Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

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Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

International Journal of Molecular Sciences ◽

10.3390/ijms21186594 ◽

2020 ◽

Vol 21 (18) ◽

pp. 6594

Author(s):

Shuting Zhang ◽

Qin Zhou ◽

Feng Chen ◽

Lan Wu ◽

Baojun Liu ◽

...

Keyword(s):

Transcription Factors ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Leaf Morphogenesis ◽

Systematic Analysis ◽

Genome Wide ◽

A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

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Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

10.21203/rs.3.rs-53464/v1 ◽

2020 ◽

Author(s):

Songfeng Diao ◽

Hong Liu ◽

Zhongrui Lv ◽

Caiyun He ◽

Aiguo Duan ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Gene Families ◽

Sea Buckthorn ◽

Bhlh Transcription Factor ◽

Systematic Analysis ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Genome Wide ◽

A Genome

Abstract Background The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, organ development, and stress responses. However, limited studies are available on the gene family in sea buckthorn. Results In this study, we focused on 144 HrbHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 15 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 108 HrbHLH genes that expressed in five sea buckthorn tissue, including root nodule, root, leaf, stem and fruit. Furthermore, we found 11 increased expressed HrbHLH genes during sea buckthorn fruit development. We validated the expression pattern of HrbHLH genes using reverse transcription quantitative real-time PCR. Conclusions This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms. We performed a genome-wide, systematic analysis of bHLH proteins in sea buckthorn. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs.

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Research progress of NPR genes in signal pathway of salicylic acid mediated plant disease resistance

E3S Web of Conferences ◽

10.1051/e3sconf/202014501038 ◽

2020 ◽

Vol 145 ◽

pp. 01038

Author(s):

Pan Wang ◽

Meiqin Xiang

Keyword(s):

Salicylic Acid ◽

Disease Resistance ◽

Plant Disease Resistance ◽

Plant Disease ◽

Systemic Acquired Resistance ◽

Acquired Resistance ◽

Signal Transduction Pathway ◽

Research Progress ◽

Signal Molecule ◽

Pathogenesis Related

Salicylic acid (SA) is considered to be an endogenous signal molecule in plants, and it is related to many resistances in plants. In Arabidopsis, Non-expressor of pathogenesis-related gene1 (NPR1) mediates the expression of pathogenesis-related genes (PRs) and systemic acquired resistance (SAR) induced by SA. NPR1 is a key factor in SA signaling pathway, and the research shows that NPR1, NPR3 and NPR4 play a key role in SA mediated plant disease resistance. In this review, the interaction between NPR and transcription factors is discussed, and we also describe the progress of NPR in SA mediated SAR signal transduction pathway, likewise, we introduce the relationship between NPR1 and its paralogues NPR3/NPR4. This paper analyzes the research prospect of NPR as the intersection of multiple signal paths.

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Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

PeerJ ◽

10.7717/peerj.8358 ◽

2020 ◽

Vol 8 ◽

pp. e8358 ◽

Cited By ~ 2

Author(s):

Yong Zhou ◽

Yuan Cheng ◽

Chunpeng Wan ◽

Jingwen Li ◽

Youxin Yang ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Patterns ◽

Future Research ◽

Promoter Regions ◽

Syntenic Relationship ◽

Specific Expression ◽

Qrt Pcr ◽

Genome Wide ◽

Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

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Genome-Wide Investigation of the ZF-HD Gene Family in Two Varieties of Alfalfa (Medicago sativa L.) and Its Expression Pattern Under Alkaline Stress

10.21203/rs.3.rs-911266/v1 ◽

2021 ◽

Author(s):

Kai He ◽

Chunxin Li ◽

ZhenYue Zhang ◽

Lifeng Zhan ◽

Chunlong Cong ◽

...

Keyword(s):

Stress Response ◽

Gene Family ◽

Stress Responses ◽

Growth Regulation ◽

Biological Information ◽

Functional Study ◽

Alkaline Stress ◽

Genome Wide ◽

The Difference ◽

Genome Level

Abstract Background:Zinc finger homeodomain (ZHD) protein is a plant-specific transcription factor and a potential regulator of phosphoenolpyruvate carboxylase (PEPCase)-coding genes, and it also participates in plant growth regulation and abiotic stress responses. To study the function of MsZF-HD genes in the alkaline stress response, this paper assessed biological information and performed transcriptome analyses of the MsZF-HD gene family by using the genomes of two different varieties of alfalfa (XinJiangDa Ye and Zhongmu No. 1). Results:In total, 49 and 11 MsZF-HD genes were identified in these varieties, respectively, including the alleles of XinJiangDa Ye. According to their phylogenetic relationships, the 60 MsZF-HD genes were divided into 5 ZHD subfamilies and 1 MIF subfamily. A total of 88.3% of MsZF-HD genes do not contain introns and are unevenly distributed among the 6 chromosomes of alfalfa. A collinearity analysis indicated that 26 genes of XinJiangDa Ye have no orthologous genes in Zhongmu No. 1, although these genes (such as ZHD-X1–2, ZHD-X3–2 and ZHD-X4–2) have homologous genes in Arabidopsis thaliana, Medicago truncatula and Glycine max. Through RNA-seq and qRT–PCR verification, it was found that MsZF-HD genes are downregulated to participate in the alkaline stress response. Conclusion:The results of this study may lay the foundation for the cloning and functional study of MsZF-HD genes and provide a theoretical basis for revealing the difference between XinJiangDa Ye and Zhongmu No. 1 at the genome level.

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Overexpression of (At)NPR1 in Rice Leads to a BTH- and Environment-Induced Lesion-Mimic/Cell Death Phenotype

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2004.17.2.140 ◽

2004 ◽

Vol 17 (2) ◽

pp. 140-151 ◽

Cited By ~ 134

Author(s):

Heather A. Fitzgerald ◽

Maw-Sheng Chern ◽

Roy Navarre ◽

Pamela C. Ronald

Keyword(s):

Cell Death ◽

Broad Spectrum ◽

Stress Responses ◽

Systemic Acquired Resistance ◽

Plant Stress ◽

Acquired Resistance ◽

Bacterial Pathogen ◽

Lesion Mimic ◽

Pathogenesis Related ◽

Plant Stress Responses

Systemic acquired resistance (SAR) is an inducible defense response that protects plants against a broad spectrum of pathogens. A central regulator of SAR in Arabidopsis is NPR1 (nonexpresser of pathogenesis-related genes). In rice, overexpression of Arabidopsis NPR1 enhances plant resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae. This report demonstrates that overexpression of (At)NPR1 in rice also triggers a lesion-mimic/cell death (LMD) phenotype. The LMD phenotype is environmentally regulated and heritable. In addition, the development of lesions and death correlates with the expression of rice defense genes and the accumulation of hydrogen peroxide. Application of the salicylic acid (SA) analog, benzo(1,2,3) thiadiazole-7-carbothioc acid S-methyl ester (BTH), potentiates this phenotype. Endogenous SA levels are reduced in rice overexpressing (At)NPR1 when compared with wild-type plants, supporting the idea that (At)NPR1 may perceive and modulate the accumulation of SA. The association of (At)NPR1 expression in rice with the development of an LMD phenotype suggests that (At)NPR1 has multiple roles in plant stress responses that may affect its efficacy as a transgenic tool for engineering broad-spectrum resistance.

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Molecular and functional analysis of new members of the wheat PR4 gene family

Biological Chemistry ◽

10.1515/bc.2006.136 ◽

2006 ◽

Vol 387 (8) ◽

pp. 1101-1111 ◽

Cited By ~ 15

Author(s):

Laura Bertini ◽

Annunziata Cascone ◽

Marina Tucci ◽

Rosalinda D'Amore ◽

Iris Di Berardino ◽

...

Keyword(s):

Gene Family ◽

Systemic Acquired Resistance ◽

Expression Patterns ◽

Acquired Resistance ◽

Plant Defence ◽

Untranslated Regions ◽

High Sequence Identity ◽

New Members ◽

New Genes ◽

Pathogenesis Related

Abstract Five new genes belonging to the pathogenesis-related (PR) 4 family have been cloned and characterised in Triticum aestivum. Two full-length genes, named wPR4e and wPR4f-b, were isolated by library screening, demonstrating the presence of a small intron only in wPR4f-b. Two other PR4 genes (wPR4f-a and wPR4f-c) were isolated by PCR, showing very high sequence identity with wPR4f-b and constituting a new sub-family. Transcription start analysis was performed by RLM-RACE, leading to the isolation of a fifth gene, named wPR4g, that is highly homologous to wPR4e; both encode putative vacuolar PR4 proteins (Wheatwin7 and Wheatwin5, respectively). wPR4e and wPR4f sub-family genes are induced by F. culmorum infection, by chemicals that lead to systemic acquired resistance and by wounding, showing different spatial and temporal induction pathways. In silico analysis of the 5′ untranslated regions of wPR4e and wPR4f-b revealed the presence of several abiotic and biotic stress-responsive elements. wPR4e and wPR4f-b putative promoters were fused to the β-glucuronidase (GUS) reporter gene, and transient and stable expression assays demonstrated that both are able to drive expression of GUS. Characterisation of these new PR4 genes and particularly of their 5′ untranslated regions, as well as the determination of their expression patterns, will contribute to our understanding of the responsiveness of this gene family to various stress conditions and of its role in plant defence.

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Spatial and temporal regulation of biosynthesis of the plant immune signal salicylic acid

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1511182112 ◽

2015 ◽

Vol 112 (30) ◽

pp. 9166-9173 ◽

Cited By ~ 94

Author(s):

Xiao-yu Zheng ◽

Mian Zhou ◽

Heejin Yoo ◽

Jose L. Pruneda-Paz ◽

Natalie Weaver Spivey ◽

...

Keyword(s):

Salicylic Acid ◽

Systemic Acquired Resistance ◽

Acquired Resistance ◽

Signal Transduction Pathway ◽

Temporal Regulation ◽

Calmodulin Binding ◽

Regulation Of Biosynthesis ◽

Pathogen Entry ◽

Transcription Activators ◽

Transcriptional Induction

The plant hormone salicylic acid (SA) is essential for local defense and systemic acquired resistance (SAR). When plants, such as Arabidopsis, are challenged by different pathogens, an increase in SA biosynthesis generally occurs through transcriptional induction of the key synthetic enzyme isochorismate synthase 1 (ICS1). However, the regulatory mechanism for this induction is poorly understood. Using a yeast one-hybrid screen, we identified two transcription factors (TFs), NTM1-LIKE 9 (NTL9) and CCA1 HIKING EXPEDITION (CHE), as activators of ICS1 during specific immune responses. NTL9 is essential for inducing ICS1 and two other SA synthesis-related genes, PHYTOALEXIN-DEFICIENT 4 (PAD4) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), in guard cells that form stomata. Stomata can quickly close upon challenge to block pathogen entry. This stomatal immunity requires ICS1 and the SA signaling pathway. In the ntl9 mutant, this response is defective and can be rescued by exogenous application of SA, indicating that NTL9-mediated SA synthesis is essential for stomatal immunity. CHE, the second identified TF, is a central circadian clock oscillator and is required not only for the daily oscillation in SA levels but also for the pathogen-induced SA synthesis in systemic tissues during SAR. CHE may also regulate ICS1 through the known transcription activators CALMODULIN BINDING PROTEIN 60g (CBP60g) and SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1) because induction of these TF genes is compromised in the che-2 mutant. Our study shows that SA biosynthesis is regulated by multiple TFs in a spatial and temporal manner and therefore fills a gap in the signal transduction pathway between pathogen recognition and SA production.

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Systemic Acquired Resistance in Canola Is Linked with Pathogenesis-Related Gene Expression and Requires Salicylic Acid

Phytopathology ◽

10.1094/phyto-97-7-0794 ◽

2007 ◽

Vol 97 (7) ◽

pp. 794-802 ◽

Cited By ~ 29

Author(s):

Shobha D. Potlakayala ◽

Darwin W. Reed ◽

Patrick S. Covello ◽

Pierre R. Fobert

Keyword(s):

Salicylic Acid ◽

Pseudomonas Syringae ◽

Systemic Acquired Resistance ◽

Induced Defense ◽

Acquired Resistance ◽

Microbial Pathogens ◽

Broad Host Range ◽

Avirulent Strain ◽

Enhanced Resistance ◽

Pathogenesis Related

Systemic acquired resistance (SAR) is an induced defense response that confers long-lasting protection against a broad range of microbial pathogens. Here we show that treatment of Brassica napus plants with the SAR-inducing chemical benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) significantly enhanced resistance against virulent strains of the bacterial pathogen Pseudomonas syringae pv. maculicola and the fungal pathogen Leptosphaeria maculans. Localized preinoculation of plants with an avirulent strain of P. syringae pv. maculicola also enhanced resistance to these pathogens but was not as effective as BTH treatment. Single applications of either SAR-inducing pretreatment were effective against P. syringae pv. maculicola, even when given more than 3 weeks prior to the secondary challenge. The pretreatments also led to the accumulation of pathogenesis-related (PR) genes, including BnPR-1 and BnPR-2, with higher levels of transcripts observed in the BTH-treatment material. B. napus plants expressing a bacterial salicylate hydroxylase transgene (NahG) that metabolizes salicylic acid to catechol were substantially compromised in SAR and accumulated reduced levels of PR gene transcripts when compared with untransformed controls. Thus, SAR in B. napus displays many of the hallmarks of classical SAR including long lasting and broad host range resistance, association with PR gene activation, and a requirement for salicylic acid.

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