Lotus japonicus LjKUP is induced late during nodule development and encodes a potassium transporter of the plasma membrane

Boosting Rhizobium-legume symbiosis: The role of nodule non-rhizobial bacteria in hormonal and nutritional regulation under stress

Legumes are vital for sustainable agriculture due to their unique ability to fix atmospheric nitrogen through symbiosis with rhizobia. Recent research has highlighted the significant role of non-rhizobial bacteria (NRB) within root nodules in enhancing this symbiotic relationship, particularly under stress conditions. These NRB exhibit plant growth-promoting (PGP) metabolites by modulating phytohormones and enhancing nutrient availability, thereby improving nodule development and function. Bacteria produce essential hormones, such as auxin (indole-3-acetic acid), cytokinins, gibberellic acids abscisic acid, jasmonic acid, and salicylic acid, and enzymes like 1-aminocyclopropane-1-carboxylate deaminase, which mitigate ethylene's inhibitory effects on nodulation. Furthermore, NRB contribute to nutrient cycling by solubilizing minerals like phosphate, potassium, silicate, zinc, and iron, essential for effective nitrogen fixation. The co-inoculation of legumes with both rhizobia and NRB with multiple PGP metabolites has shown synergistic effects on plant growth, yield, and resilience against environmental stresses. This review emphasizes the need to further explore the diversity and functional roles of nodule-associated non-rhizobial endophytes, aiming to optimize legume productivity through improved nutrient and hormonal management. Understanding these interactions is crucial for developing sustainable agricultural practices that enhance the efficiency of legume-rhizobia symbiosis, ultimately contributing to food security and ecosystem health.

The interaction of nutrient uptake with biotic and abiotic stresses in plants

Plants depend heavily on efficient nutrient uptake and utilization for optimal growth and development. However, plants are constantly subjected to a diverse array of biotic stresses, such as pathogen infections, insect pests, and herbivory, as well as abiotic stress like drought, salinity, extreme temperatures, and nutrient imbalances. These stresses significantly impact the plant's ability to take up nutrient and use it efficiency. Understanding how plants maintain nutrient uptake and use efficiency under biotic and abiotic stress conditions is crucial for improving crop resilience and sustainability. This review explores the recent advancements in elucidating the mechanisms underlying nutrient uptake and utilization efficiency in plants under such stress conditions. Our aim is to offer a comprehensive perspective that can guide the breeding of stress-tolerant and nutrition-efficient crop varieties, ultimately contributing to the advancement of sustainable agriculture.

OsHAK4 functions in retrieving sodium from the phloem at the reproductive stage of rice

Soil salinity significantly limits rice productivity, but it is poorly understood how excess sodium (Na+) is delivered to the grains at the reproductive stage. Here, we functionally characterized OsHAK4, a member of the clade IV HAK/KUP/KT transporter subfamily in rice. OsHAK4 was localized to the plasma membrane and exhibited influx transport activity for Na+, but not for K+. Analysis of organ- and growth stage-dependent expression patterns showed that very low expression levels of OsHAK4 were detected at the vegetative growth stage, but its high expression in uppermost node I, peduncle, and rachis was found at the reproductive stage. Immunostaining indicated OsHAK4 localization in the phloem region of node I, peduncle, and rachis. Knockout of OsHAK4 did not affect the growth and Na+ accumulation at the vegetative stage. However, at the reproductive stage, the hak4 mutants accumulated higher Na+ in the peduncle, rachis, husk, and brown rice compared to the wild-type rice. Element imaging revealed higher Na+ accumulation at the phloem region of the peduncle in the mutants. These results indicate that OsHAK4 plays a crucial role in retrieving Na+ from the phloem in the upper nodes, peduncle, and rachis, thereby preventing Na+ distribution to the grains at the reproductive stage of rice.

Metal nutrition and transport in the process of symbiotic nitrogen fixation

Symbiotic nitrogen fixation (SNF) facilitated by the interaction between legumes and rhizobia is a well-documented and eco-friendly alternative to chemical nitrogen fertilizers. Host plants obtain fixed nitrogen from rhizobia by providing carbon and mineral nutrients. These mineral nutrients, which are mostly in the form of metal ions, are implicated in various stages of the SNF process. This review describes the functional roles played by metal ions in nodule formation and nitrogen fixation and specifically addresses their transport mechanisms and associated transporters within root nodules. Future research directions and potential strategies for enhancing SNF efficiency are also discussed.

Genome-wide identification and expression analysis of HAK/KUP/KT potassium transporter provides insights into genes involved in responding to potassium deficiency and salt stress in pepper (Capsicum annuum L.)

In plants, the HAK/KUP/KT family is the largest group of potassium transporters, and it plays an important role in mineral element absorption, plant growth, environmental stress adaptation, and symbiosis. Although these important genes have been investigated in many plant species, limited information is currently available on the HAK/KUP/KT genes for Pepper (Capsicum annuum L.). In the present study, a total of 20 CaHAK genes were identified from the pepper genome and the CaHAK genes were numbered 1 - 20 based on phylogenetic analysis. For the genes and their corresponding proteins, the physicochemical properties, phylogenetic relationship, chromosomal distribution, gene structure, conserved motifs, gene duplication events, and expression patterns were analyzed. Phylogenetic analysis divided CaHAK genes into four cluster (I-IV) based on their structural features and the topology of the phylogenetic tree. Purifying selection played a crucial role in the evolution of CaHAK genes, while whole-genome triplication contributed to the expansion of the CaHAK gene family. The expression patterns showed that CaHAK proteins exhibited functional divergence in terms of plant K⁺ uptake and salt stress response. In particular, transcript abundance of CaHAK3 and CaHAK7 was strongly and specifically up-regulated in pepper roots under low K⁺ or high salinity conditions, suggesting that these genes are candidates for high-affinity K⁺ uptake transporters and may play crucial roles in the maintenance of the Na⁺/K⁺ balance during salt stress in pepper. In summary, the results not only provided the important information on the characteristics and evolutionary relationships of CaHAKs, but also provided potential genes responding to potassium deficiency and salt stress.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-022-03136-z.

Genome-Wide Identification, Genomic Organization, and Characterization of Potassium Transport-Related Genes in Cajanus cajan and Their Role in Abiotic Stress

Potassium is the most important and abundant inorganic cation in plants and it can comprise up to 10% of a plant's dry weight. Plants possess complex systems of transporters and channels for the transport of K+ from soil to numerous parts of plants. Cajanus cajan is cultivated in different regions of the world as an economical source of carbohydrates, fiber, proteins, and fodder for animals. In the current study, 39 K+ transport genes were identified in C. cajan, including 25 K+ transporters (17 carrier-like K+ transporters (KUP/HAK/KTs), 2 high-affinity potassium transporters (HKTs), and 6 K+ efflux transporters (KEAs) and 14 K+ channels (9 shakers and 5 tandem-pore K+ channels (TPKs). Chromosomal mapping indicated that these genes were randomly distributed among 10 chromosomes. A comparative phylogenetic analysis including protein sequences from Glycine max, Arabidopsis thaliana, Oryza sativa, Medicago truncatula Cicer arietinum, and C. cajan suggested vital conservation of K+ transport genes. Gene structure analysis showed that the intron/exon organization of K+ transporter and channel genes is highly conserved in a family-specific manner. In the promoter region, many cis-regulatory elements were identified related to abiotic stress, suggesting their role in abiotic stress response. Abiotic stresses (salt, heat, and drought) adversely affect chlorophyll, carotenoids contents, and total soluble proteins. Furthermore, the activities of catalase, superoxide, and peroxidase were altered in C. cajan leaves under applied stresses. Expression analysis (RNA-seq data and quantitative real-time PCR) revealed that several K+ transport genes were expressed in abiotic stress-responsive manners. The present study provides an in-depth understanding of K+ transport system genes in C. cajan and serves as a basis for further characterization of these genes.

Recent Advances in Genome-wide Analyses of Plant Potassium Transporter Families

Plants require potassium (K⁺) as a macronutrient to support numerous physiological processes. Understanding how this nutrient is transported, stored, and utilized within plants is crucial for breeding crops with high K⁺ use efficiency. As K⁺ is not metabolized, cross-membrane transport becomes a rate-limiting step for efficient distribution and utilization in plants. Several K⁺ transporter families, such as KUP/HAK/KT and KEA transporters and Shaker-like and TPK channels, play dominant roles in plant K⁺ transport processes. In this review, we provide a comprehensive contemporary overview of our knowledge about these K⁺ transporter families in angiosperms, with a major focus on the genome-wide identification of K⁺ transporter families, subcellular localization, spatial expression, function and regulation. We also expanded the genome-wide search for the K⁺ transporter genes and examined their tissue-specific expression in Camelina sativa, a polyploid oil-seed crop with a potential to adapt to marginal lands for biofuel purposes and contribution to sustainable agriculture. In addition, we present new insights and emphasis on the study of K⁺ transporters in polyploids in an effort to generate crops with high K⁺ Utilization Efficiency (KUE).

Potassium content diminishes in infected cells of Medicago truncatula nodules due to the mislocation of channels MtAKT1 and MtSKOR/GORK

Rhizobia establish a symbiotic relationship with legumes that results in the formation of root nodules, where bacteria encapsulated by a membrane of plant origin (symbiosomes), convert atmospheric nitrogen into ammonia. Nodules are more sensitive to ionic stresses than the host plant itself. We hypothesize that such a high vulnerability might be due to defects in ion balance in the infected tissue. Low temperature SEM (LTSEM) and X-ray microanalysis of Medicago truncatula nodules revealed a potassium (K⁺) decrease in symbiosomes and vacuoles during the life span of infected cells. To clarify K⁺ homeostasis in the nodule, we performed phylogenetic and gene expression analyses, and confocal and electron microscopy localization of two key plant Shaker K⁺ channels, AKT1 and SKOR/GORK. Phylogenetic analyses showed that the genome of some legume species, including the Medicago genus, contained one SKOR/GORK and one AKT1 gene copy, while other species contained more than one copy of each gene. Localization studies revealed mistargeting and partial depletion of both channels from the plasma membrane of M. truncatula mature nodule-infected cells that might compromise ion transport. We propose that root nodule-infected cells have defects in K⁺ balance due to mislocation of some plant ion channels, as compared with non-infected cells. The putative consequences are discussed.

Genome-Wide Survey and Expression Analysis of the KT/HAK/KUP Family in Brassica napus and Its Potential Roles in the Response to K+ Deficiency

The KT/HAK/KUP (HAK) family is the largest potassium (K⁺) transporter family in plants, which plays key roles in K⁺ uptake and homeostasis, stress resistance, and root and embryo development. However, the HAK family has not yet been characterized in Brassica napus. In this study, 40 putative B. napus HAK genes (BnaHAKs) are identified and divided into four groups (Groups I–III and V) on the basis of phylogenetic analysis. Gene structure analysis revealed 10 conserved intron insertion sites across different groups. Collinearity analysis demonstrated that both allopolyploidization and small-scale duplication events contributed to the large expansion of BnaHAKs. Transcription factor (TF)-binding network construction, cis-element analysis, and microRNA prediction revealed that the expression of BnaHAKs is regulated by multiple factors. Analysis of RNA-sequencing data further revealed extensive expression profiles of the BnaHAKs in groups II, III, and V, with limited expression in group I. Compared with group I, most of the BnaHAKs in groups II, III, and V were more upregulated by hormone induction based on RNA-sequencing data. Reverse transcription-quantitative polymerase reaction analysis revealed that the expression of eight BnaHAKs of groups I and V was markedly upregulated under K⁺-deficiency treatment. Collectively, our results provide valuable information and key candidate genes for further functional studies of BnaHAKs.

Genome-Wide Investigation and Expression Analysis of K+-Transport-Related Gene Families in Chinese Cabbage (Brassica rapa ssp. pekinensis)

Potassium (K⁺) transport and channel systems play vital roles in plant growth, development and responses to various stresses. In this study, 44 putative K⁺-transport-related genes (18K⁺ uptake permease (KUP)/high-affinity K⁺ (HAK)/K⁺ transporter (KT) family genes and 26 channel genes, including 18 Shaker family genes and 8K⁺ channel outward (KCO) family genes) were identified in the genome of Chinese cabbage (Brassica rapa ssp. pekinensis). To clarify the molecular evolution of each family in Chinese cabbage, phylogenetic analysis and assessments of the gene structures, conserved motifs, chromosomal locations, gene duplications, expression patterns and cis-acting elements of the 44 putative K⁺-transport-related genes were performed. The phylogenetic analysis showed that these genes could be classified into five clades [KUP/HAK/KTs, KCOs, K_out, K_in (KAT) and K_in (AKT)] and that the members of a given clade shared conserved exon-intron distributions and motif compositions. These K⁺-transport-related genes were unevenly distributed over all ten chromosomes, including four duplicated gene pairs that implied an expansion of K⁺-transport-related genes in Chinese cabbage. Analyses of Illumina RNA-seq data for these 44K⁺-transport-related genes indicated tissue-/organ-specific expression patterns. In addition, an overall evaluation showed that the expression levels of KUP/HAK/KT genes were significantly higher than those of potassium channel genes in six tissues. Promoter cis-acting element analysis revealed that these 44K⁺-transport-related genes may be associated with responses to 10 abiotic stresses, primarily light, methyl jasmonate (MeJA) and abscisic acid (ABA). Our results provide a systematic and comprehensive overview of K⁺-transport-related gene families in Chinese cabbage and establish a foundation for further research on K⁺ absorption and transport functions.

Loss of salt tolerance during tomato domestication conferred by variation in a Na+ /K+ transporter

Domestication has resulted in reduced salt tolerance in tomato. To identify the genetic components causing this deficiency, we performed a genome-wide association study (GWAS) for root Na⁺ /K⁺ ratio in a population consisting of 369 tomato accessions with large natural variations. The most significant variations associated with root Na⁺ /K⁺ ratio were identified within the gene SlHAK20 encoding a member of the clade IV HAK/KUP/KT transporters. We further found that SlHAK20 transports Na⁺ and K⁺ and regulates Na⁺ and K⁺ homeostasis under salt stress conditions. A variation in the coding sequence of SlHAK20 was found to be the causative variant associated with Na⁺ /K⁺ ratio and confer salt tolerance in tomato. Knockout mutations in tomato SlHAK20 and the rice homologous genes resulted in hypersensitivity to salt stress. Together, our study uncovered a previously unknown molecular mechanism of salt tolerance responsible for the deficiency in salt tolerance in cultivated tomato varieties. Our findings provide critical information for molecular breeding to improve salt tolerance in tomato and other crops.

Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia-legume symbiosis

Symbiotic nitrogen fixation in root nodules of grain legumes is essential for high yielding. Protein phosphorylation/dephosphorylation plays important role in root nodule development. Differences in the phosphoproteomes may either be developmental specific and related to nitrogen fixation activity. An iTRAQ-based quantitative phosphoproteomic analyses during nodule development enables identification of specific phosphorylation signaling in the Lotus-rhizobia symbiosis. During evolution, legumes (Fabaceae) have evolved a symbiotic relationship with rhizobia, which fix atmospheric nitrogen and produce ammonia that host plants can then absorb. Root nodule development depends on the activation of protein phosphorylation-mediated signal transduction cascades. To investigate possible molecular mechanisms of protein modulation during nodule development, we used iTRAQ-based quantitative proteomic analyses to identify root phosphoproteins during rhizobial colonization and infection of Lotus japonicus. 1154 phosphoproteins with 2957 high-confidence phosphorylation sites were identified. Gene ontology enrichment analysis of functional groups of these genes revealed that the biological processes mediated by these proteins included cellular processes, signal transduction, and transporter activity. Quantitative data highlighted the dynamics of protein phosphorylation during nodule development and, based on regulatory trends, seven groups were identified. RNA splicing and brassinosteroid (BR) signaling pathways were extensively affected by phosphorylation, and most Ser/Arg-rich (SR) proteins were multiply phosphorylated. In addition, many proposed kinase-substrate pairs were predicted, and in these MAPK6 substrates were found to be highly enriched. This study offers insights into the regulatory processes underlying nodule development, provides an accessible resource cataloging the phosphorylation status of thousands of Lotus proteins during nodule development, and develops our understanding of post-translational regulatory mechanisms in the Lotus-rhizobia symbiosis.

Genome-wide analysis of the HAK potassium transporter gene family reveals asymmetrical evolution in tobacco (Nicotiana tabacum)

Being an essential mineral nutrient, potassium (K+) plays numerous important roles in plant growth and development and determines the yield and quality of crop products. The cellular level of K+ is controlled to a large extent by the K+ transporter, which belongs to the KT/HAK/KUP (HAK) family. However, little is known about these genes in tobacco. In this study, we surveyed the tobacco genome and identified 41 putative NtHAK genes (NtHAKS1-NtHAKS21 and NtHAKT1-NtHAKT20). Investigation of the cis-elements in upstream regions of these NtHAK genes suggests that members of this family respond to environmental cues and phytohormones. Expression data mining reveals that NtHAK genes showed clear sub-genome dominance. In all, these results will provide molecular insights into K+ transporter research in tobacco.

KT-HAK-KUP transporters in major terrestrial photosynthetic organisms: A twenty years tale

Since their discovery, twenty years ago, KT-HAK-KUP transporters have become a keystone to understand how alkali cation fluxes are controlled in major land-dwelling photosynthetic organisms. In this review we focus on their discovery, phylogeny, and functions, as well as the regulation of its canonical member, AtHAK5. We also address issues related to structure-function studies, and the technological possibilities opened up by recent findings. Available evidence suggests that this family of transporters underwent an early divergence into major groups following the conquest of land by embryophytes. KT-HAK-KUPs are necessary to accomplish several major developmental and growth processes, as well as to ensure plant responses to environmental injuries. Although the primary function of these transporters is to mediate potassium (K⁺) fluxes, some of them can also mediate sodium (Na⁺) and cesium (Cs⁺) transport, and contribute to maintenance of K⁺ (and Na⁺) homeostasis in different plant tissues. In addition, there is evidence for a role of some members of this family in auxin movement and in adenylate cyclase activity. Recent research, focusing on the regulation of the canonical member of this family, AtHAK5, revealed the existence of a complex network that involves transcriptional and post-transcriptional phenomena which control the enhancement of AtHAK5-mediated K⁺ uptake when Arabidopsis thaliana plants are faced with low K⁺ supply. In spite of the formidable advances made since their discovery, important subjects remain to be elucidated to gain a more complete knowledge of the roles and regulation of KT-HAK-KUPs, as well as to improve their use for innovative procedures in crop breeding.

In-Depth Genomic and Transcriptomic Analysis of Five K+ Transporter Gene Families in Soybean Confirm Their Differential Expression for Nodulation

Plants have evolved a sophisticated network of K⁺ transport systems to regulate growth and development. Limited K⁺ resources are now forcing us to investigate how plant demand can be satisfied. To answer this complex question, we must understand the genomic and transcriptomic portfolio of K⁺ transporters in plants. Here, we have identified 70 putative K⁺ transporter genes from soybean, including 29 HAK/KT/KUP genes, 16 genes encoding voltage-gated K⁺ channels, 9 TPK/KCO genes, 4 HKT genes, and 12 KEA genes. To clarify the molecular evolution of each family in soybean, we analyzed their phylogeny, mode of duplication, exon structures and splice sites, and paralogs. Additionally, ortholog clustering and syntenic analysis across five other dicots further explored the evolution of these gene families and indicated that the soybean data is suitable as a model for all other legumes. Available microarray data sets from Genevestigator about nodulation was evaluated and further confirmed with the RNA sequencing data available by a web server. For each family, expression models were designed based on Transcripts Per Kilobase Million (TPM) values; the outcomes indicated differential expression linked to nodulation and confirmed the genes' putative roles. In-depth studies such as ours provides the basis for understanding K⁺ inventories in all other plants.

Uneven HAK/KUP/KT Protein Diversity Among Angiosperms: Species Distribution and Perspectives

HAK/KUP/KT K(+) transporters have been widely associated with K(+) transport across membranes in bacteria, fungi, and plants. Indeed some members of the plant HAK/KUP/KT family contribute to root K(+) uptake, notably at low external concentrations. Besides such role in acquisition, several studies carried out in Arabidopsis have shown that other members are also involved in developmental processes. With the publication of new plant genomes, a growing interest on plant species other than Arabidopsis has become evident. In order to understand HAK/KUP/KT diversity in these new plant genomes, we discuss the evolutionary trends of 913 HAK/KUP/KT sequences identified in 46 genomes revealing five major groups with an uneven distribution among angiosperms, notably between dicotyledonous and monocotyledonous species. This information evidenced the richness of crop genomes in HAK/KUP/KT transporters and supports their study for unraveling novel physiological roles of such transporters in plants.

Molecular Cloning and Functional Analysis of a Na+-Insensitive K+ Transporter of Capsicum chinense Jacq

High-affinity K⁺ (HAK) transporters are encoded by a large family of genes and are ubiquitous in the plant kingdom. These HAK-type transporters participate in low- and high-affinity potassium (K⁺) uptake and are crucial for the maintenance of K⁺ homeostasis under hostile conditions. In this study, the full-length cDNA of CcHAK1 gene was isolated from roots of the habanero pepper (Capsicum chinense). CcHAK1 expression was positively regulated by K⁺ starvation in roots and was not inhibited in the presence of NaCl. Phylogenetic analysis placed the CcHAK1 transporter in group I of the HAK K⁺ transporters, showing that it is closely related to Capsicum annuum CaHAK1 and Solanum lycopersicum LeHAK5. Characterization of the protein in a yeast mutant deficient in high-affinity K⁺ uptake (WΔ3) suggested that CcHAK1 function is associated with high-affinity K⁺ uptake, with K_m and V_max for Rb of 50 μM and 0.52 nmol mg^-1 min^-1, respectively. K⁺ uptake in yeast expressing the CcHAK1 transporter was inhibited by millimolar concentrations of the cations ammonium ([Formula: see text]) and cesium (Cs⁺) but not by sodium (Na⁺). The results presented in this study suggest that the CcHAK1 transporter may contribute to the maintenance of K⁺ homeostasis in root cells in C. chinense plants undergoing K⁺-deficiency and salt stress.

Molecular biology of K+ transport across the plant cell membrane: what do we learn from comparison between plant species?

Cloning and characterizations of plant K(+) transport systems aside from Arabidopsis have been increasing over the past decade, favored by the availability of more and more plant genome sequences. Information now available enables the comparison of some of these systems between species. In this review, we focus on three families of plant K(+) transport systems that are active at the plasma membrane: the Shaker K(+) channel family, comprised of voltage-gated channels that dominate the plasma membrane conductance to K(+) in most environmental conditions, and two families of transporters, the HAK/KUP/KT K(+) transporter family, which includes some high-affinity transporters, and the HKT K(+) and/or Na(+) transporter family, in which K(+)-permeable members seem to be present in monocots only. The three families are briefly described, giving insights into the structure of their members and on functional properties and their roles in Arabidopsis or rice. The structure of the three families is then compared between plant species through phylogenic analyses. Within clusters of ortologues/paralogues, similarities and differences in terms of expression pattern, functional properties and, when known, regulatory interacting partners, are highlighted. The question of the physiological significance of highlighted differences is also addressed.

Transport and metabolism in legume-rhizobia symbioses

Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems.

Genome-wide and molecular evolution analysis of the Poplar KT/HAK/KUP potassium transporter gene family

As the largest K(+) transport gene family, KT/HAK/KUP family plays an important role in plant growth, development, and stress adaptation. However, there is limited information about this family in woody plant species. In this study, with genome-wide in-depth investigation, 31 Poplar KT/HAK/KUP transporter genes including six pairs of tandem duplicated and eight pairs of segmental duplicated paralogs have been identified, suggesting segmental and tandem duplication events contributed to the expansion of this family in Poplar. The combination of phylogenetic, exon structure and splice site, and paragon analysis revealed 11 pairs of Poplar KT/HAK/KUP duplicates. For these 11 pairs, all pairs are subject to purify selection, and asymmetric evolutionary rates have been found to occur in three pairs. This study might provide more insights into the underlying evolution mechanisms of trees acclimating to their natural habitat.

Genome-wide analysis and identification of HAK potassium transporter gene family in maize (Zea mays L.)

The high-affinity K(+) (HAK) transporter gene family constitutes the largest family that functions as potassium transporter in plant and is important for various cellular processes of plant life. In spite of their physiological importance, systematic analyses of ZmHAK genes have not yet been investigated. In this paper, we indicated the isolation and characterization of ZmHAK genes in whole-genome wide by using bioinformatics methods. A total of 27 members (ZmHAK1-ZmHAK27) of this family were identified in maize genome. ZmHAK genes were distributed in all the maize 10 chromosomes. These genes expanded in the maize genome partly due to tandem and segmental duplication events. Multiple alignment and motif display results revealed major maize ZmHAK proteins share all the three conserved domains. Phylogenetic analysis indicated ZmHAK family can be divided into six subfamilies. Putative cis-elements involved in Ca(2+) response, abiotic stress adaption, light and circadian rhythms regulation and seed development were observed in the promoters of ZmHAK genes. Expression data mining suggested maize ZmHAK genes have temporal and spatial expression pattern. In all, these results will provide molecular insights into the potassium transporter research in maize.

Genomic inventory and transcriptional analysis of Medicago truncatula transporters

Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, and signaling and, consequently, in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least 5-fold during nodule development and 44 in roots during arbuscular mycorrhizal symbiosis. Among the nodule- and mycorrhiza-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for the selection and functional characterization of legume transporters.

KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice (Oryza sativa)

KT/HAK/KUP potassium transporter protein-encoding genes constitute a large family in the plant kingdom. The KT/HAK/KUP family is important for various physiological processes of plant life. In this study, we identified 27 potential KT/HAK/KUP family genes in rice (Oryza sativa) by database searching. Analysis of these KT/HAK/KUP family members identified three conserved motifs with unknown functions, and 11-15 trans-membrane segments, most of which are conserved. A total of 144 putative cis-elements were found in the 2 kb upstream region of these genes, of which a Ca2+-responsive cis-element, two light-responsive cis-elements, and a circadian-regulated cis-element were identified in the majority of the members, suggesting regulation of these genes by these signals. A comprehensive expression analysis of these genes was performed using data from microarrays hybridized with RNA samples of 27 tissues covering the entire life cycle from three rice genotypes, Minghui 63, Zhenshan 97, and Shanyou 63. We identified preferential expression of two OsHAK genes in stamen at 1 day before flowering compared with all the other tissues. OsHAK genes were also found to be differentially upregulated or downregulated in rice seedlings subjected to treatments with three hormones. These results would be very useful for elucidating the roles of these genes in growth, development, and stress response of the rice plant.

Potassium transporters in plants--involvement in K+ acquisition, redistribution and homeostasis

Potassium is a major plant nutrient which has to be accumulated in great quantity by roots and distributed throughout the plant and within plant cells. Membrane transport of potassium can be mediated by potassium channels and secondary potassium transporters. Plant potassium transporters are present in three families of membrane proteins: the K(+) uptake permeases (KT/HAK/KUP), the K(+) transporter (Trk/HKT) family and the cation proton antiporters (CPA). This review will discuss the contribution of members of each family to potassium acquisition, redistribution and homeostasis.

Functional genomics of plant transporters in legume nodules

Over the past few decades, a combination of physiology, biochemistry, molecular and cell biology, and genetics has given us a basic understanding of some of the key transport processes at work in nitrogen-fixing legume nodules, especially those involved in nutrient exchange between infected plant cells and their endosymbiotic rhizobia. However, our knowledge in this area remains patchy and dispersed over numerous legume species. Recent progress in the areas of genomics and functional genomics of the two model legumes, Medicago truncatula and Lotus japonicus is rapidly filling the gap in knowledge about which plant transporter genes are expressed constitutively in nodules and other organs, and which are induced or expressed specifically in nodules. The latter class in particular is the focus of current efforts to understand specialised, nodule-specific roles of transporters. This article briefly reviews past work on the biochemistry and molecular biology of plant transporters in nodules, before describing recent work in the areas of transcriptomics and bioinformatics. Finally, we consider where functional genomics together with more classical approaches are likely to lead us in this area of research in the future.