Identification of a delta-TIP cDNA clone and determination of related A and D genome subfamilies in Gossypium species

Identification of early Al-responsive genes in rice bean (Vigna umbellata) roots provides new clues to molecular mechanisms of Al toxicity and tolerance

Significant secretion of citrate from root apex of rice bean (Vigna umbellata) is delayed by several hours under aluminium (Al) stress. However, the molecular basis of regulation of VuMATE1, a gene encoding an Al-activated citrate transporter, remains unclear. In this study, we used suppression subtractive hybridization together with reverse northern blot analysis and qRT-PCR to identify genes with altered transcript levels in the root apex after treatment with low (5 μm) or high (25 μm) concentration of AlCl(3) for a short time (4 h). We found that in addition to VuMATE1, 393 genes showed an early response to Al. Among functionally annotated genes, those related to 'metabolism and energy', 'signal transduction and transcription' and 'transport' was predominantly up-regulated, whereas those associated with 'protein translation, processing and degradation' was predominantly down-regulated. Comparative analysis of transcriptional profiles highlighted candidate genes associated with citrate secretion and revealed several new aspects of the molecular processes underlying Al toxicity and tolerance. Based on the data, it is proposed that metabolic changes represent adaptive mechanisms to Al stress, whereas inhibition of both cell elongation and cell division underlies Al-induced root growth inhibition.

Identification of the family of aquaporin genes and their expression in upland cotton (Gossypium hirsutum L.)

BACKGROUND

Cotton (Gossypium spp.) is produced in over 30 countries and represents the most important natural fiber in the world. One of the primary factors affecting both the quantity and quality of cotton production is water. A major facilitator of water movement through cell membranes of cotton and other plants are the aquaporin proteins. Aquaporin proteins are present as diverse forms in plants, where they function as transport systems for water and other small molecules. The plant aquaporins belong to the large major intrinsic protein (MIP) family. In higher plants, they consist of five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). Although a great deal is known about aquaporins in plants, very little is known in cotton.

RESULTS

From a molecular cloning effort, together with a bioinformatic homology search, 71 upland cotton (G. hirsutum) aquaporin genes were identified. The cotton aquaporins consist of 28 PIP and 23 TIP members with high sequence similarity. We also identified 12 NIP and 7 SIP members that showed more divergence. In addition, one XIP member was identified that formed a distinct 5th subfamily. To explore the physiological roles of these aquaporin genes in cotton, expression analyses were performed for a select set of aquaporin genes from each subfamily using semi-quantitative reverse transcription (RT)-PCR. Our results suggest that many cotton aquaporin genes have high sequence similarity and diverse roles as evidenced by analysis of sequences and their expression.

CONCLUSION

This study presents a comprehensive identification of 71 cotton aquaporin genes. Phylogenetic analysis of amino acid sequences divided the large and highly similar multi-gene family into the known 5 aquaporin subfamilies. Together with expression and bioinformatic analyses, our results support the idea that the genes identified in this study represent an important genetic resource providing potential targets to modify the water use properties of cotton.

Characterization and expression of plasma and tonoplast membrane aquaporins in elongating cotton fibers

Cotton fiber (Gossypium hirsutum L. and G. barbadense L.) is a good model for studies of plant cell elongation and cell wall biogenesis. Aquaporins are ancient membrane channel proteins that facilitate the permeation of water across biological membranes. We studied GhPIP1-2, encoding plasma membrane intrinsic protein, and GhgammaTIP1, encoding tonoplast intrinsic protein, during cotton fiber development. The full-length cDNAs of GhPIP1-2 and GhgammaTIP1 were obtained through 5' RACE. The deduced amino acid sequences of GhPIP1-2 and GhgammaTIP1 share high sequence identity with aquaporins from diverse plant species. Phylogenetic analysis of GhPIP1-2 and GhgammaTIP1 with other plant aquaporins showed that GhPIP1-2 belongs to the PIP1 group of the PIP subfamily and GhgammaTIP1 belongs to the gammaTIP group of the TIP subfamily. GhPIP1-2 and GhgammaTIP1 contain three and two introns, respectively. Genomic Southern blot analysis indicated that GhPIP1-2 and GhgammaTIP1 have several copies and multiple homologous genes in allotetraploid cotton. Northern blot analysis with gene-specific probes and real-time PCR demonstrated that GhPIP1-2 and GhgammaTIP1 are predominantly expressed during cotton fiber elongation, with the highest expression levels at 5 days post-anthesis. Moreover, expression patterns of the two genes in G. hirsutum and G. barbadense are similar, whereas the expression levels in G. barbadense are much lower than that in G. hirsutum. The high and preferential expression of GhPIP1-2 and GhgammaTIP1 during fiber cell elongation suggests that they may play important roles in supporting the rapid influx of water into vacuoles during cotton fiber cell expansion.

Expression profile analysis of genes involved in cell wall regeneration during protoplast culture in cotton by suppression subtractive hybridization and macroarray

The molecular mechanisms underlying cell wall biosynthesis are poorly understood. In this study, microscopic analysis showed that protoplasts generated a new cell wall within 48 h after transfer to a wall-regeneration medium. To identify genes related to cell wall biosynthesis in cotton, suppression subtractive hybridization was used to visualize differential gene expression at seven time points within the first 48 h. In total, 412 differentially expressed sequence tags (ESTs; >3-fold) were identified, and 210 unigenes were sequenced successfully. As confirmed by reverse-transcription PCR (RT-PCR) and real-time quantitative reverse-transcription PCR (QRT-PCR) analysis, the selected genes displayed complex expression patterns during cell wall regeneration from protoplasts and included most previously published cell-wall-associated genes. ESTs similar to cell-wall-protein genes, such as proline-rich protein (PRPL), glycine-rich protein (GRP), extension (EPR1), fasciclin-like arabinogalactan protein (FLA2), and expensing-like protein (EXLA and EXLB), which might participate in primary cell wall or secondary cell wall construction and modification, were up-regulated during cell wall regeneration from protoplasts. Sucrose synthase, an important enzyme in the sugar signalling pathway, played important roles in cellulose biosynthesis. Our findings also highlighted the function of some transcription factors during cell wall regeneration from protoplasts, including the squamosa promoter binding protein-like 14 (SPL14), NAC, Gbiaa-re, MYB, WRKY, swellmap 1 (SMP1), RAD5, and zinc finger family protein, as well as the enrichment of Ca(2+)-calmodulin signal molecules. On the basis of the gene expression profiles, a model of cell wall regeneration from protoplasts derived from cotton suspension cultures is proposed.

Molecular cloning, differential expression, and functional characterization of a family of class I ubiquitin-conjugating enzyme (E2) genes in cotton (Gossypium)

Two cDNAs and their corresponding genes (GhUBC1 and GhUBC2) encoding ubiquitin-conjugating enzymes (E2s) have been cloned and characterized from allotetraploid cotton Gossypium hirsutum ((AD)(1) genome). Three additional E2 genes (GaUBC1, GtUBC2, and GrUBC2) have also been identified from diploid cottons Gossypium arboreum (A(2) genome), Gossypium thurberi (D(1) genome), and Gossypium raimondii (D(5) genome), respectively. The derived amino acid sequences of the five closely related cotton E2s are 77-79% identical to yeast ScUBC4 and ScUBC5. The GhUBC1/2 gene family is composed of two members, and genomic origin analysis indicates that GhUBC1 and 2 are individually present in the A and D subgenomes of G. hirsutum. The transcript levels of GhUBC1/2 increased significantly in leaves and flowers at senescence, suggesting that GhUBC1/2 may play a role in the degradation of target proteins that function in the delay of the senescence program. Correlated with high auxin content and auxin-associated effects, GhUBC1/2 are also highly expressed in the youngest leaves, the apical part of lateral roots, and elongating fibers. Genetic complementation experiments revealed that GhUBC1 and 2 can substitute for the function of ScUBC4 and 5 required for the selective degradation of abnormal and short-lived proteins in a yeast ubc4ubc5 double mutant.

Expressed sequence tag-based gene expression analysis under aluminum stress in rye

To understand the mechanisms responsible for aluminum (Al) toxicity and tolerance in plants, an expressed sequence tag (EST) approach was used to analyze changes in gene expression in roots of rye (Secale cereale L. cv Blanco) under Al stress. Two cDNA libraries were constructed (Al stressed and unstressed), and a total of 1,194 and 774 ESTs were generated, respectively. The putative proteins encoded by these cDNAs were uncovered by Basic Local Alignment Search Tool searches, and those ESTs showing similarity to proteins of known function were classified according to 13 different functional categories. A total of 671 known function genes were used to analyze the gene expression patterns in rye cv Blanco root tips under Al stress. Many of the previously identified Al-responsive genes showed expression differences between the libraries within 6 h of Al stress. Certain genes were selected, and their expression profiles were studied during a 48-h period using northern analysis. A total of 13 novel genes involved in cell elongation and division (tonoplast aquaporin and ubiquitin-like protein SMT3), oxidative stress (glutathione peroxidase, glucose-6-phosphate-dehydrogenase, and ascorbate peroxidase), iron metabolism (iron deficiency-specific proteins IDS3a, IDS3b, and IDS1; S-adenosyl methionine synthase; and methionine synthase), and other cellular mechanisms (pathogenesis-related protein 1.2, heme oxygenase, and epoxide hydrolase) were demonstrated to be regulated by Al stress. These genes provide new insights about the response of Al-tolerant plants to toxic levels of Al.

Molecular physiology of aquaporins in plants

In plants, membrane channels of the major intrinsic protein (MIP) super-family exhibit a high diversity with, for instance, 35 homologues in the model species Arabidopsis thaliana. As has been found in other organisms, plant MIPs function as membrane channels permeable to water (aquaporins) and in some cases to small nonelectrolytes. The aim of the present article is to integrate into plant physiology what has been recently learned about the molecular and functional properties of aquaporins in plants. Exhaustive compilation of data in the literature shows that the numerous aquaporin isoforms of plants have specific expression patterns throughout plant development and in response to environmental stimuli. The diversity of aquaporin homologues in plants can also be explained in part by their presence in multiple subcellular compartments. In recent years, there have been numerous reports that describe the activity of water channels in purified membrane vesicles, in isolated organelles or protoplasts, and in intact plant cells or even tissues. Altogether, these data suggest that the transport of water and solutes across plant membranes concerns many facets of plant physiology. Because of the high degree of compartmentation of plant cells, aquaporins may play a critical role in cell osmoregulation. Water uptake in roots represents a typical process in which to investigate the role of aquaporins in transcellular water transport, and the mechanisms and regulations involved are discussed.

TONOPLAST TRANSPORTERS: Organization and Function

Regulation of the contents and volume of vacuoles in plant cells depends on the coordinated activities of transporters and channels located in the tonoplast (vacuolar membrane). The three major components of the tonoplast are two proton pumps, the vacuolar H+-ATPase (V-ATPase) and H+-pyrophosphatase (V-PPase), and aquaporins. The tertiary structure of the V-ATPase complex and properties of its subunits have been characterized by biochemical and genetic techniques. These studies and a comparison with the F-type ATPase have enabled estimation of the dynamics of V-ATPase activity during catalysis. V-PPase, a simple proton pump, has been identified and cloned from various plant species and other organisms, such as algae and phototrophic bacteria, and functional motifs of the enzyme have been determined. Aquaporin, serving as the water channel, is the most abundant protein in the tonoplast in most plants. A common molecular architecture of aquaporins in mammals and plants has been determined by two-dimensional crystallographic analysis. Furthermore, recent molecular biological studies have revealed several other types of tonoplast transporters, such as the Ca2+-ATPase, Ca2+/H+ antiporter and Na+/H+ antiporter. Many other transporters and channels in the tonoplast remain to be identified; their activities have already been detected. This review presents an overview of the field and discusses recent findings on the tonoplast protein components that have been identified and their physiological consequences.

Expression of a lipid transfer protein gene family during cotton fibre development

There are six to eight lipid transfer protein-related genes in the allotetraploid Gossypium hirsutum genome, three of which, FSltp1, FSltp2 and FSltp3, were isolated in two genomic clones. All three genes potentially encode full-length lipid transfer proteins (LTPs), but sequence differences between these and the cotton fibre-specific cDNA previously reported, pFS6, suggest that none is likely to encode the fibre transcripts. Gene-specific RT-PCR experiments showed that expression patterns of the three new LTP genes are similar to each other, with transcripts present in all aerial cotton tissues tested, and only pFS6 transcripts are present in fibre cells at elevated levels. PCR analysis of cotton genomic DNA suggested that FSltp1 and FSltp3 are alloalleles, with FSltp3 being derived from the ancestral A genome, and FSltp1 from the D genome. The fibre-specific gene, yet to be isolated, and FSltp2 are also derived from the ancestral D genome of G. hirsutum.

Genes involved in osmoregulation during turgor-driven cell expansion of developing cotton fibers are differentially regulated

Cotton (Gossypium hirsutum L.) fibers are single-celled trichomes that synchronously undergo a phase of rapid cell expansion, then a phase including secondary cell wall deposition, and finally maturation. To determine if there is coordinated regulation of gene expression during fiber expansion, we analyzed the expression of components involved in turgor regulation and a cytoskeletal protein by measuring levels of mRNA and protein accumulation and enzyme activity. Fragments of the genes for the plasma membrane proton-translocating ATPase, vacuole-ATPase, proton-translocating pyrophosphatase (PPase), phosphoenolpyruvate carboxylase, major intrinsic protein, and alpha-tubulin were amplified by polymerase chain reaction and used as probes in ribonuclease protection assays of RNA from a fiber developmental series, revealing two discrete patterns of mRNA accumulation. Transcripts of all but the PPase accumulated to highest levels during the period of peak expansion (+12-15 d postanthesis [dpa]), then declined with the onset of secondary cell wall synthesis. The PPase was constitutively expressed through fiber development. Activity of the two proton-translocating-ATPases peaked at +15 dpa, whereas PPase activity peaked at +20 dpa, suggesting that all are involved in the process of cell expansion but with varying roles. Patterns of protein accumulation and enzyme activity for some of the proteins examined suggest posttranslational regulation through fiber development.