Research

20 pages, 7332 KiB

Open AccessArticle

Cloning and Characterization of Two Novel PR4 Genes from Picea asperata

by Weidong Zhao, Lijuan Liu, Chengsong Li, Chunlin Yang, Shujiang Li, Shan Han, Tiantian Lin and Yinggao Liu

Int. J. Mol. Sci. 2022, 23(23), 14906; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232314906 - 28 Nov 2022

Cited by 1 | Viewed by 1306

Abstract

Pathogenesis-related (PR) proteins are important in plant pathogenic resistance and comprise 17 families, including the PR4 family, with antifungal and anti-pathogenic functions. PR4 proteins contain a C-terminal Barwin domain and are divided into Classes I and II based on the presence of an [...] Read more.

Pathogenesis-related (PR) proteins are important in plant pathogenic resistance and comprise 17 families, including the PR4 family, with antifungal and anti-pathogenic functions. PR4 proteins contain a C-terminal Barwin domain and are divided into Classes I and II based on the presence of an N-terminal chitin-binding domain (CBD). This study is the first to isolate two PR4 genes, PaPR4-a and PaPR4-b, from Picea asperata, encoding PaPR4-a and PaPR4-b, respectively. Sequence analyses suggested that they were Class II proteins, owing to the presence of an N-terminal signal peptide and a C-terminal Barwin domain, but no CBD. Tertiary structure analyses using the Barwin-like protein of papaya as a template revealed structural similarity, and therefore, functional similarity between the proteins. Predictive results revealed an N-terminal transmembrane domain, and subcellular localization studies confirmed its location on cell membrane and nuclei. Real-time quantitative PCR (RT-qPCR) demonstrated that PaPR4-a and PaPR4-b expression levels were upregulated following infection with Lophodermium piceae. Additionally, PaPR4-a and PaPR4-b were induced in Escherichia coli, where the recombinant proteins existed in inclusion bodies. The renatured purified proteins showed antifungal activity. Furthermore, transgenic tobacco overexpressing PaPR4-a and PaPR4-b exhibited improved resistance to fungal infection. The study can provide a basis for further molecular mechanistic insights into PR4-induced defense responses. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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22 pages, 5865 KiB

Open AccessArticle

Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.)

by Venura Herath and Jeanmarie Verchot

Int. J. Mol. Sci. 2022, 23(22), 13795; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232213795 - 09 Nov 2022

Cited by 3 | Viewed by 1576

Abstract

We treated potato (Solanum tuberosum L.) plantlets with TM and performed gene expression studies to identify genome-wide changes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). An extensive network of responses was identified, including chromatin remodeling, transcriptional reprogramming, [...] Read more.

We treated potato (Solanum tuberosum L.) plantlets with TM and performed gene expression studies to identify genome-wide changes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). An extensive network of responses was identified, including chromatin remodeling, transcriptional reprogramming, as well as changes in the structural components of the endomembrane network system. Limited genome-wide changes in alternative RNA splicing patterns of protein-coding transcripts were also discovered. Significant changes in RNA metabolism, components of the translation machinery, as well as factors involved in protein folding and maturation occurred, which included a broader set of genes than expected based on Arabidopsis research. Antioxidant defenses and oxygen metabolic enzymes are differentially regulated, which is expected of cells that may be experiencing oxidative stress or adapting to protect proteins from oxidation. Surges in protein kinase expression indicated early signal transduction events. This study shows early genomic responses including an array of differentially expressed genes that have not been reported in Arabidopsis. These data describe novel ER stress responses in a solanaceous host. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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11 pages, 2600 KiB

Open AccessArticle

Natural Variation of Fatty Acid Desaturase Gene Affects Linolenic Acid Content and Starch Pasting Viscosity in Rice Grains

by Liting Zhang, Yu Xia, Yage Dong, Tianyi Xie, Wenqiang Sun and Sibin Yu

Int. J. Mol. Sci. 2022, 23(19), 12055; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231912055 - 10 Oct 2022

Cited by 5 | Viewed by 1697

Abstract

Rice, as one of the main food crops, provides a vital source of dietary energy for over half the world’s population. The OsFAD3 gene encodes fatty acid desaturase, catalyzing the conversion of linoleic acid (LA) to alpha-linolenic acid (ALA) in rice. However, the [...] Read more.

Rice, as one of the main food crops, provides a vital source of dietary energy for over half the world’s population. The OsFAD3 gene encodes fatty acid desaturase, catalyzing the conversion of linoleic acid (LA) to alpha-linolenic acid (ALA) in rice. However, the genetic characterization of OsFAD3 and its role in the conversion of LA to ALA remains elusive. Here, we validated the effects of two homologous genes, OsFAD3-1 and OsFAD3-2, on the ALA and LA/ALA ratio in rice grains using near-isogenic lines. Two major haplotypes of OsFAD3-1 are identified with different effects on the ALA and LA/ALA ratio in rice germplasm. High expression of OsFAD3-1 is associated with high ALA accumulation and eating quality of rice grains. Overexpression of OsFAD3-1 driven by a seed-specific promoter increases the ALA content up to 16-fold in the endosperm. A diagnostic marker is designed based on an 8-bp insertion/deletion in the OsFAD3-1 promoter, which can recognize OsFAD3-1 alleles in rice. These results indicate that OsFAD3-1 is a useful target gene in marker-assisted breeding programs to improve varieties with high ALA and appropriate LA/ALA ratio in brown rice. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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25 pages, 4717 KiB

Open AccessArticle

OsSPLs Regulate Male Fertility in Response to Different Temperatures by Flavonoid Biosynthesis and Tapetum PCD in PTGMS Rice

by Yujun Sun, Ming Fu, Lei Wang, Yunxiu Bai, Xueliang Fang, Qian Wang, Ying He and Hanlai Zeng

Int. J. Mol. Sci. 2022, 23(7), 3744; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23073744 - 29 Mar 2022

Cited by 9 | Viewed by 2284

Abstract

Photoperiod and thermo-sensitive genic male sterile (PTGMS) rice is an important resource for two line hybrid rice production. The SQUAMOSA–promoter binding, such as the (SPL) gene family, encode the plant specific transcription factors that regulate development and defense responses in plants. [...] Read more.

Photoperiod and thermo-sensitive genic male sterile (PTGMS) rice is an important resource for two line hybrid rice production. The SQUAMOSA–promoter binding, such as the (SPL) gene family, encode the plant specific transcription factors that regulate development and defense responses in plants. However, the reports about SPLs participating in male fertility regulation are limited. Here, we identified 19 OsSPL family members and investigated their involvement in the fertility regulation of the PTGMS rice lines, PA2364S and PA2864S, with different fertility transition temperatures. The results demonstrated that OsSPL2, OsSPL4, OsSPL16 and OsSPL17 affect male fertility in response to temperature changes through the MiR156-SPL module. WGCNA (weighted gene co-expression network analysis) revealed that CHI and APX1 were co-expressed with OsSPL17. Targeted metabolite and flavonoid biosynthetic gene expression analysis revealed that OsSPL17 regulates the expression of flavonoid biosynthesis genes CHI, and the up regulation of flavanones (eriodictvol and naringenin) and flavones (apigenin and luteolin) content contributed to plant fertility. Meanwhile, OsSPL17 negatively regulates APX1 to affect APX (ascorbate peroxidase) activity, thereby regulating ROS (reactive oxygen species) content in the tapetum, controlling the PCD (programmed cell death) process and regulating male fertility in rice. Overall, this report highlights the potential role of OsSPL for the regulation of male fertility in rice and provides a new insight for the further understanding of fertility molecular mechanisms in PTGMS rice. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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13 pages, 6271 KiB

Open AccessArticle

Genome-Wide Analysis of LBD Transcription Factor Genes in Dendrobium catenatum

by Ru Jia, Cheng Li, Yuhua Wang, Xiangshi Qin, Lihua Meng and Xudong Sun

Int. J. Mol. Sci. 2022, 23(4), 2089; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23042089 - 14 Feb 2022

Cited by 5 | Viewed by 1937

Abstract

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family comprises plant-specific transcription factors that control cell proliferation and differentiation during growth and development in many plant species. However, to date, no studies of the LBD gene family in Dendrobium catenatum have been reported. In [...] Read more.

The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) gene family comprises plant-specific transcription factors that control cell proliferation and differentiation during growth and development in many plant species. However, to date, no studies of the LBD gene family in Dendrobium catenatum have been reported. In this study, a genome-wide analysis of LBD genes was performed in D. catenatum and 24 LBD genes were identified. The genes were classified into two classes (I and II) based on phylogenetic relationships and motif structure. Subcellular localization analysis for DcaLBD6 and DcaLBD18 from class I and DcaLBD37 and DcaLBD41 from class II revealed that the proteins were localized in the nucleus. Transient expression analysis of DcaLBD6, DcaLBD18, DcaLBD37, and DcaLBD41 indicated that class I and class II members have opposite roles in regulating VASCULAR-RELATED NAC-DOMAIN 7 (VND7) expression. DcaLBD genes showed diverse expression patterns in response to different phytohormone treatments. Heat maps revealed diverse patterns of DcaLBD gene expression in different organs. These results lay the foundation for further detailed studies of the LBD gene family in D. catenatum. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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28 pages, 7001 KiB

Open AccessArticle

Telomerase Interaction Partners–Insight from Plants

by Jana Fulnečková, Ladislav Dokládal, Karolína Kolářová, Martina Nešpor Dadejová, Klára Procházková, Sabina Gomelská, Martin Sivčák, Kateřina Adamusová, Martin Lyčka, Vratislav Peska, Martina Dvořáčková and Eva Sýkorová

Int. J. Mol. Sci. 2022, 23(1), 368; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010368 - 29 Dec 2021

Cited by 2 | Viewed by 2553

Abstract

Telomerase, an essential enzyme that maintains chromosome ends, is important for genome integrity and organism development. Various hypotheses have been proposed in human, ciliate and yeast systems to explain the coordination of telomerase holoenzyme assembly and the timing of telomerase performance at telomeres [...] Read more.

Telomerase, an essential enzyme that maintains chromosome ends, is important for genome integrity and organism development. Various hypotheses have been proposed in human, ciliate and yeast systems to explain the coordination of telomerase holoenzyme assembly and the timing of telomerase performance at telomeres during DNA replication or repair. However, a general model is still unclear, especially pathways connecting telomerase with proposed non-telomeric functions. To strengthen our understanding of telomerase function during its intracellular life, we report on interactions of several groups of proteins with the Arabidopsis telomerase protein subunit (AtTERT) and/or a component of telomerase holoenzyme, POT1a protein. Among these are the nucleosome assembly proteins (NAP) and the minichromosome maintenance (MCM) system, which reveal new insights into the telomerase interaction network with links to telomere chromatin assembly and replication. A targeted investigation of 176 candidate proteins demonstrated numerous interactions with nucleolar, transport and ribosomal proteins, as well as molecular chaperones, shedding light on interactions during telomerase biogenesis. We further identified protein domains responsible for binding and analyzed the subcellular localization of these interactions. Moreover, additional interaction networks of NAP proteins and the DOMINO1 protein were identified. Our data support an image of functional telomerase contacts with multiprotein complexes including chromatin remodeling and cell differentiation pathways. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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19 pages, 2857 KiB

Open AccessArticle

In-Depth Sequence Analysis of Bread Wheat VRN1 Genes

by Beáta Strejčková, Zbyněk Milec, Kateřina Holušová, Petr Cápal, Tereza Vojtková, Radim Čegan and Jan Šafář

Int. J. Mol. Sci. 2021, 22(22), 12284; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212284 - 13 Nov 2021

Cited by 13 | Viewed by 2790

Abstract

The VERNALIZATION1 (VRN1) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of VRN1 homoeologs has been associated with large differences in flowering time. The aim of [...] Read more.

The VERNALIZATION1 (VRN1) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of VRN1 homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of VRN1 homoeologs (VRN-A1, VRN-B1 and VRN-D1). We performed an in-depth sequence analysis of VRN1 homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele Vrn-B1f with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the Vrn-A1b allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of VRN1 homoeologs showed that VRN-B1 and VRN-D1 are present in only one copy. The copy number of recessive vrn-A1 ranged from one to four, while that of dominant Vrn-A1 was one or two. Different numbers of Vrn-A1a copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more vrn-A1 copies. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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22 pages, 17935 KiB

Open AccessArticle

Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences

by Zhenhua Dang, Yuanyuan Jia, Yunyun Tian, Jiabin Li, Yanan Zhang, Lei Huang, Cunzhu Liang, Peter J. Lockhart, Cory Matthew and Frank Yonghong Li

Int. J. Mol. Sci. 2021, 22(21), 11882; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111882 - 02 Nov 2021

Cited by 6 | Viewed by 1693

Abstract

Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term [...] Read more.

Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Here, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. As a result, a total of 2357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified in RNA-Seq and qRT-PCR analyses that indicated the modulation of the Calvin–Benson cycle and photorespiration metabolic pathways. The key gene expression profiles encoding various proteins (e.g., ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase, etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection and identifying important questions to address in future transcriptome studies. Full article

(This article belongs to the Special Issue Plant Genome Dynamics)

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