1
|
Photenhauer AL, Villafuerte-Vega RC, Cerqueira FM, Armbruster KM, Mareček F, Chen T, Wawrzak Z, Hopkins JB, Vander Kooi CW, Janeček Š, Ruotolo BT, Koropatkin NM. The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch. Nat Struct Mol Biol 2024; 31:255-265. [PMID: 38177679 PMCID: PMC11081458 DOI: 10.1038/s41594-023-01166-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 10/27/2023] [Indexed: 01/06/2024]
Abstract
Resistant starch is a prebiotic accessed by gut bacteria with specialized amylases and starch-binding proteins. The human gut symbiont Ruminococcus bromii expresses Sas6 (Starch Adherence System member 6), which consists of two starch-specific carbohydrate-binding modules from family 26 (RbCBM26) and family 74 (RbCBM74). Here, we present the crystal structures of Sas6 and of RbCBM74 bound with a double helical dimer of maltodecaose. The RbCBM74 starch-binding groove complements the double helical α-glucan geometry of amylopectin, suggesting that this module selects this feature in starch granules. Isothermal titration calorimetry and native mass spectrometry demonstrate that RbCBM74 recognizes longer single and double helical α-glucans, while RbCBM26 binds short maltooligosaccharides. Bioinformatic analysis supports the conservation of the amylopectin-targeting platform in CBM74s from resistant-starch degrading bacteria. Our results suggest that RbCBM74 and RbCBM26 within Sas6 recognize discrete aspects of the starch granule, providing molecular insight into how this structure is accommodated by gut bacteria.
Collapse
Affiliation(s)
- Amanda L Photenhauer
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Filipe M Cerqueira
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krista M Armbruster
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Filip Mareček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tiantian Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Zdzislaw Wawrzak
- Northwestern Synchrotron Research Center-LS-CAT, Northwestern University, Argonne, IL, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Craig W Vander Kooi
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Nicole M Koropatkin
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
2
|
Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species. Genes Genomics 2022; 44:733-746. [PMID: 35486322 DOI: 10.1007/s13258-022-01254-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/31/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available. OBJECTIVE The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation. METHODS Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle. RESULTS Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. CONCLUSIONS The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.
Collapse
|
3
|
Kim SY, Kim H, Kim YJ, Jung DH, Seo DH, Jung JH, Park CS. Enzymatic analysis of truncation mutants of a type II pullulanase from Bifidobacterium adolescentis P2P3, a resistant starch-degrading gut bacterium. Int J Biol Macromol 2021; 193:1340-1349. [PMID: 34740684 DOI: 10.1016/j.ijbiomac.2021.10.193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/28/2022]
Abstract
A putative type II pullulanase gene, pulP, was identified in Bifidobacterium adolescentis P2P3. PulP possesses an α-amylase domain at the N-terminus and a pullulanase type I domain at the C-terminus, as well as three carbohydrate-binding modules (one CBM25 and two CBM41s) between them. The native PulP and four truncated mutant recombinant proteins (PulPΔCΔP, PulPΔP, PulPΔAΔC, and PulPΔA), in which each of the two catalytic domains and/or the CBMs were deleted, were produced in Escherichia coli and their specific properties were characterized. The removal of either catalytic domain abolished the corresponding catalytic activity of the wild-type enzyme. Deletion of the C-terminal domain resulted in a drastic decrease in the optimal temperature and thermostability, indicating that the pullulanase domain might be related to the temperature dependency of the enzyme. In addition, the elimination of the CBMs in the mutant proteins led to a loss of binding affinity toward raw substrates as well as the loss of their hydrolysis activities compared to the wild-type enzyme. HPAEC and TLC analyses proved that PulP and its mutants could hydrolyze α-glucans into maltotriose as their main product. These results suggest that PulP may play an important role in α-glucan metabolism in B. adolescentis P2P3.
Collapse
Affiliation(s)
- Sun-Young Kim
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyeran Kim
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Ye-Jin Kim
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Dong-Hyun Jung
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Dong-Ho Seo
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Cheon-Seok Park
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea.
| |
Collapse
|
4
|
Han SR, Kim B, Jang JH, Park H, Oh TJ. Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation. BMC Genomics 2021; 22:403. [PMID: 34078272 PMCID: PMC8171050 DOI: 10.1186/s12864-021-07734-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. RESULTS Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. CONCLUSIONS We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.
Collapse
Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea
| | - Jong Hwa Jang
- Department of Dental Hygiene, College of Health Science, Dankook University, 119 Dandae-ro, Dongnam-gu, 31116, Cheonan-si, Chungnam, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, 02841, Seoul, Republic of Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Genome-based BioIT Convergence Institute, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea. .,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, 31460, Asan-si, Chungnam, Republic of Korea.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Janíčková Z, Janeček Š. Fungal α-amylases from three GH13 subfamilies: their sequence-structural features and evolutionary relationships. Int J Biol Macromol 2020; 159:763-772. [DOI: 10.1016/j.ijbiomac.2020.05.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 01/12/2023]
|
7
|
Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
Collapse
Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| |
Collapse
|
8
|
Comparative Genomic Study of Polar Lichen-Associated Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 Reveals the Presence of Polysaccharide-Degrading Ability Based on Habitat. Curr Microbiol 2020; 77:2940-2952. [PMID: 32681312 DOI: 10.1007/s00284-020-02120-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
The genus Hymenobacter is classified in the family Hymenobacteraceae under the phylum Bacteroidetes. They have been isolated from diverse environments, such as air, soil, and lichen, along with extreme polar environments, including the Arctic and Antarctic regions. The polar regions have attracted intense research interest for the discovery of novel microorganisms and their functions. Analysis of the polysaccharide utilization-related carbohydrate-active enzyme among the two lichen-associated polar organisms Hymenobacter sp. PAMC 26554 and Hymenobacter sp. PAMC 26628 was performed, along with its comparison with the complete genome of the same genus available in the NCBI database. The study was conducted relying on the AZCL screening data for the two polar lichen-associated species. While comparing with eight other complete genomes, differences in polysaccharide preferences based on the isolation environment and biosample source were discovered. All the species showed almost similar percentage of cellulose synthesis and degradation genes. However, the polar lichen-associated microorganism was found to have a high percentage of hemicellulose degradation genes, and less starch and laminarin degradation. The Hymenobacter species with higher number of hemicellulose degradation genes was found to have a lower number of starch and laminarin degradation genes and vice versa, highlighting the differences in polysaccharide utilization among the species.
Collapse
|
9
|
Datta D, Halder G. Blending of phthalated starch and surface functionalized rice husk extracted nanosilica with LDPE towards developing an efficient packaging substitute. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1533-1557. [PMID: 31755061 DOI: 10.1007/s11356-019-06430-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Starch was transformed to hydrophobic starch phthalate (contact angle 109°) in order to achieve a good dispersion in LDPE matrix. Nanosilica derived from rice husk after aminopropyltrimethoxysilane functionalization was also incorporated into the blend as property-enhancing filler. The produced crystalline starch phthalate had a lower particle size of 9.87 μm and a higher surface area of 2.87 m2/g compared to starch (40.28 μm, 1.91 m2/g). The potential quality modification of starch phthalate as a substitute for starch towards the production of a perfect biodegradable blend was quantified in terms of mechanical (tensile, tear, stiffness), optical (haze, transmittance), and biodegradation assessments. Interfacial adhesion between LDPE and starch phthalate was well justified by the morphology and enhancement in mechanical properties like tensile and tear strength from 8.87 to 12.67 MPa and 96.57 to 187.10 N/mm for 30% of starch or starch phthalate in LDPE matrix, respectively. Starch phthalate compared to starch blended films showed a higher biodegradation rate of 14.8 and 13.5% in garden soil and vegetable waste respectively in 1 year (at 30% biofiller), with a good first-order kinetics fit of the weight loss data having a higher degradation rate constant at higher content of biofiller in the blend.
Collapse
Affiliation(s)
- Deepshikha Datta
- Department of Chemical Engineering, National Institute of Technology, Durgapur, 713209, India
- Department of Polymer Science, Central Institute of Plastic Engineering and Technology, Bhubaneswar, 751024, India
| | - Gopinath Halder
- Department of Chemical Engineering, National Institute of Technology, Durgapur, 713209, India.
| |
Collapse
|
10
|
Thakur K, Rajhans A, Kandasubramanian B. Starch/PVA hydrogels for oil/water separation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:32013-32028. [PMID: 31493081 DOI: 10.1007/s11356-019-06327-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/26/2019] [Indexed: 05/06/2023]
Abstract
PVA polymers have been well-known as water-absorbing materials but their brittle nature hinders their applicability. In this study, we enhanced the strength of hydrogel and its water-absorbing capabilities by glutaraldehyde-assisted crosslinking of starch with PVA and blending BMIM-BF4 to enhance the plasticity and generate porosity within the hydrogel multiplying the swelling capacity up to 300% and understand the kinetics and mechanism of water absorption based on the structure of the hydrogel. The ability of starch/PVA hydrogel to selectively adsorb water from oil-water emulsions was determined by establishing the underwater oleophobic nature (oil contact angle ~ 153.6°), subjecting the hydrogel to oil-water emulsion to determine the water absorbed. The hydrogels' biodegradable nature was tested by an efficient in-house biotic system and mechanisms for biodegradation have been discussed. The biodegradability (~ 90%) was determined for 50% starch in PVA sample in 28 days. These properties observed in the hydrogels will find applications in irrigating arid and semi-arid areas and also in developing superabsorbent hydrogels for hygiene-related product development etc. which can be biodegraded in an economic way. Graphical abstract.
Collapse
Affiliation(s)
- Kirti Thakur
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Aditya Rajhans
- Department of Chemical Engineering, National Institute of Technology, Rourkela, India
| | - Balasubramanian Kandasubramanian
- Nano Surface Texturing Lab, Department of Metallurgical & Materials Engineering, DIAT (DU), Ministry of Defence, Girinagar, Pune, India.
| |
Collapse
|
11
|
Han SR, Kim DW, Kim B, Chi YM, Kang S, Park H, Jung SH, Lee JH, Oh TJ. Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation. Microb Pathog 2019; 137:103759. [PMID: 31560973 DOI: 10.1016/j.micpath.2019.103759] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022]
Abstract
Shigella sp. PAMC 28760 (isolated from Himantormia sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated S. sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus Shigella, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. S. sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding Shigella survival adaptation mechanisms under extremely cold Antarctic conditions.
Collapse
Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Do Wan Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Young Min Chi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Sang-Hee Jung
- Department of Dental Hygiene, Gangneung Yeongdong University, Gangneung, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea; Genome-based BioIT Convergence Institute, Asan, South Korea; Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Gangoiti J, Corwin SF, Lamothe LM, Vafiadi C, Hamaker BR, Dijkhuizen L. Synthesis of novel α-glucans with potential health benefits through controlled glucose release in the human gastrointestinal tract. Crit Rev Food Sci Nutr 2018; 60:123-146. [PMID: 30525940 DOI: 10.1080/10408398.2018.1516621] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The glycemic carbohydrates we consume are currently viewed in an unfavorable light in both the consumer and medical research worlds. In significant part, these carbohydrates, mainly starch and sucrose, are looked upon negatively due to their rapid and abrupt glucose delivery to the body which causes a high glycemic response. However, dietary carbohydrates which are digested and release glucose in a slow manner are recognized as providing health benefits. Slow digestion of glycemic carbohydrates can be caused by several factors, including food matrix effect which impedes α-amylase access to substrate, or partial inhibition by plant secondary metabolites such as phenolic compounds. Differences in digestion rate of these carbohydrates may also be due to their specific structures (e.g. variations in degree of branching and/or glycosidic linkages present). In recent years, much has been learned about the synthesis and digestion kinetics of novel α-glucans (i.e. small oligosaccharides or larger polysaccharides based on glucose units linked in different positions by α-bonds). It is the synthesis and digestion of such structures that is the subject of this review.
Collapse
Affiliation(s)
- Joana Gangoiti
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Sarah F Corwin
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Lisa M Lamothe
- Nestlé Research Center, Vers-Chez-Les-Blanc, Lausanne, Switzerland
| | | | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| |
Collapse
|
14
|
Peng H, Zhai L, Xu S, Xu P, He C, Xiao Y, Gao Y. Efficient Hydrolysis of Raw Microalgae Starch by an α-Amylase (AmyP) of Glycoside Hydrolase Subfamily GH13_37. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12748-12755. [PMID: 30441891 DOI: 10.1021/acs.jafc.8b03524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Microalgae starch is receiving increasing attention as a renewable feedstock for biofuel production. Raw microalgae starch from Tetraselmis subcordiformis was proven to be very efficiently hydrolyzed by an α-amylase (AmyP) of glycoside hydrolase subfamily GH13_37 below the temperature of gelatinization (40 °C). The hydrolysis degree reached 74.4 ± 2.2% for 4% raw microalgae starch and 53.2 ± 1.7% for 8% raw microalgae starch after only 2 h. The hydrolysis efficiency was significantly stimulated by calcium ions. The enzyme catalysis of AmyP and its mutants (Q306A and E347A) suggested that calcium ions contributed to the hydrolysis of cyclic structures in raw microalgae starch by a distinctive calcium-binding site Ca2 of AmyP. The study explored raw microalgae starch as a new resource for cold enzymatic hydrolysis and extended our knowledge on the function of calcium in amylolytic enzyme.
Collapse
Affiliation(s)
- Hui Peng
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Lu Zhai
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Suo Xu
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Peng Xu
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Yazhong Xiao
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| | - Yi Gao
- Anhui Key Laboratory of Modern Biomanufacturing, School of Life Sciences, School of Resources and Environmental Engineering , Anhui University , Hefei 230601 , Anhui P.R. China
| |
Collapse
|
15
|
Huang XF, Nazarian F, Vincken JP, Visser RGF, Trindade LM. A tandem CBM25 domain of α-amylase from Microbacterium aurum as potential tool for targeting proteins to starch granules during starch biosynthesis. BMC Biotechnol 2017; 17:86. [PMID: 29202734 PMCID: PMC5715617 DOI: 10.1186/s12896-017-0406-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/27/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Starch-binding domains from carbohydrate binding module family 20 have been used as a tool for starch engineering. Previous studies showed that expression of starch binding domain fusion proteins in planta resulted in modified starch granule structures and physicochemical properties. However, although 13 carbohydrate binding module families have been reported to contain starch-binding domains, only starch-binding domains from carbohydrate binding module family 20 have been well studied and introduced into plants successfully. In this study, two fragments, the tandem CBM25 domain and the tandem CBM25 with multiple fibronectin type III (FN3) domains of the α-amylase enzyme from Microbacterium aurum, were expressed in the tubers of a wild type potato cultivar (cv. Kardal) and an amylose-free (amf) potato mutant. RESULTS The (CBM25)2 and FN3 protein were successfully accumulated in the starch granules of both Kardal and amf transformants. The accumulation of (CBM25)2 protein did not result in starch morphological alterations in Kardal but gave rise to rough starch granules in amf, while the FN3 resulted in morphological changes of starch granules (helical starch granules in Kardal and rough surface granules in amf) but only at a very low frequency. The starches of the different transformants did not show significant differences in starch size distribution, apparent amylose content, and physico-chemical properties in comparison to that of untransformed controls. CONCLUSION These results suggest that the starch-binding domains from carbohydrate binding module family 25 can be used as a novel tool for targeting proteins to starch granules during starch biosynthesis without side-effects on starch morphology, composition and properties.
Collapse
Affiliation(s)
- Xing-Feng Huang
- Wageningen University and Research, Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
- Present address: Department of Chemical and Biological Engineering, Colorado State University, Campus delivery 1370, Fort Collins, CO 80523 USA
| | - Farhad Nazarian
- Wageningen University and Research, Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
- Present address: Agronomy and plant breeding group, Faculty of Agriculture, University of Lorestan, P.O.Box 465, Khorramabad, Iran
| | - Jean-Paul Vincken
- Wageningen University and Research, Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
- Present address: Laboratory of Food Chemistry, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Richard G. F. Visser
- Wageningen University and Research, Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Luisa M. Trindade
- Wageningen University and Research, Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| |
Collapse
|
16
|
Cockburn DW, Suh C, Medina KP, Duvall RM, Wawrzak Z, Henrissat B, Koropatkin NM. Novel carbohydrate binding modules in the surface anchored α-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut. Mol Microbiol 2017; 107:249-264. [PMID: 29139580 PMCID: PMC6939882 DOI: 10.1111/mmi.13881] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2017] [Indexed: 12/30/2022]
Abstract
Gut bacteria recognize accessible glycan substrates within a complex environment. Carbohydrate binding modules (CBMs) of cell surface glycoside hydrolases often drive binding to the target substrate. Eubacterium rectale, an important butyrate-producing organism in the gut, consumes a limited range of substrates, including starch. Host consumption of resistant starch increases the abundance of E. rectale in the intestine, likely because it successfully captures the products of resistant starch degradation by other bacteria. Here, we demonstrate that the cell wall anchored starch-degrading α-amylase, Amy13K of E. rectale harbors five CBMs that all target starch with differing specificities. Intriguingly these CBMs efficiently bind to both regular and high amylose corn starch (a type of resistant starch), but have almost no affinity for potato starch (another type of resistant starch). Removal of these CBMs from Amy13K reduces the activity level of the enzyme toward corn starches by ∼40-fold, down to the level of activity toward potato starch, suggesting that the CBMs facilitate activity on corn starch and allow its utilization in vivo. The specificity of the Amy13K CBMs provides a molecular rationale for why E. rectale is able to only use certain starch types without the aid of other organisms.
Collapse
Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Food Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Carolyn Suh
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Krizia Perez Medina
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Rebecca M Duvall
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zdzislaw Wawrzak
- Life Sciences Collaborative Access Team (LS-CAT), Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL, 60439, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, F-13288, France.,Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
17
|
Zhou J, Song Z, Zhang R, Liu R, Wu Q, Li J, Tang X, Xu B, Ding J, Han N, Huang Z. Distinctive molecular and biochemical characteristics of a glycoside hydrolase family 20 β-N-acetylglucosaminidase and salt tolerance. BMC Biotechnol 2017; 17:37. [PMID: 28399848 PMCID: PMC5387316 DOI: 10.1186/s12896-017-0358-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/04/2017] [Indexed: 12/05/2022] Open
Abstract
Background Enzymatic degradation of chitin has attracted substantial attention because chitin is an abundant renewable natural resource, second only to lignocellulose, and because of the promising applications of N-acetylglucosamine in the bioethanol, food and pharmaceutical industries. However, the low activity and poor tolerance to salts and N-acetylglucosamine of most reported β-N-acetylglucosaminidases limit their applications. Mining for novel enzymes from new microorganisms is one way to address this problem. Results A glycoside hydrolase family 20 (GH 20) β-N-acetylglucosaminidase (GlcNAcase) was identified from Microbacterium sp. HJ5 harboured in the saline soil of an abandoned salt mine and was expressed in Escherichia coli. The purified recombinant enzyme showed specific activities of 1773.1 ± 1.1 and 481.4 ± 2.3 μmol min−1 mg−1 towards p-nitrophenyl β-N-acetylglucosaminide and N,N'-diacetyl chitobiose, respectively, a Vmax of 3097 ± 124 μmol min−1 mg−1 towards p-nitrophenyl β-N-acetylglucosaminide and a Ki of 14.59 mM for N-acetylglucosamine inhibition. Most metal ions and chemical reagents at final concentrations of 1.0 and 10.0 mM or 0.5 and 1.0% (v/v) had little or no effect (retaining 84.5 − 131.5% activity) on the enzyme activity. The enzyme can retain more than 53.6% activity and good stability in 3.0–20.0% (w/v) NaCl. Compared with most GlcNAcases, the activity of the enzyme is considerably higher and the tolerance to salts and N-acetylglucosamine is much better. Furthermore, the enzyme had higher proportions of aspartic acid, glutamic acid, alanine, glycine, random coils and negatively charged surfaces but lower proportions of cysteine, lysine, α-helices and positively charged surfaces than its homologs. These molecular characteristics were hypothesised as potential factors in the adaptation for salt tolerance and high activity of the GH 20 GlcNAcase. Conclusions Biochemical characterization revealed that the GlcNAcase had novel salt–GlcNAc tolerance and high activity. These characteristics suggest that the enzyme has versatile potential in biotechnological applications, such as bioconversion of chitin waste and the processing of marine materials and saline foods. Molecular characterization provided an understanding of the molecular–function relationships for the salt tolerance and high activity of the GH 20 GlcNAcase. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0358-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Zhifeng Song
- College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Rui Liu
- College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Junjun Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China.,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China.,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, 650500, People's Republic of China. .,College of Life Sciences, Yunnan Normal University, No. 768 Juxian Street, Chenggong, Kunming, Yunnan, 650500, People's Republic of China. .,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan, Kunming, 650500, People's Republic of China. .,Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China.
| |
Collapse
|
18
|
Božić N, Lončar N, Slavić MŠ, Vujčić Z. Raw starch degrading α-amylases: an unsolved riddle. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/amylase-2017-0002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractStarch is an important food ingredient and a substrate for the production of many industrial products. Biological and industrial processes involve hydrolysis of raw starch, such as digestion by humans and animals, starch metabolism in plants, and industrial starch conversion for obtaining glucose, fructose and maltose syrup or bioethanol. Raw starch degrading α-amylases (RSDA) can directly degrade raw starch below the gelatinization temperature of starch. Knowledge of the structures and properties of starch and RSDA has increased significantly in recent years. Understanding the relationships between structural peculiarities and properties of RSDA is a prerequisite for efficient application in different aspects of human benefit from health to the industry. This review summarizes recent advances on RSDA research with emphasizes on representatives of glycoside hydrolase family GH13. Definite understanding of raw starch digesting ability is yet to come with accumulating structural and functional studies of RSDA.
Collapse
|
19
|
Exploring the effect of bisphenol S on sludge hydrolysis and mechanism of the interaction between bisphenol S and α-Amylase through spectrophotometric methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 167:128-135. [DOI: 10.1016/j.jphotobiol.2016.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/27/2016] [Accepted: 12/16/2016] [Indexed: 01/13/2023]
|
20
|
Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization. Sci Rep 2016; 6:36100. [PMID: 27808246 PMCID: PMC5093618 DOI: 10.1038/srep36100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/10/2016] [Indexed: 11/09/2022] Open
Abstract
The bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed.
Collapse
|
21
|
Valk V, Lammerts van Bueren A, Kaaij RM, Dijkhuizen L. Carbohydrate‐binding module 74 is a novel starch‐binding domain associated with large and multidomain α‐amylase enzymes. FEBS J 2016; 283:2354-68. [DOI: 10.1111/febs.13745] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/01/2016] [Accepted: 04/20/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Vincent Valk
- Microbial Physiology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) The Netherlands
| | | | - Rachel M. Kaaij
- Microbial Physiology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) The Netherlands
| |
Collapse
|