Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis

Enrichment of a set of microRNAs during the cotton fiber development

Background

Cotton (Gossypium hirsutum) is one of the most important economic crops and provides excellent fibers for textile manufacture. In addition to its industrial and agricultural importance, the fiber cell (plant trichome) also is a biological model system for exploring gene expression and regulation. Small RNAs regulate many aspects of plant growth and development. However, whether small RNAs are involved in regulation of fiber cell development is unknown.

Results

We adopted a deep sequencing approach developed by Solexa (Illumina Inc.) to investigate global expression and complexity of small RNAs during cotton fiber initiation and development. We constructed two small RNA libraries prepared from wild type (WT) and fuzz/lintless (fl Mutant in the WT background) cotton ovules, respectively. Each library was sequenced individually and generated more than 6-7 million short sequences, resulting in a total of over 13 million sequence reads. At least 22 conserved candidate miRNA families including 111 members were identified. Seven families make up the vast majority of expressed miRNAs in developing cotton ovules. In total 120 unique target genes were predicted for most of conserved miRNAs. In addition, we identified 2 cell-type-specific novel miRNA candidates in cotton ovules. Our study has demonstrated significant differences in expression abundance of miRNAs between the wild-type and mutant, and suggests that these differentially expressed miRNAs potentially regulate transcripts distinctly involved in cotton fiber development.

Conclusion

The present study is the first to deep sequence the small RNA population of G. hirsutum ovules where cotton fibers initiate and develop. Millions of unique miRNA sequences ranging from 18~28 nt in length were detected. Our results support the importance of miRNAs in regulating the development of different cell types and indicate that identification of a comprehensive set of miRNAs in cotton fiber cells would facilitate our understanding of the regulatory mechanisms for fiber cell initiation and elongation.

Isolation and characterization of a class III homeodomain-leucine zipper-like gene fromGossypium barbadense

Class III homeodomain-leucine zipper (HD-Zip III) genes are important plant-specific transcription factors which have key roles in different stages of vascular and interfascicular fiber differentiation. A novel HD-Zip III gene, designated GbHB1, was isolated by suppression subtraction hybridization and RACE (rapid amplification of cDNA ends) from Gossypium barbadense (sea-island cotton). The GbHB1 cDNA has a total length of 3061 bp with an open reading frame of 2508 bp, encoding a predicated polypeptide of 836 amino acids with a molecular weight of 91.6 kDa and a calculated pI of 5.93. The putative polypeptide of GbHB1 is structurally characterized by a homeodomain positioned adjacent to a leucine zipper domain, which shares high identity with other reported HD-Zip III domains. DNA gel blotting analysis shows that GbHB1 is a low-copy gene. Organ expression pattern analysis reveals that GbHB1 expressed highly in ovule and stem, followed by in root, and low in leaf and cotyledon. The result suggests that GbHB1 may play a regulatory role in cotton interfascicular fiber development.

Molecular and biochemical evidence for phenylpropanoid synthesis and presence of wall-linked phenolics in cotton fibers

The mature cotton (Gossypium hirsutum L.) fiber is a single cell with a typically thickened secondary cell wall. The aim of this research was to use molecular, spectroscopic and chemical techniques to investigate the possible occurrence of previously overlooked accumulation of phenolics during secondary cell wall formation in cotton fibers. Relative quantitative reverse transcription-polymerase chain reaction analysis showed that GhCAD6 and GhCAD1 were predominantly expressed among seven gene homologs, only GhCAD6 was up-regulated during secondary wall formation in cotton fibers. Phylogenic analysis revealed that GhCAD6 belonged to Class I and was proposed to have a major role in monolignol biosynthesis, and GhCAD1 belonged to Class III and was proposed to have a compensatory mechanism for monolignol biosynthesis. Amino acid sequence comparison showed that the cofactor binding sites of GhCADs were highly conserved with high similarity and identity to bona fide cinnamyl alcohol dehydrogenases. The substrate binding site of GhCAD1 is different from GhCAD6. This difference was confirmed by the different catalytic activities observed with the enzymes. Cell wall auto-fluorescence, Fourier transform infrared spectroscopy (FTIR), high-performance liquid chromatography (HPLC) and chemical analyses confirmed that phenolic compounds were bound to the cell walls of mature cotton fibers. Our findings may suggest a potential for genetic manipulation of cotton fiber properties, which are of central importance to agricultural, cotton processing and textile industries.

A specialized outer layer of the primary cell wall joins elongating cotton fibers into tissue-like bundles

Cotton (Gossypium hirsutum) provides the world's dominant renewable textile fiber, and cotton fiber is valued as a research model because of its extensive elongation and secondary wall thickening. Previously, it was assumed that fibers elongated as individual cells. In contrast, observation by cryo-field emission-scanning electron microscopy of cotton fibers developing in situ within the boll demonstrated that fibers elongate within tissue-like bundles. These bundles were entrained by twisting fiber tips and consolidated by adhesion of a cotton fiber middle lamella (CFML). The fiber bundles consolidated via the CFML ultimately formed a packet of fiber around each seed, which helps explain how thousands of cotton fibers achieve their great length within a confined space. The cell wall nature of the CFML was characterized using transmission electron microscopy, including polymer epitope labeling. Toward the end of elongation, up-regulation occurred in gene expression and enzyme activities related to cell wall hydrolysis, and targeted breakdown of the CFML restored fiber individuality. At the same time, losses occurred in certain cell wall polymer epitopes (as revealed by comprehensive microarray polymer profiling) and sugars within noncellulosic matrix components (as revealed by gas chromatography-mass spectrometry analysis of derivatized neutral and acidic glycosyl residues). Broadly, these data show that adhesion modulated by an outer layer of the primary wall can coordinate the extensive growth of a large group of cells and illustrate dynamic changes in primary wall structure and composition occurring during the differentiation of one cell type that spends only part of its life as a tissue.

Cloning and expression of two sterol C-24 methyltransferase genes from upland cotton (Gossypium hirsuturm L.)

Brassinosteroids (BRs) are an important class of plant steroidal hormones that are essential in a wide variety of physiological processes. Two kinds of intermediates, sitosterol and campesterol, play a crucial role in cell elongation, cellulose biosynthesis, and accumulation. To illuminate the effects of sitosterol and campesterol on the development of cotton (Gossypium hirsuturm L.) fibers through screening cotton fiber EST database and contigging the candidate ESTs, two key genes GhSMT2-1 and GhSMT2-2 controlling the sitosterol biosynthesis were cloned from developing fibers of upland cotton cv. Xuzhou 142. The full length of GhSMT2-1 was 1,151 bp, including an 8 bp 5'-untranslated region (UTR), a 1,086 bp open reading frame (ORF), and a 57 bp 3'-UTR. GhSMT2-1 gene encoded a polypeptide of 361 amino acid residues with a predicted molecular mass of 40 kDa. The full length of GhSMT2-2 was 1,166 bp, including an 18 bp 5'-UTR, a 1,086 bp ORF, and a 62 bp 3'-UTR. GhSMT2-2 gene encoded a polypeptide of 361 amino acid residues with a predicted molecular mass of 40 kDa. The two deduced amino acid sequences had high homology with the SMT2 from Arabidopsis thaliana and Nicotiana tabacum. Furthermore, the typical conserved structures characterized by the sterol C-24 methyltransferase, such as region I (LDVGCGVGGPMRAI), region II (IEATCHAP), and region III (YEWGWGQSFHF), were present in both deduced proteins. Southern blotting analysis indicated that GhSMT2-1 or GhSMT2-2 was a single copy in upland cotton genome. Quantitative real-time RT-PCR analysis revealed that the highest expression levels of both genes were detected in 10 DPA (day post anthesis) fibers, while the lowest levels were observed in cotyledon and leaves. The expression level of GhSMT2-1 was 10 times higher than that of GhSMT2-2 in all the organs and tissues detected. These results indicate that the homologue of sterol C-24 methyltransferase gene was cloned from upland cotton and both GhSMT2 genes play a crucial role in fiber elongation. The role of GhSMT2-1 may be more important than that of GhSMT2-2.

Down-regulation of GhADF1 gene expression affects cotton fibre properties

Cotton fibre is the most important natural fibres for textile industry. To date, the mechanism that governs the development of fibre traits is largely unknown. In this study, we have characterized the function of a member of the actin depolymerizing factor (ADF) family in Gossypium hirsutum by down-regulation of the gene (designated as GhADF1) expression in the transgenic cotton plants. We observed that both the fibre length and strength of the GhADF1-underexpressing plants increased as compared to the wild-type fibre, and transgenic fibres contained more abundant F-actin filaments in the cortical region of the cells. Moreover, the secondary cell wall of the transgenic fibre appeared thicker and the cellulose content was higher than that of the control fibre. Our results suggest that organization of actin cytoskeleton regulated by actin-associated proteins such as GhADF1 plays a critical role in the processes of elongation and secondary cell wall formation during fibre development. Additionally, our study provided a candidate intrinsic gene for the improvement of fibre traits via genetic engineering.

Cloning and characterization of a calcium dependent protein kinase gene associated with cotton fiber development

The gene GhCPK1 encoding a calcium dependent protein kinase was identified from cotton. Transcripts of GhCPK1 accumulated primarily in the elongating fiber, and Arabidopsis plants transformed with GhCPK1 promoter-GUS construct exhibited GUS activity mainly in the developing trichomes, roots, young leaves and sepals. In the bombarded onion epidermal cells, GhCPK1-GFP fusion proteins showed a subcellular distribution in the plasma membrane. In vitro assays indicated that GhCPK1 was a functional calcium-dependent kinase able to undergo autophosphorylation and phosphorylation of the known substrate histone III-S. Together, these results suggest that GhCPK1 may play a role in the calcium signaling events associated with fiber elongation.

Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells

A reverse genetic approach was used to investigate the functions of three members of the cellulose synthase superfamily in Arabidopsis (Arabidopsis thaliana), CELLULOSE SYNTHASE-LIKE D1 (CSLD1), CSLD2, and CSLD4. CSLD2 is required for normal root hair growth but has a different role from that previously described for CSLD3 (KOJAK). CSLD2 is required during a later stage of hair development than CSLD3, and CSLD2 mutants produce root hairs with a range of abnormalities, with many root hairs rupturing late in development. Remarkably, though, it was often the case that in CSLD2 mutants, tip growth would resume after rupturing of root hairs. In silico, semiquantitative reverse transcription-polymerase chain reaction, and promoter-reporter construct analyses indicated that the expression of both CSLD2 and CSLD3 is elevated at reduced temperatures, and the phenotypes of mutants homozygous for insertions in these genes were partially rescued by reduced temperature growth. However, this was not the case for a double mutant homozygous for insertions in both CSLD2 and CSLD3, suggesting that there may be partial redundancy in the functions of these genes. Mutants in CSLD1 and CSLD4 had a defect in male transmission, and plants heterozygous for insertions in CSLD1 or CSLD4 were defective in their ability to produce pollen tubes, although the number and morphology of pollen grains was normal. We propose that the CSLD family of putative glycosyltransferases synthesize a polysaccharide that has a specialized structural role in the cell walls of tip-growing cells.

Co-expression and preferential interaction between two calcineurin B-like proteins and a CBL-interacting protein kinase from cotton

The CBL/CIPK signaling system mediates a variety of responses to environmental stimuli in plants. In this work, we identified four CBL genes from Gossypium hirsutum, two of which (designated GhCBL2 and GhCBL3) showed preferential expression in the elongating fiber cells. Moreover, the expression patterns of these two CBL genes coincided with that of a putative CBL-interacting protein kinase gene (GhCIPK1) that we isolated in a previous study. Yeast two-hybrid assay indicated that among the four CBLs, GhCIPK1 interacted selectively with GhCBL2 and GhCBL3. The co-expression and interactions of these proteins suggest that they are components of the same signaling pathway. These findings strengthen our previous prediction that CBL/CIPK signaling plays a critical role in the regulation of cotton fiber elongation.

The R2R3 MYB transcription factor GhMYB109 is required for cotton fiber development

Cotton (Gossypium hirsutum L.) fibers are single highly elongated cells derived from the outer epidermis of ovules. A large number of genes are required for fiber differentiation and development, but so far, little is known about how these genes control and regulate the process of fiber development. Here we examine the role of the cotton-fiber-specific R2R3 MYB gene GhMYB109 in cotton fiber development. Transgenic reporter gene analysis revealed that a 2-kb GhMYB109 promoter was sufficient to confirm its fiber-specific expression. Antisense-mediated suppression of GhMYB109 led to a substantial reduction in fiber length. Consistently, several genes related to cotton fiber growth were found to be significantly reduced in the transgenic cotton. Our results showed that GhMYB109 is required for cotton fiber development and reveal a largely conserved mechanism of the R2R3 MYB transcription factor in cell fate determination in plants.

Geminivirus-mediated gene silencing from Cotton leaf crumple virus is enhanced by low temperature in cotton

A silencing vector for cotton (Gossypium hirsutum) was developed from the geminivirus Cotton leaf crumple virus (CLCrV). The CLCrV coat protein gene was replaced by up to 500 bp of DNA homologous to one of two endogenous genes, the magnesium chelatase subunit I gene (ChlI) or the phytoene desaturase gene (PDS). Cotyledons of cotton cultivar 'Deltapine 5415' bombarded with the modified viral vectors manifested chlorosis due to silencing of either ChlI or PDS in approximately 70% of inoculated plants after 2 to 3 weeks. Use of the green fluorescence protein gene showed that replication of viral DNA was restricted to vascular tissue and that the viral vector could transmit to leaves, roots, and the ovule integument from which fibers originate. Temperature had profound effects on vector DNA accumulation and the spread of endogenous gene silencing. Consistent with reports that silencing against viruses increases at higher temperatures, plants grown at a 30 degrees C/26 degrees C day/night cycle had a greater than 10-fold reduction in viral DNA accumulation compared to plants grown at 22 degrees C/18 degrees C. However, endogenous gene silencing decreased at 30 degrees C/26 degrees C. There was an approximately 7 d delay in the onset of gene silencing at 22 degrees C/18 degrees C, but silencing was extensive and persisted throughout the life of the plant. The extent of silencing in new growth could be increased or decreased by changing temperature regimes at various times following the onset of silencing. Our experiments establish the use of the CLCrV silencing vector to study gene function in cotton and show that temperature can have a major impact on the extent of geminivirus-induced gene silencing.

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.

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.

Gene-rich islands for fiber development in the cotton genome

Cotton fiber is an economically important seed trichome and the world's leading natural fiber used in the manufacture of textiles. As a step toward elucidating the genomic organization and distribution of gene networks responsible for cotton fiber development, we investigated the distribution of fiber genes in the cotton genome. Results revealed the presence of gene-rich islands for fiber genes with a biased distribution in the tetraploid cotton (Gossypium hirsutum L.) genome that was also linked to discrete fiber developmental stages based on expression profiles. There were 3 fiber gene-rich islands associated with fiber initiation on chromosome 5, 3 islands for the early to middle elongation stage on chromosome 10, 3 islands for the middle to late elongation stage on chromosome 14, and 1 island on chromosome 15 for secondary cell wall deposition, for a total of 10 fiber gene-rich islands. Clustering of functionally related gene clusters in the cotton genome displaying similar transcriptional regulation indicates an organizational hierarchy with significant implications for the genetic enhancement of particular fiber quality traits. The relationship between gene-island distribution and functional expression profiling suggests for the first time the existence of functional coupling gene clusters in the cotton genome.

Cu/Zn superoxide dismutases in developing cotton fibers: evidence for an extracellular form

Hydrogen peroxide and other reactive oxygen species are important signaling molecules in diverse physiological processes. Previously, we discovered superoxide dismutase (SOD) activity in extracellular protein preparations from fiber-bearing cotton (Gossypium hirsutum L.) seeds. We show here, based on immunoreactivity, that the enzyme is a Cu/Zn-SOD (CSD). Immunogold localization shows that CSD localizes to secondary cell walls of developing cotton fibers. Five cotton CSD cDNAs were cloned from cotton fiber and classified into three subfamilies (Group 1: GhCSD1; Group 2: GhCSD2a and GhCSD2b; Group 3: GhCSD3 and GhCSD3s). Members of Group 1 and 2 are expressed throughout fiber development, but predominant during the elongation stage. Group 3 CSDs are also expressed throughout fiber development, but transiently increase in abundance at the transition period between cell elongation and secondary cell wall synthesis. Each of the three GhCSDs also has distinct patterns of expression in tissues other than fiber. Overexpression of cotton CSDs fused to green fluorescent protein in transgenic Arabidopsis demonstrated that GhCSD1 localizes to the cytosol, GhCSD2a localizes to plastids, and GhCSD3 is translocated to the cell wall. Subcellular fractionation of proteins from transgenic Arabidopsis seedlings confirmed that only c-myc epitope-tagged GhCSD3 co-purifies with cell wall proteins. Extracellular CSDs have been suggested to be involved in lignin formation in secondary cell walls of other plants. Since cotton fibers are not lignified, we suggest that extracellular CSDs may be involved in other plant cell wall growth and development processes.

A preliminary analysis of genome structure and composition in Gossypium hirsutum

Background

Upland cotton has the highest yield, and accounts for > 95% of world cotton production. Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural, functional, and evolutionary studies of the species. Here, we employed GeneTrek and BAC tagging information approaches to predict the general composition and structure of the allotetraploid cotton genome.

Results

142 BAC sequences from Gossypium hirsutum cv. Maxxa were downloaded and confirmed. These BAC sequence analysis revealed that the tetraploid cotton genome contains over 70,000 candidate genes with duplicated gene copies in homoeologous A- and D-subgenome regions. Gene distribution is uneven, with gene-rich and gene-free regions of the genome. Twenty-one percent of the 142 BACs lacked genes. BAC gene density ranged from 0 to 33.2 per 100 kb, whereas most gene islands contained only one gene with an average of 1.5 genes per island. Retro-elements were found to be a major component, first an enriched LTR/gypsy and second LTR/copia. Most LTR retrotransposons were truncated and in nested structures. In addition, 166 polymorphic loci amplified with SSRs developed from 70 BAC clones were tagged on our backbone genetic map. Seventy-five percent (125/166) of the polymorphic loci were tagged on the D-subgenome. By comprehensively analyzing the molecular size of amplified products among tetraploid G. hirsutum cv. Maxxa, acc. TM-1, and G. barbadense cv. Hai7124, and diploid G. herbaceum var. africanum and G. raimondii, 37 BACs, 12 from the A- and 25 from the D-subgenome, were further anchored to their corresponding subgenome chromosomes. After a large amount of genes sequence comparison from different subgenome BACs, the result showed that introns might have no contribution to different subgenome size in Gossypium.

Conclusion

This study provides us with the first glimpse of cotton genome complexity and serves as a foundation for tetraploid cotton whole genomesequencing in the future.

Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton

A putative advantage of allopolyploidy is the possibility of differential selection of duplicated (homeologous) genes originating from two different progenitor genomes. In this note we explore this hypothesis using a high throughput, SNP-specific microarray technology applied to seed trichomes (cotton) harvested from three developmental time points in wild and modern accessions of two independently domesticated cotton species, Gossypium hirsutum and G. barbadense. We show that homeolog expression ratios are dynamic both developmentally and over the several-thousand-year period encompassed by domestication and crop improvement, and that domestication increased the modulation of homeologous gene expression. In both species, D-genome expression was preferentially enhanced under human selection pressure, but for nonoverlapping sets of genes for the two independent domestication events. Our data suggest that human selection may have operated on different components of the fiber developmental genetic program in G. hirsutum and G. barbadense, leading to convergent rather than parallel genetic alterations and resulting morphology.

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

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.

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.

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.

Cloning and characterization of cotton GhBG gene encoding beta-glucosidase

Beta-1,4-glucosidase (BG, EC3.2.1.21), one of three cellulases, is a widespread family of enzymes involved in the metabolism of cell wall polysaccharides in both prokaryocytes and eukaryotes. Here, we report the isolation of a full-length cDNA encoding beta-1,4-glucosidase protein (designated as GhBG) and its putative function in the process of fiber development and in yeast. Through random sequencing of the cotton fiber cDNA library from 7235 germplasm line, with elite fiber quality in Gossypium hirsutum L. and utilizing the 5' rapid amplification of cDNA ends (RACE) technique, a 2133 bp cDNA clone encoding a cotton fiber specifically expressed protein (accession number: DQ103699) was isolated. GhBG was composed of a 1884 bp open reading frame (ORF) encoding 627 amino acid residues. This putative protein had an isoelectric point of 8.17, a calculated molecular weight of 68.78 KD and a signal peptide with 23 amino acid residues at the N-terminal. RT-PCR analysis indicated GhBG was specifically expressed in fiber cells and was highly abundant in 5-17 day post anthesis (DPA). It was not, however, expressed in root, hypocotyls or leaves. Southern blotting analysis showed there were two copies of GhBG in the upland cotton genome; most likely contained in sub-genome A and sub-genome D. GhBG was then integrated into a yeast expression vector, pREP-5N and electro-transformed into fission yeast Schizosaccharomyces pombe Q-01. The results demonstrated that GhBG led to a significant increase in cell length and width and a remarkable decrease of the length/width ratio. Compared to vector control transformants, cells were significantly larger and rounder and their growth velocity was also reduced.

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.

Rapid cell expansion and cellulose synthesis regulated by plasmodesmata and sugar: insights from the single-celled cotton fibre

Higher plants comprise mixtures of some 40 different cell types, and this often complicates the interpretation of data obtained at the tissue level. Studies for a given cell type may provide novel insights into the mechanisms underlying defined cellular and developmental processes. In this regard, the cotton fibre represents an excellent single-cell model to study the control of rapid cell elongation and cellulose synthesis. These single cells, initiated from the ovule epidermis at anthesis, typically elongate to ~3-5 cm in the tetraploid species before they switch to intensive secondary cell wall cellulose synthesis. By maturity, more than 94% of fibre weight is cellulose. To unravel the mechanisms of fibre elongation and cellulose synthesis, two hypotheses have been examined: (a) that sucrose degradation and utilisation mediated by sucrose synthase (Sus) may play roles in fibre development and (b) that symplastic isolation of the fibre cells may be required for their rapid elongation. Reverse genetic and biochemical analyses have revealed the critical role that Sus plays in fibre initiation and early elongation. Late in development, plasma-membrane and cell wall association of Sus protein seems to be involved in rapid cellulose synthesis. Cell biology and gene expression studies showed a temporary closure of fibre plasmodesmata (PD), probably due to the deposition of callose, at the rapid phase of elongation. The duration of the PD closure correlates positively with the final fibre length attained. These data support the view that PD closure may be required for fibres to achieve extended elongation. The branching of PD towards the secondary cell wall stage is postulated to function as a molecule sieve for tight control of macromolecule trafficking into fibres to sustain intensive cellulose synthesis.

A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation

The transcriptional regulators for anthocyanin pigmentation include proteins containing R2R3-MYB domains, bHLH domains and conserved WD40 repeats, and their interactions determine the set of genes to be expressed. Spontaneous ivory seed (ivs) mutants of Ipomoea purpurea displaying pale pigmented flowers and ivory seeds are caused by insertions of DNA transposons into the bHLH2 gene that encodes a bHLH transcriptional regulator. A partial reduction in the expression of all structural genes encoding enzymes for anthocyanin biosynthesis was observed in the young flower buds of these ivs mutants. The DFR-B and ANS transcripts were completely abolished in the ivs seed coats, whereas the early biosynthetic genes for flavonol biosynthesis remained active. The production and accumulation of both proanthocyanidin and phytomelanin pigments in the ivory seed coats were drastically reduced. Moreover, the unbranched trichomes in the ivory seeds were smaller in size and fewer in number than those in the wild-type dark-brown seeds, and the surface of the epidermis without trichomes in the dark-brown seeds looked rougher, due to the protruding tangential walls, than that in the ivory seeds. Although the I. purpurea bHLH2 gene is the most closely related to the petunia AN1 gene, whose mutation is known to confer white flowers and to be deficient in acidification of their vacuoles, the vacuolar alkalization in the epidermal flower limbs of I. purpurea ivs mutants appears to occur normally. These results are discussed with regard to the function of bHLH transcriptional regulators controlling flower and seed pigmentation as well as other epidermal traits.

Functional analysis of a cotton glucuronosyltransferase promoter in transgenic tobaccos

The 5' fragment (1 647 bp) of the cotton glucuronosyltransferase gene (GhGlcAT1) was transcriptionally fused to the beta-glucuronidase (GUS) gene, and functionally analyzed for important regulatory regions controlling gene expression in transgenic tobacco plants. GUS activity analysis revealed that the full-length promoter drives efficient expression of the GUS gene in the root cap, seed coat, pollen grains and trichomes. Exposure of the transgenic tobacco to various abiotic stresses showed that the promoter was mainly responsive to the sugars (glucose and sucrose) as well as gibberellic acid. Progressive upstream deletion analyses of the promoter showed that the region from -281 to +30 bp is sufficient to drive strong GUS expression in the trichomes of shoot, suggesting that the 311 bp region contains all cis-elements needed for trichome-specific expression. Furthermore, deletion analysis also revealed that the essential cis-element(s) for sucrose induction might be located between -635 and -281 bp. In addition, sequence analysis of the regulatory region indicated several conserved motifs among which some were shared with previously reported seed-specific elements and sugar-responsive elements, while others were related with trichome expression. These findings indicate that a 1 647-bp fragment of the cotton GhGlcAT1 promoter contains specific transcription regulatory elements, and provide clues about the roles of GhGlcAT1 in cotton fiber development. Further analyses of these elements will help to elucidate the molecular mechanisms regulating the expression of the GhGlcAT1 gene during fiber elongation.

An efficient protein preparation for proteomic analysis of developing cotton fibers by 2-DE

Preparation of high-quality proteins from cotton fiber tissues is difficult due to high endogenous levels of polysaccharides, polyphenols, and other interfering compounds. To establish a routine procedure for the application of proteomic analysis to cotton fiber tissues, a new protocol for protein extraction was developed by optimizing a phenol extraction method combined with methanol/ammonium acetate precipitation. The protein extraction for 2-DE was remarkably improved by the combination of chemically and physically modified processes including polyvinylpolypyrrolidone (PVPP) addition, acetone cleaning, and SDS replacement. The protocol gave a higher protein yield and vastly greater resolution and spot intensity. The efficiency of this protocol and its feasibility in fiber proteomic study were demonstrated by comparison of the cotton fiber proteomes at two growth stages. Furthermore, ten protein spots changed significantly were identified by MS/tandem MS and their potential relationships to fiber development were discussed. To the best of our knowledge, this is the first time that a protocol for protein extraction from cotton fiber tissues appears to give satisfactory and reproductive 2-D protein profiles. The protocol is expected to accelerate the process of the proteomic study of cotton fibers and also to be applicable to other recalcitrant plant tissues.

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.

The cotton fiber zinc-binding domain of cellulose synthase A1 from Gossypium hirsutum displays rapid turnover in vitro and in vivo

Little is known about the assembly and turnover of cellulose synthase complexes commonly called rosettes. Recent work indicates that rosette assembly could involve the dimerization of CesA (cellulose synthase catalytic subunit) proteins regulated by the redox state of the CesA zinc-binding domain (ZnBD). Several studies in the 1980s led to the suggestion that synthase complexes may have very short half-lives in vivo, but no recent work has directly addressed this issue. In the present work, we show that the half-life of cotton fiber GhCesA1 protein is <30 min in vivo, far less than the average membrane protein. We also show that the reduced monomer of GhCesA1 ZnBD is rapidly degraded when exposed to cotton fiber extracts, whereas the oxidized dimer is resistant to degradation. Low rates of degradation activity were detected in vitro by using extracts from fibers harvested during primary cell-wall formation, but activity increased markedly during transition to secondary cell-wall synthesis. In vitro degradation of reduced GhCesA1 ZnBD is inhibited by proteosome inhibitor MG132 and also by E64 and EGTA, suggesting that proteolysis is initiated by cysteine protease activity rather than the proteosome. We used a yeast two-hybrid system to identify a putative cotton fiber metallothionein and to confirm it as a protein that could interact with the GhCesA1 ZnBD. A model is proposed wherein active cellulose synthase complexes contain CesA proteins in dimerized form, and turnover and degradation of the complexes are mediated through reductive zinc insertion by metallothionein and subsequent proteolysis involving a cysteine protease.

Isolation of the promoter of a cotton beta-galactosidase gene (GhGal1) and its expression in transgenic tobacco plants

Beta-galactosidases (EC 3.2.1.23) constitute a widespread family of glycosyl hydrolases in plants and are thought to be involved in metabolism of cell wall polysaccharides. A cDNA of the cotton (Gossypium hirsutum) beta-galactosidase gene, designated GhGal1, has previously been identified and its transcripts are highly abundant at the elongation stage of the cotton fiber. To examine the temporal and spatial control of GhGal1 expression, a transcriptional fusion of the GhGal1 promoter region (1770 bp) with the beta-glucuronidase (GUS) reporter gene was introduced into tobacco plants by the Agrobacterium infection method. The resulting transgenic plants showed higher GUS activity of fruit in the transgenic plants than that in the negative and positive controls. Histochemical localization of GUS activity demonstrated that the expression of the GUS gene could be found in the meristem zones of roots, cotyledons, vascular tissues, fruit and trichomes in transgenic tobacco plants. Additionally, sequence analysis of the regulatory region also revealed several conserved motifs among which some were shared with previously reported fruit/seed-specific elements and the others were related with trichome expression. These results indicated the temporal and spatial expression characterization of the GhGal1 promoter in transgenic tobacco plants and provided an important insight into the roles of GhGal1 in cotton fiber development.

Leafing through the genomes of our major crop plants: strategies for capturing unique information

Crop plants not only have economic significance, but also comprise important botanical models for evolution and development. This is reflected by the recent increase in the percentage of publicly available sequence data that are derived from angiosperms. Further genome sequencing of the major crop plants will offer new learning opportunities, but their large, repetitive, and often polyploid genomes present challenges. Reduced-representation approaches - such as EST sequencing, methyl filtration and Cot-based cloning and sequencing - provide increased efficiency in extracting key information from crop genomes without full-genome sequencing. Combining these methods with phylogenetically stratified sampling to allow comparative genomic approaches has the potential to further accelerate progress in angiosperm genomics.

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

Upland cotton (Gossypium hirsutum) produces the most widely used natural fibers, yet the regulatory mechanisms governing fiber cell elongation are not well understood. Through sequencing of a cotton fiber cDNA library and subsequent microarray analysis, we found that ethylene biosynthesis is one of the most significantly upregulated biochemical pathways during fiber elongation. The 1-Aminocyclopropane-1-Carboxylic Acid Oxidase1-3 (ACO1-3) genes responsible for ethylene production were expressed at significantly higher levels during this growth stage. The amount of ethylene released from cultured ovules correlated with ACO expression and the rate of fiber growth. Exogenously applied ethylene promoted robust fiber cell expansion, whereas its biosynthetic inhibitor l-(2-aminoethoxyvinyl)-glycine (AVG) specifically suppressed fiber growth. The brassinosteroid (BR) biosynthetic pathway was modestly upregulated during this growth stage, and treatment with BR or its biosynthetic inhibitor brassinazole (BRZ) also promoted or inhibited, respectively, fiber growth. However, the effect of ethylene treatment was much stronger than that of BR, and the inhibitory effect of BRZ on fiber cells could be overcome by ethylene, but the AVG effect was much less reversed by BR. These results indicate that ethylene plays a major role in promoting cotton fiber elongation. Furthermore, ethylene may promote cell elongation by increasing the expression of sucrose synthase, tubulin, and expansin genes.

Isolation of a cotton reversibly glycosylated polypeptide (GhRGP1) promoter and its expression activity in transgenic tobacco

Reversibly glycosylated polypeptides (RGPs) are thought to be involved in polysaccharide metabolism. A cDNA of the cotton (Gossypium hirsutum) RGP gene, designated GhRGP1, has previously been characterized, and is preferentially expressed in fiber cells. In order to investigate its temporal and spatial control, we isolated a 624bp fragment upstream of the GhRGP1 coding sequence using a polymerase chain reaction (PCR)-based genomic walking method, transcriptionally fused the 624bp promoter sequence to the beta-glucuronidase (GUS) gene, and analyzed the stable gene expression in tobacco (Nicotiana tabacum). In 4-week-old transgenic tobacco plants, the highest expression level was observed in roots, and the GUS activity was 1.13- and 6.65-fold higher than that in stems and leaves, respectively. In the reproductive growth stage, the GUS expression level was highest in the pistils and the GUS activity in the stigmas and styles were 17.6-fold higher than that in the ovaries. High GUS activity was also detected in the anthers. In addition, histochemical staining for GUS activity on transgenic tobacco plants further indicated a higher expression in the trichomes, seeds and vascular tissues of stems. Abiotic stress treatments on transgenic tobacco plants showed that wounding and dehydration induced GUS expression. These results demonstrated the spatial and temporal regulation of a cotton RGP promoter in a model plant, and provided an important insight into the factors that control the fiber development and stress responses of the gene.

Developmental and gene expression analyses of a cotton naked seed mutant

Cotton fiber development is a fundamental biological phenomenon, yet the molecular basis of fiber cell initiation is poorly understood. We examined molecular and cellular events of fiber cell development in the naked seed mutant (N1N1) and its isogenic line of cotton (Gossypium hirsutum L. cv. Texas Marker-1, TM-1). The dominant mutation not only delayed the process of fiber cell formation and elongation but also reduced the total number of fiber cells, resulting in sparsely distributed short fibers. Gene expression changes in TM-1 and N1N1 mutant lines among four tissues were analyzed using spotted cotton oligo-gene microarrays. Using the Arabidopsis genes, we selected and designed approximately 1,334 70-mer oligos from a subset of cotton fiber ESTs. Statistical analysis of the microarray data indicates that the number of significantly differentially expressed genes was 856 in the leaves compared to the ovules (3 days post-anthesis, DPA), 632 in the petals relative to the ovules (3 DPA), and 91 in the ovules at 0 DPA compared to 3 DPA, all in TM-1. Moreover, 117 and 30 genes were expressed significantly different in the ovules at three and 0 DPA, respectively, between TM-1 and N1N1. Quantitative RT-PCR analysis of 23 fiber-associated genes in seven tissues including ovules, fiber-bearing ovules, fibers, and non-fiber tissues in TM-1 and N1N1 indicates a mode of temporal regulation of the genes involved in transcriptional and translational regulation, signal transduction, and cell differentiation during early stages of fiber development. Suppression of the fiber-associated genes in the mutant may suggest that the N1N1 mutation disrupts temporal regulation of gene expression, leading to a defective process of fiber cell elongation and development.

Identification and quantification of glycerolipids in cotton fibers: reconciliation with metabolic pathway predictions from DNA databases

The lipid profiles of cotton fiber cells were determined from total lipid extracts of elongating and maturing cotton fiber cells to see whether the membrane lipid composition changed during the phases of rapid cell elongation or secondary cell wall thickening. Total FA content was highest or increased during elongation and was lower or decreased thereafter, likely reflecting the assembly of the expanding cell membranes during elongation and the shift to membrane maintenance (and increase in secondary cell wall content) in maturing fibers. Analysis of lipid extracts by electrospray ionization and tandem MS (ESI-MS/MS) revealed that in elongating fiber cells (7-10 d post-anthesis), the polar lipids-PC, PE, PI, PA, phosphatidylglycerol, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and phosphatidylglycerol-were most abundant. These same glycerolipids were found in similar proportions in maturing fiber cells (21 dpa). Detailed molecular species profiles were determined by ESI-MS/MS for all glycerolipid classes, and ESI-MS/MS results were consistent with lipid profiles determined by HPLC and ELSD. The predominant molecular species of PC, PE, PI, and PA was 34:3 (16:0, 18:3), but 36:6 (18:3,18:3) also was prevalent. Total FA analysis of cotton lipids confirmed that indeed linolenic (18:3) and palmitic (16:0) acids were the most abundant FA in these cell types. Bioinformatics data were mined from cotton fiber expressed sequence tag databases in an attempt to reconcile expression of lipid metabolic enzymes with lipid metabolite data. Together, these data form a foundation for future studies of the functional contribution of lipid metabolism to the development of this unusual and economically important cell type.

Functional characterization of Gossypium hirsutum profilin 1 gene (GhPFN1) in tobacco suspension cells. Characterization of in vivo functions of a cotton profilin gene

Cotton fiber is an extremely long plant cell. Fiber elongation is a complex process and the genes that are crucial for elongation are largely unknown. We previously cloned a cDNA encoding an isoform of cotton profilin and found that the gene (designated GhPFN1) was preferentially expressed in cotton fibers. In the present study, we have further analyzed the expression pattern of GhPFN1 during fiber development and studied its cellular function using tobacco suspension cells as an experimental system. We report that expression of GhPFN1 is tightly associated with fast elongation of cotton fibers whose growth requires an intact actin cytoskeleton. Overexpression of GhPFN1 in the transgenic tobacco cells was correlated with the formation of elongated cells that contained thicker and longer microfilament cables. Quantitative analyses revealed a 2.5-3.6 fold increase in total profilin levels and a 1.6-2.6 fold increase in the F-actin levels in six independent transgenic lines. In addition to the effect on cell elongation, we also observed delayed cell cycle progression and a slightly lower mitotic index in the transgenic cells. Based on these data, we propose that GhPFN1 may play a critical role in the rapid elongation of cotton fibers by promoting actin polymerization.

A versatile promoter for the expression of proteins in glandular and non-glandular trichomes from a variety of plants

A DNA regulatory fragment was isolated from the promoter region of the OASA1 gene, encoding the cytosolic O-acetylserine(thiol)lyase enzyme that is highly expressed in Arabidopsis thaliana trichomes. This DNA fragment has been named an ATP fragment and comprises 1435 bp of the genomic region upstream of the OASA1 gene and 375 bp of the transcriptional initiation start site containing the first intron of the gene. The ATP fragment, fused to the green fluorescent protein (GFP) and beta-glucuronidase (GUS) reporter genes, is able to drive high-level gene expression in A. thaliana trichomes. Deletion analysis of the ATP fragment determined that the region from -266 to -66 contains regulatory elements required for trichome expression. In addition, the region from +112 to +375, comprising the first intronic region of the gene, is also essential for trichome gene expression. Expression of the full-length ATP fragment in tobacco and peppermint shows that this fragment is also able to drive expression in glandular trichomes and suggests additional biotechnological applications for this promoter.

Brassinosteroid regulates fiber development on cultured cotton ovules

Our current understanding of the role of phytohormones in the development of cotton fibers is derived largely from an amenable culture system in which cotton ovules, collected on the day of anthesis, are floated on liquid media. Under these conditions, supplemental auxin and gibberellin were found to promote fiber initiation and elongation. More recently, addition of low concentrations of the brassinosteroid brassinolide (BL) were also found to promote fiber elongation while a brassinosteroid biosynthesis inhibitor brassinazole2001 (Brz) inhibited fiber development. In order to elucidate the role of brassinosteroid in cotton fiber development further, we have performed a more detailed analysis of the effects of these chemicals on cultured cotton ovules. Our results confirm that exogenous BL promotes fiber elongation while treatment with Brz inhibits it. Furthermore, treatment of cotton floral buds with Brz results in the complete absence of fiber differentiation, indicating that BR is required for fiber initiation as well as elongation. Expression of fiber genes associated with cell elongation increased in ovules treated with BL and was suppressed by Brz treatment, establishing a correlation between brassinosteroid-regulated gene expression and fiber elongation. These results establish a clear connection between brassinosteroid and fiber development and open the door for genetic analysis of cotton development through direct modification of the brassinosteroid signal transduction pathway.

A plant-specific kinesin binds to actin microfilaments and interacts with cortical microtubules in cotton fibers

A novel kinesin, GhKCH1, has been identified from cotton (Gossypium hirsutum) fibers. GhKCH1 has a centrally located kinesin catalytic core, a signature neck peptide of minus end-directed kinesins, and a unique calponin homology (CH) domain at its N terminus. GhKCH1 and other CH domain-containing kinesins (KCHs) belong to a distinct branch of the minus end-directed kinesin subfamily. To date the KCH kinesins have been found only in higher plants. Because the CH domain is often found in actin-binding proteins, we proposed that GhKCH1 might play a role in mediating dynamic interaction between microtubules and actin microfilaments in cotton fibers. In an in vitro actin-binding assay, GhKCH1's N-terminal region including the CH domain interacted directly with actin microfilaments. In cotton fibers, GhKCH1 decorated cortical microtubules in a punctate manner. Occasionally GhKCH1 was found to be associated with transverse-cortical actin microfilaments, but never with axial actin cables in cotton fibers. Localization of GhKCH1 on cortical microtubules was independent of the integrity of actin microfilaments. Thus, GhKCH1 may play a role in organizing the actin network in coordination with the cortical microtubule array. These data also suggest that flowering plants may employ unique KCHs to coordinate actin microfilaments and microtubules during cell growth.

A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium)

We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM ( approximately 600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM ( approximately 500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6-11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the "portability" of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome.

Characterization of GhRac1 GTPase expressed in developing cotton (Gossypium hirsutum L.) fibers

Cytoskeleton assembly plays an important role in determining cotton fiber cell length and morphology and is developmentally regulated. As in other plant cells, it is not clear how cytoskeletal assembly in fibers is regulated. Recently, several Rac/Rop GTPases in Arabidopsis were shown to regulate isotropic and polar cell growth of root hairs and pollen tubes by controlling assembly of the cytoskeleton. GhRac1, isolated from cottonseeds, is a member of the Rac/Rop GTPase family and is abundantly expressed in rapidly growing cotton tissues. GhRac1 shows the greatest sequence similarity to the group IV subfamily of Arabidopsis Rac/Rop genes. Overexpression of GhRac1 in E. coli led to the production of a functional GTPase as shown by in vitro enzyme activity assay. In contrast to other Rac/Rop GTPases found in cotton fiber, GhRac1 is highly expressed during the elongation stage of fiber development with expression decreasing dramatically when the rate of fiber elongation declines. The association of highest GhRac1 expression during stages of maximal cotton fiber elongation suggests that GhRac1 GTPase may be a potential regulator of fiber elongation by controlling cytoskeletal assembly.

Xyloglucan breakdown during cotton fiber development

Cotton (Gossypium herbaceum L.) fibers elongated almost linearly up to about 20 days post anthesis. The molecular mass of xyloglucans in fiber cell walls decreased gradually during the elongation stage. When enzymatically active (native) cell wall preparations of fibers were autolyzed, the molecular mass of xyloglucans decreased. The decrease was most prominent in wall preparations obtained from the rapidly elongating fibers. The xyloglucan-degrading activity was recovered from the fiber cell walls with 3 mol/L NaCl, and the activity was high at the stages in which fibers elongated vigorously. These results suggest the possible involvement of xyloglucan metabolism in the regulation of cotton fiber elongation.

Changes in the sugar composition and molecular mass distribution of matrix polysaccharides during cotton fiber development

Cotton (Gossypium herbaceum L.) fiber development consists of a fiber elongation stage (up to 20 d post-anthesis) and a subsequent cell wall thickening stage. Cell wall analysis revealed that the extractable matrix (pectic and hemicellulosic) polysaccharides accounted for 30-50% of total sugar content in the fiber elongation stage but less than 3% in the cell wall thickening stage. By contrast, cellulose increased dramatically after the fiber elongation ceased. The amounts of extractable xyloglucans and arabinose- and galactose-containing polymers per seed increased in the early fiber elongation stage and decreased thereafter. The amounts of extractable acidic polymers and non-cellulosic beta-glucans (mainly composed of beta-1,3-glucans) increased in parallel with fiber elongation and then decreased. The molecular masses of extractable non-cellulosic beta-glucans, and arabinose- and galactose-containing polymers decreased during both fiber elongation and cell wall thickening stages. The molecular mass of extractable xyloglucans also decreased during the fiber elongation stage, but this decrease ceased during the cell wall thickening stage. Conversely, the molecular size of acidic polymers in the extractable pectic fraction increased during both stages. Thus, not only the amounts but also the molecular size of the extractable matrix polysaccharides showed substantial changes during cotton fiber development.