Global Analysis of UDP Glucose Pyrophosphorylase (UDPGP) Gene Family in Plants: Conserved Evolution Involved in Cell Death

Liu, Shuai; Zhong, Hua; Wang, Qiang; Liu, Caixiang; Li, Ting; Peng, Zhaohua; Li, Yangsheng; Zhang, Hongyu; Liao, Jiang-Lin; Huang, Yongji; Wang, Zhaohai

doi:10.3389/fpls.2021.681719

Cited by 6 publications

(4 citation statements)

References 78 publications

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“…The genomes of D. nobile (https://www.ncbi.nlm.nih.gov/genome/?term=dendrobium+nobile) were downloaded to identify the candidate R2R3-MYB genes. We used the hidden Markov model (HMM) pro le of the MYB domain (PF00249) from the Pfam database to search the protein sequences [14,15]. The putative DnMYB sequences were checked by the National Center for Biotechnology Information (NCBI).…”

Section: Identi Cation and Sequence Analysismentioning

confidence: 99%

Genome-wide identification of R2R3-MYB Family Genes and their Response to Stress in Dendrobium nobile

Fan

et al. 2023

Preprint

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R2R3-MYB is one of the largest and most important gene families, participating in the regulation of plant growth and development and response to abiotic stresses. However, the function of R2R3-MYB genes in Dendrobium nobile remains largely unknown. Here, a comprehensive genome-wide analysis of D. nobile R2R3-DnMYBs was performed, investigating phylogenic relationships, gene structures, motif composition, chromosomal locations, collinearity analysis, and cis-acting elements. Totally, 125 DnMYB genes were identified in the D. nobile genome, and they could be subdivided into 26 groups by further divided through phylogenetic analysis. Most genes with similar exon-intron structures and motif compositions in eaach subgroup exhibited similar functions. All of DnMYB genes were mapped on 19 chromosomes with the co-linearity relationship. Moreover, their expression patterns were analyzed in various tissues and abiotic stresses. The results showed that DnMYBs were significantly differential expressed in different tissues, following abiotic stresses and phytohormone treatments, indicating their possible roles in biological processes and some abiotic stress tolerance and adaptation. This work provides a comprehensive understanding of the R2R3-MYB family of D. nobile, and lays a foundation for future research on the potential function of DnMYB gene in the growth and development of D. nobile.

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Section: Identi Cation and Sequence Analysismentioning

confidence: 99%

Genome-wide identification of R2R3-MYB Family Genes and their Response to Stress in Dendrobium nobile

Fan

et al. 2023

Preprint

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“…4 ). UDP-sugar pyrophosphorylase (USP) is involved in the processes of synthesis and modification of the cell wall during pectin synthesis, as pectin is the main component of the intine layer ( Liu et al, 2021 ). Deletion occurs in the USP mutant due to the impaired synthesis of pollen intine ( Mi et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Research overview on the genetic mechanism underlying the biosynthesis of polysaccharide in tuber plants

Xu,

Hu,

et al. 2024

PeerJ

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Tuber plants are of great significance in the world as human food crops. Polysaccharides, important metabolites in tuber plants, also serve as a source of innovative drugs with significant pharmacological effects. These drugs are particularly known for their immunomodulation and antitumor properties. To fully exploit the potential value of tuber plant polysaccharides and establish a synthetic system for their targeted synthesis, it is crucial to dissect their metabolic processes and genetic regulatory mechanisms. In this article, we provide a comprehensive summary of the basic pathways involved in the synthesis of various types of tuber plant polysaccharides. We also outline the key research progress that has been made in this area in recent years. We classify the main types and functions of tuber plant polysaccharides and analyze the biosynthetic processes and genetic regulation mechanisms of key enzymes involved in the metabolic pathways of starch, cellulose, pectin, and fructan in tuber plants. We have identified hexokinase and glycosyltransferase as the key enzymes involved in the polysaccharide synthesis process. By elucidating the synthesis pathway of polysaccharides in tuber plants and understanding the underlying mechanism of action of key enzymes in the metabolic pathway, we can provide a theoretical framework for enhancing the yield of polysaccharides and other metabolites in plant culture cells. This will ultimately lead to increased production efficiency.

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“…While most NSPs display specificity for both the NTP (nucleoside triphosphate) and sugar phosphate, some enzymes are capable of activating two or more sugars, such as UDP-GlcNAc/-GalNAc pyrophosphorylases ( 19 ) and UDP-sugar pyrophosphorylases (USPs) with broad substrate specificity identified in plants and some protozoan parasites [reviewed in reference ( 20 )]. A second subclade of UGP, termed UGP-B, which was more closely related to USPs, was identified exclusively in plants, whereas the UGP-A subclade is found in all eukaryotes ( 21 ). NDP-activated sugars may be further converted by, e.g., epimerases, mutases, or oxidative pathways, giving rise to additional nucleotide-sugars.…”

Section: Introductionmentioning

confidence: 99%

CryoEM analysis of the essential native UDP-glucose pyrophosphorylase from Aspergillus nidulans reveals key conformations for activity regulation and function

Han

D’Angelo

Otamendi

et al. 2023

mBio

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Invasive aspergillosis is one of the most serious clinical invasive fungal infections, resulting in a high case fatality rate among immunocompromised patients. The disease is caused by saprophytic molds in the genus Aspergillus , including Aspergillus fumigatus , the most significant pathogenic species. The fungal cell wall, an essential structure mainly composed of glucan, chitin, galactomannan, and galactosaminogalactan, represents an important target for the development of antifungal drugs. UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) is a central enzyme in the metabolism of carbohydrates that catalyzes the biosynthesis of UDP-glucose, a key precursor of fungal cell wall polysaccharides. Here, we demonstrate that the function of UGP is vital for Aspergillus nidulans ( An UGP). To understand the molecular basis of An UGP function, we describe a cryoEM structure (global resolution of 3.5 Å for the locally refined subunit and 4 Å for the octameric complex) of a native An UGP. The structure reveals an octameric architecture with each subunit comprising an N-terminal α-helical domain, a central catalytic glycosyltransferase A-like (GT-A-like) domain, and a C-terminal (CT) left-handed β-helix oligomerization domain. An UGP displays unprecedented conformational variability between the CT oligomerization domain and the central GT-A-like catalytic domain. In combination with activity measurements and bioinformatics analysis, we unveil the molecular mechanism of substrate recognition and specificity for An UGP. Altogether, our study not only contributes to understanding the molecular mechanism of catalysis/regulation of an important class of enzymes but also provides the genetic, biochemical, and structural groundwork for the future exploitation of UGP as a potential antifungal target. IMPORTANCE Fungi cause diverse diseases in humans, ranging from allergic syndromes to life-threatening invasive diseases, together affecting more than a billion people worldwide. Increasing drug resistance in Aspergillus species represents an emerging global health threat, making the design of antifungals with novel mechanisms of action a worldwide priority. The cryoEM structure of UDP (uridine diphosphate)-glucose pyrophosphorylase (UGP) from the filamentous fungus Aspergillus nidulans reveals an octameric architecture displaying unprecedented conformational variability between the C-terminal oligomerization domain and the central glycosyltransferase A-like catalytic domain in the individual protomers. While the active site and oligomerization interfaces are more highly conserved, these dynamic interfaces include motifs restricted to specific clades of filamentous fungi. Functional study of these motifs could lead to the definition of new targets for antifungals inhibiting UGP activity and, thus, the architecture of the cell wall of filamentous fungal pathogens.

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Global Analysis of UDP Glucose Pyrophosphorylase (UDPGP) Gene Family in Plants: Conserved Evolution Involved in Cell Death

Cited by 6 publications

References 78 publications

Genome-wide identification of R2R3-MYB Family Genes and their Response to Stress in Dendrobium nobile

Genome-wide identification of R2R3-MYB Family Genes and their Response to Stress in Dendrobium nobile

Research overview on the genetic mechanism underlying the biosynthesis of polysaccharide in tuber plants

CryoEM analysis of the essential native UDP-glucose pyrophosphorylase from Aspergillus nidulans reveals key conformations for activity regulation and function

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