Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation

Promoter of a cotton fibre MYB gene functional in trichomes of Arabidopsis and glandular trichomes of tobacco

Cotton fibres are unicellular seed trichomes. Our previous study suggested that the cotton R2R3 MYB transcript factor GaMYB2 is a functional homologue of the Arabidopsis trichome regulator GLABRA1 (GL1). Here, the GaMYB2 promoter activity is reported in cotton (Gossypium hirsutum), tobacco (Nicotiana tabacum), and Arabidopsis plants. A 2062 bp promoter of GaMYB2 was isolated from G. arboreum, and fused to a beta-glucuronidase (GUS) reporter gene. In cotton, the GaMYB2 promoter exhibited activities in developing fibre cells and trichomes of other aerial organs, including leaves, stems and bracts. In Arabidopsis the promoter was specific to trichomes. Different from Arabidopsis and cotton that have unicellular non-glandular simple trichomes, tobacco plants contain more than one type of trichome, including multicellular simple and glandular secreting trichomes (GSTs). Interestingly, in tobacco plants the GaMYB2 promoter directed GUS expression exclusively in glandular cells of GSTs. A series of 5'-deletions revealed that a 360 bp fragment upstream to the translation initiation codon was sufficient to drive gene expression. A putative cis-element of the T/G-box was located at -233 to -214; a yeast one-hybrid assay showed that Arabidopsis bHLH protein GLABRA3 (GL3), also a trichome regulator, and GhDEL65, a GL3-like cotton protein, had high binding activities to the T/G-box motif. Overexpression of GL3 or GhDEL65 enhanced the GaMYB2 promoter activity in transgenic Arabidopsis plants. A comparison of GaMYB2 promoter specificities in trichomes of different plant species with different types of trichomes provides a tool for further dissection of plant trichome structure and development.

Cotton benzoquinone reductase: up-regulation during early fiber development and heterologous expression and characterization in Pichia pastoris

Benzoquinone reductase (BR; EC 1.6.5.7) is an enzyme which catalyzes the bivalent redox reactions of quinones without the production of free radical intermediates. Using 2D-PAGE comparisons, two proteins were found to be up-regulated in wild-type cotton ovules during the fiber initiation stage but not in the fiberless line SL 1-7-1. These proteins were excised from the gel, partially sequenced and identified to be BR isoforms. PCR was used to amplify both full length coding regions of 609bp and once cloned, the restriction enzyme HindIII was used to distinguish the clones encoding the BR1 (one site) and BR2 (two sites) isoforms. Both deduced protein sequences had 203 residues which differed at 14 residues. The molecular mass and pIs were similar between the measured protein (2D-PAGE) and the theoretical protein (deduced). Heterologous proteins BR1 and BR2 were produced for further study by ligating the BR1 and BR2 clones in frame into the alpha-factor secretion sequence in pPICZalphaA vector and expressed with Pichia pastoris. Both BR1 and BR2 were approximately 26.5kDa and did enzymatically reduce 2,6-dimethoxybenzoquinone similar to the fungal BR.

Isolation of an 1-aminocyclopropane-1-carboxylate oxidase gene from mulberry (Morus alba L.) and analysis of the function of this gene in plant development and stresses response

Mulberry (Morus alba) is an important crop tree involved in sericulture and pharmaceuticals. To further understand the development and the environmental adaptability mechanism of mulberry, a cDNA of the gene MaACO1 encoding 1-aminocyclopropane-1-carboxylate oxidase was isolated from mulberry. This was used to investigate stress-responsive expression in mulberry. Developmental expression of ACC oxidase in mulberry leaves and spatial expression in mulberry flowers were also investigated. Damage and low-temperature treatment promoted the expression of MaACO1 in mulberry. In leaves, expression of the MaACO1 gene increased in cotyledons and the lowest leaves with leaf development, but showed reduced levels in emerging leaves. In flowers, the pollinated stigma showed the highest expression level, followed by the unpollinated stigma, ovary, and immature flowers. These results suggest that high MaACO1 expression may be predominantly associated with tissue aging or senescence in mulberry.

Complementary analysis of microRNA and mRNA expression during phorbol 12-myristate 13-acetate (TPA)-induced differentiation of HL-60 cells

MicroRNAs (miRNAs) and mRNAs constitute an important part of gene regulatory networks, influencing diverse biological phenomena. To discover novel regulatory pathways during myeloid differentiation, we performed miRNA as well as mRNA expression profiling of in vitro-differentiating HL-60 cells treated with 12-O-tetradecanoylphorbol-13-acetate (TPA). The main findings were up-regulation of miR-146a/b, miR-21, miR-221, miR-222, miR-155, miR-26a and down-regulation of miR-199a*, miR-181c, miR-142-3p, miR-92. After integrating the miRNA and mRNA expression data into a Transcriptome Interaction Database by Molecule Annotation System (MAS) software, a number of differently expressed mRNAs were revealed as potential targets of these miRNAs.

The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism

A central question in evolutionary biology concerns the developmental processes by which new phenotypes arise. An exceptional example of evolutionary innovation is the single-celled seed trichome in Gossypium (“cotton fiber”). We have used fiber development in Gossypium as a system to understand how morphology can rapidly evolve. Fiber has undergone considerable morphological changes between the short, tightly adherent fibers of G. longicalyx and the derived long, spinnable fibers of its closest relative, G. herbaceum, which facilitated cotton domestication. We conducted comparative gene expression profiling across a developmental time-course of fibers from G. longicalyx and G. herbaceum using microarrays with ∼22,000 genes. Expression changes between stages were temporally protracted in G. herbaceum relative to G. longicalyx, reflecting a prolongation of the ancestral developmental program. Gene expression and GO analyses showed that many genes involved with stress responses were upregulated early in G. longicalyx fiber development. Several candidate genes upregulated in G. herbaceum have been implicated in regulating redox levels and cell elongation processes. Three genes previously shown to modulate hydrogen peroxide levels were consistently expressed in domesticated and wild cotton species with long fibers, but expression was not detected by quantitative real time-PCR in wild species with short fibers. Hydrogen peroxide is important for cell elongation, but at high concentrations it becomes toxic, activating stress processes that may lead to early onset of secondary cell wall synthesis and the end of cell elongation. These observations suggest that the evolution of long spinnable fibers in cotton was accompanied by novel expression of genes assisting in the regulation of reactive oxygen species levels. Our data suggest a model for the evolutionary origin of a novel morphology through differential gene regulation causing prolongation of an ancestral developmental program.

Human domestication of plants has resulted in dramatic changes in mature structures, often over relatively short time frames. The availability of both wild and domesticated forms of domesticated species provides an opportunity to understand the genetic and developmental steps involved in domestication, thereby providing a model of how the evolutionary process shapes phenotypes. Here we use a comparative approach to explore the evolutionary innovations leading to modern cotton fiber, which represent some of the more remarkable single-celled hairs in the plant kingdom. We used microarrays assaying approximately 22,000 genes to elucidate expression differences across a developmental time-course of fibers from G. longicalyx, representing wild cotton, and G. herbaceum, a cultivated species. Expression changes between stages were temporally elongated in G. herbaceum relative to G. longicalyx, showing that domestication involved a prolongation of an ancestral developmental program. These data and quantitative real time-PCR experiments showed that long, spinnable fiber is associated with a number of genes implicated in regulating redox levels and cell elongation processes, suggesting that the evolution of spinnable cotton fiber entailed a novel metabolic regulatory program

Gene expression and metabolism in tomato fruit surface tissues

The cuticle, covering the surface of all primary plant organs, plays important roles in plant development and protection against the biotic and abiotic environment. In contrast to vegetative organs, very little molecular information has been obtained regarding the surfaces of reproductive organs such as fleshy fruit. To broaden our knowledge related to fruit surface, comparative transcriptome and metabolome analyses were carried out on peel and flesh tissues during tomato (Solanum lycopersicum) fruit development. Out of 574 peel-associated transcripts, 17% were classified as putatively belonging to metabolic pathways generating cuticular components, such as wax, cutin, and phenylpropanoids. Orthologs of the Arabidopsis (Arabidopsis thaliana) SHINE2 and MIXTA-LIKE regulatory factors, activating cutin and wax biosynthesis and fruit epidermal cell differentiation, respectively, were also predominantly expressed in the peel. Ultra-performance liquid chromatography coupled to a quadrupole time-of-flight mass spectrometer and gas chromatography-mass spectrometry using a flame ionization detector identified 100 metabolites that are enriched in the peel tissue during development. These included flavonoids, glycoalkaloids, and amyrin-type pentacyclic triterpenoids as well as polar metabolites associated with cuticle and cell wall metabolism and protection against photooxidative stress. Combined results at both transcript and metabolite levels revealed that the formation of cuticular lipids precedes phenylpropanoid and flavonoid biosynthesis. Expression patterns of reporter genes driven by the upstream region of the wax-associated SlCER6 gene indicated progressive activity of this wax biosynthetic gene in both fruit exocarp and endocarp. Peel-associated genes identified in our study, together with comparative analysis of genes enriched in surface tissues of various other plant species, establish a springboard for future investigations of plant surface biology.

Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant

Polyploidy is an important driver of eukaryotic evolution, evident in many animals, fungi, and plants. One consequence of polyploidy is subfunctionalization, in which the ancestral expression profile becomes partitioned among duplicated genes (termed homoeologs). Subfunctionalization appears to be a common phenomenon insofar as it has been studied, at the scale of organs. Here, we use a high-resolution methodology to investigate the expression of thousands of pairs of homoeologs during the development of a single plant cell, using as a model the seed trichomes ("cotton fiber") of allopolyploid (containing "A" and "D" genomes) cotton (Gossypium). We demonstrate that approximately 30% of the homoeologs are significantly A- or D-biased at each of three time points studied during fiber development. Genes differentially biased toward the A or D genome belong to different biological processes, illustrating the functional partitioning of genomic contributions during cellular development. Interestingly, expression of the biased genes was shifted strongly toward the agronomically inferior D genome. Analyses of homoeologous gene expression during development of this cell showed that one-fifth of the genes exhibit changes in A/D ratios, indicating that significant alteration in duplicated gene expression is fairly frequent even at the level of development and maturation of a single cell. Comparing changes in homoeolog expression in cultivated versus wild cotton showed that most homoeolog expression bias reflects polyploidy rather than domestication. Evidence suggests, however, that domestication may increase expression bias in fibers toward the D genome, potentially implicating D-genome recruitment under human selection during domestication.

The ascorbate peroxidase regulated by H(2)O(2) and ethylene is involved in cotton fiber cell elongation by modulating ROS homeostasis

Ascorbate peroxidase (APX) is a reactive oxygen species (ROSs) scavenging enzyme involved in regulation of intracellular ROS levels by reduction of H(2)O(2) to water using ascorbate as an electron donor. In New Phytologist 2007; 175:462-71, we identified a cotton cytosolic APX1 (GhAPX1) that was significantly accumulated during the fast fiber-cell elongation period, through a proteomics approach. Both the transcript levels of GhAPX1 and the total APX activity were highly induced in response to in vitro applied H(2)O(2) or ethylene. Further analysis showed that ethylene promoted H(2)O(2) production 1 day after it was included in the culture medium, suggesting that H(2)O(2) induced cell elongation processes may be placed downstream of the ethylene signal transduction pathway. In this addendum, quantitative real-time RT-PCR showed that only cytosolic APX1, not other cotton APX genes including a second cytosolic APX2, a glyoxysomal and a stromal APXs, was up-regulated during fiber cell elongating. Exogenous H(2)O(2) was found to induce ethylene production if wild-type cotton ovules were cultured for a longer period of time, implying that there was a feedback regulatory mechanism from H(2)O(2) to ethylene biosynthesis in modulating cotton fiber development.

Genome-wide analysis of gene expression profiles during the kernel development of maize (Zea mays L.)

Maize kernel is an important source of food, feed, and industrial raw materials. The elucidation of the molecular mechanisms of maize kernel development will be helpful for the manipulation of maize improvements. A microarray with approximately 58,000 probes was used to study dynamic gene expression during kernel development from fertilization to physiological maturity. By comparing six consecutive time points, 3445 differentially expressed genes were identified. These genes were then grouped into 10 clusters showing specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes elucidate the regulation mechanism underlying the important developmental processes cell division and kernel filling. The differential expression of genes involved in plant hormone signaling pathways suggested that phytohormone might play a critical role in the kernel developmental process. Moreover, regulation of some transcription factors and protein kinases might be involved in the whole developmental process.

Molecular cloning, expression profiling, and yeast complementation of 19 beta-tubulin cDNAs from developing cotton ovules

Microtubules are a major structural component of the cytoskeleton and participate in cell division, intracellular transport, and cell morphogenesis. In the present study, 795 cotton tubulin expressed sequence tags were analysed and 19 beta-tubulin genes (TUB) cloned from a cotton cDNA library. Among the group, 12 cotton TUBs (GhTUBs) are reported for the first time here. Transcription profiling revealed that nine GhTUBs were highly expressed in elongating fibre cells as compared with fuzzless-lintless mutant ovules. Treating cultured wild-type cotton ovules with exogenous phytohormones showed that individual genes can be induced by different agents. Gibberellin induced expression of GhTUB1 and GhTUB3, ethylene induced expression of GhTUB5, GhTUB9, and GhTUB12, brassinosteroids induced expression of GhTUB1, GhTUB3, GhTUB9, and GhTUB12, and lignoceric acid induced expression of GhTUB1, GhTUB3, and GhTUB12. When GhTUBs were transformed into the Saccharomyces cerevisiae inviable mutant, tub2, which is deficient in beta-tubulin, one ovule-specific and eight of nine fibre-preferential GhTUBs rescued this lethality. This study suggests that the proteins encoded by cotton GhTUBs are involved during cotton fibre development.

A majority of cotton genes are expressed in single-celled fiber

Multicellular eukaryotes contain a diversity of cell types, presumably differing from one another in the suite of genes expressed during development. At present, little is known about the proportion of the genome transcribed in most cell types, nor the degree to which global patterns of expression change during cellular differentiation. To address these questions in a model plant system, we studied the unique and highly exaggerated single-celled, epidermal seed trichomes ("cotton") of cultivated cotton (Gossypium hirsutum). By taking advantage of advances in expression profiling and microarray technology, we evaluated the transcriptome of cotton fibers across a developmental time-course, from a few days post-anthesis through primary and secondary wall synthesis stages. Comparisons of gene expression in populations of developing cotton fiber cells to genetically complex reference samples derived from 6 different cotton organs demonstrated that a remarkably high proportion of the cotton genome is transcribed, with 75-94% of the total genome transcribed at each stage. Compared to the reference samples, more than half of all genes were up-regulated during at least one stage of fiber development. These genes were clustered into seven groups of expression profiles that provided new insight into biological processes governing fiber development. Genes implicated in vesicle coating and trafficking were found to be overexpressed throughout all stages of fiber development studied, indicating their important role in maintaining rapid growth of this unique plant cell.

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.

Expression and functional analysis of ZmDWF4, an ortholog of Arabidopsis DWF4 from maize (Zea mays L.)

DWF4 encodes a rate-limiting mono-oxygenase that mediates 22alpha-hydroxylation reactions in the BR biosynthetic pathway and it is the target gene in the BR feedback loop. Knockout of DWF4 results in a dwarfed phenotype and other severe defects in Arabidopsis. Here we report on the isolation of the ZmDWF4 gene in maize. Sequence analysis revealed that the open reading frame of ZmDWF4 was 1,518 bp, which encodes a protein composed of 505 amino acid residues with a calculated molecular mass of 57.6 kD and a predicated isoelectric point (pI) of 9.54. Phylogenetic analysis indicated that ZmDWF4 was very close to the Arabidopsis DWF4. In young maize seedlings, the expression of ZmDWF4 in shoots was much higher than that in roots. The highest expression of ZmDWF4 was observed in husk leaves and the lowest in silks during flowering stage. The expression of ZmDWF4 in maize was significantly down regulated by exogenous brassinolide. A heterogeneous complementary experiment demonstrated that the defects of three Arabidopsis DWF4 mutants could be rescued by constitutive expression of ZmDWF4, with leaf expandability, inflorescence stem heights and fertile capabilities all restored to normal levels. Increases in seed and branch number as well as the height of florescence stem were observed in the over-expressed transformants. These findings suggest that ZmDWF4 may be an ortholog gene of Arabidopsis DWF4 and responsible for BR biosynthesis in maize.

Gene expression changes and early events in cotton fibre development

BACKGROUND

Cotton is the dominant source of natural textile fibre and a significant oil crop. Cotton fibres, produced by certain species in the genus Gossypium, are seed trichomes derived from individual cells of the epidermal layer of the seed coat. Cotton fibre development is delineated into four distinct and overlapping developmental stages: fibre initiation, elongation, secondary wall biosynthesis and maturation.

SCOPE

Recent advances in gene expression studies are beginning to provide new insights into a better understanding of early events in cotton fibre development. Fibre cell development is a complex process involving many pathways, including various signal transduction and transcriptional regulation components. Several analyses using expressed sequence tags and microarray have identified transcripts that preferentially accumulate during fibre development. These studies, as well as complementation and overexpression experiments using cotton genes in arabidopsis and tobacco, indicate some similar molecular events between trichome development from the leaf epidermis and fibre development from the ovule epidermis. Specifically, MYB transcription factors regulate leaf trichome development in arabidopsis and may regulate seed trichome development in cotton. In addition, transcript profiling and ovule culture experiments both indicate that several phytohormones and other signalling pathways mediate cotton fibre development. Auxin and gibberellins promote early stages of fibre initiation; ethylene- and brassinosteroid-related genes are up-regulated during the fibre elongation phase; and genes associated with calmodulin and calmodulin-binding proteins are up-regulated in fibre initials. Additional genomic data, mutant and functional analyses, and genome mapping studies promise to reveal the critical factors mediating cotton fibre cell development.

Genes and (common) pathways underlying drug addiction

Drug addiction is a serious worldwide problem with strong genetic and environmental influences. Different technologies have revealed a variety of genes and pathways underlying addiction; however, each individual technology can be biased and incomplete. We integrated 2,343 items of evidence from peer-reviewed publications between 1976 and 2006 linking genes and chromosome regions to addiction by single-gene strategies, microrray, proteomics, or genetic studies. We identified 1,500 human addiction-related genes and developed KARG (http://karg.cbi.pku.edu.cn), the first molecular database for addiction-related genes with extensive annotations and a friendly Web interface. We then performed a meta-analysis of 396 genes that were supported by two or more independent items of evidence to identify 18 molecular pathways that were statistically significantly enriched, covering both upstream signaling events and downstream effects. Five molecular pathways significantly enriched for all four different types of addictive drugs were identified as common pathways which may underlie shared rewarding and addictive actions, including two new ones, GnRH signaling pathway and gap junction. We connected the common pathways into a hypothetical common molecular network for addiction. We observed that fast and slow positive feedback loops were interlinked through CAMKII, which may provide clues to explain some of the irreversible features of addiction.

Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis

Fatty acids are essential for membrane biosynthesis in all organisms and serve as signaling molecules in many animals. Here, we found that saturated very-long-chain fatty acids (VLCFAs; C20:0 to C30:0) exogenously applied in ovule culture medium significantly promoted cotton (Gossypium hirsutum) fiber cell elongation, whereas acetochlor (2-chloro-N-[ethoxymethyl]-N-[2-ethyl-6-methyl-phenyl]-acetamide; ACE), which inhibits VLCFA biosynthesis, abolished fiber growth. This inhibition was overcome by lignoceric acid (C24:0). Elongating fibers contained significantly higher amounts of VLCFAs than those of wild-type or fuzzless-lintless mutant ovules. Ethylene nullified inhibition by ACE, whereas C24:0 was inactive in the presence of the ethylene biosynthesis inhibitor (l-[2-aminoethoxyvinyl]-glycine), indicating that VLCFAs may act upstream of ethylene. C24:0 induced a rapid and significant increase in ACO (for 1-aminocyclopropane-1-carboxylic acid oxidase) transcript levels that resulted in substantial ethylene production. C24:0 also promoted Ser palmitoyltransferase expression at a later stage, resulting in increased sphingolipid biosynthesis. Application of C24:0 not only stimulated Arabidopsis thaliana root cell growth but also complemented the cut1 phenotype. Transgenic expression of Gh KCS13/CER6, encoding the cotton 3-ketoacyl-CoA synthase, in the cut1 background produced similar results. Promotion of Arabidopsis stem elongation was accompanied by increased ACO transcript levels. Thus, VLCFAs may be involved in maximizing the extensibility of cotton fibers and multiple Arabidopsis cell types, possibly by activating ethylene biosynthesis.

Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules

Cotton (Gossypium hirsutum L.) fibre initial cells undergo a rapid cellular re-programming around anthesis to form the long cellulose fibres prized for textile manufacture. On the day of anthesis the cotton fibre initial cells balloon out from the ovule surface and so are clearly distinguished from adjacent epidermal pavement cells. To enhance our understanding of the molecular processes that determine which cells become fibres and why adjacent epidermal cells remain in a different developmental state we studied the expression profiles of the two respective cell types. Using laser-capture microdissection, coupled with an in vitro RNA amplification system, we used cDNA microarray slides to profile the gene expression in expanding fibre initials compared to the non-expanding epidermal cells at an early stage just after the fibre initials are discernable. Except for a few regulatory genes, the genes that are up-regulated in the cotton fibre initials relative to epidermal cells predominantly encode proteins involved in generating the components for the extra cell membrane and primary cell wall needed for the rapid cell expansion of the initials. This includes synthesis of enzymes and cell wall proteins, carbohydrates, and lipids. An analysis of single channel fluorescence levels confirmed that these classes of genes were also the most highly expressed genes in fibre initials. Genes involved in DNA metabolism were also well represented in the expanding fibre cell, consistent with the limited endoreduplication we previously reported to occur in fibre initial cells.

Evidence for alternative splicing of MADS-box transcripts in developing cotton fibre cells

The MADS-box family of genes encodes transcription factors that have widely ranging roles in diverse aspects of plant development. In this study, four cotton MADS-box cDNA clones of the type II (MIKC) class were isolated, with phylogenetic analysis indicating that the cotton sequences are of the AGAMOUS subclass. The corresponding transcripts were detected in developing cotton fibre cells as well as in whole ovule and flower tissue, with differential expression in stems, leaves and roots. Reverse transcription PCR showed extensive alternative splicing in one of the reactions, and 11 mRNAs of different intron/exon composition and length were characterised. Sequence differences between the transcripts indicated that they could not be derived from the same pre-mRNA and that the sequenced transcript pool was derived from two distinct MADS-box genes. Several of the alternatively spliced transcripts potentially encoded proteins with altered K-domains and/or C-terminal regions and the variant proteins may have altered cellular roles. This work is the first that describes MADS-box gene expression in elongating cotton fibres and adds to a growing body of evidence for the prevalence of alternative splicing in the expression of MADS-box and other genes.

Systematic studies of 12S seed storage protein accumulation and degradation patterns during Arabidopsis seed maturation and early seedling germination stages

Seed storage proteins (SSPs) are important for seed germination and early seedling growth. We studied the accumulation and degradation profiles of four major Arabidopsis 12S SSPs using a 2-DE scheme combined with mass spectrometric methods. On the 2-DE map of 23 dpa (days post anthesis) siliques, 48 protein spots were identified as putative full-length or partial alpha, beta subunits. Only 9 of them were found in 12 dpa siliques with none in younger than 8 dpa siliques, indicating that the accumulation of 12S SSPs started after the completion of cell elongation processes both in siliques and in developing seeds. The length and strength of transcription activity for each gene determined the final contents of respective SSP. At the beginning of imbibition, 68 SSP spots were identified while only 2 spots were found at the end of the 4 d germination period, with alpha subunits degraded more rapidly than the beta subunits. The CRC alpha subunit was found to degrade from its C-terminus with conserved sequence motifs. Our data provide an important basis for understanding the nutritional value of developing plant seeds and may serve as a useful platform for other species.

Genes expression analyses of sea-island cotton (Gossypium barbadense L.) during fiber development

Sea-island cotton (Gossypium barbadense L.) is one of the most valuable cotton species due to its silkiness, luster, long staples, and high strength, but its fiber development mechanism has not been surveyed comprehensively. We constructed a normalized fiber cDNA library (from -2 to 25 dpa) of G. barbadense cv. Pima 3-79 (the genetic standard line) by saturation hybridization with genomic DNA. We screened Pima 3-79 fiber RNA from five developmental stages using a cDNA array including 9,126 plasmids randomly selected from the library, and we selected and sequenced 929 clones that had different signal intensities between any two stages. The 887 high-quality expressed sequence tags obtained were assembled into 645 consensus sequences (582 singletons and 63 contigs), of which 455 were assigned to functional categories using gene ontology. Almost 50% of binned genes belonged to metabolism functional categories. Based on subarray analysis of the 887 high-quality expressed sequence tags with 0-, 5-, 10-, 15-, and 20-dpa RNA of Pima 3-79 fibers and a mixture of RNA of nonfiber tissues, seven types of expression profiles were elucidated. Furthermore our results showed that phytohormones may play an important role in the fiber development.

GhDET2, a steroid 5alpha-reductase, plays an important role in cotton fiber cell initiation and elongation

Cotton (Gossypium hirsutum L.) fibers, one of the most important natural raw materials for textile industry, are highly elongated trichomes from epidermal cells of cotton ovules. DET2, an Arabidopsis steroid 5d-reductase, is considered to catalyze a major rate-limiting in brassinosteroid (BR) biosynthesis. To understand the role of BRs in cotton fiber development, GhDET2, which putatively encodes a steroid 5alpha-reductase by sequence comparison, was cloned from developing fiber cells. In vitro assessment of GhDET2 protein activity confirmed that GhDET2 encodes a functional steroid 5alpha-redutase. High levels of GhDET2 transcript were detected during the fiber initiation stage and the fiber rapid elongation stage. Antisense-mediated suppression of GhDET2 inhibited both fiber initiation and fiber elongation. Similarly, treating cultured ovules with finasteride, a steroid 5alpha-reductase inhibitor, reduced fiber elongation. Inhibition of fiber cell elongation by expression of antisense GhDET2 or the finasteride treatment could be reversed by epibrassinolide, a biologically active BR. Furthermore, seed coat-specific expression of GhDET2 increased fiber number and length. Therefore, GhDET2 and BRs play a crucial role in the initiation and elongation of cotton fiber cells, suggesting that modulation of BR biosynthesis factors may improve fiber quality or yield.

Combinative effects of a bacterial type-III effector and a biocontrol bacterium on rice growth and disease resistance

Expression of HpaG(Xoo), a bacterial type-III effector, in transgenic plants induces disease resistance. Resistance also can be elicited by biocontrol bacteria. In both cases, plant growth is often promoted. Here we address whether biocontrol bacteria and HpaG(Xoo) can act together to provide better results in crop improvement. We studied effects of Pseudomonas cepacia on the rice variety R109 and the hpaG(Xoo)-expressing rice line HER1. Compared to R109, HER1 showed increased growth, grain yield, and defense responses toward diseases and salinity stress. Colonization of roots by P. cepacia caused 20% and 13% increase, in contrast to controls, in root growth of R109 and HER1. Growth of leaves and stems also increased in R109 but that of HER1 was inhibited. When P. cepacia colonization was subsequent to plant inoculation with Rhizoctonia solani, a pathogen that causes sheath blight, the disease was less severe than controls in both R109 and HER1; HER1, nevertheless, was more resistant, suggesting that P. cepacia and HpaG(Xoo) cooperate in inducing disease resistance. Several genes that critically regulate growth and defense behaved differentially in HER1 and R109 while responding to P. cepacia. In R109 leaves, the OsARF1 gene, which regulates plant growth, was expressed in consistence with growth promotion by P. cepacia. Inversely, OsARF1 expression was coincident with inhibition in growth of HER1 leaves. In both plants, the expression of OsEXP1, which encodes an expansin protein involved in plant growth,was concomitant with growth promotion in leaves instead of roots,in response to P. cepacia . We also studied OsMAPK, a gene that encodes a mitogen-activated protein kinase and controls defense responses toward salinity and infection by pathogens in rice. In response to P. cepacia, an early expression of OsMAPK was coincident with R109 resistance to the disease, while HER1 expressed the gene similarly whether P. cepacia was present or not. Evidently, P. cepacia and G(Xoo)-gene mediated resistance may act differently in rice growth and resistance. Whereas combinative effects of P. cepacia and HpaG(Xoo) in disease resistance have a great potential in agricultural use, it is interesting to study mechanisms that underlie interactions involving biocontrol bacteria, type-III effectors and pathogens.

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.

Heterotrimeric G protein alpha subunit is involved in rice brassinosteroid response

Heterotrimeric G proteins are known to function as messengers in numerous signal transduction pathways. The null mutation of RGA (rice heterotrimeric G protein alpha subunit), which encodes the alpha subunit of heterotrimeric G protein in rice, causes severe dwarfism and reduced responsiveness to gibberellic acid in rice. However, less is known about heterotrimeric G protein in brassinosteroid (BR) signaling, one of the well-understood phytohormone pathways. In the present study, we used root elongation inhibition assay, lamina inclination assay and coleoptile elongation analysis to demonstrated reduced sensitivity of d1 mutant plants (caused by the null mutation of RGA) to 24-epibrassinolide (24-epiBL), which belongs to brassinosteroids and plays a wide variety of roles in plant growth and development. Moreover, RGA transcript level was decreased in 24-epiBL-treated seedlings in a dose-dependent manner. Our results show that RGA is involved in rice brassinosteroid response, which may be beneficial to elucidate the molecular mechanisms of G protein signaling and provide a novel perspective to understand BR signaling in higher plants.

Identification of proteins expressed at extremely low level in Arabidopsis leaves

2-DE related techniques have been broadly used for protein separation and identification in recent years. However, many important cellular components often escape detection by 2-DE due to its inherent low resolution. Here we use a polyU-affinity column to enrich proteins with nucleotide-binding motifs. As a result, 26 enriched protein spots, including three new Arabidopsis RNA-binding proteins cp31A, cp31B, and CSP41, are identified by MALDI-TOF-MS. In the sum, 15 protein spots encoded by 12 individual genes are observed on the 2-DE only after binding to the polyU-affinity column. Two of these genes are expressed at lower than 0.1% the level of TUB4 that were considered mainly as non-expressed genes in several ATH1 microarray analysis of Arabidopsis leaf samples. Our results suggest that polyU or similar media may be combined with 2-DE techniques to identify cellular proteins with extremely low transcription levels to fulfill specific research needs.

Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis

Cotton fibers elongate rapidly after initiation of elongation, eventually leading to the deposit of a large amount of cellulose. To reveal features of cotton fiber cells at the fast elongation and the secondary cell wall synthesis stages, we compared the respective transcriptomes and metabolite profiles. Comparative analysis of transcriptomes by cDNA array identified 633 genes that were differentially regulated during fiber development. Principal component analysis (PCA) using expressed genes as variables divided fiber samples into four groups, which are diagnostic of developmental stages. Similar grouping results are also found if we use non-polar or polar metabolites as variables for PCA of developing fibers. Auxin signaling, wall-loosening and lipid metabolism are highly active during fiber elongation, whereas cellulose biosynthesis is predominant and many other metabolic pathways are downregulated at the secondary cell wall synthesis stage. Transcript and metabolite profiles and enzyme activities are consistent in demonstrating a specialization process of cotton fiber development toward cellulose synthesis. These data demonstrate that cotton fiber cell at a certain stage has its own unique feature, and developmental stages of cotton fiber cells can be distinguished by their transcript and metabolite profiles. During the secondary cell wall synthesis stage, metabolic pathways are streamed into cellulose synthesis.

Microarray expression analysis of the early N-methy-N-nitrosourea-induced retinal degeneration in rat

The study was undertaken to investigate the gene expressions in N-methy-N-nitrosourea (MNU)-induced rat retinal degeneration (RD) by performing microarray analysis of retinal RNA at 12h. All rats were randomly divided into a normal group, a 12h model group and a 24h model group. Rats in the two model groups received a single intraperitoneal injection of 40 mg/kg body weight of MNU, while those in the normal group were injected with equivalent volume of physiological saline. After 12h and 24h of the injection, rats in each respective group were sacrificed, respectively. One eye of each animal was used for hematoxylin and erosin (H&E) staining, and fresh retinas of the other eye of each animal in the both normal group and 12h model group were used to extract total RNA, which was analyzed by microarray and real time RT-PCR. Retinal histological alteration was found in the 24h model group. There were 75 genes differently expressed (ratio > or =2.0), including 64 genes up-regulated and 11 genes down-regulated. Seven genes were assayed by real time RT-PCR and demonstrated the same alteration tendency as in microarray analysis. These genes that expressed differently mainly involved signal transduction, development, immune and defense, and apoptosis, etc. The major pathways were MAP-kinase signaling pathways, Toll-like receptor signaling pathway and apoptosis pathway involved. The results suggest that there are significant changes of gene expression in the early stage of MNU-induced RD. These microarray results provide clues to understand the molecular pathways underlying photoreceptor degeneration and indicate directions for future studies.

A cotton ascorbate peroxidase is involved in hydrogen peroxide homeostasis during fibre cell development

Reactive oxygen species (ROS) play important roles in multiple physiological processes such as cellular signalling and stress responses, whereas, the hydrogen peroxide (H(2)O(2)) scavenging enzyme ascorbate peroxidase (APX) participates in the regulation of intracellular ROS levels. Here, a cotton (Gossypium hirsutum) cytosolic APX1 (GhAPX1) was identified to be highly accumulated during cotton fibre elongation by proteomic analysis. GhAPX1 cDNA contained an open reading frame of 753-bp encoding a protein of 250 amino acid residues. When GhAPX1 was expressed in Escherichia coli, the purified GhAPX1 was a dimer consisting of two identical subunits with a molecular mass of 28 kDa. GhAPX1 showed the highest substrate specificity for ascorbate. Quantitative real-time polymerase chain reaction (PCR) analyses showed that GhAPX1 was highly expressed in wild-type 5-d postanthesis fibres with much lower transcript levels in the fuzzless-lintless mutant ovules. Treating in vitro cultured wild-type cotton ovules with exogenous H(2)O(2) or ethylene induced the expression of GhAPX1 and hence increased total APX activity proportionally, followed by extended fibre cell elongation. These data suggest that GhAPX1 expression is upregulated in response to an increase in cellular H(2)O(2) and ethylene. GhAPX1 encodes a functional enzyme that is involved in hydrogen peroxide homeostasis during cotton fibre development.

Molecular characterization and expression analysis of nine cotton GhEF1A genes encoding translation elongation factor 1A

The translation elongation factor 1A, eEF1A, plays an important role in protein synthesis, catalyzing the binding of aminoacyl-tRNA to the A-site of the ribosome by a GTP-dependent mechanism. To investigate the role of eEF1A for protein synthesis in cotton fiber development, nine different cDNA clones encoding eukaryotic translation elongation factor 1A were isolated from cotton (Gossypium hirsutum) fiber cDNA libraries. The isolated genes (cDNAs) were designated cotton elongation factor 1A gene GhEF1A1, GhEF1A2, GhEF1A3, GhEF1A4, GhEF1A5, GhEF1A6, GhEF1A7, GhEF1A8, GhEF1A9, respectively. They share high sequence homology at nucleotide level (71-99% identity) in the coding region and at amino acid level (96-99% identity) among each other. Phylogenetic analysis demonstrated that the nine GhEF1A genes can be divided into 5-6 subfamilies, indicating the divergence occurred in structures of the genes as well as the deduced proteins during evolution. Real-time quantitative RT-PCR analysis revealed that GhEF1A genes are differentially expressed in different tissues/organs. Of the nine GhEF1A genes, five are expressed at relatively high levels in young fibers. Further analysis indicated that expressions of the GhEF1As in fiber are highly developmental-regulated, suggesting that protein biosynthesis is very active at the early fiber elongation.

Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton

Gene expression during the early stages of fiber cell development and in allopolyploid crops is poorly understood. Here we report computational and expression analyses of 32 789 high-quality ESTs derived from Gossypium hirsutum L. Texas Marker-1 (TM-1) immature ovules (GH_TMO). The ESTs were assembled into 8540 unique sequences including 4036 tentative consensus sequences (TCs) and 4504 singletons, representing approximately 15% of the unique sequences in the cotton EST collection. Compared with approximately 178 000 existing ESTs derived from elongating fibers and non-fiber tissues, GH_TMO ESTs showed a significant increase in the percentage of genes encoding putative transcription factors such as MYB and WRKY and genes encoding predicted proteins involved in auxin, brassinosteroid (BR), gibberellic acid (GA), abscisic acid (ABA) and ethylene signaling pathways. Cotton homologs related to MIXTA, MYB5, GL2 and eight genes in the auxin, BR, GA and ethylene pathways were induced during fiber cell initiation but repressed in the naked seed mutant (N1N1) that is impaired in fiber formation. The data agree with the known roles of MYB and WRKY transcription factors in Arabidopsis leaf trichome development and the well-documented phytohormonal effects on fiber cell development in immature cotton ovules cultured in vitro. Moreover, the phytohormonal pathway-related genes were induced prior to the activation of MYB-like genes, suggesting an important role of phytohormones in cell fate determination. Significantly, AA sub-genome ESTs of all functional classifications including cell-cycle control and transcription factor activity were selectively enriched in G. hirsutum L., an allotetraploid derived from polyploidization between AA and DD genome species, a result consistent with the production of long lint fibers in AA genome species. These results suggest general roles for genome-specific, phytohormonal and transcriptional gene regulation during the early stages of fiber cell development in cotton allopolyploids.

KOBAS server: a web-based platform for automated annotation and pathway identification

There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experiments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously demonstrated the KEGG Orthology (KO) as an effective alternative controlled vocabulary and developed a standalone KO-Based Annotation System (KOBAS). Here we report a KOBAS server with a friendly web-based user interface and enhanced functionalities. The server can support input by nucleotide or amino acid sequences or by sequence identifiers in popular databases and can annotate the input with KO terms and KEGG pathways by BLAST sequence similarity or directly ID mapping to genes with known annotations. The server can then identify both frequent and statistically enriched pathways, offering the choices of four statistical tests and the option of multiple testing correction. The server also has a ‘User Space’ in which frequent users may store and manage their data and results online. We demonstrate the usability of the server by finding statistically enriched pathways in a set of upregulated genes in Alzheimer's Disease (AD) hippocampal cornu ammonis 1 (CA1). KOBAS server can be accessed at .