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Chen B, Liu G, Chen Q, Wang H, Liu L, Tang K. Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes. Comput Struct Biotechnol J 2024; 23:406-416. [PMID: 38235362 PMCID: PMC10792170 DOI: 10.1016/j.csbj.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024] Open
Abstract
Members of the phylum Bacteroidetes play a key role in the marine carbon cycle through their degradation of polysaccharides via carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs). The discovery of novel CAZymes and PULs is important for our understanding of the marine carbon cycle. In this study, we isolated and identified a potential new genus of the family Catalimonadaceae, in the phylum Bacteroidetes, from the southwest Indian Ocean. Strain TK19036, the type strain of the new genus, is predicted to encode CAZymes that are relatively abundant in marine Bacteroidetes genomes. Tunicatimonas pelagia NBRC 107804T, Porifericola rhodea NBRC 107748T and Catalinimonas niigatensis NBRC 109829T, which exhibit 16 S rRNA similarities exceeding 90% with strain TK19036, and belong to the same family, were selected as reference strains. These organisms possess a highly diverse repertoire of CAZymes and PULs, which may enable them to degrade a wide range of polysaccharides, especially pectin and alginate. In addition, some secretory CAZymes in strain TK19036 and its relatives were predicted to be transported by type IX secretion system (T9SS). Further, to the best of our knowledge, we propose the first reported "hybrid" PUL targeting alginates in T. pelagia NBRC 107804T. Our findings provide new insights into the polysaccharide degradation capacity of marine Bacteroidetes, and suggest that T9SS may play a more important role in this process than previously believed.
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Guohua Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Huanyu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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2
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Mei X, Tao W, Sun H, Liu G, Chen G, Zhang Y, Xue C, Chang Y. Characterization and structural identification of a novel alginate-specific carbohydrate-binding module (CBM): The founding member of a new CBM family. Int J Biol Macromol 2024; 277:134221. [PMID: 39069041 DOI: 10.1016/j.ijbiomac.2024.134221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Alginate is a commercially important polysaccharide widely distributed in brown algae. Carbohydrate-binding modules (CBMs), a class of commonly used polysaccharide-binding proteins, have greatly facilitated the investigations of polysaccharides. Few alginate-binding CBMs have been hitherto reported and structurally characterized. Herein, an unknown domain from a potential PL6 family alginate lyase in the marine bacterium Vibrio breoganii was discovered and recombinantly expressed. The obtained protein, designated VbCBM106, displayed the favorable specificity to alginate. The unique sequence and well-defined function of VbCBM106 reveal a new CBM family (CBM106). Moreover, the structure of VbCBM106 was determined at a 1.5 Å resolution by the X-ray crystallography, which shows a typical β-sandwich fold comprised of two antiparallel β-sheets. Site-directed mutagenesis assays confirmed that positively charged polar residues are crucial for the ligand binding of VbCBM106. The discovery of VbCBM106 enriches the toolbox of alginate-binding proteins, and the elucidation of critical residues would guide the future practical applications of VbCBM106.
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Affiliation(s)
- Xuanwei Mei
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China
| | - Wenwen Tao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China
| | - Haitao Sun
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China
| | - Guanchen Liu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China
| | - Guangning Chen
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China
| | - Yuying Zhang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China
| | - Changhu Xue
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China
| | - Yaoguang Chang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao, 266404, China.
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3
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Sakoh T, Satoh N, Domon Y, Nakamura M, Kawakita M, Sakaguchi M. Aromatic residues in N-terminal domain of archaeal trehalase affect the folding and activity of catalytic domain. Appl Microbiol Biotechnol 2024; 108:441. [PMID: 39145831 PMCID: PMC11327188 DOI: 10.1007/s00253-024-13205-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 08/16/2024]
Abstract
Considering the structure of the bacterial GH15 family glucoamylase (GA), Thermoplasma trehalase Tvn1315 may be composed of a β-sandwich domain (BD) and a catalytic domain (CD). Tvn1315 BD weakly binds to insoluble β-glucans, such as cellulose, and helps fold CD. To determine how aromatic residues contribute to proper folding and enzyme activity, we performed alanine scanning for 32 aromatic residues in the BD. The study did not identify a single residue involved in glucan binding. However, several aromatic residues were found to be involved in BD or CD folding and in modulating the activity of the full-length enzyme. Among those aromatic residue mutations, the W43A mutation led to reduced solubility of the BD and full-length protein and resulted in a full-length enzyme with significantly lower activity. The activity of W43F and W43Y was significantly higher than that of W43A. In addition, Ala substitutions of Tyr83, Tyr113, and Tyr17 led to a reduction in trehalase activity, but Phe substitutions of these residues could be tolerated, as these mutants maintained activities similar to WT activity. Thus, these aromatic residues in BD may interact with CD and modulate enzyme activity. KEY POINTS: • Aromatic residues in the BD are involved in BD and CD folding. • Aromatic residues in the BD near the CD active site modulate enzyme activity. • BD interacts with CD and closely modulates enzyme activity.
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Affiliation(s)
- Takumi Sakoh
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-Cho, Hachioji, Tokyo, 192-0015, Japan
| | - Nagisa Satoh
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-Cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yumeka Domon
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-Cho, Hachioji, Tokyo, 192-0015, Japan
| | - Maho Nakamura
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-Cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masao Kawakita
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-Cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masayoshi Sakaguchi
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-Cho, Hachioji, Tokyo, 192-0015, Japan.
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Dong N, Jiao G, Cao R, Li S, Zhao S, Duan Y, Ma L, Li X, Lu F, Wang H, Wang S, Shao G, Sheng Z, Hu S, Tang S, Wei X, Hu P. OsLESV and OsESV1 promote transitory and storage starch biosynthesis to determine rice grain quality and yield. PLANT COMMUNICATIONS 2024; 5:100893. [PMID: 38581128 PMCID: PMC11287174 DOI: 10.1016/j.xplc.2024.100893] [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: 01/22/2024] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Transitory starch is an important carbon source in leaves, and its biosynthesis and metabolism are closely related to grain quality and yield. The molecular mechanisms controlling leaf transitory starch biosynthesis and degradation and their effects on rice (Oryza sativa) quality and yield remain unclear. Here, we show that OsLESV and OsESV1, the rice orthologs of AtLESV and AtESV1, are associated with transitory starch biosynthesis in rice. The total starch and amylose contents in leaves and endosperms are significantly reduced, and the final grain quality and yield are compromised in oslesv and osesv1 single and oslesv esv1 double mutants. Furthermore, we found that OsLESV and OsESV1 bind to starch, and this binding depends on a highly conserved C-terminal tryptophan-rich region that acts as a starch-binding domain. Importantly, OsLESV and OsESV1 also interact with the key enzymes of starch biosynthesis, granule-bound starch synthase I (GBSSI), GBSSII, and pyruvate orthophosphote dikiase (PPDKB), to maintain their protein stability and activity. OsLESV and OsESV1 also facilitate the targeting of GBSSI and GBSSII from plastid stroma to starch granules. Overexpression of GBSSI, GBSSII, and PPDKB can partly rescue the phenotypic defects of the oslesv and osesv1 mutants. Thus, we demonstrate that OsLESV and OsESV1 play a key role in regulating the biosynthesis of both leaf transitory starch and endosperm storage starch in rice. These findings deepen our understanding of the molecular mechanisms underlying transitory starch biosynthesis in rice leaves and reveal how the transitory starch metabolism affects rice grain quality and yield, providing useful information for the genetic improvement of rice grain quality and yield.
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Affiliation(s)
- Nannan Dong
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ruijie Cao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Sanfeng Li
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaolu Zhao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Yingqing Duan
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Liuyang Ma
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xinwei Li
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Feifei Lu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Hong Wang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shiwen Wang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Peisong Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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5
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You Y, Kong H, Li C, Gu Z, Ban X, Li Z. Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes. Biotechnol Adv 2024; 73:108365. [PMID: 38677391 DOI: 10.1016/j.biotechadv.2024.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Carbohydrate binding modules (CBMs) are independent non-catalytic domains widely found in carbohydrate-active enzymes (CAZymes), and they play an essential role in the substrate binding process of CAZymes by guiding the appended catalytic modules to the target substrates. Owing to their precise recognition and selective affinity for different substrates, CBMs have received increasing research attention over the past few decades. To date, CBMs from different origins have formed a large number of families that show a variety of substrate types, structural features, and ligand recognition mechanisms. Moreover, through the modification of specific sites of CBMs and the fusion of heterologous CBMs with catalytic domains, improved enzymatic properties and catalytic patterns of numerous CAZymes have been achieved. Based on cutting-edge technologies in computational biology, gene editing, and protein engineering, CBMs as auxiliary components have become portable and efficient tools for the evolution and application of CAZymes. With the aim to provide a theoretical reference for the functional research, rational design, and targeted utilization of novel CBMs in the future, we systematically reviewed the function-related characteristics and potentials of CAZyme-derived CBMs in this review, including substrate recognition and binding mechanisms, non-catalytic contributions to enzyme performances, module modifications, and innovative applications in various fields.
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Affiliation(s)
- Yuxian You
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Haocun Kong
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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6
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Zhuang Y, Guo W, Cui K, Tu Y, Diao Q, Zhang N, Bi Y, Ma T. Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer. Microbiol Spectr 2024; 12:e0131423. [PMID: 38014976 PMCID: PMC10871699 DOI: 10.1128/spectrum.01314-23] [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: 03/27/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.
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Affiliation(s)
- Yimin Zhuang
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Kai Cui
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Tu
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiyu Diao
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Naifeng Zhang
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanliang Bi
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Ma
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
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Brown HA, DeVeaux AL, Juliano BR, Photenhauer AL, Boulinguiez M, Bornschein RE, Wawrzak Z, Ruotolo BT, Terrapon N, Koropatkin NM. BoGH13A Sus from Bacteroides ovatus represents a novel α-amylase used for Bacteroides starch breakdown in the human gut. Cell Mol Life Sci 2023; 80:232. [PMID: 37500984 PMCID: PMC10540511 DOI: 10.1007/s00018-023-04812-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 07/29/2023]
Abstract
Members of the Bacteroidetes phylum in the human colon deploy an extensive number of proteins to capture and degrade polysaccharides. Operons devoted to glycan breakdown and uptake are termed polysaccharide utilization loci or PUL. The starch utilization system (Sus) is one such PUL and was initially described in Bacteroides thetaiotaomicron (Bt). BtSus is highly conserved across many species, except for its extracellular α-amylase, SusG. In this work, we show that the Bacteroides ovatus (Bo) extracellular α-amylase, BoGH13ASus, is distinguished from SusG in its evolutionary origin and its domain architecture and by being the most prevalent form in Bacteroidetes Sus. BoGH13ASus is the founding member of both a novel subfamily in the glycoside hydrolase family 13, GH13_47, and a novel carbohydrate-binding module, CBM98. The BoGH13ASus CBM98-CBM48-GH13_47 architecture differs from the CBM58 embedded within the GH13_36 of SusG. These domains adopt a distinct spatial orientation and invoke a different association with the outer membrane. The BoCBM98 binding site is required for Bo growth on polysaccharides and optimal enzymatic degradation thereof. Finally, the BoGH13ASus structure features bound Ca2+ and Mn2+ ions, the latter of which is novel for an α-amylase. Little is known about the impact of Mn2+ on gut bacterial function, much less on polysaccharide consumption, but Mn2+ addition to Bt expressing BoGH13ASus specifically enhances growth on starch. Further understanding of bacterial starch degradation signatures will enable more tailored prebiotic and pharmaceutical approaches that increase starch flux to the gut.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Anna L DeVeaux
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Matthieu Boulinguiez
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | | | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Lemont, IL, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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An Y, Tran PL, Yoo MJ, Song HN, Park KH, Kim TJ, Park JT, Woo EJ. The Distinctive Permutated Domain Structure of Periplasmic α-Amylase (MalS) from Glycoside Hydrolase Family 13 Subfamily 19. Molecules 2023; 28:molecules28103972. [PMID: 37241718 DOI: 10.3390/molecules28103972] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Periplasmic α-amylase MalS (EC. 3.2.1.1), which belongs to glycoside hydrolase (GH) family 13 subfamily 19, is an integral component of the maltose utilization pathway in Escherichia coli K12 and used among Ecnterobacteriaceae for the effective utilization of maltodextrin. We present the crystal structure of MalS from E. coli and reveal that it has unique structural features of circularly permutated domains and a possible CBM69. The conventional C-domain of amylase consists of amino acids 120-180 (N-terminal) and 646-676 (C-terminal) in MalS, and the whole domain architecture shows the complete circular permutation of C-A-B-A-C in domain order. Regarding substrate interaction, the enzyme has a 6-glucosyl unit pocket binding it to the non-reducing end of the cleavage site. Our study found that residues D385 and F367 play important roles in the preference of MalS for maltohexaose as an initial product. At the active site of MalS, β-CD binds more weakly than the linear substrate, possibly due to the positioning of A402. MalS has two Ca2+ binding sites that contribute significantly to the thermostability of the enzyme. Intriguingly, the study found that MalS exhibits a high binding affinity for polysaccharides such as glycogen and amylopectin. The N domain, of which the electron density map was not observed, was predicted to be CBM69 by AlphaFold2 and might have a binding site for the polysaccharides. Structural analysis of MalS provides new insight into the structure-evolution relationship in GH13 subfamily 19 enzymes and a molecular basis for understanding the details of catalytic function and substrate binding of MalS.
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Affiliation(s)
- Yan An
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Phuong Lan Tran
- Department of Food Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- Department of Food Technology, An Giang University, Long Xuyen 880000, Vietnam
- Vietnam National University-Ho Chi Minh City, Ho Chi Minh 700000, Vietnam
| | - Min-Jee Yoo
- Department of Food Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Hyung-Nam Song
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Kwang-Hyun Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Tae-Jip Kim
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jong-Tae Park
- Department of Food Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Eui-Jeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
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Sequence-structural features and evolution of the α-amylase family GH119 revealed by the in silico analysis of its relatedness to the family GH57. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01349-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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10
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Wang Y, Wu Y, Christensen SJ, Janeček Š, Bai Y, Møller MS, Svensson B. Impact of Starch Binding Domain Fusion on Activities and Starch Product Structure of 4-α-Glucanotransferase. Molecules 2023; 28:molecules28031320. [PMID: 36770986 PMCID: PMC9920598 DOI: 10.3390/molecules28031320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
A broad range of enzymes are used to modify starch for various applications. Here, a thermophilic 4-α-glucanotransferase from Thermoproteus uzoniensis (TuαGT) is engineered by N-terminal fusion of the starch binding domains (SBDs) of carbohydrate binding module family 20 (CBM20) to enhance its affinity for granular starch. The SBDs are N-terminal tandem domains (SBDSt1 and SBDSt2) from Solanum tuberosum disproportionating enzyme 2 (StDPE2) and the C-terminal domain (SBDGA) of glucoamylase from Aspergillus niger (AnGA). In silico analysis of CBM20s revealed that SBDGA and copies one and two of GH77 DPE2s belong to well separated clusters in the evolutionary tree; the second copies being more closely related to non-CAZyme CBM20s. The activity of SBD-TuαGT fusions increased 1.2-2.4-fold on amylose and decreased 3-9 fold on maltotriose compared with TuαGT. The fusions showed similar disproportionation activity on gelatinised normal maize starch (NMS). Notably, hydrolytic activity was 1.3-1.7-fold elevated for the fusions leading to a reduced molecule weight and higher α-1,6/α-1,4-linkage ratio of the modified starch. Notably, SBDGA-TuαGT and-SBDSt2-TuαGT showed Kd of 0.7 and 1.5 mg/mL for waxy maize starch (WMS) granules, whereas TuαGT and SBDSt1-TuαGT had 3-5-fold lower affinity. SBDSt2 contributed more than SBDSt1 to activity, substrate binding, and the stability of TuαGT fusions.
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Affiliation(s)
- Yu Wang
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Yazhen Wu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Stefan Jarl Christensen
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
| | - Yuxiang Bai
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Marie Sofie Møller
- Applied Molecular Enzyme Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Correspondence: (M.S.M.); (B.S.)
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Correspondence: (M.S.M.); (B.S.)
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11
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Duan K, Ban X, Wang Y, Li C, Gu Z, Li Z. Improving the Product Specificity of Maltotetraose-Forming Amylase from Pseudomonas saccharophila STB07 by Removing the Carbohydrate-Binding Module. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13709-13718. [PMID: 36238980 DOI: 10.1021/acs.jafc.2c05580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Maltotetraose (G4) is composed of four glucose units linked by the α-1,4-glycosidic bond, which has excellent adaptability in food processing and specific physiological functions. Maltotetraose-forming amylases (MFAses) are used in the industry as a promising tool for G4 production. The MFAse from Pseudomonas saccharophila STB07 (MFAPS), which belongs to the GH13, can preferentially hydrolyze substrates to G4. MFAPS contains a carbohydrate-binding module (CBM). In this study, we removed the CBM to obtain the mutant MFAPS-ΔCBM. We explored the aspects affecting the catalytic performance of enzymes through structural simulations and molecular docking. Results showed that when the CBM was removed, the thermal stability of MFAPS was slightly reduced, and its catalytic ability for long-chain substrates, such as corn starch, was significantly reduced. However, the catalytic ability and product specificity of the substrates with shorter chain length, such as maltodextrin (DE 7-9), were improved. The G1-G7 (glucose (G1), maltose (G2), maltotriose (G3), maltotetraose (G4), maltopentaose (G5), maltohexaose (G6), and maltoheptaose (G7)) contents and G4 proportion of the mutant MFAPS-ΔCBM reaction at 24 h were 11.1 and 11.6% higher than those of MFAPS, respectively. The results also showed that the forces of MFAPS on the substrate near the -4, -1, +1, and +3 subsites were critical for its product specificity.
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Affiliation(s)
- Kaiwen Duan
- School of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
| | - Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
| | - Yinglan Wang
- School of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu214122, People's Republic of China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu214122, People's Republic of China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi214122, People's Republic of China
- Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu214122, People's Republic of China
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12
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In-Depth Characterization of Debranching Type I Pullulanase from Priestia koreensis HL12 as Potential Biocatalyst for Starch Saccharification and Modification. Catalysts 2022. [DOI: 10.3390/catal12091014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pullulanase is an effective starch debranching enzyme widely used in starch saccharification and modification. In this work, the biochemical characteristics and potential application of a new type I pullulanase from Priestia koreensis HL12 (HL12Pul) were evaluated and reported for the first time. Through in-depth evolutionary analysis, HL12Pul was classified as type I pullulanase belonging to glycoside hydrolase family 13, subfamily 14 (GH13_14). HL12Pul comprises multi-domains architecture, including two carbohydrate-binding domains, CBM68 and CBM48, at the N-terminus, the TIM barrel structure of glycoside hydrolase family 13 (GH13) and C-domain. Based on sequence analysis and experimental cleavage profile, HL12Pul specifically hydrolyzes only α-1,6 glycosidic linkage-rich substrates. The enzyme optimally works at 40 °C, pH 6.0, with the maximum specific activity of 181.14 ± 3.55 U/mg protein and catalytic efficiency (kcat/Km) of 49.39 mL/mg·s toward pullulan. In addition, HL12Pul worked in synergy with raw starch-degrading α-amylase, promoting raw cassava starch hydrolysis and increasing the sugar yield by 2.9-fold in comparison to the α-amylase alone in a short reaction time. Furthermore, HL12Pul effectively produces type III-resistant starch (RSIII) from cassava starch with a production yield of 70%. These indicate that HL12Pul has the potential as a biocatalyst for starch saccharification and modification.
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13
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Chen L, Du M, Wang L, Yu W, Chen Y, Cheng B, Wu J. Maize STARCH SYNTHESIS REGULATING PROTEIN1 positively regulates starch biosynthesis in rice endosperm. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:773-783. [PMID: 35491402 DOI: 10.1071/fp21338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Starch is a major component of the endosperm, directly determining grain yield and quality. Although the key enzymes of starch synthesis have been identified and characterised, the regulatory mechanisms remain unclear. In this study, we identified the novel maize STARCH SYNTHESIS REGULATING PROTEIN1 (ZmSSRP1 ), which encodes a typical carbohydrate-binding module 48 (CBM48) protein. Expression analysis revealed that ZmSSRP1 was highly expressed in the maize endosperm, while transient expression in maize leaf protoplasts showed localisation in the plastids, dependent on the N-terminal transit peptide. In addition, overexpression of ZmSSRP1 in rice resulted in a decrease in grain thickness and the 1000-grain weight, as well as affecting the starch content and structure of the rice endosperm. The physicochemical properties of starch in the rice endosperm were also altered compared with the wild-type seeds. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was subsequently performed to determine the expression of starch synthesis-related genes, revealing upregulation of mRNA expression of most genes in the transgenic compared with wild-type lines. Collectively, these findings suggest that ZmSSRP1 acts as a potential regulator of starch synthesis, providing new insight for molecular breeding of high-yielding high-quality maize.
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Affiliation(s)
- Long Chen
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Ming Du
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China; and Shanghai Zhongke Quanyin Molecular Breeding Technology, Shanghai 200030, China
| | - Long Wang
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Wei Yu
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yirong Chen
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Jiandong Wu
- National Engineering Laboratory of Crop Stress Resistance, College of Life Science, Anhui Agricultural University, Hefei 230036, Anhui, China
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14
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A Maize CBM Domain Containing the Protein ZmCBM48-1 Positively Regulates Starch Synthesis in the Rice Endosperm. Int J Mol Sci 2022; 23:ijms23126598. [PMID: 35743040 PMCID: PMC9223709 DOI: 10.3390/ijms23126598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 12/05/2022] Open
Abstract
Starch directly determines the grain yield and quality. The key enzymes participating in the process of starch synthesis have been cloned and characterized. Nevertheless, the regulatory mechanisms of starch synthesis remain unclear. In this study, we identified a novel starch regulatory gene, ZmCBM48-1, which contained a carbohydrate-binding module 48 (CBM48) domain. ZmCBM48-1 was highly expressed in the maize endosperm and was localized in the plastids. Compared with the wild type lines, the overexpression of ZmCBM48-1 in rice altered the grain size and 1000-grain weight, increased the starch content, and decreased the soluble sugar content. Additionally, the transgenic rice seeds exhibited an alterant endosperm cell shape and starch structure. Meanwhile, the physicochemical characteristics (gelatinization properties) of starch were influenced in the transgenic lines of the endosperm compared with the wild type seeds. Furthermore, ZmCBM48-1 played a positive regulatory role in the starch synthesis pathway by up-regulating several starch synthesis-related genes. Collectively, the results presented here suggest that ZmCBM48-1 acts as a key regulatory factor in starch synthesis, and could be helpful for devising strategies for modulating starch production for a high yield and good quality in maize endosperm.
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15
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Hedin N, Velazquez MB, Barchiesi J, Gomez-Casati DF, Busi MV. CBM20CP, a novel functional protein of starch metabolism in green algae. PLANT MOLECULAR BIOLOGY 2022; 108:363-378. [PMID: 34546521 DOI: 10.1007/s11103-021-01190-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/20/2021] [Indexed: 05/29/2023]
Abstract
Ostreococcus tauri is a picoalga that contains a small and compact genome, which resembles that of higher plants in the multiplicity of enzymes involved in starch synthesis (ADP-glucose pyrophosphorylase, ADPGlc PPase; granule bound starch synthase, GBSS; starch synthases, SSI, SSII, SSIII; and starch branching enzyme, SBE, between others), except starch synthase IV (SSIV). Although its genome is fully sequenced, there are still many genes and proteins to which no function was assigned. Here, we identify the OT_ostta06g01880 gene that encodes CBM20CP, a plastidial protein which contains a central carbohydrate binding domain of the CBM20 family, and a coiled coil domain at the C-terminus that lacks catalytic activity. We demonstrate that CBM20CP has the ability to bind starch, amylose and amylopectin with different affinities. Furthermore, this protein interacts with OsttaSSIII-B, increasing its binding to starch granules, its catalytic efficiency and promoting granule growth. The results allow us to postulate a functional role for CBM20CP in starch metabolism in green algae. KEY MESSAGE: CBM20CP, a plastidial protein that has a modular structure but lacks catalytic activity, regulates the synthesis of starch in Ostreococcus tauri.
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Affiliation(s)
- Nicolas Hedin
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Maria B Velazquez
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Julieta Barchiesi
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Maria V Busi
- CEFOBI - CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas Y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
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16
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Zhang L, Li N, Zhang J, Zhao L, Qiu J, Wei C. The CBM48 domain-containing protein FLO6 regulates starch synthesis by interacting with SSIVb and GBSS in rice. PLANT MOLECULAR BIOLOGY 2022; 108:343-361. [PMID: 34387795 DOI: 10.1007/s11103-021-01178-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/30/2021] [Indexed: 05/27/2023]
Abstract
FLO6 is involved in starch synthesis by interacting with SSIVb and GBSS in rice. Starch synthesized and stored in plastids including chloroplasts and amyloplasts plays a vital role in plant growth and provides the major energy for human diet. However, the molecular mechanisms by which regulate starch synthesis remain largely unknown. In this study, we identified and characterized a rice floury endosperm mutant M39, which exhibited defective starch granule formation in pericarp and endosperm, accompanied by the decreased starch content and amylose content. The abnormal starch accumulation in M39 pollen grains caused a significant decrease in plant fertility. Chloroplasts in M39 leaves contained no or only one large starch granule. Positional cloning combined with complementary experiment demonstrated that the mutant phenotypes were restored by the FLOURY ENDOSPERM6 (FLO6). FLO6 was generally expressed in various tissues, including leaf, anther and developing endosperm. FLO6 is a chloroplast and amyloplast-localized protein that is able to bind to starch by its carbohydrate-binding module 48 (CBM48) domain. Interestingly, we found that FLO6 interacted with starch synthase IVb (SSIVb) and granule-bound starch synthase (GBSSI and GBSSII). Together, our results suggested that FLO6 plays a critical role in starch synthesis through cooperating with several starch synthesis enzymes throughout plant growth and development.
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Affiliation(s)
- Long Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Ning Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Jing Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Linglong Zhao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Jiajing Qiu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Cunxu Wei
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
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17
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Ban X, Xi S, Jiang H, Gu Z, Li C, Cheng L, Hong Y, Li Z. The amino acid on the top of the active groove allosterically modulates product specificity of the 1,4-α-glucan branching enzyme. Food Chem 2022; 384:132458. [PMID: 35219229 DOI: 10.1016/j.foodchem.2022.132458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 01/02/2023]
Abstract
The 1,4-α-glucan branching enzymes (GBEs, EC 2.4.1.18) catalyse the formation of α-1,6 branching points in starch, presenting several potential applications in modifying starch. Previous study proved that W285 is considered to act as a "switch" to stop extension of substrates in the structure of GBE from Cyanothece sp. (cceBE). In the structure of GBE from Rhodothermus obamensis STB05 (RoGBE), the amino acid 160 site is structurally similar to the W285 in cceBE. In order to explore the role of this site in RoGBE, several engineered mutants individually substituted with Arg, Phe and Ala at G160 were studied in our research. The results show that substitution with Arg and Phe increased branching activity significantly, and the ratio of short glucan chains among all oligosaccharides increased. Finally, we proposed that the G160 is a 'door model' to elucidate introduced mutagenesis that triggers and controls the length of binding glucan chains of starch.
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Affiliation(s)
- Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shixia Xi
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Haimin Jiang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China
| | - Caiming Li
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Li Cheng
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yan Hong
- The Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi 214122, China.
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18
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Conchou L, Martin J, Gonçalves IR, Galisson F, Violot S, Guillière F, Aghajari N, Ballut L. The Candida glabrata glycogen branching enzyme structure reveals unique features of branching enzymes of the Saccharomycetaceae phylum. Glycobiology 2021; 32:343-355. [PMID: 34939121 DOI: 10.1093/glycob/cwab110] [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: 07/21/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Branching enzymes (BE) are responsible for the formation of branching points at the 1,6 position in glycogen and starch, by catalyzing the cleavage of α-1,4-linkages and the subsequent transfer by introducing α-1,6-linked glucose branched points. BEs are found in the large GH13 family, eukaryotic BEs being mainly classified in the GH13_8 subfamily, GH13_9 grouping almost exclusively prokaryotic enzymes. With the aim of contributing to the understanding of the mode of recognition and action of the enzymes belonging to GH13_8, and to the understanding of features distinguishing these enzymes from those belonging to subfamily 13_9 we solved the crystal structure of the glycogen branching enzyme (GBE) from the yeast Candida glabrata, CgGBE, in ligand free forms and in complex with a maltotriose. The structures revealed the presence of a domain already observed in Homo sapiens and Oryza sativa BEs and that we named α-helical N-terminal domain, in addition to the three conserved domains found in BE. We confirmed by phylogenetic analysis that this α-helical N-terminal domain is always present in the GH13_8 enzymes suggesting that it could actually present a signature for this subfamily. We identified two binding sites (BS) in the α-helical N-terminal domain and in the carbohydrate binding module 48 (CBM48), respectively, which show a unique structural organization only present in the Saccharomycotina phylum. Our structural and phylogenetic investigation provides new insight into the structural characterization of GH13_8 GBE revealing unique structural features only present in the Saccharomycotina phylum thereby conferring original properties to this group of enzymes.
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Affiliation(s)
- Léa Conchou
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Isabelle R Gonçalves
- Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS Université de Lyon, Villeurbanne 69622, France
| | - Frédéric Galisson
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Florence Guillière
- Institut des Sciences Analytiques, UMR 5280 CNRS Université de Lyon, Villeurbanne, France
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
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19
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Yu J, Wang K, Beckles DM. Starch branching enzymes as putative determinants of postharvest quality in horticultural crops. BMC PLANT BIOLOGY 2021; 21:479. [PMID: 34674662 PMCID: PMC8529802 DOI: 10.1186/s12870-021-03253-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Starch branching enzymes (SBEs) are key determinants of the structure and amount of the starch in plant organs, and as such, they have the capacity to influence plant growth, developmental, and fitness processes, and in addition, the industrial end-use of starch. However, little is known about the role of SBEs in determining starch structure-function relations in economically important horticultural crops such as fruit and leafy greens, many of which accumulate starch transiently. Further, a full understanding of the biological function of these types of starches is lacking. Because of this gap in knowledge, this minireview aims to provide an overview of SBEs in horticultural crops, to investigate the potential role of starch in determining postharvest quality. A systematic examination of SBE sequences in 43 diverse horticultural species, identified SBE1, 2 and 3 isoforms in all species examined except apple, olive, and Brassicaceae, which lacked SBE1, but had a duplicated SBE2. Among our findings after a comprehensive and critical review of published data, was that as apple, banana, and tomato fruits ripens, the ratio of the highly digestible amylopectin component of starch increases relative to the more digestion-resistant amylose fraction, with parallel increases in SBE2 transcription, fruit sugar content, and decreases in starch. It is tempting to speculate that during the ripening of these fruit when starch degradation occurs, there are rearrangements made to the structure of starch possibly via branching enzymes to increase starch digestibility to sugars. We propose that based on the known action of SBEs, and these observations, SBEs may affect produce quality, and shelf-life directly through starch accumulation, and indirectly, by altering sugar availability. Further studies where SBE activity is fine-tuned in these crops, can enrich our understanding of the role of starch across species and may improve horticulture postharvest quality.
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Affiliation(s)
- Jingwei Yu
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Graduate Group of Horticulture & Agronomy, University of California, Davis, CA, 95616, USA
- Present Address: Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, PR China
| | - Keyun Wang
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Diane M Beckles
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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20
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Cockburn DW, Kibler R, Brown HA, Duvall R, Moraïs S, Bayer E, Koropatkin NM. Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases. J Struct Biol 2021; 213:107765. [PMID: 34186214 DOI: 10.1016/j.jsb.2021.107765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 01/15/2023]
Abstract
Pullulanases are glycoside hydrolase family 13 (GH13) enzymes that target α1,6 glucosidic linkages within starch and aid in the degradation of the α1,4- and α1,6- linked glucans pullulan, glycogen and amylopectin. The human gut bacterium Ruminococcus bromii synthesizes two extracellular pullulanases, Amy10 and Amy12, that are incorporated into the multiprotein amylosome complex that enables the digestion of granular resistant starch from the diet. Here we provide a comparative biochemical analysis of these pullulanases and the x-ray crystal structures of the wild type and the nucleophile mutant D392A of Amy12 complexed with maltoheptaose and 63-α-D glucosyl-maltotriose. While Amy10 displays higher catalytic efficiency on pullulan and cleaves only α1,6 linkages, Amy12 has some activity on α1,4 linkages suggesting that these enzymes are not redundant within the amylosome. Our structures of Amy12 include a mucin-binding protein (MucBP) domain that follows the C-domain of the GH13 fold, an atypical feature of these enzymes. The wild type Amy12 structure with maltoheptaose captured two oligosaccharides in the active site arranged as expected following catalysis of an α1,6 branch point in amylopectin. The nucleophile mutant D392A complexed with maltoheptaose or 63-α-D glucosyl-maltotriose captured β-glucose at the reducing end in the -1 subsite, facilitated by the truncation of the active site aspartate and stabilized by stacking with Y279. The core interface between the co-crystallized ligands and Amy12 occurs within the -2 through + 1 subsites, which may allow for flexible recognition of α1,6 linkages within a variety of starch structures.
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Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Ryan Kibler
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Rebecca Duvall
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Sarah Moraïs
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Edward Bayer
- Faculty of Natural Sciences, Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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21
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A putative novel starch-binding domain revealed by in silico analysis of the N-terminal domain in bacterial amylomaltases from the family GH77. 3 Biotech 2021; 11:229. [PMID: 33968573 DOI: 10.1007/s13205-021-02787-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022] Open
Abstract
The family GH77 contains 4-α-glucanotransferase acting on α-1,4-glucans, known as amylomaltase in prokaryotes and disproportionating enzyme in plants. A group of bacterial GH77 members, represented by amylomaltases from Escherichia coli and Corynebacterium glutamicum, possesses an N-terminal extension that forms a distinct immunoglobulin-like fold domain, of which no function has been identified. Here, in silico analysis of 100 selected sequences of N-terminal domain homologues disclosed several well-conserved residues, among which Tyr108 (E. coli amylomaltase numbering) may be involved in α-glucan binding. These N-terminal domains, therefore, may represent a new type of starch-binding domain and define a new CBM family. This hypothesis is supported by docking of maltooligosaccharides to the N-terminal domain in amylomaltases, representing the four clusters of the phylogenetic tree. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02787-8.
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22
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Dittmer KE, Pradhan P, Tompkins QC, Brittingham A, Wilson WA. Cloning and characterization of glycogen branching and debranching enzymes from the parasitic protist Trichomonas vaginalis. Biochimie 2021; 186:59-72. [PMID: 33895247 DOI: 10.1016/j.biochi.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/09/2021] [Accepted: 04/18/2021] [Indexed: 11/15/2022]
Abstract
The protist Trichomonas vaginalis is an obligate parasite of humans and the causative agent of trichomoniasis, a common sexually transmitted infection. The organism has long been known to accumulate glycogen, a branched polymer of glucose, and to mobilize this reserve in response to carbohydrate limitation. However, the enzymes required for the synthesis and degradation of glycogen by T. vaginalis have been little studied. Previously, we characterized T. vaginalis glycogen synthase and glycogen phosphorylase, the key enzymes of glycogen synthesis and degradation, respectively. We determined that their regulatory properties differed from those of well-characterized animal and fungal enzymes. Here, we turn our attention to how glycogen attains its branched structure. We first determined that the glycogen from T. vaginalis resembled that from a related organism, T. gallinae. To determine how the branched structure of T. vaginalis glycogen arose, we identified open reading frames encoding putative T. vaginalis branching and debranching enzymes. When the open reading frames TVAG_276310 and TVAG_330630 were expressed recombinantly in bacteria, the resulting proteins exhibited branching and debranching activity, respectively. Specifically, recombinant TVAG_276310 had affinity for polysaccharides with long outer branches and could add branches to both amylose and amylopectin. TVAG_330630 displayed both 4-α-glucanotransferase and α1,6-glucosidase activity and could efficiently debranch phosphorylase limit dextrin. Furthermore, expression of TVAG_276310 and TVAG_330630 in yeast cells lacking endogenous glycogen branching or debranching enzyme activity, restored normal glycogen accumulation and branched structure. We now have access to the suite of enzymes required for glycogen synthesis and degradation in T. vaginalis.
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Affiliation(s)
- Karoline E Dittmer
- Departments of Biochemistry & Nutrition, and Microbiology & Immunology, Des Moines University, Des Moines, IA, 50312, USA
| | - Prajakta Pradhan
- Departments of Microbiology & Immunology, Des Moines University, Des Moines, IA, 50312, USA
| | - Quentin C Tompkins
- Departments of Microbiology & Immunology, Des Moines University, Des Moines, IA, 50312, USA
| | - Andrew Brittingham
- Departments of Microbiology & Immunology, Des Moines University, Des Moines, IA, 50312, USA
| | - Wayne A Wilson
- Departments of Biochemistry & Nutrition, and Microbiology & Immunology, Des Moines University, Des Moines, IA, 50312, USA.
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23
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Abstract
Resistant starch, microbiome, and precision modulation. Mounting evidence has positioned the gut microbiome as a nexus of health. Modulating its phylogenetic composition and function has become an attractive therapeutic prospect. Resistant starches (granular amylase-resistant α-glycans) are available as physicochemically and morphologically distinguishable products. Attempts to leverage resistant starch as microbiome-modifying interventions in clinical studies have yielded remarkable inter-individual variation. Consequently, their utility as a potential therapy likely depends predominantly on the selected resistant starch and the subject's baseline microbiome. The purpose of this review is to detail i) the heterogeneity of resistant starches, ii) how resistant starch is sequentially degraded and fermented by specialized gut microbes, and iii) how resistant starch interventions yield variable effects on the gut microbiome.
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Affiliation(s)
- Peter A. Dobranowski
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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24
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Extension of the taxonomic coverage of the family GH126 outside Firmicutes and in silico characterization of its non-catalytic terminal domains. 3 Biotech 2020; 10:420. [PMID: 32953382 PMCID: PMC7479077 DOI: 10.1007/s13205-020-02415-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/27/2020] [Indexed: 01/01/2023] Open
Abstract
The family GH126 is a family of glycoside hydrolases established in 2011. Officially, in the CAZy database, it counts ~ 1000 sequences originating solely from bacterial phylum Firmicutes. Two members, the proteins CPF_2247 from Clostridium perfringens and PssZ from Listeria monocytogenes have been characterized as a probable α-amylase and an exopolysaccharide-specific glycosidase, respectively; their three-dimensional structures being also solved as possessing catalytic (α/α)6-barrel fold. Previously, based on a detailed in silico analysis, the seven conserved sequence regions (CSRs) were identified for the family along with elucidating basic evolutionary relationships within the family members. The present study represents a continuation study focusing on two particular aims: (1) to find out whether the taxonomic coverage of the family GH126 might be extended outside the Firmicutes and, if positive, to deliver those out-of-Firmicutes proteins with putting them into the context of the family; and (2) to identify the family members containing the N- and/or C-terminal extensions of their polypeptide chain, additional to the catalytic (α/α)6-barrel domain, and perform the bioinformatics characterization of the extra domains. The main results could be summarized as follows: (1) 17 bacterial proteins caught by BLAST searches outside Firmicutes (especially from phyla Proteobacteria, Actinobacteria and Bacteroidetes) have been found and convincingly suggested as new family GH126 members; and (2) a thioredoxin-like fold and various leucine-rich repeat motifs identified by Phyre2 structure homology modelling have been recognized as extra domains occurring most frequently in the N-terminal extensions of family GH126 members possessing a modular organization.
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25
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Tetlow IJ, Bertoft E. A Review of Starch Biosynthesis in Relation to the Building Block-Backbone Model. Int J Mol Sci 2020; 21:E7011. [PMID: 32977627 PMCID: PMC7582286 DOI: 10.3390/ijms21197011] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/31/2023] Open
Abstract
Starch is a water-insoluble polymer of glucose synthesized as discrete granules inside the stroma of plastids in plant cells. Starch reserves provide a source of carbohydrate for immediate growth and development, and act as long term carbon stores in endosperms and seed tissues for growth of the next generation, making starch of huge agricultural importance. The starch granule has a highly complex hierarchical structure arising from the combined actions of a large array of enzymes as well as physicochemical self-assembly mechanisms. Understanding the precise nature of granule architecture, and how both biological and abiotic factors determine this structure is of both fundamental and practical importance. This review outlines current knowledge of granule architecture and the starch biosynthesis pathway in relation to the building block-backbone model of starch structure. We highlight the gaps in our knowledge in relation to our understanding of the structure and synthesis of starch, and argue that the building block-backbone model takes accurate account of both structural and biochemical data.
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Affiliation(s)
- Ian J. Tetlow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada
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26
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Wang W, Wei X, Jiao G, Chen W, Wu Y, Sheng Z, Hu S, Xie L, Wang J, Tang S, Hu P. GBSS-BINDING PROTEIN, encoding a CBM48 domain-containing protein, affects rice quality and yield. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:948-966. [PMID: 31449354 DOI: 10.1111/jipb.12866] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/20/2019] [Indexed: 05/20/2023]
Abstract
The percentage of amylose in the endosperm of rice (Oryza sativa) largely determines grain cooking and eating qualities. Granule-bound starch synthase I (GBSSI) and GBSSII are responsible for amylose biosynthesis in the endosperm and leaf, respectively. Here, we identified OsGBP, a rice GBSS-binding protein that interacted with GBSSI and GBSSII in vitro and in vivo. The total starch and amylose contents in osgbp mutants were significantly lower than those of wild type in leaves and grains, resulting in reduced grain weight and quality. The carbohydrate-binding module 48 (CBM48) domain present in the C-terminus of OsGBP is crucial for OsGBP binding to starch. In the osgbp mutant, the extent of GBSSI and GBSSII binding to starch in the leaf and endosperm was significantly lower than wild type. Our data suggest that OsGBP plays an important role in leaf and endosperm starch biosynthesis by mediating the binding of GBSS proteins to developing starch granules. This elucidation of the function of OsGBP enhances our understanding of the molecular basis of starch biosynthesis in rice and contributes information that can be potentially used for the genetic improvement of yield and grain quality.
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Affiliation(s)
- Wei Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Wenqiang Chen
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yawen Wu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiayu Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peisong Hu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
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27
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A detailed in silico analysis of the amylolytic family GH126 and its possible relatedness to family GH76. Carbohydr Res 2020; 494:108082. [PMID: 32634753 DOI: 10.1016/j.carres.2020.108082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/13/2020] [Accepted: 06/14/2020] [Indexed: 11/21/2022]
Abstract
The glycoside hydrolase (GH) family 126 was established based on the X-ray structure determination of the amylolytic enzyme CPF_2247 from Clostridium perfringens genome. Its original identification as a putative carbohydrate-active enzyme was based on its low, yet significant sequence identity to members of the family GH8, which are inverting endo-β-1,4-glucanases. As the family GH8 forms the clan GH-M with GH48, the CPF_2247 protein also exhibits similarities with members of the family GH48. The original screening of the CPF_2247 on carbohydrate substrates demonstrated its activity on glycogen and amylose, thus classifying this protein as an "α-amylase". It should be pointed out, however, there are apparent inconsistencies concerning the exact enzyme specificity of the "amylase" CPF_2247, since it exhibits both the endo- and exo-fashion of action. The family GH126 currently counts ~1000 amino acid sequences solely from Bacteria; all belonging to the phylum Firmicutes. The present study delivers the first detailed bioinformatics study of 117 selected amino acid sequences from the family GH126, featuring the insightful sequence-structure comparison with the aim to define seven conserved sequence regions and elucidate the evolutionary relationships within the family. In addition, a comparative structural analysis of the GH126 members with representatives of other GH families adopting the same (α/α)6-barrel catalytic domain fold indicates the possible sharing a catalytic residue between the families GH126 and GH76.
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28
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Carrillo JB, Torresi F, Morales LL, Ricordi M, Gomez-Casati DF, Busi MV, Martín M. Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga. Arch Biochem Biophys 2020; 680:108235. [PMID: 31877265 DOI: 10.1016/j.abb.2019.108235] [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: 10/27/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022]
Abstract
Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes.
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Affiliation(s)
- Julieta B Carrillo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Florencia Torresi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Luisina L Morales
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Micaela Ricordi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina
| | - Maria V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina.
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000, Rosario, Santa Fe, Argentina.
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29
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Li Q, Zhang M, Wu T, Liu R. Potential correlation between carbohydrate-active enzyme family 48 expressed by gut microbiota and the expression of intestinal epithelial AMP-activated protein kinase β. J Food Biochem 2019; 44:e13123. [PMID: 31837163 DOI: 10.1111/jfbc.13123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/19/2019] [Accepted: 11/24/2019] [Indexed: 12/12/2022]
Abstract
The expression of the carbohydrate-active enzyme family and related genes is known to be influenced by the response of intestinal microbiota to dietary changes. However, it is uncertain whether this is caused by variation in the intestinal microecology. In this study, metabolite analysis, 16S rDNA sequencing, metagenomics, and Western blotting were employed to investigate the effects of dietary intervention on the composition of gut microbiota and microbiota-mediated changes. The results showed that compared with the low fiber-fed group, the fiber diet-fed mice displayed a shift in gut microbiota composition to contain more members of phylum Bacteroidetes, accompanied by higher proportions of Akkermansia and typical probiotic Bifidobacterium. Moreover, correlations were found between microbial genes coding for carbohydrate-binding module family 48 (CBM48) and intestinal epithelial expression levels of AMPK β. This finding provides new insight for elucidating the contribution of dietary intervention through AMPK regulation linked to the microbial carbohydrate-binding family. PRACTICAL APPLICATIONS: The relationship suggested by these data will provide theoretical and applied foundations for the development of potential intervention targeting the interaction between gut microbiota and host health, particularly the use of dietary fiber as a medically relevant food. Additionally, a better understanding of the interactions between gut microbiota and intestinal epithelial will inform the development of gut microbiota intervention as a health-promoting procedure.
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Affiliation(s)
- Qian Li
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Ministry of Science and Technology, Tianjin, P.R. China
| | - Min Zhang
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Ministry of Science and Technology, Tianjin, P.R. China.,School of Food Science and Bioengineering, Tianjin Agricultural University, Tianjin, P.R. China
| | - Tao Wu
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Ministry of Science and Technology, Tianjin, P.R. China.,Engineering Research Center of Food Biotechnology, Ministry of Education, Tianjin, P.R. China
| | - Rui Liu
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Ministry of Science and Technology, Tianjin, P.R. China
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30
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A new GH13 subfamily represented by the α-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 2019; 24:207-217. [PMID: 31734852 DOI: 10.1007/s00792-019-01147-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/05/2019] [Indexed: 01/16/2023]
Abstract
α-Amylase catalyzes the endohydrolysis of α-1,4-glucosidic linkages in starch and related α-glucans. In the CAZy database, most α-amylases have been classified into the family GH13 counting at present more than 80,000 sequences and ~ 30 different enzyme specificities. The family has already been divided into 42 subfamilies, but additional subfamilies are still emerging. The present bioinformatics study was undertaken in an effort to propose a novel GH13 subfamily around the experimentally characterized α-amylase from the halophilic archaeon Haloarcula hispanica, which until now has not been assigned to any GH13 subfamily. The in silico analysis resulted in collecting a convincing group of putative haloarchaeal α-amylase homologues sharing sequence similarities mainly in their conserved sequence regions (CSRs) and forming a cluster in the evolutionary tree, which is well separated from representatives of established GH13 subfamilies. One of the most exclusive sequence features of the novel GH13 subfamily is the tyrosine (Tyr79 in H. hispanica α-amylase numbering) succeeding the glycine at the beginning of the CSR-VI at the β2 strand of the catalytic TIM-barrel. Evolutionarily, the novel GH13 α-amylase subfamily was most closely related to two clusters of GH13 subfamilies with the specificity of α-amylase, i.e. subfamilies GH13_5, 6 and 7 as well as GH13_15, 24, 27 and 28.
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31
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Structural and Functional Characterization of Three Novel Fungal Amylases with Enhanced Stability and pH Tolerance. Int J Mol Sci 2019; 20:ijms20194902. [PMID: 31623309 PMCID: PMC6801514 DOI: 10.3390/ijms20194902] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Amylases are probably the best studied glycoside hydrolases and have a huge biotechnological value for industrial processes on starch. Multiple amylases from fungi and microbes are currently in use. Whereas bacterial amylases are well suited for many industrial processes due to their high stability, fungal amylases are recognized as safe and are preferred in the food industry, although they lack the pH tolerance and stability of their bacterial counterparts. Here, we describe three amylases, two of which have a broad pH spectrum extending to pH 8 and higher stability well suited for a broad set of industrial applications. These enzymes have the characteristic GH13 α-amylase fold with a central (β/α)8-domain, an insertion domain with the canonical calcium binding site and a C-terminal β-sandwich domain. The active site was identified based on the binding of the inhibitor acarbose in form of a transglycosylation product, in the amylases from Thamnidium elegans and Cordyceps farinosa. The three amylases have shortened loops flanking the nonreducing end of the substrate binding cleft, creating a more open crevice. Moreover, a potential novel binding site in the C-terminal domain of the Cordyceps enzyme was identified, which might be part of a starch interaction site. In addition, Cordyceps farinosa amylase presented a successful example of using the microseed matrix screening technique to significantly speed-up crystallization.
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32
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Holck J, Fredslund F, Møller MS, Brask J, Krogh KBRM, Lange L, Welner DH, Svensson B, Meyer AS, Wilkens C. A carbohydrate-binding family 48 module enables feruloyl esterase action on polymeric arabinoxylan. J Biol Chem 2019; 294:17339-17353. [PMID: 31558605 DOI: 10.1074/jbc.ra119.009523] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/17/2019] [Indexed: 12/25/2022] Open
Abstract
Feruloyl esterases (EC 3.1.1.73), belonging to carbohydrate esterase family 1 (CE1), hydrolyze ester bonds between ferulic acid (FA) and arabinose moieties in arabinoxylans. Recently, some CE1 enzymes identified in metagenomics studies have been predicted to contain a family 48 carbohydrate-binding module (CBM48), a CBM family associated with starch binding. Two of these CE1s, wastewater treatment sludge (wts) Fae1A and wtsFae1B isolated from wastewater treatment surplus sludge, have a cognate CBM48 domain and are feruloyl esterases, and wtsFae1A binds arabinoxylan. Here, we show that wtsFae1B also binds to arabinoxylan and that neither binds starch. Surface plasmon resonance analysis revealed that wtsFae1B's Kd for xylohexaose is 14.8 μm and that it does not bind to starch mimics, β-cyclodextrin, or maltohexaose. Interestingly, in the absence of CBM48 domains, the CE1 regions from wtsFae1A and wtsFae1B did not bind arabinoxylan and were also unable to catalyze FA release from arabinoxylan. Pretreatment with a β-d-1,4-xylanase did enable CE1 domain-mediated FA release from arabinoxylan in the absence of CBM48, indicating that CBM48 is essential for the CE1 activity on the polysaccharide. Crystal structures of wtsFae1A (at 1.63 Å resolution) and wtsFae1B (1.98 Å) revealed that both are folded proteins comprising structurally-conserved hydrogen bonds that lock the CBM48 position relative to that of the CE1 domain. wtsFae1A docking indicated that both enzymes accommodate the arabinoxylan backbone in a cleft at the CE1-CBM48 domain interface. Binding at this cleft appears to enable CE1 activities on polymeric arabinoxylan, illustrating an unexpected and crucial role of CBM48 domains for accommodating arabinoxylan.
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Affiliation(s)
- Jesper Holck
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Folmer Fredslund
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, DK-2800 Kongens Lyngby, Denmark
| | - Marie S Møller
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Jesper Brask
- Novozymes A/S, Biologiens Vej 2, DK-2800 Kongens Lyngby, Denmark
| | | | - Lene Lange
- LLa-Bioeconomy, Research and Advisory, Karensgade 5, DK-2500 Valby, Denmark
| | - Ditte H Welner
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, DK-2800 Kongens Lyngby, Denmark
| | - Birte Svensson
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Anne S Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
| | - Casper Wilkens
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
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Janeček Š, Mareček F, MacGregor EA, Svensson B. Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv 2019; 37:107451. [PMID: 31536775 DOI: 10.1016/j.biotechadv.2019.107451] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 09/15/2019] [Indexed: 01/05/2023]
Abstract
The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - E Ann MacGregor
- 2 Nicklaus Green, Livingston EH54 8RX, West Lothian, United Kingdom
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
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Karim KMR, Husaini A, Sing NN, Tasnim T, Mohd Sinang F, Hussain H, Hossain MA, Roslan H. Characterization and expression in Pichia pastoris of a raw starch degrading glucoamylase (GA2) derived from Aspergillus flavus NSH9. Protein Expr Purif 2019; 164:105462. [PMID: 31351992 DOI: 10.1016/j.pep.2019.105462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/19/2019] [Accepted: 07/24/2019] [Indexed: 11/25/2022]
Abstract
The Aspergillus flavus NSH9 gene, encoding a pH and thermostable glucoamylase with a starch binding domain (SBD), was expressed in Pichia pastoris to produce recombinant glucoamylase (rGA2). The full-length glucoamylase gene (2039 bp), and cDNA (1839 bp) encode a 612 amino acid protein most similar to glucoamylase from Aspergillus oryzae RIB40; the first 19 amino acids are presumed to be a signal peptide for secretion, and the SBD is at the C-terminal. The cDNA was successfully secreted by Pichia at 8.23 U mL-1, and the rGA2 was found to be: a 80 kDa monomer, stable from pH 3.0-9.0, with optimum catalytic activity at pH 5.0, active at temperatures up to 80°C (rGA2 retained 58% of its activity after 60 min of incubation at 70°C), and metal ions such as Na+, K+, Ca++ and Mg++ enhanced rGA2 enzyme activity. The starch degrading ability of rGA2 was also observed on raw sago starch and where prolonged incubation generated larger, deeper, holes on the starch granules, indicating rGA2 is an excellent candidate for industrial starch processing applications.
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Affiliation(s)
| | - Ahmad Husaini
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia.
| | - Ngieng Ngui Sing
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
| | - Tasmia Tasnim
- Department of Nutrition and Food Engineering, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Fazia Mohd Sinang
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
| | - Hasnain Hussain
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
| | - Md Anowar Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Hairul Roslan
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota, Samarahan, Sarawak, Malaysia
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Kundu S. Insights into the mechanism(s) of digestion of crystalline cellulose by plant class C GH9 endoglucanases. J Mol Model 2019; 25:240. [PMID: 31338614 PMCID: PMC7385011 DOI: 10.1007/s00894-019-4133-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 07/11/2019] [Indexed: 02/03/2023]
Abstract
Biofuels such as γ-valerolactone, bioethanol, and biodiesel are derived from potentially fermentable cellulose and vegetable oils. Plant class C GH9 endoglucanases are CBM49-encompassing hydrolases that cleave the β (1 → 4) glycosidic linkage of contiguous D-glucopyranose residues of crystalline cellulose. Here, I analyse 3D-homology models of characterised and putative class C enzymes to glean insights into the contribution of the GH9, linker, and CBM49 to the mechanism(s) of crystalline cellulose digestion. Crystalline cellulose may be accommodated in a surface groove which is imperfectly bounded by the GH9_CBM49, GH9_linker, and linker_CBM49 surfaces and thence digested in a solvent accessible subsurface cavity. The physical dimensions and distortions thereof, of the groove, are mediated in part by the bulky side chains of aromatic amino acids that comprise it and may also result in a strained geometry of the bound cellulose polymer. These data along with an almost complete absence of measurable cavities, along with poorly conserved, hydrophobic, and heterogeneous amino acid composition, increased atomic motion of the CBM49_linker junction, and docking experiements with ligands of lower degrees of polymerization suggests a modulatory rather than direct role for CBM49 in catalysis. Crystalline cellulose is the de facto substrate for CBM-containing plant and non-plant GH9 enzymes, a finding supported by exceptional sequence- and structural-homology. However, despite the implied similarity in general acid-base catalysis of crystalline cellulose, this study also highlights qualitative differences in substrate binding and glycosidic bond cleavage amongst class C members. Results presented may aid the development of novel plant-based GH9 endoglucanases that could extract and utilise potential fermentable carbohydrates from biomass. Crystalline cellulose digestion by plant class C GH9 endoglucanases - an in silico assessment of function. ![]()
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, Army College of Medical Sciences, Brar Square, Delhi Cantt., New Delhi, 110010, India.
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Findinier J, Laurent S, Duchêne T, Roussel X, Lancelon-Pin C, Cuiné S, Putaux JL, Li-Beisson Y, D'Hulst C, Wattebled F, Dauvillée D. Deletion of BSG1 in Chlamydomonas reinhardtii leads to abnormal starch granule size and morphology. Sci Rep 2019; 9:1990. [PMID: 30760823 PMCID: PMC6374437 DOI: 10.1038/s41598-019-39506-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 01/03/2019] [Indexed: 11/09/2022] Open
Abstract
Chlamydomonas reinhardtii represents an ideal model microbial system to decipher starch metabolism. In this green algae, in cells growing in photosynthetic conditions, starch mainly accumulates as a sheath surrounding the pyrenoid while in cells subjected to a nutrient starvation, numerous starch granules are filling up the plastid stroma. The mechanisms underlying and regulating this switch from photosynthetic to storage starch metabolisms are not known. In this work, we have isolated a Chlamydomonas mutant strain containing a deletion in chromosome 2 which displays abnormal starch granule distribution. Under nitrogen starvation, this strain contains an additional starch granules population. These granules are twice as big as the wild-type granules and display characteristics of photosynthetic starch. Genetic and functional complementation analyses allowed us to identify the gene responsible for this original phenotype which was called BSG1 for "Bimodal Starch Granule". Possible roles of BSG1 in starch metabolism modifications during the transition from photosynthetic to starved growth conditions are discussed.
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Affiliation(s)
- Justin Findinier
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Sylvain Laurent
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Thierry Duchêne
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Xavier Roussel
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | | | - Stéphan Cuiné
- CEA, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108, Saint-Paul-lez-Durance, France
| | - Jean-Luc Putaux
- University Grenoble Alpes, CNRS, CERMAV, F-38000, Grenoble, France
| | - Yonghua Li-Beisson
- CEA, Institut de Biologie Environnementale et de Biotechnologie, Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, F-13108, Saint-Paul-lez-Durance, France
| | - Christophe D'Hulst
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - Fabrice Wattebled
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France
| | - David Dauvillée
- University Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000, Lille, France.
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Seung D, Smith AM. Starch granule initiation and morphogenesis-progress in Arabidopsis and cereals. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:771-784. [PMID: 30452691 DOI: 10.1093/jxb/ery412] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/06/2018] [Indexed: 05/13/2023]
Abstract
Starch, the major storage carbohydrate in plants, is synthesized in plastids as semi-crystalline, insoluble granules. Many organs and cell types accumulate starch at some point during their development and maturation. The biosynthesis of the starch polymers, amylopectin and amylose, is relatively well understood and mostly conserved between organs and species. However, we are only beginning to understand the mechanism by which starch granules are initiated, and the factors that control the number of granules per plastid and the size/shape of granules. Here, we review recent progress in understanding starch granule initiation and morphogenesis. In Arabidopsis, granule initiation requires several newly discovered proteins with specific locations within the chloroplast, and also on the availability of maltooligosaccharides which act as primers for initiation. We also describe progress in understanding granule biogenesis in the endosperm of cereal grains-within which there is large interspecies variation in granule initiation patterns and morphology. Investigating whether this diversity results from differences between species in the functions of known proteins, and/or from the presence of novel, unidentified proteins, is a promising area of future research. Expanding our knowledge in these areas will lead to new strategies for improving the quality of cereal crops by modifying starch granule size and shape in vivo.
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Affiliation(s)
- David Seung
- John Innes Centre, Norwich Research Park, Norwich, UK
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Brewer MK, Gentry MS. Brain Glycogen Structure and Its Associated Proteins: Past, Present and Future. ADVANCES IN NEUROBIOLOGY 2019; 23:17-81. [PMID: 31667805 PMCID: PMC7239500 DOI: 10.1007/978-3-030-27480-1_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter reviews the history of glycogen-related research and discusses in detail the structure, regulation, chemical properties and subcellular distribution of glycogen and its associated proteins, with particular focus on these aspects in brain tissue.
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Affiliation(s)
- M Kathryn Brewer
- Department of Molecular and Cellular Biochemistry, Epilepsy and Brain Metabolism Center, Lafora Epilepsy Cure Initiative, and Center for Structural Biology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, Epilepsy and Brain Metabolism Center, Lafora Epilepsy Cure Initiative, and Center for Structural Biology, University of Kentucky College of Medicine, Lexington, KY, USA.
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Wilkens C, Svensson B, Møller MS. Functional Roles of Starch Binding Domains and Surface Binding Sites in Enzymes Involved in Starch Biosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1652. [PMID: 30483298 PMCID: PMC6243121 DOI: 10.3389/fpls.2018.01652] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/24/2018] [Indexed: 05/07/2023]
Abstract
Biosynthesis of starch is catalyzed by a cascade of enzymes. The activity of a large number of these enzymes depends on interaction with polymeric substrates via carbohydrate binding sites, which are situated outside of the catalytic site and its immediate surroundings including the substrate-binding crevice. Such secondary binding sites can belong to distinct starch binding domains (SBDs), classified as carbohydrate binding modules (CBMs), or be surface binding sites (SBSs) exposed on the surface of catalytic domains. Currently in the Carbohydrate-Active enZYmes (CAZy) database SBDs are found in 13 CBM families. Four of these families; CBM20, CBM45, CBM48, and CBM53 are represented in enzymes involved in starch biosynthesis, namely starch synthases, branching enzymes, isoamylases, glucan, water dikinases, and α-glucan phosphatases. A critical role of the SBD in activity has not been demonstrated for any of these enzymes. Among the well-characterized SBDs important for starch biosynthesis are three CBM53s of Arabidopsis thaliana starch synthase III, which have modest affinity. SBSs, which are overall less widespread than SBDs, have been reported in some branching enzymes, isoamylases, synthases, phosphatases, and phosphorylases active in starch biosynthesis. SBSs appear to exert roles similar to CBMs. SBSs, however, have also been shown to modulate specificity for example by discriminating the length of chains transferred by branching enzymes. Notably, the difference in rate of occurrence between SBDs and SBSs may be due to lack of awareness of SBSs. Thus, SBSs as opposed to CBMs are not recognized at the protein sequence level, which hampers their identification. Moreover, only a few SBSs in enzymes involved in starch biosynthesis have been functionally characterized, typically by structure-guided site-directed mutagenesis. The glucan phosphatase Like SEX4 2 from A. thaliana has two SBSs with weak affinity for β-cyclodextrin, amylose and amylopectin, which were indicated by mutational analysis to be more important than the active site for initial substrate recognition. The present review provides an update on occurrence of functional SBDs and SBSs in enzymes involved in starch biosynthesis.
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Affiliation(s)
- Casper Wilkens
- Enzyme Technology, Department of Bioengineering and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Bioengineering and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Marie Sofie Møller
- Enzyme and Protein Chemistry, Department of Bioengineering and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Ruiz-Gayosso A, Rodríguez-Sotres R, Martínez-Barajas E, Coello P. A role for the carbohydrate-binding module (CBM) in regulatory SnRK1 subunits: the effect of maltose on SnRK1 activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:163-175. [PMID: 30003611 DOI: 10.1111/tpj.14026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/19/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
SnRK1 is a protein kinase complex that is involved in several aspects of plant growth and development. There are published data indicative of a participation of SnRK1 in the regulation of the synthesis and degradation of starch, although the molecular mechanism is not known. In this work, we performed electron microscopy to explore the in vivo localization of the regulatory and catalytic subunits that constitute the SnRK1 complex. The results indicated that all the subunits are present in the chloroplast and, in particular, the SnRK1 βγ and SnRK1 β3 subunits are associated with starch. Furthermore, the regulatory subunits bind maltose, a relevant product of starch degradation. The kinase activity of immunoprecipitated complexes containing the βγ regulatory subunit was positively regulated by maltose only in the complexes obtained from Arabidopsis leaves collected at dusk. Recombinant complexes with the SnRK1α1 catalytic subunit, SnRK1βγ and three different β subunits showed that maltose only had an effect on a complex formed with the β3 subunit. Truncation of the CBM domain form SnRK1 βγ abolished the maltose activation of the complex and the activity was significantly reduced, indicating that the CBM is a positive regulator of SnRK1. A model of the SnRK1α1/βγ/β3 complex suggests the presence of two putative maltose-binding sites, both involving ligand interactions with the βγ subunit and the α subunit.
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Affiliation(s)
- Ana Ruiz-Gayosso
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Eleazar Martínez-Barajas
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Patricia Coello
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
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Craig PM, Moyes CD, LeMoine CM. Sensing and responding to energetic stress: Evolution of the AMPK network. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:156-169. [DOI: 10.1016/j.cbpb.2017.11.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/01/2017] [Accepted: 11/01/2017] [Indexed: 01/24/2023]
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Ben Imeddourene A, Esque J, André I. Combining multi-scale modelling methods to decipher molecular motions of a branching sucrase from glycoside-hydrolase family 70. PLoS One 2018; 13:e0201323. [PMID: 30067837 PMCID: PMC6070258 DOI: 10.1371/journal.pone.0201323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/12/2018] [Indexed: 01/23/2023] Open
Abstract
Among α-transglucosylases from Glycoside-Hydrolase family 70, the ΔN123-GB-CD2 enzyme derived from the bifunctional DSR-E from L. citreum NRRL B-1299 is particularly interesting as it was the first described engineered Branching Sucrase, not able to elongate glucan polymers from sucrose substrate. The previously reported overall structural organization of this multi-domain enzyme is an intricate U-shape fold conserved among GH70 enzymes which showed a certain conformational variability of the so-called domain V, assumed to play a role in the control of product structures, in available X-ray structures. Understanding the role of functional dynamics on enzyme reaction and substrate recognition is of utmost interest although it remains a challenge for biophysical methods. By combining long molecular dynamics simulation (1μs) and multiple analyses (NMA, PCA, Morelet Continuous Wavelet Transform and Cross Correlations Dynamics), we investigated here the dynamics of ΔN123-GB-CD2 alone and in interaction with sucrose substrate. Overall, our results provide the detailed picture at atomic level of the hierarchy of motions occurring along different timescales and how they are correlated, in agreement with experimental structural data. In particular, detailed analysis of the different structural domains revealed cooperative dynamic behaviors such as twisting, bending and wobbling through anti- and correlated motions, and also two structural hinge regions, of which one was unreported. Several highly flexible loops surrounding the catalytic pocket were also highlighted, suggesting a potential role in the acceptor promiscuity of ΔN123-GBD-CD2. Normal modes and essential dynamics underlined an interesting two-fold dynamic of the catalytic domain A, pivoting about an axis splitting the catalytic gorge in two parts. The comparison of the conformational free energy landscapes using principal component analysis of the enzyme in absence or in presence of sucrose, also revealed a more harmonic basin when sucrose is bound with a shift population of the bending mode, consistent with the substrate binding event.
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Affiliation(s)
- Akli Ben Imeddourene
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jérémy Esque
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
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Lafora Disease: A Ubiquitination-Related Pathology. Cells 2018; 7:cells7080087. [PMID: 30050012 PMCID: PMC6116066 DOI: 10.3390/cells7080087] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 11/17/2022] Open
Abstract
Lafora disease (LD, OMIM254780) is a rare and fatal form of progressive myoclonus epilepsy (PME). Among PMEs, LD is unique because of the rapid neurological deterioration of the patients and the appearance in brain and peripheral tissues of insoluble glycogen-like (polyglucosan) inclusions, named Lafora bodies (LBs). LD is caused by mutations in the EPM2A gene, encoding the dual phosphatase laforin, or the EPM2B gene, encoding the E3-ubiquitin ligase malin. Laforin and malin form a functional complex that is involved in the regulation of glycogen synthesis. Thus, in the absence of a functional complex glycogen accumulates in LBs. In addition, it has been suggested that the laforin-malin complex participates in alternative physiological pathways, such as intracellular protein degradation, oxidative stress, and the endoplasmic reticulum unfolded protein response. In this work we review the possible cellular functions of laforin and malin with a special focus on their role in the ubiquitination of specific substrates. We also discuss here the pathological consequences of defects in laforin or malin functions, as well as the therapeutic strategies that are being explored for LD.
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Arredondo-Santoyo M, Vázquez-Garcidueñas MS, Vázquez-Marrufo G. Identification and characterization of the biotechnological potential of a wild strain of Paraconiothyrium
sp. Biotechnol Prog 2018; 34:846-857. [DOI: 10.1002/btpr.2653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 04/21/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Marina Arredondo-Santoyo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo; Michoacán México
| | - Ma. Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas Dr. Ignacio Chávez, Universidad Michoacana de San Nicolás de Hidalgo; Michoacán México
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo; Michoacán México
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45
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Kuchtová A, Gentry MS, Janeček Š. The unique evolution of the carbohydrate-binding module CBM20 in laforin. FEBS Lett 2018; 592:586-598. [PMID: 29389008 DOI: 10.1002/1873-3468.12994] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 12/30/2022]
Abstract
Laforin catalyses glycogen dephosphorylation. Mutations in its gene result in Lafora disease, a fatal progressive myoclonus epilepsy, the hallmark being water-insoluble, hyperphosphorylated carbohydrate inclusions called Lafora bodies. Human laforin consists of an N-terminal carbohydrate-binding module (CBM) from family CBM20 and a C-terminal dual-specificity phosphatase domain. Laforin is conserved in all vertebrates, some basal metazoans and a small group of protozoans. The present in silico study defines the evolutionary relationships among the CBM20s of laforin with an emphasis on newly identified laforin orthologues. The study reveals putative laforin orthologues in Trichinella, a parasitic nematode, and identifies two sequence inserts in the CBM20 of laforin from parasitic coccidia. Finally, we identify that the putative laforin orthologues from some protozoa and algae possess more than one CBM20.
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Affiliation(s)
- Andrea Kuchtová
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia.,Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia.,Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, Slovakia
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Li X, Yu J, Zhang J, Sun H, Zhang X. Backbone and side-chain assignments for a novel CBM69 starch binding domain AmyP-SBD. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:235-237. [PMID: 28795344 DOI: 10.1007/s12104-017-9755-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
Starch binding domains (SBDs) are important for the functions of glycoside hydrolysis enzymes such as α-amylases, they have great application potential in biotechnology and industries. AmyP is a newly identified α-amylase belonging to a new subfamily 37 of glycoside hydrolysis enzyme family 13. AmyP shows preferential degradation to soluble starch, in which its C-terminal starch binding domain, AmyP-SBD, plays an important role. AmyP-SBD shares very low sequence similarity with other biochemically characterized SBDs and was assigned to a new carbohydrate binding module family CBM69. Intriguingly, AmyP-SBD is unfolded in free form, and substrate analogue β-cyclodextrin may induce it to fold into a relatively rigid state. Structure determination for AmyP-SBD will be helpful for understanding its unique properties. Here, we report the backbone and side-chain 1H, 13C and 15N resonance assignments of folded AmyP-SBD, as a basis for structure determination and further studies.
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Affiliation(s)
- Xinxin Li
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Jigang Yu
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, Anhui, People's Republic of China
| | - Hongbin Sun
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Academy of Sciences of China, Hefei, 230031, People's Republic of China
| | - Xuecheng Zhang
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China.
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Fungal Hybrid B heme peroxidases - unique fusions of a heme peroxidase domain with a carbohydrate-binding domain. Sci Rep 2017; 7:9393. [PMID: 28839281 PMCID: PMC5571214 DOI: 10.1038/s41598-017-09581-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/26/2017] [Indexed: 01/03/2023] Open
Abstract
Heme peroxidases, essential peroxide converting oxidoreductases are divided into four independently evolved superfamilies. Within the largest one – the peroxidase-catalase superfamily - two hybrid lineages were described recently. Whereas Hybrid A heme peroxidases represent intermediate enzymes between ascorbate peroxidases and cytochrome c peroxidases, Hybrid B heme peroxidases are unique fusion proteins comprised of a conserved N-terminal heme peroxidase domain and a C-terminal domain of various sugar binding motifs. So far these peculiar peroxidases are only found in the kingdom of Fungi. Here we present a phylogenetic reconstruction of the whole superfamily with focus on Hybrid B peroxidases. We analyse the domain assembly and putative structure and function of the newly discovered oligosaccharide binding domains. Two distinct carbohydrate binding modules (CBM21 and CBM34) are shown to occur in phytopathogenic ascomycetous orthologs of Hybrid B heme peroxidases only. Based on multiple sequence alignment and homology modeling the structure-function relationships are discussed with respect to physiological function. A concerted action of peroxide cleavage with specific cell-wall carbohydrate binding can support phytopathogens survival within the plant host.
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Affiliation(s)
- Yasunori Nakamura
- Akita Natural Science Laboratory; Tennoh, Katagami, Akita Japan
- Faculty of Bioresource Sciences; Akita Prefectural University; Shimoshinjo-Nakano, Akita Japan
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Janeček Š, Majzlová K, Svensson B, MacGregor EA. The starch-binding domain family CBM41-Anin silicoanalysis of evolutionary relationships. Proteins 2017; 85:1480-1492. [DOI: 10.1002/prot.25309] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/05/2017] [Accepted: 04/17/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Štefan Janeček
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
- Department of Biology; Faculty of Natural Sciences, University of SS. Cyril and Methodius; Trnava Slovakia
| | - Katarína Majzlová
- Institute of Molecular Biology, Slovak Academy of Sciences; Bratislava Slovakia
| | - Birte Svensson
- Department of Biotechnology and Biomedicine; Technical University of Denmark; Kgs. Lyngby Denmark
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Jia X, Guo Y, Lin X, You M, Lin C, Chen L, Chen J. Fusion of a family 20 carbohydrate-binding module (CBM20) with cyclodextrin glycosyltransferase of Geobacillus
sp. CHB1 improves catalytic efficiency. J Basic Microbiol 2017; 57:471-480. [DOI: 10.1002/jobm.201600628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/14/2017] [Accepted: 03/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Xianbo Jia
- Institute of Applied Ecology; Fujian Agriculture and Forestry University; Fuzhou China
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Yonghua Guo
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Xinjian Lin
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Minsheng You
- Institute of Applied Ecology; Fujian Agriculture and Forestry University; Fuzhou China
| | - Chenqiang Lin
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Longjun Chen
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
| | - Jichen Chen
- Institute of Soil and Fertilizer; Fujian Academy of Agricultural and Sciences; Fuzhou China
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