Isolation and RNA gel blot analysis of genes that could serve as potential molecular markers for leaf senescence in Arabidopsis thaliana

MYB3R-mediated and cell cycle-dependent transcriptional regulation of a tobacco ortholog of SCARECROW-LIKE28 in synchronized cultures of BY-2 cells

Although it is well known that hierarchical transcriptional networks are essential for various aspects of plant development and environmental response, little has been investigated about whether and how they also regulate the plant cell cycle. Recent studies on cell cycle regulation in Arabidopsis thaliana identified SCARECROW-LIKE28 (SCL28), a GRAS-type transcription factor, that constitutes a hierarchical transcriptional pathway comprised of MYB3R, SCL28 and SIAMESE-RELATED (SMR). In this pathway, MYB3R family proteins regulate the G2/M-specific transcription of the SCL28 gene, of which products, in turn, positively regulate the transcription of SMR genes encoding a group of plant-specific inhibitor proteins of cyclin-dependent kinases. However, this pathway with a role in cell cycle inhibition is solely demonstrated in A. thaliana, thus leaving open the question of whether and to what extent this pathway is evolutionarily conserved in plants. In this study, we conducted differential display RT-PCR on synchronized Nicotiana tabacum (tobacco) BY-2 cells and identified several M-phase-specific cDNA clones, one of which turned out to be a tobacco ortholog of SCL28 and was designated NtSCL28. We showed that NtSCL28 is expressed specifically during G2/M and early G1 in the synchronized cultures of BY-2 cells. NtSCL28 contains MYB3R-binding promoter elements, so-called mitosis-specific activator elements, and is upregulated by a hyperactive form of NtmybA2, one of the MYB3R proteins from tobacco. Our study indicated that a part of the hierarchical pathway identified in A. thaliana is equally operating in tobacco cells, suggesting the conservation of this pathway across different families in evolution of angiosperm.

Gene co-expression network analysis for the selection of candidate early warning indicators of heat and nutrient stress in Posidonia oceanica

The continuous worldwide seagrasses decline calls for immediate actions in order to preserve this precious marine ecosystem. The main stressors that have been linked with decline in seagrasses are 1) the increasing ocean temperature due to climate change and 2) the continuous inputs of nutrients (eutrophication) associated with coastal human activities. To avoid the loss of seagrass populations, an "early warning" system is needed. We used Weighed Gene Co-expression Network Analysis (WGCNA), a systems biology approach, to identify potential candidate genes that can provide an early warning signal of stress in the Mediterranean iconic seagrass Posidonia oceanica, anticipating plant mortality. Plants were collected from both eutrophic (EU) and oligotrophic (OL) environments and were exposed to thermal and nutrient stress in a dedicated mesocosm. By correlating the whole-genome gene expression after 2-weeks exposure with the shoot survival percentage after 5-weeks exposure to stressors, we were able to identify several transcripts that indicated an early activation of several biological processes (BP) including: protein metabolic process, RNA metabolic process, organonitrogen compound biosynthetic process, catabolic process and response to stimulus, which were shared among OL and EU plants and among leaf and shoot apical meristem (SAM), in response to excessive heat and nutrients. Our results suggest a more dynamic and specific response of the SAM compared to the leaf, especially the SAM from plants coming from a stressful environment appeared more dynamic than the SAM from a pristine environment. A vast list of potential molecular markers is also provided that can be used as targets to assess field samples.

Cryptochromes suppress leaf senescence in response to blue light in Arabidopsis

The induction and progression of leaf senescence are effectively changed according to the light environment. The leaf senescence response is enhanced when plants are grown under a dense shade cast by neighboring vegetation. Although the fluence rate of the red and blue regions in the light spectrum is strongly attenuated under shade, photosensory mechanisms that underpin the blue light response are still unclear. In this study, we analyzed leaf senescence in response to blue light in Arabidopsis (Arabidopsis thaliana). We found that leaf senescence was promoted by the elimination of active phytochrome Pfr by pulsed far-red (FR) light, whereas irradiation with blue light suppressed leaf senescence in the wild type but not in the cryptochrome (CRY)-deficient mutant, cry1 cry2. Hence, two light-sensing modes contributed to the suppression of leaf senescence that was dependent on light spectrum features. First was the leaf senescence response to blue light, which was mediated exclusively by cryptochromes. Second was the phytochrome-mediated leaf senescence response to red/FR light. Physiological analysis of transgenic plants expressing green fluorescent protein (GFP)-tagged CRY2 revealed that photo-activation of cryptochromes was required to suppress leaf senescence in response to blue light. Transcriptomic analysis further uncovered the molecular and cellular processes involved in the regulation of leaf senescence downstream of cryptochromes. Furthermore, analysis of cryptochrome-downstream components indicated that ELONGATED HYPOCOTYL 5 (HY5) and PHYTOCHROME INTERACTING FACTOR (PIF) 4 and PIF5 were required for suppression and promotion of leaf senescence, respectively.

I Choose You: Selecting Accurate Reference Genes for qPCR Expression Analysis in Reproductive Tissues in Arabidopsis thaliana

Quantitative real-time polymerase chain reaction (qPCR) is a widely used method to analyse the gene expression pattern in the reproductive tissues along with detecting gene levels in mutant backgrounds. This technique requires stable reference genes to normalise the expression level of target genes. Nonetheless, a considerable number of publications continue to present qPCR results normalised to a single reference gene and, to our knowledge, no comparative evaluation of multiple reference genes has been carried out in specific reproductive tissues of Arabidopsis thaliana. Herein, we assessed the expression stability levels of ten candidate reference genes (UBC9, ACT7, GAPC-2, RCE1, PP2AA3, TUA2, SAC52, YLS8, SAMDC and HIS3.3) in two conditional sets: one across flower development and the other using inflorescences from different genotypes. The stability analysis was performed using the RefFinder tool, which combines four statistical algorithms (geNorm, NormFinder, BestKeeper and the comparative ΔCt method). Our results showed that RCE1, SAC52 and TUA2 had the most stable expression in different flower developmental stages while YLS8, HIS3.3 and ACT7 were the top-ranking reference genes for normalisation in mutant studies. Furthermore, we validated our results by analysing the expression pattern of genes involved in reproduction and examining the expression of these genes in published mutant backgrounds. Overall, we provided a pool of appropriate reference genes for expression studies in reproductive tissues of A. thaliana, which will facilitate further gene expression studies in this context. More importantly, we presented a framework that will promote a consistent and accurate analysis of gene expression in any scientific field. Simultaneously, we highlighted the relevance of clearly defining and describing the experimental conditions associated with qPCR to improve scientific reproducibility.

Brassica napus Transcription Factor Bna.A07.WRKY70 Negatively Regulates Leaf Senescence in Arabidopsis thaliana

Leaf senescence is the final stage of leaf development and is essential for storage properties and crop productivity. WRKY transcription factors have been revealed to play crucial roles in several biological processes during plant growth and development, especially in leaf senescence. However, the functions of Brassica napus WRKY transcription factors in leaf senescence remain unclear. In the present study, Bna.A07.WRKY70, one paralogue of Brassica napus WRKY70, was cloned from the B. napus cultivar "Zhongshuang11 (ZS11)". We found that Bna.A07.WRKY70 contains a highly conserved WRKY domain and is most closely related to Arabidopsis thaliana WRKY70. The subcellular localization and transcriptional self-activation assays indicated that Bna.A07.WRKY70 functions as a transcription factor. Meanwhile, RT-qPCR and promoter-GUS analysis showed that Bna.A07.WRKY70 is predominantly expressed in the leaves of B. napus and rosette leaves of A. thaliana. In addition, our results demonstrated that ectopic expression of Bna.A07.WRKY70 in A. thaliana wrky70 mutants could restore the senescence phenotypes to wild-type levels. Consistently, the expression levels of three senescence-related marker genes of wrky70 mutants were restored to wild-type levels by ectopic expression of Bna.A07.WRKY70. These findings improve our understanding of the function of Bna.A07.WRKY70 in B. napus and provide a novel strategy for breeding the new stay-green cultivars in rapeseed through genetic manipulation.

Integrated analyses reveal the response of peanut to phosphorus deficiency on phenotype, transcriptome and metabolome

BACKGROUND

Phosphorus (P) is one of the most essential macronutrients for crops. The growth and yield of peanut (Arachis hypogaea L.) are always limited by P deficiency. However, the transcriptional and metabolic regulatory mechanisms were less studied. In this study, valuable phenotype, transcriptome and metabolome data were analyzed to illustrate the regulatory mechanisms of peanut under P deficiency stress.

RESULT

In present study, two treatments of P level in deficiency with no P application (-P) and in sufficiency with 0.6 mM P application (+ P) were used to investigate the response of peanut on morphology, physiology, transcriptome, microRNAs (miRNAs), and metabolome characterizations. The growth and development of plants were significantly inhibited under -P treatment. A total of 6088 differentially expressed genes (DEGs) were identified including several transcription factor family genes, phosphate transporter genes, hormone metabolism related genes and antioxidant enzyme related genes that highly related to P deficiency stress. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that 117 genes were annotated in the phenylpropanoid biosynthesis pathway under P deficiency stress. A total of 6 miRNAs have been identified significantly differential expression between + P and -P group by high-throughput sequencing of miRNAs, including two up-regulated miRNAs (ahy-miR160-5p and ahy-miR3518) and four down-regulated miRNAs (ahy-miR408-5p, ahy-miR408-3p, ahy-miR398, and ahy-miR3515). Further, the predicted 22 target genes for 6 miRNAs and cis-elements in 2000 bp promoter region of miRNA genes were analyzed. A total of 439 differentially accumulated metabolites (DAMs) showed obviously differences in two experimental conditions.

CONCLUSIONS

According to the result of transcripome and metabolome analyses, we can draw a conclusion that by increasing the content of lignin, amino acids, and levan combining with decreasing the content of LPC, cell reduced permeability, maintained stability, raised the antioxidant capacity, and increased the P uptake in struggling for survival under P deficiency stress.

A Non-Shedding Fruit Elaeis oleifera Palm Reveals Perturbations to Hormone Signaling, ROS Homeostasis, and Hemicellulose Metabolism

The developmentally programmed loss of a plant organ is called abscission. This process is characterized by the ultimate separation of adjacent cells in the abscission zone (AZ). The discovery of an American oil palm (Elaeis oleifera) variant that does not shed its has allowed for the study of the mechanisms of ripe fruit abscission in this species. A comparative transcriptome analysis was performed to compare the fruit AZs of the non-shedding E. oleifera variant to an individual of the same progeny that sheds its ripe fruit normally. The study provides evidence for widespread perturbation to gene expression in the AZ of the non-shedding variant, compared to the normal fruit-shedding control, and offers insight into abscission-related functions. Beyond the genes with known or suspected roles during organ abscission or indehiscence that were identified, a list of genes with hormone-related functions, including ethylene, jasmonic acid, abscisic acid, cytokinin and salicylic acid, in addition to reactive oxygen species (ROS) metabolism, transcriptional responses and signaling pathways, was compiled. The results also allowed a comparison between the ripe fruit abscission processes of the African and American oil palm species at the molecular level and revealed commonalities with environmental stress pathways.

Increased expression of ANAC017 primes for accelerated senescence

Recent studies in Arabidopsis (Arabidopsis thaliana) have reported conflicting roles for NAC DOMAIN CONTAINING PROTEIN 17 (ANAC017), a transcription factor regulating mitochondria-to-nuclear signaling, and its closest paralog NAC DOMAIN CONTAINING PROTEIN 16 (ANAC016), in leaf senescence. By synchronizing senescence in individually darkened leaves of knockout and overexpressing mutants from these contrasting studies, we demonstrate that elevated ANAC017 expression consistently causes accelerated senescence and cell death. A time-resolved transcriptome analysis revealed that senescence-associated pathways such as autophagy are not constitutively activated in ANAC017 overexpression lines, but require a senescence-stimulus to trigger accelerated induction. ANAC017 transcript and ANAC017-target genes are constitutively upregulated in ANAC017 overexpression lines, but surprisingly show a transient "super-induction" 1 d after senescence induction. This induction of ANAC017 and its target genes is observed during the later stages of age-related and dark-induced senescence, indicating the ANAC017 pathway is also activated in natural senescence. In contrast, knockout mutants of ANAC017 showed lowered senescence-induced induction of ANAC017 target genes during the late stages of dark-induced senescence. Finally, promoter binding analyses show that the ANAC016 promoter sequence is directly bound by ANAC017, so ANAC016 likely acts downstream of ANAC017 and is directly transcriptionally controlled by ANAC017 in a feed-forward loop during late senescence.

Identification of a delayed leaf greening gene from a mutation of pummelo

Delayed greening of young leaves is an unusual phenomenon of plants in nature. Citrus are mostly evergreen tree species. Here, a natural mutant of "Guanxi" pummelo (Citrus maxima), which shows yellow leaves at the young stage, was characterized to identify the genes underlying the trait of delayed leaf greening in plants. A segregating population with this mutant as the seed parent and a normal genotype as the pollen parent was generated. Two DNA pools respectively from the leaves of segregating seedlings with extreme phenotypes of normal leaf greening and delayed leaf greening were collected for sequencing. Bulked segregant analysis (BSA) and InDel marker analysis demonstrated that the delayed leaf greening trait is governed by a 0.3 Mb candidate region on chromosome 6. Gene expression analysis further identified a key candidate gene (Citrus Delayed Greening gene 1, CDG1) in the 0.3 Mb region, which showed significantly differential expression between the genotypes with delayed and normal leaf greening phenotypes. There was a 67 bp InDel region difference in the CDG1 promoter and the InDel region contains a TATA-box element. Confocal laser-scanning microscopy revealed that the CDG1-GFP fusion protein signals were co-localized with the chloroplast signals in the protoplasts. Overexpression of CDG1 in tobacco and Arabidopsis led to the phenotype of delayed leaf greening. These results suggest that the CDG1 gene is involved in controlling the delayed leaf greening phenotype with important functions in chloroplast development.

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/ . We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena

Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.

Unusual DNA-binding properties of the Arabidopsis thaliana WRKY50 transcription factor at target gene promoters

WRKY50 from A. thaliana requires WT-boxes at target gene promoters for activation and binding. Based on the genome-wide prediction of WRKY50 target genes and the similarity of a WRKY50 binding site to WT-boxes in microbe-associated molecular pattern (MAMP)-responsive cis-regulatory modules (CRM), four WT-box containing CRMs from the promoter region of three WRKY50 target genes were investigated for their interaction with WRKY50. These target genes are DJ1E, WRKY30 and ATBBE4. Two of the four CRMs, one from DJ1E and one from WRKY30, were able to activate reporter gene expression in the presence of WRKY50. Activation requires the WT-boxes GGACTTTT, GGACTTTG from DJ1E and GGACTTTC from WRKY30. WRKY50 does not activate a second CRM from WRKY30 and the CRM from ATBBE4, both containing the WT-box TGACTTTT. In vitro gel-shift assays demonstrate WT-box-specific binding of the WRKY50 DNA-binding domain to all four CRMs. This work shows a high flexibility of WRKY50 binding site recognition beyond the classic W-box TTGACC/T.

The expression pattern of OsDim1 in rice and its proposed function

Development of plant tissues is dependent on numerous factors, including hormone activity, signaling, cell division, and elongation. In plants, Defective Entry into Mitosis 1 (Dim1) homologs are recognized as pivotal in leaf senescence and progress of normal growth, but their role in rice has not been functionally characterized. The findings presented in this paper suggest that OsDim1 is important in early seedling development, pollen tube elongation, and impacts rice yield components. The gene is expressed in the scutellum, endosperm, embryonic root, shoot, pollen grains and tubes, as well as in several organs of the rice flower. According to the present study findings, RNAi mediated knockdown of OsDim1 resulted in phytohormonal imbalance, reduced amylase activity, affected differentiation of embryonic root elongation zone tissues, suppressed embryonic root and shoot growth, and impaired pollen tube elongation. In contrast, overexpression of OsDim1 showed significant growth in embryonic roots and shoots, while it increased culm length, total number of tillers per plant, seed setting rate, and total number of grains per panicle compared to its wild type line. In summary, we propose OsDim1 plays an important role in seedling growth and pollen tube elongation, and has pleiotropic effects on reproductive tissues.

Genome-Wide Characterization of AspATs in Populus: Gene Expression Variation and Enzyme Activities in Response to Nitrogen Perturbations

Aspartate aminotransferase (AspAT) catalyzes a reversible transamination reaction between glutamate and oxaloacetate to yield aspartate and 2-oxoglutarate, exerting a primary role in amino acid biosynthesis and homeostasis of nitrogen (N) and carbon metabolism within all cellular organisms. While progress in biochemical characterization of AspAT has been made for decades, the molecular and physiological characteristics of different members of the AspAT gene family remain poorly known particularly in forest trees. Here, extensive genome-wide survey of AspAT encoding genes was implemented in black cottonwood (Populus trichocarpa Torr. & A. Gray), a model species of woody plants. Thorough inspection of the phylogenies, gene structures, chromosomal distribution, cis-elements, conserved motifs, and subcellular targeting resulted in the identification of 10 AspAT isogenes (PtAspAT1-10) in the Populus genome. RNA-seq along with quantitative real-time polymerase chain reaction (qRT-PCR) validation revealed that PtAspATs displayed diverse patterns of tissue-specific expression. Spatiotemporal expressions of homologous AspATs in the poplar hybrid clone ‘Nanlin895’ were further evaluated, showing that gene expressions varied depending on source-sink dynamics. The impact on AspAT transcripts upon N starvation and seasonal senescence showed the upregulation of five AspAT in leaves concurrent with drastic downregulation of six or more AspATs in roots. Additionally, marked reductions of many more AspATs transcripts were observed in roots upon N excess. Accordingly, AspAT activities were significantly suppressed upon N starvation by an in-gel assay, prompting the argument that enzyme activity was a more direct indicator of the growth morphology under a N stress regime. Taken together, the expression profiling and enzyme activities upon stress cues provide a theoretical basis for unraveling the physiological significance of specific gene(s) in regulation of N acquisition and remobilization in woody plants.

Tomato fruit ripening factor NOR controls leaf senescence

NAC transcription factors (TFs) are important regulators of expressional reprogramming during plant development, stress responses, and leaf senescence. NAC TFs also play important roles in fruit ripening. In tomato (Solanum lycopersicum), one of the best characterized NACs involved in fruit ripening is NON-RIPENING (NOR), and the non-ripening (nor) mutation has been widely used to extend fruit shelf life in elite varieties. Here, we show that NOR additionally controls leaf senescence. Expression of NOR increases with leaf age, and developmental as well as dark-induced senescence are delayed in the nor mutant, while overexpression of NOR promotes leaf senescence. Genes associated with chlorophyll degradation as well as senescence-associated genes (SAGs) show reduced and elevated expression, respectively, in nor mutants and NOR overexpressors. Overexpression of NOR also stimulates leaf senescence in Arabidopsis thaliana. In tomato, NOR supports senescence by directly and positively regulating the expression of several senescence-associated genes including, besides others, SlSAG15 and SlSAG113, SlSGR1, and SlYLS4. Finally, we find that another senescence control NAC TF, namely SlNAP2, acts upstream of NOR to regulate its expression. Our data support a model whereby NAC TFs have often been recruited by higher plants for both the control of leaf senescence and fruit ripening.

Comparative Transcriptomic Analysis of Biological Process and Key Pathway in Three Cotton (Gossypium spp.) Species Under Drought Stress

Drought is one of the most important abiotic stresses that seriously affects cotton growth, development, and production worldwide. However, the molecular mechanism, key pathway, and responsible genes for drought tolerance incotton have not been stated clearly. In this research, high-throughput next generation sequencing technique was utilized to investigate gene expression profiles of three cotton species (Gossypium hirsutum, Gossypium arboreum, and Gossypium barbadense L.) under drought stress. A total of 6968 differentially expressed genes (DEGs) were identified, where 2053, 742, and 4173 genes were tested as statistically significant; 648, 320, and 1998 genes were up-regulated, and 1405, 422, and 2175 were down-regulated in TM-1, Zhongmian-16, and Pima4-S, respectively. Total DEGs were annotated and classified into functional groups under gene ontology analysis. The biological process was present only in tolerant species(TM-1), indicating drought tolerance condition. The Kyoto encyclopedia of genes and genomes showed the involvement of plant hormone signal transduction and metabolic pathways enrichment under drought stress. Several transcription factors associated with ethylene-responsive genes (ICE1, MYB44, FAMA, etc.) were identified as playing key roles in acclimatizing to drought stress. Drought also caused significant changes in the expression of certain functional genes linked to abscisic acid (ABA) responses (NCED, PYL, PP2C, and SRK2E), reactive oxygen species (ROS) related in small heat shock protein and 18.1 kDa I heat shock protein, YLS3, and ODORANT1 genes. These results will provide deeper insights into the molecular mechanisms of drought stress adaptation in cotton.

Accumulation patterns of endogenous β-aminobutyric acid during plant development and defence in Arabidopsis thaliana

We recently discovered that β-aminobutyric acid (BABA), a molecule known for its ability to prime defences in plants, is a natural plant metabolite. However, the role played by endogenous BABA in plants is currently unknown. In this study we investigated the systemic accumulation of BABA during pathogen infection, levels of BABA during plant growth and development and analysed mutants possibly involved in BABA transport or regulation. BABA was quantified by LC-MS using an improved method adapted from a previously published protocol. Systemic accumulation of BABA was determined by analysing non-infected leaves and roots after localised infections with Plectosphaerella cucumerina or Pseudomonas syringae pv. tomato (Pst) DC3000 avrRpt2. The levels of BABA were also quantified in different plant tissues and organs during normal plant growth, and in leaves during senescence. Mutants affecting amino acid transport (aap6, aap3, prot1 and gat1), γ-aminobutyric acid levels (pop2) and senescence/defence (cpr5-2) were analysed. BABA was found to accumulate only locally after bacterial or fungal infection, with no detectable increase in non-infected systemic plant parts. In leaves, BABA content increased during natural and induced senescence. Reproductive organs had the highest levels of BABA, and the mutant cpr5-2 produced constitutively high levels of BABA. Synthetic BABA is highly mobile in the receiving plant, whereas endogenous BABA appears to be produced and accumulated locally in a tissue-specific way. We discuss a possible role for BABA in age-related resistance and propose a comprehensive model for endogenous and synthetic BABA.

A rust fungal effector binds plant DNA and modulates transcription

The basidiomycete Melampsora larici-populina causes poplar rust disease by invading leaf tissues and secreting effector proteins through specialized infection structures known as haustoria. The mechanisms by which rust effectors promote pathogen virulence are poorly understood. The present study characterized Mlp124478, a candidate effector of M. larici-populina. We used the models Arabidopsis thaliana and Nicotiana benthamiana to investigate the function of Mlp124478 in plant cells. We established that Mlp124478 accumulates in the nucleus and nucleolus, however its nucleolar accumulation is not required to promote growth of the oomycete pathogen Hyaloperonospora arabidopsidis. Stable constitutive expression of Mlp124478 in A. thaliana repressed the expression of genes involved in immune responses, and also altered leaf morphology by increasing the waviness of rosette leaves. Chip-PCR experiments showed that Mlp124478 associats'e with the TGA1a-binding DNA sequence. Our results suggest that Mlp124478 exerts a virulence activity and binds the TGA1a promoter to suppress genes induced in response to pathogen infection.

The Direct Involvement of Dark-Induced Tic55 Protein in Chlorophyll Catabolism and Its Indirect Role in the MYB108-NAC Signaling Pathway during Leaf Senescence in Arabidopsis thaliana

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 Arabidopsis. Here, a tic55-II-knockout mutant of Arabidopsis thaliana 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 tic55-II-knockout mutant. The IDLs of the tic55-II-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 tic55-II-knockout mutant: ASP3, APG7, DIN2, DIN11, SAG12, SAG13, and YLS9. 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 A. thaliana by indirectly regulating downstream SAGs expression. In addition, the expression of four NAC genes, including ANAC003, ANAC010, ANAC042, and ANAC075 of IDL treated tic55-II-knockout mutant appeared to be downregulated. Yeast one hybrid assay revealed that only ANAC003 promoter region can be bound by MYB108, suggesting that a MYB-NAC regulatory network is involved in dark-stressed senescence.

De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech

Despite the ecological and economic importance of European beech (Fagus sylvatica L.) genomic resources of this species are still limited. This hampers an understanding of the molecular basis of adaptation to stress. Since beech will most likely be threatened by the consequences of climate change, an understanding of adaptive processes to climate change-related drought stress is of major importance. Here, we used RNA-seq to provide the first drought stress-related transcriptome of beech. In a drought stress trial with beech saplings, 50 samples were taken for RNA extraction at five points in time during a soil desiccation experiment. De novo transcriptome assembly and analysis of differential gene expression revealed 44,335 contigs, and 662 differentially expressed genes between the stress and normally watered control group. Gene expression was specific to the different time points, and only five genes were significantly differentially expressed between the stress and control group on all five sampling days. GO term enrichment showed that mostly genes involved in lipid- and homeostasis-related processes were upregulated, whereas genes involved in oxidative stress response were downregulated in the stressed seedlings. This study gives first insights into the genomic drought stress response of European beech, and provides new genetic resources for adaptation research in this species.

Comparative Transcriptome and Microscopy Analyses Provide Insights into Flat Shape Formation in Peach (Prunus persica)

Fruit shape is an important external characteristic that consumers use to select preferred fruit cultivars. In peach, the flat fruit cultivars have become more and more popular worldwide. Genetic markers closely linking to the flat fruit trait have been identified and are useful for marker-assisted breeding. However, the cellular and genetic mechanisms underpinning flat fruit formation are still poorly understood. In this study, we have revealed the differences in fruit cell number, cell size, and in gene expression pattern between the traditional round fruit and modern flat fruit cultivars. Flat peach cultivars possessed significantly lower number of cells in the vertical axis because cell division in the vertical direction stopped early in the flat fruit cultivars at 15 DAFB (day after full bloom) than in round fruit cultivars at 35 DAFB. This resulted in the reduction in vertical development in the flat fruit. Significant linear relationship was observed between fruit vertical diameter and cell number in vertical axis for the four examined peach cultivars (R² = 0.9964) at maturation stage, and was also observed between fruit vertical diameter and fruit weight (R² = 0.9605), which indicated that cell number in vertical direction contributed to the flat shape formation. Furthermore, in RNA-seq analysis, 4165 differentially expressed genes (DEGs) were detected by comparing RNA-seq data between flat and round peach cultivars at different fruit development stages. In contrast to previous studies, we discovered 28 candidate genes potentially responsible for the flat shape formation, including 19 located in the mapping site and 9 downstream genes. Our study indicates that flat and round fruit shape in peach is primarily determined by the regulation of cell production in the vertical direction during early fruit development.

Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research

Leaf senescence is a complex but tightly regulated developmental process involving a coordinated sequence of multiple molecular events, which ultimately leads to death of the leaf. Efforts to understand the mechanistic principles underlying leaf senescence have been largely made by transcriptomic, proteomic, and metabolomic studies over the past decade. This review focuses on recent milestones in leaf senescence research obtained using multi-omics technologies, as well as future endeavors toward systems understanding of leaf senescence processes. In particular, we discuss recent advances in understanding molecular events during leaf senescence through genome-wide transcriptome analyses in Arabidopsis. We also describe comparative transcriptome analyses used to unveil the commonality and diversity of regulatory mechanisms governing leaf senescence in the plant kingdom. Finally, we provide current illustrations of epigenomic, proteomic, and metabolomic landscapes of leaf senescence. We envisage that integration of multi-omics leaf senescence data will enable us to address unresolved questions regarding leaf senescence, including determining the molecular principles that coordinate concurrent and ordered changes in biological events during leaf senescence.

Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa

Background. Xylella fastidiosa, the causative agent of various plant diseases including Pierce’s disease in the US, and Citrus Variegated Chlorosis in Brazil, remains a continual source of concern and economic losses, especially since almost all commercial varieties are sensitive to this Gammaproteobacteria. Differential expression of proteins in infected tissue is an established methodology to identify key elements involved in plant defense pathways.

Methods. In the current work, we developed a methodology named CHURNER that emphasizes relevant protein functions from proteomic data, based on identification of proteins with similar structures that do not necessarily have sequence homology. Such clustering emphasizes protein functions which have multiple copies that are up/down-regulated, and highlights similar proteins which are differentially regulated. As a working example we present proteomic data enumerating differentially expressed proteins in xylem sap from grapevines that were infected with X. fastidiosa.

Results. Analysis of this data by CHURNER highlighted pathogenesis related PR-1 proteins, reinforcing this as the foremost protein function in xylem sap involved in the grapevine defense response to X. fastidiosa. β-1, 3-glucanase, which has both anti-microbial and anti-fungal activities, is also up-regulated. Simultaneously, chitinases are found to be both up and down-regulated by CHURNER, and thus the net gain of this protein function loses its significance in the defense response.

Discussion. We demonstrate how structural data can be incorporated in the pipeline of proteomic data analysis prior to making inferences on the importance of individual proteins to plant defense mechanisms. We expect CHURNER to be applicable to any proteomic data set.

Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum

In Arabidopsis, jasmonate (JA)-signaling plays a key role in mediating Fusarium oxysporum disease outcome. However, the roles of JASMONATE ZIM-domain (JAZ) proteins that repress JA-signaling have not been characterized in host resistance or susceptibility to this pathogen. Here, we found most JAZ genes are induced following F. oxysporum challenge, and screening T-DNA insertion lines in Arabidopsis JAZ family members identified a highly disease-susceptible JAZ7 mutant (jaz7-1D). This mutant exhibited constitutive JAZ7 expression and conferred increased JA-sensitivity, suggesting activation of JA-signaling. Unlike jaz7 loss-of-function alleles, jaz7-1D also had enhanced JA-responsive gene expression, altered development and increased susceptibility to the bacterial pathogen PstDC3000 that also disrupts host JA-responses. We also demonstrate that JAZ7 interacts with transcription factors functioning as activators (MYC3, MYC4) or repressors (JAM1) of JA-signaling and contains a functional EAR repressor motif mediating transcriptional repression via the co-repressor TOPLESS (TPL). We propose through direct TPL recruitment, in wild-type plants JAZ7 functions as a repressor within the JA-response network and that in jaz7-1D plants, misregulated ectopic JAZ7 expression hyper-activates JA-signaling in part by disturbing finely-tuned COI1-JAZ-TPL-TF complexes.

Sequence/structural analysis of xylem proteome emphasizes pathogenesis-related proteins, chitinases and β-1, 3-glucanases as key players in grapevine defense against Xylella fastidiosa

Background. Xylella fastidiosa, the causative agent of various plant diseases including Pierce's disease in the US, and Citrus Variegated Chlorosis in Brazil, remains a continual source of concern and economic losses, especially since almost all commercial varieties are sensitive to this Gammaproteobacteria. Differential expression of proteins in infected tissue is an established methodology to identify key elements involved in plant defense pathways. Methods. In the current work, we developed a methodology named CHURNER that emphasizes relevant protein functions from proteomic data, based on identification of proteins with similar structures that do not necessarily have sequence homology. Such clustering emphasizes protein functions which have multiple copies that are up/down-regulated, and highlights similar proteins which are differentially regulated. As a working example we present proteomic data enumerating differentially expressed proteins in xylem sap from grapevines that were infected with X. fastidiosa. Results. Analysis of this data by CHURNER highlighted pathogenesis related PR-1 proteins, reinforcing this as the foremost protein function in xylem sap involved in the grapevine defense response to X. fastidiosa. β-1, 3-glucanase, which has both anti-microbial and anti-fungal activities, is also up-regulated. Simultaneously, chitinases are found to be both up and down-regulated by CHURNER, and thus the net gain of this protein function loses its significance in the defense response. Discussion. We demonstrate how structural data can be incorporated in the pipeline of proteomic data analysis prior to making inferences on the importance of individual proteins to plant defense mechanisms. We expect CHURNER to be applicable to any proteomic data set.

Functional dissection of a strong and specific microbe-associated molecular pattern-responsive synthetic promoter

Synthetic promoters are important for temporal and spatial gene expression in transgenic plants. To identify novel microbe-associated molecular pattern (MAMP)-responsive cis-regulatory sequences for synthetic promoter design, a combination of bioinformatics and experimental approaches was employed. One cis-sequence was identified which confers strong MAMP-responsive reporter gene activity with low background activity. The 35-bp-long cis-sequence was identified in the promoter of the Arabidopsis thaliana DJ1E gene, a homologue of the human oncogene DJ1. In this study, this cis-sequence is shown to be a tripartite cis-regulatory module (CRM). A synthetic promoter with four copies of the CRM linked to a minimal promoter increases MAMP-responsive reporter gene expression compared to the wild-type DJ1E promoter. The CRM consists of two WT-boxes (GGACTTTT and GGACTTTG) and a variant of the GCC-box (GCCACC), all required for MAMP and salicylic acid (SA) responsivity. Yeast one-hybrid screenings using a transcription factor (TF)-only prey library identified two AP2/ERFs, ORA59 and ERF10, interacting antagonistically with the CRM. ORA59 activates reporter gene activity and requires the consensus core sequence GCCNCC for gene expression activation. ERF10 down-regulates MAMP-responsive gene expression. No TFs interacting with the WT-boxes GGACTTTT and GGACTTTG were selected in yeast one-hybrid screenings with the TF-only prey library. In transgenic Arabidopsis, the synthetic promoter confers strong and specific reporter gene activity in response to biotrophs and necrotrophs as well as SA.

Leaf senescence induced by EGY1 defection was partially restored by glucose in Arabidopsis thaliana

BACKGROUND

Ethylene-dependent gravitropism-deficient and yellow-green 1 (EGY1) protein is required for chloroplast development and photosynthesis conduction. The egy1 deletion mutants have a yellow-green phenotype and reduced granal thylakoids. Furthermore, the yellow-green phenotype of egy1 mutants is more obvious than that of wild-type (WT) plants with increasing leaf age, suggesting an early senescence in the egy1 mutants. However, the relationship between EGY1 functions and leaf senescence still remains poorly understood.

RESULTS

We observed that egy1 mutant leaves were more yellow than those of WT (the same age) in Arabidopsis thaliana. In accompany with this phenotype, leaf survival, chlorophyll content, Fv/Fm and soluble protein content decreased, and ion leakage increased significantly in egy1 mutants compared to WT plants. At molecular level, the expressions of senescence-associated genes increased, and photosynthesis genes decreased significantly in the mutants compared to those in WT plants. Furthermore, after darkness treatment, the yellow-green phenotype of egy1 mutants was more obvious than that of WT. These results indicate that the loss-of-function of egy1 gene induces leaf senescence in A. thaliana. In addition, our results showed that the yellow-green phenotype, chlorophyll content and ion leakage of egy1 mutants was partially restored after exogenously applied glucose for 5 weeks. At the same time, the expression of hexokinase 1 (HXK1) and/or senescence-associated gene 12 (SAG12) in egy1 mutants growing on 2 % glucose was lower than that in egy1 mutants without glucose.

CONCLUSION

EGY1-defection induced leaf senescence and this senescence was partially restored by glucose in A. thaliana.

SnRK1-triggered switch of bZIP63 dimerization mediates the low-energy response in plants

Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.

DOI:http://dx.doi.org/10.7554/eLife.05828.001

Organisms need to adjust their metabolism in response to changing environmental conditions to ensure that they balance their energy intake with the demands of growth and reproduction. In plants, an enzyme called SnRK1 plays a crucial role in responses to starvation in two ways: by altering the activities of enzymes involved in metabolism and by regulating the expression of genes. To perform the second job, SnRK1 is thought to control the activity of proteins called transcription factors—which alter the expression of genes by binding to DNA—but it is not known which ones.

SnRK1 has ‘kinase’ activity, that is, it can alter the activities of other proteins by adding small molecules called phosphates to them. It has been suggested that a group of transcription factors called the bZIP proteins may be regulated by SnRK1. Two bZIP proteins work together to switch on a gene, and the combination of bZIP proteins that interact can influence which genes are switched on. Here, Mair et al. studied the role of a bZIP protein called bZIP63 during starvation in the plant Arabidopsis.

The experiments show that bZIP63 is involved in controlling responses to starvation. Furthermore, its activity is regulated by SnRK1, which adds phosphates to three specific locations on the protein. These phosphates alter the ability of bZIP63 to interact with other bZIP proteins, leading to changes in gene expression during starvation.

Mair et al. triggered starvation in Arabidopsis plants by keeping the plants in darkness for several days. The leaves of normal plants turn yellow in response to starvation, but the leaves of mutant plants that lacked bZIP63 remained green. In contrast, plants containing higher amounts of this bZIP protein showed the opposite effect and their leaves turned yellow much more quickly than normal plants. The mutant plants that lacked bZIP63 could be rescued by the normal protein, but not by another version of the protein that SnRK1 is unable to add phosphates to.

These data suggest that SnRK1 regulates bZIP63 activity to alter metabolism in response to starvation. Mair et al. propose a model in which the ability of bZIP63 to interact with other bZIPs is normally rather low. However, when the plants are starved, SnRK1 adds phosphates to bZIP63, which increases its ability to bind to other bZIP proteins and leads to changes in gene expression. The bZIP proteins are also found in animals; therefore a future challenge is to find out whether these proteins are also regulated in a similar way.

DOI:http://dx.doi.org/10.7554/eLife.05828.002

Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short-day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome-wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co-located with a QTL mapped in the RIL population.

Transcriptional analyses of natural leaf senescence in maize

Leaf senescence is an important biological process that contributes to grain yield in crops. To study the molecular mechanisms underlying natural leaf senescence, we harvested three different developmental ear leaves of maize, mature leaves (ML), early senescent leaves (ESL), and later senescent leaves (LSL), and analyzed transcriptional changes using RNA-sequencing. Three sets of data, ESL vs. ML, LSL vs. ML, and LSL vs. ESL, were compared, respectively. In total, 4,552 genes were identified as differentially expressed. Functional classification placed these genes into 18 categories including protein metabolism, transporters, and signal transduction. At the early stage of leaf senescence, genes involved in aromatic amino acids (AAAs) biosynthetic process and transport, cellular polysaccharide biosynthetic process, and the cell wall macromolecule catabolic process, were up-regulated. Whereas, genes involved in amino acid metabolism, transport, apoptosis, and response to stimulus were up-regulated at the late stage of leaf senescence. Further analyses reveals that the transport-related genes at the early stage of leaf senescence potentially take part in enzyme and amino acid transport and the genes upregulated at the late stage are involved in sugar transport, indicating nutrient recycling mainly takes place at the late stage of leaf senescence. Comparison between the data of natural leaf senescence in this study and previously reported data for Arabidopsis implies that the mechanisms of leaf senescence in maize are basically similar to those in Arabidopsis. A comparison of natural and induced leaf senescence in maize was performed. Athough many basic biological processes involved in senescence occur in both types of leaf senescence, 78.07% of differentially expressed genes in natural leaf senescence were not identifiable in induced leaf senescence, suggesting that differences in gene regulatory network may exist between these two leaf senescence programs. Thus, this study provides important information for understanding the mechanism of leaf senescence in maize.

Senescence, nutrient remobilization, and yield in wheat and barley

Cereals including wheat and barley are of primary importance to ensure food security for the 21st century. A combination of lab- and field-based approaches has led to a considerably improved understanding of the importance of organ and particularly of whole-plant (monocarpic) senescence for wheat and barley yield and quality. A delicate balance between senescence timing, grain nutrient content, nutrient-use efficiency, and yield needs to be considered to (further) improve cereal varieties for a given environment and end use. The recent characterization of the Gpc-1 (NAM-1) genes in wheat and barley demonstrates the interdependence of these traits. Lines or varieties with functional Gpc-1 genes demonstrate earlier senescence and enhanced grain protein and micronutrient content but, depending on the environment, somewhat reduced yields. A major effort is needed to dissect regulatory networks centred on additional wheat and barley transcription factors and signalling pathways influencing the senescence process. Similarly, while important molecular details of nutrient (particularly nitrogen) remobilization from senescing organs to developing grains have been identified, important knowledge gaps remain. The genes coding for the major proteases involved in senescence-associated plastidial protein degradation are largely unknown. Membrane transport proteins involved in the different transport steps occurring between senescing organ (such as leaf mesophyll) cells and protein bodies in the endosperm of developing grains remain to be identified or further characterized. Existing data suggest that an improved understanding of all these steps will reveal additional, important targets for continued cereal improvement.

Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance

In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants of Mendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed.

Drying without senescence in resurrection plants

Research into extreme drought tolerance in resurrection plants using species such as Craterostigma plantagineum, C. wilmsii, Xerophyta humilis, Tortula ruralis, and Sporobolus stapfianus has provided some insight into the desiccation tolerance mechanisms utilized by these plants to allow them to persist under extremely adverse environmental conditions. Some of the mechanisms used to ensure cellular preservation during severe dehydration appear to be peculiar to resurrection plants. Apart from the ability to preserve vital cellular components during drying and rehydration, such mechanisms include the ability to down-regulate growth-related metabolism rapidly in response to changes in water availability, and the ability to inhibit dehydration-induced senescence programs enabling reconstitution of photosynthetic capacity quickly following a rainfall event. Extensive research on the molecular mechanism of leaf senescence in non-resurrection plants has revealed a multi-layered regulatory network operates to control programed cell death pathways. However, very little is known about the molecular mechanisms that resurrection plants employ to avoid undergoing drought-related senescence during the desiccation process. To survive desiccation, dehydration in the perennial resurrection grass S. stapfianus must proceed slowly over a period of 7 days or more. Leaves detached from the plant before 60% relative water content (RWC) is attained are desiccation-sensitive indicating that desiccation tolerance is conferred in vegetative tissue of S. stapfianus when the leaf RWC has declined to 60%. Whilst some older leaves remaining attached to the plant during dehydration will senesce, suggesting dehydration-induced senescence may be influenced by leaf age or the rate of dehydration in individual leaves, the majority of leaves do not senesce. Rather these leaves dehydrate to air-dryness and revive fully following rehydration. Hence it seems likely that there are genes expressed in younger leaf tissues of resurrection plants that enable suppression of drought-related senescence pathways. As very few studies have directly addressed this phenomenon, this review aims to discuss current literature surrounding the activation and suppression of senescence pathways and how these pathways may differ in resurrection plants.

Transcriptional and biochemical responses of monoacylglycerol acyltransferase-mediated oil synthesis and associated senescence-like responses in Nicotiana benthamiana

Triacylglycerol (TAG) accumulates in plant seeds as a major renewable source of carbon for food, fuel and industrial feedstock. Approaches to enhance TAG content by altering lipid pathways and genes in vegetative parts have gained significant attention for biofuel and other applications. However, consequences of these modifications are not always studied in detail. In an attempt to increase TAG levels in leaves we previously demonstrated that a novel substrate, monoacylglycerol (MAG), can be used for the biosynthesis of diacylglycerol (DAG) and TAG. Transient expression of the Mus musculus monoacylglycerol acyltransferases MGAT1 and 2 in the model plant Nicotiana benthamiana increased TAG levels at 5 days post-infiltration (dpi). Here we show that increased TAG and DAG levels can be achieved as early as 2 dpi. In addition, the MGAT1 infiltrated areas showed senescence-like symptoms from 3 dpi onwards. To unravel underlying molecular mechanisms, Illumina deep sequencing was carried out (a) for de-novo assembling and annotation of N. benthamiana leaf transcripts and (b) to characterize MGAT1-responsive transcriptome. We found that MGAT1-responsive genes are involved in several processes including TAG biosynthesis, photosynthesis, cell-wall, cutin, suberin, wax and mucilage biosynthesis, lipid and hormone metabolism. Comparative analysis with transcript profiles from other senescence studies identified characteristic gene expression changes involved in senescence induction. We confirmed that increased TAG and observed senescence-symptoms are due to the MAG depletion caused by MGAT1 activity and suggest a mechanism for MGAT1 induced TAG increase and senescence-like symptoms. The data generated will serve as a valuable resource for oil and senescence related studies and for future N. benthamiana transcriptome studies.

Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L

Background

Cotton (Gossypium hirsutum L.) is one of the world’s most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence.

Methodology/Principal Findings

In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR), which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves.

Conclusions/Significance

These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence assembly and annotation in G. hirsutum and comparative genomics among Gossypium species.

Transcriptome profiling of low temperature-treated cassava apical shoots showed dynamic responses of tropical plant to cold stress

BACKGROUND

Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signalling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions.

RESULTS

A 60-mer oligonucleotide microarray representing 20,840 genes was used to perform transcriptome profiling in apical shoots of cassava subjected to cold at 7°C for 0, 4 and 9 h. A total of 508 transcripts were identified as early cold-responsive genes in which 319 sequences had functional descriptions when aligned with Arabidopsis proteins. Gene ontology annotation analysis identified many cold-relevant categories, including 'Response to abiotic and biotic stimulus', 'Response to stress', 'Transcription factor activity', and 'Chloroplast'. Various stress-associated genes with a wide range of biological functions were found, such as signal transduction components (e.g., MAP kinase 4), transcription factors (TFs, e.g., RAP2.11), and reactive oxygen species (ROS) scavenging enzymes (e.g., catalase 2), as well as photosynthesis-related genes (e.g., PsaL). Seventeen major TF families including many well-studied members (e.g., AP2-EREBP) were also involved in the early response to cold stress. Meanwhile, KEGG pathway analysis uncovered many important pathways, such as 'Plant hormone signal transduction' and 'Starch and sucrose metabolism'. Furthermore, the expression changes of 32 genes under cold and other abiotic stress conditions were validated by real-time RT-PCR. Importantly, most of the tested stress-responsive genes were primarily expressed in mature leaves, stem cambia, and fibrous roots rather than apical buds and young leaves. As a response to cold stress in cassava, an increase in transcripts and enzyme activities of ROS scavenging genes and the accumulation of total soluble sugars (including sucrose and glucose) were also detected.

CONCLUSIONS

The dynamic expression changes reflect the integrative controlling and transcriptome regulation of the networks in the cold stress response of cassava. The biological processes involved in the signal perception and physiological response might shed light on the molecular mechanisms related to cold tolerance in tropical plants and provide useful candidate genes for genetic improvement.

The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator

Correct interpretation of the coding capacity of RNA polymerase II transcribed eukaryotic genes is determined by the recognition and removal of intronic sequences of pre-mRNAs by the spliceosome. Our current knowledge on dynamic assembly and subunit interactions of the spliceosome mostly derived from the characterization of yeast, Drosophila, and human spliceosomal complexes formed on model pre-mRNA templates in cell extracts. In addition to sequential structural rearrangements catalyzed by ATP-dependent DExH/D-box RNA helicases, catalytic activation of the spliceosome is critically dependent on its association with the NineTeen Complex (NTC) named after its core E3 ubiquitin ligase subunit PRP19. NTC, isolated recently from Arabidopsis, occurs in a complex with the essential RNA helicase and GTPase subunits of the U5 small nuclear RNA particle that are required for both transesterification reactions of splicing. A compilation of mass spectrometry data available on the composition of NTC and spliceosome complexes purified from different organisms indicates that about half of their conserved homologs are encoded by duplicated genes in Arabidopsis. Thus, while mutations of single genes encoding essential spliceosome and NTC components lead to cell death in other organisms, differential regulation of some of their functionally redundant Arabidopsis homologs permits the isolation of partial loss of function mutations. Non-lethal pleiotropic defects of these mutations provide a unique means for studying the roles of NTC in co-transcriptional assembly of the spliceosome and its crosstalk with DNA repair and cell death signaling pathways.

Ammonium secretion during Colletotrichum coccodes infection modulates salicylic and jasmonic acid pathways of ripe and unripe tomato fruit

The postharvest pathogens Colletotrichum coccodes remains quiescent after infection of unripe fruit. However, during fruit ripening, the pathogen assumes a necrotrophic life style, rapidly colonizing the tissue. C. coccodes secretes ammonium during germination and colonization of host tissue that induces host programmed cell death. We further examined the role of ammonia in the infection process by analyzing transcriptome expression from infected and ammonia-treated fruit tissue compared with healthy tissue. The analysis revealed 82 and 237 common upregulated and downregulated genes, respectively. Quantitative reverse-transcriptase polymerase chain reaction analysis of select transcripts in normal and transgenic NADPH oxidase antisense plants revealed that their expression was NADPH oxidase dependent. Common-upregulated genes showed overrepresentation of salicylic acid (SA)-dependent genes as well as genes related to biotic stress. The downregulated genes showed overrepresentation of jasmonic acid (JA)-dependent genes. Indeed, direct application of SA to the fruit enhanced C. coccodes necrotrophic colonization, whereas the application of JA delayed colonization. Importantly, green fruit and red fruit displayed similar gene expression patterns although only red fruit is susceptible to colonization. Thus, it is likely that the resistance of green fruit to C. coccodes colonization is due to additional factors.

Overexpression of Arabidopsis ACBP3 enhances NPR1-dependent plant resistance to Pseudomonas syringe pv tomato DC3000

ACBP3 is one of six Arabidopsis (Arabidopsis thaliana) genes, designated ACBP1 to ACBP6, that encode acyl-coenzyme A (CoA)-binding proteins (ACBPs). These ACBPs bind long-chain acyl-CoA esters and phospholipids and are involved in diverse cellular functions, including acyl-CoA homeostasis, development, and stress tolerance. Recombinant ACBP3 binds polyunsaturated acyl-CoA esters and phospholipids in vitro. Here, we show that ACBP3 plays a role in the plant defense response to the bacterial pathogen Pseudomonas syringae pv tomato DC3000. ACBP3 mRNA was up-regulated upon pathogen infection and treatments using pathogen elicitors and defense-related phytohormones. Transgenic Arabidopsis ACBP3 overexpressors (ACBP3-OEs) showed constitutive expression of pathogenesis-related genes (PR1, PR2, and PR5), cell death, and hydrogen peroxide accumulation in leaves. Consequently, ACBP3-OEs displayed enhanced resistance to the bacterial pathogen P. syringae DC3000. In contrast, the acbp3 T-DNA insertional mutant was more susceptible and exhibited lower PR gene transcript levels upon infection. Using the ACBP3 OE-1 line in combination with nonexpressor of PR genes1 (npr1-5) or coronatine-insensitive1 (coi1-2), we concluded that the enhanced PR gene expression and P. syringae DC3000 resistance in the ACBP3-OEs are dependent on the NPR1-mediated, but not the COI1-mediated, signaling pathway. Given that ACBP3-OEs showed greater susceptibility to infection by the necrotrophic fungus Botrytis cinerea while the acbp3 mutant was less susceptible, we suggest that ACBP3 plays a role in the plant defense response against biotrophic pathogens that is distinct from necrotrophic pathogens. ACBP3 function in plant defense was supported further by bioinformatics data showing up-regulation of many biotic and abiotic stress-related genes in ACBP3 OE-1 in comparison with the wild type.

Utility of leaf senescence-associated gene homologs as developmental markers in common wheat

Senescence is the final stage of development in plant tissues. In the senescence process, many senescence-associated genes (SAGs) are reportedly transcriptionally up-regulated. Here, we reported the isolation of nine wheat SAG cDNA clones named TaSAG1 to TaSAG9, and evaluated the usefulness of the SAG homologs for wheat developmental molecular markers based on their expression patterns. The nine wheat SAGs were identified in wheat EST libraries based on their homology to rice SAGs. All wheat SAG transcripts were up-regulated during natural senescence as well as during dark-induced senescence in seedling leaves. However, the expression patterns of wheat SAGs in the flag leaf did not necessarily correspond to those in seedling leaves during senescence. The nine wheat SAGs also showed variable expression patterns in developing and ripening seeds. The transcript accumulation patterns of TaSAG5 and TaSAG6 increased linearly during the period examined in the flag leaf and seed, and are therefore available as molecular markers to respectively evaluate the degree of wheat flag leaf senescence and seed maturation. Transcript accumulation levels of the six SAGs were increased before apparent necrotic cell death of seeding leaves exhibiting wheat hybrid necrosis. These results suggested that necrotic cell death in wheat hybrid necrosis could be closely related not only to senescence but also to defense responses.

TRICHOME BIREFRINGENCE and its homolog AT5G01360 encode plant-specific DUF231 proteins required for cellulose biosynthesis in Arabidopsis

The Arabidopsis (Arabidopsis thaliana) trichome birefringence (tbr) mutant has severely reduced crystalline cellulose in trichomes, but the molecular nature of TBR was unknown. We determined TBR to belong to the plant-specific DUF231 domain gene family comprising 46 members of unknown function in Arabidopsis. The genes harbor another plant-specific domain, called the TBL domain, which contains a conserved GDSL motif known from some esterases/lipases. TBR and TBR-like3 (TBL3) are transcriptionally coordinated with primary and secondary CELLULOSE SYNTHASE (CESA) genes, respectively. The tbr and tbl3 mutants hold lower levels of crystalline cellulose and have altered pectin composition in trichomes and stems, respectively, tissues generally thought to contain mainly secondary wall crystalline cellulose. In contrast, primary wall cellulose levels remain unchanged in both mutants as measured in etiolated tbr and tbl3 hypocotyls, while the amount of esterified pectins is reduced and pectin methylesterase activity is increased in this tissue. Furthermore, etiolated tbr hypocotyls have reduced length with swollen epidermal cells, a phenotype characteristic for primary cesa mutants or the wild type treated with cellulose synthesis inhibitors. Taken together, we show that two TBL genes contribute to the synthesis and deposition of secondary wall cellulose, presumably by influencing the esterification state of pectic polymers.

Powdery mildew resistance conferred by loss of the ENHANCED DISEASE RESISTANCE1 protein kinase is suppressed by a missense mutation in KEEP ON GOING, a regulator of abscisic acid signaling

Loss-of-function mutations in the Arabidopsis (Arabidopsis thaliana) ENHANCED DISEASE RESISTANCE1 (EDR1) gene confer enhanced resistance to infection by powdery mildew (Golovinomyces cichoracearum). EDR1 encodes a protein kinase, but its substrates and the pathways regulated by EDR1 are unknown. To identify components of the EDR1 signal transduction pathway(s), we conducted a forward genetic screen for mutations that suppressed edr1-mediated disease resistance. Genetic mapping and cloning of one of these suppressor mutations revealed a recessive missense mutation in the KEEP ON GOING gene (KEG; At5g13530), which we designated keg-4. KEG encodes a multidomain protein that includes a RING E3 ligase domain, a kinase domain, ankyrin repeats, and HERC2-like repeats. The KEG protein has previously been shown to have ubiquitin ligase activity and to negatively regulate protein levels of the transcription factor ABCISIC ACID INSENSITIVE5. KEG mRNA levels were found to be 3-fold higher in edr1 mutant plants compared to wild type. Loss-of-function mutations in KEG are seedling lethal and are hypersensitive to glucose and abscisic acid (ABA). The keg-4 mutation, in contrast, conferred resistance to 6% glucose and suppressed edr1-mediated hypersensitivity to ABA, suggesting that the keg-4 mutation suppresses ABA signaling by altering KEG function. Several ABA-responsive genes were found to be further up-regulated in the edr1 mutant following ABA treatment, and this up-regulation was suppressed by the keg-4 mutation. We conclude that edr1-mediated resistance to powdery mildew is mediated, in part, by enhanced ABA signaling.

Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function

BACKGROUND

StWhy1, a member of the plant-specific Whirly single-stranded DNA-binding protein family, was first characterized as a transcription factor involved in the activation of the nuclear PR-10a gene following defense-related stress in potato. In Arabidopsis thaliana, Whirlies have recently been shown to be primarily localized in organelles. Two representatives of the family, AtWhy1 and AtWhy3 are imported into plastids while AtWhy2 localizes to mitochondria. Their function in organelles is currently unknown.

RESULTS

To understand the role of mitochondrial Whirlies in higher plants, we produced A. thaliana lines with altered expression of the atwhy2 gene. Organellar DNA immunoprecipitation experiments demonstrated that AtWhy2 binds to mitochondrial DNA. Overexpression of atwhy2 in plants perturbs mitochondrial function by causing a diminution in transcript levels and mtDNA content which translates into a low activity level of respiratory chain complexes containing mtDNA-encoded subunits. This lowered activity of mitochondria yielded plants that were reduced in size and had distorted leaves that exhibited accelerated senescence. Overexpression of atwhy2 also led to early accumulation of senescence marker transcripts in mature leaves. Inactivation of the atwhy2 gene did not affect plant development and had no detectable effect on mitochondrial morphology, activity of respiratory chain complexes, transcription or the amount of mtDNA present. This lack of phenotype upon abrogation of atwhy2 expression suggests the presence of functional homologues of the Whirlies or the activation of compensating mechanisms in mitochondria.

CONCLUSION

AtWhy2 is associated with mtDNA and its overexpression results in the production of dysfunctional mitochondria. This report constitutes the first evidence of a function for the Whirlies in organelles. We propose that they could play a role in the regulation of the gene expression machinery of organelles.

Increased senescence-associated gene expression and lipid peroxidation induced by iron deficiency in rice roots

Iron deficiency is among the most common nutritional disorders in plants. Low iron supply causes decreased root growth and even plant death. However, there are no reports about the specific pathways that lead Fe-deficient roots to senescence and death. To investigate the molecular mechanisms that regulate rice roots response to Fe-deficiency, rice seedlings were grown for 3, 6 and 9 days in the presence or absence of Fe. Sequences of 28 induced genes in rice roots under Fe-deficiency were identified by representational difference analysis (RDA). About 40% of these sequences have been previously reported as senescence-related. Differential expression of selected genes was confirmed by semi-quantitative RT-PCR analysis. Classical senescence-related sequences, such as MYB and WRKY transcription factors, cysteine protease, ubiquitin-conjugating enzyme, lipid transfer protein, fatty acid hydroxylase, beta-glucosidase and cytochrome P450 oxydoreductase were identified. Fe-deficiency also resulted in decreased dry weight, increased lipid peroxidation (detected by TBA and histochemical methods) as well as evident membrane damage in Fe-deficient roots. Taken together, the results indicate that Fe-deficiency in roots is linked to typical senescence pathways, associated with lipid peroxidation.

Iron deficiency in rice shoots: identification of novel induced genes using RDA and possible relation to leaf senescence

Rice plants are highly susceptible to Fe-deficiency. Under nutrient deprivation, plant cells undergo extensive metabolic changes for their continued survival. To provide further insight into the pathways induced during Fe-deficiency, rice seedlings were grown for 3, 6 and 9 days in the presence or absence of Fe. Using RDA (Representational Difference Analysis), sequences of 32 induced genes in rice shoots under Fe-deficiency were identified. About 30% of the sequences found have been previously reported as responsive to other abiotic and even biotic stresses. However, this is the first report that indicates their relation to Fe deprivation. Differential expression of selected genes was confirmed by semi-quantitative RT-PCR analysis. The identification of classical senescence-related sequences, such as lipase EC 3.1.1.-, ubiquitin-conjugating enzyme EC 6.3.2.19, beta-Glucosidase EC 3.2.1.21 and cysteine synthase EC 2.5.1.47, besides the higher accumulation of total soluble sugars prior to the decrease of total chlorophyll content in Fe-deficient leaves, indicate that sugar accumulation may be one of the factors leading to premature leaf senescence induced by Fe-deficiency.

The WRKY70 transcription factor of Arabidopsis influences both the plant senescence and defense signaling pathways

Regulatory proteins play critical roles in controlling the kinetics of various cellular processes during the entire life span of an organism. Leaf senescence, an integral part of the plant developmental program, is fine-tuned by a complex transcriptional regulatory network ensuring a successful switch to the terminal life phase. To expand our understanding on how transcriptional control coordinates leaf senescence, we characterized AtWRKY70, a gene encoding a WRKY transcription factor that functions as a negative regulator of developmental senescence. To gain insight into the interplay of senescence and plant defense signaling pathways, we employed a collection of mutants, allowing us to specifically define the role of AtWRKY70 in the salicylic acid-mediated signaling cascades and to further dissect the cross-talk of signal transduction pathways during the onset of senescence in Arabidopsis thaliana. Our results provide strong evidence that AtWRKY70 influences plant senescence and defense signaling pathways. These studies could form the basis for further unraveling of these two complex interlinked regulatory networks.

Arabidopsis ESK1 encodes a novel regulator of freezing tolerance

The eskimo1 (esk1) mutation of Arabidopsis resulted in a 5.5 degrees C improvement in freezing tolerance in the absence of cold acclimation. Here we show that the increase in freezing tolerance is not associated with any increase in the ability to survive drought or salt stresses, which are similar to freezing in their induction of cellular dehydration. Genome-wide comparisons of gene expression between esk1-1 and wild type indicate that mutations at esk1 result in altered expression of transcription factors and signaling components and of a set of stress-responsive genes. Interestingly, the list of 312 genes regulated by ESK1 shows greater overlap with sets of genes regulated by salt, osmotic and abscisic acid treatments than with genes regulated by cold acclimation or by the transcription factors CBF3 and ICE1, which have been shown to control genetic pathways for freezing tolerance. Map-based cloning identified the esk1 locus as At3g55990. The wild-type ESK1 gene encodes a 57-kDa protein and is a member of a large gene family of DUF231 domain proteins whose members encode a total of 45 proteins of unknown function. Our results indicate that ESK1 is a novel negative regulator of cold acclimation. Mutations in the ESK1 gene provide strong freezing tolerance through genetic regulation that is apparently very different from previously described genetic mechanisms of cold acclimation.

Subtractive hybridization techniques to study cellular senescence

Molecular and cellular processes related to the senescence syndrome are determined by programs of differential gene expression. Subtractive cDNA hybridization is a powerful approach to identify and isolate differentially expressed genes in various systems. A highly effective method, termed suppression subtractive hybridization (SSH), has been applied for the generation of subtracted cDNA library of senescing leaves. The method consists of two main stages, the normalization step that equalizes the abundance of cDNAs within the target population and the subtraction step that eliminates the common sequences between the target and the driver populations. The successful generation of library containing high numbered of rare and abundant cDNA clones in senescing plant cells proves the applicability of this method for global identification of differentially expressed genes during cellular senescence.

Senescence-associated genes induced during compatible viral interactions with grapevine and Arabidopsis

The senescence process is the last stage in leaf development and is characterized by dramatic changes in cellular metabolism and the degeneration of cellular structures. Several reports of senescence-associated genes (SAGs) have appeared, and an overlap in some of the genes induced during senescence and pathogen infections has been observed. For example, the enhanced expression of SAGs in response to diseases caused by fungi, bacteria, and viruses that trigger the hypersensitive response (HR) or during infections induced by virulent fungi and bacteria that elicit necrotic symptoms has been observed. The present work broadens the search for SAGs induced during compatible viral interactions with both the model plant Arabidopsis thaliana and a commercially important grapevine cultivar. The transcript profiles of Arabidopsis ecotype Uk-4 infected with tobacco mosaic virus strain Cg (TMV-Cg) and Vitis vinifera cv. Carménère infected with grapevine leafroll-associated virus strain 3 (GLRaV-3) were analysed using microarray slides of the reference species Arabidopsis. A large number of SAGs exhibited altered expression during these two compatible interactions. Among the SAGs were genes that encode proteins such as proteases, lipases, proteins involved in the mobilization of nutrients and minerals, transporters, transcription factors, proteins related to translation and antioxidant enzymes, among others. Thus, part of the plant's response to virus infection appears to be the activation of the senescence programme. Finally, it was demonstrated that several virus-induced genes are also expressed at elevated levels during natural senescence in healthy plants.