Arabidopsis ALF5, a multidrug efflux transporter gene family member, confers resistance to toxins

Comprehensive characterization of the ALMT and MATE families on Populus trichocarpa and gene co-expression network analysis of its members during aluminium toxicity and phosphate starvation stresses

Aluminium (Al) toxicity and phosphate deficit on soils are some of the main problems of modern agriculture and are usually associated. Some plants are able to overcome these stresses through exuding organic acids on the rhizosphere, such as citrate and malate, which are exported by MATE (Multi drug and toxin extrusion) and ALMT (Aluminium-activated malate transporter) transporters, respectively. Despite its co-action on acidic soils, few studies explore these two families' correlation, especially on tree crops, therefore we performed a comprehensive description of MATE and ALMT families on Populus trichocarpa as a model species for arboreal plants. We found 20 and 56 putative members of ALMT and MATE families, respectively. Then, a gene co-expression network analysis was performed using broad transcriptomic data to analyze which members of each family were transcriptionally associated. Four independent networks were generated, one of which is composed of members putatively related to phosphate starvation and aluminum toxicity stresses. The PoptrALMT10 and PoptrMATE54 genes were selected from this network for a deeper analysis, which revealed that in roots under phosphate starvation stress the two genes have independent transcriptional profiles, however, on the aluminum toxicity stress they share some common correlations with other genes. The data presented here help on the description of these gene families, of which some members are potentially involved in plant responses to acid soil-related stresses and its exploration is an important step towards using this knowledge on breeding programs for P. trichocarpa and other tree crops.

Mechanisms of organic acids and boron induced tolerance of aluminum toxicity: A review

Aluminum is a major limiting abiotic factor for plant growth and productivity on acidic soils. The primary disorder of aluminum toxicity is the rapid cessation of root elongation. The root apex is the most sensitive part of this organ. Although significant literature evidence and hypothesis exist on aluminum toxicity, the explicit mechanism through which aluminum ceases root growth is still indefinable. The mechanisms of tolerance in plants have been the focus of intense research. Some plant species growing on acidic soils have developed tolerance mechanisms to overcome and mitigate aluminum toxicity, either by avoiding entry of Al³⁺ into roots (exclusion mechanism) or by being able to counterbalance toxic Al³⁺ engrossed by the root system (internal tolerance mechanism). Genes belonging to ALMT (Aluminum-activated malate transporter) and MATE (Multidrug and toxin compounds extrusion) have been identified that are involved in the aluminum-activated secretion of organic acids from roots. However, different plant species show different gene expression pattern. On the other hand, boron (B) (indispensable micronutrient) is a promising nutrient in the tolerance to aluminum toxicity. It not only hinders the adsorption of aluminum to the cell wall but also improves plant growth. This review mainly explains the critical roles of organic acid and B-induced tolerance to aluminum by summarizing the mechanisms of ALMT, MATE, internal detoxification, molecular traits and genetic engineering of crops.

GsMATE encoding a multidrug and toxic compound extrusion transporter enhances aluminum tolerance in Arabidopsis thaliana

BACKGROUND

Multidrug and toxic compound extrusion (MATE) transporters, which exist widely in plants, function as crucial regulators in plant resistance to aluminum (Al) toxicity by inducing citrate efflux. However, the functions of most MATE family members in soybean (Glycine soja) remain to be elucidated.

RESULTS

Expression pattern analysis showed that GsMATE was constitutively expressed in different soybean organs, with the highest level in root compared with those in stem, leaf and cotyledon. In addition, Al stress induced expression of GsMATE in soybean. Temporal analysis indicated that GsMATE expression was greatly enhanced by increasing concentrations of aluminum [Al3+] after short exposure, reaching the high levels detected in the BW69 (Al-resistant) and the JW81 (Al-sensitive) lines of Glycine soja of wild soybean at 6 h and 8 h, respectively. Furthermore, transient GsMATE expression in Arabidopsis protoplasts showed that GsMATE protein localized to the plasma membrane. Overexpression of GsMATE on an Arabidopsis columbia-0 (Col-0) background resulted in increased Al tolerance in transgenic plants. Analysis of hematoxylin staining showed that the roots of GsMATE transgenic lines were stained less intensely than those of the wild-type exposured to the same AlCl3 concentrations. Therefore, GsMATE enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots.

CONCLUSIONS

In summary, our results indicate that GsMATE is responsive to aluminum stress and may participate in the regulation of sensitivity to Al toxicity in Arabidopsis. In addition, the GsMATE protein is an Al-induced citrate transporter of the MATE family and exerts an essential role in Al tolerance in Glycine soja.

Expression of rice MATE family transporter OsMATE2 modulates arsenic accumulation in tobacco and rice

KEY MESSAGE

The OsMATE2 upon constitutive expression in tobacco decreases root-to-shoot As transfer coefficient and its endosperm-specific silencing in rice reduces grain As content, broadening the role of MATE proteins in planta. Rice (Oryza sativa) is capable of accumulating significant amount of arsenic (As) in grains, causing serious health hazard for rice consuming population. The multidrug and toxic compound extrusion (MATE) protein family comprises a large group of secondary transporters present universally in living organisms, and transports metabolites and/or xenobiotic compounds. OsMATE2, one of the MATE family members of rice was found to be transcriptionally up-regulated (sixfolds) in the developing seeds during As stress, and showed positive correlation with the As content in mature grains. Therefore, to understand the role of OsMATE2 in As accumulation, constitutive expression in tobacco was carried out. Transgenic tobacco plants exhibited decreased root-to-shoot As transfer coefficient (33.3-39.6%) along with augmented As sensitivity by increasing oxidative stress compared to untransformed control plants, indicating the involvement of OsMATE2 in As accumulation. Consequently, RNAi strategy was utilized for endosperm-specific silencing of endogenous OsMATE2 to mitigate As accumulation in rice grains. Transgenic rice lines demonstrated significant reduction of both OsMATE2 transcript (~ 38-87%) and grain As content (36.9-47.8%) compared to the control plants without undesirable effects on agronomical traits. Together, the present findings indicate the connection of OsMATE2 in As accumulation, and could expand the functional role of MATE proteins in planta.

Slow darkening of pinto bean seed coat is associated with significant metabolite and transcript differences related to proanthocyanidin biosynthesis

Background

Postharvest seed coat darkening in pinto bean is an undesirable trait resulting in a loss in the economic value of the crop. The extent of darkening varies between the bean cultivars and their storage conditions.

Results

Metabolite analysis revealed that the majority of flavonoids including proanthocyanidin monomer catechin accumulated at higher level in a regular darkening (RD) pinto line CDC Pintium than in a slow darkening (SD) line 1533–15. A transcriptome analysis was conducted to compare gene expression between CDC Pintium and 1533–15 and identify the gene (s) that may play a role in slow darkening processes in 1533–15 pinto.

RNAseq against total RNA from RD and SD cultivars found several phenylpropanoid genes, metabolite transporter genes and genes involved in gene regulation or modification to be differentially expressed between CDC Pintium and 1533–15.

Conclusion

RNAseq analysis and metabolite data of seed coat tissue from CDC Pintium and 1533–15 revealed that the whole proanthocyanidin biosynthetic pathway was downregulated in 1533–15. Additionally, genes that encode for putative transporter proteins were also downregulated in 1533–15 suggesting both synthesis and accumulation of proanthocyanidin is reduced in SD pintos.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4550-z) contains supplementary material, which is available to authorized users.

Global analysis of the MATE gene family of metabolite transporters in tomato

BACKGROUND

Species in the Solanaceae family are known for producing plethora of specialized metabolites. In addition to biosynthesis pathways, a full comprehension of secondary metabolism must also take into account the transport and subcellular compartmentalization of substances. Here, we examined the MATE (Multidrug and Toxic Compound Extrusion, or Multi-Antimicrobial Extrusion) gene family in the tomato (Solanum lycopersicum) genome with the objective of better understanding the transport of secondary metabolites in this model species. MATE membrane effluxers encompass an ancient gene family of secondary transporters present in all kingdoms of life, but with a remarkable expansion in plants. They mediate the transport of primary and secondary metabolites using the proton motive force through several membrane systems of the cell.

RESULTS

We identified 67 genes coding for MATE transporters in the tomato genome, 33 of which are expressed constitutively whereas 34 are expressed in specific cell types or environmental conditions. Synteny analyses revealed bona fide paralogs and Arabidopsis orthologs. Co-expression analysis between MATE and regulatory genes revealed 78 positive and 8 negative strong associations (ρ≥|0.8|). We found no evidence of MATE transporters belonging to known metabolic gene clusters in tomato.

CONCLUSIONS

Altogether, our expression data, phylogenetic analyses, and synteny study provide strong evidence of functional homologies between MATE genes of tomato and Arabidopsis thaliana. Our co-expression study revealed potential transcriptional regulators of MATE genes that warrant further investigation. This work sets the stage for genome-wide functional analyses of MATE transporters in tomato and other Solanaceae species of economic relevance.

Diverse functions of multidrug and toxin extrusion (MATE) transporters in citric acid efflux and metal homeostasis in Medicago truncatula

The multidrug and toxin extrusion (MATE) transporter family comprises 70 members in the Medicago truncatula genome, and they play seemingly important, yet mostly uncharacterized, physiological functions. Here, we employed bioinformatics and molecular genetics to identify and characterize MATE transporters involved in citric acid export, Al³⁺ tolerance and Fe translocation. MtMATE69 is a citric acid transporter induced by Fe-deficiency. Overexpression of MtMATE69 in hairy roots altered Fe homeostasis and hormone levels under Fe-deficient or Fe-oversupplied conditions. MtMATE66 is a plasma membrane citric acid transporter primarily expressed in root epidermal cells. The mtmate66 mutant had less root growth than the wild type under Al³⁺ stress, and seedlings were chlorotic under Fe-deficient conditions. Overexpression of MtMATE66 rendered hairy roots more tolerant to Al³⁺ toxicity. MtMATE55 is involved in seedling development and iron homeostasis, as well as hormone signaling. The mtmate55 mutant had delayed development and chlorotic leaves in mature plants. Both knock-out and overexpression mutants of MtMATE55 showed altered Fe accumulation and abnormal hormone levels compared with the wild type. We demonstrate that the zinc-finger transcription factor MtSTOP is essentially required for MtMATE66 expression and plant resistance to H⁺ and Al³⁺ toxicity. The proper expression of two previously characterized MATE flavonoid transporters MtMATE1 and MtMATE2 also depends on several transcription factors. This study reveals not only functional diversity of MATE transporters and regulatory mechanisms in legumes against H⁺ and Al³⁺ stresses, but also casts light on their role in metal nutrition and hormone signaling under various stresses.

Genomewide analysis of MATE-type gene family in maize reveals microsynteny and their expression patterns under aluminum treatment

Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro-exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The Ka/Ks ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize.

The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana

BACKGROUND

Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection.

RESULTS

Forty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies. In both species, the MATE gene family has expanded mainly through tandem and segmental duplications. A transcriptome atlas showed considerable differences in expression among the genes, in terms of transcript abundance and expression patterns under normal growth conditions, indicating wide functional divergence in this family. In both rice and Arabidopsis, the MATE genes showed consistent functional divergence trends, with highly significant Type-I divergence in each subfamily, while Type-II divergence mainly occurred in subfamily III. The Type-II coefficients between rice subfamilies I/III, II/III, and IV/III were all significantly greater than zero, while only the Type-II coefficient between Arabidopsis IV/III subfamilies was significantly greater than zero. A site-specific model analysis indicated that MATE genes have relatively conserved evolutionary trends. A branch-site model suggested that the extent of positive selection on each subfamily of rice and Arabidopsis was different: subfamily II of Arabidopsis showed higher positive selection than other subfamilies, whereas in rice, positive selection was highest in subfamily III. In addition, the analyses identified 18 rice sites and 7 Arabidopsis sites that were responsible for positive selection and for Type-I and Type-II functional divergence; there were no common sites between rice and Arabidopsis. Five coevolving amino acid sites were identified in rice and three in Arabidopsis; these sites might have important roles in maintaining local structural stability and protein functional domains.

CONCLUSIONS

We demonstrate that the MATE gene family expanded through tandem and segmental duplication in both rice and Arabidopsis. Overall, the results of our analyses contribute to improved understanding of the molecular evolution and functions of the MATE gene family in plants.

ELS1, a novel MATE transporter related to leaf senescence and iron homeostasis in Arabidopsis thaliana

The multidrug and toxic compound extrusion (MATE) transporters mediate the coupled exchange of organic substrates and monovalent cations have been recently implicated in various plant biological activities. In this work, we isolated a dominant mutant from an Arabidopsis activation-tagging mutant pool. This mutant exhibits pleiotropic phenotype including early flowering, dwarf and bushy architecture, minified lateral organs and early leaf senescence, and is therefore designated early leaf senescence 1-Dominaint (els1-D). Genotyping assays showed that els1-D is a gain-of-function mutant of a novel MATE transporter gene, ELS1, which encodes a close homolog of the previously reported ADP1, BCD1 and DTX50. Further investigations revealed that the overexpression of ELS1 reduces iron content in els1-D, and the accelerated senescence of the detached els1-D leaves can be recovered by exogenous iron supply. In addition, we also found that ELS1 is an iron responsive gene. Based on these findings, we proposed that ELS1 is related to leaf senescence and iron homeostasis in Arabidopsis.

Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean

BACKGROUND

Multidrug and toxic compound extrusion (MATE) family is an important group of the multidrug efflux transporters that extrude organic compounds, transporting a broad range of substrates such as organic acids, plant hormones and secondary metabolites. However, genome-wide analysis of MATE family in plant species is limited and no such studies have been reported in soybean.

RESULTS

A total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean (Glycine max), which were denominated as GmMATE1 - GmMATE117. These 117 GmMATE genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. Soybean MATE family could be classified into four subfamilies comprising ten smaller subgroups, with diverse potential functions such as transport and accumulation of flavonoids or alkaloids, extrusion of plant-derived or xenobiotic compounds, regulation of disease resistance, and response to abiotic stresses. Eight soybean MATE transporters clustered together with the previously reported MATE proteins related to aluminum (Al) detoxification and iron translocation were further analyzed. Seven stress-responsive cis-elements such as ABRE, ARE, HSE, LTR, MBS, as well as a cis-element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight GmMATE genes. Differential gene expression analysis of these eight GmMATE genes in response to Al stress helps us identify GmMATE75 as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related MATE genes.

CONCLUSIONS

A total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. The cis-elements and expression patterns of eight soybean MATE genes related to Al detoxification/iron translocation were analyzed, and GmMATE75 was identified as a candidate gene for Al tolerance in soybean. This study provides a first insight on soybean MATE family and their potential roles in soybean response to abiotic stresses especially Al toxicity.

Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana

Background

m⁶A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m⁶A patterns in Arabidopsis have been assayed recently. However, differential m⁶A patterns between organs have not been well characterized.

Results

Over two-third of the transcripts in Arabidopsis are modified by m⁶A. In contrast to a recent observation of m⁶A enrichment in 5′ mRNA, we find that m⁶A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m⁶A methylation extent compared to their transcript level. The 290 highly methylated transcripts are mainly associated with transporters, stress responses, redox, regulation factors, and some non-coding RNAs. On average, the proportion of transcripts showing differential methylation between two plant organs is higher than that showing differential transcript levels. The transcripts with extensively higher m⁶A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m⁶A may be another important contributor to organ differentiation in Arabidopsis. Highly expressed genes are relatively less methylated and vice versa, and different RNAs have distinct m⁶A patterns, which hint at mRNA fate. Intriguingly, most of the transposable element transcripts maintained a fragmented form with a relatively low transcript level and high m⁶A methylation in the cells.

Conclusions

This is the first study to comprehensively analyze m⁶A patterns in a variety of RNAs, the relationship between transcript level and m⁶A methylation extent, and differential m⁶A patterns across organs in Arabidopsis.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0839-2) contains supplementary material, which is available to authorized users.

A subgroup of MATE transporter genes regulates hypocotyl cell elongation in Arabidopsis

The growth of higher plants is under complex regulation to ensure the elaboration of developmental programmes under a changing environment. To dissect these regulatory circuits, we carried out genetic screens for Arabidopsis abnormal shoot (abs) mutants with altered shoot development. Here, we report the isolation of two dominant mutants, abs3-1D and abs4-1D, through activation tagging. Both mutants showed a 'bushy' loss of apical dominance phenotype. ABS3 and ABS4 code for two closely related putative Multidrug and Toxic Compound Extrusion (MATE) family of efflux transporters, respectively. ABS3 and ABS4, as well as two related MATE genes, ABS3-Like1 (ABS3L1) and ABS3L2, showed diverse tissue expression profiles but their gene products all localized to the late endosome/prevacuole (LE/PVC) compartment. The over-expression of these four genes individually led to the inhibition of hypocotyl cell elongation in the light. On the other hand, the quadruple knockout mutant (mateq) showed the opposite phenotype of an enhanced hypocotyl cell elongation in the light. Hypocotyl cell elongation and de-etiolation processes in the dark were also affected by the mutations of these genes. Exogenously applied sucrose attenuated the inhibition of hypocotyl elongation caused by abs3-1D and abs4-1D in the dark, and enhanced the hypocotyl elongation of mateq under prolonged dark treatment. We determined that ABS3 genetically interacts with the photoreceptor gene PHYTOCHROME B (PHYB). Our results demonstrate that ABS3 and related MATE family transporters are potential negative regulators of hypocotyl cell elongation and support a functional link between the endomembrane system, particularly the LE/PVC, and the regulation of plant cell elongation.

Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.)

Histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. Genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. We report the genome-wide profiling of histone methylation (H3K9me2) and acetylation (H4K12ac) in common bean (Phaseolus vulgaris L.) under rust (Uromyces appendiculatus) stress using two high-throughput approaches, chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq). ChIP-Seq analysis revealed 1,235 and 556 histone methylation and acetylation responsive genes from common bean leaves treated with the rust pathogen at 0, 12 and 84 hour-after-inoculation (hai), while RNA-Seq analysis identified 145 and 1,763 genes differentially expressed between mock-inoculated and inoculated plants. The combined ChIP-Seq and RNA-Seq analyses identified some key defense responsive genes (calmodulin, cytochrome p450, chitinase, DNA Pol II, and LRR) and transcription factors (WRKY, bZIP, MYB, HSFB3, GRAS, NAC, and NMRA) in bean-rust interaction. Differential methylation and acetylation affected a large proportion of stress-responsive genes including resistant (R) proteins, detoxifying enzymes, and genes involved in ion flux and cell death. The genes identified were functionally classified using Gene Ontology (GO) and EuKaryotic Orthologous Groups (KOGs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified a putative pathway with ten key genes involved in plant-pathogen interactions. This first report of an integrated analysis of histone modifications and gene expression involved in the bean-rust interaction as reported here provides a comprehensive resource for other epigenomic regulation studies in non-model species under stress.

Localization and expression of EDS5H a homologue of the SA transporter EDS5

BACKGROUND

An important signal transduction pathway in plant defence depends on the accumulation of salicylic acid (SA). SA is produced in chloroplasts and the multidrug and toxin extrusion transporter ENHANCED DISEASE SUSCEPTIBILITY5 (EDS5; At4g39030) is necessary for the accumulation of SA after pathogen and abiotic stress. EDS5 is localized at the chloroplast and functions in transporting SA from the chloroplast to the cytoplasm. EDS5 has a homologue called EDS5H (EDS5 HOMOLOGUE; At2g21340) but its relationship to EDS5 has not been described and its function is not known.

RESULTS

EDS5H exhibits about 72% similarity and 59% identity to EDS5. In contrast to EDS5 that is induced after pathogen inoculation, EDS5H was constitutively expressed in all green tissues, independently of pathogen infection. Both transporters are located at the envelope of the chloroplast, the compartment of SA biosynthesis. EDS5H is not involved with the accumulation of SA after inoculation with a pathogen or exposure to UV stress. A phylogenetic analysis supports the hypothesis that EDS5H may be an H(+)/organic acid antiporter like EDS5.

CONCLUSIONS

The data based on genetic and molecular studies indicate that EDS5H despite its homology to EDS5 does not contribute to pathogen-induced SA accumulation like EDS5. EDS5H most likely transports related substances such as for example phenolic acids, but unlikely SA.

Identification and expression analysis of MATE genes involved in flavonoid transport in blueberry plants

Multidrug and toxic compound extrusion (MATE) proteins are the most recently identified family of multidrug transporters. In plants, this family is remarkably large compared to the human and bacteria counterpart, highlighting the importance of MATE proteins in this kingdom. Here 33 Unigenes annotated as MATE transporters were found in the blueberry fruit transcriptome, of which eight full-length cDNA sequences were identified and cloned. These proteins are composed of 477-517 residues, with molecular masses ~54 kDa, and theoretical isoelectric points from 5.35 to 8.41. Bioinformatics analysis predicted 10-12 putative transmembrane segments for VcMATEs, and localization to the plasma membrane without an N-terminal signal peptide. All blueberry MATE proteins shared 32.1-84.4% identity, among which VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8, and VcMATE9 were more similar to the MATE-type flavonoid transporters. Phylogenetic analysis showed VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8 and VcMATE9 clustered with MATE-type flavonoid transporters, indicating that they might be involved in flavonoid transport. VcMATE1 and VcMATE4 may be involved in the transport of secondary metabolites, the detoxification of xenobiotics, or the export of toxic cations. Real-time quantitative PCR demonstrated that the expression profile of the eight VcMATE genes varied spatially and temporally. Analysis of expression and anthocyanin accumulation indicated that there were some correlation between the expression profile and the accumulation of anthocyanins. These results showed VcMATEs might be involved in diverse physiological functions, and anthocyanins across the membranes might be mutually maintained by MATE-type flavonoid transporters and other mechanisms. This study will enrich the MATE-based transport mechanisms of secondary metabolite, and provide a new biotechonology strategy to develop better nutritional blueberry cultivars.

Involvement of the leaf-specific multidrug and toxic compound extrusion (MATE) transporter Nt-JAT2 in vacuolar sequestration of nicotine in Nicotiana tabacum

Alkaloids play a key role in higher plant defense against pathogens and herbivores. Following its biosynthesis in root tissues, nicotine, the major alkaloid of Nicotiana species, is translocated via xylem transport toward the accumulation sites, leaf vacuoles. Our transcriptome analysis of methyl jasmonate-treated tobacco BY-2 cells identified several multidrug and toxic compound extrusion (MATE) transporter genes. In this study, we characterized a MATE gene, Nicotiana tabacum jasmonate-inducible alkaloid transporter 2 (Nt-JAT2), which encodes a protein that has 32% amino acid identity with Nt-JAT1. Nt-JAT2 mRNA is expressed at a very low steady state level in whole plants, but is rapidly upregulated by methyl jasmonate treatment in a leaf-specific manner. To characterize the function of Nt-JAT2, yeast cells were used as the host organism in a cellular transport assay. Nt-JAT2 was localized at the plasma membrane in yeast cells. When incubated in nicotine-containing medium, the nicotine content in Nt-JAT2-expressing cells was significantly lower than in control yeast. Nt-JAT2-expressing cells also showed lower content of other alkaloids like anabasine and anatabine, but not of flavonoids, suggesting that Nt-JAT2 transports various alkaloids including nicotine. Fluorescence assays in BY-2 cells showed that Nt-JAT2-GFP was localized to the tonoplast. These findings indicate that Nt-JAT2 is involved in nicotine sequestration in leaf vacuoles following the translocation of nicotine from root tissues.

Beyond cellular detoxification: a plethora of physiological roles for MDR transporter homologs in plants

Higher plants possess a multitude of Multiple Drug Resistance (MDR) transporter homologs that group into three distinct and ubiquitous families—the ATP-Binding Cassette (ABC) superfamily, the Major Facilitator Superfamily (MFS), and the Multidrug And Toxic compound Extrusion (MATE) family. As in other organisms, such as fungi, mammals, and bacteria, MDR transporters make a primary contribution to cellular detoxification processes in plants, mainly through the extrusion of toxic compounds from the cell or their sequestration in the central vacuole. This review aims at summarizing the currently available information on the in vivo roles of MDR transporters in plant systems. Taken together, these data clearly indicate that the biological functions of ABC, MFS, and MATE carriers are not restricted to xenobiotic and metal detoxification. Importantly, the activity of plant MDR transporters also mediates biotic stress resistance and is instrumental in numerous physiological processes essential for optimal plant growth and development, including the regulation of ion homeostasis and polar transport of the phytohormone auxin.

ADP1 affects plant architecture by regulating local auxin biosynthesis

Plant architecture is one of the key factors that affect plant survival and productivity. Plant body structure is established through the iterative initiation and outgrowth of lateral organs, which are derived from the shoot apical meristem and root apical meristem, after embryogenesis. Here we report that ADP1, a putative MATE (multidrug and toxic compound extrusion) transporter, plays an essential role in regulating lateral organ outgrowth, and thus in maintaining normal architecture of Arabidopsis. Elevated expression levels of ADP1 resulted in accelerated plant growth rate, and increased the numbers of axillary branches and flowers. Our molecular and genetic evidence demonstrated that the phenotypes of plants over-expressing ADP1 were caused by reduction of local auxin levels in the meristematic regions. We further discovered that this reduction was probably due to decreased levels of auxin biosynthesis in the local meristematic regions based on the measured reduction in IAA levels and the gene expression data. Simultaneous inactivation of ADP1 and its three closest homologs led to growth retardation, relative reduction of lateral organ number and slightly elevated auxin level. Our results indicated that ADP1-mediated regulation of the local auxin level in meristematic regions is an essential determinant for plant architecture maintenance by restraining the outgrowth of lateral organs.

Plant architecture is one of the key factors that affect plant survival and productivity. It is well established that the plant hormone auxin plays an essential role in organ initiation and pattern formation, thus affecting plant architecture. We found that a putative MATE (multidrug and toxic compound extrusion) transporter, ADP1, which was expressed in the meristematic regions, through regulating the level of auxin biosynthesis, controls lateral organ outgrowth so as to maintain normal architecture in Arabidopsis. The more ADP1 was expressed, the less levels of local auxin were detected in the meristematic regions of the plant, resulting in increased growth rate and a greater number of axillary branches and flowers. The reduction of auxin levels is probably due to decreased level of auxin biosynthesis in the local meristematic regions. Down-regulated expression of ADP1 and its three closely related genes caused plants to grow slower and to produce less lateral organs. Our results indicated that ADP1-mediated regulation of the local auxin levels in meristematic regions is an essential determinant for plant architecture by restraining the outgrowth of lateral organs.

The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate Monosiga brevicollis

Background

It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown.

Results

Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids.

Conclusions

Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-729) contains supplementary material, which is available to authorized users.

Comprehensive analysis of genic male sterility-related genes in Brassica rapa using a newly developed Br300K oligomeric chip

To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassicarapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility.

New insights into the transport mechanisms in plant vacuoles

The vacuole is the largest compartment in plant cells, often occupying more than 80% of the total cell volume. This organelle accumulates a large variety of endogenous ions, metabolites, and xenobiotics. The compartmentation of divergent substances is relevant for a wide range of biological processes, such as the regulation of stomata movement, defense mechanisms against herbivores, flower coloration, etc. Progress in molecular and cellular biology has revealed that a large number of transporters and channels exist at the tonoplast. In recent years, various biochemical and physiological functions of these proteins have been characterized in detail. Some are involved in maintaining the homeostasis of ions and metabolites, whereas others are related to defense mechanisms against biotic and abiotic stresses. In this review, we provide an updated inventory of vacuolar transport mechanisms and a comprehensive summary of their physiological functions.

Mechanisms for cellular transport and release of allelochemicals from plant roots into the rhizosphere

Allelochemicals and other metabolites released by plant roots play important roles in rhizosphere signalling, plant defence and responses to abiotic stresses. Plants use a variety of sequestration and transport mechanisms to move and export bioactive products safely into the rhizosphere. The use of mutants and molecular tools to study gene expression has revealed new information regarding the diverse group of transport proteins and conjugation processes employed by higher plants. Transport systems used for moving secondary products into and out of root cells are similar to those used elsewhere in the plant but are closely linked to soil environmental conditions and local root health. Root cells can rapidly generate and release large quantities of allelochemicals in response to stress or local rhizosphere conditions, so the production and transport of these compounds in cells are often closely linked. Plants need to manage the potentially toxic allelochemicals and metabolites they produce by sequestering them to the vacuole or other membrane-bound vesicles. These compartments provide secure storage areas and systems for safely moving bioactive chemicals throughout the cytosol. Release into the apoplast occurs either by exocytosis or through membrane-bound transport proteins. This review discusses the possible transport mechanisms involved in releasing specific root-produced allelochemicals by combining microscopic observations of the specialized root cells with the physical and chemical properties of the exudates.

ADS1 encodes a MATE-transporter that negatively regulates plant disease resistance

Multidrug and toxic compound extrusion (MATE) proteins comprise the most recently identified family of multidrug transporters. In plants, the numbers of MATE proteins has undergone a remarkable expansion, underscoring the importance of these transporters within this kingdom. Here, we describe the identification and characterization of Activated Disease Susceptibility 1 (ADS1) which encodes a putative MATE transport protein. An activation tagging screen uncovered the ads1-Dominant (ads1-D) mutant, which was subsequently characterized by molecular, genetic and biochemical approaches. The ads1-D mutant was compromised in both basal and nonhost resistance against microbial pathogens. Further, plant defence responses conferred by RPS4 were also disabled in ads1-D plants. By contrast, depletion of ADS1 transcripts by RNA-interference (RNAi) promoted basal disease resistance. Unexpectedly, ads1-D plants were found to constitutively accumulate reactive oxygen intermediates (ROIs). However, analysis of ads1-D Arabidopsis thaliana respiratory burst oxidase (atrboh) double and triple mutants indicated that an increase in ROIs did not impact ads1-D-mediated disease susceptibility. Our findings imply that ADS1 negatively regulates the accumulation of the plant immune activator salicylic acid (SA) and cognate Pathogenesis-Related 1 (PR1) gene expression. Collectively, these data highlight an important role for MATE proteins in the establishment of plant disease resistance.

From organelle to organ: ZRIZI MATE-Type transporter is an organelle transporter that enhances organ initiation

Plant architecture is a predictable but flexible trait. The timing and position of organ initiation from the shoot apical meristem (SAM) contribute to the final plant form. While much progress has been made recently in understanding how the site of leaf initiation is determined, the mechanism underlying the temporal interval between leaf primordia is still largely unknown. The Arabidopsis ZRIZI (ZRZ) gene belongs to a large gene family encoding multidrug and toxic compound extrusion (MATE) transporters. Unique among plant MATE transporters identified so far, ZRZ is localized to the membrane of a small organelle, possibly the mitochondria. Plants overexpressing ZRZ in initiating leaves are short, produce leaves much faster than wild-type plants and show enhanced growth of axillary buds. These results suggest that ZRZ is involved in communicating a leaf-borne signal that determines the rate of organ initiation.

Exploring multiple drug and herbicide resistance in plants--spotlight on transporter proteins

Multiple drug resistance (MDR) has been extensively studied in bacteria, yeast, and mammalian cells due to the great clinical significance of this problem. MDR is not well studied in plant systems, although plant genomes contain large numbers of genes encoding putative MDR transporters (MDRTs). Biochemical pathways in the chloroplast are the targets of many herbicides and antibiotics, yet very little data is available regarding mechanisms of drug transport across the chloroplast membrane. MDRTs typically have broad substrate specificities, and may transport essential compounds and metabolites in addition to toxins. Indeed, plant transporters belonging to MDR families have also been implicated in the transport of a wide variety of compounds including auxins, flavonoids, glutathione conjugates, metal chelators, herbicides and antibiotics, although definitive evidence that a single transporter is capable of moving both toxins and metabolites has not yet been provided. Current understanding of plant MDR can be expanded via the characterization of candidate genes, especially MDRTs predicted to localize to the chloroplast, and also via traditional forward genetic approaches. Novel plant MDRTs have the potential to become endogenous selectable markers, aid in phytoremediation strategies, and help us to understand how plants have evolved to cope with toxins in their environment.

Sequestration and transport of lignin monomeric precursors

Lignin is the second most abundant terrestrial biopolymer after cellulose. It is essential for the viability of vascular plants. Lignin precursors, the monolignols, are synthesized within the cytosol of the cell. Thereafter, these monomeric precursors are exported into the cell wall, where they are polymerized and integrated into the wall matrix. Accordingly, transport of monolignols across cell membranes is a critical step affecting deposition of lignin in the secondarily thickened cell wall. While the biosynthesis of monolignols is relatively well understood, our knowledge of sequestration and transport of these monomers is sketchy. In this article, we review different hypotheses on monolignol transport and summarize the recent progresses toward the understanding of the molecular mechanisms underlying monolignol sequestration and transport across membranes. Deciphering molecular mechanisms for lignin precursor transport will support a better biotechnological solution to manipulate plant lignification for more efficient agricultural and industrial applications of cell wall biomass.

How a microbial drug transporter became essential for crop cultivation on acid soils: aluminium tolerance conferred by the multidrug and toxic compound extrusion (MATE) family

BACKGROUND

Aluminium (Al) toxicity is a major agricultural constraint for crop cultivation on acid soils, which comprise a large portion of the world's arable land. One of the most widely accepted mechanisms of Al tolerance in plants is based on Al-activated organic acid release into the rhizosphere, with organic acids forming stable, non-toxic complexes with Al. This mechanism has recently been validated by the isolation of bona-fide Al-tolerance genes in crop species, which encode membrane transporters that mediate Al-activated organic acid release leading to Al exclusion from root apices. In crop species such as sorghum and barley, members in the multidrug and toxic compound extrusion (MATE) family underlie Al tolerance by a mechanism based on Al-activated citrate release.

SCOPE AND CONCLUSIONS

The study of Al tolerance in plants as conferred by MATE family members is in its infancy. Therefore, much is yet to be discovered about the functional diversity and evolutionary dynamics that led MATE proteins to acquire transport properties conducive to Al tolerance in plants. In this paper we review the major characteristics of transporters in the MATE family and will relate this knowledge to Al tolerance in plants. The MATE family is clearly extremely flexible with respect to substrate specificity, which raises the possibility that Al tolerance as encoded by MATE proteins may not be restricted to Al-activated citrate release in plant species. There are also indications that regulatory loci may be of pivotal importance to fully explore the potential for Al-tolerance improvement based on MATE genes.

Deficiencies in jasmonate-mediated plant defense reveal quantitative variation in Botrytis cinerea pathogenesis

Despite the described central role of jasmonate signaling in plant defense against necrotrophic pathogens, the existence of intraspecific variation in pathogen capacity to activate or evade plant jasmonate-mediated defenses is rarely considered. Experimental infection of jasmonate-deficient and jasmonate-insensitive Arabidopsis thaliana with diverse isolates of the necrotrophic fungal pathogen Botrytis cinerea revealed pathogen variation for virulence inhibition by jasmonate-mediated plant defenses and induction of plant defense metabolites. Comparison of the transcriptional effects of infection by two distinct B. cinerea isolates showed only minor differences in transcriptional responses of wild-type plants, but notable isolate-specific transcript differences in jasmonate-insensitive plants. These transcriptional differences suggest B. cinerea activation of plant defenses that require plant jasmonate signaling for activity in response to only one of the two B. cinerea isolates tested. Thus, similar infection phenotypes observed in wild-type plants result from different signaling interactions with the plant that are likely integrated by jasmonate signaling.

While many important elements of plant defense signaling have been identified, the function of these defense signaling pathways may mask additional variation in the plant–pathogen interaction, including both pathogen variation and variation in downstream plant defense responses. Jasmonate plant hormones contribute to both plant development and defense, including plant defense against necrotrophic fungal pathogens such as the grey mold Botrytis cinerea. Ten diverse B. cinerea isolates all showed increased virulence and decreased induction of a plant antimicrobial metabolite in experimental infections of Arabidopsis thaliana lacking functional jasmonate signaling. Yet within this consistent result, B. cinerea isolates varied considerably. Through comparing the transcript profiles of A. thaliana infected with the two most disparate B. cinerea isolates, we found that wild-type plants showed similar transcriptional responses to infection with these two isolates, but the absence of functional jasmonate signaling revealed dramatic differences in plant response, including groups of co-regulated genes that may participate in undescribed plant response networks. Jasmonate signaling appears to integrate plant responses to diverse pathogen inputs, and its absence may reveal novel aspects of plant–pathogen interaction.

The 'ins' and 'outs' of flavonoid transport

The sites of plant flavonoid biosynthesis, storage and final function often differ at the subcellular, cell, and even tissue and organ levels. Efficient transport systems for flavonoids across endomembranes and the plasma membrane are therefore required. However, a clear picture of the dynamic trafficking of flavonoids is only now beginning to emerge and appears to have many players. Here, we review current hypotheses for flavonoid transport, discuss whether these are mutually exclusive, highlight the importance of flavonoid efflux from vacuoles to the cytosol and consider future efforts to catch flavonoids 'in the act' of moving within and between cells. An improved understanding of transport mechanisms will facilitate the successful metabolic engineering of flavonoids for plant protection and human health.

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

A powerful way to map functional genomic variation and reveal the genetic basis of local adaptation is to associate allele frequency across the genome with environmental conditions. Serpentine soils, characterized by high heavy-metal content and low calcium-to-magnesium ratios, are a classic context for studying adaptation of plants to local soil conditions. To investigate whether Arabidopsis lyrata is locally adapted to serpentine soil, and to map the polymorphisms responsible for such adaptation, we pooled DNA from individuals from serpentine and nonserpentine soils and sequenced each 'gene pool' with the Illumina Genome Analyzer. The polymorphisms that are most strongly associated with soil type are enriched at heavy-metal detoxification and calcium and magnesium transport loci, providing numerous candidate mutations for serpentine adaptation. Sequencing of three candidate loci in the European subspecies of A. lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution.

Flavonoids: new roles for old molecules

Flavonoids are ubiquitous in the plant kingdom and have many diverse functions including defense, UV protection, auxin transport inhibition, allelopathy, and flower coloring. Interestingly, these compounds also have considerable biological activity in plant, animal and bacterial systems - such broad activity is accomplished by few compounds. Yet, for all the research over the last three decades, many of the cellular targets of these secondary metabolites are unknown. The many mutants available in model plant species such as Arabidopsis thaliana and Medicago truncatula are enabling the intricacies of the physiology of these compounds to be deduced. In the present review, we cover recent advances in flavonoid research, discuss deficiencies in our understanding of the physiological processes, and suggest approaches to identify the cellular targets of flavonoids.

An Arabidopsis flavonoid transporter is required for anther dehiscence and pollen development

FLOWER FLAVONOID TRANSPORTER (FFT) encodes a multidrug and toxin efflux family transporter in Arabidopsis thaliana. FFT (AtDTX35) is highly transcribed in floral tissues, the transcript being localized to epidermal guard cells, including those of the anthers, stigma, siliques and nectaries. Mutant analysis demonstrates that the absence of FFT transcript affects flavonoid levels in the plant and that the altered flavonoid metabolism has wide-ranging consequences. Root growth, seed development and germination, and pollen development, release and viability are all affected. Spectrometry of mutant versus wild-type flowers shows altered levels of a glycosylated flavonol whereas anthocyanin seems unlikely to be the substrate as previously speculated. Thus, as well as adding FFT to the incompletely described flavonoid transport network, it is found that correct reproductive development in Arabidopsis is perturbed when this particular transporter is missing.

Salicylic acid confers resistance to a biotrophic rust pathogen, Puccinia substriata, in pearl millet (Pennisetum glaucum)

Studies were undertaken to assess the induction of defence response pathways in pearl millet (Pennisetum glaucum) in response to infection with the leaf rust fungus Puccinia substriata. Pretreatment of pearl millet with salicylic acid (SA) conferred resistance to a virulent isolate of the rust fungus, whereas methyl jasmonate (MeJA) did not significantly reduce infection levels. These results suggest that the SA defence pathway is involved in rust resistance. In order to identify pearl millet genes that are specifically regulated in response to SA and not MeJA, and thus could play a role in resistance to P. substriata, gene expression profiling was performed. Substantial overlap in gene expression responses between the treatments was observed, with MeJA and SA treatments exhibiting 17% co-regulated transcripts. However, 34% of transcripts were differentially expressed in response to SA treatment, but not in response to MeJA treatment. SA-responsive transcripts represented genes involved in SA metabolism, defence response, signal transduction, protection from oxidative stress and photosynthesis. The expression profiles of pearl millet plants after treatment with SA or MeJA were more similar to one another than to the response during a compatible infection with P. substriata. However, some SA-responsive genes were repressed during P. substriata infection, indicating possible manipulation of host responses by the pathogen.

Aluminum-activated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance

Aluminum-activated root malate and citrate exudation play an important role in plant Al tolerance. This paper characterizes AtMATE, a homolog of the recently discovered sorghum and barley Al-tolerance genes, shown here to encode an Al-activated citrate transporter in Arabidopsis. Together with the previously characterized Al-activated malate transporter, AtALMT1, this discovery allowed us to examine the relationship in the same species between members of the two gene families for which Al-tolerance genes have been identified. AtMATE is expressed primarily in roots and is induced by Al. An AtMATE T-DNA knockdown line exhibited very low AtMATE expression and Al-activated root citrate exudation was abolished. The AtALMT1 AtMATE double mutant lacked both Al-activated root malate and citrate exudation and showed greater Al sensitivity than the AtALMT1 mutant. Therefore, although AtALMT1 is a major contributor to Arabidopsis Al tolerance, AtMATE also makes a significant but smaller contribution. The expression patterns of AtALMT1 and AtMATE and the profiles of Al-activated root citrate and malate exudation are not affected by the presence or absence of the other gene. These results suggest that AtALMT1-mediated malate exudation and AtMATE-mediated citrate exudation evolved independently to confer Al tolerance in Arabidopsis. However, a link between regulation of expression of the two transporters in response to Al was identified through work on STOP1, a transcription factor that was previously shown to be necessary for AtALMT1 expression. Here we show that STOP1 is also required for AtMATE expression and Al-activated citrate exudation.

Multidrug efflux transporters in the MATE family

The MATE (Multidrug And Toxic Compound Extrusion) family is the most recently categorized one among five multidrug efflux transporter families. As far as we know, about twenty MATE transporters have been characterized so far. According to the information in sequence databases, huge numbers of MATE transporters seem to be present in various microorganisms. In this review, we would like to summarize the properties of the MATE-family transporters.

Expression profiling and mapping of defence response genes associated with the barley-Pyrenophora teres incompatible interaction

Barley net- and spot-form of net blotch disease are caused by two formae of the hemibiotrophic fungus Pyrenophora teres (P. t. f. teres and P. t. f. maculata). In the present study, suppression subtractive hybridization (SSH) was used in combination with quantitative real-time reverse transcriptase PCR to identify and profile the expression of defence response (DR) genes in the early stages of both barley-P. teres incompatible and compatible interactions. From a pool of 307 unique gene transcripts identified by SSH, 45 candidate DR genes were selected for temporal expression profiling in infected leaf epidermis. Differential expression profiles were observed for 28 of the selected candidates, which were grouped into clusters depending on their expression profiles within the first 48 h after inoculation. The expression profiles characteristic of each gene cluster were very similar in both barley-P. t. f. teres and barley-P. t. f. maculata interactions, indicating that resistance to both pathogens could be mediated by induction of the same group of DR genes. Chromosomal map locations for 21 DR genes were identified using four doubled-haploid mapping populations. The mapped DR genes were distributed across all seven barley chromosomes, with at least one gene mapping to within 15 cM of another on chromosomes 1H, 2H, 5H and 7H. Additionally, some DR genes appeared to co-localize with loci harbouring known resistance genes or quantitative trait loci for net blotch resistance on chromosomes 6H and 7H, as well as loci associated with resistance to other barley diseases. The DR genes are discussed with respect to their map locations and potential functional role in contributing to net blotch disease resistance.

Spatial distribution of transcript changes in the maize primary root elongation zone at low water potential

BACKGROUND

Previous work showed that the maize primary root adapts to low Psiw (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low Psiw. To identify mechanisms that determine these responses to low Psiw, transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation.

RESULTS

Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit.

CONCLUSION

The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance

Background

Soluble sugars, which play a central role in plant structure and metabolism, are also involved in the responses to a number of stresses, and act as metabolite signalling molecules that activate specific or hormone-crosstalk transduction pathways. The different roles of exogenous sucrose in the tolerance of Arabidopsis thaliana plantlets to the herbicide atrazine and oxidative stress were studied by a transcriptomic approach using CATMA arrays.

Results

Parallel situations of xenobiotic stress and sucrose-induced tolerance in the presence of atrazine, of sucrose, and of sucrose plus atrazine were compared. These approaches revealed that atrazine affected gene expression and therefore seedling physiology at a much larger scale than previously described, with potential impairment of protein translation and of reactive-oxygen-species (ROS) defence mechanisms. Correlatively, sucrose-induced protection against atrazine injury was associated with important modifications of gene expression related to ROS defence mechanisms and repair mechanisms. These protection-related changes of gene expression did not result only from the effects of sucrose itself, but from combined effects of sucrose and atrazine, thus strongly suggesting important interactions of sucrose and xenobiotic signalling or of sucrose and ROS signalling.

Conclusion

These interactions resulted in characteristic differential expression of gene families such as ascorbate peroxidases, glutathione-S-transferases and cytochrome P450s, and in the early induction of an original set of transcription factors. These genes used as molecular markers will eventually be of great importance in the context of xenobiotic tolerance and phytoremediation.

CSR1, the sole target of imidazolinone herbicide in Arabidopsis thaliana

The imidazolinone-tolerant mutant of Arabidopsis thaliana, csr1-2(D), carries a mutation equivalent to that found in commercially available Clearfield crops. Despite their widespread usage, the mechanism by which Clearfield crops gain imidazolinone herbicide tolerance has not yet been fully characterized. Transcription profiling of imazapyr (an imidazolinone herbicide)-treated wild-type and csr1-2(D) mutant plants using Affymetrix ATH1 GeneChip microarrays was performed to elucidate further the biochemical and genetic mechanisms of imidazolinone resistance. In wild-type shoots, the genes which responded earliest to imazapyr treatment were detoxification-related genes which have also been shown to be induced by other abiotic stresses. Early-response genes included steroid sulfotransferase (ST) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), as well as members of the glycosyltransferase, glutathione transferase (GST), cytochrome P450, ATP-binding cassette (ABC) transporter, multidrug and toxin extrusion (MATE) and alternative oxidase (AOX) protein families. Later stages of the imazapyr response involved regulation of genes participating in biosynthesis of amino acids, secondary metabolites and tRNA. In contrast to the dynamic changes in the transcriptome profile observed in imazapyr-treated wild-type plants, the transcriptome of csr1-2(D) did not exhibit significant changes following imazapyr treatment, compared with mock-treated csr1-2(D). Further, no substantial difference was observed between wild-type and csr1-2(D) transcriptomes in the absence of imazapyr treatment. These results indicate that CSR1 is the sole target of imidazolinone and that the csr1-2(D) mutation has little or no detrimental effect on whole-plant fitness.

A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum

Crop yields are significantly reduced by aluminum toxicity on highly acidic soils, which comprise up to 50% of the world's arable land. Candidate aluminum tolerance proteins include organic acid efflux transporters, with the organic acids forming non-toxic complexes with rhizosphere aluminum. In this study, we used positional cloning to identify the gene encoding a member of the multidrug and toxic compound extrusion (MATE) family, an aluminum-activated citrate transporter, as responsible for the major sorghum (Sorghum bicolor) aluminum tolerance locus, Alt(SB). Polymorphisms in regulatory regions of Alt(SB) are likely to contribute to large allelic effects, acting to increase Alt(SB) expression in the root apex of tolerant genotypes. Furthermore, aluminum-inducible Alt(SB) expression is associated with induction of aluminum tolerance via enhanced root citrate exudation. These findings will allow us to identify superior Alt(SB) haplotypes that can be incorporated via molecular breeding and biotechnology into acid soil breeding programs, thus helping to increase crop yields in developing countries where acidic soils predominate.

The GLK1 'regulon' encodes disease defense related proteins and confers resistance to Fusarium graminearum in Arabidopsis

Overexpression (OE) was used to study the role of the Arabidopsis Golden2-like (GLK1) transcriptional activator in regulating gene expression. Affymetrix Gene Chip and RT-PCR analyses indicated that GLK1 OE in Arabidopsis reprogrammed gene expression networks to enhance a high constitutive expression of genes encoding disease defense related proteins. These include PR10, isochorismate synthase, antimicrobial peptides, glycosyl hydrolases, MATE efflux and other genes associated with pathogen response and detoxification. However, PR1, an indicator of systemic acquired resistance (SAR), was downregulated in GLK1 OE. GLK1 OE in Arabidopsis confers resistance to Fusarium graminearum, a broad host pathogen responsible for major losses in cereal crops. This is the first identification of the GLK1 'regulon' and a novel role for GLK1 in plant defense, suggesting its potential use for providing disease resistance in crop plants.

Analysis of gene expression in cotton fiber initials

BACKGROUND

Cotton (Gossypium hirsutum L.) fibers are trichomes that initiate from the ovule epidermis. Little is known about the developmental pathway causing fiber to differentiate from ovular epidermal cells even though limits on the number of cells that differentiate into fiber will limit yield.

RESULTS

A method was developed to isolate RNA from fiber initials 1 day post anthesis (dpa). Complementary DNA libraries representing 1 dpa fibers and other cotton tissues were sequenced and analyzed. Assembly of G. hirsutum Expressed Sequenced Tags (ESTs) identified over 11,000 sequences not previously represented in GenBank. New genes identified among these ESTs were represented on microarrays. The microarrays were used to identify genes enriched in fiber initials (1 dpa fibers) and elongating fibers. Analyses of Gene Ontologies (GO) of differentially expressed genes determined that terms associated with the "membranes" were statistically over represented among genes increased in expression in fiber initials and 10 dpa fibers. Staining ovules with a fluorescent dye confirmed an increase in Endoplasmic Reticulum (ER) occurred in fiber initials on the day of anthesis, persisted through 3 dpa and was absent in a fiberless mutant. Two genes similar to the CAPRICE/TRIPTYCHON (CPC) gene that inhibits differentiation of leaf trichomes in Arabidopsis were also characterized. Genes associated with novel regulation of brassinosterols, GTP mediated signal transduction and cell cycle control and components of a Ca+2 mediated signaling pathway were identified. Staining of cellular Ca+2 indicated that fiber initials had more Ca+2 than other ovule cells supporting a role for Ca+2 in fiber development.

CONCLUSION

Analysis of genes expressed in fiber initials identified a unique stage in fiber development characterized by an increase in ER and Ca+2 levels that occurred between 0 and 1 dpa. The gene similar to CPC has a MYB domain but appears to lack a transcription activating domain similar to the Arabisopsis gene. The method used to stain the ER also can be used to count fiber initials and showed fiber cells develop from adjacent cells unlike leaf trichomes.

Retrograde regulation of nuclear gene expression in CW-CMS of rice

The CW-cytoplasmic male sterility (CMS) line has the cytoplasm of Oryza rufipogon Griff, and mature pollen is morphologically normal under an optical microscope but lacks the ability to germinate; restorer gene Rf17 has been identified as restoring this ability. The difference between nuclear gene expression in mature anthers was compared for the CW-CMS line, [cms-CW] rf17rf17, and a maintainer line with normal cytoplasm of Oryza sativa L., [normal] rf17rf17. Using a 22-k rice oligoarray we detected 58 genes that were up-regulated more than threefold in the CW-CMS line. Expression in other organs was further investigated for 20 genes using RT-PCR. Five genes, including genes for alternative oxidase, were found to be preferentially expressed in [cms-CW] rf17rf17 but not in [normal] rf17rf17 or [cms-CW] Rf17Rf17. Such [cms-CW] rf17rf17-specific gene expression was only observed in mature anthers but not in leaves, stems, or roots, indicating the presence of anther-specific mitochondrial retrograde regulation of nuclear gene expression, and that Rf17 has a role in restoring the ectopic gene expression. We also used a proteomic approach to discover the retrograde regulated proteins and identified six proteins that were accumulated differently. These results reveal organ-specific induced mitochondrial retrograde pathways affecting nuclear gene expression possibly related to CMS.

Use of RNA fingerprinting to identify fungal genes specifically expressed during ectomycorrhizal interaction

The ecosystem soil is characterized by interactions between microorganisms and plants including mycorrhiza--mutualistic interactions between fungi and plant roots. Species of the basidiomycete genus Tricholoma form ectomycorrhiza with tree roots which is characterized by morphological and metabolic changes of both partners, yet molecular mechanisms of the interaction are poorly understood. We performed differential display with arbitrarily primed RT-PCR using ectomycorrhiza between the basidiomycete Tricholoma vaccinum and its compatible host spruce (Picea abies) to isolate mycorrhiza-specific fungal gene fragments. 76 differentially expressed PCR fragments were verified and checked for plant or fungal origin and expression pattern. Of 20 fungal fragments with mycorrhiza-specific expression, sequence analyses were performed to identify homologs with known function of the encoded protein. Among the genes identified were orthologs to an aldehyde dehydrogenase, an alcohol dehydrogenase and a protein of the MATE transporter family, all with possible function in plant pathogen response. A phospholipase B, a beta-glucosidase and a binding protein of basic amino acids might play a role in nutrient exchange and growth in planta. A protein similar to inactive E2 compounds of ubiquitin-conjugating enzymes like CROC-1 and MMS2, a Ras protein and an APS kinase were placed in signal transduction and two retrotransposons of the Ty3-gypsy and the Ty1-copia family are expressed most likely due to stress.

The MATE proteins as fundamental transporters of metabolic and xenobiotic organic cations

Multidrug and toxic compound extrusion (MATE) proteins, comprising the most recently designated family of multidrug transporter proteins, are widely distributed in all kingdoms of living organisms, although their function is far from understood. The bacterial MATE-type transporters that have been characterized function as exporters of cationic drugs, such as norfloxacin and ethidium, through H(+) or Na(+) exchange. Plant MATE-type transporters are involved in the detoxification of secondary metabolites, including alkaloids. Mammalian MATE-type transporters are responsible for the final step in the excretion of metabolic waste and xenobiotic organic cations in the kidney and liver through electroneutral exchange of H(+). Thus, we propose that members of the MATE family are organic cation exporters that excrete metabolic or xenobiotic organic cations from the body.