Coexpression-based clustering of Arabidopsis root genes predicts functional modules in early phosphate deficiency signaling

Skewing in Arabidopsis roots involves disparate environmental signaling pathways

BACKGROUND

Skewing root patterns provide key insights into root growth strategies and mechanisms that produce root architectures. Roots exhibit skewing and waving when grown on a tilted, impenetrable surface. The genetics guiding these morphologies have been examined, revealing that some Arabidopsis ecotypes skew and wave (e.g. WS), while others skew insignificantly but still wave (e.g. Col-0). The underlying molecular mechanisms of skewing and waving remain unclear. In this study, transcriptome data were derived from two Arabidopsis ecotypes, WS and Col-0, under three tilted growth conditions in order to identify candidate genes involved in skewing.

RESULTS

This work identifies a number of genes that are likely involved in skewing, using growth conditions that differentially affect skewing and waving. Comparing the gene expression profiles of WS and Col-0 in different tilted growth conditions identified 11 candidate genes as potentially involved in the control of skewing. These 11 genes are involved in several different cellular processes, including sugar transport, salt signaling, cell wall organization, and hormone signaling.

CONCLUSIONS

This study identified 11 genes whose change in expression level is associated with root skewing behavior. These genes are involved in signaling and perception, rather than the physical restructuring of root. Future work is needed to elucidate the potential role of these candidate genes during root skewing.

The Understanding of the Plant Iron Deficiency Responses in Strategy I Plants and the Role of Ethylene in This Process by Omic Approaches

Iron (Fe) is an essential plant micronutrient but is toxic in excess. Fe deficiency chlorosis is a major constraint for plant growth and causes severe losses of crop yields and quality. Under Fe deficiency conditions, plants have developed sophisticated mechanisms to keep cellular Fe homeostasis via various physiological, morphological, metabolic, and gene expression changes to facilitate the availability of Fe. Ethylene has been found to be involved in the Fe deficiency responses of plants through pharmacological studies or by the use of ethylene mutants. However, how ethylene is involved in the regulations of Fe starvation responses remains not fully understood. Over the past decade, omics approaches, mainly focusing on the RNA and protein levels, have been used extensively to investigate global gene expression changes under Fe-limiting conditions, and thousands of genes have been found to be regulated by Fe status. Similarly, proteome profiles have uncovered several hallmark processes that help plants adapt to Fe shortage. To find out how ethylene participates in the Fe deficiency response and explore putatively novel regulators for further investigation, this review emphasizes the integration of those genes and proteins, derived from omics approaches, regulated both by Fe deficiency, and ethylene into a systemic network by gene co-expression analysis.

Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs

Plants and other multicellular organisms consist of many types of specialized cells. Systems-wide exploration of large-scale information from singe cell level is essential to understand how cell works. Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, in the interaction with microbe, and in plant anchorage, and represent an ideal model to study the biology of a single cell type. Single cell sampling combined with omics approaches has been applied to study plant root hairs. This review emphasizes the integration of omics approaches towards understanding the systems biology of root hairs, unraveling the common and plant species-specific properties of root hairs, as well as the concordance of protein and transcript abundance. Understanding plant root hair biology by mining the integrated omics data will provide a way to know how a single cell differentiates, elongates, and functions, which might help molecularly modify crops for developing sustainable agriculture practices.

Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots

Manganese (Mn) is pivotal for plant growth and development, but little information is available regarding the strategies that evolved to improve Mn acquisition and cellular homeostasis of Mn. Using an integrated RNA-based transcriptomic and high-throughput shotgun proteomics approach, we generated a comprehensive inventory of transcripts and proteins that showed altered abundance in response to Mn deficiency in roots of the model plant Arabidopsis. A suite of 22,385 transcripts was consistently detected in three RNA-seq runs; LC-MS/MS-based iTRAQ proteomics allowed the unambiguous determination of 11,606 proteins. While high concordance between mRNA and protein expression (R = 0.87) was observed for transcript/protein pairs in which both gene products accumulated differentially upon Mn deficiency, only approximately 10% of the total alterations in the abundance of proteins could be attributed to transcription, indicating a large impact of protein-level regulation. Differentially expressed genes spanned a wide range of biological functions, including the maturation, translation, and transport of mRNAs, as well as primary and secondary metabolic processes. Metabolic analysis by UPLC-qTOF-MS revealed that the steady-state levels of several major glucosinolates were significantly altered upon Mn deficiency in both roots and leaves, possibly as a compensation for increased pathogen susceptibility under conditions of Mn deficiency.

Mitochondrial and Chloroplast Stress Responses Are Modulated in Distinct Touch and Chemical Inhibition Phases

Previous studies have identified a range of transcription factors that modulate retrograde regulation of mitochondrial and chloroplast functions in Arabidopsis (Arabidopsis thaliana). However, the relative importance of these regulators and whether they act downstream of separate or overlapping signaling cascades is still unclear. Here, we demonstrate that multiple stress-related signaling pathways, with distinct kinetic signatures, converge on overlapping gene sets involved in energy organelle function. The transcription factor ANAC017 is almost solely responsible for transcript induction of marker genes around 3 to 6 h after chemical inhibition of organelle function and is a key regulator of mitochondrial and specific types of chloroplast retrograde signaling. However, an independent and highly transient gene expression phase, initiated within 10 to 30 min after treatment, also targets energy organelle functions, and is related to touch and wounding responses. Metabolite analysis demonstrates that this early response is concurrent with rapid changes in tricarboxylic acid cycle intermediates and large changes in transcript abundance of genes encoding mitochondrial dicarboxylate carrier proteins. It was further demonstrated that transcription factors AtWRKY15 and AtWRKY40 have repressive regulatory roles in this touch-responsive gene expression. Together, our results show that several regulatory systems can independently affect energy organelle function in response to stress, providing different means to exert operational control.

ROS Regulation of Polar Growth in Plant Cells

Root hair cells and pollen tubes, like fungal hyphae, possess a typical tip or polar cell expansion with growth limited to the apical dome. Cell expansion needs to be carefully regulated to produce a correct shape and size. Polar cell growth is sustained by oscillatory feedback loops comprising three main components that together play an important role regulating this process. One of the main components are reactive oxygen species (ROS) that, together with calcium ions (Ca(2+)) and pH, sustain polar growth over time. Apoplastic ROS homeostasis controlled by NADPH oxidases as well as by secreted type III peroxidases has a great impact on cell wall properties during cell expansion. Polar growth needs to balance a focused secretion of new materials in an extending but still rigid cell wall in order to contain turgor pressure. In this review, we discuss the gaps in our understanding of how ROS impact on the oscillatory Ca(2+) and pH signatures that, coordinately, allow root hair cells and pollen tubes to expand in a controlled manner to several hundred times their original size toward specific signals.

Discriminative gene co-expression network analysis uncovers novel modules involved in the formation of phosphate deficiency-induced root hairs in Arabidopsis

Cell fate and differentiation in the Arabidopsis root epidermis are genetically defined but remain plastic to environmental signals such as limited availability of inorganic phosphate (Pi). Root hairs of Pi-deficient plants are more frequent and longer than those of plants grown under Pi-replete conditions. To dissect genes involved in Pi deficiency-induced root hair morphogenesis, we constructed a co-expression network of Pi-responsive genes against a customized database that was assembled from experiments in which differentially expressed genes that encode proteins with validated functions in root hair development were over-represented. To further filter out less relevant genes, we combined this procedure with a search for common cis-regulatory elements in the promoters of the selected genes. In addition to well-described players and processes such as auxin signalling and modifications of primary cell walls, we discovered several novel aspects in the biology of root hairs induced by Pi deficiency, including cell cycle control, putative plastid-to-nucleus signalling, pathogen defence, reprogramming of cell wall-related carbohydrate metabolism, and chromatin remodelling. This approach allows the discovery of novel of aspects of a biological process from transcriptional profiles with high sensitivity and accuracy.

Identification of phosphorus deficiency responsive proteins in a high phosphorus acquisition soybean (Glycine max) cultivar through proteomic analysis

As one of the major oil crops, soybean might be seriously affected by phosphorus deficiency on both yield and quality. Understanding the molecular basis of phosphorus uptake and utilization in soybean may help to develop phosphorus (P) efficient cultivars. On this purpose, we conducted a comparative proteomic analysis on a high P acquisition soybean cultivar BX10 under low and high P conditions. A total of 61 unique proteins were identified as putative P deficiency responsive proteins. These proteins were involved in carbohydrate metabolism, protein biosynthesis/processing, energy metabolism, cellular processes, environmental defense/interaction, nucleotide metabolism, signal transduction, secondary metabolism and other metabolism related processes. Several proteins involved in energy metabolism, cellular processes, and protein biosynthesis and processing were found to be up-regulated in both shoots and roots, whereas, proteins involved in carbohydrate metabolism appeared to be down-regulated. These proteins are potential candidates for improving P acquisition. These findings provide a useful starting point for further research that will provide a more comprehensive understanding of molecular mechanisms through which soybeans adapt to P deficiency condition.

Comparative expression profiling reveals a role of the root apoplast in local phosphate response

BACKGROUND

Plant adaptation to limited phosphate availability comprises a wide range of responses to conserve and remobilize internal phosphate sources and to enhance phosphate acquisition. Vigorous restructuring of root system architecture provides a developmental strategy for topsoil exploration and phosphate scavenging. Changes in external phosphate availability are locally sensed at root tips and adjust root growth by modulating cell expansion and cell division. The functionally interacting Arabidopsis genes, LOW PHOSPHATE RESPONSE 1 and 2 (LPR1/LPR2) and PHOSPHATE DEFICIENCY RESPONSE 2 (PDR2), are key components of root phosphate sensing. We recently demonstrated that the LOW PHOSPHATE RESPONSE 1 - PHOSPHATE DEFICIENCY RESPONSE 2 (LPR1-PDR2) module mediates apoplastic deposition of ferric iron (Fe(3+)) in the growing root tip during phosphate limitation. Iron deposition coincides with sites of reactive oxygen species generation and triggers cell wall thickening and callose accumulation, which interfere with cell-to-cell communication and inhibit root growth.

RESULTS

We took advantage of the opposite phosphate-conditional root phenotype of the phosphate deficiency response 2 mutant (hypersensitive) and low phosphate response 1 and 2 double mutant (insensitive) to investigate the phosphate dependent regulation of gene and protein expression in roots using genome-wide transcriptome and proteome analysis. We observed an overrepresentation of genes and proteins that are involved in the regulation of iron homeostasis, cell wall remodeling and reactive oxygen species formation, and we highlight a number of candidate genes with a potential function in root adaptation to limited phosphate availability. Our experiments reveal that FERRIC REDUCTASE DEFECTIVE 3 mediated, apoplastic iron redistribution, but not intracellular iron uptake and iron storage, triggers phosphate-dependent root growth modulation. We further highlight expressional changes of several cell wall-modifying enzymes and provide evidence for adjustment of the pectin network at sites of iron accumulation in the root.

CONCLUSION

Our study reveals new aspects of the elaborate interplay between phosphate starvation responses and changes in iron homeostasis. The results emphasize the importance of apoplastic iron redistribution to mediate phosphate-dependent root growth adjustment and suggest an important role for citrate in phosphate-dependent apoplastic iron transport. We further demonstrate that root growth modulation correlates with an altered expression of cell wall modifying enzymes and changes in the pectin network of the phosphate-deprived root tip, supporting the hypothesis that pectins are involved in iron binding and/or phosphate mobilization.

Vascular-mediated signalling involved in early phosphate stress response in plants

Depletion of finite global rock phosphate (Pi) reserves will impose major limitations on future agricultural productivity and food security. Hence, modern breeding programmes seek to develop Pi-efficient crops with sustainable yields under reduced Pi fertilizer inputs. In this regard, although the long-term responses of plants to Pi stress are well documented, the early signalling events have yet to be elucidated. Here, we show plant tissue-specific responses to early Pi stress at the transcription level and a predominant role of the plant vascular system in this process. Specifically, imposition of Pi stress induces rapid and major changes in the mRNA population in the phloem translocation stream, and grafting studies have revealed that many hundreds of phloem-mobile mRNAs are delivered to specific sink tissues. We propose that the shoot vascular system acts as the site of root-derived Pi stress perception, and the phloem serves to deliver a cascade of signals to various sinks, presumably to coordinate whole-plant Pi homeostasis.

The histone deacetylase HDA19 controls root cell elongation and modulates a subset of phosphate starvation responses in Arabidopsis

The length of root epidermal cells and their patterning into files of hair-bearing and non-hair cells are genetically determined but respond with high plasticity to environmental cues. Limited phyto-availability of the essential mineral nutrient phosphate (Pi) increases the number of root hairs by longitudinal shortening of epidermal cells and by reprogramming the fate of cells in positions normally occupied by non-hair cells. Through analysis of the root morphology and transcriptional profiles from transgenic Arabidopsis lines with altered expression of the histone deacetylase HDA19, we show that in an intricate interplay of Pi availability and intrinsic factors, HDA19 controls the epidermal cell length, probably by altering the positional bias that dictates epidermal patterning. In addition, HDA19 regulates several Pi-responsive genes that encode proteins with important regulatory or metabolic roles in the acclimation to Pi deficiency. In particular, HDA19 affects genes encoding SPX (SYG1/Pho81/XPR) domain-containing proteins and genes involved in membrane lipid remodeling, a key response to Pi starvation that increases the free Pi in plants. Our data add a novel, non-transcriptionally regulated component of the Pi signaling network and emphasize the importance of reversible post-translational histone modification for the integration of external signals into intrinsic developmental and metabolic programs.

The histone deacetylase HDA19 controls root cell elongation and modulates a subset of phosphate starvation responses in Arabidopsis

The length of root epidermal cells and their patterning into files of hair-bearing and non-hair cells are genetically determined but respond with high plasticity to environmental cues. Limited phyto-availability of the essential mineral nutrient phosphate (Pi) increases the number of root hairs by longitudinal shortening of epidermal cells and by reprogramming the fate of cells in positions normally occupied by non-hair cells. Through analysis of the root morphology and transcriptional profiles from transgenic Arabidopsis lines with altered expression of the histone deacetylase HDA19, we show that in an intricate interplay of Pi availability and intrinsic factors, HDA19 controls the epidermal cell length, probably by altering the positional bias that dictates epidermal patterning. In addition, HDA19 regulates several Pi-responsive genes that encode proteins with important regulatory or metabolic roles in the acclimation to Pi deficiency. In particular, HDA19 affects genes encoding SPX (SYG1/Pho81/XPR) domain-containing proteins and genes involved in membrane lipid remodeling, a key response to Pi starvation that increases the free Pi in plants. Our data add a novel, non-transcriptionally regulated component of the Pi signaling network and emphasize the importance of reversible post-translational histone modification for the integration of external signals into intrinsic developmental and metabolic programs.

Genome-wide analysis of overlapping genes regulated by iron deficiency and phosphate starvation reveals new interactions in Arabidopsis roots

Background

Iron (Fe) and phosphorus (P) are essential mineral nutrients in plants. Knowledge regarding global changes in the abundance of Fe-responsive genes under Pi deficiency as well as the processes these genes are involved in remains largely unavailable at the genome level. In the current study, we comparatively analyzed RNA sequencing data sets relative to Fe deficiency (NCBI: SRP044814) and Pi starvation (NCBI: SRA050356.1).

Results

Analysis showed a total of 579 overlapping genes that are responsible for both Fe deficiency and Pi starvation in Arabidopsis roots. A subset of 137 genes had greater than twofold changes in transcript abundant as a result of the treatments. Gene ontology (GO) analysis showed that the stress-related processes ‘response to salt stress’, ‘response to oxidative stress’, and ‘response to zinc ion’ were enriched in the 579 genes, while Fe response-related processes, including ‘cellular response to nitric oxide’, ‘cellular response to iron ion’, and ‘cellular iron ion homeostasis’, were also enriched in the subset of 137 genes. Co-expression analysis of the 579 genes using the MACCU toolbox yielded a network consisting of 292 nodes (genes). Further analysis revealed that a subset of 90 genes were up-regulated under Fe shortage, but down-regulated under Pi starvation. GO analysis in this group of genes revealed an increased cellular response to iron ion/nitric oxide/ethylene stimuli. Promoter analysis was performed in 35 of the 90 genes with a 1.5-fold or greater change in abundance, showing that 12 genes contained the PHOSPHATE STARVATION RESPONSE1-binding GNATATNC cis-element within their promoter regions. Quantitative real-time PCR showed that the decreased abundance of Fe acquisition genes under Pi deficiency exclusively relied on Fe concentration in Pi-deficient media.

Conclusions

Comprehensive analysis of the overlapping genes derived from Fe deficiency and Pi starvation provides more information to understand the link between Pi and Fe homeostasis. Gene clustering and root-specific co-expression analysis revealed several potentially important genes which likely function as putative novel players in response to Fe and Pi deficiency or in cross-talk between Fe-deficient responses and Pi-deficient signaling.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-015-1524-y) contains supplementary material, which is available to authorized users.

Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response

Time course transcriptome datasets are commonly used to predict key gene regulators associated with stress responses and to explore gene functionality. Techniques developed to extract causal relationships between genes from high throughput time course expression data are limited by low signal levels coupled with noise and sparseness in time points. We deal with these limitations by proposing the Cluster and Differential Alignment Algorithm (CDAA). This algorithm was designed to process transcriptome data by first grouping genes based on stages of activity and then using similarities in gene expression to predict influential connections between individual genes. Regulatory relationships are assigned based on pairwise alignment scores generated using the expression patterns of two genes and some inferred delay between the regulator and the observed activity of the target. We applied the CDAA to an iron deficiency time course microarray dataset to identify regulators that influence 7 target transcription factors known to participate in the Arabidopsis thaliana iron deficiency response. The algorithm predicted that 7 regulators previously unlinked to iron homeostasis influence the expression of these known transcription factors. We validated over half of predicted influential relationships using qRT-PCR expression analysis in mutant backgrounds. One predicted regulator-target relationship was shown to be a direct binding interaction according to yeast one-hybrid (Y1H) analysis. These results serve as a proof of concept emphasizing the utility of the CDAA for identifying unknown or missing nodes in regulatory cascades, providing the fundamental knowledge needed for constructing predictive gene regulatory networks. We propose that this tool can be used successfully for similar time course datasets to extract additional information and infer reliable regulatory connections for individual genes.

CaM and CML emergence in the green lineage

Calmodulin (CaM) is a well-studied calcium sensor that is ubiquitous in all eukaryotes and contributes to signaling during developmental processes and adaptation to environmental stimuli. Among eukaryotes, plants have a remarkable variety of CaM-like proteins (CMLs). The expansion of genomic data sets offers the opportunity to explore CaM and CML evolution among the green lineage from algae to land plants. Database analysis indicates that a striking diversity of CaM and CMLs evolved in angiosperms during terrestrial colonization and reveals the emergence of new CML classes throughout the green lineage that correlate with the acquisition of novel biological traits. Here, we speculate that expansion of the CML family was driven by selective pressures to process environmental signals efficiently as plants adapted to land environments.

The paralogous R3 MYB proteins CAPRICE, TRIPTYCHON and ENHANCER OF TRY AND CPC1 play pleiotropic and partly non-redundant roles in the phosphate starvation response of Arabidopsis roots

Phosphate (Pi) deficiency alters root hair length and frequency as a means of increasing the absorptive surface area of roots. Three partly redundant single R3 MYB proteins, CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1) and TRIPTYCHON (TRY), positively regulate the root hair cell fate by participating in a lateral inhibition mechanism. To identify putative targets and processes that are controlled by these three transcription factors (TFs), we conducted transcriptional profiling of roots from Arabidopsis thaliana wild-type plants, and cpc, etc1 and try mutants grown under Pi-replete and Pi-deficient conditions using RNA-seq. The data show that in an intricate interplay between the three MYBs regulate several developmental, physiological and metabolic processes that are putatively located in different tissues. When grown on media with a low Pi concentration, all three TFs acquire additional functions that are related to the Pi starvation response, including transition metal transport, membrane lipid remodelling, and the acquisition, uptake and storage of Pi. Control of gene activity is partly mediated through the regulation of potential antisense transcripts. The current dataset extends the known functions of R3 MYB proteins, provides a suite of novel candidates with critical function in root hair development under both control and Pi-deficient conditions, and challenges the definition of genetic redundancy by demonstrating that environmental perturbations may confer specific functions to orthologous proteins that could have similar roles under control conditions.

Soybean kinome: functional classification and gene expression patterns

The protein kinase (PK) gene family is one of the largest and most highly conserved gene families in plants and plays a role in nearly all biological functions. While a large number of genes have been predicted to encode PKs in soybean, a comprehensive functional classification and global analysis of expression patterns of this large gene family is lacking. In this study, we identified the entire soybean PK repertoire or kinome, which comprised 2166 putative PK genes, representing 4.67% of all soybean protein-coding genes. The soybean kinome was classified into 19 groups, 81 families, and 122 subfamilies. The receptor-like kinase (RLK) group was remarkably large, containing 1418 genes. Collinearity analysis indicated that whole-genome segmental duplication events may have played a key role in the expansion of the soybean kinome, whereas tandem duplications might have contributed to the expansion of specific subfamilies. Gene structure, subcellular localization prediction, and gene expression patterns indicated extensive functional divergence of PK subfamilies. Global gene expression analysis of soybean PK subfamilies revealed tissue- and stress-specific expression patterns, implying regulatory functions over a wide range of developmental and physiological processes. In addition, tissue and stress co-expression network analysis uncovered specific subfamilies with narrow or wide interconnected relationships, indicative of their association with particular or broad signalling pathways, respectively. Taken together, our analyses provide a foundation for further functional studies to reveal the biological and molecular functions of PKs in soybean.

Exposure of barley plants to low Pi leads to rapid changes in root respiration that correlate with specific alterations in amino acid substrates

The majority of inorganic phosphate (Pi ) stress studies in plants have focused on the response after growth has been retarded. Evidence from transcript analysis, however, shows that a Pi -stress specific response is initiated within minutes of transfer to low Pi and in crop plants precedes the expression of Pi transporters and depletion of vacuolar Pi reserves by days. In order to investigate the physiological and metabolic events during early exposure to low Pi in grain crops, we monitored the response of whole barley plants during the first hours following Pi withdrawal. Lowering the concentration of Pi led to rapid changes in root respiration and leaf gas exchange throughout the early phase of the light course. Combining amino and organic acid analysis with (15) N labelling we show a root-specific effect on nitrogen metabolism linked to specific substrates of respiration as soon as 1 h following Pi withdrawal; this explains the respiratory responses observed and was confirmed by stimulation of respiration by exogenous addition of these respiratory substrates to roots. The rapid adjustment of substrates for respiration in roots during short-term Pi -stress is highlighted and this could help guide roots towards Pi -rich soil patches without compromising biomass accumulation of the plant.

Physiological and molecular alterations in plants exposed to high [CO2] under phosphorus stress

Atmospheric [CO2] has increased substantially in recent decades and will continue to do so, whereas the availability of phosphorus (P) is limited and unlikely to increase in the future. P is a non-renewable resource, and it is essential to every form of life. P is a key plant nutrient controlling the responsiveness of photosynthesis to [CO2]. Increases in [CO2] typically results in increased biomass through stimulation of net photosynthesis, and hence enhance the demand for P uptake. However, most soils contain low concentrations of available P. Therefore, low P is one of the major growth-limiting factors for plants in many agricultural and natural ecosystems. The adaptive responses of plants to [CO2] and P availability encompass alterations at morphological, physiological, biochemical and molecular levels. In general low P reduces growth, whereas high [CO2] enhances it particularly in C3 plants. Photosynthetic capacity is often enhanced under high [CO2] with sufficient P supply through modulation of enzyme activities involved in carbon fixation such as ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). However, high [CO2] with low P availability results in enhanced dry matter partitioning towards roots. Alterations in below-ground processes including root morphology, exudation and mycorrhizal association are influenced by [CO2] and P availability. Under high P availability, elevated [CO2] improves the uptake of P from soil. In contrast, under low P availability, high [CO2] mainly improves the efficiency with which plants produce biomass per unit P. At molecular level, the spatio-temporal regulation of genes involved in plant adaptation to low P and high [CO2] has been studied individually in various plant species. Genome-wide expression profiling of high [CO2] grown plants revealed hormonal regulation of biomass accumulation through complex transcriptional networks. Similarly, differential transcriptional regulatory networks are involved in P-limitation responses in plants. Analysis of expression patterns of some typical P-limitation induced genes under high [CO2] suggests that long-term exposure of plants to high [CO2] would have a tendency to stimulate similar transcriptional responses as observed under P-limitation. However, studies on the combined effect of high [CO2] and low P on gene expression are scarce. Such studies would provide insights into the development of P efficient crops in the context of anticipated increases in atmospheric [CO2].

Identification of three potent hydroxyproline O-galactosyltransferases in Arabidopsis

Arabinogalactan proteins (AGPs) are plant-specific extracellular glycoproteins implicated in a variety of processes during growth and development. AGP biosynthesis involves O-galactosylation of hydroxyproline (Hyp) residues followed by a stepwise elongation of the complex sugar chains. However, functionally dominant Hyp O-galactosyltransferases, such that their disruption produces phenocopies of AGP-deficient mutants, remain to be identified. Here, we purified and identified three potent Hyp O-galactosyltransferases, HPGT1, HPGT2 and HPGT3, from Arabidopsis microsomal fractions. Loss-of-function analysis indicated that approximately 90% of the endogenous Hyp O-galactosylation activity is attributable to these three enzymes. AGP14 expressed in the triple mutant migrated much faster on SDS-PAGE than when expressed in wild-type, confirming a considerable decrease in levels of glycosylation of AGPs in the mutant. Loss-of-function mutant plants exhibited a pleiotropic phenotype of longer lateral roots, longer root hairs, radial expansion of the cells in the root tip, small leaves, shorter inflorescence stems, reduced fertility and shorter siliques. Our findings provide genetic evidence that Hyp-linked arabinogalactan polysaccharide chains are critical for AGP function and clues to how arabinogalactan moieties of AGPs contribute to cell-to-cell communication during plant growth and development.

Re-analysis of RNA-seq transcriptome data reveals new aspects of gene activity in Arabidopsis root hairs

Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, interaction with microbe, and in plant anchorage. As a specialized cell type, root hairs, especially in Arabidopsis, provide a pragmatic research system for various aspects of studies. Here, we re-analyzed the RNA-seq transcriptome profile of Arabidopsis root hair cells by Tophat software and used Cufflinks program to mine the differentially expressed genes. Results showed that ERD14, RIN4, AT5G64401 were among the most abundant genes in the root hair cells; while ATGSTU2, AT5G54940, AT4G30530 were highly expressed in non-root hair tissues. In total, 5409 genes, with a fold change greater than two-fold (FDR adjusted P < 0.05), showed differential expression between root hair cells and non-root hair tissues. Of which, 61 were expressed only in root hair cells. One hundred and thirty-six out of 5409 genes have been reported to be "core" root epidermal genes, which could be grouped into nine clusters according to expression patterns. Gene ontology (GO) analysis of the 5409 genes showed that processes of "response to salt stress," "ribosome biogenesis," "protein phosphorylation," and "response to water deprivation" were enriched. Whereas only process of "intracellular signal transduction" was enriched in the subset of 61 genes expressed only in the root hair cells. One hundred and twenty-one unannotated transcripts were identified and 14 of which were shown to be differentially expressed between root hair cells and non-root hair tissues, with transcripts XLOC_000763, XLOC_031361, and XLOC_005665 being highly expressed in the root hair cells. The comprehensive transcriptomic analysis provides new information on root hair gene activity and sets the stage for follow-up experiments to certify the biological functions of the newly identified genes and novel transcripts in root hair cell morphogenesis.

Exploring the role of a stigma-expressed plant U-box gene in the pollination responses of transgenic self-incompatible Arabidopsis thaliana

Recognition of "self" pollen in the self-incompatibility (SI) response of the Brassicaceae is determined by allele-specific interaction between the S-locus receptor kinase (SRK), a transmembrane protein of the stigma epidermis, and its ligand, the pollen coat-localized S-locus cysteine-rich (SCR) protein. The current model for SRK-mediated signaling proposes a central role for the plant U-box (PUB) Armadillo repeat-containing protein ARC1, an E3 ligase that interacts with, and is phosphorylated by, the kinase domain of SRK. According to the model, activated ARC1 causes the degradation of factors required for successful pollen tube growth. However, Arabidopsis thaliana plants transformed with functional SRK and SCR genes isolated from self-incompatible A. lyrata can express an intense SI response despite lacking a functional ARC1 gene. Here, we tested the possibility that a different member of the A. thaliana PUB protein family might have assumed the role of ARC1 in SI. Toward this end, we analyzed the AtPUB2 gene, which is annotated as being highly expressed in stigmas. Our functional analysis of a T-DNA insertion pub2 allele, together with yeast two-hybrid interaction assays and reporter analysis of AtPUB2 promoter activity, demonstrates that AtPUB2 does not function in SI. The results leave open the question of whether the proposed model of ARC1-mediated signaling applies to transgenic SRK-SCR self-incompatible A. thaliana plants.

Molecular mechanisms underlying phosphate sensing, signaling, and adaptation in plants

As an essential plant macronutrient, the low availability of phosphorus (P) in most soils imposes serious limitation on crop production. Plants have evolved complex responsive and adaptive mechanisms for acquisition, remobilization and recycling of phosphate (Pi) to maintain P homeostasis. Spatio-temporal molecular, physiological, and biochemical Pi deficiency responses developed by plants are the consequence of local and systemic sensing and signaling pathways. Pi deficiency is sensed locally by the root system where hormones serve as important signaling components in terms of developmental reprogramming, leading to changes in root system architecture. Root-to-shoot and shoot-to-root signals, delivered through the xylem and phloem, respectively, involving Pi itself, hormones, miRNAs, mRNAs, and sucrose, serve to coordinate Pi deficiency responses at the whole-plant level. A combination of chromatin remodeling, transcriptional and posttranslational events contribute to globally regulating a wide range of Pi deficiency responses. In this review, recent advances are evaluated in terms of progress toward developing a comprehensive understanding of the molecular events underlying control over P homeostasis. Application of this knowledge, in terms of developing crop plants having enhanced attributes for P use efficiency, is discussed from the perspective of agricultural sustainability in the face of diminishing global P supplies.

Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments

Nitrogen (N) is an essential macronutrient for plant growth and development. Plants adapt to changes in N availability partly by changes in global gene expression. We integrated publicly available root microarray data under contrasting nitrate conditions to identify new genes and functions important for adaptive nitrate responses in Arabidopsis thaliana roots. Overall, more than 2000 genes exhibited changes in expression in response to nitrate treatments in Arabidopsis thaliana root organs. Global regulation of gene expression by nitrate depends largely on the experimental context. However, despite significant differences from experiment to experiment in the identity of regulated genes, there is a robust nitrate response of specific biological functions. Integrative gene network analysis uncovered relationships between nitrate-responsive genes and 11 highly co-expressed gene clusters (modules). Four of these gene network modules have robust nitrate responsive functions such as transport, signaling, and metabolism. Network analysis hypothesized G2-like transcription factors are key regulatory factors controlling transport and signaling functions. Our meta-analysis highlights the role of biological processes not studied before in the context of the nitrate response such as root hair development and provides testable hypothesis to advance our understanding of nitrate responses in plants.

Towards a comprehensive picture of the genetic landscape of complex traits

The formation of phenotypic traits, such as biomass production, tumor volume and viral abundance, undergoes a complex process in which interactions between genes and developmental stimuli take place at each level of biological organization from cells to organisms. Traditional studies emphasize the impact of genes by directly linking DNA-based markers with static phenotypic values. Functional mapping, derived to detect genes that control developmental processes using growth equations, has proven powerful for addressing questions about the roles of genes in development. By treating phenotypic formation as a cohesive system using differential equations, a different approach-systems mapping-dissects the system into interconnected elements and then map genes that determine a web of interactions among these elements, facilitating our understanding of the genetic machineries for phenotypic development. Here, we argue that genetic mapping can play a more important role in studying the genotype-phenotype relationship by filling the gaps in the biochemical and regulatory process from DNA to end-point phenotype. We describe a new framework, named network mapping, to study the genetic architecture of complex traits by integrating the regulatory networks that cause a high-order phenotype. Network mapping makes use of a system of differential equations to quantify the rule by which transcriptional, proteomic and metabolomic components interact with each other to organize into a functional whole. The synthesis of functional mapping, systems mapping and network mapping provides a novel avenue to decipher a comprehensive picture of the genetic landscape of complex phenotypes that underlie economically and biomedically important traits.

A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina

Aging of biological systems is controlled by various processes which have a potential impact on gene expression. Here we report a genome-wide transcriptome analysis of the fungal aging model Podospora anserina. Total RNA of three individuals of defined age were pooled and analyzed by SuperSAGE (serial analysis of gene expression). A bioinformatics analysis identified different molecular pathways to be affected during aging. While the abundance of transcripts linked to ribosomes and to the proteasome quality control system were found to decrease during aging, those associated with autophagy increase, suggesting that autophagy may act as a compensatory quality control pathway. Transcript profiles associated with the energy metabolism including mitochondrial functions were identified to fluctuate during aging. Comparison of wild-type transcripts, which are continuously down-regulated during aging, with those down-regulated in the long-lived, copper-uptake mutant grisea, validated the relevance of age-related changes in cellular copper metabolism. Overall, we (i) present a unique age-related data set of a longitudinal study of the experimental aging model P. anserina which represents a reference resource for future investigations in a variety of organisms, (ii) suggest autophagy to be a key quality control pathway that becomes active once other pathways fail, and (iii) present testable predictions for subsequent experimental investigations.

Root systems biology: integrative modeling across scales, from gene regulatory networks to the rhizosphere

Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment.

Expression changes of ribosomal proteins in phosphate- and iron-deficient Arabidopsis roots predict stress-specific alterations in ribosome composition

Background

Ribosomes are essential ribonucleoprotein complexes that are engaged in translation and thus indispensable for growth. Arabidopsis thaliana ribosomes are composed of 80 distinct ribosomal proteins (RPs), each of which is encoded by two to seven highly similar paralogous genes. Little information is available on how RP genes respond to a shortage of essential mineral nutrients such as phosphate (Pi) or iron (Fe). In the present study, the expression of RP genes and the differential accumulation of RPs upon Pi or Fe deficiency in Arabidopsis roots were comprehensively analyzed.

Results

Comparison of 3,106 Pi-responsive genes with 3,296 Fe-responsive genes revealed an overlap of 579 genes that were differentially expressed under both conditions in Arabidopsis roots. Gene ontology (GO) analysis revealed that these 579 genes were mainly associated with abiotic stress responses. Among the 247 RP genes retrieved from the TAIR10 release of the Arabidopsis genome (98 small subunit RP genes, 143 large subunit RP genes and six ribosome-related genes), seven RP genes were not detected in Arabidopsis roots by RNA sequencing under control conditions. Transcripts from 20 and 100 RP genes showed low and medium abundance, respectively; 120 RP genes were highly expressed in Arabidopsis roots. As anticipated, gene ontology (GO) analysis indicated that most RP genes were related to translation and ribosome assembly, but some of the highly expressed RP genes were also involved in the responses to cold, UV-B, and salt stress. Only three RP genes derived from three ‘sets’ of paralogous genes were differentially expressed between Pi-sufficient and Pi-deficient roots, all of which were induced by Pi starvation. In Fe-deficient plants, 81 RP genes from 51 ’sets’ of paralagous RP genes were significantly down-regulated in response to Fe deficiency. The biological processes ’translation’ (GO: 0006412), ’ribosome biogenesis (GO: 0042254), and ’response to salt (GO: 0009651), cold (GO: 0009409), and UV-B stresses (GO: 0071493)’ were enriched in this subset of RP genes. At the protein level, 21 and two RPs accumulated differentially under Pi- and Fe-deficient conditions, respectively. Neither the differentially expressed RP genes nor the differentially expressed RPs showed any overlap between the two growth types.

Conclusions

In the present study three and 81 differentially expressed RP genes were identified under Pi and Fe deficiency, respectively. At protein level, 21 and two RP proteins were differentially accumulated under Pi- and Fe-deficient conditions. Our study shows that the expression of paralogous genes encoding RPs was regulated in a stress-specific manner in Arabidopsis roots, presumably resulting in an altered composition of ribosomes and biased translation. These findings may aid in uncovering an unexplored mechanism by which plants adapt to changing environmental conditions.

Positional signaling and expression of ENHANCER OF TRY AND CPC1 are tuned to increase root hair density in response to phosphate deficiency in Arabidopsis thaliana

Phosphate (Pi) deficiency induces a multitude of responses aimed at improving the acquisition of Pi, including an increased density of root hairs. To understand the mechanisms involved in Pi deficiency-induced alterations of the root hair phenotype in Arabidopsis (Arabidopsis thaliana), we analyzed the patterning and length of root epidermal cells under control and Pi-deficient conditions in wild-type plants and in four mutants defective in the expression of master regulators of cell fate, CAPRICE (CPC), ENHANCER OF TRY AND CPC 1 (ETC1), WEREWOLF (WER) and SCRAMBLED (SCM). From this analysis we deduced that the longitudinal cell length of root epidermal cells is dependent on the correct perception of a positional signal ('cortical bias') in both control and Pi-deficient plants; mutants defective in the receptor of the signal, SCM, produced short cells characteristic of root hair-forming cells (trichoblasts). Simulating the effect of cortical bias on the time-evolving probability of cell fate supports a scenario in which a compromised positional signal delays the time point at which non-hair cells opt out the default trichoblast pathway, resulting in short, trichoblast-like non-hair cells. Collectively, our data show that Pi-deficient plants increase root hair density by the formation of shorter cells, resulting in a higher frequency of hairs per unit root length, and additional trichoblast cell fate assignment via increased expression of ETC1.

Calmodulin-related proteins step out from the shadow of their namesake

Emerging roles for these proteins in plant development and stress response highlight their importance in plant signaling, and their functional diversity underscores the significance of Ca2+ as a second messenger in plants .

Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula

The generally low bioavailability of iron in aerobic soil systems forced plants to evolve sophisticated genetic strategies to improve the acquisition of iron from sparingly soluble and immobile iron pools. To distinguish between conserved and species-dependent components of such strategies, we analyzed iron deficiency-induced changes in the transcriptome of two model species, Arabidopsis (Arabidopsis thaliana) and Medicago truncatula. Transcriptional profiling by RNA sequencing revealed a massive up-regulation of genes coding for enzymes involved in riboflavin biosynthesis in M. truncatula and phenylpropanoid synthesis in Arabidopsis upon iron deficiency. Coexpression and promoter analysis indicated that the synthesis of flavins and phenylpropanoids is tightly linked to and putatively coregulated with other genes encoding proteins involved in iron uptake. We further provide evidence that the production and secretion of phenolic compounds is critical for the uptake of iron from sources with low bioavailability but dispensable under conditions where iron is readily available. In Arabidopsis, homozygous mutations in the Fe(II)- and 2-oxoglutarate-dependent dioxygenase family gene F6'H1 and defects in the expression of PLEIOTROPIC DRUG RESISTANCE9, encoding a putative efflux transporter for products from the phenylpropanoid pathway, compromised iron uptake from an iron source of low bioavailability. Both mutants were partially rescued when grown alongside wild-type Arabidopsis or M. truncatula seedlings, presumably by secreted phenolics and flavins. We concluded that production and secretion of compounds that facilitate the uptake of iron is an essential but poorly understood aspect of the reduction-based iron acquisition strategy, which is likely to contribute substantially to the efficiency of iron uptake in natural conditions.

Transcriptome divergence between introduced and native populations of Canada thistle, Cirsium arvense

Introduced plants may quickly evolve new adaptive traits upon their introduction. Canada thistle (Cirsium arvense - Cardueae, Asteraceae) is one of the worst invasive weeds worldwide. The goal of this study is to compare gene expression profiles of native (European) and introduced (North American) populations of this species, to elucidate the genetic mechanisms that may underlie such rapid adaptation. We explored the transcriptome of ten populations (five per range) of C. arvense in response to three treatments (control, nutrient deficiency and shading) using a customized microarray chip containing 63 690 expressed sequence tags (ESTs), and verified the expression level of 13 loci through real-time quantitative PCR. Only 2116 ESTs (3.5%) were found to be differentially expressed between the ranges, and 4458 ESTs (7.1%) exhibited a significant treatment-by-range effect. Among them was an overrepresentation of loci involved in stimulus and stress responses. Cirsium arvense has evolved different life history strategies on each continent. The two ranges notably differ with regard to R-protein mediated defence, sensitivity to abiotic stresses, and developmental timing. The fact that genotypes from the Midwest exhibit different expression kinetics than remaining North American samples further corroborates the hypothesis that the New World has been colonized twice, independently.

Mapping gene activity of Arabidopsis root hairs

Background

Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized cells in the epidermis, represent an ideal model for cell fate acquisition and differentiation in plants.

Results

Here, we provide an atlas of gene and protein expression in Arabidopsis root hair cells, generated by paired-end RNA sequencing and LC/MS-MS analysis of protoplasts from plants containing a pEXP7-GFP reporter construct. In total, transcripts of 23,034 genes were detected in root hairs. High-resolution proteome analysis led to the reliable identification of 2,447 proteins, 129 of which were differentially expressed between root hairs and non-root hair tissue. Dissection of pre-mRNA splicing patterns showed that all types of alternative splicing were cell type-dependent, and less complex in EXP7-expressing cells when compared to non-root hair cells. Intron retention was repressed in several transcripts functionally related to root hair morphogenesis, indicative of a cell type-specific control of gene expression by alternative splicing of pre-mRNA. Concordance between mRNA and protein expression was generally high, but in many cases mRNA expression was not predictive for protein abundance.

Conclusions

The integrated analysis shows that gene activity in root hairs is dictated by orchestrated, multilayered regulatory mechanisms that allow for a cell type-specific composition of functional components.

A digital compendium of genes mediating the reversible phosphorylation of proteins in fe-deficient Arabidopsis roots

Post-translational modifications of proteins such as reversible phosphorylation provide an important but understudied regulatory network that controls important nodes in the adaptation of plants to environmental conditions. Iron (Fe) is an essential mineral nutrient for plants, but due to its low solubility often a limiting factor for optimal growth. To understand the role of protein phosphorylation in the regulation of cellular Fe homeostasis, we analyzed the expression of protein kinases (PKs) and phosphatases (PPs) in Arabidopsis roots by mining differentially expressed PK and PP genes. Transcriptome analysis using RNA-seq revealed that subsets of 203 PK and 39 PP genes were differentially expressed under Fe-deficient conditions. Functional modules of these PK and PP genes were further generated based on co-expression analysis using the MACCU toolbox on the basis of 300 publicly available root-related microarray data sets. Results revealed networks comprising 87 known or annotated PK and PP genes that could be subdivided into one large and several smaller highly co-expressed gene modules. The largest module was composed of 58 genes, most of which have been assigned to the leucine-rich repeat protein kinase superfamily and associated with the biological processes "hypotonic salinity response," "potassium ion import," and "cellular potassium ion homeostasis." The comprehensive transcriptional information on PK and PP genes in iron-deficient roots provided here sets the stage for follow-up experiments and contributes to our understanding of the post-translational regulation of Fe deficiency and potassium ion homeostasis.

ALFIN-LIKE 6 is involved in root hair elongation during phosphate deficiency in Arabidopsis

Phosphate (Pi) starvation in plants induces dense and elongated root hairs, which increase the absorptive surface area of the roots and play a critical role in Pi uptake. The molecular mechanism underlying these changes remains unclear. Forward and reverse genetic approaches were employed to identify novel genes involved in root hair formation on Pi starvation. The mutant per2, with defects in root hair elongation specifically under low Pi conditions, was identified in a large-scale genetic screen of T-DNA insertion lines. The phenotype was caused by a mutation in the homeodomain protein ALFIN-LIKE 6 (AL6). From a screen of mutants defective in genes that showed lower transcript abundance in per2 relative to wild-type roots on low Pi medium, we identified four putative downstream targets of AL6, namely ETC1, NPC4, SQD2 and PS2, all of which were critical in root hair elongation of Pi-deficient plants. The results further indicate that AL6 is involved in the control of growth and several key responses to Pi starvation. Our findings demonstrate that AL6 controls the transcription of a suite of genes critical for root hair elongation under low Pi conditions, suggesting a novel physiological function for an Alfin gene in Arabidopsis.

Divergent low water potential response in Arabidopsis thaliana accessions Landsberg erecta and Shahdara

The Arabidopsis thaliana accession Shahdara (Sha) differs from Landsberg erecta (Ler) and other accessions in its responses to drought and low water potential including lower levels of proline accumulation. However, Sha maintained greater seedling root elongation at low water potential and a higher NADP/NADPH ratio than Ler. Profiling of major amino acids and organic acids found that Sha had reduced levels of all glutamate family amino acids metabolically related to proline, but increased levels of aspartate-derived amino acids (particularly isoleucine), leucine and valine at low water potential. Although Sha is known for its different abiotic stress response, RNA sequencing and co-expression clustering found that Sha differed most from Ler in defence/immune response and reactive oxygen-related gene expression. HVA22B and Osmotin34 were two of the relatively few abiotic stress-associated genes differentially expressed between Ler and Sha. Insensitivity to exogenous glutamine and a different expression profile of glutamate receptors were further factors that may underlie the differing metabolism and low water potential phenotypes of Sha. These data define the unique environmental adaptation and differing metabolism of Sha including differences in defence gene expression, and will facilitate further analysis of Sha natural variation to understand metabolic regulation and abiotic/biotic stress interaction.

Genome-wide co-expression analysis predicts protein kinases as important regulators of phosphate deficiency-induced root hair remodeling in Arabidopsis

BACKGROUND

Phosphorus (P) is one of the essential but often limiting elements for plants. Based on transcriptional profiling we reported previously that more than 3,000 genes are differentially expressed between phosphate (Pi)-deficient and Pi-sufficient Arabidopsis roots (MCP 11(11):1156-1166, 2012). The current study extends these findings by focusing on the analysis of genes that encode protein kinases (PK) and phosphatases (PP) by mining PK and PP genes that were differentially expressed in response to Pi deficiency.

RESULTS

Subsets of 1,118 and 205 annotated PK and PP genes were mined on the basis of the TAIR10 release of the Arabidopsis genome. Analysis of RNA-seq data showed that 92 PK and 19 PP genes were not detected in roots (zero reads in three biological repeats); 96 PK and 10 PP showed low abundance (≤ 10 reads). Gene ontology analysis revealed that the 188 PK genes with no or low expression level in Arabidopsis roots are mainly involved in pollen recognition, pollen tube growth or other processes not relevant for root hair formation. More than 50% of the cysteine-rich RLK (receptor-like protein kinase) subfamily genes belong to this group. Among the 29 PP genes with no or low expression level, purple acid phosphatases, haloacid dehalogenase-like hydrolases, and PP2C genes with functions in the dephosphorylation of RNA polymerase II C-terminal domain and mRNA capping were enriched. Subsets of 173 PK and 35 PP genes were differentially expressed under Pi-deficient conditions. Putative functional modules (clusters) of these PK and PP genes were constructed based on co-expression analysis using the MACCU toolbox. A co-expression network comprising 65 known or annotated PK and PP genes (60 PK and 5 PP genes, respectively) was subdivided into several highly co-expressed gene sub-clusters. The largest sub-cluster was composed of 22 genes, most of which have been assigned to the RLK superfamily and were associated with cell wall metabolism, pollen tube and/or root hair development and growth.

CONCLUSIONS

We here provide comprehensive 'digital' transcriptional information on PK and PP genes in Arabidopsis roots. The co-expression network derived from our data mining approach sets the stage for follow-up experimentation that helps to complete our understanding of the post-translational regulation of Pi deficiency-induced changes in root hair morphogenesis.

The transcriptional response of Arabidopsis leaves to Fe deficiency

Due to its ease to donate or accept electrons, iron (Fe) plays a crucial role in respiration and metabolism, including tetrapyrrole synthesis, in virtually all organisms. In plants, Fe is a component of the photosystems and thus essential for photosynthesis. Fe deficiency compromises chlorophyll (Chl) synthesis, leading to interveinal chlorosis in developing leaves and decreased photosynthetic activity. To gain insights into the responses of photosynthetically active cells to Fe deficiency, we conducted transcriptional profiling experiments on leaves from Fe-sufficient and Fe-deficient plants using the RNA-seq technology. As anticipated, genes associated with photosynthesis and tetrapyrrole metabolism were dramatically down-regulated by Fe deficiency. A sophisticated response comprising the down-regulation of HEMA1 and NYC1, which catalyze the first committed step in tetrapyrrole biosynthesis and the conversion of Chl b to Chl a at the commencement of Chl breakdown, respectively, and the up-regulation of CGLD27, which is conserved in plastid-containing organisms and putatively involved in xanthophyll biosynthesis, indicates a carefully orchestrated balance of potentially toxic tetrapyrrole intermediates and functional end products to avoid photo-oxidative damage. Comparing the responses to Fe deficiency in leaves to that in roots confirmed subgroup 1b bHLH transcription factors and POPEYE/BRUTUS as important regulators of Fe homeostasis in both leaf and root cells, and indicated six novel players with putative roles in Fe homeostasis that were highly expressed in leaves and roots and greatly induced by Fe deficiency. The data further revealed down-regulation of organ-specific subsets of genes encoding ribosomal proteins, which may be indicative of a change in ribosomal composition that could bias translation. It is concluded that Fe deficiency causes a massive reorganization of plastid activity, which is adjusting leaf function to the availability of Fe.

A galacturonic acid-containing xyloglucan is involved in Arabidopsis root hair tip growth

Root hairs provide a model system to study plant cell growth, yet little is known about the polysaccharide compositions of their walls or the role of these polysaccharides in wall expansion. We report that Arabidopsis thaliana root hair walls contain a previously unidentified xyloglucan that is composed of both neutral and galacturonic acid-containing subunits, the latter containing the β-D-galactosyluronic acid-(1→2)-α-D-xylosyl-(1→ and/or α-L-fucosyl-(1→2)-β-D-galactosyluronic acid-(1→2)-α-D-xylosyl-(1→) side chains. Arabidopsis mutants lacking root hairs have no acidic xyloglucan. A loss-of-function mutation in At1g63450, a root hair-specific gene encoding a family GT47 glycosyltransferase, results in the synthesis of xyloglucan that lacks galacturonic acid. The root hairs of this mutant are shorter than those of the wild type. This mutant phenotype and the absence of galacturonic acid in the root xyloglucan are complemented by At1g63450. The leaf and stem cell walls of wild-type Arabidopsis contain no acidic xyloglucan. However, overexpression of At1g63450 led to the synthesis of galacturonic acid-containing xyloglucan in these tissues. We propose that At1g63450 encodes XYLOGLUCAN-SPECIFIC GALACTURONOSYLTRANSFERASE1, which catalyzes the formation of the galactosyluronic acid-(1→2)-α-D-xylopyranosyl linkage and that the acidic xyloglucan is present only in root hair cell walls. The role of the acidic xyloglucan in root hair tip growth is discussed.

Unique drought resistance functions of the highly ABA-induced clade A protein phosphatase 2Cs

Six Arabidopsis (Arabidopsis thaliana) clade A protein phosphatase 2Cs (PP2Cs) have established abscisic acid (ABA) signaling roles; however, phenotypic roles of the remaining three "HAI" PP2Cs, Highly ABA-Induced1 (HAI1), AKT1-Interacting PP2C1/HAI2, and HAI3, have remained unclear. HAI PP2C mutants had enhanced proline and osmoregulatory solute accumulation at low water potential, while mutants of other clade A PP2Cs had no or lesser effect on these drought resistance traits. hai1-2 also had increased expression of abiotic stress-associated genes, including dehydrins and late embryogenesis abundant proteins, but decreased expression of several defense-related genes. Conversely, the HAI PP2Cs had relatively less impact on several ABA sensitivity phenotypes. HAI PP2C single mutants were unaffected in ABA sensitivity, while double and triple mutants were moderately hypersensitive in postgermination ABA response but ABA insensitive in germination. The HAI PP2Cs interacted most strongly with PYL5 and PYL7 to -10 of the PYL/RCAR ABA receptor family, with PYL7 to -10 interactions being relatively little affected by ABA in yeast two-hybrid assays. HAI1 had especially limited PYL interaction. Reduced expression of the main HAI1-interacting PYLs at low water potential when HAI1 expression was strongly induced also suggests limited PYL regulation and a role of HAI1 activity in negatively regulating specific drought resistance phenotypes. Overall, the HAI PP2Cs had greatest effect on ABA-independent low water potential phenotypes and lesser effect on classical ABA sensitivity phenotypes. Both this and their distinct PYL interaction demonstrate a new level of functional differentiation among the clade A PP2Cs and a point of cross talk between ABA-dependent and ABA-independent drought-associated signaling.

Complementary proteome and transcriptome profiling in phosphate-deficient Arabidopsis roots reveals multiple levels of gene regulation

Phosphate (Pi) deficiency impairs plant growth and productivity in many agricultural ecosystems, causing severe reductions in crop yield. To uncover novel aspects in acclimation to Pi starvation, we investigated the correlation between Pi deficiency-induced changes in transcriptome and proteome profiles in Arabidopsis roots. Using exhaustive tandem mass spectrometry-based shotgun proteomics and whole-genome RNA sequencing to generate a nearly complete catalog of expressed mRNAs and proteins, we reliably identified 13,298 proteins and 24,591 transcripts, subsets of 356 proteins and 3106 mRNAs were differentially expressed during Pi deficiency. Most dramatic changes were noticed for genes involved in Pi acquisition and in processes that either liberate Pi or bypass Pi/ATP-consuming metabolic steps, for example during membrane lipid remodeling and glycolytic carbon flux. The concordance between the abundance of mRNA and its encoded protein was generally high for highly up-regulated genes, but the analysis also revealed numerous discordant changes in mRNA/protein pairs, indicative of divergent regulation of transcription and post-transcriptional processes. In particular, a decreased abundance of proteins upon Pi deficiency was not closely correlated with changes in the corresponding mRNAs. In several cases, up-regulation of gene activity was observed solely at the protein level, adding novel aspects to key processes in the adaptation to Pi deficiency. We conclude that integrated measurement and interpretation of changes in protein and transcript abundance are mandatory for generating a complete inventory of the components that are critical in the response to environmental stimuli.

The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis

Plastoglobules (PGs) in chloroplasts are thylakoid-associated monolayer lipoprotein particles containing prenyl and neutral lipids and several dozen proteins mostly with unknown functions. An integrated view of the role of the PG is lacking. Here, we better define the PG proteome and provide a conceptual framework for further studies. The PG proteome from Arabidopsis (Arabidopsis thaliana) leaf chloroplasts was determined by mass spectrometry of isolated PGs and quantitative comparison with the proteomes of unfractionated leaves, thylakoids, and stroma. Scanning electron microscopy showed the purity and size distribution of the isolated PGs. Compared with previous PG proteome analyses, we excluded several proteins and identified six new PG proteins, including an M48 metallopeptidase and two Absence of bc1 complex (ABC1) atypical kinases, confirmed by immunoblotting. This refined PG proteome consisted of 30 proteins, including six ABC1 kinases and seven fibrillins together comprising more than 70% of the PG protein mass. Other fibrillins were located predominantly in the stroma or thylakoid and not in PGs; we discovered that this partitioning can be predicted by their isoelectric point and hydrophobicity. A genome-wide coexpression network for the PG genes was then constructed from mRNA expression data. This revealed a modular network with four distinct modules that each contained at least one ABC1K and/or fibrillin gene. Each module showed clear enrichment in specific functions, including chlorophyll degradation/senescence, isoprenoid biosynthesis, plastid proteolysis, and redox regulators and phosphoregulators of electron flow. We propose a new testable model for the PGs, in which sets of genes are associated with specific PG functions.