1
|
Salgado JCS, Alnoch RC, Polizeli MDLTDM, Ward RJ. Microenzymes: Is There Anybody Out There? Protein J 2024; 43:393-404. [PMID: 38507106 DOI: 10.1007/s10930-024-10193-1] [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] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Biological macromolecules are found in different shapes and sizes. Among these, enzymes catalyze biochemical reactions and are essential in all organisms, but is there a limit size for them to function properly? Large enzymes such as catalases have hundreds of kDa and are formed by multiple subunits, whereas most enzymes are smaller, with molecular weights of 20-60 kDa. Enzymes smaller than 10 kDa could be called microenzymes and the present literature review brings together evidence of their occurrence in nature. Additionally, bioactive peptides could be a natural source for novel microenzymes hidden in larger peptides and molecular downsizing could be useful to engineer artificial enzymes with low molecular weight improving their stability and heterologous expression. An integrative approach is crucial to discover and determine the amino acid sequences of novel microenzymes, together with their genomic identification and their biochemical biological and evolutionary functions.
Collapse
Affiliation(s)
- Jose Carlos Santos Salgado
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-900, São Paulo, Brazil.
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil.
| | - Robson Carlos Alnoch
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-901, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| | - Richard John Ward
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto, 14040-900, São Paulo, Brazil
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, 14049-900, São Paulo, Brazil
| |
Collapse
|
2
|
Chen J, Si X, Wang Y, Ren Z, Liu Q, Lu F. Efficient Fractionation and Catalytic Valorization of Raw Biomass in ϵ-Caprolactone and Water. CHEMSUSCHEM 2023; 16:e202202162. [PMID: 36610014 DOI: 10.1002/cssc.202202162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Efficient fractionation and utilization of the whole biomass is particularly attractive but remains a great challenge, owing to the recalcitrance of biomass. In this study, a simple and efficient approach is developed to obtain high-purity cellulose with a delignification degree of 97.5 % in ϵ-caprolactone and water. FTIR spectroscopy reveals that ϵ-caprolactone and water act in synergy to remove lignin from raw biomass and afford cellulose with clear macrofibrils. A linear positive correlation between the contents of hemicellulose and lignin is observed for the separated cellulose pulp. This mixed solvent exhibits good performance for the removal of lignin from various agricultural and forestry wastes. Moreover, nearly complete transformation of the whole biomass constituents is achieved with Ni-Al catalyst.
Collapse
Affiliation(s)
- Jiali Chen
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, P. R. China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Xiaoqin Si
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Yubao Wang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, P. R. China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Zhiwen Ren
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Qian Liu
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, P. R. China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Fang Lu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| |
Collapse
|
3
|
Sayad A, Oduntan Y, Bokros N, DeBolt S, Benzecry A, Robertson DJ, Stubbs CJ. The semi-automated development of plant cell wall finite element models. PLANT METHODS 2023; 19:3. [PMID: 36624506 PMCID: PMC9827646 DOI: 10.1186/s13007-023-00979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
This study presents a methodology for a high-throughput digitization and quantification process of plant cell walls characterization, including the automated development of two-dimensional finite element models. Custom algorithms based on machine learning can also analyze the cellular microstructure for phenotypes such as cell size, cell wall curvature, and cell wall orientation. To demonstrate the utility of these models, a series of compound microscope images of both herbaceous and woody representatives were observed and processed. In addition, parametric analyses were performed on the resulting finite element models. Sensitivity analyses of the structural stiffness of the resulting tissue based on the cell wall elastic modulus and the cell wall thickness; demonstrated that the cell wall thickness has a three-fold larger impact of tissue stiffness than cell wall elastic modulus.
Collapse
Affiliation(s)
- Andrew Sayad
- School of Computer Sciences and Engineering, Fairleigh Dickinson University, Teaneck, NJ, USA
| | - Yusuf Oduntan
- Department of Mechanical Engineering, University of Idaho, Moscow, ID, USA
| | - Norbert Bokros
- Department of Horticulture, University of Kentucky, Lexington, KY, 40546, USA
| | - Seth DeBolt
- Department of Horticulture, University of Kentucky, Lexington, KY, 40546, USA
| | - Alice Benzecry
- Department of Biological Sciences, Fairleigh Dickinson University, Teaneck, NJ, USA
| | - Daniel J Robertson
- Department of Mechanical Engineering, University of Idaho, Moscow, ID, USA
| | - Christopher J Stubbs
- School of Computer Sciences and Engineering, Fairleigh Dickinson University, Teaneck, NJ, USA.
| |
Collapse
|
4
|
Structural and functional insights into the glycoside hydrolase family 30 xylanase of the rumen bacterium Ruminococcus flavefaciens. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
5
|
Song W, Du Q, Li X, Wang S, Song G. Sustainable Production of Bioactive Molecules from C-Lignin-Derived Propenylcatechol. CHEMSUSCHEM 2022; 15:e202200646. [PMID: 35548878 DOI: 10.1002/cssc.202200646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Catechyl lignin (C-lignin) is a naturally occurring linear homogeneous biopolymer composed solely of caffeyl alcohol subunits with cleavable benzodioxane linkages. The inherent structural features of propenylcatechol, a direct depolymerized product of castor seed coats C-lignin, render it a sustainable and promising platform for the synthesis of bioactive molecules. Herein, diversified transformations of propenylcatechol, including C=C bond difunctionalization, β-modification, β,γ-rearrangement, and γ-methyl derivatization, were reported based on known or developed methods. A series of functional molecular skeletons involved in the current synthetic routes for the preparation of pharmaceuticals and bioactive molecules were obtained. Starting from castor seed coats, annuloline (natural product) and CC-5079 (antitumor) were synthesized using facile and inexpensive reagents in only four- and five-sequence reactions, respectively, thereby demonstrating a superior step-efficiency to that of reported synthetic routes. Almost all atoms in the C-lignin biopolymer were incorporated into the final products owing to the intrinsic structures of naturally occurring C-lignin. Bioactive molecules produced from C-lignin integrate a low-carbon footprint with high-quality and economical manufacture of pharmaceuticals.
Collapse
Affiliation(s)
- Weihong Song
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, P. R. China
- Institute of Drug Discovery Technology Institution, Ningbo University, Ningbo, 315000, P. R. China
| | - Qinglian Du
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Xiancheng Li
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Shuizhong Wang
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Guoyong Song
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, 100083, P. R. China
| |
Collapse
|
6
|
Yang C, Wang E, Liu J. CERK1, more than a co-receptor in plant-microbe interactions. THE NEW PHYTOLOGIST 2022; 234:1606-1613. [PMID: 35297054 DOI: 10.1111/nph.18074] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
CERK1 (Chitin Elicitor Receptor Kinase 1), a lysin motif-containing pattern recognition receptor (PRR), perceives chitooligosaccharides (COs) to mount immune and symbiotic responses. However, CERK1, for a relatively long time, has been regarded as a co-receptor in plant immunity, mainly due to its lack of high binding affinity to known elicitors. Recent studies demonstrated several novel carbohydrates as ligands of CERK1 in different plant species and recognized CERK1 as a key receptor in plant immunity and symbiosis. This review summarizes recent knowledge acquired on the role of CERK1 in plant-microbe interactions.
Collapse
Affiliation(s)
- Chao Yang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, 100193, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jun Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory for Monitoring and Green Management of Crop Pests, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
7
|
Suryadi H, Judono JJ, Putri MR, Eclessia AD, Ulhaq JM, Agustina DN, Sumiati T. Biodelignification of lignocellulose using ligninolytic enzymes from white-rot fungi. Heliyon 2022; 8:e08865. [PMID: 35141441 PMCID: PMC8814692 DOI: 10.1016/j.heliyon.2022.e08865] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/17/2021] [Accepted: 01/27/2022] [Indexed: 11/25/2022] Open
Abstract
Lignocellulose is the most abundant biomass available on earth, including wood and agricultural wastes such as rice straw, corn cobs, and oil palm empty bunches. The biopolymer content in lignocellulose has a great potential as feedstock for producing industrial raw materials such as glucose, sorbitol, xylose, xylitol, and other pharmaceutical excipients. Currently, scientists and governments agree that the enzymatic delignification method is an environmentally friendly green method to be applied. This review attempts to explain the proper preparation of the enzymes laccase, lignin peroxidase, and manganese peroxidase, as well as the important factors influencing their activity. The recent applications of the enzymes for detoxification of hazardous substances, proper enzyme immobilization technique, and future prospect combination with DESs extraction of lignin are also discussed.
Collapse
Affiliation(s)
- Herman Suryadi
- Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| | - Jessica J. Judono
- Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| | - Merianda R. Putri
- Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| | - Alma D. Eclessia
- Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| | - Jiihan M. Ulhaq
- Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| | - Dinar N. Agustina
- Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| | - Triyani Sumiati
- Faculty of Pharmacy, Universitas Indonesia, Depok, 16424, West Java, Indonesia
| |
Collapse
|
8
|
Abstract
The lignocellulosic perennial crop miscanthus, especially Miscanthus × giganteus, is particularly interesting for bioenergy production as it combines high biomass production with low environmental impact. However, there are several varieties that pose a hazard due to susceptibility to disease. This review contains links showing genotype and ecological variability of important characteristics related to yield and biomass composition of miscanthus that may be useful in plant breeding programs to increase bioenergy production. Some clones of Miscanthus × giganteus and Miscanthus sinensis are particularly interesting due to their high biomass production per hectare. Although the compositional requirements for industrial biomass have not been fully defined for the various bioenergy conversion processes, the lignin-rich species Miscanthus × giganteus and Miscanthus sacchariflorus seem to be more suitable for thermochemical conversion processes. At the same time, the species Miscanthus sinensis and some clones of Miscanthus × giganteus with low lignin content are of interest for the biochemical transformation process. The species Miscanthus sacchariflorus is suitable for various bioenergy conversion processes due to its low ash content, so this species is also interesting as a pioneer in breeding programs. Mature miscanthus crops harvested in winter are favored by industrial enterprises to improve efficiency and reduce processing costs. This study can be attributed to other monocotyledonous plants and perennial crops that can be used as feedstock for biofuels.
Collapse
|
9
|
Anaerobic Acidogenic Fermentation of Cellobiose by Immobilized Cells: Prediction of Organic Acids Production by Response Surface Methodology. Processes (Basel) 2021. [DOI: 10.3390/pr9081441] [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
Response surface methodology was used to derive a prediction model for organic acids production by anaerobic acidogenic fermentation of cellobiose, using a mixed culture immobilized on γ-alumina. Three parameters (substrate concentration, temperature, and initial pH) were evaluated. In order to determine the limits of the parameters, preliminary experiments at 37 °C were conducted using substrates of various cellobiose concentrations and pH values. Cellobiose was used as a model sugar for subsequent experiments with lignocellulosic biomass. The culture was well adapted to cellobiose by successive subculturing at 37 °C in synthetic media (with 100:5:1 COD:N:P ratio). The experimental data of successive batch fermentations were fitted into a polynomial model for the total organic acids concentration in order to derive a predictive model that could be utilized as a tool to predict fermentation results when lignocellulosic biomass is used as a substrate. The quadratic effect of temperature was the most significant, followed by the quadratic effect of initial pH and the linear effect of cellobiose concentration. The results corroborated the validity and effectiveness of the model.
Collapse
|
10
|
Xia Y, Li J, Zhang Z, Luo S, Liu S, Ma C, Li W. Decoding biomass recalcitrance: Dispersion of ionic liquid in aqueous solution and efficient extraction of lignans with microwave magnetic field. PLoS One 2020; 15:e0226901. [PMID: 32084140 PMCID: PMC7034798 DOI: 10.1371/journal.pone.0226901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 12/07/2019] [Indexed: 11/25/2022] Open
Abstract
Alkaline ionic liquid aqueous solutions were used to extract biphenyl cyclooctene lignans derivatives, and hydrolyze to the free-state biphenyl cyclooctene lignans simultaneously from Schisandra chinensis by microwave-assisted heating. The hydrogen bonds formatted between ionic liquid and water molecular attacks the amorphous region of cellulose. Selective heating by microwave produce the more polar regions, which results in swelling and fragmentation of raw materials near the hot spots. Therefore, ionic liquid-microwave-assisted extraction method of free-state biphenyl cyclooctene lignans was set up. The solid residue after treatment was characterized by infrared spectroscopy and scanning electron microscopy, which showed that cellulose, hemicellulose, and lignin were removed partially. The water content of ionic liquid solution affected its viscosity and diffusivity, and in turns the extraction efficiency of lignans. The IL solutions with different mole fractions of IL were detected by FTIR and Raman spectroscopy, the result shows that IL solutions with higher water contents (>0.6) won't form clusters. The optimum hydrolysis conditions were 0.2 g of ionic liquid catalyst per 5.0 g of S. chinensis fruits, a microwave irradiation power of 600 W, and heating time of 12 min, which gave a yield of free-state biphenyl cyclooctene lignans of 4.12±0.37 mg g-1. Besides, a hydrolysis mechanism of ester-bond biphenyl cyclooctene lignans and decreasing "biomass recalcitrance effect" by ionic liquid microwave-assisted method was proposed.
Collapse
Affiliation(s)
- Yu Xia
- College of Material Science and Engineering, Northeast Forestry University, Harbin, China
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, China
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Jingdu Li
- College of Material Science and Engineering, Northeast Forestry University, Harbin, China
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Zhijun Zhang
- College of Material Science and Engineering, Northeast Forestry University, Harbin, China
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Sha Luo
- College of Material Science and Engineering, Northeast Forestry University, Harbin, China
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Shouxin Liu
- College of Material Science and Engineering, Northeast Forestry University, Harbin, China
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Chunhui Ma
- College of Material Science and Engineering, Northeast Forestry University, Harbin, China
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Wei Li
- College of Material Science and Engineering, Northeast Forestry University, Harbin, China
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| |
Collapse
|
11
|
Wan Y, Zhang M, Hong A, Lan X, Yang H, Liu Y. Transcriptome and weighted correlation network analyses provide insights into inflorescence stem straightness in Paeonia lactiflora. PLANT MOLECULAR BIOLOGY 2020; 102:239-252. [PMID: 31832900 DOI: 10.1007/s11103-019-00945-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Lack of structural components results in inflorescence stem bending. Differentially expressed genes involved in lignin and hemicellulose biosynthesis are vital; genes involved in cellulose and glycan biosynthesis are also relevant. An erect inflorescence stem is essential for high-quality cut herbaceous peony flowers. To explore the factors underlying inflorescence stem bending, major cell walls contents were measured, and stem structure was observed in two herbaceous peony varieties with contrasting stem straightness traits ('Da Fugui', upright; 'Chui Touhong', bending). In addition, Illumina sequencing was performed and weighted correlation network analysis (WGCNA) was used to analyze the results. The results showed significant differences in lignin, hemicellulose and soluble sugar contents, sclerenchyma and xylem areas and thickening in cell walls in pith at stage S3, when bending begins. In addition, 44,182 significantly differentially expressed genes (DEGs) were found, and these DEGs were mainly enriched in 36 pathways. Among the DEGs, hub genes involved in lignin, cellulose, and xylan biosynthesis and transcription factors that regulated these process were identified by WGCNA. These results suggested that the contents of compounds that provided cell wall rigidity were vital factors affecting inflorescence stem straightness in herbaceous peony. Genes involved in or regulating the biosynthesis of these compounds are thus important; lignin and hemicellulose are of great interest, and cellulose and glycan should not be ignored. This paper lays a foundation for developing new herbaceous peony varieties suitable for cut flowers by molecular-assisted breeding.
Collapse
Affiliation(s)
- Yingling Wan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Min Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Aiying Hong
- Management Office of Caozhou Peony Garden, Heze, 274000, Shandong, People's Republic of China
| | - Xinyu Lan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Huiyan Yang
- Management Office of Caozhou Peony Garden, Heze, 274000, Shandong, People's Republic of China
| | - Yan Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| |
Collapse
|
12
|
Sharma K, Fontes CMGA, Najmudin S, Goyal A. Small angle X-ray scattering based structure, modeling and molecular dynamics analyses of family 43 glycoside hydrolase α-L-arabinofuranosidase from Clostridium thermocellum. J Biomol Struct Dyn 2019; 39:209-218. [PMID: 31856699 DOI: 10.1080/07391102.2019.1707119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Enzymes that participate in the hydrolysis of complex carbohydrates display a modular architecture, although the significance of enzyme modularity to flexibility and catalytic efficacy is not fully understood. α-L-arabinofuranosidase from Clostridium thermocellum (CtAraf43) catalyzes the release of α-1,2-, α-1,3-, or α-1,5- linked L-arabinose from arabinose decorated polysaccharides. CtAraf43 comprises an N-terminal catalytic domain (CtAbf43A) connected with two family 6 carbohydrate-binding modules (CBMs), termed as CtCBM6A and CtCBM6B, through flexible linker peptides. Here, we modeled the structure of CtAraf43 revealing that the module, CtAbf43A displays a 5-fold β-propeller fold and the CBMs the typical jellyroll type β-sandwich folds. Ramachandran plot showed 98.5% residues in the favored region and 1.5% residues in the disallowed region. Molecular dynamics simulation analysis of CtAraf43 revealed significant flexibility that is more expressive in the C-terminal CtCBM6B module in terms of structure and orientation. Small angle X-ray scattering analysis of CtAraf43 revealed its elongated structure. CtAraf43 at 1.2 mg/mL demonstrated the monomeric nature and a multi-modular shaped molecular envelope in solution with a Dmax of 12 nm. However, at 4.7 mg/mL, CtAraf43 displayed a dimeric structure and elongated molecular envelope. Kratky plot analysis revealed the folded state of CtAraf43 with limited flexibility at both concentrations. The data revealed higher flexibility at the C-terminal of CtAraf43 suggesting a coordinated action of the N-terminal catalytic module CtAbf43A and the internal CtCBM6A.AbbreviationCBMsCarbohydrate Binding ModulesCtAraf43α-L-arabinofuranosidaseGHsGlycoside HydrolasesMDMolecular DynamicsRMSDRoot Mean Square DeviationRMSFRoot Mean Square FluctuationSAXSSmall angle X-ray scatteringCommunicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| |
Collapse
|
13
|
Nawaz A, Mukhtar H, ul Haq I, Mazhar Z, Mumtaz MW. Laccase: An Environmental Benign Pretreatment Agent for Efficient Bioconversion of Lignocellulosic Residues to Bioethanol. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190722163046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abrupt urbanization and industrialization around the world resulted in elevated environmental pollution and depletion of natural energy resources. An eco-friendly and economical alternative for energy production is the need of an hour. This can be achieved by converting the waste material into energy. One such waste is lignocellulosic agricultural residues, produced in billions of tons every year all around the world, which can be converted into bioethanol. The main challenge in this bioconversion is the recalcitrant nature of lignocellulosic material. The removal of cementing material is lignin and to overcome the potential inhibitors produced during the disintegration of lignin is the challenging task for biotechnologist. This task can be achieved by a number of different methods but laccase is the most effective and eco-friendly method that can be used for effective removal of lignin along with the increase the accessibility of cellulose and bioethanol yield.
Collapse
Affiliation(s)
- Ali Nawaz
- Institute of Industrial Biotechnology, GC University, Lahore, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, GC University, Lahore, Pakistan
| | - Ikram ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore, Pakistan
| | - Zainab Mazhar
- Institute of Industrial Biotechnology, GC University, Lahore, Pakistan
| | | |
Collapse
|
14
|
Sharma K, Fontes CMGA, Najmudin S, Goyal A. Molecular organization and protein stability of the Clostridium thermocellum glucuronoxylan endo-β-1,4-xylanase of family 30 glycoside hydrolase in solution. J Struct Biol 2019; 206:335-344. [PMID: 30959107 DOI: 10.1016/j.jsb.2019.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
Abstract
Glucuronoxylan-β-1,4-xylanohydrolase from Clostridium thermocellum (CtXynGH30) hydrolyzes β-1,4-xylosidic linkages in 4-O-Methyl-D-glucuronoxylan. CtXynGH30 comprises an N-terminal catalytic domain, CtXyn30A, joined by a typical linker sequence to a family 6 carbohydrate-binding module, termed CtCBM6. ITC, mass spectrometric and enzyme activity analyses of CtXyn30A:CtCBM6 (1:1 M ratio), CtXyn30A and CtXynGH30 showed that the linker peptide plays a key role in connecting and orienting CtXyn30A and CtCBM6 modules resulting in the enhanced activity of CtXynGH30. To visualize the disposition of the two protein domains of CtXynGH30, SAXS analysis revealed that CtXynGH30 is monomeric and has a boot-shaped molecular envelope in solution with a Dmax of 18 nm and Rg of 3.6 nm. Kratky plot displayed the protein in a fully folded and flexible state. The ab initio derived dummy atom model of CtXynGH30 superposed well with the modelled structure.
Collapse
Affiliation(s)
- Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| |
Collapse
|
15
|
Pandey G. Biomass based bio-electro fuel cells based on carbon electrodes: an alternative source of renewable energy. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0409-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
|
16
|
Chang C, Brooke C, Piao H, Mack J, Babnigg G, Joachimiak A, Hess M. A 2.08 Å resolution structure of HLB5, a novel cellulase from the anaerobic gut bacterium Parabacteroides johnsonii DSM 18315. Protein Sci 2019; 28:794-799. [PMID: 30687968 DOI: 10.1002/pro.3582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 11/05/2022]
Abstract
Cellulases play a significant role in the degradation of complex carbohydrates. In the human gut, anaerobic bacteria are essential to the well-being of the host by producing these essential enzymes that convert plant polymers into simple sugars that can then be further metabolized by the host. Here, we report the 2.08 Å resolution structure of HLB5, a chemically verified cellulase that was identified previously from an anaerobic gut bacterium and that has no structural cellulase homologues in PDB nor possesses any conserved region typical for glycosidases. We anticipate that the information presented here will facilitate the identification of additional cellulases for which no homologues have been identified to date and enhance our understanding how these novel cellulases bind and hydrolyze their substrates.
Collapse
Affiliation(s)
- Changsoo Chang
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439
| | | | - Hailan Piao
- Washington State University, Richland, WA, USA
| | - Jamey Mack
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics Argonne National Laboratory, Argonne, Illinois 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439
| | | |
Collapse
|
17
|
Zhu Y, Han Z, Fu L, Liu C, Zhang D. Cleavage of the β–O–4 bond in a lignin model compound using the acidic ionic liquid 1-H-3-methylimidazolium chloride as catalyst: a DFT mechanistic study. J Mol Model 2018; 24:322. [DOI: 10.1007/s00894-018-3854-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/04/2018] [Indexed: 12/28/2022]
|
18
|
Sakamoto S, Somssich M, Nakata MT, Unda F, Atsuzawa K, Kaneko Y, Wang T, Bågman AM, Gaudinier A, Yoshida K, Brady SM, Mansfield SD, Persson S, Mitsuda N. Complete substitution of a secondary cell wall with a primary cell wall in Arabidopsis. NATURE PLANTS 2018; 4:777-783. [PMID: 30287954 DOI: 10.1038/s41477-018-0260-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/21/2018] [Indexed: 05/22/2023]
Abstract
The bulk of a plant's biomass, termed secondary cell walls, accumulates in woody xylem tissues and is largely recalcitrant to biochemical degradation and saccharification1. By contrast, primary cell walls, which are chemically distinct, flexible and generally unlignified2, are easier to deconstruct. Thus, engineering certain primary wall characteristics into xylem secondary walls would be interesting to readily exploit biomass for industrial processing. Here, we demonstrated that by expressing AP2/ERF transcription factors from group IIId and IIIe in xylem fibre cells of mutants lacking secondary walls, we could generate plants with thickened cell wall characteristics of primary cell walls in the place of secondary cell walls. These unique, newly formed walls displayed physicochemical and ultrastructural features consistent with primary walls and had gene expression profiles illustrative of primary wall synthesis. These data indicate that the group IIId and IIIe AP2/ERFs are transcription factors regulating primary cell wall deposition and could form the foundation for exchanging one cell wall type for another in plants.
Collapse
Affiliation(s)
- Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Marc Somssich
- School of Biosciences, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Miyuki T Nakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Faride Unda
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kimie Atsuzawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yasuko Kaneko
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ting Wang
- Max-Planck Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Yokohama, Japan
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
| |
Collapse
|
19
|
Duque E, Daddaoua A, Cordero BF, Udaondo Z, Molina‐Santiago C, Roca A, Solano J, Molina‐Alcaide E, Segura A, Ramos J. Ruminal metagenomic libraries as a source of relevant hemicellulolytic enzymes for biofuel production. Microb Biotechnol 2018; 11:781-787. [PMID: 29663699 PMCID: PMC6011990 DOI: 10.1111/1751-7915.13269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/01/2022] Open
Abstract
The success of second-generation (2G) ethanol technology relies on the efficient transformation of hemicellulose into monosaccharides and, particularly, on the full conversion of xylans into xylose for over 18% of fermentable sugars. We sought new hemicellulases using ruminal liquid, after enrichment of microbes with industrial lignocellulosic substrates and preparation of metagenomic libraries. Among 150 000 fosmid clones tested, we identified 22 clones with endoxylanase activity and 125 with β-xylosidase activity. These positive clones were sequenced en masse, and the analysis revealed open reading frames with a low degree of similarity with known glycosyl hydrolases families. Among them, we searched for enzymes that were thermostable (activity at > 50°C) and that operate at high rate at pH around 5. Upon a wide series of assays, the clones exhibiting the highest endoxylanase and β-xylosidase activities were identified. The fosmids were sequenced, and the corresponding genes cloned, expressed and proteins purified. We found that the activity of the most active β-xylosidase was at least 10-fold higher than that in commercial enzymatic fungal cocktails. Endoxylanase activity was in the range of fungal enzymes. Fungal enzymatic cocktails supplemented with the bacterial hemicellulases exhibited enhanced release of sugars from pretreated sugar cane straw, a relevant agricultural residue.
Collapse
Affiliation(s)
- Estrella Duque
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Abdelali Daddaoua
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Faculty of PharmacyDepartment of PharmacologyUniversity of Granada18071GranadaSpain
| | - Baldo F. Cordero
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Zulema Udaondo
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Carlos Molina‐Santiago
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Amalia Roca
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | - Jennifer Solano
- BioIliberis R&DPolígono JuncarilCalle Capileira 718220AlboloteGranadaSpain
| | | | - Ana Segura
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| | - Juan‐Luis Ramos
- Estación Experimental del Zaidín (CSIC)Calle Profesor Albareda, 118008GranadaSpain
- Department of BiotechnologyAbengoa ResearchCampus Palmas Altas, Avenida de la Energia 141014SevilleSpain
| |
Collapse
|
20
|
Low-resolution SAXS and comparative modeling based structure analysis of endo-β-1,4-xylanase a family 10 glycoside hydrolase from Pseudopedobacter saltans comb. nov. Int J Biol Macromol 2018; 112:1104-1114. [DOI: 10.1016/j.ijbiomac.2018.02.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/05/2018] [Accepted: 02/07/2018] [Indexed: 11/20/2022]
|
21
|
Perera D, Magbanua ZV, Thummasuwan S, Mukherjee D, Arick M, Chouvarine P, Nairn CJ, Schmutz J, Grimwood J, Dean JFD, Peterson DG. Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis. Gene 2018; 663:165-177. [PMID: 29655895 DOI: 10.1016/j.gene.2018.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 03/20/2018] [Accepted: 04/10/2018] [Indexed: 02/06/2023]
Abstract
Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production.
Collapse
Affiliation(s)
- Dinum Perera
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Zenaida V Magbanua
- National Institute of Molecular Biology & Biotechnology, National Science Complex, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Supaphan Thummasuwan
- Department of Agricultural Sciences, Naresuan University, Phitsanulok, Thailand.
| | - Dipaloke Mukherjee
- Department of Food Science, Nutrition, & Health Promotion, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Mark Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Philippe Chouvarine
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Campbell J Nairn
- Warnell School of Forest Resources, University of Georgia, Athens, GA 30602, USA.
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35801, USA.
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35801, USA.
| | - Jeffrey F D Dean
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA; Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
| |
Collapse
|
22
|
Carbon-Based Nanomaterials in Biomass-Based Fuel-Fed Fuel Cells. SENSORS 2017; 17:s17112587. [PMID: 29125564 PMCID: PMC5713132 DOI: 10.3390/s17112587] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/05/2017] [Accepted: 11/07/2017] [Indexed: 12/15/2022]
Abstract
Environmental and sustainable economical concerns are generating a growing interest in biofuels predominantly produced from biomass. It would be ideal if an energy conversion device could directly extract energy from a sustainable energy resource such as biomass. Unfortunately, up to now, such a direct conversion device produces insufficient power to meet the demand of practical applications. To realize the future of biofuel-fed fuel cells as a green energy conversion device, efforts have been devoted to the development of carbon-based nanomaterials with tunable electronic and surface characteristics to act as efficient metal-free electrocatalysts and/or as supporting matrix for metal-based electrocatalysts. We present here a mini review on the recent advances in carbon-based catalysts for each type of biofuel-fed/biofuel cells that directly/indirectly extract energy from biomass resources, and discuss the challenges and perspectives in this developing field.
Collapse
|
23
|
Walker JA, Pattathil S, Bergeman LF, Beebe ET, Deng K, Mirzai M, Northen TR, Hahn MG, Fox BG. Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:31. [PMID: 28184246 PMCID: PMC5288845 DOI: 10.1186/s13068-017-0703-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/06/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine soluble sugar products of their reactions. RESULTS Single, purified enzymes from the GH5_4, GH10, and GH11 families of glycoside hydrolases hydrolyzed hemicelluloses as evidenced by the loss of specific epitopes from the glycome profiles in enzyme-treated plant biomass. The glycome profiling data were further substantiated by oxime-NIMS, which identified hexose products from hydrolysis of cellulose, and pentose-only and mixed hexose-pentose products from the hydrolysis of hemicelluloses. The GH10 enzyme proved to be reactive with the broadest diversity of xylose-backbone polysaccharide epitopes, but was incapable of reacting with glucose-backbone polysaccharides. In contrast, the GH5 and GH11 enzymes studied here showed the ability to react with both glucose- and xylose-backbone polysaccharides. CONCLUSIONS The identification of enzyme specificity for a wide diversity of polysaccharide structures provided by glycome profiling, and the correlated identification of soluble oligosaccharide hydrolysis products provided by oxime-NIMS, offers a unique combination to understand the hydrolytic capabilities and constraints of individual enzymes as they interact with plant biomass.
Collapse
Affiliation(s)
- Johnnie A. Walker
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Sivakumar Pattathil
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Lai F. Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Emily T. Beebe
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kai Deng
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Maryam Mirzai
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Trent R. Northen
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Michael G. Hahn
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Brian G. Fox
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| |
Collapse
|
24
|
Falade AO, Nwodo UU, Iweriebor BC, Green E, Mabinya LV, Okoh AI. Lignin peroxidase functionalities and prospective applications. Microbiologyopen 2017; 6:e00394. [PMID: 27605423 PMCID: PMC5300883 DOI: 10.1002/mbo3.394] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/18/2016] [Accepted: 06/28/2016] [Indexed: 11/18/2022] Open
Abstract
Ligninolytic extracellular enzymes, including lignin peroxidase, are topical owing to their high redox potential and prospective industrial applications. The prospective applications of lignin peroxidase span through sectors such as biorefinery, textile, energy, bioremediation, cosmetology, and dermatology industries. The litany of potentials attributed to lignin peroxidase is occasioned by its versatility in the degradation of xenobiotics and compounds with both phenolic and non-phenolic constituents. Over the years, ligninolytic enzymes have been studied however; research on lignin peroxidase seems to have been lagging when compared to other ligninolytic enzymes which are extracellular in nature including laccase and manganese peroxidase. This assertion becomes more pronounced when the application of lignin peroxidase is put into perspective. Consequently, a succinct documentation of the contemporary functionalities of lignin peroxidase and, some prospective applications of futuristic relevance has been advanced in this review. Some articulated applications include delignification of feedstock for ethanol production, textile effluent treatment and dye decolourization, coal depolymerization, treatment of hyperpigmentation, and skin-lightening through melanin oxidation. Prospective application of lignin peroxidase in skin-lightening functions through novel mechanisms, hence, it holds high value for the cosmetics sector where it may serve as suitable alternative to hydroquinone; a potent skin-lightening agent whose safety has generated lots of controversy and concern.
Collapse
Affiliation(s)
- Ayodeji O. Falade
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Uchechukwu U. Nwodo
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Benson C. Iweriebor
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Ezekiel Green
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Leonard V. Mabinya
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| | - Anthony I. Okoh
- SAMRC Microbial Water Quality Monitoring CentreUniversity of Fort HareAliceSouth Africa
- Applied and Environmental Microbiology Research Group (AEMREG)Department of Biochemistry and MicrobiologyUniversity of Fort HareAliceSouth Africa
| |
Collapse
|
25
|
Healey AL, Lee DJ, Lupoi JS, Papa G, Guenther JM, Corno L, Adani F, Singh S, Simmons BA, Henry RJ. Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa. FRONTIERS IN PLANT SCIENCE 2016; 7:1705. [PMID: 27917179 PMCID: PMC5114311 DOI: 10.3389/fpls.2016.01705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/31/2016] [Indexed: 05/23/2023]
Abstract
In order for a lignocellulosic bioenergy feedstock to be considered sustainable, it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application, it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin, glucan, and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7-21.3%) among parental and hybrid populations, whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28-38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age, with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase), and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%, respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass, with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass, respectively), with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate, biomass composition, and further optimization of enzymatic saccharification yield, high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.
Collapse
Affiliation(s)
- Adam L. Healey
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt. Lucia, QLD, Australia
| | - David J. Lee
- Forest Industries Research Centre, University of the Sunshine CoastMaroochydore, QLD, Australia
- Forestry & Biosciences, Agri-Science Queensland, Department of Agriculture and FisheriesGympie, QLD, Australia
| | | | - Gabriella Papa
- Joint BioEnergy Institute, Lawrence Berkeley National LaboratoryEmeryville, CA, USA
| | - Joel M. Guenther
- Joint BioEnergy Institute, Lawrence Berkeley National LaboratoryEmeryville, CA, USA
- Biological and Engineering Sciences Center, Sandia National LaboratoriesLivermore, CA, USA
| | - Luca Corno
- Gruppo Ricicla – Biomass and Bioenergy Laboratory, DiSAA, University of MilanMilan, Italy
| | - Fabrizio Adani
- Gruppo Ricicla – Biomass and Bioenergy Laboratory, DiSAA, University of MilanMilan, Italy
| | - Seema Singh
- Joint BioEnergy Institute, Lawrence Berkeley National LaboratoryEmeryville, CA, USA
- Biological and Engineering Sciences Center, Sandia National LaboratoriesLivermore, CA, USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Lawrence Berkeley National LaboratoryEmeryville, CA, USA
- Biological and Engineering Sciences Center, Sandia National LaboratoriesLivermore, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt. Lucia, QLD, Australia
| |
Collapse
|
26
|
Liu B, Gómez LD, Hua C, Sun L, Ali I, Huang L, Yu C, Simister R, Steele-King C, Gan Y, McQueen-Mason SJ. Linkage Mapping of Stem Saccharification Digestibility in Rice. PLoS One 2016; 11:e0159117. [PMID: 27415441 PMCID: PMC4944936 DOI: 10.1371/journal.pone.0159117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/27/2016] [Indexed: 12/19/2022] Open
Abstract
Rice is the staple food of almost half of the world population, and in excess 90% of it is grown and consumed in Asia, but the disposal of rice straw poses a problem for farmers, who often burn it in the fields, causing health and environmental problems. However, with increased focus on the development of sustainable biofuel production, rice straw has been recognized as a potential feedstock for non-food derived biofuel production. Currently, the commercial realization of rice as a biofuel feedstock is constrained by the high cost of industrial saccharification processes needed to release sugar for fermentation. This study is focused on the alteration of lignin content, and cell wall chemotypes and structures, and their effects on the saccharification potential of rice lignocellulosic biomass. A recombinant inbred lines (RILs) population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 271 molecular markers for quantitative trait SNP (QTS) analyses was used. After association analysis of 271 markers for saccharification potential, 1 locus and 4 pairs of epistatic loci were found to contribute to the enzymatic digestibility phenotype, and an inverse relationship between reducing sugar and lignin content in these recombinant inbred lines was identified. As a result of QTS analyses, several cell-wall associated candidate genes are proposed that may be useful for marker-assisted breeding and may aid breeders to produce potential high saccharification rice varieties.
Collapse
Affiliation(s)
- Bohan Liu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Leonardo D. Gómez
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Cangmei Hua
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lili Sun
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Ali
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Linli Huang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunyan Yu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Clare Steele-King
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Simon J. McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom
| |
Collapse
|
27
|
Galkin MV, Samec JSM. Lignin Valorization through Catalytic Lignocellulose Fractionation: A Fundamental Platform for the Future Biorefinery. CHEMSUSCHEM 2016; 9:1544-58. [PMID: 27273230 DOI: 10.1002/cssc.201600237] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Indexed: 05/08/2023]
Abstract
Current processes for the fractionation of lignocellulosic biomass focus on the production of high-quality cellulosic fibers for paper, board, and viscose production. The other fractions that constitute a major part of lignocellulose are treated as waste or used for energy production. The transformation of lignocellulose beyond paper pulp to a commodity (e.g., fine chemicals, polymer precursors, and fuels) is the only feasible alternative to current refining of fossil fuels as a carbon feedstock. Inspired by this challenge, scientists and engineers have developed a plethora of methods for the valorization of biomass. However, most studies have focused on using one single purified component from lignocellulose that is not currently generated by the existing biomass fractionation processes. A lot of effort has been made to develop efficient methods for lignin depolymerization. The step to take this fundamental research to industrial applications is still a major challenge. This review covers an alternative approach, in which the lignin valorization is performed in concert with the pulping process. This enables the fractionation of all components of the lignocellulosic biomass into valorizable streams. Lignocellulose fractions obtained this way (e.g., lignin oil and glucose) can be utilized in a number of existing procedures. The review covers historic, current, and future perspectives, with respect to catalytic lignocellulose fractionation processes.
Collapse
Affiliation(s)
- Maxim V Galkin
- Department of Organic Chemistry, Stockholm University, 106 91, Stockholm, Sweden
| | - Joseph S M Samec
- Department of Organic Chemistry, Stockholm University, 106 91, Stockholm, Sweden.
| |
Collapse
|
28
|
Abdel-Hamid AM, Solbiati JO, Cann IKO. Insights into lignin degradation and its potential industrial applications. ADVANCES IN APPLIED MICROBIOLOGY 2016; 82:1-28. [PMID: 23415151 DOI: 10.1016/b978-0-12-407679-2.00001-6] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lignocellulose is an abundant biomass that provides an alternative source for the production of renewable fuels and chemicals. The depolymerization of the carbohydrate polymers in lignocellulosic biomass is hindered by lignin, which is recalcitrant to chemical and biological degradation due to its complex chemical structure and linkage heterogeneity. The role of fungi in delignification due to the production of extracellular oxidative enzymes has been studied more extensively than that of bacteria. The two major groups of enzymes that are involved in lignin degradation are heme peroxidases and laccases. Lignin-degrading peroxidases include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). LiP, MnP, and VP are class II extracellular fungal peroxidases that belong to the plant and microbial peroxidases superfamily. LiPs are strong oxidants with high-redox potential that oxidize the major non-phenolic structures of lignin. MnP is an Mn-dependent enzyme that catalyzes the oxidation of various phenolic substrates but is not capable of oxidizing the more recalcitrant non-phenolic lignin. VP enzymes combine the catalytic activities of both MnP and LiP and are able to oxidize Mn(2+) like MnP, and non-phenolic compounds like LiP. DyPs occur in both fungi and bacteria and are members of a new superfamily of heme peroxidases called DyPs. DyP enzymes oxidize high-redox potential anthraquinone dyes and were recently reported to oxidize lignin model compounds. The second major group of lignin-degrading enzymes, laccases, are found in plants, fungi, and bacteria and belong to the multicopper oxidase superfamily. They catalyze a one-electron oxidation with the concomitant four-electron reduction of molecular oxygen to water. Fungal laccases can oxidize phenolic lignin model compounds and have higher redox potential than bacterial laccases. In the presence of redox mediators, fungal laccases can oxidize non-phenolic lignin model compounds. In addition to the peroxidases and laccases, fungi produce other accessory oxidases such as aryl-alcohol oxidase and the glyoxal oxidase that generate the hydrogen peroxide required by the peroxidases. Lignin-degrading enzymes have attracted the attention for their valuable biotechnological applications especially in the pretreatment of recalcitrant lignocellulosic biomass for biofuel production. The use of lignin-degrading enzymes has been studied in various applications such as paper industry, textile industry, wastewater treatment and the degradation of herbicides.
Collapse
Affiliation(s)
- Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois, IL, USA; Institute for Genomic Biology, University of Illinois, IL, USA
| | | | | |
Collapse
|
29
|
Healey AL, Lee DJ, Furtado A, Simmons BA, Henry RJ. Efficient Eucalypt Cell Wall Deconstruction and Conversion for Sustainable Lignocellulosic Biofuels. Front Bioeng Biotechnol 2015; 3:190. [PMID: 26636077 PMCID: PMC4653827 DOI: 10.3389/fbioe.2015.00190] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 11/04/2015] [Indexed: 11/13/2022] Open
Abstract
In order to meet the world's growing energy demand and reduce the impact of greenhouse gas emissions resulting from fossil fuel combustion, renewable plant-based feedstocks for biofuel production must be considered. The first-generation biofuels, derived from starches of edible feedstocks, such as corn, create competition between food and fuel resources, both for the crop itself and the land on which it is grown. As such, biofuel synthesized from non-edible plant biomass (lignocellulose) generated on marginal agricultural land will help to alleviate this competition. Eucalypts, the broadly defined taxa encompassing over 900 species of Eucalyptus, Corymbia, and Angophora are the most widely planted hardwood tree in the world, harvested mainly for timber, pulp and paper, and biomaterial products. More recently, due to their exceptional growth rate and amenability to grow under a wide range of environmental conditions, eucalypts are a leading option for the development of a sustainable lignocellulosic biofuels. However, efficient conversion of woody biomass into fermentable monomeric sugars is largely dependent on pretreatment of the cell wall, whose formation and complexity lend itself toward natural recalcitrance against its efficient deconstruction. A greater understanding of this complexity within the context of various pretreatments will allow the design of new and effective deconstruction processes for bioenergy production. In this review, we present the various pretreatment options for eucalypts, including research into understanding structure and formation of the eucalypt cell wall.
Collapse
Affiliation(s)
- Adam L. Healey
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - David J. Lee
- Forest Industries Research Centre, University of the Sunshine Coast, Maroochydore, QLD, Australia
- Department of Agriculture and Fisheries, Forestry and Biosciences, Agri-Science Queensland, Gympie, QLD, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Blake A. Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| |
Collapse
|
30
|
Hoang NV, Furtado A, Botha FC, Simmons BA, Henry RJ. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels. Front Bioeng Biotechnol 2015; 3:182. [PMID: 26636072 PMCID: PMC4646955 DOI: 10.3389/fbioe.2015.00182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels.
Collapse
Affiliation(s)
- Nam V. Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Blake A. Simmons
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| |
Collapse
|
31
|
Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module. PLoS One 2015; 10:e0142107. [PMID: 26562160 PMCID: PMC4643050 DOI: 10.1371/journal.pone.0142107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/16/2015] [Indexed: 01/08/2023] Open
Abstract
Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.
Collapse
|
32
|
Banoub J, Delmas GH, Joly N, Mackenzie G, Cachet N, Benjelloun-Mlayah B, Delmas M. A critique on the structural analysis of lignins and application of novel tandem mass spectrometric strategies to determine lignin sequencing. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:5-48. [PMID: 25601673 DOI: 10.1002/jms.3541] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 05/27/2023]
Abstract
This review is devoted to the application of MS using soft ionization methods with a special emphasis on electrospray ionization, atmospheric pressure photoionization and matrix-assisted laser desorption/ionization MS and tandem MS (MS/MS) for the elucidation of the chemical structure of native and modified lignins. We describe and critically evaluate how these soft ionization methods have contributed to the present-day knowledge of the structure of lignins. Herein, we will introduce new nomenclature concerning the chemical state of lignins, namely, virgin released lignins (VRLs) and processed modified lignins (PML). VRLs are obtained by liberation of lignins through degradation of vegetable matter by either chemical hydrolysis and/or enzymatic hydrolysis. PMLs are produced by subjecting the VRL to a series of further chemical transformations and purifications that are likely to alter their original chemical structures. We are proposing that native lignin polymers, present in the lignocellulosic biomass, are not made of macromolecules linked to cellulose fibres as has been frequently reported. Instead, we propose that the lignins are composed of vast series of linear related oligomers, having different lengths that are covalently linked in a criss-cross pattern to cellulose and hemicellulose fibres forming the network of vegetal matter. Consequently, structural elucidation of VRLs, which presumably have not been purified and processed by any other type of additional chemical treatment and purification, may reflect the structure of the native lignin. In this review, we present an introduction to a MS/MS top-down concept of lignin sequencing and how this technique may be used to address the challenge of characterizing the structure of VRLs. Finally, we offer the case that although lignins have been reported to have very high or high molecular weights, they might not exist on the basis that such polymers have never been identified by the mild ionizing techniques used in modern MS.
Collapse
Affiliation(s)
- Joseph Banoub
- Department of Chemistry, Memorial University of Newfoundland, St John's, Newfoundland, A1C 5X1, Canada; Science Branch, Special Projects, Fisheries and Oceans Canada, St John's, NL, A1C 5X1, Canada
| | | | | | | | | | | | | |
Collapse
|
33
|
Pyroligneous acid—the smoky acidic liquid from plant biomass. Appl Microbiol Biotechnol 2014; 99:611-22. [DOI: 10.1007/s00253-014-6242-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 12/17/2022]
|
34
|
Furtado A, Lupoi JS, Hoang NV, Healey A, Singh S, Simmons BA, Henry RJ. Modifying plants for biofuel and biomaterial production. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1246-58. [PMID: 25431201 DOI: 10.1111/pbi.12300] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/28/2014] [Accepted: 10/23/2014] [Indexed: 05/08/2023]
Abstract
The productivity of plants as biofuel or biomaterial crops is established by both the yield of plant biomass per unit area of land and the efficiency of conversion of the biomass to biofuel. Higher yielding biofuel crops with increased conversion efficiencies allow production on a smaller land footprint minimizing competition with agriculture for food production and biodiversity conservation. Plants have traditionally been domesticated for food, fibre and feed applications. However, utilization for biofuels may require the breeding of novel phenotypes, or new species entirely. Genomics approaches support genetic selection strategies to deliver significant genetic improvement of plants as sources of biomass for biofuel manufacture. Genetic modification of plants provides a further range of options for improving the composition of biomass and for plant modifications to assist the fabrication of biofuels. The relative carbohydrate and lignin content influences the deconstruction of plant cell walls to biofuels. Key options for facilitating the deconstruction leading to higher monomeric sugar release from plants include increasing cellulose content, reducing cellulose crystallinity, and/or altering the amount or composition of noncellulosic polysaccharides or lignin. Modification of chemical linkages within and between these biomass components may improve the ease of deconstruction. Expression of enzymes in the plant may provide a cost-effective option for biochemical conversion to biofuel.
Collapse
Affiliation(s)
- Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
| | | | | | | | | | | | | |
Collapse
|
35
|
Marriott PE, Sibout R, Lapierre C, Fangel JU, Willats WGT, Hofte H, Gómez LD, McQueen-Mason SJ. Range of cell-wall alterations enhance saccharification in Brachypodium distachyon mutants. Proc Natl Acad Sci U S A 2014; 111:14601-6. [PMID: 25246540 PMCID: PMC4209982 DOI: 10.1073/pnas.1414020111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lignocellulosic plant biomass is an attractive feedstock for the production of sustainable biofuels, but the commercialization of such products is hampered by the high costs of processing this material into fermentable sugars (saccharification). One approach to lowering these costs is to produce crops with cell walls that are more susceptible to hydrolysis to reduce preprocessing and enzyme inputs. To deepen our understanding of the molecular genetic basis of lignocellulose recalcitrance, we have screened a mutagenized population of the model grass Brachypodium distachyon for improved saccharification with an industrial polysaccharide-degrading enzyme mixture. From an initial screen of 2,400 M2 plants, we selected 12 lines that showed heritable improvements in saccharification, mostly with no significant reduction in plant size or stem strength. Characterization of these putative mutants revealed a variety of alterations in cell-wall components. We have mapped the underlying genetic lesions responsible for increased saccharification using a deep sequencing approach, and here we report the mapping of one of the causal mutations to a narrow region in chromosome 2. The most likely candidate gene in this region encodes a GT61 glycosyltransferase, which has been implicated in arabinoxylan substitution. Our work shows that forward genetic screening provides a powerful route to identify factors that impact on lignocellulose digestibility, with implications for improving feedstock for cellulosic biofuel production.
Collapse
Affiliation(s)
- Poppy E Marriott
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Richard Sibout
- Institut National de la Recherche Agronomique and AgroParisTech, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Équipes de Recherche Labellisées Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France; and
| | - Catherine Lapierre
- Institut National de la Recherche Agronomique and AgroParisTech, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Équipes de Recherche Labellisées Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France; and
| | - Jonatan U Fangel
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Copenhagen, Denmark
| | - William G T Willats
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, DK-1871 Copenhagen, Denmark
| | - Herman Hofte
- Institut National de la Recherche Agronomique and AgroParisTech, Institut Jean-Pierre Bourgin, Unité Mixte de Recherche 1318, Équipes de Recherche Labellisées Centre National de la Recherche Scientifique 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France; and
| | - Leonardo D Gómez
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom;
| |
Collapse
|
36
|
Zhao X, Moates G, Wellner N, Collins S, Coleman M, Waldron K. Chemical characterisation and analysis of the cell wall polysaccharides of duckweed (Lemna minor). Carbohydr Polym 2014; 111:410-8. [DOI: 10.1016/j.carbpol.2014.04.079] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/15/2014] [Accepted: 04/18/2014] [Indexed: 11/16/2022]
|
37
|
Sahoo DK, Maiti IB. Biomass derived from transgenic tobacco expressing the Arabidopsis CESA3ixr1-2 gene exhibits improved saccharification. ACTA BIOLOGICA HUNGARICA 2014; 65:189-204. [PMID: 24873912 DOI: 10.1556/abiol.65.2014.2.7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Studies in Arabidopsis thaliana and Nicotiana tabacum L. variety Samsun NN demonstrated that expression of the CESA3 cellulose synthase gene that contains a point mutation, named ixr1-2, results in greater conversion of plant-derived cellulose to fermentable sugars. The present study was designed to examine the improved enzymatic saccharification efficiency of lignocellulosic biomass of tobacco plants expressing AtCESA3ixr1-2. Three-month-old AtCESA3ixr1-2 transgenic and wild-type tobacco plants (Nicotiana tabacum L. variety Samsun NN) were grown in the presence and absence of isoxaben. Biomass obtained from leaf, stem, and root tissues were analyzed for enzymatic saccharification rates. During enzymatic saccharification, 45% and 25% more sugar was released from transgenic leaf and stem samples, respectively, when compared to the wild-type samples. This gain in saccharification efficiency was achieved without chemical or heat pretreatment. Additionally, leaf and stem biomass from transgenic AtCESA3ixr1-2 requires a reduced amount of enzyme for saccharification compared to biomass from wild-type plants. From a practical standpoint, a similar strategy could be employed to introduce the mutated CESA into energy crops like poplar and switchgrass to improve the efficiency of biomass conversion.
Collapse
Affiliation(s)
- Dipak Kumar Sahoo
- University of Kentucky KTRDC, College of Agriculture, Food and Environment Lexington KY 40546-0236 USA
| | - Indu B Maiti
- University of Kentucky KTRDC, College of Agriculture, Food and Environment Lexington KY 40546-0236 USA
| |
Collapse
|
38
|
Piao H, Froula J, Du C, Kim TW, Hawley ER, Bauer S, Wang Z, Ivanova N, Clark DS, Klenk HP, Hess M. Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation. Biotechnol Bioeng 2014; 111:1550-65. [PMID: 24728961 DOI: 10.1002/bit.25250] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 02/21/2014] [Accepted: 03/24/2014] [Indexed: 11/06/2022]
Abstract
Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.
Collapse
Affiliation(s)
- Hailan Piao
- School of Molecular Biosciences, Washington State University, Richland, Washington, 99352; Pacific Northwest National Laboratory, Richland, Washington
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Yu Y, Hu R, Wang H, Cao Y, He G, Fu C, Zhou G. MlWRKY12, a novel Miscanthus transcription factor, participates in pith secondary cell wall formation and promotes flowering. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 212:1-9. [PMID: 24094048 DOI: 10.1016/j.plantsci.2013.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/18/2013] [Accepted: 07/20/2013] [Indexed: 05/19/2023]
Abstract
WRKY proteins play crucial roles in various plant processes. An AtWRKY12 homologous gene, named MlWRKY12, was isolated from Miscanthus lutarioriparius. The MlWRKY12 gene encodes a WRKY transcription factor belonging to the group IIc subfamily. MlWRKY12 is a nuclear protein. Gene expression pattern analysis revealed a relatively high MlWRKY12 expression level in rhizomes, stems and leaf sheaths. In situ hybridization analysis further demonstrated that MlWRKY12 was expressed in vascular bundle sheath, sclerenchyma and parenchyma tissues. The heterologous expression of MlWRKY12 in an atwrky12 background mutant successfully rescued the phenotype of pith cell walls caused by the defect of AtWRKY12. Most strikingly, the transgenic Arabidopsis plants overexpressing MlWRKY12 exhibited early flowering. The transcript abundance of flowering related genes was measured by quantitative RT-PCR analysis, suggesting that overexpression of MlWRKY12 in Arabidopsis had a significant impact on the expression level of CONSTANS (CO). Moreover, the expression levels of FLOWERING LOCUS T (FT), LFY (LEAFY), APETALA1 (AP1), CAULIFLOWER (CAL) and FRUITFULL (FUL) were upregulated in transgenic plants. These results demonstrated the conserved function of MlWRKY12 existing in secondary cell wall formation of monocotyledonous species and implied a possible impact of MlWRKY12 on flowering control.
Collapse
Affiliation(s)
- Yanchong Yu
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS), Qingdao, Shandong, China
| | | | | | | | | | | | | |
Collapse
|
40
|
Wang YH, Acharya A, Burrell AM, Klein RR, Klein PE, Hasenstein KH. Mapping and candidate genes associated with saccharification yield in sorghum. Genome 2013; 56:659-65. [PMID: 24299105 DOI: 10.1139/gen-2013-0134] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a high-yielding, stress tolerant energy crop for lignocellulosic-based biofuel production. Saccharification is a process by which hydrolytic enzymes break down lignocellulosic materials to fermentable sugars for biofuel production, and mapping and identifying genes underlying saccharification yield is an important first step to genetically improve the plant for higher biofuel productivity. In this study, we used the ICRISAT sorghum mini core germplasm collection and 14 739 single nucleotide polymorphism markers to map saccharification yield. Seven marker loci were associated with saccharification yield and five of these loci were syntenic with regions in the maize genome that contain quantitative trait loci underlying saccharification yield and cell wall component traits. Candidate genes from the seven loci were identified but must be validated, with the most promising candidates being β-tubulin, which determines the orientation of cellulose microfibrils in plant secondary cell walls, and NST1, a master transcription factor controlling secondary cell wall biosynthesis in fibers. Other candidate genes underlying the different saccharification loci included genes that play a role in vascular development and suberin deposition in plants. The identified loci and candidate genes provide information into the factors controlling saccharification yield and may facilitate increasing biofuel production in sorghum.
Collapse
Affiliation(s)
- Yi-Hong Wang
- a Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | | | | | | | | | | |
Collapse
|
41
|
The role of coproporphyrinogen III oxidase and ferrochelatase genes in heme biosynthesis and regulation in Aspergillus niger. Appl Microbiol Biotechnol 2013; 97:9773-85. [PMID: 24113826 DOI: 10.1007/s00253-013-5274-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 10/26/2022]
Abstract
Heme is a suggested limiting factor in peroxidase production by Aspergillus spp., which are well-known suitable hosts for heterologous protein production. In this study, the role of genes coding for coproporphyrinogen III oxidase (hemF) and ferrochelatase (hemH) was analyzed by means of deletion and overexpression to obtain more insight in fungal heme biosynthesis and regulation. These enzymes represent steps in the heme biosynthetic pathway downstream of the siroheme branch and are suggested to play a role in regulation of the pathway. Based on genome mining, both enzymes deviate in cellular localization and protein domain structure from their Saccharomyces cerevisiae counterparts. The lethal phenotype of deletion of hemF or hemH could be remediated by heme supplementation confirming that Aspergillus niger is capable of hemin uptake. Nevertheless, both gene deletion mutants showed an extremely impaired growth even with hemin supplementation which could be slightly improved by media modifications and the use of hemoglobin as heme source. The hyphae of the mutant strains displayed pinkish coloration and red autofluorescence under UV indicative of cellular porphyrin accumulation. HPLC analysis confirmed accumulation of specific porphyrins, thereby confirming the function of the two proteins in heme biosynthesis. Overexpression of hemH, but not hemF or the aminolevulinic acid synthase encoding hemA, modestly increased the cellular heme content, which was apparently insufficient to increase activity of endogenous peroxidase and cytochrome P450 enzyme activities. Overexpression of all three genes increased the cellular accumulation of porphyrin intermediates suggesting regulatory mechanisms operating in the final steps of the fungal heme biosynthesis pathway.
Collapse
|
42
|
Optimization of β-glucosidase, β-xylosidase and xylanase production by Colletotrichum graminicola under solid-state fermentation and application in raw sugarcane trash saccharification. Int J Mol Sci 2013; 14:2875-902. [PMID: 23364611 PMCID: PMC3588020 DOI: 10.3390/ijms14022875] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/12/2012] [Accepted: 01/09/2013] [Indexed: 12/02/2022] Open
Abstract
Efficient, low-cost enzymatic hydrolysis of lignocellulosic residues is essential for cost-effective production of bioethanol. The production of β-glucosidase, β-xylosidase and xylanase by Colletotrichum graminicola was optimized using Response Surface Methodology (RSM). Maximal production occurred in wheat bran. Sugarcane trash, peanut hulls and corncob enhanced β-glucosidase, β-xylosidase and xylanase production, respectively. Maximal levels after optimization reached 159.3 ± 12.7 U g−1, 128.1 ± 6.4 U g−1 and 378.1 ± 23.3 U g−1, respectively, but the enzymes were produced simultaneously at good levels under culture conditions optimized for each one of them. Optima of pH and temperature were 5.0 and 65 °C for the three enzymes, which maintained full activity for 72 h at 50 °C and for 120 min at 60 °C (β-glucosidase) or 65 °C (β-xylosidase and xylanase). Mixed with Trichoderma reesei cellulases, C. graminicola crude extract hydrolyzed raw sugarcane trash with glucose yield of 33.1% after 48 h, demonstrating good potential to compose efficient cocktails for lignocellulosic materials hydrolysis.
Collapse
|
43
|
Abstract
Lignocellulosic biomass is a promising feedstock to produce biofuels and other valuable biocommodities. A major obstacle to its commercialization is the high cost of degrading biomass into fermentable sugars, which is typically achieved using cellulolytic enzymes from Trichoderma reesei. Here, we explore the use of microbes to break down biomass. Bacillus subtilis was engineered to display a multicellulase-containing minicellulosome. The complex contains a miniscaffoldin protein that is covalently attached to the cell wall and three noncovalently associated cellulase enzymes derived from Clostridium cellulolyticum (Cel48F, Cel9E, and Cel5A). The minicellulosome spontaneously assembles, thus increasing the practicality of the cells. The recombinant bacteria are highly cellulolytic and grew in minimal medium containing industrially relevant forms of biomass as the primary nutrient source (corn stover, hatched straw, and switch grass). Notably, growth did not require dilute acid pretreatment of the biomass and the cells achieved densities approaching those of cells cultured with glucose. An analysis of the sugars released from acid-pretreated corn stover indicates that the cells have stable cellulolytic activity that enables them to break down 62.3% ± 2.6% of the biomass. When supplemented with beta-glucosidase, the cells liberated 21% and 33% of the total available glucose and xylose in the biomass, respectively. As the cells display only three types of enzymes, increasing the number of displayed enzymes should lead to even more potent cellulolytic microbes. This work has important implications for the efficient conversion of lignocellulose to value-added biocommodities.
Collapse
|
44
|
Kiyota E, Mazzafera P, Sawaya ACHF. Analysis of soluble lignin in sugarcane by ultrahigh performance liquid chromatography-tandem mass spectrometry with a do-it-yourself oligomer database. Anal Chem 2012; 84:7015-20. [PMID: 22830944 DOI: 10.1021/ac301112y] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lignin is a polymer found in the cell wall of plants and is one of the main obstacles to the implementation of second-generation ethanol production because it confers the recalcitrance of the lignocellulosic material. The recalcitrance of biomass is affected by the amount of lignin, by its monomer composition, and the way the monomers are arranged in the plant cell wall. Analysis of lignin structure demands mass spectrometry analysis, and identification of oligomers is usually based on libraries produced by laborious protocols. A robust method to build a do-it-yourself lignin oligomer library was tested. This library can be built using commercially available enzymes, standards, and reagents and is relatively easy to accomplish. An ultrahigh performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the separation and characterization of monomers and oligomers was developed and was equally applicable to the synthetic lignin and to soluble lignin extracted from a sample of sugar cane.
Collapse
Affiliation(s)
- Eduardo Kiyota
- Plant Biology Department, Biology Institute, State University of Campinas, Unicamp, Campinas, São Paulo, 13083-970, Brazil
| | | | | |
Collapse
|
45
|
Fiasconaro ML, Gogorcena Y, Muñoz F, Andueza D, Sánchez-Díaz M, Antolín MC. Effects of nitrogen source and water availability on stem carbohydrates and cellulosic bioethanol traits of alfalfa plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:16-23. [PMID: 22682561 DOI: 10.1016/j.plantsci.2012.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/16/2012] [Accepted: 04/18/2012] [Indexed: 06/01/2023]
Abstract
Symbiotic association of legumes with rhizobia frequently results in higher photosynthesis and soluble carbohydrates in comparison with nitrate-fed plants, which might improve its potential for biomass conversion into bioethanol. A greenhouse experiment was conducted to examine the effects of nitrogen source and water availability on stem characteristics and on relationships between carbohydrates, phenolic metabolism activity and cell wall composition in alfalfa (Medicago sativa L. cv. Aragón). The experiment included three treatments: (1) plants fed with ammonium nitrate (AN); (2) plants inoculated with rhizobia (R); and (3) plants inoculated with rhizobia and amended with sewage sludge (RS). Two levels of irrigation were imposed: (1) well-watered and (2) drought stress. Under well-watered conditions, nitrogen-fixing plants have increased photosynthesis and stem fermentable carbohydrate concentrations, which result in higher potential for biomass conversion to bioethanol than in AN plants. The latter had higher lignin due to enhanced activities of phenolic metabolism-related enzymes. Under drought conditions, the potential for bioethanol conversion decreased to a similar level in all treatments. Drought-stressed nitrogen-fixing plants have high concentrations of fermentable carbohydrates and cell wall cellulose, but ammonium nitrate-fed plants produced higher plant and stem biomass, which might compensate the decreasing stem carbohydrates and cellulose concentrations.
Collapse
Affiliation(s)
- M Laura Fiasconaro
- Dpto. Biología Vegetal, Sección Biología Vegetal, Unidad Asociada al CSIC-EEAD, Zaragoza, ICVV, Logroño, Facultades de Ciencias y Farmacia, Universidad de Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain
| | | | | | | | | | | |
Collapse
|
46
|
Production of a xylose-stimulated β-glucosidase and a cellulase-free thermostable xylanase by the thermophilic fungus Humicola brevis var. thermoidea under solid state fermentation. World J Microbiol Biotechnol 2012; 28:2689-701. [PMID: 22806195 DOI: 10.1007/s11274-012-1079-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/05/2012] [Indexed: 10/28/2022]
Abstract
Humicola brevis var. thermoidea cultivated under solid state fermentation in wheat bran and water (1:2 w/v) was a good producer of β-glucosidase and xylanase. After optimization using response surface methodology the level of xylanase reached 5,791.2 ± 411.2 U g(-1), while β-glucosidase production was increased about 2.6-fold, reaching 20.7 ± 1.5 U g(-1). Cellulase levels were negligible. Biochemical characterization of H. brevis β-glucosidase and xylanase activities showed that they were stable in a wide pH range. Optimum pH for β-glucosidase and xylanase activities were 5.0 and 5.5, respectively, but the xylanase showed 80 % of maximal activity when assayed at pH 8.0. Both enzymes presented high thermal stability. The β-glucosidase maintained about 95 % of its activity after 26 h in water at 55 °C, with half-lives of 15.7 h at 60 °C and 5.1 h at 65 °C. The presence of xylose during heat treatment at 65 °C protected β-glucosidase against thermal inactivation. Xylanase maintained about 80 % of its activity after 200 h in water at 60 °C. Xylose stimulated β-glucosidase activity up to 1.7-fold, at 200 mmol L(-1). The notable features of both xylanase and β-glucosidase suggest that H. brevis crude culture extract may be useful to compose efficient enzymatic cocktails for lignocellulosic materials treatment or paper pulp biobleaching.
Collapse
|
47
|
Chavigneau H, Goué N, Delaunay S, Courtial A, Jouanin L, Reymond M, Méchin V, Barrière Y. QTL for floral stem lignin content and degradability in three recombinant inbred line (RIL) progenies of <i>Arabidopsis thaliana</i> and search for candidate genes involved in cell wall biosynthesis and degradability. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojgen.2012.21002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
48
|
Kwon SI, Cho HJ, Lee JS, Jin H, Shin SJ, Kwon M, Noh EW, Park OK. Overexpression of constitutively active Arabidopsis RabG3b promotes xylem development in transgenic poplars. PLANT, CELL & ENVIRONMENT 2011; 34:2212-24. [PMID: 21895694 DOI: 10.1111/j.1365-3040.2011.02416.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An Arabidopsis small GTPase, RabG3b, was previously characterized as a component of autophagy and as a positive regulator for xylem development in Arabidopsis. In this work, we assessed whether RabG3b modulates xylem-associated traits in poplar in a similar way as in Arabidopsis. We generated transgenic poplars (Populus alba × Populus tremula var. glandulosa) overexpressing a constitutively active form of RabG3b (RabG3bCA) and performed a range of morphological, histochemical and molecular analyses to examine xylogenesis. RabG3bCA transgenic poplars showed increased stem growth due to enhanced xylem development. Autophagic structures were observed in differentiating xyelm cells undergoing programmed cell death (PCD) in wild-type poplar, and were more abundant in RabG3bCA transgenic poplar plants and cultured cells. Xylogenic activation was also accompanied by the expression of secondary wall-, PCD- and autophagy-related genes. Collectively, our results suggest that Arabidopsis RabG3b functions to regulate xylem growth through the activation of autophagy during wood formation in Populus, as does the same in Arabidopsis.
Collapse
Affiliation(s)
- Soon Il Kwon
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Mendu V, Harman-Ware AE, Crocker M, Jae J, Stork J, Morton S, Placido A, Huber G, DeBolt S. Identification and thermochemical analysis of high-lignin feedstocks for biofuel and biochemical production. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:43. [PMID: 22018114 PMCID: PMC3224766 DOI: 10.1186/1754-6834-4-43] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 10/21/2011] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lignin is a highly abundant biopolymer synthesized by plants as a complex component of plant secondary cell walls. Efforts to utilize lignin-based bioproducts are needed. RESULTS Herein we identify and characterize the composition and pyrolytic deconstruction characteristics of high-lignin feedstocks. Feedstocks displaying the highest levels of lignin were identified as drupe endocarp biomass arising as agricultural waste from horticultural crops. By performing pyrolysis coupled to gas chromatography-mass spectrometry, we characterized lignin-derived deconstruction products from endocarp biomass and compared these with switchgrass. By comparing individual pyrolytic products, we document higher amounts of acetic acid, 1-hydroxy-2-propanone, acetone and furfural in switchgrass compared to endocarp tissue, which is consistent with high holocellulose relative to lignin. By contrast, greater yields of lignin-based pyrolytic products such as phenol, 2-methoxyphenol, 2-methylphenol, 2-methoxy-4-methylphenol and 4-ethyl-2-methoxyphenol arising from drupe endocarp tissue are documented. CONCLUSIONS Differences in product yield, thermal decomposition rates and molecular species distribution among the feedstocks illustrate the potential of high-lignin endocarp feedstocks to generate valuable chemicals by thermochemical deconstruction.
Collapse
Affiliation(s)
- Venugopal Mendu
- Department of Horticulture, University of Kentucky, 1100 Nicholasville Road, Lexington, KY 40546, USA
| | - Anne E Harman-Ware
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY 40511, USA
| | - Mark Crocker
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY 40511, USA
| | - Jungho Jae
- Department of Chemical Engineering, University of Massachusetts, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Jozsef Stork
- Department of Horticulture, University of Kentucky, 1100 Nicholasville Road, Lexington, KY 40546, USA
| | - Samuel Morton
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY 40511, USA
| | - Andrew Placido
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY 40511, USA
| | - George Huber
- Department of Chemical Engineering, University of Massachusetts, 686 North Pleasant Street, Amherst, MA 01003, USA
| | - Seth DeBolt
- Department of Horticulture, University of Kentucky, 1100 Nicholasville Road, Lexington, KY 40546, USA
| |
Collapse
|
50
|
Cook C, Devoto A. Fuel from plant cell walls: recent developments in second generation bioethanol research. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2011; 91:1729-32. [PMID: 21681755 DOI: 10.1002/jsfa.4455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
As bioethanol from sugarcane and wheat falls out of favour due to concerns about food security, research is ongoing into genetically engineering model plants and microorganisms to find the optimum cell wall structure for the ultimate second generation bioethanol crop. Charis Cook and Alessandra Devoto highlight here the progress made to tailor the plant cell wall to improve the accessibility of cellulose by acting on the regulation, the structure or the relative composition of other cell wall components to ultimately improve saccharification efficiency. They also consider possible side effects of cell wall modification and focus on the latest advances made to improve the efficiency of digestion of lignocellulosic materials by cell wall degrading microorganisms.
Collapse
Affiliation(s)
- Charis Cook
- Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey TW200EX, UK.
| | | |
Collapse
|