Aluminum-Activated Malate Transporters Can Facilitate GABA Transport

Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)

SQUAMOSA promoter-binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play roles in plant growth and development. The characteristics of SBP-box genes in rice (Oryza sativa) and Arabidopsis have been reported, but their potential roles in wheat (Triticum aestivum) are not fully understood. In this study, 48 SBP-box genes (TaSBPs) were identified; they were located in all wheat chromosomes except for 4B and 4D. Six TaSBPs were identified as tandem duplication genes that formed three tandem duplication pairs, while 22 were segmentally duplicated genes that formed 16 segmental duplication pairs. Subcellular localization prediction showed TaSBPs were located in nucleus. Among the 48 TaSBPs, 24 were predicted to be putative targets of TamiR156. Phylogenetic analysis showed that TaSBPs, AtSBPs, and OsSBPs that shared similar functions were clustered into the same subgroups. The phylogenetic relationships between the TaSBPs were supported by the identification of highly conserved motifs and gene structures. Four types of cis-elements––transcription-related, development-related, hormone-related, and abiotic stress-related elements––were found in the TaSBP promoters. Expression profiles indicated most TaSBPs participate in flower development and abiotic stress responses. This study establishes a foundation for further investigation of TaSBP genes and provides novel insights into their biological functions.

Physiological and proteomics responses of nitrogen assimilation and glutamine/glutamine family of amino acids metabolism in mulberry (Morus alba L.) leaves to NaCl and NaHCO3 stress

In order to find out the response mechanism of nitrogen assimilation and glutamine/glutamine family of amino acids metabolism in mulberry (Morus alba L.) leaves under NaCl and NaHCO3 stress, and to reveal its role in salt alkali adaptation. The effects of the nitrogen metabolism of mulberry leaves were studied under 100 mmol L-1 NaCl and NaHCO3 stress.The results showed that the activity of NR and the content of TN and SP did not change significantly, the expression of NiR, Fd-NiR, Fd-NiR gene and theactivity of NiR increased significantly under NaCl stress, but nitrogen assimilation was inhibited under NaHCO3 stress. NaCl stress had no significant effect on the expression and activity of GS and GOGAT in mulberry leaves. Under NaHCO3 stress, the expression of Fd-GOGAT, Fd-GOGAT2, Fd-GOGAT gene, and the activity of GS and GOGAT were significantly decreased. NaCl stress can promote the accumulation of Pro, Put and Spd in mulberry leaves. The accumulation of Pro under NaHCO3 stress is greater than that under NaCl stress. NaCl stress also induced the up-regulation of GAD, GAD1 and GAD1 gene expression, so promoting the synthesis of GABA may be an adaptive mechanism for mulberry to cope with NaCl stress, but the expression of GAD did not change significantly and GAD gene expression lower than CK under NaHCO3 stress. Although both NaCl and NaHCO3 stress could promote the synthesis of GSH by up-regulation of GCLM expression, GSH under NaHCO3 stress was significantly higher than that under NaCl stress, the content of H2O2 was still significantly higher than that of NaCl stress, that means GSH may not play a key role in alleviating the oxidative damage in mulberry leaves caused by salt and alkali.

Role of TaALMT1 malate-GABA transporter in alkaline pH tolerance of wheat

Malate exudation through wheat (Triticum aestivum L) aluminium-activated malate transporter 1 (TaALMT1) confers Al³⁺ tolerance at low pH, but is also activated by alkaline pH, and is regulated by and facilitates significant transport of gamma-aminobutyric acid (GABA, a zwitterionic buffer). Therefore, TaALMT1 may facilitate acidification of an alkaline rhizosphere by promoting exudation of both malate and GABA. Here, the performance of wheat near isogenic lines ET8 (Al⁺³ -tolerant, high TaALMT1 expression) and ES8 (Al⁺³ -sensitive, low TaALMT1 expression) are compared. Root growth (at 5 weeks) was higher for ET8 than ES8 at pH 9. ET8 roots exuded more malate and GABA at high pH and acidified the rhizosphere more rapidly. GABA and malate exudation was enhanced at high pH by the addition of aluminate in both ET8 and transgenic barley expressing TaALMT1. Xenopus laevis oocytes expressing TaALMT1 acidified an alkaline media more rapidly than controls corresponding to higher GABA efflux. TaALMT1 expression did not change under alkaline conditions but key genes involved in GABA turnover changed in accordance with a high rate of GABA synthesis. We propose that TaALMT1 plays a role in alkaline tolerance by exuding malate and GABA, possibly coupled to proton efflux.

Does the GABA Shunt Regulate Cytosolic GABA?

The GABA shunt has long been known as a metabolic pathway that produces GABA in, and removes GABA from, the cytosol. There is no consensus regarding its function. The hypothesis presented here is that the GABA shunt regulates cytosolic GABA levels and GABA signaling.

Effects of GABA and Vigabatrin on the Germination of Chinese Chestnut Recalcitrant Seeds and Its Implications for Seed Dormancy and Storage

Recalcitrant chestnut seeds are rich in γ-aminobutyric acid (GABA), which negatively regulates adventitious root development by altering carbon/nitrogen metabolism. However, little is known regarding the role of this metabolite in chestnut seeds. In this study, we investigated the effects of GABA changes on the germination of chestnut seeds treated with exogenous GABA and vigabatrin (VGB, which inhibits GABA degradation). Both treatments significantly inhibited seed germination and primary root growth and resulted in the considerable accumulation of H₂O₂, but the endogenous GABA content decreased before germination at 48 h. Soluble sugar levels increased before germination, but subsequently decreased, whereas starch contents were relatively unchanged. Changes to organic acids were observed at 120 h after sowing, including a decrease and increase in citrate and malate levels, respectively. Similarly, soluble protein contents increased at 120 h, but the abundance of most free amino acids decreased at 48 h. Moreover, the total amino acid levels increased only in response to VGB at 0 h. Accordingly, GABA and VGB altered the balance of carbon and nitrogen metabolism, thereby inhibiting chestnut seed germination. These results suggested that changes to GABA levels in chestnut seeds might prevent seed germination. The study data may also help clarify the dormancy and storage of chestnut seeds, as well as other recalcitrant seeds.

GABA negatively regulates adventitious root development in poplar

γ-Aminobutyric acid (GABA) influences plant growth, but little is known about how this metabolite regulates adventitious root (AR) development. Here, we investigate the effects of GABA on ARs using poplar lines overexpressing glutamate decarboxilase 2 (GAD2) and by treating poplar stem cuttings with exogenous GABA or vigabatrin (VGB; a specific GABA transaminase inhibitor). Endogenous GABA accumulation not only inhibited AR growth, but it also suppressed or delayed AR formation. Anatomical observations revealed that the GABA and VGB treatments resulted in a 1 d delay in the formation of AR primordia and the appearance of ARs. This delay coincided with changes in primary metabolism, including transient increases in hexose and amino acid levels. GABA-dependent changes in the expression of genes related to hormone synthesis and signalling, as well as analysis of hormone levels revealed that ethylene-dependent pathways were decreased at the earliest stage of AR formation. In contrast, auxin and abscisic acid were increased at 1-5 d as well as GA4 over a 5 d period of AR formation. These results demonstrate that GABA plays a crucial role in AR development. Evidence is presented demonstrating that GABA can interact with hormone-related pathways as well as carbon/nitrogen metabolism. These findings also elucidate the functions of GABA in plant development.

Apple ALMT9 Requires a Conserved C-Terminal Domain for Malate Transport Underlying Fruit Acidity

Malate accumulation in the vacuole largely determines apple (Malus domestica) fruit acidity, and low fruit acidity is strongly associated with truncation of Ma1, an ortholog of ALUMINUM-ACTIVATED MALATE TRANSPORTER9 (ALMT9) in Arabidopsis (Arabidopsis thaliana). A mutation at base 1,455 in the open reading frame of Ma1 leads to a premature stop codon that truncates the protein by 84 amino acids at its C-terminal end. Here, we report that both the full-length protein, Ma1, and its naturally occurring truncated protein, ma1, localize to the tonoplast; when expressed in Xenopus laevis oocytes and Nicotiana benthamiana cells, Ma1 mediates a malate-dependent inward-rectifying current, whereas the ma1-mediated transmembrane current is much weaker, indicating that ma1 has significantly lower malate transport activity than Ma1. RNA interference suppression of Ma1 expression in 'McIntosh' apple leaves, 'Empire' apple fruit, and 'Orin' apple calli results in a significant decrease in malate level. Genotyping and phenotyping of 186 apple accessions from a diverse genetic background of 17 Malus species combined with the functional analyses described above indicate that Ma1 plays a key role in determining fruit acidity and that the truncation of Ma1 to ma1 is genetically responsible for low fruit acidity in apple. Furthermore, we identified a C-terminal domain conserved in all tonoplast-localized ALMTs essential for Ma1 function; protein truncations into this conserved domain significantly lower Ma1 transport activity. We conclude that the truncation of Ma1 to ma1 reduces its malate transport function by removing a conserved C-terminal domain, leading to low fruit acidity in apple.

Genome-Wide Identification of Aluminum-Activated Malate Transporter (ALMT) Gene Family in Rubber Trees (Hevea brasiliensis) Highlights Their Involvement in Aluminum Detoxification

The rubber tree (Hevea brasiliensis) is a widely cultivated crop in tropical acidic soil that is tolerant to high concentration of aluminum and the aluminum-activated malate transporter (ALMT) plays an important role in plant aluminum detoxification. However, the effects of ALMT on rubber tree aluminum tolerance, growth performance, and latex production are unclear. In this study, 17 HbALMT genes were identified from the genome of rubber trees. The physiological and biochemical characteristics, phylogenetic relationships, gene structures, conserved motifs, cis-elements of promoter, and expression patterns of the identified HbALMT genes were studied. Phylogenetic relationships indicated that these genes were divided into four clusters and genes in the same cluster have similar gene structures and conserved motifs. The promoters of HbALMT genes contain many cis-elements associated with biotic stress and abiotic stress. Quantitative real-time PCR analysis revealed HbALMTs showed various expression patterns in different tissues, indicating the functional diversity of HbALMT genes in different tissues of rubber trees. Transcriptome analysis and qRT-PCR assay showed that most of the HbALMT genes responded to aluminum stress, and among the 17 HbALMTs, HbALMT1, HbALMT2, HbALMT13, and HbALMT15 displayed higher expression levels in roots after two or five days of Al treatments, indicating their potential involvement in aluminum detoxification. Taken together, this study laid a foundation for further understanding the molecular evolution of the ALMT genes and their involvement in rubber tree aluminum adaption.

Cytosolic GABA inhibits anion transport by wheat ALMT1

Anion transport by aluminium-activated malate transporter (ALMT) proteins is negatively regulated by gamma-aminobutyric acid (GABA), which increases in concentration during stress. Here, the interaction between GABA and wheat (Triticum aestivum, Ta) TaALMT1 heterologously-expressed in Xenopus laevis oocytes was investigated. GABA inhibited anion transport by TaALMT1 in membrane patches from the cytosolic, not extracellular membrane face, via a reduction in open probability (NP_open ), not an inhibition of channel current magnitude. TaALMT1 currents in patches frequently exhibited rundown with complete removal of cytosolic factors, but were partially sustained by protein kinase C dependent phosphorylation. When applied to whole oocytes a GABA-analogue-BODIPY conjugate inhibited TaALMT1 anion currents from the cytoplasmic face only, whereas free GABA inhibited from both the inside and outside consistent with GABA traversing the TaALMT1 pore then acting from the inside. We propose GABA does not competitively inhibit ALMT conductance through the same pore but rather leads to an allosteric effect, reducing anion channel opening frequency. Across plants GABA is a conserved regulator of anion transport via ALMTs - a family with numerous physiological roles beyond Al³⁺ tolerance. Our data suggests that a GABA-ALMT interaction from the cytosolic face has the potential to form part of a novel plant signalling pathway.

Roles of membrane transporters: connecting the dots from sequence to phenotype

BACKGROUND

Plant membrane transporters are involved in diverse cellular processes underpinning plant physiology, such as nutrient acquisition, hormone movement, resource allocation, exclusion or sequestration of various solutes from cells and tissues, and environmental and developmental signalling. A comprehensive characterization of transporter function is therefore key to understanding and improving plant performance.

SCOPE AND CONCLUSIONS

In this review, we focus on the complexities involved in characterizing transporter function and the impact that this has on current genomic annotations. Specific examples are provided that demonstrate why sequence homology alone cannot be relied upon to annotate and classify transporter function, and to show how even single amino acid residue variations can influence transporter activity and specificity. Misleading nomenclature of transporters is often a source of confusion in transporter characterization, especially for people new to or outside the field. Here, to aid researchers dealing with interpretation of large data sets that include transporter proteins, we provide examples of transporters that have been assigned names that misrepresent their cellular functions. Finally, we discuss the challenges in connecting transporter function at the molecular level with physiological data, and propose a solution through the creation of new databases. Further fundamental in-depth research on specific transport (and other) proteins is still required; without it, significant deficiencies in large-scale data sets and systems biology approaches will persist. Reliable characterization of transporter function requires integration of data at multiple levels, from amino acid residue sequence annotation to more in-depth biochemical, structural and physiological studies.

Characteristics and Expression Pattern of MYC Genes in Triticum aestivum, Oryza sativa, and Brachypodium distachyon

Myelocytomatosis oncogenes (MYC) transcription factors (TFs) belong to basic helix-loop-helix (bHLH) TF family and have a special bHLH_MYC_N domain in the N-terminal region. Presently, there is no detailed and systematic analysis of MYC TFs in wheat, rice, and Brachypodium distachyon. In this study, 26 TaMYC, 7 OsMYC, and 7 BdMYC TFs were identified and their features were characterized. Firstly, they contain a JAZ interaction domain (JID) and a putative transcriptional activation domain (TAD) in the bHLH_MYC_N region and a BhlH region in the C-terminal region. In some cases, the bHLH region is followed by a leucine zipper region; secondly, they display tissue-specific expression patterns: wheat MYC genes are mainly expressed in leaves, rice MYC genes are highly expressed in stems, and B. distachyon MYC genes are mainly expressed in inflorescences. In addition, three types of cis-elements, including plant development/growth-related, hormone-related, and abiotic stresses-related were identified in different MYC gene promoters. In combination with the previous studies, these results indicate that MYC TFs mainly function in growth and development, as well as in response to stresses. This study laid a foundation for the further functional elucidation of MYC genes.

Molecular and electrophysiological characterization of anion transport in Arabidopsis thaliana pollen reveals regulatory roles for pH, Ca2+ and GABA

We investigated the molecular basis and physiological implications of anion transport during pollen tube (PT) growth in Arabidopsis thaliana (Col-0). Patch-clamp whole-cell configuration analysis of pollen grain protoplasts revealed three subpopulations of anionic currents differentially regulated by cytoplasmic calcium ([Ca²⁺ ]_cyt ). We investigated the pollen-expressed proteins AtSLAH3, AtALMT12, AtTMEM16 and AtCCC as the putative anion transporters responsible for these currents. AtCCC-GFP was observed at the shank and AtSLAH3-GFP at the tip and shank of the PT plasma membrane. Both are likely to carry the majority of anion current at negative potentials, as extracellular anionic fluxes measured at the tip of PTs with an anion vibrating probe were significantly lower in slah3^-/- and ccc^-/- mutants, but unaffected in almt12^-/- and tmem16^-/- . We further characterised the effect of pH and GABA by patch clamp. Strong regulation by extracellular pH was observed in the wild-type, but not in tmem16^-/- . Our results are compatible with AtTMEM16 functioning as an anion/H⁺ cotransporter and therefore, as a putative pH sensor. GABA presence: (1) inhibited the overall currents, an effect that is abrogated in the almt12^-/- and (2) reduced the current in AtALMT12 transfected COS-7 cells, strongly suggesting the direct interaction of GABA with AtALMT12. Our data show that AtSLAH3 and AtCCC activity is sufficient to explain the major component of extracellular anion fluxes, and unveils a possible regulatory system linking PT growth modulation by pH, GABA, and [Ca²⁺ ]_cyt through anionic transporters.

Molecular Mechanisms for Coping with Al Toxicity in Plants

Aluminum (Al) toxicity is one of the major constraints to agricultural production in acid soils. Molecular mechanisms of coping with Al toxicity have now been investigated in a range of plant species. Two main mechanisms of Al tolerance in plants are Al exclusion from the roots and the ability to tolerate Al in the roots. This review focuses on the recent discovery of novel genes and mechanisms that confer Al tolerance in plants and summarizes our understanding of the physiological, genetic, and molecular basis for plant Al tolerance. We hope this review will provide a theoretical basis for the genetic improvement of Al tolerance in plants.

The botanical multiverse of Peter Barlow

Dr Peter Barlow, who died in 2017, was one of the most respected botanists and biologists of the latter half of the 20th Century. His interests covered a wide range of plant biological topics, e.g. root growth and development, plant cytoskeleton, effects of gravity, plant intelligence, pattern formation, and evolution of eukaryotic cells. Here we consider Peter's numerous contributions to the: elucidation of plant patterns; understanding of root biology; role of the plant cytoskeleton in growth and development; influence of the Moon on terrestrial vegetation; Cell Body concept; and plant neurobiology. In so doing we attempt not only to provide an overview of Peter's important work in many areas of plant biology, but also to place that work in the context of recent advances in plant and biological sciences.

Engineering Strategies to Boost Crop Productivity by Cutting Respiratory Carbon Loss

Roughly half the carbon that crop plants fix by photosynthesis is subsequently lost by respiration. Nonessential respiratory activity leading to unnecessary CO2 release is unlikely to have been minimized by natural selection or crop breeding, and cutting this large loss could complement and reinforce the currently dominant yield-enhancement strategy of increasing carbon fixation. Until now, however, respiratory carbon losses have generally been overlooked by metabolic engineers and synthetic biologists because specific target genes have been elusive. We argue that recent advances are at last pinpointing individual enzyme and transporter genes that can be engineered to (1) slow unnecessary protein turnover, (2) replace, relocate, or reschedule metabolic activities, (3) suppress futile cycles, and (4) make ion transport more efficient, all of which can reduce respiratory costs. We identify a set of engineering strategies to reduce respiratory carbon loss that are now feasible and model how implementing these strategies singly or in tandem could lead to substantial gains in crop productivity.

The role of transposable elements in the evolution of aluminium resistance in plants

Aluminium (Al) toxicity can severely reduce root growth and consequently affect plant development and yield. A mechanism by which many species resist the toxic effects of Al relies on the efflux of organic anions (OAs) from the root apices via OA transporters. Several of the genes encoding these OA transporters contain transposable elements (TEs) in the coding sequences or in flanking regions. Some of the TE-induced mutations impact Al resistance by modifying the level and/or location of gene expression so that OA efflux from the roots is increased. The importance of genomic modifications for improving the adaptation of plants to acid soils has been raised previously, but the growing number of examples linking TEs with these changes requires highlighting. Here, we review the role of TEs in creating genetic modifications that enhance the adaptation of plants to acid soils by increasing the release of OAs from the root apices. We argue that TEs have been an important source of beneficial mutations that have co-opted OA transporter proteins with other functions to perform this role. These changes have occurred relatively recently in the evolution of many species and likely facilitated their expansion into regions with acidic soils.

Emerging Pleiotropic Mechanisms Underlying Aluminum Resistance and Phosphorus Acquisition on Acidic Soils

Aluminum (Al) toxicity on acidic soils significantly damages plant roots and inhibits root growth. Hence, crops intoxicated by Al become more sensitive to drought stress and mineral nutrient deficiencies, particularly phosphorus (P) deficiency, which is highly unavailable on tropical soils. Advances in our understanding of the physiological and genetic mechanisms that govern plant Al resistance have led to the identification of Al resistance genes, both in model systems and in crop species. It has long been known that Al resistance has a beneficial effect on crop adaptation to acidic soils. This positive effect happens because the root systems of Al resistant plants show better development in the presence of soil ionic Al3+ and are, consequently, more efficient in absorbing sub-soil water and mineral nutrients. This effect of Al resistance on crop production, by itself, warrants intensified efforts to develop and implement, on a breeding scale, modern selection strategies to profit from the knowledge of the molecular determinants of plant Al resistance. Recent studies now suggest that Al resistance can exert pleiotropic effects on P acquisition, potentially expanding the role of Al resistance on crop adaptation to acidic soils. This appears to occur via both organic acid (OA)- and non-OA transporters governing a joint, iron-dependent interplay between Al resistance and enhanced P uptake, via changes in root system architecture. Current research suggests this interplay to be part of a P stress response, suggesting that this mechanism could have evolved in crop species to improve adaptation to acidic soils. Should this pleiotropism prove functional in crop species grown on acidic soils, molecular breeding based on Al resistance genes may have a much broader impact on crop performance than previously anticipated. To explore this possibility, here we review the components of this putative effect of Al resistance genes on P stress responses and P nutrition to provide the foundation necessary to discuss the recent evidence suggesting pleiotropy as a genetic linkage between Al resistance and P efficiency. We conclude by exploring what may be needed to enhance the utilization of Al resistance genes to improve crop production on acidic soils.