scholarly journals Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in Nicotiana benthamiana

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shaofei Rao ◽  
Xinyang Wu ◽  
Hongying Zheng ◽  
Yuwen Lu ◽  
Jiejun Peng ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Catharanthus Roseus ◽  
Nicotiana Benthamiana ◽  
Expression Profiles ◽  
Plant Immunity ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Phylogenetic Groups ◽  
Specific Expression ◽  
Cis Acting

Abstract Background The Catharanthus roseus RLK1-like kinase (CrRLK1L) is a subfamily of the RLK gene family, and members are sensors of cell wall integrity and regulators of cell polarity growth. Recent studies have also shown that members of this subfamily are involved in plant immunity. Nicotiana benthamiana is a model plant widely used in the study of plant-pathogen interactions. However, the members of the NbCrRLK1L subfamily and their response to pathogens have not been reported. Results In this study, a total of 31 CrRLK1L members were identified in the N. benthamiana genome, and these can be divided into 6 phylogenetic groups (I-VI). The members in each group have similar exon-intron structures and conserved motifs. NbCrRLK1Ls were predicted to be regulated by cis-acting elements such as STRE, TCA, ABRE, etc., and to be the target of transcription factors such as Dof and MYB. The expression profiles of the 16 selected NbCrRLK1Ls were determined by quantitative PCR. Most NbCrRLK1Ls were highly expressed in leaves but there were different and diverse expression patterns in other tissues. Inoculation with the bacterium Pseudomonas syringae or with Turnip mosaic virus significantly altered the transcript levels of the tested genes, suggesting that NbCrRLK1Ls may be involved in the response to pathogens. Conclusions This study systematically identified the CrRLK1L members in N. benthamiana, and analyzed their tissue-specific expression and gene expression profiles in response to different pathogens and two pathogens associated molecular patterns (PAMPs). This research lays the foundation for exploring the function of NbCrRLK1Ls in plant-microbe interactions.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals The SAL-PAP Chloroplast Retrograde Pathway Contributes to Plant Immunity by Regulating Glucosinolate Pathway and Phytohormone Signaling

2017 ◽  
Vol 30 (10) ◽  
pp. 829-841 ◽  
Author(s):  
Yasuhiro Ishiga ◽  
Mutsumi Watanabe ◽  
Takako Ishiga ◽  
Takayuki Tohge ◽  
Takakazu Matsuura ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Pseudomonas Syringae ◽  
Expression Profiles ◽  
Plant Immunity ◽  
Gene Expression Profiles ◽  
Nuclear Gene ◽  
Retrograde Signaling ◽  
Necrotrophic Pathogen ◽  
Nuclear Gene Expression

Chloroplasts have a crucial role in plant immunity against pathogens. Increasing evidence suggests that phytopathogens target chloroplast homeostasis as a pathogenicity mechanism. In order to regulate the performance of chloroplasts under stress conditions, chloroplasts produce retrograde signals to alter nuclear gene expression. Many signals for the chloroplast retrograde pathway have been identified, including chlorophyll intermediates, reactive oxygen species, and metabolic retrograde signals. Although there is a reasonably good understanding of chloroplast retrograde signaling in plant immunity, some signals are not well-understood. In order to understand the role of chloroplast retrograde signaling in plant immunity, we investigated Arabidopsis chloroplast retrograde signaling mutants in response to pathogen inoculation. sal1 mutants (fry1-2 and alx8) responsible for the SAL1-PAP retrograde signaling pathway showed enhanced disease symptoms not only to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000 but, also, to the necrotrophic pathogen Pectobacterium carotovorum subsp. carotovorum EC1. Glucosinolate profiles demonstrated the reduced accumulation of aliphatic glucosinolates in the fry1-2 and alx8 mutants compared with the wild-type Col-0 in response to DC3000 infection. In addition, quantification of multiple phytohormones and analyses of their gene expression profiles revealed that both the salicylic acid (SA)- and jasmonic acid (JA)-mediated signaling pathways were down-regulated in the fry1-2 and alx8 mutants. These results suggest that the SAL1-PAP chloroplast retrograde pathway is involved in plant immunity by regulating the SA- and JA-mediated signaling pathways.

scholarly journals Gene Expression Profiles of the Cochlea and Vestibular Endorgans

2015 ◽  
Vol 124 (1_suppl) ◽  
pp. 6S-48S ◽  
Author(s):  
Shin-ya Nishio ◽  
Mitsuru Hattori ◽  
Hideaki Moteki ◽  
Keita Tsukada ◽  
Maiko Miyagawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hearing Loss ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Vestibular Function ◽  
Specific Expression ◽  
Hereditary Hearing Loss ◽  
Vestibular Endorgans ◽  
Gene Symbols

Objectives:We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss.Methods:Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Homepage using localization, expression, and distribution as keywords.Results:Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans.Conclusions:The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.

scholarly journals Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

2020 ◽  
Author(s):  
Xinyang Wu ◽  
Yuchao Lai ◽  
Lanqing Lv ◽  
Mengfei Ji ◽  
Kelei Han ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Nicotiana Benthamiana ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Arabinogalactan Proteins ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain ◽  
Plant Pathogen Interactions

Abstract Background: Nicotiana benthamiana is widely used as a model plant to study plant-pathogen interactions. Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating plant growth, development and response to abiotic stress. However, the members of FLAs in N. benthamiana and their response to plant pathogens are unknown.Results: 38 NbFLAs were identified from a genome-wide study. NbFLAs could be divided into four subclasses, and their gene structure and motif composition were conserved in each subclass. NbFLAs may be regulated by cis-acting elements such as STRE and MBS, and could possibly be the targets of transcription factors like C2H2. Quantitative real time polymerase chain reaction (RT-qPCR) results showed that selected NbFLAs were differentially expressed in different tissues. All of the selected NbFLAs were significantly downregulated following infection by turnip mosaic virus (TuMV) and most of them also by Pseudomonas syringae pv tomato (Pst) strain DC3000 (Pst DC3000), suggesting possible roles in response to pathogenic infection.Conclusions: This study systematically identified FLAs in N. benthamiana, and indicates their potential roles in response to biotic stress. The identification of NbFLAs will facilitate further studies of their role in plant immunity in N. benthamiana.

scholarly journals Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

2020 ◽  
Author(s):  
Xinyang Wu ◽  
Yuchao Lai ◽  
Lanqing Lv ◽  
Mengfei Ji ◽  
Kelei Han ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Nicotiana Benthamiana ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Arabinogalactan Proteins ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain ◽  
Plant Pathogen Interactions

Abstract Background: Nicotiana benthamiana is widely used as a model plant to study plant-pathogen interactions. Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating plant growth, development and response to abiotic stress. However, the members of FLAs in N. benthamiana and their response to plant pathogens are unknown.Results: 38 NbFLAs were identified from a genome-wide study. NbFLAs could be divided into four subclasses, and their gene structure and motif composition were conserved in each subclass. NbFLAs may be regulated by cis-acting elements such as STRE and MBS, and may be the targets of transcription factors like C2H2. Quantitative real time polymerase chain reaction (RT-qPCR) results showed that selected NbFLAs were differentially expressed in different tissues. All of the selected NbFLAs were significantly downregulated following infection by turnip mosaic virus (TuMV) and most of them also by Pseudomonas syringae pv tomato strain DC3000 (Pst DC3000), suggesting possible roles in response to pathogenic infection.Conclusions: This study systematically identified FLAs in N. benthamiana, and indicates their potential roles in response to biotic stress. The identification of NbFLAs will facilitate further studies of their role in plant immunity in N. benthamiana.

scholarly journals Transcriptome-wide identification and characterization of WD40 genes, as well as their tissue-specific expression profiles and responses to heat stress in Dimocarpus longan Lour.

2021 ◽  
Vol 49 (1) ◽  
pp. 12191
Author(s):  
Wei ZHENG ◽  
Ziwei ZHANG ◽  
Xuefei YU ◽  
Tongtong XIE ◽  
Ning CHEN ◽  
...  
Keyword(s):  
Heat Stress ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Flavonoid Biosynthesis ◽  
Functional Verification ◽  
Specific Expression ◽  
Cis Acting ◽  
Qrt Pcr

The WD40 transcription factor (TF) family is widespread in plants and plays important roles in plant growth and development, transcriptional regulation, and tolerance to abiotic stresses. WD40 TFs have been identified and characterized in a diverse series of plant species. However, little information is available on WD40 genes from D. longan. In this study, a total of 45 DlWD40 genes were identified from D. longan RNA-Seq data, and further analysed by bioinformatics tools. Also, the expression patterns of DlWD40 genes in roots and leaves, as well as responses to heat stress, were evaluated using quantitative real-time PCR (qRT-PCR). We found that the 45 DlWD40 proteins, together with 80 WD40 proteins from Arabidopsis and Zea mays, could be categorized into six groups. Of these, the DlWD40-4 protein was highly homologous to Arabidopsis WDR5a, a protein participating in tolerance to abiotic stresses. Moreover, a total of 25 cis-acting elements, such as abiotic stress and flavonoid biosynthesis elements, were found in the promoters of DlWD40 genes. The DlWD40-33 gene is targeted by miR3627, which has been proposed to be involved in flavonoid biosynthesis. Using qRT-PCR, ten of the 45 DlWD40 genes were demonstrated to have diverse expression patterns between roots and leaves, and these ten DlWD40 genes could also respond to varying durations of a 38 °C heat stress in roots and leaves. The results reported here will provide a basis for the further functional verification of DlWD40 genes in D. longan.

scholarly journals Study on the region-specific expression of epididymis mRNA in the rams

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245933
Author(s):  
Cuiling Wu ◽  
Chunxin Wang ◽  
Bo Zhai ◽  
Yunhui Zhao ◽  
Zhuo Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Sperm Maturation ◽  
Sequencing Technology ◽  
Specific Expression ◽  
Data Resource ◽  
Specific Expression Pattern ◽  
One Year

The epididymis is divided into three regions including the caput, corpus and cauda. Gene expression profiles in different regions indicate the different functions of epididymis which are crucial for sperm maturation. In this study, three one-year-old rams was used as the experimental animal. Transcriptome sequencing technology was used to sequence mRNA in the caput, corpus and cauda of the epididymis. Based on the spatiotemporal-specific expression pattern in the epididymis, the mRNA expression profiles of the three parts of the epididymis were analysed. Region-specifically expressed genes were analysed by GO and KEGG analyses to screen the key genes involved in sheep sperm maturation. We obtained 129, 54 and 99 specifically expressed genes in the caput, corpus and cauda, respectively. And twenty specific expressed genes related to sperm maturation were used to construct functional networks. The heatmap showed that 6 genes of LCN protein family were highly expressed in the head of epididymis of sheep. We infer that sperm maturation is gradual in the epididymis and that there are significant differences in epididymal gene expression patterns between different species. This provides a data resource for analysing the regulatory mechanism of epididymis genes related to sperm maturation in rams.

scholarly journals Genome-Wide Identification and Expression Profiling of the BZR Transcription Factor Gene Family in Nicotiana benthamiana

2021 ◽  
Vol 22 (19) ◽  
pp. 10379
Author(s):  
Xuwei Chen ◽  
Xinyang Wu ◽  
Shiyou Qiu ◽  
Hongying Zheng ◽  
Yuwen Lu ◽  
...  
Keyword(s):  
Stress Resistance ◽  
Nicotiana Benthamiana ◽  
Expression Patterns ◽  
Basic Research ◽  
Drought Treatment ◽  
Specific Expression ◽  
Cis Acting ◽  
Genome Wide ◽  
Organ Specific ◽  
Organ Specific Expression

Brassinazole-resistant (BZR) family genes encode plant-specific transcription factors (TFs), play essential roles in the regulation of plant growth and development, and have multiple stress-resistance functions. Nicotiana benthamiana is a model plant widely used in basic research. However, members of the BZR family in N. benthamiana have not been identified, and little is known about their function in abiotic stress. In this study, a total of 14 BZR members were identified in the N. benthamiana genome, which could be divided into four groups according to a phylogenetic tree. NbBZRs have similar exon-intron structures and conserved motifs, and may be regulated by cis-acting elements such as STRE, TCA, and ARE, etc. Organ-specific expression analysis showed that NbBZR members have different and diverse expression patterns in different tissues, and most of the members are expressed in roots, stems, and leaves. The analysis of the expression patterns in response to different abiotic stresses showed that all the tested NbBZR members showed a significant down-regulation after drought treatment. Many NbBZR genes also responded in various ways to cold, heat and salt stress treatments. The results imply that NbBZRs have multiple functions related to stress resistance.

scholarly journals Genome Wide Identification of Respiratory Burst Oxidase Homolog (Rboh) Genes in Citrus sinensis and Functional Analysis of CsRbohD in Cold Tolerance

2022 ◽  
Vol 23 (2) ◽  
pp. 648
Author(s):  
Yueliang Zhang ◽  
Yiwu Zhang ◽  
Li Luo ◽  
Chunyi Lu ◽  
Weiwen Kong ◽  
...  
Keyword(s):  
Cold Stress ◽  
Respiratory Burst ◽  
Citrus Sinensis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Microrna Target ◽  
Specific Expression ◽  
Cis Acting ◽  
Functional Studies ◽  
Respiratory Burst Oxidase

Respiratory burst oxidase homologs (Rbohs) are critical enzymes involved in the generation of reactive oxygen species (ROS) that play an important role in plant growth and development as well as various biotic and abiotic stresses in plants. Thus far, there have been few reports on the characterization of the Rboh gene family in Citrus. In this study, seven Rboh genes (CsRbohA~CsRbohG) were identified in the Citrus sinensis genome. The CsRboh proteins were predicted to localize to the cell membrane. Most CsRbohs contained four conserved domains, an EF-hand domain, and a transmembrane region. Phylogenetic analysis demonstrated that the CsRbohs were divided into five groups, suggesting potential distinct functions and evolution. The expression profiles revealed that these seven CsRboh genes displayed tissue-specific expression patterns, and five CsRboh genes were responsive to cold stress. Fourteen putative cis-acting elements related to stress response, hormone response, and development regulation were present within the promoters of CsRboh genes. The in-silico microRNA target transcript analyses indicated that CsRbohE might be targeted by csi-miR164. Further functional and physiological analyses showed that the knockdown of CsRbohD in trifoliate orange impaired resistance to cold stress. As a whole, our results provide valuable information for further functional studies of the CsRboh genes in response to cold stress.

scholarly journals Characterization of Interactions between the Soybean Salt-Stress Responsive Membrane-Intrinsic Proteins GmPIP1 and GmPIP2

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1312
Author(s):  
Jia Liu ◽  
Weicong Qi ◽  
Haiying Lu ◽  
Hongbo Shao ◽  
Dayong Zhang
Keyword(s):  
Plasma Membrane ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Early Gene ◽  
Plant Responses ◽  
Constitutive Overexpression ◽  
Important Trait

Salt tolerance is an important trait in soybean cultivation and breeding. Plant responses to salt stress include physiological and biochemical changes that affect the movement of water across the plasma membrane. Plasma membrane intrinsic proteins (PIPs) localize to the plasma membrane and regulate the water and solutes flow. In this study, quantitative real-time PCR and yeast two-hybridization were engaged to analyze the early gene expression profiles and interactions of a set of soybean PIPs (GmPIPs) in response to salt stress. A total of 20 GmPIPs-encoding genes had varied expression profiles after salt stress. Among them, 13 genes exhibited a downregulated expression pattern, including GmPIP1;6, the constitutive overexpression of which could improve soybean salt tolerance, and its close homologs GmPIP1;7 and 1;5. Three genes showed upregulated patterns, including the GmPIP1;6 close homolog GmPIP1;4, when four genes with earlier increased and then decreased expression patterns. GmPIP1;5 and GmPIP1;6 could both physically interact strongly with GmPIP2;2, GmPIP2;4, GmPIP2;6, GmPIP2;8, GmPIP2;9, GmPIP2;11, and GmPIP2;13. Definite interactions between GmPIP1;6 and GmPIP1;7 were detected and GmPIP2;9 performed homo-interaction. The interactions of GmPIP1;5 with GmPIP2;11 and 2;13, GmPIP1;6 with GmPIP2;9, 2;11 and GmPIP2;13, and GmPIP2;9 with itself were strengthened upon salt stress rather than osmotic stress. Taken together, we inferred that GmPIP1 type and GmPIP2 type could associate with each other to synergistically function in the plant cell; a salt-stress environment could promote part of their interactions. This result provided new clues to further understand the soybean PIP–isoform interactions, which lead to potentially functional homo- and heterotetramers for salt tolerance.

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