MYB
Transcriptional activator Myb (Proto-oncogene c-Myb)
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To better understand the molecular control of leaf senescence, we examined transcriptome changes during seasonal leaf senescence in Populus trichocarpa Nisqually-1, the Populus reference genome, growing in its natural habitat. Using monthly (from May to October) transcriptomes for three years (2009, 2015, and 2016), we identified 17,974 differentially expressed genes (DEGs; false discovery rate <0.05; log-fold change cutoff = 0) from 36,007 expressed Populus gene models. A total of 14,415 DEGs were directly related to transitions between four major developmental phases - growth, senescence initiation, reorganization, and senescence termination. These DEGs were significantly (p < 0.05) enriched in 279 gene ontology (GO) terms, including those related to photosynthesis, metabolic process, catalytic activity, protein phosphorylation, kinase activity, pollination, and transport. Also, there were 881 differentially expressed transcription factor (TF) genes from 54 TF families, notably bHLH, MYB, ERF, MYB-related, NAC, and WRKY. We also examined 28 DEGs known as alternative splicing (AS) factors that regulate AS process, and found evidence for a reduced level of AS activity during leaf senescence. Furthermore, we were able to identify a number of promoter sequence motifs associated with leaf senescence. This work provides a comprehensive resource for identification of genes involved in seasonal leaf senescence in trees, and informs efforts to explore the conservation and divergence of molecular mechanisms underlying leaf senescence between annual and perennial species.
MeSH Terms
- Aging
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Genome, Plant
- Photosynthesis
- Plant Leaves
- Populus
- Seasons
- Transcription Factors
- Transcriptome
The juvenile shoots of Phyllostachys edulis have been used as a food source for thousands of years, and it is recognized as a potential source of nutraceuticals. However, its rapid senescence restricts bamboo production and consumption, and the underlying molecular mechanisms of rapid shoot senescence remain largely unclear. In the present study, transcriptome profiling was employed to investigate the molecular regulation of postharvest senescence in shoots, along with physiological assays and anatomical dissections. Results revealed a distinct shift in expression postharvest, specifically transitions from cellular division and differentiation to the relocation of nutrients and programmed cell death. A number of regulatory and signaling factors were induced during postharvest senescence. Moreover, transcription factors, including NAM, ATAF and CUC (NAC) transcription factors, basic helix-loop-helix transcription factors, basic region/leucine zipper transcription factors, MYB transcription factors and WRKY transcription factors, were critical for shoot postharvest senescence, of which NACs were the most abundant. PheNAP2 and PheNAP3 were induced in postharvest shoots and found to promote leaf senescence in Arabidopsis by inducing the expression of AtSAG12 and AtSAG113. PheNAP2 and PheNAP3 could both restore the stay-green Arabidopsis nap to the wild-type phenotype either under normal growth condition or under abscisic acid treatment. Collectively, these results suggest that PheNAPs may promote shoot senescence. These findings provide a systematic view of shoot senescence and will inform future studies on the underlying molecular mechanisms responsible for shoot degradation during storage.
MeSH Terms
- Arabidopsis
- Arabidopsis Proteins
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Plant Leaves
- Transcriptome
Keywords
Phyllostachys edulis
- NAC
- postharvest
- regulatory factors
- shoot senescence
The MYB proteins represent a large family of transcription factors and play important roles in development, senescence, and stress responses in plants. In the current study, 233 MYB transcription factor-encoding genes were identified and analyzed in the potato genome, including 119 R1-MYB, 112 R2R3-MYB, and two R1R2R3-MYB members. R2R3-MYB is the most abundant MYB subclass and potato R2R3-MYB members together with their [i]Arabidopsis[/i] homologs were divided into 35 well-supported subgroups as the result of phylogenetic analyses. Analyses on gene structure and protein motif revealed that members from the same subgroup shared similar exon/intron and motif organization, further supporting the results of phylogenetic analyses. Evolution of the potato MYB family was studied via syntenic analysis. Forty-one pairs of [i]StMYB[/i] genes were predicted to have arisen from tandem or segmental duplication events, which played important roles in the expansion of the [i]StMYB[/i] family. Expression profiling revealed that the [i]StMYB[/i] genes were expressed in various tissues and several [i]StMYB[/i] genes were identified to be induced by different stress conditions. Notably, [i]StMYB030[/i] was found to act as the homolog of [i]AtMYB44[/i] and was significantly up-regulated by salt and drought stress treatments. Furthermore, overexpression of [i]StMYB030[/i] in [i]Arabidopsis[/i] enhanced salt stress tolerance of transgenic plants. The results from this study provided information for further functional analysis and for crop improvements through genetic manipulation of these [i]StMYB[/i] genes.
MeSH Terms
- Chromosome Duplication
- Chromosomes, Plant
- Models, Molecular
- Phylogeny
- Plant Proteins
- Promoter Regions, Genetic
- Protein Conformation
- Protein Transport
- Sequence Alignment
- Solanum tuberosum
- Stress, Physiological
- Synteny
- Transcription Factors
Keywords
- MYB
- abiotic stress
- biotic stress
- leaf senescence
- potato
Lonicera japonica Thunb. flower has been used for the treatment of various diseases for a long time and attracted many studies on its potential effects. Transcription factors (TFs) regulate extensive biological processes during plant development. As the restricted reports of L. japonica on TFs, our work was carried out to better understand the TFs' regulatory roles under different developmental stages in L. japonica. In this study, 1316 TFs belonging to 52 families were identified from the transcriptomic data, and corresponding expression profiles during the L. japonica flower development were comprehensively analyzed. 917 (69.68%) TFs were differentially expressed. TFs in bHLH, ERF, MYB, bZIP, and NAC families exhibited obviously altered expression during flower growth. Based on the analysis of differentially expressed TFs (DETFs), TFs in MYB, WRKY, NAC and LSD families that involved in phenylpropanoids biosynthesis, senescence processes and antioxidant activity were detected. The expression of MYB114 exhibited a positive correlation with the contents of luteoloside; Positive correlation was observed among the expression of MYC12, chalcone synthase (CHS) and flavonol synthase (FLS), while negative correlation was observed between the expression of MYB44 and the synthases; The expression of LSD1 was highly correlated with the expression of SOD and the total antioxidant capacity, while the expression of LOL1 and LOL2 exhibited a negative correlation with them; Many TFs in NAC and WRKY families may be potentially involved in the senescence process regulated by hormones and reactive oxygen species (ROS). The expression of NAC19, NAC29, and NAC53 exhibited a positive correlation with the contents of ABA and H O , while the expression of WRKY53, WRKY54, and WRKY70 exhibited a negative correlation with the contents of JA, SA and ABA. Our study provided a comprehensive characterization of the expression profiles of TFs during the developmental stages of L. japonica. In addition, we detected the key TFs that may play significant roles in controlling active components biosynthesis, antioxidant activity and flower senescence in L. japonica, thereby providing valuable insights into the molecular networks underlying L. japonica flower development.
MeSH Terms
- Chlorogenic Acid
- Chromatography, High Pressure Liquid
- Flowers
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Glucosides
- Hydrogen Peroxide
- Lonicera
- Luteolin
- Plant Proteins
- Sequence Analysis, DNA
- Transcription Factors
Keywords
- Flower development
- Hormone
- L.japonica
- Senescence
- Transcription factor
MYB-type transcription factors (TFs) play important roles in plant growth and development, and in the rapid responses to unfavorable environmental conditions. We recently reported the isolation and characterization of a rice (Oryza sativa) MYB TF, OsMYB102, which is involved in the regulation of leaf senescence by downregulating abscisic acid (ABA) biosynthesis and the downstream signaling response. Based on the similarities of their sequences and expression patterns, OsMYB102 appears to be a homolog of the Arabidopsis thaliana AtMYB44 TF. Since AtMYB44 is a key regulator of leaf senescence and abiotic stress responses, it is important to examine whether AtMYB44 homologs in other plants also act similarly. Here, we generated transgenic Arabidopsis plants expressing OsMYB102 (OsMYB102-OX). The OsMYB102-OX plants showed a delayed senescence phenotype during dark incubation and were more susceptible to salt and drought stresses, considerably similar to Arabidopsis plants overexpressing AtMYB44. Real-time quantitative PCR (RT-qPCR) revealed that, in addition to known senescence-associated genes, genes encoding the ABA catabolic enzymes AtCYP707A3 and AtCYP707A4 were also significantly upregulated in OsMYB102- OX, leading to a significant decrease in ABA accumulation. Furthermore, protoplast transient expression and chromatin immunoprecipitation assays revealed that OsMYB102 directly activated AtCYP707A3 expression. Based on our findings, it is probable that the regulatory functions of AtMYB44 homologs in plants are highly conserved and they have vital roles in leaf senescence and the abiotic stress responses. [BMB Reports 2019; 52(11): 653-658].
MeSH Terms
- Aging
- Arabidopsis
- Arabidopsis Proteins
- Droughts
- Gene Expression Regulation, Plant
- Oryza
- Plant Leaves
- Plants, Genetically Modified
- Signal Transduction
- Stress, Physiological
- Transcription Factors
Premature senescence can reduce the yield and quality of crops. WRKY transcription factors (TFs) play important roles during leaf senescence, but little is known about their ageing mechanisms in cotton. In this study, a group III WRKY TF, GhWRKY27, was isolated and characterized. The expression of GhWRKY27 was induced by leaf senescence and was higher in an early-ageing cotton variety than in a non-early-ageing cotton variety. Overexpression of GhWRKY27 in Arabidopsis promoted leaf senescence, as determined by reduced chlorophyll content and elevated expression of senescence-associated genes (SAGs). Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhWRKY27 interacted with an MYB TF, GhTT2. Putative target genes of GhWRKY27 were identified via chromatin immunoprecipitation followed by sequencing (ChIP-seq). Yeast one-hybrid (Y1H) assay and electrophoretic mobility shift assay (EMSA) revealed that GhWRKY27 binds directly to the promoters of cytochrome P450 94C1 (GhCYP94C1) and ripening-related protein 2 (GhRipen2-2). In addition, the expression patterns of GhTT2, GhCYP94C1 and GhRipen2-2 were identified during leaf senescence. Transient dual-luciferase reporter assay indicated that GhWRKY27 could activate the expression of GhCYP94C1 and GhRipen2-2. Our work lays the foundation for further study of the functional roles of WRKY genes during leaf senescence in cotton. In addition, our data provide new insights into the senescence-associated mechanisms of WRKY genes in cotton.
MeSH Terms
- Arabidopsis
- Binding Sites
- Chromatin Immunoprecipitation
- Electrophoretic Mobility Shift Assay
- Gene Expression Regulation, Plant
- Gossypium
- Plant Leaves
- Plant Proteins
- Plants, Genetically Modified
- Promoter Regions, Genetic
- Transcription Factors
- Two-Hybrid System Techniques
Keywords
- ChIP-seq
- Cotton
- GhWRKY27
- Leaf senescence
- SAGs
- Transcription factor
MYB-type transcription factors (TFs) play important roles in plant growth and development, and in the responses to several abiotic stresses. In rice (Oryza sativa), the roles of MYB-related TFs in leaf senescence are not well documented. Here, we examined rice MYB TF gene OsMYB102 and found that an OsMYB102 T-DNA activation-tagged line (termed osmyb102-D), which constitutively expresses OsMYB102 under the control of four tandem repeats of the 35S promoter, and OsMYB102-overexpressing transgenic lines (35S:OsMYB102 and 35S:GFP-OsMYB102) maintain green leaves much longer than the wild-type under natural, dark-induced, and abscisic acid (ABA)-induced senescence conditions. Moreover, an osmyb102 knockout mutant showed an accelerated senescence phenotype under dark-induced and ABA-induced leaf senescence conditions. Microarray analysis showed that a variety of senescence-associated genes (SAGs) were down-regulated in the osmyb102-D line. Further studies demonstrated that overexpression of OsMYB102 controls the expression of SAGs, including genes associated with ABA degradation and ABA signaling (OsABF4, OsNAP, and OsCYP707A6), under dark-induced senescence conditions. OsMYB102 inhibits ABA accumulation by directly activating the transcription of OsCYP707A6, which encodes the ABA catabolic enzyme ABSCISIC ACID 8'-HYDROXYLASE. OsMYB102 also indirectly represses ABA-responsive genes, such as OsABF4 and OsNAP. Collectively, these results demonstrate that OsMYB102 plays a critical role in leaf senescence by down-regulating ABA accumulation and ABA signaling responses.
MeSH Terms
- Abscisic Acid
- Oryza
- Plant Leaves
- Plant Proteins
- Signal Transduction
- Time Factors
- Transcription Factors
Keywords
OsCYP707A6
OsMYB102
- Abscisic acid
- chlorophyll degradation
- leaf senescence
- rice
- senescence-associated genes
- transcriptional regulation
Red clover ([i]Trifolium pratense[/i] L.) is an important cool-season legume plant, which is used as forage. Leaf senescence is a critical developmental process that negatively affects plant quality and yield. The regulatory mechanism of leaf senescence has been studied, and genes involved in leaf senescence have been cloned and characterized in many plants. However, those works mainly focused on model plants. Information about regulatory pathways and the genes involved in leaf senescence in red clover is very sparse. In this study, to better understand leaf senescence in red clover, transcriptome analysis of mature and senescent leaves was investigated using RNA-Seq. A total of about 35,067 genes were identified, and 481 genes were differentially expressed in mature and senescent leaves. Some identified differentially expressed genes showed similar expression patterns as those involved in leaf senescence in other species, such as Arabidopsis, [i]Medicago truncatula[/i] and rice. Differentially expressed genes were confirmed by quantitative real-time PCR (qRT-PCR). Genes involved in signal transduction, transportation and metabolism of plant hormones, transcription factors and plant senescence were upregulated, while the downregulated genes were primarily involved in nutrient cycling, lipid/carbohydrate metabolism, hormone response and other processes. There were 64 differentially expressed transcription factor genes identified by RNA-Seq, including ERF, WRKY, bHLH, MYB and NAC. A total of 90 genes involved in biosynthesis, metabolism and transduction of plant hormones, including abscisic acid, jasmonic acid, cyokinin, brassinosteroid, salicylic acid and ethylene, were identified. Furthermore, 207 genes with direct roles in leaf senescence were demonstrated, such as senescence-associated genes. These genes were associated with senescence in other plants. Transcriptome analysis of mature and senescent leaves in red clover provides a large number of differentially expressed genes. Further analysis and identification of senescence-associated genes can provide new insight into the regulatory mechanisms of leaf development and senescence in legume plant and red clover.
Keywords
- Early stage of leaf senescence
- RNA-Seq
- Red clover
- Senescence associated gene
The chloroplast relies on proteins encoded in the nucleus, synthesized in the cytosol and subsequently transported into chloroplast through the protein complexes Toc and Tic (Translocon at the outer/inner membrane of chloroplasts). A Tic complex member, Tic55, contains a redox-related motif essential for protein import into chloroplasts in peas. However, Tic55 is not crucial for protein import in [i]Arabidopsis[/i]. Here, a [i]tic55-II[/i]-knockout mutant of [i]Arabidopsis thaliana[/i] was characterized for Tic55 localization, its relationship with other translocon proteins, and its association with plant leaf senescence when compared to the wild type. Individually darkened leaves (IDLs) obtained through dark-induced leaf senescence were used to demonstrate chlorophyll breakdown and its relationship with plant senescence in the [i]tic55-II[/i]-knockout mutant. The IDLs of the [i]tic55-II[/i]-knockout mutant contained higher chlorophyll concentrations than those of the wild type. Our microarray analysis of IDLs during leaf senescence identified seven senescence-associated genes (SAGs) that were downregulated in the [i]tic55-II[/i]-knockout mutant: [i]ASP3[/i], [i]APG7[/i], [i]DIN2[/i], [i]DIN11[/i], [i]SAG12[/i], [i]SAG13[/i], and [i]YLS9[/i]. Real-time quantitative PCR confirmed the reliability of microarray analysis by showing the same expression patterns with those of the microarray data. Thus, Tic55 functions in dark-induced aging in [i]A. thaliana[/i] by indirectly regulating downstream SAGs expression. In addition, the expression of four NAC genes, including [i]ANAC003[/i], [i]ANAC010[/i], [i]ANAC042[/i], and [i]ANAC075[/i] of IDL treated [i]tic55-II[/i]-knockout mutant appeared to be downregulated. Yeast one hybrid assay revealed that only [i]ANAC003[/i] promoter region can be bound by MYB108, suggesting that a MYB-NAC regulatory network is involved in dark-stressed senescence.
MeSH Terms
- Amino Acid Sequence
- Arabidopsis
- Arabidopsis Proteins
- Cellular Senescence
- Chlorophyll
- Chloroplasts
- Darkness
- Gene Expression Regulation, Plant
- Gene Knockout Techniques
- Membrane Transport Proteins
- Phylogeny
- Plant Cells
- Plant Leaves
- Promoter Regions, Genetic
- Protein Binding
- Sequence Alignment
- Sequence Homology, Amino Acid
- Signal Transduction
- Transcription Factors
- Two-Hybrid System Techniques
Keywords
- ANAC proteins
- MYB108
- Tic55 proteins of chloroplasts
- dark-induced leaf senescence
Leaf senescence is a complex process, which has dramatic consequences on crop yield. In sunflower, gap between potential and actual yields reveals the economic impact of senescence. Indeed, sunflower plants are incapable of maintaining their green leaf area over sustained periods. This study characterizes the leaf senescence process in sunflower through a systems biology approach integrating transcriptomic and metabolomic analyses: plants being grown under both glasshouse and field conditions. Our results revealed a correspondence between profile changes detected at the molecular, biochemical and physiological level throughout the progression of leaf senescence measured at different plant developmental stages. Early metabolic changes were detected prior to anthesis and before the onset of the first senescence symptoms, with more pronounced changes observed when physiological and molecular variables were assessed under field conditions. During leaf development, photosynthetic activity and cell growth processes decreased, whereas sucrose, fatty acid, nucleotide and amino acid metabolisms increased. Pathways related to nutrient recycling processes were also up-regulated. Members of the NAC, AP2-EREBP, HB, bZIP and MYB transcription factor families showed high expression levels, and their expression level was highly correlated, suggesting their involvement in sunflower senescence. The results of this study thus contribute to the elucidation of the molecular mechanisms involved in the onset and progression of leaf senescence in sunflower leaves as well as to the identification of candidate genes involved in this process.
MeSH Terms
- Gas Chromatography-Mass Spectrometry
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Gene Ontology
- Genes, Plant
- Helianthus
- Ions
- Metabolomics
- Oligonucleotide Array Sequence Analysis
- Plant Leaves
- Principal Component Analysis
- RNA, Messenger
- Transcription Factors
Keywords
- candidate genes
- data integration
- leaf senescence
- metabolomics
- sunflower
- transcriptomics
Cellular senescence is a stable cell cycle arrest, caused by insults, such as: telomere erosion, oncogene activation, irradiation, DNA damage, oxidative stress, and viral infection. Extrinsic stimuli such as cell culture stress can also trigger this growth arrest. Senescence is thought to have evolved as an example of antagonistic pleiotropy, as it acts as a tumor suppressor mechanism during the reproductive age, but can promote organismal aging by disrupting tissue renewal, repair, and regeneration later in life. The mechanisms underlying the senescence growth arrest are broadly considered to involve p16(INK4A) -pRB and p53-p21(CIP1/WAF1/SDI1) tumor suppressor pathways; but it is not known what makes the senescence arrest stable and what the critical downstream targets are, as they are likely to be key to the establishment and maintenance of the senescent state. MYB-related protein B (B-MYB/MYBL2), a member of the myeloblastosis family of transcription factors, has recently emerged as a potential candidate for regulating entry into senescence. Here, we review the evidence which indicates that loss of B-MYB expression has an important role in causing senescence growth arrest. We discuss how B-MYB acts, as the gatekeeper, to coordinate transit through the cell cycle, in conjunction with the multivulval class B (MuvB) complex and FOXM1 transcription factors. We also evaluate the evidence connecting B-MYB to the mTOR nutrient signaling pathway and suggest that inhibition of this pathway leading to an extension of healthspan may involve activation of B-MYB.
MeSH Terms
- Aging
- Animals
- Cell Cycle Checkpoints
- Cell Proliferation
- Cellular Senescence
- Humans
- Proto-Oncogene Proteins c-myb
- Signal Transduction
Keywords
- B-MYB
- MuvB
- aging
- cellular senescence
- growth arrest
The transcriptomes of senescing flag leaves collected from barley field plots with standard or high nitrogen supply were compared to identify genes specifically associated with nitrogen remobilization during leaf senescence under agronomically relevant conditions. In flag leaves collected in field plots with high nitrogen supply, the decline in chlorophyll content was delayed. By comparing changes in gene expression for the two nitrogen levels, it was possible to discriminate genes related to nitrogen remobilization during senescence and genes involved in other processes associated with the late development of leaves under field conditions. Predominant genes that were more strongly upregulated during senescence of flag leaves from plants with standard nitrogen supply included genes encoding the transcription factor HvNAC026, serine type protease SCPL51, and the autophagy factors APG7 and ATG18F. Elevated expression of these genes in senescing leaves from plants with standard nitrogen supply indicates important roles of the corresponding proteins in nitrogen remobilization. In comparison, the genes upregulated in both flag leaf samples might have roles in general senescence processes associated with late leaf development. Among these genes were the transcription factor genes HvNAC001, HvNAC005, HvNAC013, HvWRKY12 and MYB, genes encoding the papain-like cysteine peptidases HvPAP14 and HvPAP20, as well as a subtilase gene.
MeSH Terms
- Gene Expression Regulation, Plant
- Genes, Plant
- Hordeum
- Nitrogen
- Oligonucleotide Array Sequence Analysis
- Plant Leaves
- Real-Time Polymerase Chain Reaction
Keywords
- Barley
- Hordeum vulgare L.
- HvNAC026.
- field experiment
- flag leaf
- leaf senescence
- nitrogen remobilization
- nitrogen supply