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Abena T, Simachew A. Production and characterization of acidophilic xylanase from wood degrading white rot fungus by solid-state fermentation of wheat straw. Heliyon 2024; 10:e35496. [PMID: 39170105 PMCID: PMC11337099 DOI: 10.1016/j.heliyon.2024.e35496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Xylanases (EC 3.2.1.8) catalyze the breakdown of xylan, which is the second most abundant polysaccharide in plant cell walls. Biological catalysts have gained greater global attention than chemical catalysts in different industrial processes because they are highly selective, easy to control and have a negligible environmental impact. The aim of this study was to investigate the xylanolytic potential of white-rot fungi, optimize their physicochemical conditions and characterize the resulting xylanase. Sixty-eight white-rot fungus (WRF) isolates were screened for their xylanolytic potential and growth conditions for maximal xylanase production using cheap agricultural residue (wheat straw) as the sole carbon source. Five WRF isolates with high xylanase yields (73.63 ± 0.0283-63.6 ± 0.01247 U/ml) were selected by qualitative and quantitative screening methods. The optimum xylanase production occurred at pH 5.0 and 28 °C. Solid-state fermentation (SSF) yielded a high amount of xylanase. The highest xylanase activity (80.9-61.274 U/mL) was recorded in the pH range of 5.0-6.5 and at 50 °C. The metal ions Mg2+, Ca2+ and Mn2+ enhanced the activity of xylanase (127.28-110.06 %), while Cu2+, Fe2+ and K+ inhibited the activity with 43.4-17 % losses. The km and Vmax were 0.32-0.545 mg/mL and 86.95-113.63 μmol/min/mg, respectively. This finding indicates that wheat straw can be used for large-scale xylanase production under SSF conditions. The pH and temperature profiles and stabilities indicate that the xylanase produced in the present study can be applied in food and animal feed industries.
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Affiliation(s)
- Tariku Abena
- Microbial Biotechnology Research Program, National Agricultural Biotechnology Research Center (NABRC), Ethiopian Institute of Agricultural Research, Ethiopia
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Ethiopia
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2
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Zhong R, Phillips DR, Clark KD, Adams ER, Lee C, Ye ZH. Biochemical Characterization of Rice Xylan Biosynthetic Enzymes in Determining Xylan Chain Elongation and Substitutions. PLANT & CELL PHYSIOLOGY 2024; 65:1065-1079. [PMID: 38501734 DOI: 10.1093/pcp/pcae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
Grass xylan consists of a linear chain of β-1,4-linked xylosyl residues that often form domains substituted only with either arabinofuranose (Araf) or glucuronic acid (GlcA)/methylglucuronic acid (MeGlcA) residues, and it lacks the unique reducing end tetrasaccharide sequence found in dicot xylan. The mechanism of how grass xylan backbone elongation is initiated and how its distinctive substitution pattern is determined remains elusive. Here, we performed biochemical characterization of rice xylan biosynthetic enzymes, including xylan synthases, glucuronyltransferases and methyltransferases. Activity assays of rice xylan synthases demonstrated that they required short xylooligomers as acceptors for their activities. While rice xylan glucuronyltransferases effectively glucuronidated unsubstituted xylohexaose acceptors, they transferred little GlcA residues onto (Araf)-substituted xylohexaoses and rice xylan 3-O-arabinosyltransferase could not arabinosylate GlcA-substituted xylohexaoses, indicating that their intrinsic biochemical properties may contribute to the distinctive substitution patterns of rice xylan. In addition, we found that rice xylan methyltransferase exhibited a low substrate binding affinity, which may explain the partial GlcA methylation in rice xylan. Furthermore, immunolocalization of xylan in xylem cells of both rice and Arabidopsis showed that it was deposited together with cellulose in secondary walls without forming xylan-rich nanodomains. Together, our findings provide new insights into the biochemical mechanisms underlying xylan backbone elongation and substitutions in grass species.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dennis R Phillips
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Kevin D Clark
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Earle R Adams
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Chanhui Lee
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Plant & Environmental New Resources, College of Life Sciences, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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3
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Delmer D, Dixon RA, Keegstra K, Mohnen D. The plant cell wall-dynamic, strong, and adaptable-is a natural shapeshifter. THE PLANT CELL 2024; 36:1257-1311. [PMID: 38301734 PMCID: PMC11062476 DOI: 10.1093/plcell/koad325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024]
Abstract
Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms-with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type-specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.
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Affiliation(s)
- Deborah Delmer
- Section of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Kenneth Keegstra
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48823, USA
| | - Debra Mohnen
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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4
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Sahu S, Sharma S, Kaur A, Singh G, Khatri M, Arya SK. Algal carbohydrate polymers: Catalytic innovations for sustainable development. Carbohydr Polym 2024; 327:121691. [PMID: 38171696 DOI: 10.1016/j.carbpol.2023.121691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Algal polysaccharides, harnessed for their catalytic potential, embody a compelling narrative in sustainable chemistry. This review explores the complex domains of algal carbohydrate-based catalysis, revealing its diverse trajectory. Starting with algal polysaccharide synthesis and characterization methods as catalysts, the investigation includes sophisticated techniques like NMR spectroscopy that provide deep insights into the structural variety of these materials. Algal polysaccharides undergo various preparation and modification techniques to enhance their catalytic activity such as immobilization. Homogeneous catalysis, revealing its significance in practical applications like crafting organic compounds and facilitating chemical transformations. Recent studies showcase how algal-derived catalysts prove to be remarkably versatile, showcasing their ability to customise reactions for specific substances. Heterogeneous catalysis, it highlights the significance of immobilization techniques, playing a central role in ensuring stability and the ability to reuse catalysts. The practical applications of heterogeneous algal catalysts in converting biomass and breaking down contaminants, supported by real-life case studies, emphasize their effectiveness. In sustainable chemistry, algal polysaccharides emerge as compelling catalysts, offering a unique intersection of eco-friendliness, structural diversity, and versatile catalytic properties. Tackling challenges such as dealing with complex structural variations, ensuring the stability of the catalyst, and addressing economic considerations calls for out-of-the-box and inventive solutions. Embracing the circular economy mindset not only assures sustainable catalyst design but also promotes efficient recycling practices. The use of algal carbohydrates in catalysis stands out as a source of optimism, paving the way for a future where chemistry aligns seamlessly with nature, guiding us toward a sustainable, eco-friendly, and thriving tomorrow. This review encapsulates-structural insights, catalytic applications, challenges, and future perspectives-invoking a call for collective commitment to catalyze a sustainable scientific revolution.
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Affiliation(s)
- Sudarshan Sahu
- Department of Biotechnology Engineering, University Institute of Engineering & Technology, Panjab University, Chandigarh, India
| | - Shalini Sharma
- Department of Biotechnology Engineering, University Institute of Engineering & Technology, Panjab University, Chandigarh, India
| | - Anupreet Kaur
- Department of Biotechnology Engineering, University Institute of Engineering & Technology, Panjab University, Chandigarh, India
| | - Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Madhu Khatri
- Department of Biotechnology Engineering, University Institute of Engineering & Technology, Panjab University, Chandigarh, India
| | - Shailendra Kumar Arya
- Department of Biotechnology Engineering, University Institute of Engineering & Technology, Panjab University, Chandigarh, India.
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Xu R, Liu Z, Wang X, Zhou Y, Zhang B. Xylan clustering on the pollen surface is required for exine patterning. PLANT PHYSIOLOGY 2023; 194:153-167. [PMID: 37801619 DOI: 10.1093/plphys/kiad529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/07/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
Xylan is a crosslinking polymer that plays an important role in the assembly of heterogeneous cell wall structures in plants. The pollen wall, a specialized cell wall matrix, exhibits diverse sculpted patterns that serve to protect male gametophytes and facilitate pollination during plant reproduction. However, whether xylan is precisely anchored into clusters and its influence on pollen wall patterning remain unclear. Here, we report xylan clustering on the mature pollen surface in different plant species that is indispensable for the formation of sculpted exine patterns in dicot and monocot plants. Chemical composition analyses revealed that xylan is generally present at low abundance in the mature pollen of flowering plants and shows plentiful variations in terms of substitutions and modifications. Consistent with the expression profiles of their encoding genes, genetic characterization revealed IRREGULAR XYLEM10-LIKE (IRX10L) and its homologous proteins in the GT47 family of glycosyltransferases as key players in the formation of these xylan micro-/nano-compartments on the pollen surface in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). A deficiency in xylan biosynthesis abolished exine patterning on pollen and compromised male fertility. Therefore, our study outlines a mechanism of exine patterning and provides a tool for manipulating male fertility in crop breeding.
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Affiliation(s)
- Rui Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuolin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Domozych DS, LoRicco JG. The extracellular matrix of green algae. PLANT PHYSIOLOGY 2023; 194:15-32. [PMID: 37399237 PMCID: PMC10762512 DOI: 10.1093/plphys/kiad384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
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Affiliation(s)
- David S Domozych
- Department of Biology, Skidmore College, Saratoga Springs, NY 12866, USA
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7
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Rapin MN, Murray L, Sadler IH, Bothwell JH, Fry SC. Same but different - pseudo-pectin in the charophytic alga Chlorokybus atmophyticus. PHYSIOLOGIA PLANTARUM 2023; 175:e14079. [PMID: 38148229 PMCID: PMC10953000 DOI: 10.1111/ppl.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 12/28/2023]
Abstract
All land-plant cell walls possess hemicelluloses, cellulose and anionic pectin. The walls of their cousins, the charophytic algae, exhibit some similarities to land plants' but also major differences. Charophyte 'pectins' are extractable by conventional land-plant methods, although they differ significantly in composition. Here, we explore 'pectins' of an early-diverging charophyte, Chlorokybus atmophyticus, characterising the anionic polysaccharides that may be comparable to 'pectins' in other streptophytes. Chlorokybus 'pectin' was anionic and upon acid hydrolysis gave GlcA, GalA and sulphate, plus neutral sugars (Ara≈Glc>Gal>Xyl); Rha was undetectable. Most Gal was the l-enantiomer. A relatively acid-resistant disaccharide was characterised as β-d-GlcA-(1→4)-l-Gal. Two Chlorokybus 'pectin' fractions, separable by anion-exchange chromatography, had similar sugar compositions but different sulphate-ester contents. No sugars were released from Chlorokybus 'pectin' by several endo-hydrolases [(1,5)-α-l-arabinanase, (1,4)-β-d-galactanase, (1,4)-β-d-xylanase, endo-polygalacturonase] and exo-hydrolases [α- and β-d-galactosidases, α-(1,6)-d-xylosidase]. 'Driselase', which hydrolyses most land-plant cell wall polysaccharides to mono- and disaccharides, released no sugars except traces of starch-derived Glc. Thus, the Ara, Gal, Xyl and GalA of Chlorokybus 'pectin' were not non-reducing termini with configurations familiar from land-plant polysaccharides (α-l-Araf, α- and β-d-Galp, α- and β-d-Xylp and α-d-GalpA), nor mid-chain residues of α-(1→5)-l-arabinan, β-(1→4)-d-galactan, β-(1→4)-d-xylan or α-(1→4)-d-galacturonan. In conclusion, Chlorokybus possesses anionic 'pectic' polysaccharides, possibly fulfilling pectic roles but differing fundamentally from land-plant pectin. Thus, the evolution of land-plant pectin since the last common ancestor of Chlorokybus and land plants is a long and meandering path involving loss of sulphate, most l-Gal and most d-GlcA; re-configuration of Ara, Xyl and GalA; and gain of Rha.
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Affiliation(s)
- Marie N. Rapin
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's BuildingsEdinburghUK
| | - Lorna Murray
- EastChem School of Chemistry, The University of EdinburghEdinburghUK
| | - Ian H. Sadler
- EastChem School of Chemistry, The University of EdinburghEdinburghUK
| | | | - Stephen C. Fry
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's BuildingsEdinburghUK
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8
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Dutschei T, Beidler I, Bartosik D, Seeßelberg JM, Teune M, Bäumgen M, Ferreira SQ, Heldmann J, Nagel F, Krull J, Berndt L, Methling K, Hein M, Becher D, Langer P, Delcea M, Lalk M, Lammers M, Höhne M, Hehemann JH, Schweder T, Bornscheuer UT. Marine Bacteroidetes enzymatically digest xylans from terrestrial plants. Environ Microbiol 2023; 25:1713-1727. [PMID: 37121608 DOI: 10.1111/1462-2920.16390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Irena Beidler
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Julia-Maria Seeßelberg
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michelle Teune
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Soraia Querido Ferreira
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Julia Heldmann
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Felix Nagel
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Martin Hein
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Peter Langer
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Matthias Höhne
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
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9
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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10
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Curry TM, Peña MJ, Urbanowicz BR. An update on xylan structure, biosynthesis, and potential commercial applications. Cell Surf 2023; 9:100101. [PMID: 36748082 PMCID: PMC9898438 DOI: 10.1016/j.tcsw.2023.100101] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 01/30/2023] Open
Abstract
•Xylan is an abundant carbohydrate component of plant cell walls that is vital for proper cell wall structure and vascular tissue development.•Xylan structure is known to vary between different tissues and species.•The role of xylan in the plant cell wall is to interact with cellulose, lignin, and hemicelluloses.•Xylan synthesis is directed by several types of Golgi-localized enzymes.•Xylan is being explored as an eco-friendly resource for diverse commercial applications.
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Key Words
- AGX, arabinoglucuronoxylan
- Araf, L-α-arabinofuranose, TBL, Trichome Birefringence Like
- GAX, glucuronoarabinoxylan
- GX, glucuronoxylan
- GXMT/GXM, glucuronoxylan methyltransferase
- GlcpA, glucuronic acid
- Glycosyltransferase
- Hemicellulose
- IRX10, Irregular Xylem 10
- IRX14, Irregular Xylem 14
- IRX9, Irregular Xylem 9
- MeGlcpA, 4-O-methylglucuronic acid
- NMR, Nuclear magnetic resonance
- Plant cell wall
- UDP-sugar, uridine diphosphate-linked sugar
- XOATs, xylan O-acetyltransferases
- XSC, xylan synthase complex
- Xylan
- Xylan biosynthesis
- glucuronoarabinoxylan (GAX)
- glucuronoxylan (GX)
- or arabinoglucuronoxylan (AGX)
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Affiliation(s)
- Thomas M. Curry
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA,Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Maria J. Peña
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA,Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Breeanna R. Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA,Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA,Corresponding author at: Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
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11
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The In Silico Characterization of Monocotyledonous α-l-Arabinofuranosidases on the Example of Maize. Life (Basel) 2023; 13:life13020266. [PMID: 36836625 PMCID: PMC9964162 DOI: 10.3390/life13020266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/26/2022] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
Plant α-l-arabinofuranosidases remove terminal arabinose from arabinose-containing substrates such as plant cell wall polysaccharides, including arabinoxylans, arabinogalactans, and arabinans. In plants, de-arabinosylation of cell wall polysaccharides accompanies different physiological processes such as fruit ripening and elongation growth. In this report, we address the diversity of plant α-l-arabinofuranosidases of the glycoside hydrolase (GH) family 51 through their phylogenetic analysis as well as their structural features. The CBM4-like domain at N-terminus was found to exist only in GH51 family proteins and was detected in almost 90% of plant sequences. This domain is similar to bacterial CBM4, but due to substitutions of key amino acid residues, it does not appear to be able to bind carbohydrates. Despite isoenzymes of GH51 being abundant, in particular in cereals, almost half of the GH51 proteins in Poales have a mutation of the acid/base residue in the catalytic site, making them potentially inactive. Open-source data on the transcription and translation of GH51 isoforms in maize were analyzed to discuss possible functions of individual isoenzymes. The results of homology modeling and molecular docking showed that the substrate binding site can accurately accommodate terminal arabinofuranose and that arabinoxylan is a more favorable ligand for all maize GH51 enzymes than arabinan.
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Anders N, Wilson LFL, Sorieul M, Nikolovski N, Dupree P. β-1,4-Xylan backbone synthesis in higher plants: How complex can it be? FRONTIERS IN PLANT SCIENCE 2023; 13:1076298. [PMID: 36714768 PMCID: PMC9874913 DOI: 10.3389/fpls.2022.1076298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Xylan is a hemicellulose present in the cell walls of all land plants. Glycosyltransferases of the GT43 (IRX9/IRX9L and IRX14/IRX14L) and GT47 (IRX10/IRX10L) families are involved in the biosynthesis of its β-1,4-linked xylose backbone, which can be further modified by acetylation and sugar side chains. However, it remains unclear how the different enzymes work together to synthesize the xylan backbone. A xylan synthesis complex (XSC) has been described in the monocots wheat and asparagus, and co-expression of asparagus AoIRX9, AoIRX10 and AoIRX14A is required to form a catalytically active complex for secondary cell wall xylan biosynthesis. Here, we argue that an equivalent XSC exists for the synthesis of the primary cell wall of the eudicot Arabidopsis thaliana, consisting of IRX9L, IRX10L and IRX14. This would suggest the existence of distinct XSCs for primary and secondary cell wall xylan synthesis, reminiscent of the distinct cellulose synthesis complexes (CSCs) of the primary and secondary cell wall. In contrast to the CSC, in which each CESA protein has catalytic activity, the XSC seems to contain proteins with non-catalytic function with each component bearing potentially unique but crucial roles. Moreover, the core XSC formed by a combination of IRX9/IRX9L, IRX10/IRX10L and IRX14/IRX14L might not be stable in its composition during transit from the endoplasmic reticulum to the Golgi apparatus. Instead, potential dynamic changes of the XSC might be a means of regulating xylan biosynthesis to facilitate coordinated deposition of tailored polysaccharides in the plant cell wall.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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14
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Ye ZH, Zhong R. Outstanding questions on xylan biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111476. [PMID: 36174800 DOI: 10.1016/j.plantsci.2022.111476] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/25/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Xylan is the second most abundant polysaccharide in plant biomass. It is a crucial component of cell wall structure as well as a significant factor contributing to biomass recalcitrance. Xylan consists of a linear chain of β-1,4-linked xylosyl residues that are often substituted with glycosyl side chains, such as glucuronosyl/methylglucuronosyl and arabinofuranosyl residues, and acetylated at O-2 and/or O-3. Xylan from gymnosperms and dicots contains a unique reducing end tetrasaccharide sequence that is not detected in xylan from grasses, bryophytes and seedless vascular plants. Grass xylan is heavily decorated at O-3 with arabinofuranosyl residues that are frequently esterified with hydroxycinnamates. Genetic and biochemical studies have uncovered a number of genes involved in xylan backbone elongation and acetylation, xylan glycosyl substitutions and their modifications, and the synthesis of the unique xylan reducing end tetrasaccharide sequence, but some outstanding issues on the biosynthesis of xylan still remain unanswered. Here, we provide a brief overview of xylan structure and focus on discussion of the current understanding and open questions on xylan biosynthesis. Further elucidation of the biochemical mechanisms underlying xylan biosynthesis will not only shed new insights into cell wall biology but also provide molecular tools for genetic modification of biomass composition tailored for diverse end uses.
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Affiliation(s)
- Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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15
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Domozych DS, Bagdan K. The cell biology of charophytes: Exploring the past and models for the future. PLANT PHYSIOLOGY 2022; 190:1588-1608. [PMID: 35993883 PMCID: PMC9614468 DOI: 10.1093/plphys/kiac390] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Charophytes (Streptophyta) represent a diverse assemblage of extant green algae that are the sister lineage to land plants. About 500-600+ million years ago, a charophyte progenitor successfully colonized land and subsequently gave rise to land plants. Charophytes have diverse but relatively simple body plans that make them highly attractive organisms for many areas of biological research. At the cellular level, many charophytes have been used for deciphering cytoskeletal networks and their dynamics, membrane trafficking, extracellular matrix secretion, and cell division mechanisms. Some charophytes live in challenging habitats and have become excellent models for elucidating the cellular and molecular effects of various abiotic stressors on plant cells. Recent sequencing of several charophyte genomes has also opened doors for the dissection of biosynthetic and signaling pathways. While we are only in an infancy stage of elucidating the cell biology of charophytes, the future application of novel analytical methodologies in charophyte studies that include a broader survey of inclusive taxa will enhance our understanding of plant evolution and cell dynamics.
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Affiliation(s)
| | - Kaylee Bagdan
- Department of Biology, Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866, USA
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16
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Zhong R, Phillips DR, Ye ZH. Independent recruitment of glycosyltransferase family 61 members for xylan substitutions in conifers. PLANTA 2022; 256:70. [PMID: 36068444 DOI: 10.1007/s00425-022-03989-x] [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: 07/13/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Several pine members of the gymnosperm-specific GT61 clades were demonstrated to be arabinosyltransferases and xylosyltransferases catalyzing the transfer of 2-O-Araf, 3-O-Araf and 2-O-Xyl side chains onto xylooligomer acceptors, indicating their possible involvement in Araf and Xyl substitutions of xylan in pine. Xylan in conifer wood is substituted at O-2 with methylglucuronic acid (MeGlcA) as well as at O-3 with arabinofuranose (Araf), which differs from xylan in dicot wood that is typically decorated with MeGlcA but not Araf. Currently, glycosyltransferases responsible for conifer xylan arabinosylation have not been identified. Here, we investigated the roles of pine glycosyltransferase family 61 (GT61) members in xylan substitutions. Biochemical characterization of four pine wood-associated GT61 members showed that they exhibited three distinct glycosyltransferase activities involved in xylan substitutions. Two of them catalyzed the addition of 2-O-α-Araf or 3-O-α-Araf side chains onto xylooligomer acceptors and thus were named Pinus taeda xylan 2-O-arabinosyltransferase 1 (PtX2AT1) and 3-O-arabinosyltransferase 1 (PtX3AT1), respectively. Two other pine GT61 members were found to be xylan 2-O-xylosyltransferases (PtXYXTs) adding 2-O-β-Xyl side chains onto xylooligomer acceptors. Furthermore, sequential reactions with PtX3AT1 and the PtGUX1 xylan glucuronyltransferase demonstrated that PtX3AT1 could efficiently arabinosylate glucuronic acid (GlcA)-substituted xylooligomers and likewise, PtGUX1 was able to add GlcA side chains onto 3-O-Araf-substituted xylooligomers. Phylogenetic analysis revealed that PtX2AT1, PtX3AT1 and PtXYXTs resided in three gymnosperm-specific GT61 clades that are separated from the grass-expanded GT61 clade harboring xylan 3-O-arabinosyltransferases and 2-O-xylosyltransferases, suggesting that they might have been recruited independently for xylan substitutions in gymnosperms. Together, our findings have established several pine GT61 members as xylan 2-O- and 3-O-arabinosyltransferases and 2-O-xylosyltransferases and they indicate that pine xylan might also be substituted with 2-O-Araf and 2-O-Xyl side chains.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Dennis R Phillips
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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17
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Sørensen M, Andersen-Ranberg J, Hankamer B, Møller BL. Circular biomanufacturing through harvesting solar energy and CO 2. TRENDS IN PLANT SCIENCE 2022; 27:655-673. [PMID: 35396170 DOI: 10.1016/j.tplants.2022.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Using synthetic biology, it is now time to expand the biosynthetic repertoire of plants and microalgae by utilizing the chloroplast to augment the production of desired high-value compounds and of oil-, carbohydrate-, or protein-enriched biomass based on direct harvesting of solar energy and the consumption of CO2. Multistream product lines based on separate commercialization of the isolated high-value compounds and of the improved bulk products increase the economic potential of the light-driven production system and accelerate commercial scale up. Here we outline the scientific basis for the establishment of such green circular biomanufacturing systems and highlight recent results that make this a realistic option based on cross-disciplinary basic and applied research to advance long-term solutions.
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Affiliation(s)
- Mette Sørensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johan Andersen-Ranberg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ben Hankamer
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
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18
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Zhu CQ, Wei Q, Hu WJ, Kong YL, Xiang XJ, Zhang H, Cao XC, Zhu LF, Liu J, Tian WH, Jin QY, Zhang JH. Unearthing the alleviatory mechanisms of hydrogen sulfide in aluminum toxicity in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 182:133-144. [PMID: 35490639 DOI: 10.1016/j.plaphy.2022.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Hydrogen sulfide (H2S) improves aluminum (Al) resistance in rice, however, the underlying mechanism remains unclear. In the present study, treatment with 30-μM Al significantly inhibited rice root growth and increased the total Al content, apoplastic and cytoplasm Al concentration in the rice roots. However, pretreatment with NaHS (H2S donor) reversed these negative effects. Pretreatment with NaHS significantly increased energy production under Al toxicity conditions, such as by increasing the content of ATP and nonstructural carbohydrates. In addition, NaHS stimulated the AsA-GSH cycle to decrease the peroxidation damage induced by Al toxicity. Pretreatment with NaHS significantly inhibited ethylene emissions in the rice and then inhibited pectin synthesis and increased the pectin methylation degree to reduce cell wall Al deposition. The phytohormones indole-3-acetic and brassinolide were also involved in the alleviation of Al toxicity by H2S. The transcriptome results further confirmed that H2S alleviates Al toxicity by increasing the pathways relating to material and energy metabolism, redox reactions, cell wall components, and signal transduction. These findings improve our understanding of how H2S affects rice responses to Al toxicity, which will facilitate further studies on crop safety.
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Affiliation(s)
- Chun Quan Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - QianQian Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China; Anhui University, Hefei, Anhui Province, China
| | - Wen Jun Hu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, 310021, China
| | - Ya Li Kong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | | | - Hui Zhang
- Agricultural Resources and Environment Institute, Jiangsu Academy of Agricultural Sciences, 210014, Jiangsu, PR China
| | - Xiao Chuang Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lian Feng Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jia Liu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi Province, China
| | - Wen Hao Tian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Yu Jin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jun Hua Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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19
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Qu L, Cai R, Hu Z, Wang H. Metagenomic assemblage genomes analyses reveal the polysaccharides hydrolyzing potential of marine group II euryarchaea. ENVIRONMENTAL RESEARCH 2022; 209:112865. [PMID: 35120891 DOI: 10.1016/j.envres.2022.112865] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/02/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Marine group II euryarchaea (MGII) dominates the planktonic archaeal community in global surface seawater and is associated to particulate organic matters mainly composed of polysaccharides. However, the polysaccharides metabolism of MGII euryarchaea is unclear. In this study, the distribution and polysaccharides metabolism potential of MGII euryarchaea in the estuary were investigated. High-throughput sequencing of 16S rRNA genes showed that MGII euryarchaea was the predominant archaeal group in the Pearl River Estuary (PRE), and the relative abundance of MGII euryarchaea in particle-attached fraction was higher than that in free-living fractions. A total of 19 metagenome-assembled genomes (MAGs) were successfully reconstructed from metagenomic data, of which 10 MAGs were grouped as MGII euryarchaea according to phylogenomic analysis. Genes encoding a variety of carbohydrate-active enzymes (CAZymes) were found in MAGs/genomes of MGII euryarchaea. These CAZymes annotated in MAGs were capable of hydrolyzing many polysaccharides, including α-glucans, β-glucans, xylans, nitrogen-containing polysaccharides, and some insoluble galactans. The results also indicated that MGII euryarchaea has some unique enzymes that can hydrolyze starch, β-1,3-glucans, complex xylans, carrageenan, and agarose. Collectively, our results demonstrated that MGII euryarchaea has great polysaccharides hydrolysis potential and could play an important role in the carbon cycle of marine ecosystem.
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Affiliation(s)
- Liping Qu
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Runlin Cai
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Zhong Hu
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China
| | - Hui Wang
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China.
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20
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Sushytskyi L, Synytsya A, Mirzayeva T, Kalouskova T, Bleha R, Čopíková J, Kubač D, Grivalský T, Ulbrich P, Kaštánek P. Fractionation of the water insoluble part of the heterotrophic mutant green microalga Parachlorella kessleri HY1 (Chlorellaceae) biomass: Identification and structure of polysaccharides. Int J Biol Macromol 2022; 213:27-42. [PMID: 35623455 DOI: 10.1016/j.ijbiomac.2022.05.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 11/17/2022]
Abstract
The water-insoluble part of Parachlorella kessleri HY1 biomass was subjected to the extraction of cell-wall polysaccharides using polar aprotic solvents (DMSO, LiCl/DMSO) and aqueous alkaline solutions (0.1, 1 and 4 mol·l-1 of NaOH). Proteins predominated in all the crude extracts and in the insoluble residues were partially removed by treatment with proteolytic enzymes (pepsin and pronase), and in some cases with the HCl/H2O2 reagent, yielding purified polysaccharide-enriched fractions. These treatments led to the solubilisation of some products in water. The composition and structure of isolated polysaccharides were characterised based on monosaccharide composition, glycosidic linkage and spectroscopic analyses. The DMSO extract contained mainly proteins, and polysaccharides were not detected. The water-soluble parts isolated from the LiCl/DMSO extract contained α-l-rhamnan, α-d-glucan and β-d-glucogalactan; the water-insoluble part contained (1 → 4)-β-d-xylan, first isolated from the biomass of green microalgae. The alkali extracts contained polysaccharides of similar structure, and also water-insoluble (1 → 4)-β-d-mannan. The insoluble part after all extractions contained α-chitin as the main polysaccharide, which was confirmed by spectroscopic methods. All these polysaccharides can play a certain role in the cell wall structure of this microalga.
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Affiliation(s)
- Leonid Sushytskyi
- Department of Carbohydrates and Cereals, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Czech Republic.
| | - Andriy Synytsya
- Department of Carbohydrates and Cereals, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Czech Republic
| | - Tamilla Mirzayeva
- Department of Carbohydrates and Cereals, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Czech Republic
| | - Tereza Kalouskova
- Department of Carbohydrates and Cereals, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Czech Republic
| | - Roman Bleha
- Department of Carbohydrates and Cereals, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Czech Republic
| | - Jana Čopíková
- Department of Carbohydrates and Cereals, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Czech Republic
| | - David Kubač
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 81 Třebon, Czech Republic
| | - Tomáš Grivalský
- Institute of Microbiology, Czech Academy of Sciences, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 81 Třebon, Czech Republic
| | - Pavel Ulbrich
- Department of Biotechnology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Technická 5, 166 28 Prague 6 Dejvice, Czech Republic
| | - Petr Kaštánek
- Department of Biotechnology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Technická 5, 166 28 Prague 6 Dejvice, Czech Republic; EcoFuel Laboratories s.r.o, Ocelářská 9, Prague 9 Libeň 190 00, Czech Republic
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21
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Bachy C, Wittmers F, Muschiol J, Hamilton M, Henrissat B, Worden AZ. The Land-Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:585-616. [PMID: 35259927 DOI: 10.1146/annurev-arplant-071921-100530] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems-the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages.
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Affiliation(s)
- Charles Bachy
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jan Muschiol
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Maria Hamilton
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille Université (AMU), Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Marine Biological Laboratories, Woods Hole, Massachusetts, USA
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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22
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Raghav D, Jyoti A, Siddiqui AJ, Saxena J. Plant associated endophytic fungi as potential bio-factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches. J Appl Microbiol 2022; 133:287-310. [PMID: 35396804 DOI: 10.1111/jam.15574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/04/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022]
Abstract
There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant-associated endophytic contain industrially important enzymes and have the potential to fulfill their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation, and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state-of-the-art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants-derived endophytic fungal enzymes and their applications in various sectors. Further, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.
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Affiliation(s)
- Divyangi Raghav
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Anupam Jyoti
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha'il, Ha'il, P O Box, Saudi Arabia
| | - Juhi Saxena
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.,Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, SAS, Nagar, Punjab
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23
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Smith P, Curry TM, Yang JY, Barnes WJ, Ziegler SJ, Mittal A, Moremen KW, York WS, Bomble YJ, Peña MJ, Urbanowicz BR. Enzymatic Synthesis of Xylan Microparticles with Tunable Morphologies. ACS MATERIALS AU 2022; 2:440-452. [PMID: 35856073 PMCID: PMC9284610 DOI: 10.1021/acsmaterialsau.2c00006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xylans are a diverse family of hemicellulosic polysaccharides found in abundance within the cell walls of nearly all flowering plants. Unfortunately, naturally occurring xylans are highly heterogeneous, limiting studies of their synthesis and structure-function relationships. Here, we demonstrate that xylan synthase 1 from the charophyte alga Klebsormidium flaccidum is a powerful biocatalytic tool for the bottom-up synthesis of pure β-1,4 xylan polymers that self-assemble into microparticles in vitro. Using uridine diphosphate-xylose (UDP-xylose) and defined saccharide primers as substrates, we demonstrate that the shape, composition, and properties of the self-assembling xylan microparticles could be readily controlled via the fine structure of the xylan oligosaccharide primer used to initiate polymer elongation. Furthermore, we highlight two approaches for bottom-up and surface functionalization of xylan microparticles with chemical probes and explore the susceptibility of xylan microparticles to enzymatic hydrolysis. Together, these results provide a useful platform for structural and functional studies of xylans to investigate cell wall biosynthesis and polymer-polymer interactions and suggest possible routes to new biobased materials with favorable properties for biomedical and renewable applications.
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Affiliation(s)
- Peter
J. Smith
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States,Bioscience
Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, Colorado 80401, United States
| | - Thomas M. Curry
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States,Department
of Biochemistry and Molecular Biology, University
of Georgia, 315 Riverbend
Road, Athens, Georgia 30602, United States
| | - Jeong-Yeh Yang
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States,Department
of Biochemistry and Molecular Biology, University
of Georgia, 315 Riverbend
Road, Athens, Georgia 30602, United States
| | - William J. Barnes
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States
| | - Samantha J. Ziegler
- Bioscience
Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, Colorado 80401, United States
| | - Ashutosh Mittal
- Bioscience
Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, Colorado 80401, United States
| | - Kelley W. Moremen
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States,Department
of Biochemistry and Molecular Biology, University
of Georgia, 315 Riverbend
Road, Athens, Georgia 30602, United States
| | - William S. York
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States
| | - Yannick J. Bomble
- Bioscience
Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, Colorado 80401, United States
| | - Maria J. Peña
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States
| | - Breeanna R. Urbanowicz
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United
States,Department
of Biochemistry and Molecular Biology, University
of Georgia, 315 Riverbend
Road, Athens, Georgia 30602, United States,. Tel: +1 706-542-4419. Fax: +1 706-542-4412
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24
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Wang H, Yang H, Wen Z, Gao C, Gao Y, Tian Y, Xu Z, Liu X, Persson S, Zhang B, Zhou Y. Xylan-based nanocompartments orchestrate plant vessel wall patterning. NATURE PLANTS 2022; 8:295-306. [PMID: 35318447 DOI: 10.1038/s41477-022-01113-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Nanoclustering of biomacromolecules allows cells to efficiently orchestrate biological processes. The plant cell wall is a highly organized polysaccharide network but is heterogeneous in chemistry and structure. However, polysaccharide-based nanocompartments remain ill-defined. Here, we identify a xylan-rich nanodomain at pit borders of xylem vessels. We show that these nanocompartments maintain distinct wall patterns by anchoring cellulosic nanofibrils at the pit borders, critically supporting vessel robustness, water transport and leaf transpiration. The nanocompartments are produced by the activity of IRREGULAR XYLEM (IRX)10 and its homologues, which we show are de novo xylan synthases. Our study hence outlines a mechanism of how xylans are synthesized, how they assemble into nanocompartments and how the nanocompartments sustain cell wall pit patterning to support efficient water transport throughout the plant body.
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Affiliation(s)
- Hang Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Hanlei Yang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhao Wen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengxu Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yihong Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanbao Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zuopeng Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Xiangling Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Staffan Persson
- Department for Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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25
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Paramjeet S, Manasa P, Korrapati N. Biochemical Characterization of Low Molecular Weight Thermostable Xylanase from Aspergillus fumigatus JCM 10253. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821100094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Wang HT, Bharadwaj VS, Yang JY, Curry TM, Moremen KW, Bomble YJ, Urbanowicz BR. Rational enzyme design for controlled functionalization of acetylated xylan for cell-free polymer biosynthesis. Carbohydr Polym 2021; 273:118564. [PMID: 34560975 DOI: 10.1016/j.carbpol.2021.118564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/13/2021] [Indexed: 11/18/2022]
Abstract
Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.
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Affiliation(s)
- Hsin-Tzu Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, CO 80401, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Thomas M Curry
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Yannick J Bomble
- Bioscience Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, CO 80401, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
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27
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Franková L, Fry SC. Hemicellulose-remodelling transglycanase activities from charophytes: towards the evolution of the land-plant cell wall. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:7-28. [PMID: 34547150 DOI: 10.1111/tpj.15500] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Transglycanases remodel cell-wall polymers, having a critical impact on many physiological processes. Unlike xyloglucan endotransglucosylase (XET) activity, widely studied in land plants, very little is known about charophyte wall-modifying enzymes - information that would promote our understanding of the 'primordial' wall, revealing how the wall matrix is remodelled in the closest living algal relatives of land plants, and what changed during terrestrialisation. We conducted various in-vitro assays for wall-remodelling transglycosylases, monitoring either (a) polysaccharide-to-[3 H]oligosaccharide transglycosylation or (b) non-radioactive oligosaccharide-to-oligosaccharide transglycosylation. We screened a wide collection of enzyme extracts from charophytes (and early-diverging land plants for comparison) and discovered several homo- and hetero-transglycanase activities. In contrast to most land plants, charophytes possess high trans-β-1,4-mannanase activity, suggesting that land plants' algal ancestors prioritised mannan remodelling. Trans-β-1,4-xylanase activity was also found, most abundantly in Chara, Nitella and Klebsormidium. Exo-acting transglycosidase activities (trans-β-1,4-xylosidase and trans-β-1,4-mannosidase) were also detected. In addition, charophytes exhibited homo- and hetero-trans-β-glucanase activities (XET, mixed-linkage glucan [MLG]:xyloglucan endotransglucosylase and cellulose:xyloglucan endotransglucosylase) despite the paucity or lack of land-plant-like xyloglucan and MLG as potential donor substrates in their cell walls. However, trans-α-xylosidase activity (which remodels xyloglucan in angiosperms) was absent in charophytes and early-diverging land plants. Transglycanase action was also found in situ, acting on endogenous algal polysaccharides as donor substrates and fluorescent xyloglucan oligosaccharides as acceptor substrates. We conclude that trans-β-mannanase and trans-β-xylanase activities are present and thus may play key roles in charophyte walls (most of which possess little or no xyloglucan and MLG, but often contain abundant β-mannans and β-xylans), comparable to the roles of XET in xyloglucan-rich land plants.
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Affiliation(s)
- Lenka Franková
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Stephen C Fry
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
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28
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Sørensen M, Møller BL. Metabolic Engineering of Photosynthetic Cells – in Collaboration with Nature. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Ancient origin of fucosylated xyloglucan in charophycean green algae. Commun Biol 2021; 4:754. [PMID: 34140625 PMCID: PMC8211770 DOI: 10.1038/s42003-021-02277-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023] Open
Abstract
The charophycean green algae (CGA or basal streptophytes) are of particular evolutionary significance because their ancestors gave rise to land plants. One outstanding feature of these algae is that their cell walls exhibit remarkable similarities to those of land plants. Xyloglucan (XyG) is a major structural component of the cell walls of most land plants and was originally thought to be absent in CGA. This study presents evidence that XyG evolved in the CGA. This is based on a) the identification of orthologs of the genetic machinery to produce XyG, b) the identification of XyG in a range of CGA and, c) the structural elucidation of XyG, including uronic acid-containing XyG, in selected CGA. Most notably, XyG fucosylation, a feature considered as a late evolutionary elaboration of the basic XyG structure and orthologs to the corresponding biosynthetic enzymes are shown to be present in Mesotaenium caldariorum.
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30
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A Pipeline towards the Biochemical Characterization of the Arabidopsis GT14 Family. Int J Mol Sci 2021; 22:ijms22031360. [PMID: 33572987 PMCID: PMC7866395 DOI: 10.3390/ijms22031360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
Glycosyltransferases (GTs) catalyze the synthesis of glycosidic linkages and are essential in the biosynthesis of glycans, glycoconjugates (glycolipids and glycoproteins), and glycosides. Plant genomes generally encode many more GTs than animal genomes due to the synthesis of a cell wall and a wide variety of glycosylated secondary metabolites. The Arabidopsis thaliana genome is predicted to encode over 573 GTs that are currently classified into 42 diverse families. The biochemical functions of most of these GTs are still unknown. In this study, we updated the JBEI Arabidopsis GT clone collection by cloning an additional 105 GT cDNAs, 508 in total (89%), into Gateway-compatible vectors for downstream characterization. We further established a functional analysis pipeline using transient expression in tobacco (Nicotiana benthamiana) followed by enzymatic assays, fractionation of enzymatic products by reversed-phase HPLC (RP-HPLC) and characterization by mass spectrometry (MS). Using the GT14 family as an exemplar, we outline a strategy for identifying effective substrates of GT enzymes. By addition of UDP-GlcA as donor and the synthetic acceptors galactose-nitrobenzodiazole (Gal-NBD), β-1,6-galactotetraose (β-1,6-Gal4) and β-1,3-galactopentose (β-1,3-Gal5) to microsomes expressing individual GT14 enzymes, we verified the β-glucuronosyltransferase (GlcAT) activity of three members of this family (AtGlcAT14A, B, and E). In addition, a new family member (AT4G27480, 248) was shown to possess significantly higher activity than other GT14 enzymes. Our data indicate a likely role in arabinogalactan-protein (AGP) biosynthesis for these GT14 members. Together, the updated Arabidopsis GT clone collection and the biochemical analysis pipeline present an efficient means to identify and characterize novel GT catalytic activities.
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31
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Tingley JP, Low KE, Xing X, Abbott DW. Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:16. [PMID: 33422151 PMCID: PMC7797155 DOI: 10.1186/s13068-020-01869-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/24/2020] [Indexed: 05/08/2023]
Abstract
The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common "-omics"-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.
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Affiliation(s)
- Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
- Department of Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 6T5, Canada
| | - Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada.
- Department of Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 6T5, Canada.
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32
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Žárský J, Žárský V, Hanáček M, Žárský V. Cryogenian Glacial Habitats as a Plant Terrestrialisation Cradle - The Origin of the Anydrophytes and Zygnematophyceae Split. FRONTIERS IN PLANT SCIENCE 2021; 12:735020. [PMID: 35154170 PMCID: PMC8829067 DOI: 10.3389/fpls.2021.735020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/17/2021] [Indexed: 05/05/2023]
Abstract
For tens of millions of years (Ma), the terrestrial habitats of Snowball Earth during the Cryogenian period (between 720 and 635 Ma before present-Neoproterozoic Era) were possibly dominated by global snow and ice cover up to the equatorial sublimative desert. The most recent time-calibrated phylogenies calibrated not only on plants but on a comprehensive set of eukaryotes indicate that within the Streptophyta, multicellular charophytes (Phragmoplastophyta) evolved in the Mesoproterozoic to the early Neoproterozoic. At the same time, Cryogenian is the time of the likely origin of the common ancestor of Zygnematophyceae and Embryophyta and later, also of the Zygnematophyceae-Embryophyta split. This common ancestor is proposed to be called Anydrophyta; here, we use anydrophytes. Based on the combination of published phylogenomic studies and estimated diversification time comparisons, we deem it highly likely that anydrophytes evolved in response to Cryogenian cooling. Also, later in the Cryogenian, secondary simplification of multicellular anydrophytes and loss of flagella resulted in Zygnematophyceae diversification as an adaptation to the extended cold glacial environment. We propose that the Marinoan geochemically documented expansion of first terrestrial flora has been represented not only by Chlorophyta but also by Streptophyta, including the anydrophytes, and later by Zygnematophyceae, thriving on glacial surfaces until today. It is possible that multicellular early Embryophyta survived in less abundant (possibly relatively warmer) refugia, relying more on mineral substrates, allowing the retention of flagella-based sexuality. The loss of flagella and sexual reproduction by conjugation evolved in Zygnematophyceae and zygomycetous fungi during the Cryogenian in a remarkably convergent way. Thus, we support the concept that the important basal cellular adaptations to terrestrial environments were exapted in streptophyte algae for terrestrialization and propose that this was stimulated by the adaptation to glacial habitats dominating the Cryogenian Snowball Earth. Including the glacial lifestyle when considering the rise of land plants increases the parsimony of connecting different ecological, phylogenetic, and physiological puzzles of the journey from aquatic algae to terrestrial floras.
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Affiliation(s)
- Jakub Žárský
- CryoEco Research Group, Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Jakub Žárský,
| | - Vojtěch Žárský
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Martin Hanáček
- Polar-Geo-Lab, Department of Geography, Faculty of Science, Masaryk University, Brno, Czechia
- Regional Museum in Jeseník, Jeseník, Czechia
| | - Viktor Žárský
- Laboratory of Cell Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
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33
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Crowe JD, Hao P, Pattathil S, Pan H, Ding SY, Hodge DB, Jensen JK. Xylan Is Critical for Proper Bundling and Alignment of Cellulose Microfibrils in Plant Secondary Cell Walls. FRONTIERS IN PLANT SCIENCE 2021; 12:737690. [PMID: 34630488 PMCID: PMC8495263 DOI: 10.3389/fpls.2021.737690] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/24/2021] [Indexed: 05/07/2023]
Abstract
Plant biomass represents an abundant and increasingly important natural resource and it mainly consists of a number of cell types that have undergone extensive secondary cell wall (SCW) formation. These cell types are abundant in the stems of Arabidopsis, a well-studied model system for hardwood, the wood of eudicot plants. The main constituents of hardwood include cellulose, lignin, and xylan, the latter in the form of glucuronoxylan (GX). The binding of GX to cellulose in the eudicot SCW represents one of the best-understood molecular interactions within plant cell walls. The evenly spaced acetylation and 4-O-methyl glucuronic acid (MeGlcA) substitutions of the xylan polymer backbone facilitates binding in a linear two-fold screw conformation to the hydrophilic side of cellulose and signifies a high level of molecular specificity. However, the wider implications of GX-cellulose interactions for cellulose network formation and SCW architecture have remained less explored. In this study, we seek to expand our knowledge on this by characterizing the cellulose microfibril organization in three well-characterized GX mutants. The selected mutants display a range of GX deficiency from mild to severe, with findings indicating even the weakest mutant having significant perturbations of the cellulose network, as visualized by both scanning electron microscopy (SEM) and atomic force microscopy (AFM). We show by image analysis that microfibril width is increased by as much as three times in the severe mutants compared to the wild type and that the degree of directional dispersion of the fibrils is approximately doubled in all the three mutants. Further, we find that these changes correlate with both altered nanomechanical properties of the SCW, as observed by AFM, and with increases in enzymatic hydrolysis. Results from this study indicate the critical role that normal GX composition has on cellulose bundle formation and cellulose organization as a whole within the SCWs.
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Affiliation(s)
- Jacob D. Crowe
- Department of Chemical Engineering & Materials Science, Michigan State University, East Lansing, MI, United States
| | - Pengchao Hao
- Department of Chemistry, Michigan State University, East Lansing, MI, United States
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, United States
| | - Henry Pan
- Department of Chemical Engineering, University of Texas, Austin, TX, United States
| | - Shi-You Ding
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - David B. Hodge
- Department of Chemical & Biological Engineering, Montana State University, Bozeman, MT, United States
| | - Jacob Krüger Jensen
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Jacob Krüger Jensen
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34
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Kasirajan L, Maupin-Furlow JA. Halophilic archaea and their potential to generate renewable fuels and chemicals. Biotechnol Bioeng 2020; 118:1066-1090. [PMID: 33241850 DOI: 10.1002/bit.27639] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.
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Affiliation(s)
- Lakshmi Kasirajan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Coimbatore, India
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Genetics Institute, University of Florida, Gainesville, Florida, USA
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Hassan MM, Yuan G, Chen JG, Tuskan GA, Yang X. Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research. BIODESIGN RESEARCH 2020; 2020:9350905. [PMID: 37849904 PMCID: PMC10530660 DOI: 10.34133/2020/9350905] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 10/19/2023] Open
Abstract
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as "prime editing," has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
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Affiliation(s)
- Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Prabhakar PK, Wang HT, Smith PJ, Yang JY, Barnes WJ, Peña MJ, Moremen KW, Urbanowicz BR. Heterologous expression of plant glycosyltransferases for biochemistry and structural biology. Methods Cell Biol 2020; 160:145-165. [PMID: 32896313 PMCID: PMC7593805 DOI: 10.1016/bs.mcb.2020.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Much of the carbon captured by photosynthesis is converted into the polysaccharides that constitute plant cell walls. These complex macrostructures are composed of cellulose, hemicellulose, and pectins, together with small amounts of structural proteins, minerals, and in many cases lignin. Wall components assemble and interact with one another to produce dynamic structures with many capabilities, including providing mechanical support to plant structures and determining plant cell shape and size. Despite their abundance, major gaps in our knowledge of the synthesis of the building blocks of these polymers remain, largely due to ineffective methods for expression and purification of active synthetic enzymes for in vitro biochemical analyses. The hemicellulosic polysaccharide, xyloglucan, comprises up to 25% of the dry weight of primary cell walls in plants. Most of the knowledge about the glycosyltransferases (GTs) involved in the xyloglucan biosynthetic pathway has been derived from the identification and carbohydrate analysis of knockout mutants, lending little information on how the catalytic biosynthesis of xyloglucan occurs in planta. In this chapter we describe methods for the heterologous expression of plant GTs using the HEK293 expression platform. As a demonstration of the utility of this platform, nine xyloglucan-relevant GTs from three different CAZy families were evaluated, and methods for expression, purification, and construct optimization are described for biochemical and structural characterization.
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Affiliation(s)
- Pradeep K Prabhakar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Hsin-Tzu Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Peter J Smith
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Jeong-Yeh Yang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - William J Barnes
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Maria J Peña
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States.
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Wang S, Li L, Li H, Sahu SK, Wang H, Xu Y, Xian W, Song B, Liang H, Cheng S, Chang Y, Song Y, Çebi Z, Wittek S, Reder T, Peterson M, Yang H, Wang J, Melkonian B, Van de Peer Y, Xu X, Wong GKS, Melkonian M, Liu H, Liu X. Genomes of early-diverging streptophyte algae shed light on plant terrestrialization. NATURE PLANTS 2020; 6:95-106. [PMID: 31844283 PMCID: PMC7027972 DOI: 10.1038/s41477-019-0560-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/28/2019] [Indexed: 05/18/2023]
Abstract
Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.
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Affiliation(s)
- Sibo Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Linzhou Li
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Haoyuan Li
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hongli Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wenfei Xian
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Hongping Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Shifeng Cheng
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yue Song
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Zehra Çebi
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Sebastian Wittek
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Tanja Reder
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Morten Peterson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Barbara Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB/UGent Center for Plant Systems Biology, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Gane Ka-Shu Wong
- BGI-Shenzhen, Shenzhen, China.
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael Melkonian
- Botanical Institute, Cologne Biocenter, University of Cologne, Cologne, Germany.
- University of Duisburg-Essen, Campus Essen, Faculty of Biology, Essen, Germany.
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China.
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Cheng S, Xian W, Fu Y, Marin B, Keller J, Wu T, Sun W, Li X, Xu Y, Zhang Y, Wittek S, Reder T, Günther G, Gontcharov A, Wang S, Li L, Liu X, Wang J, Yang H, Xu X, Delaux PM, Melkonian B, Wong GKS, Melkonian M. Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution. Cell 2019; 179:1057-1067.e14. [DOI: 10.1016/j.cell.2019.10.019] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/27/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023]
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Bhardwaj N, Kumar B, Verma P. A detailed overview of xylanases: an emerging biomolecule for current and future prospective. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0276-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Xylan is the second most abundant naturally occurring renewable polysaccharide available on earth. It is a complex heteropolysaccharide consisting of different monosaccharides such as l-arabinose, d-galactose, d-mannoses and organic acids such as acetic acid, ferulic acid, glucuronic acid interwoven together with help of glycosidic and ester bonds. The breakdown of xylan is restricted due to its heterogeneous nature and it can be overcome by xylanases which are capable of cleaving the heterogeneous β-1,4-glycoside linkage. Xylanases are abundantly present in nature (e.g., molluscs, insects and microorganisms) and several microorganisms such as bacteria, fungi, yeast, and algae are used extensively for its production. Microbial xylanases show varying substrate specificities and biochemical properties which makes it suitable for various applications in industrial and biotechnological sectors. The suitability of xylanases for its application in food and feed, paper and pulp, textile, pharmaceuticals, and lignocellulosic biorefinery has led to an increase in demand of xylanases globally. The present review gives an insight of using microbial xylanases as an “Emerging Green Tool” along with its current status and future prospective.
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Origin, evolution and functional characterization of the land plant glycoside hydrolase subfamily GH5_11. Mol Phylogenet Evol 2019; 138:205-218. [DOI: 10.1016/j.ympev.2019.05.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 01/20/2023]
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Amoozegar MA, Safarpour A, Noghabi KA, Bakhtiary T, Ventosa A. Halophiles and Their Vast Potential in Biofuel Production. Front Microbiol 2019; 10:1895. [PMID: 31507545 PMCID: PMC6714587 DOI: 10.3389/fmicb.2019.01895] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/31/2019] [Indexed: 11/13/2022] Open
Abstract
Global warming and the limitations of using fossil fuels are a main concern of all societies, and thus, the development of alternative fuel sources is crucial to improving the current global energy situation. Biofuels are known as the best alternatives of unrenewable fuels and justify increasing extensive research to develop new and less expensive methods for their production. The most frequent biofuels are bioethanol, biobutanol, biodiesel, and biogas. The production of these biofuels is the result of microbial activity on organic substrates like sugars, starch, oil crops, non-food biomasses, and agricultural and animal wastes. Several industrial production processes are carried out in the presence of high concentrations of NaCl and therefore, researchers have focused on halophiles for biofuel production. In this review, we focus on the role of halophilic microorganisms and their current utilization in the production of all types of biofuels. Also, the outstanding potential of them and their hydrolytic enzymes in the hydrolysis of different kind of biomasses and the production of biofuels are discussed.
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Atefeh Safarpour
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Kambiz Akbari Noghabi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Tala Bakhtiary
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, Seville, Spain
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Yue H, Nie X, Yan Z, Weining S. N6-methyladenosine regulatory machinery in plants: composition, function and evolution. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1194-1208. [PMID: 31070865 PMCID: PMC6576107 DOI: 10.1111/pbi.13149] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 05/04/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation, one of the most pivotal internal modifications of RNA, is a conserved post-transcriptional mechanism to enrich and regulate genetic information in eukaryotes. The scope and function of this modification in plants has been an intense focus of study, especially in model plant systems. The characterization of plant m6A writers, erasers and readers, as well as the elucidation of their functions, is currently one of the most fascinating hotspots in plant biology research. The functional analysis of m6A in plants will be booming in the foreseeable future, which could contribute to crop genetic improvement through epitranscriptome manipulation. In this review, we systematically analysed and summarized recent advances in the understanding of the structure and composition of plant m6A regulatory machinery, and the biological functions of m6A in plant growth, development and stress response. Finally, our analysis showed that the evolutionary relationships between m6A modification components were highly conserved across the plant kingdom.
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Affiliation(s)
- Hong Yue
- College of Life SciencesState Key Laboratory of Crop Stress Biology in Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaojun Nie
- College of Life SciencesState Key Laboratory of Crop Stress Biology in Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhaogui Yan
- College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanHubeiChina
| | - Song Weining
- College of Life SciencesState Key Laboratory of Crop Stress Biology in Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
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Zhong R, Cui D, Ye ZH. Secondary cell wall biosynthesis. THE NEW PHYTOLOGIST 2019; 221:1703-1723. [PMID: 30312479 DOI: 10.1111/nph.15537] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/28/2018] [Indexed: 05/19/2023]
Abstract
Contents Summary 1703 I. Introduction 1703 II. Cellulose biosynthesis 1705 III. Xylan biosynthesis 1709 IV. Glucomannan biosynthesis 1713 V. Lignin biosynthesis 1714 VI. Concluding remarks 1717 Acknowledgements 1717 References 1717 SUMMARY: Secondary walls are synthesized in specialized cells, such as tracheary elements and fibers, and their remarkable strength and rigidity provide strong mechanical support to the cells and the plant body. The main components of secondary walls are cellulose, xylan, glucomannan and lignin. Biochemical, molecular and genetic studies have led to the discovery of most of the genes involved in the biosynthesis of secondary wall components. Cellulose is synthesized by cellulose synthase complexes in the plasma membrane and the recent success of in vitro synthesis of cellulose microfibrils by a single recombinant cellulose synthase isoform reconstituted into proteoliposomes opens new doors to further investigate the structure and functions of cellulose synthase complexes. Most genes involved in the glycosyl backbone synthesis, glycosyl substitutions and acetylation of xylan and glucomannan have been genetically characterized and the biochemical properties of some of their encoded enzymes have been investigated. The genes and their encoded enzymes participating in monolignol biosynthesis and modification have been extensively studied both genetically and biochemically. A full understanding of how secondary wall components are synthesized will ultimately enable us to produce plants with custom-designed secondary wall composition tailored to diverse applications.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Dongtao Cui
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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Hsieh YSY, Harris PJ. Xylans of Red and Green Algae: What Is Known about Their Structures and How They Are Synthesised? Polymers (Basel) 2019; 11:polym11020354. [PMID: 30960338 PMCID: PMC6419167 DOI: 10.3390/polym11020354] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/15/2019] [Accepted: 02/17/2019] [Indexed: 01/14/2023] Open
Abstract
Xylans with a variety of structures have been characterised in green algae, including chlorophytes (Chlorophyta) and charophytes (in the Streptophyta), and red algae (Rhodophyta). Substituted 1,4-β-d-xylans, similar to those in land plants (embryophytes), occur in the cell wall matrix of advanced orders of charophyte green algae. Small proportions of 1,4-β-d-xylans have also been found in the cell walls of some chlorophyte green algae and red algae but have not been well characterised. 1,3-β-d-Xylans occur as triple helices in microfibrils in the cell walls of chlorophyte algae in the order Bryopsidales and of red algae in the order Bangiales. 1,3;1,4-β-d-Xylans occur in the cell wall matrix of red algae in the orders Palmariales and Nemaliales. In the angiosperm Arabidopsis thaliana, the gene IRX10 encodes a xylan 1,4-β-d-xylosyltranferase (xylan synthase), and, when heterologously expressed, this protein catalysed the production of the backbone of 1,4-β-d-xylans. An orthologous gene from the charophyte green alga Klebsormidium flaccidum, when heterologously expressed, produced a similar protein that was also able to catalyse the production of the backbone of 1,4-β-d-xylans. Indeed, it is considered that land plant xylans evolved from xylans in ancestral charophyte green algae. However, nothing is known about the biosynthesis of the different xylans found in chlorophyte green algae and red algae. There is, thus, an urgent need to identify the genes and enzymes involved.
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Affiliation(s)
- Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden.
| | - Philip J Harris
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
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Fitzek E, Orton L, Entwistle S, Grayburn WS, Ausland C, Duvall MR, Yin Y. Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion. FRONTIERS IN PLANT SCIENCE 2019; 10:732. [PMID: 31231410 PMCID: PMC6566377 DOI: 10.3389/fpls.2019.00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/16/2019] [Indexed: 05/20/2023]
Abstract
Previous analysis of charophyte green algal (CGA) genomes and transcriptomes for specific protein families revealed that numerous land plant characteristics had already evolved in CGA. In this study, we have sequenced and assembled the transcriptome of Zygnema circumcarinatum UTEX 1559, and combined its predicted protein sequences with those of 13 additional species [five embryophytes (Emb), eight charophytes (Cha), and two chlorophytes (Chl) as the outgroup] for a comprehensive comparative genomics analysis. In total 25,485 orthologous gene clusters (OGCs, equivalent to protein families) of the 14 species were classified into nine OGC groups. For example, the Cha+Emb group contains 4,174 OGCs found in both Cha and Emb but not Chl species, representing protein families that have evolved in the common ancestor of Cha and Emb. Different OGC groups were subjected to a Gene Ontology (GO) enrichment analysis with the Chl+Cha+Emb group (including 5,031 OGCs found in Chl and Cha and Emb) as the control. Interestingly, nine of the 20 top enriched GO terms in the Cha+Emb group are cell wall-related, such as biological processes involving celluloses, pectins, lignins, and xyloglucans. Furthermore, three glycosyltransferase families (GT2, 8, 43) were selected for in-depth phylogenetic analyses, which confirmed their presence in UTEX 1559. More importantly, of different CGA groups, only Zygnematophyceae has land plant cellulose synthase (CesA) orthologs, while other charophyte CesAs form a CGA-specific CesA-like (Csl) subfamily (likely also carries cellulose synthesis activity). Quantitative real-time-PCR experiments were performed on selected GT family genes in UTEX 1559. After osmotic stress treatment, significantly elevated expression was found for GT2 family genes ZcCesA, ZcCslC and ZcCslA-like (possibly mannan and xyloglucan synthases, respectively), as well as for GT8 family genes (possibly pectin synthases). All these suggest that the UTEX 1559 cell wall polysaccharide synthesis-related genes respond to osmotic stress in a manner that is similar to land plants.
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Affiliation(s)
- Elisabeth Fitzek
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
- Department of Computational Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld, Germany
| | - Lauren Orton
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Sarah Entwistle
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - W. Scott Grayburn
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Catherine Ausland
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Melvin R. Duvall
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Yanbin Yin
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska – Lincoln, Lincoln, NE, United States
- *Correspondence: Yanbin Yin, ;
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Herburger K, Xin A, Holzinger A. Homogalacturonan Accumulation in Cell Walls of the Green Alga Zygnema sp. (Charophyta) Increases Desiccation Resistance. FRONTIERS IN PLANT SCIENCE 2019; 10:540. [PMID: 31105732 PMCID: PMC6494968 DOI: 10.3389/fpls.2019.00540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/09/2019] [Indexed: 05/13/2023]
Abstract
Land plants inherited several traits from their green algal ancestors (Zygnematophyceae), including a polysaccharide-rich cell wall, which is a prerequisite for terrestrial survival. A major component of both land plant and Zygnematophyceaen cell walls is the pectin homogalacturonan (HG), and its high water holding capacity may have helped algae to colonize terrestrial habitats, characterized by water scarcity. To test this, HG was removed from the cell walls of Zygnema filaments by pectate lyase (PL), and their effective quantum yield of photosystem II (YII) as a proxy for photosynthetic performance was measured in response to desiccation stress by pulse amplitude modulation (PAM). Old filaments were found to contain more HG and are more resistant against desiccation stress but relatively lose more desiccation resistance after HG removal than young filaments. After rehydration, the photosynthetic performance recovered less efficiently in filaments with a HG content reduced by PL, independently of filament age. Immunolabeling showed that partial or un-methylesterified HG occurs throughout the longitudinal cell walls of both young and old filaments, while no labeling signal occurred when filaments were treated with PL prior labeling. This confirmed that most HG can be removed from the cell walls by PL. The initial labeling pattern was restored after ~3 days. A different form of methylesterified HG was restricted to cell poles and cross cell walls. In conclusion, it was shown that the accumulation of HG in Zygnema filaments increases their resistance against desiccation stress. This trait might have played an important role during the colonization of land by Zygnematophyceae, which founded the evolution of all land plants.
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Affiliation(s)
- Klaus Herburger
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Functional Plant Biology, Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Anzhou Xin
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Andreas Holzinger
- Functional Plant Biology, Department of Botany, University of Innsbruck, Innsbruck, Austria
- *Correspondence: Andreas Holzinger,
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47
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Amos RA, Mohnen D. Critical Review of Plant Cell Wall Matrix Polysaccharide Glycosyltransferase Activities Verified by Heterologous Protein Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:915. [PMID: 31379900 PMCID: PMC6646851 DOI: 10.3389/fpls.2019.00915] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 05/02/2023]
Abstract
The life cycle and development of plants requires the biosynthesis, deposition, and degradation of cell wall matrix polysaccharides. The structures of the diverse cell wall matrix polysaccharides influence commercially important properties of plant cells, including growth, biomass recalcitrance, organ abscission, and the shelf life of fruits. This review is a comprehensive summary of the matrix polysaccharide glycosyltransferase (GT) activities that have been verified using in vitro assays following heterologous GT protein expression. Plant cell wall (PCW) biosynthetic GTs are primarily integral transmembrane proteins localized to the endoplasmic reticulum and Golgi of the plant secretory system. The low abundance of these enzymes in plant tissues makes them particularly difficult to purify from native plant membranes in quantities sufficient for enzymatic characterization, which is essential to study the functions of the different GTs. Numerous activities in the synthesis of the major cell wall matrix glycans, including pectins, xylans, xyloglucan, mannans, mixed-linkage glucans (MLGs), and arabinogalactan components of AGP proteoglycans have been mapped to specific genes and multi-gene families. Cell wall GTs include those that synthesize the polymer backbones, those that elongate side branches with extended glycosyl chains, and those that add single monosaccharide linkages onto polysaccharide backbones and/or side branches. Three main strategies have been used to identify genes encoding GTs that synthesize cell wall linkages: analysis of membrane fractions enriched for cell wall biosynthetic activities, mutational genetics approaches investigating cell wall compositional phenotypes, and omics-directed identification of putative GTs from sequenced plant genomes. Here we compare the heterologous expression systems used to produce, purify, and study the enzyme activities of PCW GTs, with an emphasis on the eukaryotic systems Nicotiana benthamiana, Pichia pastoris, and human embryonic kidney (HEK293) cells. We discuss the enzymatic properties of GTs including kinetic rates, the chain lengths of polysaccharide products, acceptor oligosaccharide preferences, elongation mechanisms for the synthesis of long-chain polymers, and the formation of GT complexes. Future directions in the study of matrix polysaccharide biosynthesis are proposed.
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Affiliation(s)
- Robert A. Amos
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Debra Mohnen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Debra Mohnen
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Xu H, Ding A, Chen S, Marowa P, Wang D, Chen M, Hu R, Kong Y, O’Neill M, Chai G, Zhou G. Genome-Wide Analysis of Sorghum GT47 Family Reveals Functional Divergences of MUR3-Like Genes. FRONTIERS IN PLANT SCIENCE 2018; 9:1773. [PMID: 30619385 PMCID: PMC6302003 DOI: 10.3389/fpls.2018.01773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/15/2018] [Indexed: 05/13/2023]
Abstract
Sorghum (Sorghum bicolor) is an important bioenergy crop. Its biomass mainly consists of the cellulosic and non-cellulosic polysaccharides, both which can be converted to biofuels. The biosynthesis of non-cellulosic polysaccharides involves several glycosyltransferases (GT) families including GT47. However, there was no systemic study on GT47 family in sorghum to date. Here, we identified 39 sorghum GT47 family members and showed the functional divergences of MURUS3 (MUR3) homologs. Sorghum GT47 proteins were phylogenetically clustered into four distinct subfamilies. Within each subfamily, gene structure was relatively conserved between the members. Ten gene pairs were identified from the 39 GT47 genes, of which two pairs might be originated from tandem duplication. 25.6% (10/39) of sorghum GT47 genes were homologous to Arabidopsis MUR3, a xyloglucan biosynthesis gene in primary cell walls. SbGT47_2, SbGT47_7, and SbGT47_8, three most homologous genes of MUR3, exhibited different tissue expression patterns and were selected for complementation into Arabidopsis mur3-3. Physiological and cell wall analyses showed that SbGT47_2 and SbGT47_7 may be two functional xyloglucan galactosyltransferases in sorghum. Further studies found that MUR3-like genes are widely present in the seed plants but not in the chlorophytic alga Chlamydomonas reinhardtii. Our results provide novel information for evolutionary analysis and functional dissection of sorghum GT47 family members.
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Affiliation(s)
- Hua Xu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Anming Ding
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Sihui Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Prince Marowa
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Dian Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Min Chen
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Ruibo Hu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingzhen Kong
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Malcolm O’Neill
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Guohua Chai
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Gongke Zhou
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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49
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Raven JA. How long have photosynthetic organisms been aggregating soils? THE NEW PHYTOLOGIST 2018; 219:1139-1141. [PMID: 30133846 DOI: 10.1111/nph.15309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Biological Sciences, University of Western Australia (M084), 35 Stirling Highway, Crawley, WA 6009, Australia
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50
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Pauly M, Ramírez V. New Insights Into Wall Polysaccharide O-Acetylation. FRONTIERS IN PLANT SCIENCE 2018; 9:1210. [PMID: 30186297 PMCID: PMC6110886 DOI: 10.3389/fpls.2018.01210] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/27/2018] [Indexed: 05/19/2023]
Abstract
The extracellular matrix of plants, algae, bacteria, fungi, and some archaea consist of a semipermeable composite containing polysaccharides. Many of these polysaccharides are O-acetylated imparting important physiochemical properties to the polymers. The position and degree of O-acetylation is genetically determined and varies between organisms, cell types, and developmental stages. Despite the importance of wall polysaccharide O-acetylation, only recently progress has been made to elucidate the molecular mechanism of O-acetylation. In plants, three protein families are involved in the transfer of the acetyl substituents to the various polysaccharides. In other organisms, this mechanism seems to be conserved, although the number of required components varies. In this review, we provide an update on the latest advances on plant polysaccharide O-acetylation and related information from other wall polysaccharide O-acetylating organisms such as bacteria and fungi. The biotechnological impact of understanding wall polysaccharide O-acetylation ranges from the design of novel drugs against human pathogenic bacteria to the development of improved lignocellulosic feedstocks for biofuel production.
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Affiliation(s)
| | - Vicente Ramírez
- Institute for Plant Cell Biology and Biotechnology – Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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