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Advances in Functional Genomics of Plant Cell Wall Metabolism
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Advances in Functional Genomics of Plant Cell Wall Metabolism

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: closed (15 August 2021) | Viewed by 10597

Special Issue Editors

Prof. Ahmed Faik

E-Mail Website
Guest Editor
Environmental and Plant Biology Department, Ohio University, Athens, OH 45701, USA
Interests: plant cell wall; polysaccharides biosynthesis; glycosyltransferases trafficking; high-throughput analytical methods; wheat; rice
Dr. Michael Held

E-Mail Website
Guest Editor
Ohio University, Chemistry and Biochemistry Department, Athens, OH 45701, USA
Interests: plant cell wall biosynthesis and architecture; regulation of cell wall biosynthesis; secretion of cell wall polysaccharides

Special Issue Information

Dear Colleagues,

Plants build an extracellular matrix called the cell wall that is considered to be their first protective barrier from disease, water loss, and other abiotic stresses. Cell walls form a network that is thought to regulate cell elongation and plant growth. Manipulating the composition and structure of plant cell walls could provide opportunities to design plant products and plants with specific characteristics relevant to food and agricultural applications. Although tremendous progress has been made in elucidating the composition of plant cell walls in a variety of species, many functional aspects (including metabolism) of plant cell walls remain elusive. Fortunately, efforts are being made to develop new technologies and tools to analyze and manipulate plant cell walls, which will help to advance our molecular understanding of cell wall functions. The goal of this Special Issue of Plants is to provide insightful and critical advances in the field of functional genomics of plant cell wall metabolism. This includes research and reviews. Reviews should discuss experiments or technical constraints needed to advance the field, including suggestion of novel approaches to discover missing links and speculations that go beyond current knowledge but based on sound science. Research papers should highlight new developments and directions that would advance the field.

Prof. Ahmed Faik
Dr. Michael Held
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant cell wall
  • glycosyltransferases
  • functional genomics

Published Papers (4 papers)

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Research

26 pages, 15694 KiB  
Article
The Arabinogalactan Protein Family of Centaurium erythraea Rafn
by Danijela M. Paunović, Katarina B. Ćuković, Milica D. Bogdanović, Slađana I. Todorović, Milana M. Trifunović-Momčilov, Angelina R. Subotić, Ana D. Simonović and Milan B. Dragićević
Plants 2021, 10(9), 1870; https://doi.org/10.3390/plants10091870 - 9 Sep 2021
Cited by 3 | Viewed by 2292
Abstract
Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family [...] Read more.
Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family of O-glycosylated plant cell surface hydroxyproline-rich glycoproteins (HRGPs). HRGPs/AGPs are intrinsically disordered and not well conserved, making their homology-based mining ineffective. We have applied a recently developed pipeline for HRGP/AGP mining, ragp, which is based on machine learning prediction of proline hydroxylation, to identify HRGP sequences in centaury transcriptome and to classify them into motif and amino acid bias (MAAB) classes. AGP sequences with low AG glycomotif representation were also identified. Six members of each of the three AGP subclasses, fasciclin-like AGPs, receptor kinase-like AGPs and AG peptides, were selected for phylogenetic and expression analyses. The expression of these 18 genes was recorded over 48 h following leaf mechanical wounding, as well as in 16 tissue samples representing plants from nature, plants cultivated in vitro, and developmental stages during shoot organogenesis and somatic embryogenesis. None of the selected genes were upregulated during both wounding recovery and regeneration. Possible functions of AGPs with the most interesting expression profiles are discussed. Full article
(This article belongs to the Special Issue Advances in Functional Genomics of Plant Cell Wall Metabolism)
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19 pages, 4170 KiB  
Article
Three β-Glucuronosyltransferase Genes Involved in Arabinogalactan Biosynthesis Function in Arabidopsis Growth and Development
by Oyeyemi O. Ajayi, Michael A. Held and Allan M. Showalter
Plants 2021, 10(6), 1172; https://doi.org/10.3390/plants10061172 - 9 Jun 2021
Cited by 9 | Viewed by 2934
Abstract
Arabinogalactan proteins (AGPs) contain arabinogalactan (AG) polysaccharides that are biologically relevant to plant growth processes. Here, the biochemical and physiological roles of three Golgi localized β-glucuronosyltransferase genes (GLCAT14A, GLCAT14B and GLCAT14C) in Arabidopsis thaliana, responsible for the addition of glucuronic [...] Read more.
Arabinogalactan proteins (AGPs) contain arabinogalactan (AG) polysaccharides that are biologically relevant to plant growth processes. Here, the biochemical and physiological roles of three Golgi localized β-glucuronosyltransferase genes (GLCAT14A, GLCAT14B and GLCAT14C) in Arabidopsis thaliana, responsible for the addition of glucuronic acid to AG chains, were further investigated using single, double and triple glcat14 mutant plants. These proteins were localized to the Golgi apparatus when transiently expressed in Nicotiana benthamiana. Sugar analysis of AGP extracts from Arabidopsis stem, leaf and siliques showed a consistent reduction in glucuronic acid in glcat14 mutants relative to wild type, with concomitant effects resulting in tissue-specific alterations, especially in arabinose and galactose sugars. Although we observed defects in trichome branching in glca14a/b and glca14a/b/c mutants, scanning electron microscope analysis/energy dispersive microanalysis (SEM/EDX) showed no difference in the calcium content of trichomes in these mutants relative to wild type. Immunoblot analyses of the stem and leaf showed a reduction in AGPs as detected with the LM2 antibody in glcat14a/b and glcat14a/b/c mutants relative to wild type. The current work exemplifies the possibility of conducting structure-function assessment of cell wall biosynthetic genes to identify their physiological roles in plant growth and development. Full article
(This article belongs to the Special Issue Advances in Functional Genomics of Plant Cell Wall Metabolism)
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10 pages, 3077 KiB  
Article
Transcriptional Changes of Cell Wall Organization Genes and Soluble Carbohydrate Alteration during Leaf Blade Development of Rice Seedlings
by Jae-Yeon Joo, Me-Sun Kim and Jwakyung Sung
Plants 2021, 10(5), 823; https://doi.org/10.3390/plants10050823 - 21 Apr 2021
Cited by 1 | Viewed by 1850
Abstract
Plant cell walls have two constituent parts with different components and developmental stages. Much of the mystery concerning the mechanisms of synthesis, decomposition, modification, and so forth, has been resolved using omics and microscopic techniques. However, it still remains to be determined how [...] Read more.
Plant cell walls have two constituent parts with different components and developmental stages. Much of the mystery concerning the mechanisms of synthesis, decomposition, modification, and so forth, has been resolved using omics and microscopic techniques. However, it still remains to be determined how cell wall development progresses over time after leaf emergence. Our focus in the present study was to expand our knowledge of the molecular mechanisms associated with cell wall synthesis in rice leaf blade during three distinct stages (sink, sink-to-source transition, and source). The RNA-seq, quantitative reverse transcription PCR (qRT-PCR) and carbohydrate concentrations were evaluated using developing fifth leaf blades harvested at different time points. The results revealed that some of the essential genes for the primary cell wall (PCW) were highly upregulated in the sink-to-source transition compared to the sink stage, whereas those essential to the secondary cell wall (SCW) displayed relatively higher levels (p < 0.05) during the source stage. The concentrations of soluble carbohydrates differed via type rather than stage; we observed higher monosaccharides during the sink stage and higher di- and oligo-saccharides during the sink-to-source transition and source stages. In conclusion, our findings suggest that the transcriptional regulation of plant cell wall biosynthesis genes are both synchronistic with and independent of, and directly and indirectly governed by, the abundance of soluble carbohydrates in the developing leaf blade, and, finally, raffinose is likely to play a transport role comparable to sucrose. Full article
(This article belongs to the Special Issue Advances in Functional Genomics of Plant Cell Wall Metabolism)
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12 pages, 1325 KiB  
Article
Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana
by Yichao Li, Maxwell Mullin, Yingnan Zhang, Frank Drews, Lonnie R. Welch and Allan M. Showalter
Plants 2020, 9(12), 1751; https://doi.org/10.3390/plants9121751 - 10 Dec 2020
Cited by 4 | Viewed by 2803
Abstract
Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized protein sequence signatures for three family members in the HRGP superfamily: the hyperglycosylated [...] Read more.
Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized protein sequence signatures for three family members in the HRGP superfamily: the hyperglycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). However, the mechanism of pollen-specific HRGP gene expression remains unexplored. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences to identify cis-regulatory motifs responsible for pollen-specific expression of HRGP genes in Arabidopsis thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery identified 15 conserved promoter elements between A.thaliana and A. lyrata. Motif scanning revealed two pollen related transcription factors: GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Finally, we performed a regression analysis and demonstrated that the 15 motifs provided a good model of HRGP gene expression in pollen (R = 0.61). In conclusion, we performed the first integrative analysis of cis-regulatory motifs in pollen-specific HRGP genes, revealing important insights into transcriptional regulation in pollen tissue. Full article
(This article belongs to the Special Issue Advances in Functional Genomics of Plant Cell Wall Metabolism)
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