.2016.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/12/2016] [Accepted: 02/14/2016] [Indexed: 05/19/2023]
Abstract
Pectin is the most complex polysaccharide in nature and highly abundant in plant cell walls and middle lamellae, where it functions in plant growth and development. Phytopathogens utilize plant pectin as an energy source through enzyme-mediated degradation. These pectolytic enzymes include polygalacturonases (PGs) of the GH28 family and pectin methylesterases (PMEs) of the CE8 family. Recently, PGs were also identified in herbivorous insects of the distantly related plant bug, stick insect and Phytophaga beetle lineages. Unlike all other insects, weevils possess PMEs in addition to PGs. To investigate pectin digestion in insects and the role of PMEs in weevils, all PME and PG family members of the rice weevil Sitophilus oryzae were heterologously expressed and functionally characterized. Enzymatically active and inactive PG and PME family members were identified. The loss of activity can be explained by a lack of substrate binding correlating with substitutions of functionally important amino acid residues. We found subfunctionalization in both enzyme families, supported by expression pattern and substrate specificities as well as evidence for synergistic pectin breakdown. Our data suggest that the rice weevil might be able to use pectin as an energy source, and illustrates the potential of both PG and PME enzyme families to functionally diversify after horizontal gene transfer.
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Affiliation(s)
- Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, Jena, 07745, Germany.
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, Jena, 07745, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, Jena, 07745, Germany.
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Teller DC, Behnke CA, Pappan K, Shen Z, Reese JC, Reeck GR, Stenkamp RE. The structure of rice weevil pectin methylesterase. Acta Crystallogr F Struct Biol Commun 2014; 70:1480-4. [PMID: 25372813 PMCID: PMC4231848 DOI: 10.1107/s2053230x14020433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/11/2014] [Indexed: 11/10/2022] Open
Abstract
Rice weevils (Sitophilus oryzae) use a pectin methylesterase (EC 3.1.1.11), along with other enzymes, to digest cell walls in cereal grains. The enzyme is a right-handed β-helix protein, but is circularly permuted relative to plant and bacterial pectin methylesterases, as shown by the crystal structure determination reported here. This is the first structure of an animal pectin methylesterase. Diffraction data were collected to 1.8 Å resolution some time ago for this crystal form, but structure solution required the use of molecular-replacement techniques that have been developed and similar structures that have been deposited in the last 15 years. Comparison of the structure of the rice weevil pectin methylesterase with that from Dickeya dandantii (formerly Erwinia chrysanthemi) indicates that the reaction mechanisms are the same for the insect, plant and bacterial pectin methylesterases. The similarity of the structure of the rice weevil enzyme to the Escherichia coli lipoprotein YbhC suggests that the evolutionary origin of the rice weevil enzyme was a bacterial lipoprotein, the gene for which was transferred to a primitive ancestor of modern weevils and other Curculionidae. Structural comparison of the rice weevil pectin methylesterase with plant and bacterial enzymes demonstrates that the rice weevil protein is circularly permuted relative to the plant and bacterial molecules.
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Affiliation(s)
- David C. Teller
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
| | - Craig A. Behnke
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
| | - Kirk Pappan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Zicheng Shen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - John C. Reese
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Gerald R. Reeck
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Ronald E. Stenkamp
- Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA
- Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195-7742, USA
- Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195-7420, USA
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Evangelista DE, Schutzer de Godoy A, Fonseca Pereira de Paula F, Henrique-Silva F, Polikarpov I. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the pectin methylesterase from the sugar cane weevil Sphenophorus levis. Acta Crystallogr F Struct Biol Commun 2014; 70:331-4. [PMID: 24598920 PMCID: PMC3944695 DOI: 10.1107/s2053230x14001630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 01/22/2014] [Indexed: 11/11/2022] Open
Abstract
Pectin methylesterase removes the methyl groups from the main chain of pectin, the major component of the middle lamella of the plant cell wall. The enzyme is involved in plant cell-wall development, is part of the enzymatic arsenal used by microorganisms to attack plants and also has a wide range of applications in the industrial sector. Therefore, there is a considerable interest in studies of the structure and function of this enzyme. In this work, the pectin methylesterase from Sphenophorus levis was produced in Pichia pastoris and purified. Crystals belonging to the monoclinic space group C2, with unit-cell parameters a = 122.181, b = 82.213, c = 41.176 Å, β = 97.48°, were obtained by the sitting-drop vapour-diffusion method and an X-ray diffraction data set was collected to 2.1 Å resolution. Structure refinement and model building are in progress.
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Affiliation(s)
- Danilo Elton Evangelista
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Andre Schutzer de Godoy
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Fernando Fonseca Pereira de Paula
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Carlos-SP, Brazil
| | - Flavio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235, 13565-905 São Carlos-SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Sãocarlense 400, 13566-590 São Carlos-SP, Brazil
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Boraston AB, Abbott DW. Structure of a pectin methylesterase from Yersinia enterocolitica. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:129-33. [PMID: 22297983 DOI: 10.1107/s1744309111055400] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 12/23/2011] [Indexed: 11/11/2022]
Abstract
Pectin methylesterases (PMEs) are family 8 carbohydrate esterases (CE8s) which remove the methyl group from methylesterified galacturonic acid (GalA) residues within pectin. Although the role of pectinases such as PMEs within dedicated phytopathogens has been well established, the significance of homologous enzymes found within the genomes of human enteropathogens remains to be determined. Presented here is the low-resolution (3.5 Å) structure of the CE8 from Yersinia enterocolitica (YeCE8). The high degree of structural conservation in the topology of the active-site cleft and catalytic apparatus that is shared with a characterized PME from a bacterial phytopathogen (i) indicates that YeCE8 is active on methylated pectin and (ii) highlights a more prominent role for pectin utilization in Yersinia than in other enteropathogenic species.
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Affiliation(s)
- Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Pectin methylesterase and its proteinaceous inhibitor: a review. Carbohydr Res 2010; 345:2583-95. [DOI: 10.1016/j.carres.2010.10.002] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 09/30/2010] [Accepted: 10/03/2010] [Indexed: 11/23/2022]
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