Co-expression analysis reveals a group of genes potentially involved in regulation of plant response to iron-deficiency

The potential of arbuscular mycorrhizal fungi to enhance metallic micronutrient uptake and mitigate food contamination in agriculture: prospects and challenges

Optimizing agroecosystems and crops for micronutrient uptake while reducing issues with inorganic contaminants (metal(loid)s) is a challenging task. One promising approach is to use arbuscular mycorrhizal fungi (AMF) and investigate the physiological, molecular and epigenetic changes that occur in their presence and that lead to changes in plant metal(loid) concentration (biofortification of micronutrients or mitigation of contaminants). Moreover, it is important to understand these mechanisms in the context of the soil microbiome, particularly those interactions of AMF with other soil microbes that can further shape crop nutrition. To address these challenges, a two-pronged approach is recommended: exploring molecular mechanisms and investigating microbiome management and engineering. Combining both approaches can lead to benefits in human health by balancing nutrition and contamination caused by metal(loid)s in the agro-ecosystem.

Indole-3-acetaldoxime delays root iron-deficiency responses and modify auxin homeostasis in Medicago truncatula

Iron (Fe) is an essential plant micronutrient, being a major limiting growth factor in calcareous soils. To increase Fe uptake, plants induce lateral roots growth, the expression of a Fe(III)-chelate reductase (FCR), a Fe(II)-transporter and a H⁺-ATPase and the secretion of flavins. Furthermore, auxin hormone family is involved in the Fe-deficiency responses but the action mechanism remains elusive. In this work, we evaluated the effect of the auxin-precursor indole-3-acetaldoxime (IAOx) on hydroponically grown Medicago truncatula plants under different Fe conditions. Upon 4-days of Fe starvation, the pH of the nutrient solution decreased, while both the FCR activity and the presence of flavins increased. Exogenous IAOx increased lateral roots growth contributing to superroot phenotype, decreased chlorosis, and delayed up to 3-days the pH-decrease, the FCR-activity increase, and the presence of flavins, compared to Fe-deficient plants. Gene expression levels were in concordance with the physiological responses. RESULTS: showed that IAOx was immediately transformed to IAN in roots and shoots to maintain auxin homeostasis. IAOx plays an active role in iron homeostasis delaying symptoms and responses in Fe-deficient plants. We may speculate that IAOx or its derivatives remobilize Fe from root cells to alleviate Fe-deficiency. Overall, these results point out that the IAOx-derived phenotype may have advantages to overcome nutritional stresses.

Saline-alkali stress tolerance is enhanced by MhPR1 in Malus halliana leaves as shown by transcriptomic analyses

qRT-PCR analysis showed that MhPR1 was strongly induced by saline-alkali stress. Overexpression of MhPR1 enhanced tolerance to saline-alkali stress in transgenic tobacco (Nicotiana tabacum L.) and apple calli. Abstract: Soil salinization seriously threaten apple growth in Northwest loess plateau of China. Malus halliana has developed special system to adapt to saline-alkali environmental stress. To obtain a more detailed understanding of the adaptation mechanisms involved in M. halliana, a transcriptomic approach was used to analyze the leaves' pathways in the stress and its regulatory mechanisms. RNA-Seq showed that among the 16,246 investigated unigenes under saline-alkali stress, 7268 genes were up-regulated and 8978 genes were down-regulated. KEGG analysis indicated that most of the enriched saline-alkali-responsive genes were mainly involved in plant hormone, calcium signal transduction, amino acids, carotenoid and flavonoids biosynthesis, carbon and phenylalanine metabolism, and other secondary metabolites. Expression profile analysis by quantitative real-time PCR confirmed that the maximum up-regulation of MhPR1 under saline-alkali stress was 7.1 folds in leaves. Overexpression of MhPR1 enhanced tolerance to saline-alkali stress in transgenic tobacco (Nicotiana tabacum L.) and apple calli. Taken together, our results demonstrate that MhPR1 encodes a saline-alkali-responsive transcriptional activator and provide valuable information for further study of PR1 functions in apple.

Loss-of-function mutations in the ERF96 gene enhance iron-deficient tolerance in Arabidopsis

Iron is an essential micronutrient for plant growth and development. Here we provide evidence for a role of ERF96 in iron-deficiency response in Arabidopsis thaliana. The ERF96-loss-of-function mutants were found to be more tolerant to iron-deficiency stress than wild type (WT) and to have higher iron and chlorophyll content. Further studies showed that the transcriptional levels of iron-uptake related genes IRT1, FRO2, AHA2, FIT and bHLH38 in mutants were significantly higher than in WT under iron deficiency. Comparative transcriptome analysis suggested that the differentially expressed genes (DEGs) between ERF96-loss-of-function mutant and WT under iron deficiency were mainly enriched in iron uptake and chlorophyll degradation. According to the specific analysis of these two kinds of DEGs, the expression of iron uptake and transport related genes in ERF96-loss-of-function mutant was higher and the expression of chlorophyll degradation related genes was lower under iron deficiency. Furthermore, loss-of-function of ERF96 influenced the plant hormone, especially auxin and ethylene signal transduction. Altogether, our results demonstrate that loss-of-function of ERF96 increased Fe uptake and chlorophyll level through ethylene and auxin signal pathway in the regulation of iron-deficiency response in Arabidopsis.

Identification of Malus halliana R2R3-MYB gene family under iron deficiency stress and functional characteristics of MhR2R3-MYB4 in Arabidopsis thaliana

Iron (Fe) is an essential element for plant growth and development. Fe deficiency can trigger leaf chlorosis and reduce fruit yield. Therefore, it is necessary to explore transcription factors in response to Fe deficiency stress. A total of 29 MhR2R3-MYB transcription factors were identified based on the transcriptome of Malus halliana under Fe deficiency stress. A comprehensive analysis of physical and chemical properties, gene structures, conserved motif composition, evolutionary relationship and chromosome distribution was performed. Subsequently, based on the transcriptome, 14 genes with the most significant expression under Fe deficiency stress were screened for qRT-PCR verification. Among them,the functional characteristics of MhR2R3-MYB4 (MD05G1089600) were further studied in Arabidopsis thaliana. Expression of 13 out of these 14 genes was upregulated, only one was downregulated. Maximum upregulation of MhR2R3-MYB4 under Fe deficiency was 36.39-fold and 58.21-fold compared with day 0 in leaves and roots, respectively. Overexpression of MhR2R3-MYB4 enhanced tolerance to Fe deficiency in A. thaliana and led to multiple biochemical changes: transgenic lines have higher chl a, chl b and Fe²⁺ content, higher enzyme activity (SOD, POD, CAT and FCR) and lower chlorosis than the wild type in Fe deficiency conditions. We suggest that MhR2R3-MYB4 plays an important part in Fe deficiency stress, which may contribute to improve Fe deficiency tolerance of apple in future.

MfbHLH38, a Myrothamnus flabellifolia bHLH transcription factor, confers tolerance to drought and salinity stresses in Arabidopsis

BACKGROUND

The basic helix-loop-helix (bHLH) proteins, a large transcription factors family, are involved in plant growth and development, and defensive response to various environmental stresses. The resurrection plant Myrothamnus flabellifolia is known for its extremely strong drought tolerance, but few bHLHs taking part in abiotic stress response have been unveiled in M. flabellifolia.

RESULTS

In the present research, we cloned and characterized a dehydration-inducible gene, MfbHLH38, from M. flabellifolia. The MfbHLH38 protein is localized in the nucleus, where it may act as a transcription factor. Heterologous expression of MfbHLH38 in Arabidopsis improved the tolerance to drought and salinity stresses, as determined by the studies on physiological indexes, such as contents of chlorophyll, malondialdehyde (MDA), proline (Pro), soluble protein, and soluble sugar, water loss rate of detached leaves, reactive oxygen species (ROS) accumulation, as well as antioxidant enzyme activities. Besides, MfbHLH38 overexpression increased the sensitivity of stomatal closure to mannitol and abscisic acid (ABA), improved ABA level under drought stress, and elevated the expression of genes associated with ABA biosynthesis and ABA responding, sucha as NCED3, P5CS, and RD29A.

CONCLUSIONS

Our results presented evidence that MfbHLH38 enhanced tolerance to drought and salinity stresses in Arabidopsis through increasing water retention ability, regulating osmotic balance, decreasing stress-induced oxidation damage, and possibly participated in ABA-dependent stress-responding pathway.

Comprehensive Understanding of the Interaction Among Stress Hormones Signalling Pathways by Gene Co-expression Network

Background:

Plants respond to various stresses at the same time. Recent studies show that interactions of various phytohormones can play important roles in response to stresses.

Objective:

Although many studies have been done about the effects of the individual hormones, little information exists about the crosstalk among the hormone signalling pathways in plants.

Methods:

In this work, the weighted gene co-expression network analysis method was used to define modules containing genes with highly correlated expression patterns in response to abscisic acid, jasmonic acid, and salicylic acid in Arabidopsis.

Results:

Results indicate that plant hormones cause major changes the expression profile and control diverse cell functions, including response to environmental stresses and external factors, cell cycle, and antioxidant activity. In addition, AtbHLH15 and HY5 transcription factors can participate in phytochrome pathways in response to the phytohormones. It is probable that some Type III WRKY transcription factors control the response to bacterium separately from the other stresses. The E2Fa/DPa transcription factor also regulates the cell cycle.

Conclusion:

In general, many processes and pathways in plants may be regulated using a combination of abscisic acid, jasmonic acid, and salicylic acid.

Understanding the Role of the Antioxidant System and the Tetrapyrrole Cycle in Iron Deficiency Chlorosis

Iron deficiency chlorosis (IDC) is an abiotic stress often experienced by soybean, owing to the low solubility of iron in alkaline soils. Here, soybean lines with contrasting Fe efficiencies were analyzed to test the hypothesis that the Fe efficiency trait is linked to antioxidative stress signaling via proper management of tissue Fe accumulation and transport, which in turn influences the regulation of heme and non heme containing enzymes involved in Fe uptake and ROS scavenging. Inefficient plants displayed higher oxidative stress and lower ferric reductase activity, whereas root and leaf catalase activity were nine-fold and three-fold higher, respectively. Efficient plants do not activate their antioxidant system because there is no formation of ROS under iron deficiency; while inefficient plants are not able to deal with ROS produced under iron deficiency because ascorbate peroxidase and superoxide dismutase are not activated because of the lack of iron as a cofactor, and of heme as a constituent of those enzymes. Superoxide dismutase and peroxidase isoenzymatic regulation may play a determinant role: 10 superoxide dismutase isoenzymes were observed in both cultivars, but iron superoxide dismutase activity was only detected in efficient plants; 15 peroxidase isoenzymes were observed in the roots and trifoliate leaves of efficient and inefficient cultivars and peroxidase activity levels were only increased in roots of efficient plants.

Co-expression networks for plant biology: why and how

Co-expression network analysis is one of the most powerful approaches for interpretation of large transcriptomic datasets. It enables characterization of modules of co-expressed genes that may share biological functional linkages. Such networks provide an initial way to explore functional associations from gene expression profiling and can be applied to various aspects of plant biology. This review presents the applications of co-expression network analysis in plant biology and addresses optimized strategies from the recent literature for performing co-expression analysis on plant biological systems. Additionally, we describe the combined interpretation of co-expression analysis with other genomic data to enhance the generation of biologically relevant information.

Physiological and transcriptomic data highlight common features between iron and phosphorus acquisition mechanisms in white lupin roots

In agricultural soil, the bioavailability of iron (Fe) and phosphorus (P) is often below the plant's requirement causing nutritional deficiency in crops. Under P-limiting conditions, white lupin (Lupinus albus L.) activates mechanisms that promote P solubility in the soil through morphological, physiological and molecular adaptations. Similar changes occur also in Fe-deficient white lupin roots; however, no information is available on the molecular bases of the response. In the present work, responses to Fe and P deficiency and their reciprocal interactions were studied. Transcriptomic analyses indicated that white lupin roots upregulated Fe-responsive genes ascribable to Strategy-I response, this behaviour was mainly evident in cluster roots. The upregulation of some components of Fe-acquisition mechanism occurred also in P-deficient cluster roots. Concerning P acquisition, some P-responsive genes (as phosphate transporters and transcription factors) were upregulated by P deficiency as well by Fe deficiency. These data indicate a strong cross-connection between the responses activated under Fe or P deficiency in white lupin. The activation of Fe- and P-acquisition mechanisms might play a crucial role to enhance the plant's capability to mobilize both nutrients in the rhizosphere, especially P from its associated metal cations.

The basic helix-loop-helix transcription factor, bHLH11 functions in the iron-uptake system in Arabidopsis thaliana

Iron (Fe) is a micronutrient that is essential for plant development and growth. Basic helix-loop-helix (bHLH) transcription factors are a superfamily of transcription factors that are important regulatory components in transcriptional networks in plants. bHLH transcription factors have been divided into subclasses based on their amino acid sequences and domain structures. Among the members of clade IVb (PYE, bHLH121, and bHLH11), the functions of bHLH11 remain unclear. In the present study, we characterized bHLH11 as a negative regulator of Fe homeostasis. bHLH11 expression levels were high in the roots and up-regulated after plants were transferred to Fe sufficient conditions. Although T-DNA knockout mutants of bHLH11 were lethal, dominant negative (DN-) and overexpression (OX-) of bHLH11 plants exhibited sensitivity to Fe deficiency. Furthermore, the expression of FIT, a master regulator of Fe deficiency responses, was suppressed in the transgenic plants. These results suggest that the transcriptional repressor bHLH11 functions as a negative regulator of FIT-dependent Fe uptake and modulates Fe levels in Arabidopsis plants. Salicylic acid (SA) modulates the expression of genes involved in Fe-deficient responses. We found that SA levels were elevated in DN- and OX-bHLH11 plants. The T-DNA insertion mutant sid2-1, which was defective for the production of SA, did not exhibit sensitivity to Fe deficiency; however, the crossed plants of OX-bHLH11 and sid2-1 relieved sensitivity to the Fe deficiency observed in OX-bHLH11 plants. These results suggest that the accumulation of SA is closely related to iron homeostasis.

The ethylene response factor AtERF4 negatively regulates the iron deficiency response in Arabidopsis thaliana

Iron (Fe) deficiency is one of many conditions that can seriously damage crops. Low levels of photosynthesis can lead to the degradation of chlorophyll content and impaired respiration in affected plants, which together cause poor growth and reduce quality. Although ethylene plays an important role in responses to Fe deficiency, a limited number of studies have been carried out on ethylene response factor (ERFs) as components of plant regulation mechanisms. Thus, this study aimed to investigate the role of AtERF4 in plant responses to Fe deficiency. Results collected when Arabidopsis thaliana was grown under Fe deficient conditions as well as in the presence of 1-aminocyclopropane-1-carboxylic acid (ACC) revealed that leaf chlorosis did not occur over short timescales and that chloroplast structural integrity was retained. At the same time, expression of the chlorophyll degradation-related genes AtPAO and AtCLH1 was inhibited and net H+ root flux was amplified. Our results show that chlorophyll content was enhanced in the mutant erf4, while expression of the chlorophyll degradation gene AtCLH1 was reduced. Ferric reductase activity in roots was also significantly higher in the mutant than in wild type plants, while erf4 caused high levels of expression of the genes AtIRT1 and AtHA2 under Fe deficient conditions. We also utilized yeast one-hybrid technology in this study to determine that AtERF4 binds directly to the AtCLH1 and AtITR1 promoter. Observations show that transient over-expression of AtERF4 resulted in rapid chlorophyll degradation in the leaves of Nicotiana tabacum and the up-regulation of gene AtCLH1 expression. In summary, AtERF4 plays an important role as a negative regulator of Fe deficiency responses, we hypothesize that AtERF4 may exert a balancing effect on plants subject to nutrition stress.

Genome-wide analysis of gene expression profiling revealed that COP9 signalosome is essential for correct expression of Fe homeostasis genes in Arabidopsis

In plant cells, either excess or insufficient iron (Fe) concentration triggers stress responses, therefore it is strictly controlled. Proteasome-mediated degradation through ubiquitination of Fe homeostasis proteins has just become the focus of research in recent years. Deactivating ubiquitin ligases, COP9 signalosome has a central importance in the translational control of various stress responses. The aim of the study was to investigate COP9 signalosome in Fe deficiency response of Strategy I plants. In silico analysis of a set of Fe-deficiency-responsive genes was conducted against the transcriptome of Arabidopsis csn mutant lines using Genevestigator software. Induced and suppressed genes were clustered in a hierarchical way and gene ontology enrichment categories were identified. In wild-type Arabidopsis, CSN genes did not respond to iron deficiency. In csn mutant lines, under Fe-sufficient conditions, hundreds of Fe-deficiency-responsive genes were misregulated. Among the ones previously characterized for their physiological roles under Fe deficiency IRT1, NAS4, BTS, NRAMP1 were down-regulated while AHA2, MTP8, FRD3 were up-regulated. Unexpectedly, from those which were regulated in opposite ways, some had been repeatedly shown to be tightly co-regulated by the same transcription factor, FIT. Two proteins from DELLA family, which were reported to interact with FIT to repress its downstream, were found to be strikingly repressed in csn mutants. Overall, the study underlined that the absence of a functional CSN greatly impacted the regulation of Fe homeostasis-related genes, in a manner which cannot be explained simply by the induction of the master transcription factor, FIT. Correct expression of Fe deficiency-responsive genes requires an intact COP9 signalosome in Arabidopsis.

Ethylene response factor AtERF72 negatively regulates Arabidopsis thaliana response to iron deficiency

Ethylene regulates the plant's response to stress caused by iron (Fe) deficiency. However, specific roles of ERF proteins in response to Fe deficiency remain poorly understood. Here, we investigated the role of ERF72 in response to iron deficiency in Arabidopsis thaliana. In this study, the levels of the ethylene response factor AtERF72 increased in leaves and roots induced under the iron deficient conditions. erf72 mutant plants showed increased growth compared to wild type (WT) when grown in iron deficient medium for 5 d. erf72 mutants had increased root H⁺ velocity and the ferric reductase activity, and increase in the expression of the iron deficiency response genes iron-regulated transporter 1 (IRT1) and H⁺-ATPase (HA2) levels in iron deficient conditions. Compared to WT plants, erf72 mutants retained healthy chloroplast structure with significantly higher Fe and Mg content, and decreased chlorophyll degradation gene pheophorbide a oxygenase (PAO) and chlorophyllase (CLH1) expression when grown in iron deficient media. Yeast one-hybrid analysis showed that ERF72 could directly bind to the promoter regions of iron deficiency responses genes IRT1, HA2 and CLH1. Based on our results, we suggest that ethylene released from plants under iron deficiency stress can activate the expression of ERF72, which responds to iron deficiency in the negative regulation.

Transcriptional and physiological analyses of Fe deficiency response in maize reveal the presence of Strategy I components and Fe/P interactions

Background

Under limited iron (Fe) availability maize, a Strategy II plant, improves Fe acquisition through the release of phytosiderophores (PS) into the rhizosphere and the subsequent uptake of Fe-PS complexes into root cells. Occurrence of Strategy-I-like components and interactions with phosphorous (P) nutrition has been hypothesized based on molecular and physiological studies in grasses.

Results

In this report transcriptomic analysis (NimbleGen microarray) of Fe deficiency response revealed that maize roots modulated the expression levels of 724 genes (508 up- and 216 down-regulated, respectively). As expected, roots of Fe-deficient maize plants overexpressed genes involved in the synthesis and release of 2’-deoxymugineic acid (the main PS released by maize roots). A strong modulation of genes involved in regulatory aspects, Fe translocation, root morphological modification, primary metabolic pathways and hormonal metabolism was induced by the nutritional stress. Genes encoding transporters for Fe²⁺ (ZmNRAMP1) and P (ZmPHT1;7 and ZmPHO1) were also up-regulated under Fe deficiency.

Fe-deficient maize plants accumulated higher amounts of P than the Fe-sufficient ones, both in roots and shoots. The supply of 1 μM ⁵⁹Fe, as soluble (Fe-Citrate and Fe-PS) or sparingly soluble (Ferrihydrite) sources to deficient plants, caused a rapid down-regulation of genes coding for PS and Fe(III)-PS transport, as well as of ZmNRAMP1 and ZmPHT1;7.

Levels of ³²P absorption essentially followed the rates of ⁵⁹Fe uptake in Fe-deficient plants during Fe resupply, suggesting that P accumulation might be regulated by Fe uptake in maize plants.

Conclusions

The transcriptional response to Fe-deficiency in maize roots confirmed the modulation of known genes involved in the Strategy II and revealed the presence of Strategy I components usually described in dicots. Moreover, data here presented provide evidence of a close relationship between two essential nutrients for plants, Fe and P, and highlight a key role played by Fe and P transporters to preserve the homeostasis of these two nutrients in maize plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3478-4) contains supplementary material, which is available to authorized users.

Involvement of endogenous salicylic acid in iron-deficiency responses in Arabidopsis

Several phytohormones have been demonstrated to be involved in iron (Fe) homeostasis. We took advantage of a salicylic acid (SA) biosynthesis defective mutant phytoalexin deficient 4 (pad4: T-DNA Salk_089936) to explore the possible effects of endogenous SA on the morphological and physiological responses to Fe deprivation. The morphological and physiological analysis was carried out between Col-0 and the pad4 mutant. Under an Fe-deficiency treatment, Col-0 showed more severe leaf chlorosis and root growth inhibition compared with the pad4 mutant. The soluble Fe concentrations were significantly higher in pad4 than in Col-0 under the Fe-deficiency treatment. Fe deficiency significantly induced SA accumulation in Col-0 and the loss-of-function of PAD4 blocked this process. The requirement of endogenous SA accumulation for Fe-deficiency responses was confirmed using a series of SA biosynthetic mutants and transgenic lines. Furthermore, a comparative RNA sequencing analysis of the whole seedling transcriptomes between Col-0 and the pad4 mutant was also performed. Based on the transcriptome data, the expression levels of many auxin- and ethylene-response genes were altered in pad4 compared with Col-0. Fe deficiency increases SA contents which elevates auxin and ethylene signalling, thereby activating Fe translocation via the bHLH38/39-mediated transcriptional regulation of downstream Fe genes.

A cotton miRNA is involved in regulation of plant response to salt stress

The present study functionally identified a new microRNA (microRNA ovual line 5, miRNVL5) with its target gene GhCHR from cotton (Gossypium hirsutum). The sequence of miRNVL5 precursor is 104 nt long, with a well developed secondary structure. GhCHR contains two DC1 and three PHD Cys/His-rich domains, suggesting that GhCHR encodes a zinc-finger domain-containing transcription factor. miRNVL5 and GhCHR express at various developmental stages of cotton. Under salt stress (50-400 mM NaCl), miRNVL5 expression was repressed, with concomitant high expression of GhCHR in cotton seedlings. Ectopic expression of GhCHR in Arabidopsis conferred salt stress tolerance by reducing Na(+) accumulation in plants and improving primary root growth and biomass. Interestingly, Arabidopsis constitutively expressing miRNVL5 showed hypersensitivity to salt stress. A GhCHR orthorlous gene At2g44380 from Arabidopsis that can be cleaved by miRNVL5 was identified by degradome sequencing, but no confidential miRNVL5 homologs in Arabidopsis have been identified. Microarray analysis of miRNVL5 transgenic Arabidopsis showed six downstream genes (CBF1, CBF2, CBF3, ERF4, AT3G22920, and AT3G49200), which were induced by salt stress in wild-type but repressed in miRNVL5-expressing Arabidopsis. These results indicate that miRNVL5 is involved in regulation of plant response to salt stress.

Early transcriptomic response to Fe supply in Fe-deficient tomato plants is strongly influenced by the nature of the chelating agent

BACKGROUND

It is well known that in the rhizosphere soluble Fe sources available for plants are mainly represented by a mixture of complexes between the micronutrient and organic ligands such as carboxylates and phytosiderophores (PS) released by roots, as well as fractions of humified organic matter. The use by roots of these three natural Fe sources (Fe-citrate, Fe-PS and Fe complexed to water-extractable humic substances, Fe-WEHS) have been already studied at physiological level but the knowledge about the transcriptomic aspects is still lacking.

RESULTS

The (59)Fe concentration recorded after 24 h in tissues of tomato Fe-deficient plants supplied with (59)Fe complexed to WEHS reached values about 2 times higher than those measured in response to the supply with Fe-citrate and Fe-PS. However, after 1 h no differences among the three Fe-chelates were observed considering the (59)Fe concentration and the root Fe(III) reduction activity. A large-scale transcriptional analysis of root tissue after 1 h of Fe supply showed that Fe-WEHS modulated only two transcripts leaving the transcriptome substantially identical to Fe-deficient plants. On the other hand, Fe-citrate and Fe-PS affected 728 and 408 transcripts, respectively, having 289 a similar transcriptional behaviour in response to both Fe sources.

CONCLUSIONS

The root transcriptional response to the Fe supply depends on the nature of chelating agents (WEHS, citrate and PS). The supply of Fe-citrate and Fe-PS showed not only a fast back regulation of molecular mechanisms modulated by Fe deficiency but also specific responses due to the uptake of the chelating molecule. Plants fed with Fe-WEHS did not show relevant changes in the root transcriptome with respect to the Fe-deficient plants, indicating that roots did not sense the restored cellular Fe accumulation.

Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus

Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.

Characterization of long non-coding RNAs involved in cadmium toxic response in Brassica napus

There is increasing evidence of long non-coding RNA (lncRNA) involvement in a variety of biological responses to environmental stresses.

RNA-sequencing Oryza sativa transcriptome in response to herbicide isoprotruon and characterization of genes involved in IPU detoxification

The comprehensive analysis of transcriptome and UPLC-MS/MS in rice was performed to explore the regulatory mechanism of mRNA level and chemical metabolism in response to herbicide isoproturon.

The F-box family genes as key elements in response to salt, heavy mental, and drought stresses in Medicago truncatula

F-box protein is a subunit of Skp1-Rbx1-Cul1-F-box protein (SCF) complex with typically conserved F-box motifs of approximately 40 amino acids and is one of the largest protein families in eukaryotes. F-box proteins play critical roles in selective and specific protein degradation through the 26S proteasome. In this study, we bioinformatically identified 972 putative F-box proteins from Medicago truncatula genome. Our analysis showed that in addition to the conserved motif, the F-box proteins have several other functional domains in their C-terminal regions (e.g., LRRs, Kelch, FBA, and PP2), some of which were found to be M. truncatula species-specific. By phylogenetic analysis of the F-box motifs, these proteins can be classified into three major families, and each family can be further grouped into more subgroups. Analysis of the genomic distribution of F-box genes on M. truncatula chromosomes revealed that the evolutional expansion of F-box genes in M. truncatula was probably due to localized gene duplications. To investigate the possible response of the F-box genes to abiotic stresses, both publicly available and customer-prepared microarrays were analyzed. Most of the F-box protein genes can be responding to salt and heavy metal stresses. Real-time PCR analysis confirmed that some of the F-box protein genes containing heat, drought, salicylic acid, and abscisic acid responsive cis-elements were able to respond to the abiotic stresses.