1
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Bakshani CR, Cuskin F, Lant NJ, Yau HCL, Willats WGT, Grant Burgess J. Analysis of glycans in a Burnt-on/Baked-on (BoBo) model food soil using Microarray Polymer Profiling (MAPP) and immunofluorescence microscopy. Food Chem 2023; 410:135379. [PMID: 36621331 DOI: 10.1016/j.foodchem.2022.135379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/12/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Burning of food materials during cooking can increase the difficulty in removal from solid surfaces, forming residual food soils. Using molecular probe-based technologies, the aim of this work was to elucidate the composition and relative abundance of glycans within a Burnt-On/Baked-On (BoBo) model food soil and investigate enzyme systems that may facilitate soil breakdown. Microarray Polymer Profiling identified xylan, arabinoxylan, mixed-linkage glucan and mannan as target substrates for the enzymatic cleaning of BoBo residues from surfaces. Indirect immunofluorescence microscopy revealed that burning resulted in extensive structural modifications and degradation of the three-dimensional architecture of constituent polysaccharide matrices. Results from high-throughput enzyme screening indicate that inclusion of xylan depolymerising enzymes in automatic dishwashing detergents may improve cleaning of recalcitrant, plant glycan-rich BoBo soils. Collectively, this study provides new insight into the composition and removal chemistry of complex, multi-component food soils.
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Affiliation(s)
- Cassie R Bakshani
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Fiona Cuskin
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Neil J Lant
- Procter & Gamble, Newcastle Innovation Centre, Newcastle upon Tyne NE12 9TS, UK
| | - Hamish C L Yau
- Procter & Gamble, Newcastle Innovation Centre, Newcastle upon Tyne NE12 9TS, UK
| | - William G T Willats
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - J Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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2
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Singh D, Chaudhary P, Taunk J, Singh CK, Singh D, Tomar RSS, Aski M, Konjengbam NS, Raje RS, Singh S, Sengar RS, Yadav RK, Pal M. Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence. Int J Mol Sci 2021; 22:10535. [PMID: 34638885 PMCID: PMC8509049 DOI: 10.3390/ijms221910535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250001, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal 793103, India
| | - Ranjeet Sharan Raje
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sanjay Singh
- ICAR- National Institute of Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut 250001, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Chen LH, Kračun SK, Nissen KS, Mravec J, Jørgensen B, Labavitch J, Stergiopoulos I. A diverse member of the fungal Avr4 effector family interacts with de-esterified pectin in plant cell walls to disrupt their integrity. SCIENCE ADVANCES 2021; 7:7/19/eabe0809. [PMID: 33962956 PMCID: PMC8104879 DOI: 10.1126/sciadv.abe0809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 03/18/2021] [Indexed: 05/19/2023]
Abstract
Effectors are small, secreted proteins that promote pathogen virulence. Although key to microbial infections, unlocking the intrinsic function of effectors remains a challenge. We have previously shown that members of the fungal Avr4 effector family use a carbohydrate-binding module of family 14 (CBM14) to bind chitin in fungal cell walls and protect them from host chitinases during infection. Here, we show that gene duplication in the Avr4 family produced an Avr4-2 paralog with a previously unknown effector function. Specifically, we functionally characterize PfAvr4-2, a paralog of PfAvr4 in the tomato pathogen Pseudocercospora fuligena, and show that although it contains a CBM14 domain, it does not bind chitin or protect fungi against chitinases. Instead, PfAvr4-2 interacts with highly de-esterified pectin in the plant's middle lamellae or primary cell walls and interferes with Ca2+-mediated cross-linking at cell-cell junction zones, thus loosening the plant cell wall structure and synergizing the activity of pathogen secreted endo-polygalacturonases.
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Affiliation(s)
- Li-Hung Chen
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Stjepan K Kračun
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Karen S Nissen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - John Labavitch
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
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4
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Liu E, MacMillan CP, Shafee T, Ma Y, Ratcliffe J, van de Meene A, Bacic A, Humphries J, Johnson KL. Fasciclin-Like Arabinogalactan-Protein 16 (FLA16) Is Required for Stem Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:615392. [PMID: 33362841 PMCID: PMC7758453 DOI: 10.3389/fpls.2020.615392] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/23/2020] [Indexed: 05/19/2023]
Abstract
The predominant Fascilin 1 (FAS1)-containing proteins in plants belong to the Fasciclin-Like Arabinogalactan-protein (FLA) family of extracellular glycoproteins. In addition to FAS1 domains, these multi-domain FLA proteins contain glycomotif regions predicted to direct addition of large arabinogalactan (AG) glycans and many contain signal sequences for addition of a glycosylphosphatidylinositol (GPI)-anchor to tether them to the plasma membrane. FLAs are proposed to play both structural and signaling functions by forming a range of interactions in the plant extracellular matrix, similar to FAS1-containing proteins in animals. FLA group B members contain two FAS1 domains and are not predicted to be GPI-anchored. None of the group B members have been functionally characterized or their sub-cellular location resolved, limiting understanding of their function. We investigated the group B FLA16 in Arabidopsis that is predominantly expressed in inflorescence tissues. FLA16 is the most highly expressed FLA in the stem after Group A members FLA11 and FLA12 that are stem specific. A FLA16-YFP fusion protein driven by the endogenous putative FLA16 promoter in wild type background showed expression in cells with secondary cell walls, and FLA16 displayed characteristics of cell wall glycoproteins with moderate glycosylation. Investigation of a fla16 mutant showed loss of FLA16 leads to reduced stem length and altered biomechanical properties, likely as a result of reduced levels of cellulose. Immuno-labeling indicated support for FLA16 location to the plasma-membrane and (apoplastic) cell wall of interfascicular stem fiber cells. Together these results indicate FLA16, a two-FAS1 domain FLAs, plays a role in plant secondary cell wall synthesis and function.
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Affiliation(s)
- Edgar Liu
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Colleen P. MacMillan
- CSIRO, Agriculture and Food, CSIRO Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Thomas Shafee
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Yingxuan Ma
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | | | - Antony Bacic
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - John Humphries
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim L. Johnson
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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5
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Nibbering P, Petersen BL, Motawia MS, Jørgensen B, Ulvskov P, Niittylä T. Golgi-localized exo-β1,3-galactosidases involved in cell expansion and root growth in Arabidopsis. J Biol Chem 2020; 295:10581-10592. [PMID: 32493777 DOI: 10.1074/jbc.ra120.013878] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Plant arabinogalactan proteins (AGPs) are a diverse group of cell surface- and wall-associated glycoproteins. Functionally important AGP glycans are synthesized in the Golgi apparatus, but the relationships among their glycosylation levels, processing, and functionalities are poorly understood. Here, we report the identification and functional characterization of two Golgi-localized exo-β-1,3-galactosidases from the glycosyl hydrolase 43 (GH43) family in Arabidopsis thaliana GH43 loss-of-function mutants exhibited root cell expansion defects in sugar-containing growth media. This root phenotype was associated with an increase in the extent of AGP cell wall association, as demonstrated by Yariv phenylglycoside dye quantification and comprehensive microarray polymer profiling of sequentially extracted cell walls. Characterization of recombinant GH43 variants revealed that the exo-β-1,3-galactosidase activity of GH43 enzymes is hindered by β-1,6 branches on β-1,3-galactans. In line with this steric hindrance, the recombinant GH43 variants did not release galactose from cell wall-extracted glycoproteins or AGP-rich gum arabic. These results indicate that the lack of exo-β-1,3-galactosidase activity alters cell wall extensibility in roots, a phenotype that could be explained by the involvement of galactosidases in AGP glycan biosynthesis.
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Affiliation(s)
- Pieter Nibbering
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Bent L Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Totte Niittylä
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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6
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EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. Proc Natl Acad Sci U S A 2019; 116:8597-8602. [PMID: 30944225 PMCID: PMC6486723 DOI: 10.1073/pnas.1820882116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In plants, postembryonic formation of new organs helps shape the adult organism. This requires the tight regulation of when and where a new organ is formed and a coordination of the underlying cell divisions. To build a root system, new lateral roots are continuously developing, and this process requires the tight coordination of asymmetric cell division in adjacent pericycle cells. We identified EXPANSIN A1 (EXPA1) as a cell wall modifying enzyme controlling the divisions marking lateral root initiation. Loss of EXPA1 leads to defects in the first asymmetric pericycle cell divisions and the radial swelling of the pericycle during auxin-driven lateral root formation. We conclude that a localized radial expansion of adjacent pericycle cells is required to position the asymmetric cell divisions and generate a core of small daughter cells, which is a prerequisite for lateral root organogenesis.
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7
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Raimundo SC, Pattathil S, Eberhard S, Hahn MG, Popper ZA. β-1,3-Glucans are components of brown seaweed (Phaeophyceae) cell walls. PROTOPLASMA 2017; 254:997-1016. [PMID: 27562783 DOI: 10.1007/s00709-016-1007-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 07/19/2016] [Indexed: 05/28/2023]
Abstract
LAMP is a cell wall-directed monoclonal antibody (mAb) that recognizes a β-(1,3)-glucan epitope. It has primarily been used in the immunolocalization of callose in vascular plant cell wall research. It was generated against a brown seaweed storage polysaccharide, laminarin, although it has not often been applied in algal research. We conducted in vitro (glycome profiling of cell wall extracts) and in situ (immunolabeling of sections) studies on the brown seaweeds Fucus vesiculosus (Fucales) and Laminaria digitata (Laminariales). Although glycome profiling did not give a positive signal with the LAMP mAb, this antibody clearly detected the presence of the β-(1,3)-glucan in situ, showing that this epitope is a constituent of these brown algal cell walls. In F. vesiculosus, the β-(1,3)-glucan epitope was present throughout the cell walls in all thallus parts; in L. digitata, the epitope was restricted to the sieve plates of the conductive elements. The sieve plate walls also stained with aniline blue, a fluorochrome used as a probe for callose. Enzymatic digestion with an endo-β-(1,3)-glucanase removed the ability of the LAMP mAb to label the cell walls. Thus, β-(1,3)-glucans are structural polysaccharides of F. vesiculosus cell walls and are integral components of the sieve plates in these brown seaweeds, reminiscent of plant callose.
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Affiliation(s)
- Sandra Cristina Raimundo
- Botany and Plant Science and Ryan Institute for Environmental, Marine and Energy Research, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
- Biology Department, and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, NY, 12866, USA.
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Stefan Eberhard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Zoë A Popper
- Botany and Plant Science and Ryan Institute for Environmental, Marine and Energy Research, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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8
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Geissner A, Seeberger PH. Glycan Arrays: From Basic Biochemical Research to Bioanalytical and Biomedical Applications. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:223-47. [PMID: 27306309 DOI: 10.1146/annurev-anchem-071015-041641] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A major branch of glycobiology and glycan-focused biomedicine studies the interaction between carbohydrates and other biopolymers, most importantly, glycan-binding proteins. Today, this research into glycan-biopolymer interaction is unthinkable without glycan arrays, tools that enable high-throughput analysis of carbohydrate interaction partners. Glycan arrays offer many applications in basic biochemical research, for example, defining the specificity of glycosyltransferases and lectins such as immune receptors. Biomedical applications include the characterization and surveillance of influenza strains, identification of biomarkers for cancer and infection, and profiling of immune responses to vaccines. Here, we review major applications of glycan arrays both in basic and applied research. Given the dynamic nature of this rapidly developing field, we focus on recent findings.
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Affiliation(s)
- Andreas Geissner
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany;
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9
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Lampugnani ER, Ho YY, Moller IE, Koh PL, Golz JF, Bacic A, Newbigin E. A Glycosyltransferase from Nicotiana alata Pollen Mediates Synthesis of a Linear (1,5)-α-L-Arabinan When Expressed in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1962-74. [PMID: 26850276 PMCID: PMC4825119 DOI: 10.1104/pp.15.02005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/04/2016] [Indexed: 05/09/2023]
Abstract
The walls of Nicotiana alata pollen tubes contain a linear arabinan composed of (1,5)-α-linked arabinofuranose residues. Although generally found as a side chain on the backbone of the pectic polysaccharide rhamnogalacturonan I, the arabinan in N. alata pollen tubes is considered free, as there is no detectable rhamnogalacturonan I in these walls. Carbohydrate-specific antibodies detected arabinan epitopes at the tip and along the shank of N. alata pollen tubes that are predominantly part of the primary layer of the bilayered wall. A sequence related to ARABINAN DEFICIENT1 (AtARAD1), a presumed arabinan arabinosyltransferase from Arabidopsis (Arabidopsis thaliana), was identified by searching an N alata pollen transcriptome. Transcripts for this ARAD1-like sequence, which we have named N. alata ARABINAN DEFICIENT-LIKE1 (NaARADL1), accumulate in various tissues, most abundantly in the pollen grain and tube, and encode a protein that is a type II membrane protein with its catalytic carboxyl terminus located in the Golgi lumen. The NaARADL1 protein can form homodimers when transiently expressed in Nicotiana benthamiana leaves and heterodimers when coexpressed with AtARAD1 The expression of NaARADL1 in Arabidopsis led to plants with more arabinan in their walls and that also exuded a guttation fluid rich in arabinan. Chemical and enzymatic characterization of the guttation fluid showed that a soluble, linear α-(1,5)-arabinan was the most abundant polymer present. These results are consistent with NaARADL1 having an arabinan (1,5)-α-arabinosyltransferase activity.
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Affiliation(s)
- Edwin R Lampugnani
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Yin Ying Ho
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Isabel E Moller
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Poh-Ling Koh
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - John F Golz
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Antony Bacic
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
| | - Ed Newbigin
- Plant Cell Biology Research Centre, School of BioSciences (E.R.L., Y.Y.H., I.E.M., P.-L.K., A.B., E.N.), and School of BioSciences (J.F.G.), University of Melbourne, Melbourne, Victoria, 3010 Australia; andAustralian Research Council Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia (E.R.L., Y.Y.H., I.E.M., A.B.)
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10
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Raimundo SC, Avci U, Hopper C, Pattathil S, Hahn MG, Popper ZA. Immunolocalization of cell wall carbohydrate epitopes in seaweeds: presence of land plant epitopes in Fucus vesiculosus L. (Phaeophyceae). PLANTA 2016; 243:337-54. [PMID: 26411728 DOI: 10.1007/s00425-015-2412-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/18/2015] [Indexed: 05/06/2023]
Abstract
MAIN CONCLUSION Land plant cell wall glycan epitopes are present in Fucus vesiculosus. RG-I/AG mAbs recognize distinct glycan epitopes in structurally different galactans, and 3-linked glucans are also present in the cell walls. Cell wall-directed monoclonal antibodies (mAbs) have given increased knowledge of fundamental land plant processes but are not extensively used to study seaweeds. We profiled the brown seaweed Fucus vesiculosus glycome employing 155 mAbs that recognize predominantly vascular plant cell wall glycan components. The resulting profile was used to inform in situ labeling studies. Several of the mAbs recognized and bound to epitopes present in different thallus parts of Fucus vesiculosus. Antibodies recognizing arabinogalactan epitopes were divided into four groups based on their immunolocalization patterns. Group 1 bound to the stipe, blade, and receptacles. Group 2 bound to the antheridia, oogonia and paraphyses. Group 3 recognized antheridia cell walls and Group 4 localized on the antheridia inner wall and oogonia mesochite. This study reveals that epitopes present in vascular plant cell walls are also present in brown seaweeds. Furthermore, the diverse in situ localization patterns of the RG-I/AG clade mAbs suggest that these mAbs likely detect distinct epitopes present in structurally different galactans. In addition, 3-linked glucans were also detected throughout the cell walls of the algal tissues, using the β-glucan-directed LAMP mAb. Our results give insights into cell wall evolution, and diversify the available tools for the study of brown seaweed cell walls.
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Affiliation(s)
- Sandra Cristina Raimundo
- Botany and Plant Science and Ryan Institute for Environmental, Marine and Energy Research, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
| | - Utku Avci
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
| | - Christina Hopper
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
| | - Zoë A Popper
- Botany and Plant Science and Ryan Institute for Environmental, Marine and Energy Research, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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Chavan RR, Fahey LM, Harris PJ. Quantification of (1→4)-β-d-Galactans in Compression Wood Using an Immuno-Dot Assay. PLANTS 2015; 4:29-43. [PMID: 27135316 PMCID: PMC4844332 DOI: 10.3390/plants4010029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/06/2015] [Indexed: 11/16/2022]
Abstract
Compression wood is a type of reaction wood formed on the underside of softwood stems when they are tilted from the vertical and on the underside of branches. Its quantification is still a matter of some scientific debate. We developed a new technique that has the potential to do this based on the higher proportions of (1→4)-β-d-galactans that occur in tracheid cell walls of compression wood. Wood was milled, partially delignified, and the non-cellulosic polysaccharides, including the (1→4)-β-d-galactans, extracted with 6 M sodium hydroxide. After neutralizing, the solution was serially diluted, and the (1→4)-β-d-galactans determined by an immuno-dot assay using the monoclonal antibody LM5, which specifically recognizes this polysaccharide. Spots were quantified using a dilution series of a commercially available (1→4)-β-d-galactan from lupin seeds. Using this method, compression and opposite woods from radiata pine (Pinus radiata) were easily distinguished based on the amounts of (1→4)-β-d-galactans extracted. The non-cellulosic polysaccharides in the milled wood samples were also hydrolysed using 2 M trifluoroacetic acid followed by the separation and quantification of the released neutral monosaccharides by high performance anion exchange chromatography. This confirmed that the compression woods contained higher proportions of galactose-containing polysaccharides than the opposite woods.
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Affiliation(s)
- Ramesh R Chavan
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Leona M Fahey
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Philip J Harris
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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A polysaccharide utilization locus from an uncultured bacteroidetes phylotype suggests ecological adaptation and substrate versatility. Appl Environ Microbiol 2014; 81:187-95. [PMID: 25326301 DOI: 10.1128/aem.02858-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent metagenomic analyses have identified uncultured bacteria that are abundant in the rumen of herbivores and that possess putative biomass-converting enzyme systems. Here we investigate the saccharolytic capabilities of a polysaccharide utilization locus (PUL) that has been reconstructed from an uncultured Bacteroidetes phylotype (SRM-1) that dominates the rumen microbiome of Arctic reindeer. Characterization of the three PUL-encoded outer membrane glycoside hydrolases was performed using chromogenic substrates for initial screening, followed by detailed analyses of products generated from selected substrates, using high-pressure anion-exchange chromatography with electrochemical detection. Two glycoside hydrolase family 5 (GH5) endoglucanases (GH5_g and GH5_h) demonstrated activity against β-glucans, xylans, and xyloglucan, whereas GH5_h and the third enzyme, GH26_i, were active on several mannan substrates. Synergy experiments examining different combinations of the three enzymes demonstrated limited activity enhancement on individual substrates. Binding analysis of a SusE-positioned lipoprotein revealed an affinity toward β-glucans and, to a lesser extent, mannan, but unlike the two SusD-like lipoproteins previously characterized from the same PUL, binding to cellulose was not observed. Overall, these activities and binding specificities correlated well with the glycan content of the reindeer rumen, which was determined using comprehensive microarray polymer profiling and showed an abundance of various hemicellulose glycans. The substrate versatility of this single PUL putatively expands our perceptions regarding PUL machineries, which so far have demonstrated gene organization that suggests one cognate PUL for each substrate type. The presence of a PUL that possesses saccharolytic activity against a mixture of abundantly available polysaccharides supports the dominance of SRM-1 in the Svalbard reindeer rumen microbiome.
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Xia Y, Petti C, Williams MA, DeBolt S. Experimental approaches to study plant cell walls during plant-microbe interactions. FRONTIERS IN PLANT SCIENCE 2014; 5:540. [PMID: 25352855 PMCID: PMC4196508 DOI: 10.3389/fpls.2014.00540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/23/2014] [Indexed: 05/27/2023]
Abstract
Plant cell walls provide physical strength, regulate the passage of bio-molecules, and act as the first barrier of defense against biotic and abiotic stress. In addition to providing structural integrity, plant cell walls serve an important function in connecting cells to their extracellular environment by sensing and transducing signals to activate cellular responses, such as those that occur during pathogen infection. This mini review will summarize current experimental approaches used to study cell wall functions during plant-pathogen interactions. Focus will be paid to cell imaging, spectroscopic analyses, and metabolic profiling techniques.
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Affiliation(s)
| | | | | | - Seth DeBolt
- Department of Horticulture, University of KentuckyLexington, KY, USA
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Popper ZA, Ralet MC, Domozych DS. Plant and algal cell walls: diversity and functionality. ANNALS OF BOTANY 2014; 114:1043-8. [PMID: 25453142 PMCID: PMC4195566 DOI: 10.1093/aob/mcu214] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/22/2014] [Indexed: 05/29/2023]
Abstract
BACKGROUND Although plants and many algae (e.g. the Phaeophyceae, brown, and Rhodophyceae, red) are only very distantly related they are united in their possession of carbohydrate-rich cell walls, which are of integral importance being involved in many physiological processes. Furthermore,wall components have applications within food, fuel, pharmaceuticals, fibres (e.g. for textiles and paper) and building materials and have long been an active topic of research. As shown in the 27 papers in this Special Issue, as the major deposit of photosynthetically fixed carbon, and therefore energy investment, cell walls are of undisputed importance to the organisms that possess them, the photosynthetic eukaryotes ( plants and algae). The complexities of cell wall components along with their interactions with the biotic and abiotic environment are becoming increasingly revealed. SCOPE The importance of plant and algal cell walls and their individual components to the function and survival of the organism, and for a number of industrial applications, are illustrated by the breadth of topics covered in this issue, which includes papers concentrating on various plants and algae, developmental stages, organs, cell wall components, and techniques. Although we acknowledge that there are many alternative ways in which the papers could be categorized (and many would fit within several topics), we have organized them as follows: (1) cell wall biosynthesis and remodelling, (2) cell wall diversity, and (3) application of new technologies to cell walls. Finally, we will consider future directions within plant cell wall research. Expansion of the industrial uses of cell walls and potentially novel uses of cell wall components are both avenues likely to direct future research activities. Fundamentally, it is the continued progression from characterization (structure, metabolism, properties and localization) of individual cell wall components through to defining their roles in almost every aspect of plant and algal physiology that will present many of the major challenges in future cell wall research.
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Affiliation(s)
- Zoë A. Popper
- Botany and Plant Science and The Ryan Institute for Environmental, Marine and Energy Research, National University of Ireland Galway, Galway, Ireland
| | | | - David S. Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, NY 12866, USA
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Hossain MA, Rana MM, Kimura Y, Roslan HA. Changes in biochemical characteristics and activities of ripening associated enzymes in mango fruit during the storage at different temperatures. BIOMED RESEARCH INTERNATIONAL 2014; 2014:232969. [PMID: 25136564 PMCID: PMC4129145 DOI: 10.1155/2014/232969] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/27/2014] [Accepted: 07/07/2014] [Indexed: 11/17/2022]
Abstract
As a part of the study to explore the possible strategy for enhancing the shelf life of mango fruits, we investigated the changes in biochemical parameters and activities of ripening associated enzymes of Ashwina hybrid mangoes at 4-day regular intervals during storage at -10°C, 4°C, and 30 ± 1°C. Titratable acidity, vitamin C, starch content, and reducing sugar were higher at unripe state and gradually decreased with the increasing of storage time at all storage temperatures while phenol content, total soluble solid, total sugar, and nonreducing sugar contents gradually increased. The activities of amylase, α-mannosidase, α-glucosidase, and invertase increased sharply within first few days and decreased significantly in the later stage of ripening at 30 ± 1°C. Meanwhile polyphenol oxidase, β-galactosidase, and β-hexosaminidase predominantly increased significantly with the increasing days of storage till later stage of ripening. At -10°C and 4°C, the enzymes as well as carbohydrate contents of storage mango changed slightly up to 4 days and thereafter the enzyme became fully dormant. The results indicated that increase in storage temperature and time correlated with changes in biochemical parameters and activities of glycosidases suggested the suppression of β-galactosidase and β-hexosaminidase might enhance the shelf life of mango fruits.
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Affiliation(s)
- Md. Anowar Hossain
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
- Genetic Engineering Laboratory, Department of Molecular Biology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Md. Masud Rana
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Hairul Azman Roslan
- Genetic Engineering Laboratory, Department of Molecular Biology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
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Tyler L, Fangel JU, Fagerström AD, Steinwand MA, Raab TK, Willats WGT, Vogel JP. Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines. BMC PLANT BIOLOGY 2014; 14:25. [PMID: 24423101 PMCID: PMC3925370 DOI: 10.1186/1471-2229-14-25] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 01/02/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND The model grass Brachypodium distachyon is increasingly used to study various aspects of grass biology. A large and genotypically diverse collection of B. distachyon germplasm has been assembled by the research community. The natural variation in this collection can serve as a powerful experimental tool for many areas of inquiry, including investigating biomass traits. RESULTS We surveyed the phenotypic diversity in a large collection of inbred lines and then selected a core collection of lines for more detailed analysis with an emphasis on traits relevant to the use of grasses as biofuel and grain crops. Phenotypic characters examined included plant height, growth habit, stem density, flowering time, and seed weight. We also surveyed differences in cell wall composition using near infrared spectroscopy (NIR) and comprehensive microarray polymer profiling (CoMPP). In all cases, we observed extensive natural variation including a two-fold variation in stem density, four-fold variation in ferulic acid bound to hemicellulose, and 1.7-fold variation in seed mass. CONCLUSION These characterizations can provide the criteria for selecting diverse lines for future investigations of the genetic basis of the observed phenotypic variation.
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Affiliation(s)
- Ludmila Tyler
- USDA-ARS Western Regional Research Center, Albany, CA, USA
- Current address: University of California, Berkeley, CA, USA
- Current address: University of Massachusetts, Amherst, MA, USA
| | | | - Alexandra Dotson Fagerström
- University of Copenhagen, Copenhagen, Denmark
- Current address: Energy Biosciences Institute, Berkeley, CA, USA
| | - Michael A Steinwand
- USDA-ARS Western Regional Research Center, Albany, CA, USA
- Current address: University of California, Berkeley, CA, USA
| | - Theodore K Raab
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | | | - John P Vogel
- USDA-ARS Western Regional Research Center, Albany, CA, USA
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