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Sionkowski P, Kruszewska N, Kreitschitz A, Gorb SN, Domino K. Application of Recurrence Plot Analysis to Examine Dynamics of Biological Molecules on the Example of Aggregation of Seed Mucilage Components. ENTROPY (BASEL, SWITZERLAND) 2024; 26:380. [PMID: 38785629 PMCID: PMC11119629 DOI: 10.3390/e26050380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
The goal of the research is to describe the aggregation process inside the mucilage produced by plant seeds using molecular dynamics (MD) combined with time series algorithmic analysis based on the recurrence plots. The studied biological molecules model is seed mucilage composed of three main polysaccharides, i.e. pectins, hemicellulose, and cellulose. The modeling of biological molecules is based on the assumption that a classical-quantum passage underlies the aggregation process in the mucilage, resulting from non-covalent interactions, as they affect the macroscopic properties of the system. The applied recurrence plot approach is an important tool for time series analysis and data mining dedicated to analyzing time series data originating from complex, chaotic systems. In the current research, we demonstrated that advanced algorithmic analysis of seed mucilage data can reveal some features of the dynamics of the system, namely temperature-dependent regions with different dynamics of increments of a number of hydrogen bonds and regions of stable oscillation of increments of a number of hydrophobic-polar interactions. Henceforth, we pave the path for automatic data-mining methods for the analysis of biological molecules with the intermediate step of the application of recurrence plot analysis, as the generalization of recurrence plot applications to other (biological molecules) datasets is straightforward.
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Affiliation(s)
- Piotr Sionkowski
- Institute of Theoretical and Applied Informatics, Polish Academy of Sciences, ul. Bałtycka 5, 44-100 Gliwice, Poland; (P.S.); (K.D.)
| | - Natalia Kruszewska
- Group of Modeling of Physicochemical Processes, Faculty of Chemical Technology and Engineering, Bydgoszcz University of Science and Technology, 85-796 Bydgoszcz, Poland
| | - Agnieszka Kreitschitz
- Department of Plant Developmental Biology, University of Wrocław, ul. Kanonia 6/8, 50-328 Wrocław, Poland;
| | - Stanislav N. Gorb
- Department of Functional Morphology and Biomechanics, Kiel University, Am Botanischen Garten 1-9, D-24098 Kiel, Germany;
| | - Krzysztof Domino
- Institute of Theoretical and Applied Informatics, Polish Academy of Sciences, ul. Bałtycka 5, 44-100 Gliwice, Poland; (P.S.); (K.D.)
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Kaur D, Joshi A, Sharma V, Batra N, Sharma AK. An insight into microbial sources, classification, and industrial applications of xylanases: A rapid review. Biotechnol Appl Biochem 2023; 70:1489-1503. [PMID: 37186103 DOI: 10.1002/bab.2469] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Endo 1,4-β-d-xylanases (EC3.2.1.8) are one of the key lignocellulose hydrolyzing enzymes. Xylan, which is present in copious amounts on earth, forms the primary substrate of endo-xylanases, which can unchain the constituent monosaccharides linked via β-1,4-glycosidic bonds from the xylan backbone. Researchers have shown keen interest in the xylanases belonging to glycoside hydrolase families 10 and 11, whereas those placed in other glycoside hydrolase families are yet to be investigated. Various microbes such as bacteria and fungi harbor these enzymes for the metabolism of their lignocellulose fibers. These microbes can be used as miniature biofactories of xylanase enzymes for a plethora of environmentally benign applications in pulp and paper industry, biofuel production, and for improving the quality of food in bread baking and fruit juice industry. This review highlights the potential of microbes in production of xylanase for industrial biotechnology.
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Affiliation(s)
- Damanjeet Kaur
- Department of Biotechnology, Sri Guru Gobind Singh College, Chandigarh, India
| | - Amit Joshi
- Department of Biotechnology, Sri Guru Gobind Singh College, Chandigarh, India
| | - Varruchi Sharma
- Department of Biotechnology, Sri Guru Gobind Singh College, Chandigarh, India
| | - Navneet Batra
- Department of Biotechnology, GGDSD College, Chandigarh, India
| | - Anil K Sharma
- Department of Biotechnology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar (deemed to be University), Mullana-Ambala, Haryana, India
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Mendes GGM, Mota TR, Bossoni GEB, Marchiosi R, Oliveira DMD, Constantin RP, Dos Santos WD, Ferrarese-Filho O. Inhibiting tricin biosynthesis improves maize lignocellulose saccharification. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:12-19. [PMID: 35247693 DOI: 10.1016/j.plaphy.2022.02.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/14/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Lignin is a technological bottleneck to convert polysaccharides into fermentable sugars, and different strategies of genetic-based metabolic engineering have been applied to improve biomass saccharification. Using maize seedlings grown hydroponically for 24 h, we conducted a quick non-transgenic approach with five enzyme inhibitors of the lignin and tricin pathways. Two compounds [3,4-(methylenedioxy)cinnamic acid: MDCA and 2,4-pyridinedicarboxylic acid: PDCA] revealed interesting findings on root growth, lignin composition, and saccharification. By inhibiting hydroxycinnamoyl-CoA ligase, a key enzyme of phenylpropanoid pathway, MDCA decreased the lignin content and improved saccharification, but it decreased root growth. By inhibiting flavone synthase, a key enzyme of tricin biosynthesis, PDCA decreased total lignin content and improved saccharification without affecting root growth. PDCA was three-fold more effective than MDCA, suggesting that controlling lignin biosynthesis with enzymatic inhibitors may be an attractive strategy to improve biomass saccharification.
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Affiliation(s)
| | - Thatiane Rodrigues Mota
- Ghent University, Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Rogério Marchiosi
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Dyoni Matias de Oliveira
- Ghent University, Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rodrigo Polimeni Constantin
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Wanderley Dantas Dos Santos
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Osvaldo Ferrarese-Filho
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil.
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Joshi A, Verma KK, D Rajput V, Minkina T, Arora J. Recent advances in metabolic engineering of microorganisms for advancing lignocellulose-derived biofuels. Bioengineered 2022; 13:8135-8163. [PMID: 35297313 PMCID: PMC9161965 DOI: 10.1080/21655979.2022.2051856] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Combating climate change and ensuring energy supply to a rapidly growing global population has highlighted the need to replace petroleum fuels with clean, and sustainable renewable fuels. Biofuels offer a solution to safeguard energy security with reduced ecological footprint and process economics. Over the past years, lignocellulosic biomass has become the most preferred raw material for the production of biofuels, such as fuel, alcohol, biodiesel, and biohydrogen. However, the cost-effective conversion of lignocellulose into biofuels remains an unsolved challenge at the industrial scale. Recently, intensive efforts have been made in lignocellulose feedstock and microbial engineering to address this problem. By improving the biological pathways leading to the polysaccharide, lignin, and lipid biosynthesis, limited success has been achieved, and still needs to improve sustainable biofuel production. Impressive success is being achieved by the retouring metabolic pathways of different microbial hosts. Several robust phenotypes, mostly from bacteria and yeast domains, have been successfully constructed with improved substrate spectrum, product yield and sturdiness against hydrolysate toxins. Cyanobacteria is also being explored for metabolic advancement in recent years, however, it also remained underdeveloped to generate commercialized biofuels. The bacterium Escherichia coli and yeast Saccharomyces cerevisiae strains are also being engineered to have cell surfaces displaying hydrolytic enzymes, which holds much promise for near-term scale-up and biorefinery use. Looking forward, future advances to achieve economically feasible production of lignocellulosic-based biofuels with special focus on designing more efficient metabolic pathways coupled with screening, and engineering of novel enzymes.
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Affiliation(s)
- Abhishek Joshi
- Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning - 530007, China
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, 344090, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, 344090, Russia
| | - Jaya Arora
- Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India,CONTACT Jaya Arora Laboratory of Biomolecular Technology, Department of Botany, Mohanlal Sukhadia University, Udaipur313001, India
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"Neptune Balls" Polysaccharides: Disentangling the Wiry Seagrass Detritus. Polymers (Basel) 2021; 13:polym13244285. [PMID: 34960836 PMCID: PMC8703491 DOI: 10.3390/polym13244285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 01/21/2023] Open
Abstract
Each year, high amounts of dead seagrass material are washed ashore at beaches world-wide. In the Mediterranean region, the seagrass Posidonia oceanica is responsible for huge agglomerates of ball-like seagrass litter. As these are often removed due to touristic reasons, a reuse method would be a step towards a more ecologically oriented society. In this study, the main polysaccharide components were analyzed, in order to propose possible usage options. To do this, different aqueous fractions were extracted, analyzed by classical carbohydrate analysis methods (GC-FID/MS, colorimetric assay and elemental analysis), and purified by ion-exchange chromatography, as well as selective precipitation with a detecting agent for highly glycosylated glycoproteins. The obtained purified fractions were analyzed in detail and a linkage-type analysis of the most promising extract was conducted via permethylation. Only low amounts of glycoproteins, as well as medium amounts of the characteristic apiogalacturonan were likely to be present, while xylan seemed to be the most abundant polysaccharide in most fractions. A partial structural proposal showed general accordance with land plant xylans, presenting reuse options in the field of biofuel and bioplastic generation.
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Vuong TV, Master ER. Enzymatic upgrading of heteroxylans for added-value chemicals and polymers. Curr Opin Biotechnol 2021; 73:51-60. [PMID: 34311175 DOI: 10.1016/j.copbio.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/27/2021] [Accepted: 07/02/2021] [Indexed: 02/06/2023]
Abstract
Xylan is one of the most abundant, natural polysaccharides, and much recent interest focuses on upgrading heteroxylan to make use of its unique structures and chemistries. Significant progress has been made in the discovery and application of novel enzymes for debranching and modifying heteroxylans. Debranching enzymes include acetylxylan esterases, α-l-arabinofuranosidases and α-dglucuronidases that release side groups from the xylan backbone to recover both biochemicals and less substituted xylans for polymer applications in food packaging or drug delivery systems. Besides esterases and hydrolases, many oxidoreductases including carbohydrate oxidases, lytic polysaccharide monooxygenases, laccases and peroxidases have been also applied to alter different types of xylans for improved physical and chemical properties. This review will highlight the recent discovery and application of enzymes for upgrading xylans for use as added-value chemicals and in functional polymers.
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Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.
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Recent insights, applications and prospects of xylose reductase: a futuristic enzyme for xylitol production. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-020-03674-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Mota TR, de Souza WR, Oliveira DM, Martins PK, Sampaio BL, Vinecky F, Ribeiro AP, Duarte KE, Pacheco TF, Monteiro NDKV, Campanha RB, Marchiosi R, Vieira DS, Kobayashi AK, Molinari PADO, Ferrarese-Filho O, Mitchell RAC, Molinari HBC, Dos Santos WD. Suppression of a BAHD acyltransferase decreases p-coumaroyl on arabinoxylan and improves biomass digestibility in the model grass Setaria viridis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:136-150. [PMID: 33111398 DOI: 10.1111/tpj.15046] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/28/2020] [Accepted: 09/23/2020] [Indexed: 05/11/2023]
Abstract
Grass cell walls have hydroxycinnamic acids attached to arabinosyl residues of arabinoxylan (AX), and certain BAHD acyltransferases are involved in their addition. In this study, we characterized one of these BAHD genes in the cell wall of the model grass Setaria viridis. RNAi silenced lines of S. viridis (SvBAHD05) presented a decrease of up to 42% of ester-linked p-coumarate (pCA) and 50% of pCA-arabinofuranosyl, across three generations. Biomass from SvBAHD05 silenced plants exhibited up to 32% increase in biomass saccharification after acid pre-treatment, with no change in total lignin. Molecular dynamics simulations suggested that SvBAHD05 is a p-coumaroyl coenzyme A transferase (PAT) mainly involved in the addition of pCA to the arabinofuranosyl residues of AX in Setaria. Thus, our results provide evidence of p-coumaroylation of AX promoted by SvBAHD05 acyltransferase in the cell wall of the model grass S. viridis. Furthermore, SvBAHD05 is a promising biotechnological target to engineer crops for improved biomass digestibility for biofuels, biorefineries and animal feeding.
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Affiliation(s)
- Thatiane R Mota
- Department of Biochemistry, State University of Maringá, Maringá, PR, 87020-900, Brazil
| | - Wagner R de Souza
- Embrapa Agroenergy, Brasília, DF, 70770-901, Brazil
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | - Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, PR, 87020-900, Brazil
| | | | | | | | | | | | | | - Norberto de K V Monteiro
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN, 59078-970, Brazil
- Department of Analytical and Physical Chemistry, Federal University of Ceará, Fortaleza, CE, 60455-760, Brazil
| | | | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Maringá, PR, 87020-900, Brazil
| | - Davi S Vieira
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN, 59078-970, Brazil
| | | | | | | | - Rowan A C Mitchell
- Plant Sciences, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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