Global Characterization of XRN 5′-3′ Exoribonucleases and Their Responses to Environmental Stresses in Plants

The XRN family of 5′-3′ Exoribonucleases is functionally conserved in eukaryotic organisms. However, the molecular evolution of XRN proteins in plants and their functions in plant response to environment stresses remain largely unexplored. In this study, we identified 23 XRN proteins in 6 representative plant species. Polygenetic analysis revealed that XRN2 was Arabidopsis-specific among these species, and additional branches outside the clades of XRN3 and XRN4 proteins, which we named as XRN5, were found in rice, maize, and soybean. However, XRN5 in soybean lost their entire 5′-3′ XRN Exoribonuclease domain. Protein conserved sequence analysis showed that XRN3/XRN2 contained potential bipartite nuclear-localization signals (NLS) while all the XRN4 proteins lost their second KR/RR motif of NLS, potentially leading to their cytoplasm localization. SIXRN3-2 contained one mutation in this second KR/RR motif, which may change their sub-cellular localization. The promoter cis-element analysis indicated that these XRN genes responded to multiple stresses and plant hormones diversely at transcriptional level. Finally, transcriptomic analysis suggested that OsXRN3 and ZmXRN3-1 were induced by low temperature, SIXRN4 and ZmXRN4 was inhibited by heat shock, and OsXRN5 and GmXRN5-2 were repressed by drought. However, in general, the expression patterns revealed the response diversity of XRNs to environment stimuli in different plant species. Taken together, this study characterized 23 XRNs with NLS variation that contributed to their sub-cellular localization and provided an overview of the XRNs response diversity to multiple environmental stresses, suggesting that XRNs could be used as potential gene editing candidates for precise stress-tolerant crop breeding.

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Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

Author(s):

Chenghao Zhang ◽

Wenqi Dong ◽

Zong-an Huang ◽

MyeongCheoul Cho ◽

Qingcang Yu ◽

...

Keyword(s):

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Environmental Stresses ◽

Transcriptional Level ◽

Specific Expression ◽

Capsicum Annuum L ◽

Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories

BMC Plant Biology ◽

10.1186/s12870-021-03102-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Krista L. Plett ◽

Sean L. Bithell ◽

Adrian Dando ◽

Jonathan M. Plett

Keyword(s):

Nitrogen Fixation ◽

Disease Resistance ◽

Soil Nitrogen ◽

Cellular Localization ◽

Expression Patterns ◽

Nodule Development ◽

Nodule Formation ◽

Symbiotic Relationship ◽

Plant Genotype ◽

Factors Affecting

Abstract Background The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect this symbiotic relationship including abiotic conditions, plant genotype, and disruptions to host signalling/perception networks. In order to support improved nodule formation in chickpea, we investigated how plant genotype and soil nutrient availability affect chickpea nodule formation and nitrogen fixation. Further, using transcriptomic profiling, we sought to identify gene expression patterns that characterize highly nodulated genotypes. Results A study involving six chickpea varieties demonstrated large genotype by soil nitrogen interaction effects on nodulation and further identified agronomic traits of genotypes (such as shoot weight) associated with high nodulation. We broadened our scope to consider 29 varieties and breeding lines to examine the relationship between soilborne disease resistance and the number of nodules developed and real-time nitrogen fixation. Results of this larger study supported the earlier genotype specific findings, however, disease resistance did not explain differences in nodulation across genotypes. Transcriptional profiling of six chickpea genotypes indicates that genes associated with signalling, N transport and cellular localization, as opposed to genes associated with the classical nodulation pathway, are more likely to predict whether a given genotype will exhibit high levels of nodule formation. Conclusions This research identified a number of key abiotic and genetic factors affecting chickpea nodule development and nitrogen fixation. These findings indicate that an improved understanding of genotype-specific factors affecting chickpea nodule induction and function are key research areas necessary to improving the benefits of rhizobial symbiosis in chickpea.

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Poplar protease inhibitor expression differs in an herbivore specific manner

BMC Plant Biology ◽

10.1186/s12870-021-02936-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Franziska Eberl ◽

Thomas Fabisch ◽

Katrin Luck ◽

Tobias G. Köllner ◽

Heiko Vogel ◽

...

Keyword(s):

Protease Inhibitors ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Transcriptional Level ◽

Species Identity ◽

Defense Proteins ◽

Woody Perennials ◽

Cdna Sequences ◽

Black Poplar ◽

Leaf Area Loss

Abstract Background Protease inhibitors are defense proteins widely distributed in the plant kingdom. By reducing the activity of digestive enzymes in insect guts, they reduce the availability of nutrients and thus impair the growth and development of the attacking herbivore. One well-characterized class of protease inhibitors are Kunitz-type trypsin inhibitors (KTIs), which have been described in various plant species, including Populus spp. Long-lived woody perennials like poplar trees encounter a huge diversity of herbivores, but the specificity of tree defenses towards different herbivore species is hardly studied. We therefore aimed to investigate the induction of KTIs in black poplar (P. nigra) leaves upon herbivory by three different chewing herbivores, Lymantria dispar and Amata mogadorensis caterpillars, and Phratora vulgatissima beetles. Results We identified and generated full-length cDNA sequences of 17 KTIs that are upregulated upon herbivory in black poplar leaves, and analyzed the expression patterns of the eight most up-regulated KTIs via qRT-PCR. We found that beetles elicited higher transcriptional induction of KTIs than caterpillars, and that both caterpillar species induced similar KTI expression levels. Furthermore, KTI expression strongly correlated with the trypsin-inhibiting activity in the herbivore-damaged leaves, but was not dependent on damage severity, i.e. leaf area loss, for most of the genes. Conclusions We conclude that the induction of KTIs in black poplar is controlled at the transcriptional level in a threshold-based manner and is strongly influenced by the species identity of the herbivore. However, the underlying molecular mechanisms and ecological consequences of these patterns remain to be investigated.

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Gene expression patterns and protein cellular localization suggest a novel role for DAZL in developing Tibetan sheep testes

Gene ◽

10.1016/j.gene.2020.144335 ◽

2020 ◽

Vol 731 ◽

pp. 144335 ◽

Cited By ~ 2

Author(s):

Taotao Li ◽

Xia Wang ◽

Hongyu Zhang ◽

Haolin Chen ◽

Ningbo Liu ◽

...

Keyword(s):

Gene Expression ◽

Cellular Localization ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Tibetan Sheep

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The PSY Peptide Family—Expression, Modification and Physiological Implications

Genes ◽

10.3390/genes12020218 ◽

2021 ◽

Vol 12 (2) ◽

pp. 218

Author(s):

Amalie Scheel Tost ◽

Astrid Kristensen ◽

Lene Irene Olsen ◽

Kristian Buhl Axelsen ◽

Anja Thoe Fuglsang

Keyword(s):

Plant Development ◽

Higher Plants ◽

Expression Patterns ◽

Transcriptional Level ◽

Amino Acid Peptide ◽

Developmental Factors ◽

Peptide Family ◽

The Family ◽

Modified Peptides ◽

High Conservation

Small post-translationally modified peptides are gaining increasing attention as important signaling molecules in plant development. In the family of plant peptides containing tyrosine sulfation (PSYs), only PSY1 has been characterized at the mature level as an 18-amino-acid peptide, carrying one sulfated tyrosine, and involved in cell elongation. This review presents seven additional homologs in Arabidopsis all sharing high conservation in the active peptide domain, and it shows that PSY peptides are found in all higher plants and mosses. It is proposed that all eight PSY homologs are post-translationally modified to carry a sulfated tyrosine and that subtilisin-like subtilases (SBTs) are involved in the processing of PSY propeptides. The PSY peptides show differential expression patterns indicating that they serve several distinct functions in plant development. PSY peptides seem to be at least partly regulated at the transcriptional level, as their expression is greatly influenced by developmental factors. Finally, a model including a receptor in addition to PSY1R is proposed.

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Epigenomics of Plant’s Responses to Environmental Stress

10.20944/preprints201710.0185.v2 ◽

2017 ◽

Author(s):

Suresh Kumar

Keyword(s):

Gene Expression ◽

Nuclear Dna ◽

Environmental Stresses ◽

Transcriptional Level ◽

Epigenetic Changes ◽

Post Translational Modifications ◽

Genome Wide ◽

A Cell ◽

Non Coding Rnas ◽

Function Activity

Genome-wide epigenetic changes in plants are being reported during the development and environmental stresses, which are often correlated with gene expression at the transcriptional level. Sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding RNAs in a cell is known as epigenome. These changes are often responsible for variation in expression of the gene without any change in the underlying nucleotide sequence. The changes might also cause variation in chromatin structure resulting into the changes in function/activity of the genome. The epigenomic changes are dynamic with respect to the endogenous and/or environmental stimuli which affect phenotypic plasticity of the organism. Both, the epigenetic changes and variation in gene expression might return to the pre-stress state soon after withdrawal of the stress. However, a part of the epigenetic changes may be retained which is reported to play role in acclimatization, adaptation as well as in the evolutionary processes. Understanding epigenome-engineering for improved stress tolerance in plants has become essential for better utilization of the genetic factors. This review delineates the importance of epigenomics towards possible improvement of plant’s responses to environmental stresses for climate resilient agriculture.

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Expression Patterns of ACS and ACO Gene Families and Ethylene Production in Rachis and Berry of Grapes

HortScience ◽

10.21273/hortsci11050-16 ◽

2017 ◽

Vol 52 (3) ◽

pp. 413-422 ◽

Cited By ~ 2

Author(s):

Xia Ye ◽

Xianbo Zheng ◽

Dehua Zhai ◽

Wen Song ◽

Bin Tan ◽

...

Keyword(s):

Ethylene Production ◽

Expression Patterns ◽

Acc Oxidase ◽

Gene Families ◽

Stress Factors ◽

Transcriptional Level ◽

Berry Development ◽

Thompson Seedless ◽

Expression Levels ◽

Ethephon Treatment

Ethylene is important during the berry development and in the last stages of rachis development or rachis senescence. Since grapes develop in a cluster that comprises both the fruit berry and the nonfruit rachis, we measured the release of ethylene from both tissues. Detached berries from Vitis vinifera ‘Ruby Seedless’ and ‘Thompson Seedless’ showed that ethylene release peaks at the beginning of berry development and at veraison. Ethylene production in the rachis was higher than that in the berry and had an obvious peak before harvest in ‘Thompson Seedless’. In both cultivars, ethephon treatment induced ethylene production in the rachis but not in the berry. Expression of 1-aminocyclopropane-1-carboxylate (ACC) synthase (ACS) and ACC oxidase (ACO) genes showed diverse temporal and spatial patterns in ‘Thompson Seedless’ and ‘Ruby Seedless’. For most gene family members, the low ACS expression levels were observed in berry and rachis. Expression levels of most of the ACS and ACO genes did not correlate with ethylene released in the same organ. The transcriptional level of VvACS1 did correlate with ethylene evolution in rachis of ‘Thompson Seedless’ during berry development and storage, which suggested that VvACS1 may have important roles in rachis senescence. In berries of ‘Thompson Seedless’ and ‘Ruby Seedless’, the transcriptional levels of VvACO1, VvACS2, and VvACS6 coincided with ethylene production, indicating possible roles in berry development. Expression of VvACS2–VvACO9 and VvACO1–VvACO3 was not consistent with ethylene production during storage or in response to ethephon treatment, which suggests that the expression of ACS and ACO was affected by other stress factors after harvest.

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Genome-Wide Identification and Functional Analysis of Chitinase Gene Family in Grape

10.21203/rs.2.22693/v1 ◽

2020 ◽

Author(s):

Ting Zheng ◽

Kekun Zhang ◽

Xudong Zhu ◽

Songtao Jiu ◽

Tianyu Dong ◽

...

Keyword(s):

Gene Family ◽

Fungal Pathogens ◽

Expression Patterns ◽

Hydrolytic Enzymes ◽

Bimolecular Fluorescence Complementation ◽

Microarray Data Analysis ◽

Growth Stages ◽

Transcriptional Level ◽

Fungal Cell ◽

Conserved Domains

Abstract Background: Chitinases, the important resistance-related proteins, are crucial hydrolytic enzymes, which attack fungal pathogens by catalyzing the fungal cell wall degradation. As a large gene family, the VvChis have not been systematically analyzed and effectively investigated in grape. Results: In this study, we identified 42 VvChis in grape by searching the conserved domains, and divided them into A, B, C, D and E groups according to pylogenetic relationships, gene structure and conserved domains analysis. Quantitative real-time PCR (qRT-PCR) and publicly microarray data analysis revealed distinct temporal and spatial expression patterns of VvChis in different tissues at various growth stages. The transcriptional level of most genes was high in the root of ‘Koyho’ and ‘Summer Black’. Combining cis-elements in the promoter, GO and KEGG analysis, and prediction of interaction proteins, we revealed the function of Chitinase. After the pathogen infecting the leaves and berries of grape, the expression levels of VvChis in A, B and E groups showed a significant upward trend, of which VvChi5, VvChi25, VvChi11 (leaf) and VvChi16 (fruit) were the most up-regulated. The interaction between Chi-17 and Metallothionein (MTL) was confirmed by yeast two-hybrid system and bimolecular fluorescence complementation (BiFC). In addition, VvChis in GH18 family were up-regulated under MeJA and ETH treatment, in particular to 500 mg·L -1 ETH、50 μmol·L -1 MeJA; The induction of VvChis by low temperature was more significant than that of high temperature; The expression of VvChis was positively correlated with the concentration of NaCl treatment. Conclusion: This study clarified the member composition and expression pattern of VvChi family in grape, initially explored the disease resistance function of VvChi, and analyzed the response of VvChis to hormones (MeJA and ETH) and environmental stress (temperature and NaCl) signals was analyzed, which laid a foundation for constructing the functional regulation network of VvChi in grapes.

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Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽

10.3390/f11030315 ◽

2020 ◽

Vol 11 (3) ◽

pp. 315

Author(s):

Hanzeng Wang ◽

Xue Leng ◽

Xuemei Xu ◽

Chenghao Li

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Expression Profiles ◽

Populus Trichocarpa ◽

Expression Patterns ◽

Interaction Network ◽

Pcr Analysis ◽

Phylogenetic Tree Analysis ◽

Element Analysis ◽

Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

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Multiple Regulatory Domains of IRF-5 Control Activation, Cellular Localization, and Induction of Chemokines That Mediate Recruitment of T Lymphocytes

Molecular and Cellular Biology ◽

10.1128/mcb.22.16.5721-5740.2002 ◽

2002 ◽

Vol 22 (16) ◽

pp. 5721-5740 ◽

Cited By ~ 192

Author(s):

Betsy J. Barnes ◽

Merrill J. Kellum ◽

Ann E. Field ◽

Paula M. Pitha

Keyword(s):

Cellular Localization ◽

Target Genes ◽

Nuclear Translocation ◽

Transient Transfection Assay ◽

Nuclear Localization Signals ◽

Regulatory Domains ◽

Inflammatory Protein ◽

Infected Cells ◽

Simplex Virus ◽

And Function

ABSTRACT Transcription factors of the interferon regulatory factor (IRF) family have been identified as critical mediators of early inflammatory gene transcription in infected cells. We recently determined that, besides IRF-3 and IRF-7, IRF-5 serves as a direct transducer of virus-mediated signaling. In contrast to that mediated by the other two IRFs, IRF-5-mediated activation is virus specific. We show that, in addition to Newcastle disease virus (NDV) infection, vesicular stomatitis virus (VSV) and herpes simplex virus type 1 (HSV-1) infection activates IRF-5, leading to the induction of IFNA gene subtypes that are distinct from subtypes induced by NDV. The IRF-5-mediated stimulation of inflammatory genes is not limited to IFNA since in BJAB/IRF-5-expressing cells IRF-5 stimulates transcription of RANTES, macrophage inflammatory protein 1β, monocyte chemotactic protein 1, interleukin-8, and I-309 genes in a virus-specific manner. By transient- transfection assay, we identified constitutive-activation (amino acids [aa] 410 to 489) and autoinhibitory (aa 490 to 539) domains in the IRF-5 polypeptide. We identified functional nuclear localization signals (NLS) in the amino and carboxyl termini of IRF-5 and showed that both of these NLS are sufficient for nuclear translocation and retention in infected cells. Furthermore, we demonstrated that serine residues 477 and 480 play critical roles in the response to NDV infection. Mutation of these residues from serine to alanine dramatically decreased phosphorylation and resulted in a substantial loss of IRF-5 transactivation in infected cells. Thus, this study defines the regulatory phosphorylation sites that control the activity of IRF-5 in NDV-infected cells and provides further insight into the structure and function of IRF-5. It also shows that the range of IRF-5 immunoregulatory target genes includes members of the cytokine and chemokine superfamilies.

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