AtCCS is a functional homolog of the yeast copper chaperone Ccs1/Lys7

The MIO1-MtKIX8 module regulates the organ size in Medicago truncatula

Plant organ size is an important agronomic trait tightly related to crop yield. However, the molecular mechanisms underlying organ size regulation remain largely unexplored in legumes. We previously characterized a key regulator F-box protein MINI ORGAN1 (MIO1)/SMALL LEAF AND BUSHY1 (SLB1), which controls plant organ size in the model legume Medicago truncatula. In order to further dissect the molecular mechanism, MIO1 was used as the bait to screen its interacting proteins from a yeast library. Subsequently, a KIX protein, designated MtKIX8, was identified from the candidate list. The interaction between MIO1 and MtKIX8 was confirmed further by Y2H, BiFC, split-luciferase complementation and pull-down assays. Phylogenetic analyses indicated that MtKIX8 is highly homologous to Arabidopsis KIX8, which negatively regulates organ size. Moreover, loss-of-function of MtKIX8 led to enlarged leaves and seeds, while ectopic expression of MtKIX8 in Arabidopsis resulted in decreased cotyledon area and seed weight. Quantitative reverse-transcription PCR and in situ hybridization showed that MtKIX8 is expressed in most developing organs. We also found that MtKIX8 serves as a crucial molecular adaptor, facilitating interactions with BIG SEEDS1 (BS1) and MtTOPLESS (MtTPL) proteins in M. truncatula. Overall, our results suggest that the MIO1-MtKIX8 module plays a significant and conserved role in the regulation of plant organ size. This module could be a good target for molecular breeding in legume crops and forages.

Role of TRDMT1/DNMT2 in stress adaptation and its influence on transcriptome and proteome dynamics under osmotic stress in Physcomitrium patens

Early land plants such as the moss Physcomitrium patens lack several morphological traits that offer protection to tracheophytes from environmental stresses. These plants instead have evolved several physiological and biochemical mechanisms that facilitate them to adapt to terrestrial stresses such as drought. We have previously shown that loss-of-function mutants of tRNA (cytosine(38)-C(5))-methyltransferase TRDMT1/DNMT2 in P. patens are highly sensitive to oxidative and osmotic stress. To gain insight into the role of PpTRDMT1/PpDNMT2 in modulating genetic networks under osmotic stress, genome-wide transcriptome and proteome studies were undertaken in wild-type and ppdnmt2 plants. Transcriptome analysis revealed 375 genes to be differentially expressed in the ppdnmt2 under stress compared to the WT. Most of these genes are affiliated with carbohydrate metabolic pathways, photosynthesis, cell wall biogenesis, pathways related to isotropic and polarised cell growth and transcription factors among others. Histochemical staining showed elevated levels of reactive oxygen species in ppdnmt2 while transmission electron microscopy revealed no distinct defects in the ultrastructure of chloroplasts. Immunoprecipitation using PpDNMT2-specific antibody coupled with mass spectrometry revealed core proteins of the glycolytic pathway, antioxidant enzymes, proteins of amino acid biosynthetic pathways and photosynthesis-related proteins among others to co-purify with PpTRDMT1/PpDNMT2 under osmotic stress. Yeast two-hybrid assays, protein deletion and α-galactosidase assays showed the cytosol glycolytic protein glyceraldehyde 3-phosphate dehydrogenase to bind to the catalytic motifs in PpTRDMT1/PpDNMT2. Results presented in this study allow us to better understand genetic networks linking enzymes of energy metabolism, epigenetic processes and RNA pol II-mediated transcription during osmotic stress tolerance in P. patens.

The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

MicroRNAs (miRNAs) are 21-24 nt small RNAs (sRNAs) that negatively regulate protein-coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA-producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine-protein phosphatase7 and miRc20 and ahy-miR3514 targeting penta-tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS-like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits.

Molecular Responses of Red Ripe Tomato Fruit to Copper Deficiency Stress

Fruit nutritional value, plant growth, and yield can be compromised by deficient copper (Cu) bioavailability, which often appears in arable lands. This condition causes low Cu content and modifications in the ripening-associated processes in tomato fruit. This research studies the transcriptomic changes that occur in red ripe tomato fruit grown under suboptimal Cu conditions to shed light on the molecular mechanisms underlying this stress. Comparative RNA-sequencing and functional analyses revealed that Cu deficiency during cultivation activates signals for metal ion transport, cellular redox homeostasis, pyridoxal phosphate binding, and amino acid metabolism while repressing the response to phosphate starvation in harvested fruit. Transcriptomic analyses highlighted a number of novel Cu stress-responsive genes of unknown function and indicated that Cu homeostasis regulation in tomato fruit may involve additional components than those described in model plants. It also studied the regulation of high-affinity Cu transporters and a number of well-known Cu stress-responsive genes during tomato fruit ripening depending on Cu availability, which allowed potential candidates to be targeted for biotechnological improvements in reproductive tissues. We provide the first study characterizing the molecular responses of fruit to Cu deficiency stress for any fruit crop.

Protein-protein interactions in plant antioxidant defense

The regulation of reactive oxygen species (ROS) levels in plants is ensured by mechanisms preventing their over accumulation, and by diverse antioxidants, including enzymes and nonenzymatic compounds. These are affected by redox conditions, posttranslational modifications, transcriptional and posttranscriptional modifications, Ca²⁺, nitric oxide (NO) and mitogen-activated protein kinase signaling pathways. Recent knowledge about protein-protein interactions (PPIs) of antioxidant enzymes advanced during last decade. The best-known examples are interactions mediated by redox buffering proteins such as thioredoxins and glutaredoxins. This review summarizes interactions of major antioxidant enzymes with regulatory and signaling proteins and their diverse functions. Such interactions are important for stability, degradation and activation of interacting partners. Moreover, PPIs of antioxidant enzymes may connect diverse metabolic processes with ROS scavenging. Proteins like receptor for activated C kinase 1 may ensure coordination of antioxidant enzymes to ensure efficient ROS regulation. Nevertheless, PPIs in antioxidant defense are understudied, and intensive research is required to define their role in complex regulation of ROS scavenging.

MicroRNA398: A Master Regulator of Plant Development and Stress Responses

MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance.

Adaptive Responses of Citrus grandis Leaves to Copper Toxicity Revealed by RNA-Seq and Physiology

Copper (Cu)-toxic effects on Citrus grandis growth and Cu uptake, as well as gene expression and physiological parameters in leaves were investigated. Using RNA-Seq, 715 upregulated and 573 downregulated genes were identified in leaves of C. grandis seedlings exposed to Cu-toxicity (LCGSEC). Cu-toxicity altered the expression of 52 genes related to cell wall metabolism, thus impairing cell wall metabolism and lowering leaf growth. Cu-toxicity downregulated the expression of photosynthetic electron transport-related genes, thus reducing CO₂ assimilation. Some genes involved in thermal energy dissipation, photorespiration, reactive oxygen species scavenging and cell redox homeostasis and some antioxidants (reduced glutathione, phytochelatins, metallothioneins, l-tryptophan and total phenolics) were upregulated in LCGSEC, but they could not protect LCGSEC from oxidative damage. Several adaptive responses might occur in LCGSEC. LCGSEC displayed both enhanced capacities to maintain homeostasis of Cu via reducing Cu uptake by leaves and preventing release of vacuolar Cu into the cytoplasm, and to improve internal detoxification of Cu by accumulating Cu chelators (lignin, reduced glutathione, phytochelatins, metallothioneins, l-tryptophan and total phenolics). The capacities to maintain both energy homeostasis and Ca homeostasis might be upregulated in LCGSEC. Cu-toxicity increased abscisates (auxins) level, thus stimulating stomatal closure and lowering water loss (enhancing water use efficiency and photosynthesis).

The Meloidogyne graminicola effector MgMO289 targets a novel copper metallochaperone to suppress immunity in rice

Recent studies have reported that plant-parasitic nematodes facilitate their infection by suppressing plant immunity via effectors, but the inhibitory mechanisms remain poorly understood. This study found that a novel effector MgMO289 is exclusively expressed in the dorsal esophageal gland of Meloidogyne graminicola and is up-regulated at parasitic third-/fourth-stage juveniles. In planta silencing of MgMO289 substantially increased plant resistance to M. graminicola. Moreover, we found that MgMO289 interacts with a new rice copper metallochaperone heavy metal-associated plant protein 04 (OsHPP04), and that rice cytosolic COPPER/ZINC -SUPEROXIDE DISMUTASE 2 (cCu/Zn-SOD2) is the target of OsHPP04. Rice plants overexpressing OsHPP04 or MgMO289 exhibited an increased susceptibility to M. graminicola and a higher Cu/Zn-SOD activity, but lower O2•- content, when compared with wild-type plants. Meanwhile, immune response assays showed that MgMO289 could suppress host innate immunity. These findings reveal a novel pathway for a plant pathogen effector that utilizes the host O2•--scavenging system to eliminate O2•- and suppress plant immunity.

A putative nuclear copper chaperone promotes plant immunity in Arabidopsis

Copper is essential for many metabolic processes but must be sequestrated by copper chaperones. It is well known that plant copper chaperones regulate various physiological processes. However, the functions of copper chaperones in the plant nucleus remain largely unknown. Here, we identified a putative copper chaperone induced by pathogens (CCP) in Arabidopsis thaliana. CCP harbors a classical MXCXXC copper-binding site (CBS) at its N-terminus and a nuclear localization signal (NLS) at its C-terminus. CCP mainly formed nuclear speckles in the plant nucleus, which requires the NLS and CBS domains. Overexpression of CCP induced PR1 expression and enhanced resistance against Pseudomonas syringae pv. tomato DC3000 compared with Col-0 plants. Conversely, two CRISPR/Cas9-mediated ccp mutants were impaired in plant immunity. Further biochemical analyses revealed that CCP interacted with the transcription factor TGA2 in vivo and in vitro. Moreover, CCP recruits TGA2 to the PR1 promoter sequences in vivo, which induces defense gene expression and plant immunity. Collectively, our results have identified a putative nuclear copper chaperone required for plant immunity and provided evidence for a potential function of copper in the salicylic pathway.

Functional characterization and expression patterns of PnATX genes under different abiotic stress treatments in Populus

The copper chaperone ATX1 has been investigated previously in the herbaceous plants Arabidopsis and rice. However, the molecular mechanisms of ATX1 underlying copper transport and functional characteristics in the woody plant Populus are poorly understood. In this study, PnATX1 and PnATX2 of Populus simonii × P. nigra were identified and characterized. Sequence analysis showed that PnATXs contained the metal-binding motif MXCXXC in the N-terminus and a lysine-rich region. Phylogenetic analysis of ATX protein sequences revealed that PnATXs were clustered in the same group as AtATX1. PnATX proteins were localized in the cytoplasm and nucleus. Tissue-specific expression analysis showed that PnATX1 and PnATX2 were expressed in all analyzed tissues and, in particular, expressed to a higher relative expression level in young leaves. Quantitative real-time PCR analysis indicated that each PnATX gene was differentially expressed in different tissues under treatments with copper, zinc, iron, jasmonate and salicylic acid (SA). The copper-response element GTAC, methyl jasmonate and salicylic acid responsiveness elements and other cis-acting elements were identified in the PnATX1 and PnATX2 promoters. Expression of β-glucuronidase driven by the PnATX1 promoter was observed in the apical meristem of 7-day-old Arabidopsis transgenic seedlings, and the signal strength was not influenced by deficient or excessive copper conditions. Both PnATX1 and PnATX2 functionally rescued the defective phenotypes of yeast atx1Δ and sod1Δ strains. Under copper excess and deficiency conditions, transgenic Arabidopsis atx1 mutants harboring 35S::PnATX constructs exhibited root length and fresh weight similar to those of the wild type and higher than those of Arabidopsis atx1 mutants. Superoxide dismutase activity decreased in transgenic lines compared with that of atx1 mutants, whereas peroxidase and catalase activities increased significantly under excess copper. The results provide a basis for elucidating the role of Populus PnATX genes in copper homeostasis.

Deregulated High Affinity Copper Transport Alters Iron Homeostasis in Arabidopsis

The present work describes the effects on iron homeostasis when copper transport was deregulated in Arabidopsis thaliana by overexpressing high affinity copper transporters COPT1 and COPT3 (COPT^OE ). A genome-wide analysis conducted on COPT1^OE plants, highlighted that iron homeostasis gene expression was affected under both copper deficiency and excess. Among the altered genes were those encoding the iron uptake machinery and their transcriptional regulators. Subsequently, COPT^OE seedlings contained less iron and were more sensitive than controls to iron deficiency. The deregulation of copper (I) uptake hindered the transcriptional activation of the subgroup Ib of basic helix-loop-helix (bHLH-Ib) factors under copper deficiency. Oppositely, copper excess inhibited the expression of the master regulator FIT but activated bHLH-Ib expression in COPT^OE plants, in both cases leading to the lack of an adequate iron uptake response. As copper increased in the media, iron (III) was accumulated in roots, and the ratio iron (III)/iron (II) was increased in COPT^OE plants. Thus, iron (III) overloading in COPT^OE roots inhibited local iron deficiency responses, aimed to metal uptake from soil, leading to a general lower iron content in the COPT^OE seedlings. These results emphasized the importance of appropriate spatiotemporal copper uptake for iron homeostasis under non-optimal copper supply. The understanding of the role of copper uptake in iron metabolism could be applied for increasing crops resistance to iron deficiency.

Oxidative protein folding: state-of-the-art and current avenues of research in plants

Contents Summary 1230 I. Introduction 1230 II. Formation and isomerization of disulfides in the ER and the Golgi apparatus 1231 III. The disulfide relay in the mitochondrial intermembrane space: why are plants different? 1236 IV. Disulfide bond formation on luminal proteins in thylakoids 1240 V. Conclusion 1242 Acknowledgements 1242 References 1242 SUMMARY: Disulfide bonds are post-translational modifications crucial for the structure and function of thousands of proteins. Their formation and isomerization, referred to as oxidative folding, require specific protein machineries found in oxidizing subcellular compartments, namely the endoplasmic reticulum and the associated endomembrane system, the intermembrane space of mitochondria and the thylakoid lumen of chloroplasts. At least one protein component is required for transferring electrons from substrate proteins to an acceptor that is usually molecular oxygen. For oxidation reactions, incoming reduced substrates are oxidized by thiol-oxidoreductase proteins (or domains in case of chimeric proteins), which are usually themselves oxidized by a single thiol oxidase, the enzyme generating disulfide bonds de novo. By contrast, the description of the molecular actors and pathways involved in proofreading and isomerization of misfolded proteins, which require a tightly controlled redox balance, lags behind. Herein we provide a general overview of the knowledge acquired on the systems responsible for oxidative protein folding in photosynthetic organisms, highlighting their particularities compared to other eukaryotes. Current research challenges are discussed including the importance and specificity of these oxidation systems in the context of the existence of reducing systems in the same compartments.

Functions of the C2H2 Transcription Factor Gene thmea1 in Trichoderma harzianum under Copper Stress Based on Transcriptome Analysis

Trichoderma spp. are important biocontrol filamentous fungi and have tremendous potential in soil bioremediation. In our previous studies, a C2H2 type transcription factor coding gene (thmea1) was cloned from a biocontrol agent T. harzianum Th-33; the encoded sequence of thmea1 contained 3 conserved C2H2 domains with Swi5 and Ace2 in Saccharomyces cerevisiae. The thmea1 knockout mutant Δthmea1 showed 12.9% higher copper tolerance than the wild-type Th33. To elucidate the function of thmea1 and its relationship with copper stress response, we conducted transcriptome sequencing and analysis of wild-type Th33 and Δthmea1 under 0.8 mM copper stress. A total of 1061 differentially expressed genes (DEGs) were identified between the two strains, all DEGs were assigned to KEGG pathway database, 383 DEGs were annotated in 191 individual pathways, and the categories of ribosomal protein synthesis and amino acid metabolism were the most highly enriched ones. Analysis of related DEGs showed that the expression levels of intracellular glutathione detoxification enzyme, heat shock proteins, and ribosomal proteins in Δthmea1 were higher than that of the wild-type Th33, and the expression of metallothionein (MT) gene did not change. In addition, the expression levels of genes coding for proteins associated with the Ccc2p-mediated copper chaperone Atx1p transport of copper ions into the Golgi secretory pathway increased, as well as the copper amine oxidase (CuAO). These findings suggest that Thmea1 is a negative regulated factor of copper tolerance ability in T. harzianum. It does not show metallothionein expression activator activities as that of Ace2 in S. cerevisiae. We hypothesize that after T. harzianum has lost its thmea1 gene, the ability of cells to scavenge reactive oxygen species, mainly through the glutathione antioxidant system, is enhanced, whereas protein synthesis and repair and copper secretion increase under copper stress, which increases the ability of the mutant strain to tolerate copper stress.

Comparison of ATP sulfurylase 2 from selenium hyperaccumulator Stanleya pinnata and non-accumulator Stanleya elata reveals differential intracellular localization and enzyme activity levels

BACKGROUND

The plant Stanleya pinnata hyperaccumulates Se up to 0.5% of its dry weight in organic forms, whereas the closely related Stanleya elata does not hyperaccumulate Se. ATP sulfurylase (ATPS) can catalyze the formation of adenosine 5'-phosphoselenate (APSe) from ATP and selenate. We investigated the S. pinnata ATPS2 isoform (SpATPS2) to assess its possible role in Se hyperaccumulation.

METHODS

ATPS expression and activity was compared in the two Stanleya species. The ATPS2 protein sequences were modeled. Sub-cellular locations were analyzed using GFP fusions. Enzyme activity of purified recombinant SpATPS2 was measured.

RESULTS

ATPS2 transcript levels were six-fold higher in roots of S. pinnata relative to S. elata. Overall root ATPS enzyme activity was two-fold elevated in S. pinnata. Cloning and sequencing of SpATPS2 and S. elata ATPS2 (SeATPS2) showed the predicted SeATPS2 to be canonical, while SpATPS2, although very similar in its core structure, has unique features, including an interrupted plastid targeting signal due to a stop codon in the 5' region of the coding sequence. Indeed GFP fusions revealed that SpATPS2 had exclusive cytosolic localization, while SeATPS2 showed dual localization in plastids and cytosol. SpATPS2 activity was inhibited by both sulfate and selenate, indicating that the enzyme acts on both substrates.

CONCLUSIONS

The ATPS2 from S. pinnata differs from non-accumulator ATPS2 in its elevated expression and sub-cellular localization. It likely acts on both selente and sulfate substrates.

GENERAL SIGNIFICANCE

These observations shed new light on the role of ATPS2 in the evolution of Se hyperaccumulation in plants. This article is part of a Special Issue entitled Selenium research in biochemistry and biophysics - 200 year anniversary issue, edited by Dr. Elias Arnér and Dr. Regina Brigelius-Flohe.

Transcriptomic Response of Arabidopsis thaliana Exposed to CuO Nanoparticles, Bulk Material, and Ionic Copper

Engineered nanoparticles (ENPs) exhibit unique properties advantageous in a number of applications, but they also represent potential health and environmental risks. In this study, we investigated the phytotoxic mechanism of CuO ENPs using transcriptomic analysis and compared this response with the response to CuO bulk particles and ionic Cu²⁺. Ionic Cu²⁺ at the concentration of 0.16 mg L^-1 changed transcription of 2692 genes (p value of <0.001, fold change of ≥2) after 7 days of exposure, whereas CuO ENPs and bulk particles (both in the concentration of 10 mg L^-1) altered the expression of 922 and 482 genes in Arabidopsis thaliana roots, respectively. The similarity between transcription profiles of plants exposed to ENPs and ionic Cu²⁺ indicated that the main factor in phytotoxicity was the release of Cu²⁺ ions from CuO ENPs after 7 days of exposure. The effect of Cu²⁺ ions was evident in all treatments, as indicated by the down-regulation of genes involved in metal homeostasis and transport and the up-regulation of oxidative stress response genes. ENPs were more soluble than bulk particles, resulting in the up-regulation of metallochaperone-like genes or the down-regulation of aquaporins and metal transmembrane transporters that was also characteristic for ionic Cu²⁺ exposure.

Copper and ectopic expression of the Arabidopsis transport protein COPT1 alter iron homeostasis in rice (Oryza sativa L.)

Copper deficiency and excess differentially affect iron homeostasis in rice and overexpression of the Arabidopsis high-affinity copper transporter COPT1 slightly increases endogenous iron concentration in rice grains. Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. However, the molecular mechanisms underlying the interaction between both metals remain poorly understood. In the present work, we study the effects produced on iron homeostasis by a wide range of copper concentrations in the growth media and by altered copper transport in Oryza sativa plants. Gene expression profiles in rice seedlings grown under copper excess show an altered expression of genes involved in iron homeostasis compared to standard control conditions. Thus, ferritin OsFER2 and ferredoxin OsFd1 mRNAs are down-regulated whereas the transcriptional iron regulator OsIRO2 and the nicotianamine synthase OsNAS2 mRNAs rise under copper excess. As expected, the expression of OsCOPT1, which encodes a high-affinity copper transport protein, as well as other copper-deficiency markers are down-regulated by copper. Furthermore, we show that Arabidopsis COPT1 overexpression (C1 ^OE ) in rice causes root shortening in high copper conditions and under iron deficiency. C1 ^OE rice plants modify the expression of the putative iron-sensing factors OsHRZ1 and OsHRZ2 and enhance the expression of OsIRO2 under copper excess, which suggests a role of copper transport in iron signaling. Importantly, the C1 ^OE rice plants grown on soil contain higher endogenous iron concentration than wild-type plants in both brown and white grains. Collectively, these results highlight the effects of rice copper status on iron homeostasis, which should be considered to obtain crops with optimized nutrient concentrations in edible parts.

Long-chain base kinase1 affects freezing tolerance in Arabidopsis thaliana

Long-chain base kinases (LCBKs) phosphorylate sphingolipid-derived long-chain base lipids and participate in the regulation of stress responses in plants. Here, we isolated a novel Arabidopsis thaliana mutant, lcbk1-2, which was extremely sensitive to freezing temperatures with or without cold acclimation. Physiological assays revealed that concentrations of osmolytes (proline and soluble sugars) and the activity of superoxide dismutase were significantly decreased in the lcbk1-2 mutant, compared with wild type. Also, the balance of reactive oxygen species (ROS) was disrupted in the lcbk1-2 mutant with or without cold treatment and, consistent with this, gene expression profiling analysis showed that the expression of cold-responsive ROS-scavenging genes was substantially decreased in the lcbk1-2 mutant. The expression of membrane lipid-related genes, which are linked to freezing tolerance in plants, was also impaired in the lcbk1-2 mutant. Furthermore, transgenic lines overexpressing LCBK1 showed enhanced freezing tolerance with over-accumulation of osmolytes. Collectively, our results suggested that LCBK1 functions as a novel positive regulator of freezing tolerance in Arabidopsis and may participate in the accumulation of osmolytes, the regulation of ROS homeostasis and lipid metabolism.

Transcriptome Sequencing in Response to Salicylic Acid in Salvia miltiorrhiza

Salvia miltiorrhiza is a traditional Chinese herbal medicine, whose quality and yield are often affected by diseases and environmental stresses during its growing season. Salicylic acid (SA) plays a significant role in plants responding to biotic and abiotic stresses, but the involved regulatory factors and their signaling mechanisms are largely unknown. In order to identify the genes involved in SA signaling, the RNA sequencing (RNA-seq) strategy was employed to evaluate the transcriptional profiles in S. miltiorrhiza cell cultures. A total of 50,778 unigenes were assembled, in which 5,316 unigenes were differentially expressed among 0-, 2-, and 8-h SA induction. The up-regulated genes were mainly involved in stimulus response and multi-organism process. A core set of candidate novel genes coding SA signaling component proteins was identified. Many transcription factors (e.g., WRKY, bHLH and GRAS) and genes involved in hormone signal transduction were differentially expressed in response to SA induction. Detailed analysis revealed that genes associated with defense signaling, such as antioxidant system genes, cytochrome P450s and ATP-binding cassette transporters, were significantly overexpressed, which can be used as genetic tools to investigate disease resistance. Our transcriptome analysis will help understand SA signaling and its mechanism of defense systems in S. miltiorrhiza.

Transcriptome Changes in Hirschfeldia incana in Response to Lead Exposure

Hirschfeldia incana, a pseudometallophyte belonging to the Brassicaceae family and widespread in the Mediterranean region, was selected for its ability to grow on soils contaminated by lead (Pb). The global comparison of gene expression using microarrays between a plant susceptible to Pb (Arabidopsis thaliana) and a Pb tolerant plant (H. incana) enabled the identification of a set of specific genes expressed in response to lead exposure. Three groups of genes were particularly over-represented by the Pb exposure in the biological processes categorized as photosynthesis, cell wall, and metal handling. Each of these gene groups was shown to be directly involved in tolerance or in protection mechanisms to the phytotoxicity associated with Pb. Among these genes, we demonstrated that MT2b, a metallothionein gene, was involved in lead accumulation, confirming the important role of metallothioneins in the accumulation and the distribution of Pb in leaves. On the other hand, several genes involved in biosynthesis of ABA were shown to be up-regulated in the roots and shoots of H. incana treated with Pb, suggesting that ABA-mediated signaling is a possible mechanism in response to Pb treatment in H. incana. This latest finding is an important research direction for future studies.

Comparative transcriptome analysis of grapevine in response to copper stress

Grapevine is one of the most economically important and widely cultivated fruit crop worldwide. With the industrialization and the popular application of cupric fungicides in grape industry, copper stress and copper pollution are also the factors affecting grape production and berry and wine quality. Here, 3,843 transcripts were significantly differently expressed genes in response to Cu stress by RNA-seq, which included 1,892 up-regulated and 1,951 down-regulated transcripts. During this study we found many known and novel Cu-induced and -repressed genes. Biological analysis of grape samples were indicated that exogenous Cu can influence chlorophylls metabolism and photosynthetic activities of grapevine. Most ROS detoxification systems, including antioxidant enzyme, stress-related proteins and secondary metabolites were strongly induced. Concomitantly, abscisic acid functioned as a negative regulator in Cu stress, in opposite action to ethylene, auxin, jasmonic acid, and brassinolide. This study also identified a set of Cu stress specifically activated genes coding copper transporter, P1B-type ATPase, multidrug transporters. Overall, this work was carried out to gain insights into the copper-regulated and stress-responsive mechanisms in grapevine at transcriptome level. This research can also provide some genetic information that can help us in better vinery management and breeding Cu-resistant grape cultivars.

miR408 is involved in abiotic stress responses in Arabidopsis

MicroRNAs (miRNAs) are small RNAs that regulate the expression of target genes post-transcriptionally; they are known to play major roles in development and responses to abiotic stress. miR408 is a highly conserved miRNA in plants that responds to the availability of copper and targets genes encoding copper-containing proteins. It was recently recognized to be an important component of the HY5-SPL7 gene network that mediates a coordinated response to light and copper, illustrating its central role in the response of plants to the environment. Expression of miR408 is significantly affected by a variety of developmental and ‏environmental conditions; however, its biological function is ‏unknown. Involvement of miR408 in the abiotic stress response was investigated in Arabidopsis. Expression of miR408, as well as its target genes, was investigated in response to salinity, cold, oxidative stress, drought and osmotic stress. Analyses of transgenic plants with modulated miR408 expression revealed that higher miR408 expression leads to improved tolerance to salinity, cold and oxidative stress, but enhanced sensitivity to drought and osmotic stress. Cellular antioxidant capacity was enhanced in plants with elevated miR408 expression, as manifested by reduced levels of reactive oxygen species and induced expression of genes associated with antioxidative functions, including Cu/Zn superoxide dismutases (CSD1 and CSD2) and glutathione-S-transferase (GST-U25), as well as auxiliary genes: the copper chaperone CCS1 and the redox stress-associated gene SAP12. Overall, the results demonstrate significant involvement of miR408 in abiotic stress responses, emphasizing the central function of miR408 in plant survival.

Copper-transporting ATPases: The evolutionarily conserved machineries for balancing copper in living systems

Copper ATPases (Cu-ATPases) are ubiquitous transmembrane proteins using energy from ATP to transport copper across different biological membranes of prokaryotic and eukaryotic cells. As they belong to the P-ATPase family, Cu-ATPases contain a characteristic catalytic domain with an evolutionarily conserved aspartate residue phosphorylated by ATP to form a phosphoenzyme intermediate, as well as transmembrane helices containing a cation-binding cysteine-proline-cysteine/histidine/serine (CPx) motif for catalytic activation and cation translocation. In addition, most Cu-ATPases possess the N-terminal Cu-binding CxxC motif required for regulation of enzyme activity. In cells, the Cu-ATPases receive copper from soluble chaperones and maintain intracellular copper homeostasis by efflux of copper from the cell or transport of the metal into the intracellular compartments. In addition, copper pumps play an essential role in cuproprotein biosynthesis by the uptake of copper into the cell or delivery of the metal into the chloroplasts and thylakoid lumen or into the lumen of the secretory pathway, where the metal ion is incorporated into copper-dependent enzymes. In the recent years, significant progress has been made toward understanding the function and regulation of Cu-transporting ATPases in archaea, bacteria, yeast, humans, and plants, providing new insights into the specific physiological roles of these essential proteins in various organisms and revealing some conservative regulatory mechanisms of Cu-ATPase activity. In this review, the structural, biochemical, and functional properties of Cu-ATPases from phylogenetically different organisms are summarized and discussed, with particular attention given to the recent insights into the molecular biology of copper pumps in plants.

Transporters, chaperones, and P-type ATPases controlling grapevine copper homeostasis

With more copper and copper-containing compounds used as bactericides and fungicides in viticulture, copper homeostasis in grapevine (Vitis) has become one of the serious environmental crises with great risk. To better understand the regulation of Cu homeostasis in grapevine, grapevine seedlings cultured in vitro with different levels of Cu were utilized to investigate the tolerance mechanisms of grapevine responding to copper availability at physiological and molecular levels. The results indicated that Cu contents in roots and leaves arose with increasing levels of Cu application. With copper concentration increasing, malondialdehyde (MDA) content increased in roots and leaves and the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) increased to protect the plant itself from damage. The expression patterns of 19 genes, encoding transporters, chaperones, and P-type ATPases involved in copper homeostasis in root and leaf of grapevine seedling under various levels of Cu(2+) were further analyzed. The expression patterns indicated that CTr1, CTr2, and CTr8 transporters were significantly upregulated in response both to Cu excess and deficiency. ZIP2 was downregulated in response to Cu excess and upregulated under Cu-deficient conditions, while ZIP4 had an opposite expression pattern under similar conditions. The expression of chaperones and P-type ATPases in response to Cu availability in grapevine were also briefly studied.

Copper Delivery to Chloroplast Proteins and its Regulation

Copper is required for photosynthesis in chloroplasts of plants because it is a cofactor of plastocyanin, an essential electron carrier in the thylakoid lumen. Other chloroplast copper proteins are copper/zinc superoxide dismutase and polyphenol oxidase, but these proteins seem to be dispensable under conditions of low copper supply when transcripts for these proteins undergo microRNA-mediated down regulation. Two ATP-driven copper transporters function in tandem to deliver copper to chloroplast compartments. This review seeks to summarize the mechanisms of copper delivery to chloroplast proteins and its regulation. We also delineate some of the unanswered questions that still remain in this field.

Temporal aspects of copper homeostasis and its crosstalk with hormones

To cope with the dual nature of copper as being essential and toxic for cells, plants temporarily adapt the expression of copper homeostasis components to assure its delivery to cuproproteins while avoiding the interference of potential oxidative damage derived from both copper uptake and photosynthetic reactions during light hours. The circadian clock participates in the temporal organization of coordination of plant nutrition adapting metabolic responses to the daily oscillations. This timely control improves plant fitness and reproduction and holds biotechnological potential to drive increased crop yields. Hormonal pathways, including those of abscisic acid, gibberellins, ethylene, auxins, and jasmonates are also under direct clock and light control, both in mono and dicotyledons. In this review, we focus on copper transport in Arabidopsis thaliana and Oryza sativa and the presumable role of hormones in metal homeostasis matching nutrient availability to growth requirements and preventing metal toxicity. The presence of putative hormone-dependent regulatory elements in the promoters of copper transporters genes suggests hormonal regulation to match special copper requirements during plant development. Spatial and temporal processes that can be affected by hormones include the regulation of copper uptake into roots, intracellular trafficking and compartmentalization, and long-distance transport to developing vegetative and reproductive tissues. In turn, hormone biosynthesis and signaling are also influenced by copper availability, which suggests reciprocal regulation subjected to temporal control by the central oscillator of the circadian clock. This transcriptional regulatory network, coordinates environmental and hormonal signaling with developmental pathways to allow enhanced micronutrient acquisition efficiency.

Evolution of a plant-specific copper chaperone family for chloroplast copper homeostasis

Metallochaperones traffic copper (Cu(+)) from its point of entry at the plasma membrane to its destination. In plants, one destination is the chloroplast, which houses plastocyanin, a Cu-dependent electron transfer protein involved in photosynthesis. We present a previously unidentified Cu(+) chaperone that evolved early in the plant lineage by an alternative-splicing event of the pre-mRNA encoding the chloroplast P-type ATPase in Arabidopsis 1 (PAA1). In several land plants, recent duplication events created a separate chaperone-encoding gene coincident with loss of alternative splicing. The plant-specific Cu(+) chaperone delivers Cu(+) with specificity for PAA1, which is flipped in the envelope relative to prototypical bacterial ATPases, compatible with a role in Cu(+) import into the stroma and consistent with the canonical catalytic mechanism of these enzymes. The ubiquity of the chaperone suggests conservation of this Cu(+)-delivery mechanism and provides a unique snapshot into the evolution of a Cu(+) distribution pathway. We also provide evidence for an interaction between PAA2, the Cu(+)-ATPase in thylakoids, and the Cu(+)-chaperone for Cu/Zn superoxide dismutase (CCS), uncovering a Cu(+) network that has evolved to fine-tune Cu(+) distribution.

Function and Regulation of the Plant COPT Family of High-Affinity Copper Transport Proteins

Copper (Cu) is an essential micronutrient for all eukaryotes because it participates as a redox active cofactor in multiple biological processes, including mitochondrial respiration, photosynthesis, oxidative stress protection, and iron (Fe) transport. In eukaryotic cells, Cu transport toward the cytoplasm is mediated by the conserved CTR/COPT family of high-affinity Cu transport proteins. This outlook paper reviews the contribution of our research group to the characterization of the function played by the Arabidopsis thaliana COPT1–6 family of proteins in plant Cu homeostasis. Our studies indicate that the different tissue specificity, Cu-regulated expression, and subcellular localization dictate COPT-specialized contribution to plant Cu transport and distribution. By characterizing lack-of-function Arabidopsis mutant lines, we conclude that COPT1 mediates root Cu acquisition, COPT6 facilitates shoot Cu distribution, and COPT5 mobilizes Cu from storage organelles. Furthermore, our work with copt2 mutant and COPT-overexpressing plants has also uncovered Cu connections with Fe homeostasis and the circadian clock, respectively. Future studies on the interaction between COPT transporters and other components of the Cu homeostasis network will improve our knowledge of plant Cu acquisition, distribution, regulation, and utilization by Cu-proteins.

Comparison of global responses to mild deficiency and excess copper levels in Arabidopsis seedlings

Copper is an essential micronutrient in higher plants, but it is toxic in excess. The fine adjustments required to fit copper nutritional demands for optimal growth are illustrated by the diverse, severe symptoms resulting from copper deficiency and excess. Here, a differential transcriptomic analysis was done between Arabidopsis thaliana plants suffering from mild copper deficiency and those with a slight copper excess. The effects on the genes encoding cuproproteins or copper homeostasis factors were included in a CuAt database, which was organised to collect additional information and connections to other databases. The categories overrepresented under copper deficiency and copper excess conditions are discussed. Different members of the categories overrepresented under copper deficiency conditions were both dependent and independent of the general copper deficiency transcriptional regulator SPL7. The putative regulatory elements in the promoter of the copper deficiency overrepresented genes, particularly of the iron superoxide dismutase gene FSD1, were also analysed. A 65 base pair promoter fragment, with at least three GTAC sequences, was found to be not only characteristic of them all, but was responsible for most of the FSD1 copper-dependent regulations. Moreover, a new molecular marker for the slight excess copper nutritional status is proposed. Taken together, these data further contribute to characterise copper nutritional responses in higher plants.

Regulation of the chloroplastic copper chaperone (CCS) and cuprozinc superoxide dismutase (CSD2) by alternative splicing and copper excess in Glycine max

Metal homeostasis is an important aspect of plant physiology, and the copper transport into the chloroplast and its fate after delivery is of special relevance for plants. In this work, the regulation of the chloroplastic copper chaperone for the cuprozinc superoxide dismutase (GmCCS) and its target, the cuprozinc superoxide dismutase (GmCSD2), was investigated in photosynthetic cell suspensions and entire plants from Glycine max (L.) Merr. Both genes were expressed in cell suspensions and in all plant tissues analysed, and their RNAs matured by alternative splicing with intron retention (IntronR). This mechanism generated a spliced and three non-spliced mRNAs in the case of GmCCS but only a spliced and a non-spliced mRNAs in GmCSD2. Copper excess strongly upregulated the expression of both fully spliced mRNAs but mostly unaffected the non-spliced forms. In entire plants, some tissue specificity was also observed depending on copper content status. At the protein level, the GmCCS was mostly unaffected but the GmCSD2 was strongly induced under copper excess in all subcellular fractions analysed, suggesting a post-transcriptional regulation for the former. This different protein regulation of the chaperone and its target may indicate some additional function for the CSD2 protein. In addition to its well-known superoxide dismutase (SOD) activity, it may also function as a metal sink in copper excess availability to avoid metal cell damage. Furthermore, the GmCCS seems to be present in the stroma only but the GmCSD2 was present in both stroma and thylakoids despite the general idea that the SOD enzymes are typically soluble stroma proteins. The presence of the SOD enzyme on the surface of the thylakoid membranes is reasonable considering that the superoxide radical (O2-) is preferentially formed at the acceptor side of the PSI.

Species-specific activation of Cu/Zn SOD by its CCS copper chaperone in the pathogenic yeast Candida albicans

Candida albicans is a pathogenic yeast of important public health relevance. Virulence of C. albicans requires a copper and zinc containing superoxide dismutase (SOD1), but the biology of C. albicans SOD1 is poorly understood. To this end, C. albicans SOD1 activation was examined in baker's yeast (Saccharomyces cerevisiae), a eukaryotic expression system that has proven fruitful for the study of SOD1 enzymes from invertebrates, plants, and mammals. In spite of the 80% similarity between S. cerevisiae and C. albicans SOD1 molecules, C. albicans SOD1 is not active in S. cerevisiae. The SOD1 appears incapable of productive interactions with the copper chaperone for SOD1 (CCS1) of S. cerevisiae. C. albicans SOD1 contains a proline at position 144 predicted to dictate dependence on CCS1. By mutation of this proline, C. albicans SOD1 gained activity in S. cerevisiae, and this activity was independent of CCS1. We identified a putative CCS1 gene in C. albicans and created heterozygous and homozygous gene deletions at this locus. Loss of CCS1 resulted in loss of SOD1 activity, consistent with its role as a copper chaperone. C. albicans CCS1 also restored activity to C. albicans SOD1 expressed in S. cerevisiae. C. albicans CCS1 is well adapted for activating its partner SOD1 from C. albicans, but not SOD1 from S. cerevisiae. In spite of the high degree of homology between the SOD1 and CCS1 molecules in these two fungal species, there exists a species-specific barrier in CCS-SOD interactions which may reflect the vastly different lifestyles of the pathogenic versus the noninfectious yeast.

The Populus superoxide dismutase gene family and its responses to drought stress in transgenic poplar overexpressing a pine cytosolic glutamine synthetase (GS1a)

BACKGROUND

Glutamine synthetase (GS) plays a central role in plant nitrogen assimilation, a process intimately linked to soil water availability. We previously showed that hybrid poplar (Populus tremula X alba, INRA 717-1B4) expressing ectopically a pine cytosolic glutamine synthetase gene (GS1a) display enhanced tolerance to drought. Preliminary transcriptome profiling revealed that during drought, members of the superoxide dismutase (SOD) family were reciprocally regulated in GS poplar when compared with the wild-type control, in all tissues examined. SOD was the only gene family found to exhibit such patterns.

RESULTS

In silico analysis of the Populus genome identified 12 SOD genes and two genes encoding copper chaperones for SOD (CCSs). The poplar SODs form three phylogenetic clusters in accordance with their distinct metal co-factor requirements and gene structure. Nearly all poplar SODs and CCSs are present in duplicate derived from whole genome duplication, in sharp contrast to their predominantly single-copy Arabidopsis orthologs. Drought stress triggered plant-wide down-regulation of the plastidic copper SODs (CSDs), with concomitant up-regulation of plastidic iron SODs (FSDs) in GS poplar relative to the wild type; this was confirmed at the activity level. We also found evidence for coordinated down-regulation of other copper proteins, including plastidic CCSs and polyphenol oxidases, in GS poplar under drought conditions.

CONCLUSIONS

Both gene duplication and expression divergence have contributed to the expansion and transcriptional diversity of the Populus SOD/CCS families. Coordinated down-regulation of major copper proteins in drought-tolerant GS poplars supports the copper cofactor economy model where copper supply is preferentially allocated for plastocyanins to sustain photosynthesis during drought. Our results also extend previous findings on the compensatory regulation between chloroplastic CSDs and FSDs, and suggest that this copper-mediated mechanism represents a common response to oxidative stress and other genetic manipulations, as in GS poplars, that affect photosynthesis.

Chaperonin 20 might be an iron chaperone for superoxide dismutase in activating iron superoxide dismutase (FeSOD)

Activation of Cu/Zn superoxide dismutases (CuZnSODs) is aided by Cu incorporation and disulfide isomerization by Cu chaperone of SOD (CCS). As well, an Fe-S cluster scaffold protein, ISU, might alter the incorporation of Fe or Mn into yeast MnSOD (ySOD2), thus leading to active or inactive ySOD2. However, metallochaperones involved in the activation of FeSODs are unknown. Recently, we found that a chloroplastic chaperonin cofactor, CPN20, could mediate FeSOD activity. To investigate whether Fe incorporation in FeSOD is affected by CPN20, we used inductively coupled plasma mass spectrometry to analyze the ability of CPN20 to bind Fe. CPN20 could bind Fe, and the Fe binding to FeSOD was increased with CPN20 incubation. Thus, CPN20 might be an Fe chaperone for FeSOD activation, a role independent of its well-known co-chaperonin activity.

CHAPERONIN 20 mediates iron superoxide dismutase (FeSOD) activity independent of its co-chaperonin role in Arabidopsis chloroplasts

Iron superoxide dismutases (FeSODs; FSDs) are primary antioxidant enzymes in Arabidopsis thaliana chloroplasts. The stromal FSD1 conferred the only detectable FeSOD activity, whereas the thylakoid membrane- and nucleoid-co-localized FSD2 and FSD3 double mutant showed arrested chloroplast development. FeSOD requires cofactor Fe for its activity, but its mechanism of activation is unclear. We used reversed-phase high-performance liquid chromatography (HPLC), gel filtration chromatography, LC-MS/MS, protoplast transient expression and virus-induced gene silencing (VIGS) analyses to identify and characterize a factor involved in FeSOD activation. We identified the chloroplast-localized co-chaperonin CHAPERONIN 20 (CPN20) as a mediator of FeSOD activation by direct interaction. The relationship between CPN20 and FeSOD was confirmed by in vitro experiments showing that CPN20 alone could enhance FSD1, FSD2 and FSD3 activity. The in vivo results showed that CPN20-overexpressing mutants and mutants with defective co-chaperonin activity increased FSD1 activity, without changing the chaperonin CPN60 protein level, and VIGS-induced downregulation of CPN20 also led to decreased FeSOD activity. Our findings reveal that CPN20 can mediate FeSOD activation in chloroplasts, a role independent of its known function in the chaperonin system.

MicroRNAs in metal stress: specific roles or secondary responses?

In plants, microRNAs (miRNAs) control various biological processes by negatively regulating the expression of complementary target genes, either (1) post-transcriptionally by cleavage or translational inhibition of target mRNA, or (2) transcriptionally by methylation of target DNA. Besides their role in developmental processes, miRNAs are main players in stress responses, including metal stress responses. Exposure of plants to excess metal concentrations disturbs the cellular redox balance and enhances ROS accumulation, eventually leading to oxidative damage or signaling. Plants modify their gene expression by the activity of miRNAs in response to metal toxicity to regulate (1) complexation of excess metals, (2) defense against oxidative stress and (3) signal transduction for controlling various biological responses. This review focuses on the biogenesis, working mechanisms and functioning of miRNAs in plants. In a final part, our current knowledge on the regulatory roles of miRNAs in plant metal stress responses is highlighted, and whether stress-regulated miRNAs have specific roles or are secondary consequences is discussed.

The strength of the miR398-Csd2-CCS1 regulon is subject to natural variation in Arabidopsis thaliana

miR398 links expression of the three major chloroplast copper proteins, plastocyanin, CCS1 and Csd2, to copper availability. miR398 abundance was stronger plastocyanin-controlled in accessions from cold and continental habitats (Kas-1, Ms-0, WS) than in Cvi-0 and Col-0. Target gene regulation was broken for Csd2 in Cvi-0 upon cold-treatment. Comparison of miR398 levels, target gene regulation as well as Ago1 and miR168 expression demonstrated that the miR398 regulon can be overwritten by accession specific transcriptional regulation in Cvi-0. It is concluded that the escape from the miRNA control of copper homeostasis is linked to adaptation of Cvi-0 to its harsh natural habitat.

Copper chaperone-dependent and -independent activation of three copper-zinc superoxide dismutase homologs localized in different cellular compartments in Arabidopsis

Superoxide dismutases (SODs) are important antioxidant enzymes that catalyze the disproportionation of superoxide anion to oxygen and hydrogen peroxide to guard cells against superoxide toxicity. The major pathway for activation of copper/zinc SOD (CSD) involves a copper chaperone for SOD (CCS) and an additional minor CCS-independent pathway reported in mammals. We characterized the CCS-dependent and -independent activation pathways for three CSDs localized in different cellular compartments in Arabidopsis (Arabidopsis thaliana). The main activation pathway for CSD1 in the cytoplasm involved a CCS-dependent and -independent pathway, which was similar to that for human CSD. Activation of CSD2 in chloroplasts depended totally on CCS, similar to yeast (Saccharomyces cerevisiae) CSD. Peroxisome-localized CSD3 via a CCS-independent pathway was similar to nematode (Caenorhabditis elegans) CSD in retaining activity in the absence of CCS. In Arabidopsis, glutathione played a role in CCS-independent activation, as was reported in humans, but an additional factor was required. These findings reveal a highly specific and sophisticated regulation of CSD activation pathways in planta relative to other known CCS-independent activation.

Conservation and diversity of microRNA-associated copper-regulatory networks in Populus trichocarpa

Plants develop important regulatory networks to adapt to the frequently-changing availability of copper (Cu). However, little is known about miRNA-associated Cu-regulatory networks in plant species other than Arabidopsis. Here, we report that Cu-responsive miRNAs in Populus trichocarpa (Torr. & Gray) include not only conserved miR397, miR398 and miR408, but also Populus-specific miR1444, suggesting the conservation and diversity of Cu-responsive miRNAs in plants. Copper-associated suppression of mature miRNAs is in company with the up-regulation of their target genes encoding Cu-containing proteins in Populus. The targets include miR397-targeted PtLAC5, PtLAC6 and PtLAC110a, miR398-targeted PtCSD1, PtCSD2a and PtCSD2b, miR408-targeted PtPCL1, PtPCL2, PtPCL3 and PtLAC4, and miR1444-targeted PtPPO3 and PtPPO6. Consistently, P. trichocarpa miR408 promoter-directed GUS gene expression is down-regulated by Cu in transgenic tobacco plants. Cu-response elements (CuREs) are found in the promoters of Cu-responsive miRNA genes. We identified 34 SQUAMOSA-promoter binding protein-like (SPL) genes, of which 17 are full-length PtSPL proteins or partial sequences with at least 300 amino acids. Phylogenetic analysis indicates that PtSPL3 and PtSPL4 are CuRE-binding proteins controlling Cu-responsive gene expression. Cu appears to be not involved in the regulation of these transcription factors because neither PtSPL3 nor PtSPL4 is Cu-regulated and no CuRE exists in their promoters.

MiR398 and plant stress responses

Because of their sessile nature, plants are constantly exposed to a multitude of abiotic and biotic stresses. Great progress has been made in elucidating the complex stress response mechanisms in plants. MicroRNAs (miRNAs), recently recognized as important regulators of gene expression at the posttranscriptional level, have been found to be involved in plant stress responses. Most plant miRNAs usually mediate cleavage of their target mRNAs. The observation that some miRNAs are up- or downregulated in response to stress implies that miRNAs play vital roles in plant resistance to abiotic and biotic stresses. Manipulation of miRNA-guided gene regulation may represent a new way to engineer plants with improved stress tolerance. Among stress-responsive miRNAs, miRNA398 (miR398) is a miRNA proposed to be directly linked to the plant stress regulatory network and regulates plant responses to oxidative stress, water deficit, salt stress, abscisic acid stress, ultraviolet stress, copper and phosphate deficiency, high sucrose and bacterial infection. This review highlights recent progress in understanding the crucial role of miR398 in plant stress responses, and also includes a discussion of miR398-centered gene regulatory network.

Chloroplastic and mitochondrial metal homeostasis

Transition metal deficiency has a strong impact on the growth and survival of an organism. Indeed, transition metals, such as iron, copper, manganese and zinc, constitute essential cofactors for many key cellular functions. Both photosynthesis and respiration rely on metal cofactor-mediated electron transport chains. Chloroplasts and mitochondria are, therefore, organelles with high metal ion demand and represent essential components of the metal homeostasis network in photosynthetic cells. In this review, we describe the metal requirements of chloroplasts and mitochondria, the acclimation of their functions to metal deficiency and recent advances in our understanding of their contributions to cellular metal homeostasis, the control of the cellular redox status and the synthesis of metal cofactors.

The cellular redox state as a modulator in cadmium and copper responses in Arabidopsis thaliana seedlings

The cellular redox state is an important determinant of metal phytotoxicity. In this study we investigated the influence of cadmium (Cd) and copper (Cu) stress on the cellular redox balance in relation to oxidative signalling and damage in Arabidopsis thaliana. Both metals were easily taken up by the roots, but the translocation to the aboveground parts was restricted to Cd stress. In the roots, Cu directly induced an oxidative burst, whereas enzymatic ROS (reactive oxygen species) production via NADPH oxidases seems important in oxidative stress caused by Cd. Furthermore, in the roots, the glutathione metabolism plays a crucial role in controlling the gene regulation of the antioxidative defence mechanism under Cd stress. Metal-specific alterations were also noticed with regard to the microRNA regulation of CuZnSOD gene expression in both roots and leaves. The appearance of lipid peroxidation is dual: it can be an indication of oxidative damage as well as an indication of oxidative signalling as lipoxygenases are induced after metal exposure and are initial enzymes in oxylipin biosynthesis. In conclusion, the metal-induced cellular redox imbalance is strongly dependent on the chemical properties of the metal and the plant organ considered. The stress intensity determines its involvement in downstream responses in relation to oxidative damage or signalling.

Characterization of the recombinant copper chaperone (CCS) from the plant Glycine (G.) max

The goal of the present work was to characterize the recombinant copper chaperone (CCS) from soybean. Very little is known about plant copper chaperones, which makes this study of current interest, and allows for a comparison with the better known homologues from yeast and humans. To obtain sizeable amounts of pure protein suitable for spectroscopic characterization, we cloned and overexpressed the G. max CCS chaperone in E. coli in the presence of 0.5 mM CuSO(4) and 0.5 mM ZnSO(4) in the broth. A pure protein preparation was obtained by using two IMAC steps and pH gradient chromatography. Most of the proteins were obtained as apo-form, devoid of copper atoms. The chaperone showed a high content (i.e., over 40%) of loops, turns and random coil as determined both by circular dichroism and homology modelling. The homology 3-D structural model suggests the protein might fold in three structural protein domains. The 3-D model along with the primary structure and spectroscopic data may suggest that copper atoms occupy the two metal binding sites, MKCEGC and CTC, within the N-terminal domain I and C-terminal domain III, respectively. But only one Zn-binding site was obtained spectroscopically.

The biogenesis and physiological function of chloroplast superoxide dismutases

Iron-superoxide dismutase (FeSOD) and copper/zinc-superoxide dismutase (Cu/ZnSOD) are evolutionarily conserved proteins in higher plant chloroplasts. These enzymes are responsible for the efficient removal of the superoxide formed during photosynthetic electron transport and function in reactive oxygen species metabolism. The availability of copper is a major determinant of Cu/ZnSOD and FeSOD expression. Analysis of the phenotypes of plants that over-express superoxide dismutases in chloroplasts has given support for the proposed roles of these enzymes in reactive oxygen species scavenging. However, over-production of chloroplast superoxide dismutase gives only limited protection to environmental stress and does not result in greatly improved whole plant performance. Surprisingly, plant lines that lack the most abundant Cu/ZnSOD or FeSOD activities perform as well as the wild-type under most conditions tested, indicating that these superoxide dismutases are not limiting to photoprotection or the prevention of oxidative damage. In contrast, a strong defect in chloroplast gene expression and development was seen in plants that lack the two minor FeSOD isoforms, which are expressed predominantly in seedlings and that associate closely with the chloroplast genome. These findings implicate reactive oxygen species metabolism in signaling and emphasize the critical role of sub-cellular superoxide dismutase location. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.

New insights into miR398 functions in Arabidopsis

We recently identified a new target of microRNA398 (miR398), a conserved miRNA in plants. In Arabidopsis, miR398 targets the mRNAs of two copper/zinc superoxide dismutases (Cu/Zn SODs) by triggering their cleavage or repressing their translation. We analysed the transcriptomes of mutants impaired in miR398 production, revealing that the mRNAs encoding the chaperone (CCS1), essential for copper delivering to the Cu/Zn SODs of Arabidopsis and to generate the mature proteins, were undiscovered targets of miR398. It is likely that CCS1 was not identified by previous bioinformatic predictions because of the number of mismatches between the mRNA and its target. Since CCS1 has four mismatches and one GU wobble, it would have been excluded by the majority of prediction algorithms. miR398 directs the post-transcriptional regulation of CCS1 mRNAs by cleavage and ARGONAUTE10 (AGO10)-mediated translational repression. Indeed, CCS1 protein accumulate in zwille (ago10) mutants while both miR398 and CCS1 mRNAs levels remain identical to the Landsberg erecta WT plants. Moreover, since AGO10 is a negative regulator of AGO1, the CCS1 protein is more abundant in a double ago1-27 ago10-3 Col mutant compared to the single hypomorphic ago1-27 mutant, as previously shown for CSD2.

microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis

microRNA398 (miR398) is a conserved miRNA of plants that targets two of the three copper/zinc superoxide dismutases (SOD) of Arabidopsis (CSD1 and CSD2) by triggering cleavage or inhibiting translation of their mRNAs. We analysed the transcriptomes of mutants impaired in miR398 production, and found that the mRNAs encoding the copper chaperone for superoxide dismutase (CCS1), which delivers copper to CSD1 and CSD2 apoproteins in different cellular compartments, are undiscovered targets of miR398. We identified the cleavage site in CCS1 mRNAs by 5'-RACE PCR. We further show that both CCS1 protein and mRNA levels are tightly linked to the quantities of miR398, which are themselves dependent on the copper content in the medium. We generated transgenic plants carrying a CCS1 mRNA version resistant to cleavage by miR398, and demonstrated that both CCS1 mRNAs and proteins accumulate in these plants when miR398 is abundant and copper limiting. Moreover, we show that one of the ten ARGONAUTE proteins of Arabidopsis (AGO10) is involved in miR398-directed translational inhibition of CCS1 mRNAs, as CCS1 protein, but not CCS1 mRNAs accumulates in ago10 (zll) mutants. Thus, miR398 mediates the cleavage and translational inhibition of mRNAs encoding CCS1, the chaperone protein that is essential for generating the mature copper/zinc SODs of Arabidopsis. Our results also imply that new targets that have not been identified by computing analyses have yet to be discovered, even for an extensively studied miRNA such as miR398.

Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant

Copper (Cu) is an important mineral nutrient found in chloroplasts as a cofactor associated with plastocyanin and Cu/Zn superoxide dismutase (Cu/ZnSOD). Superoxide dismutases are metallo-enzymes found in most oxygenic organisms with proposed roles in reducing oxidative stress. Several recent studies in Arabidopsis have shown that microRNAs and a SQUAMOSA promoter binding protein-like7 (SPL7) transcription factor function to down-regulate the expression of many Cu-proteins, including Cu/ZnSOD in both plastids and the cytosol, during growth on low Cu. Plants contain the Cu Chaperone for SOD (CCS) that delivers Cu to Cu/ZnSODs, and, in Arabidopsis, both cytosolic and plastidic CCS versions are encoded by one gene. In this study, we demonstrate that Arabidopsis CCS transcript levels are regulated by Cu, mediated by microRNA 398 that was not previously predicted to target CCS. The microRNA target site is conserved in CCS of Oryza sativa. The data suggest that Cu-regulated microRNAs may have more mRNA targets than was previously predicted. A CCS null mutant has no measurable SOD activity in the chloroplast and cytosol, indicating an absolute requirement for CCS. When the CCS null mutant was grown on high Cu media, it lacked both Fe superoxide dismutase (FeSOD) and Cu/ZnSOD activity. However, this did not lead to a visual phenotype and no photosynthetic deficiencies were detected, even after high light stress. These results indicate that Cu/ZnSOD is not a pivotal component of the photosynthetic anti-oxidant system during growth in laboratory conditions.

Copper homeostasis

Copper (Cu) is a cofactor in proteins that are involved in electron transfer reactions and is an essential micronutrient for plants. Copper delivery is accomplished by the concerted action of a set of evolutionarily conserved transporters and metallochaperones. As a result of regulation of transporters in the root and the rarity of natural soils with high Cu levels, very few plants in nature will experience Cu in toxic excess in their tissues. However, low Cu bioavailability can limit plant productivity and plants have an interesting response to impending Cu deficiency, which is regulated by an evolutionarily conserved master switch. When Cu supply is insufficient, systems to increase uptake are activated and the available Cu is utilized with economy. A number of Cu-regulated small RNA molecules, the Cu-microRNAs, are used to downregulate Cu proteins that are seemingly not essential. On low Cu, the Cu-microRNAs are upregulated by the master Cu-responsive transcription factor SPL7, which also activates expression of genes involved in Cu assimilation. This regulation allows the most important proteins, which are required for photo-autotrophic growth, to remain active over a wide range of Cu concentrations and this should broaden the range where plants can thrive.

Facing the challenges of Cu, Fe and Zn homeostasis in plants

Plants have recently moved into the spotlight owing to the growing realization that the world needs solutions to energy and food production that are sustainable and environmentally sound. Iron, copper and zinc are essential for plant growth and development, yet the same properties that make these transition metals indispensable can also make them deadly in excess. Iron and copper are most often used for their redox properties, whereas zinc is primarily used for its ability to act as a Lewis acid. Here we review recent advances in the field of metal homeostasis and integrate the findings on uptake and transport of these three metals.

Copper in plants: acquisition, transport and interactions

Copper is an essential metal for plants. It plays key roles in photosynthetic and respiratory electron transport chains, in ethylene sensing, cell wall metabolism, oxidative stress protection and biogenesis of molybdenum cofactor. Thus, a deficiency in the copper supply can alter essential functions in plant metabolism. However, copper has traditionally been used in agriculture as an antifungal agent, and it is also extensively released into the environment by human activities that often cause environmental pollution. Accordingly, excess copper is present in certain regions and environments, and exposure to such can be potentially toxic to plants, causing phytotoxicity by the formation of reactive oxygen radicals that damage cells, or by the interaction with proteins impairing key cellular processes, inactivating enzymes and disturbing protein structure. Plants have a complex network of metal trafficking pathways in order to appropriately regulate copper homeostasis in response to environmental copper level variations. Such strategies must prevent accumulation of the metal in the freely reactive form (metal detoxification pathways) and ensure proper delivery of this element to target metalloproteins. The mechanisms involved in the acquisition and the distribution of copper have not been clearly defined, although emerging data in last decade, mainly obtained on copper uptake, and both intra- and intercellular distribution, as well as on long-distance transport, are contributing to the understanding of copper homeostasis in plants and the response to copper stress. This review gives an overview of the current understanding of main features concerning copper function, acquisition and trafficking network as well as interactions between copper and other elements.