Global identification of target genes regulated by APETALA3 and PISTILLATA floral homeotic gene action

Two GATA transcription factors are downstream effectors of floral homeotic gene action in Arabidopsis

Floral organogenesis is dependent on the combinatorial action of MADS-box transcription factors, which in turn control the expression of suites of genes required for growth, patterning, and differentiation. In Arabidopsis (Arabidopsis thaliana), the specification of petal and stamen identity depends on the action of two MADS-box gene products, APETALA3 (AP3) and PISTILLATA (PI). In a screen for genes whose expression was altered in response to the induction of AP3 activity, we identified GNC (GATA, nitrate-inducible, carbon-metabolism-involved) as being negatively regulated by AP3 and PI. The GNC gene encodes a member of the Arabidopsis GATA transcription factor family and has been implicated in the regulation of chlorophyll biosynthesis as well as carbon and nitrogen metabolism. In addition, we found that the GNC paralog, GNL (GNC-like), is also negatively regulated by AP3 and PI. Using chromatin immunoprecipitation, we showed that promoter sequences of both GNC and GNL are bound by PI protein, suggesting a direct regulatory interaction. Analyses of single and double gnc and gnl mutants indicated that the two genes share redundant roles in promoting chlorophyll biosynthesis, suggesting that in repressing GNC and GNL, AP3/PI have roles in negatively regulating this biosynthetic pathway in flowers. In addition, coexpression analyses of genes regulated by AP3, PI, GNC, and GNL indicate a complex regulatory interplay between these transcription factors in regulating a variety of light and nutrient responsive genes. Together, these results provide new insights into the transcriptional cascades controlling the specification of floral organ identities.

Persea americana (avocado): bringing ancient flowers to fruit in the genomics era

The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary "outpost" among flowering plants, representing a basal lineage (the magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical-zone crop. Among the goals of avocado improvement are to develop varieties with fruit that will "store" better on the tree, show uniform ripening and have better post-harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non-flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms.

A spatial dissection of the Arabidopsis floral transcriptome by MPSS

BACKGROUND

We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. Comparing and contrasting these MPSS floral expression libraries enabled demarcation of transcripts enriched in the petals, stamens, stigma-style, gynoecia, and those with predicted enrichment within the sepal/sepal-petals, petal-stamens, or gynoecia-stamens.

RESULTS

By comparison of expression libraries, a total of 572 genes were found to have organ-enriched expression within the inflorescence. The bulk of characterized organ-enriched transcript diversity was noted in the gynoecia and stamens, whereas fewer genes demonstrated sepal or petal-localized expression. Validation of the computational analyses was performed by comparison with previously published expression data, in situ hybridizations, promoter-reporter fusions, and reverse transcription PCR. A number of well-characterized genes were accurately delineated within our system of transcript filtration. Moreover, empirical validations confirm MPSS predictions for several genes with previously uncharacterized expression patterns.

CONCLUSION

This extensive MPSS analysis confirms and supplements prior microarray floral expression studies and illustrates the utility of sequence survey-based expression analysis in functional genomics. Spatial floral expression data accrued by MPSS and similar methods will be advantageous in the elucidation of more comprehensive genetic regulatory networks governing floral development.

Global analysis of gene expression in flower buds of Ms-cd1 Brassica oleracea conferring male sterility by using an Arabidopsis microarray

The dominant male sterility gene Ms-cd1 is identified in Brassica oleracea. Electron microscopical observations revealed that abortion of pollen development starts after tetrad formation. This important male sterility phenotype is characterized by lack of degradation of the primary pollen mother cell (PMC) wall and delayed degradation of callose surrounding the tetrads and thus arrest of microspore release. Gene expression of the male sterile and fertile buds was analyzed by heterologous hybridization of Brassica oleracea cRNA onto an Arabidopsis whole genome oligonucleotide microarray. A total of 277 suppressed genes including 40 kinase-, 32 cell wall modification and 29 transport related genes were found to be significantly down regulated >3-fold in the male sterile mutant. The vast majority of the differentially expressed transcripts are found to present late pollen stage specific genes. Kinase genes, cell wall modification genes and ion transport genes were greatly over-represented when compared to their percentage of all flower bud expressed genes and represent 36.5% of the genes suppressed by Ms-cd1. Our results also suggest that Ms-cd1 may blocks an anther developmental pathway with a small number of genes suppressed in tapetum cells which prevent the degradation of callose and PMC wall, which further leads to the suppression of a large number of genes involved in signaling pathways, cell wall modification and ion transport in pollen grains.

Analyses of the floral organ morphogenesis and the differentially expressed genes of an apetalous flower mutant in Brassica napus

The floral organ morphogenesis of the apetalous flower mutant Apet33-10 in Brassica napus was investigated and the result showed that all the floral organ morphogenesis was normal except that petal primordium was not observed during flower development. Eighteen genes were found to be down regulated in early floral buds (less than 200 mum in length) of Apet33-10 at the stage of floral organ initiation by means of suppressive subtraction hybridization (SSH) and RT-PCR. These genes were involved in petal identity, calcium iron signal transduction, mRNA processing, protein synthesis and degradation, construction of cytoskeleton, hydrogen transportation, nucleic acid binding, alkaloid biosynthesis and unknown function. Three overall coding region cDNAs of APETALA3 (AP3) gene, BnAP3-2, BnAP3-3 and BnAP3-4 were obtained by RT-PCR, respectively. Real-time quantitative PCR analysis showed that the expression ratio among BnAP3-2, BnAP3-3 and BnAP3-4 was 3.67:3.68:1 in early floral buds of wild type Pet33-10. The expression level of BnAP3-2, BnAP3-3 and BnAP3-4 in early floral buds of Apet33-10 was down-regulated to 36.6, 28.3 and 66.8% with the comparison of that of wild type, respectively, and the overall expression level of AP3 genes in apetalous mutant amounted to 45.0% of that in wild type. The difference in the expression level of each AP3 gene in stamen between apetalous and wild type lines was not significant. It is suggested that lower abundant expression of AP3 genes during the early flower development might be enough for stamen primordium initiation, but not enough for petal primordium initiation in the apetalous line Apet33-10.

Global expression profiling applied to the analysis of Arabidopsis stamen development

To obtain detailed information about gene expression during stamen development in Arabidopsis (Arabidopsis thaliana), we compared, by microarray analysis, the gene expression profile of wild-type inflorescences to those of the floral mutants apetala3, sporocyteless/nozzle, and male sterile1 (ms1), in which different aspects of stamen formation are disrupted. These experiments led to the identification of groups of genes with predicted expression at early, intermediate, and late stages of stamen development. Validation experiments using in situ hybridization confirmed the predicted expression patterns. Additional experiments aimed at characterizing gene expression specifically during microspore formation. To this end, we compared the gene expression profiles of wild-type flowers of distinct developmental stages to those of the ms1 mutant. Computational analysis of the datasets derived from this experiment led to the identification of genes that are likely involved in the control of key developmental processes during microsporogenesis. We also identified a large number of genes whose expression is prolonged in ms1 mutant flowers compared to the wild type. This result suggests that MS1, which encodes a putative transcriptional regulator, is involved in the stage-specific repression of these genes. Lastly, we applied reverse genetics to characterize several of the genes identified in the microarray experiments and uncovered novel regulators of microsporogenesis, including the transcription factor MYB99 and a putative phosphatidylinositol 4-kinase.

The homeotic protein AGAMOUS controls late stamen development by regulating a jasmonate biosynthetic gene in Arabidopsis

The Arabidopsis thaliana floral homeotic gene AGAMOUS (AG) plays a central role in reproductive organ (stamen and carpel) development. AG RNA is expressed in the center of floral primordia from a time prior to the initiation of stamen and carpel primordia until late in flower development. While early AG expression acts in specification of stamens and carpels, the role, if any, of continued AG expression in later flower development is unknown. To examine the timing of AG action and its possible late-stage functions, we performed a series of time-course experiments using a transgenic line with inducible AG activity in an ag homozygous mutant background. We show that AG controls late-stage stamen development, including anther morphogenesis and dehiscence, as well as filament formation and elongation. We further show that AG coordinates late stamen maturation by controlling a biosynthetic gene of the lipid-derived phytohormone jasmonic acid (JA). Expression analysis and in vivo binding of AG indicate that AG directly regulates the transcription of a catalytic enzyme of JA, DEFECTIVE IN ANTHER DEHISCENCE1. Our results indicate that stamen identity and differentiation control by AG is achieved by the regulation of different transcriptional cascades in different floral stages, with organ specification induced early, followed by phytohormone biosynthesis to coordinate stamen maturation.

Transcriptional analysis of petal organogenesis in Gerbera hybrida

Understanding of the molecular interplay, which determines early steps of flower formation has grown considerably during last years. In contrast, genetic actions responsible for how flower organs acquire their size and shape at later phases of organogenesis are still poorly understood. We have exploited the large and anatomically simple Gerbera (Gerbera hybrida var. Terra regina) ray flower petals to describe transcriptional changes during organogenesis. Gerbera 9 K cDNA microarray was utilized to profile gene expression at six different developmental stages of petal organogenesis, at the earliest stage expansion of petals is starting and at the latest stage petals have reached their final size and shape. Genes potentially participating in petal opening were identified based on the similarity in expression with a known marker gene. Our results showed characteristic sets of genes expressed during the cell division and cell expansion phases of petal development. Interestingly, there was a transition stage during which neither cell division nor cell expansion marker genes were abundantly expressed. Moreover, constitutive expression of late petal specific genes indicates that they participate in petal organogenesis throughout the development and they are not involved in stage specific switch points.

Divergent regulatory OsMADS2 functions control size, shape and differentiation of the highly derived rice floret second-whorl organ

Functional diversification of duplicated genes can contribute to the emergence of new organ morphologies. Model eudicot plants like Arabidopsis thaliana and Antirrhinum majus have a single PI/GLO gene that together with AP3/DEF regulate petal and stamen formation. Lodicules of grass flowers are morphologically distinct reduced organs occupying the position of petals in other flowers. They serve a distinct function in partial and transient flower opening to allow stamen emergence and cross-pollination. Grasses have duplicated PI/GLO-like genes and in rice (Oryza sativa) one these genes, OsMADS2, controls lodicule formation without affecting stamen development. In this study, we investigate the mechanistic roles played by OsMADS2. We ascribe a function for OsMADS2 in controlling cell division and differentiation along the proximal-distal axis. OsMADS2 is required to trigger parenchymatous and lodicule-specific vascular development while maintaining a small organ size. Our data implicate the developmentally late spatially restricted accumulation of OsMADS2 transcripts in the differentiating lodicule to control growth of these regions. The global architecture of transcripts regulated by OsMADS2 gives insights into the regulation of cell division and vascular differentiation that together can form this highly modified grass organ with important functions in floret opening and stamen emergence independent of the paralogous gene OsMADS4.

GASA4, one of the 14-member Arabidopsis GASA family of small polypeptides, regulates flowering and seed development

Members of the plant-specific gibberellic acid-stimulated Arabidopsis (GASA) gene family play roles in hormone response, defense and development. We have identified six new Arabidopsis GASA genes, bringing the total number of family members to 14. Here we show that these genes all encode small polypeptides that share the common structural features of an N-terminal putative signal sequence, a highly divergent intermediate region and a conserved 60 amino acid C-terminal domain containing 12 conserved cysteine residues. Analysis of promoter::GUS (beta-glucuronidase) transgenic plants representing six different GASA loci reveals that the promoters are activated in a variety of stage- and tissue-specific patterns during development, indicating that the GASA genes are involved in diverse processes. Characterization of GASA4 shows that the promoter is active in the shoot apex region, developing flowers and developing embryos. Phenotypic analyses of GASA4 loss-of-function and gain-of-function lines indicate that GASA4 regulates floral meristem identity and also positively affects both seed size and total seed yield.

Rapid transcriptome changes induced by cytosolic Ca2+ transients reveal ABRE-related sequences as Ca2+-responsive cis elements in Arabidopsis

The regulation of gene expression by cellular calcium is crucial for plant defense against biotic and abiotic stresses. However, the number of genes known to respond to specific transient calcium signals is limited, and as yet there is no definition of a calcium-responsive cis element in plants. Here, we generated specific cytosolic calcium transients in intact Arabidopsis thaliana seedlings and linked them to early transcriptome changes, followed by bioinformatic analysis of the responsive genes. A cytosolic calcium transient induced by calmodulin antagonists and blocked by lanthanides was characterized using aequorin-based luminometry and photon imaging. Analysis of transcriptome changes revealed 230 calcium-responsive genes, of which 162 were upregulated and 68 were downregulated. These include known early stress-responsive genes as well as genes of unknown function. Analysis of their upstream regions revealed, exclusively in the upregulated genes, a highly significant occurrence of a consensus sequence (P < 10(-13)) comprising two abscisic acid-specific cis elements: the abscisic acid-responsive element (ABRE; CACGTG[T/C/G]) and its coupling element ([C/A]ACGCG[T/C/G]) [corrected] Finally, we show that a tetramer of the ABRE cis element is sufficient to confer transcriptional activation in response to cytosolic Ca(2+) transients. Thus, at least for some specific Ca(2+) transients and motif combinations, ABREs function as Ca(2+)-responsive cis elements.

Rapid transcriptome changes induced by cytosolic Ca2+ transients reveal ABRE-related sequences as Ca2+-responsive cis elements in Arabidopsis

The regulation of gene expression by cellular calcium is crucial for plant defense against biotic and abiotic stresses. However, the number of genes known to respond to specific transient calcium signals is limited, and as yet there is no definition of a calcium-responsive cis element in plants. Here, we generated specific cytosolic calcium transients in intact Arabidopsis thaliana seedlings and linked them to early transcriptome changes, followed by bioinformatic analysis of the responsive genes. A cytosolic calcium transient induced by calmodulin antagonists and blocked by lanthanides was characterized using aequorin-based luminometry and photon imaging. Analysis of transcriptome changes revealed 230 calcium-responsive genes, of which 162 were upregulated and 68 were downregulated. These include known early stress-responsive genes as well as genes of unknown function. Analysis of their upstream regions revealed, exclusively in the upregulated genes, a highly significant occurrence of a consensus sequence (P < 10(-13)) comprising two abscisic acid-specific cis elements: the abscisic acid-responsive element (ABRE; CACGTG[T/C/G]) and its coupling element ([C/A]ACGCG[T/C/G]) [corrected] Finally, we show that a tetramer of the ABRE cis element is sufficient to confer transcriptional activation in response to cytosolic Ca(2+) transients. Thus, at least for some specific Ca(2+) transients and motif combinations, ABREs function as Ca(2+)-responsive cis elements.

Evolutionary divergence of LFY function in the mustards Arabidopsis thaliana and Leavenworthia crassa

LEAFY (LFY), a transcription factor involved in the regulation of flower development in Arabidopsis thaliana, has been identified as a candidate gene in the diversification of plant architecture in Brassicaceae. Previous research with Leavenworthia crassa, which produces solitary flowers in the axils of rosette leaves, has shown that the L. crassa LFY ortholog, LcrLFY, rescues most aspects of flower development in A. thaliana but showed two novel traits: flowers produced additional petals and inflorescences produced terminal flowers. In this paper, we explore the molecular mechanisms responsible for these novel phenotypes. We used microarray hybridizations to identify 32 genes differentially expressed between a transgenic LcrLFY line and a control transgenic LFY line. Of particular interest, TERMINAL FLOWER 1 (TFL1) transcripts were found at elevated levels in LcrLFY lines. To distinguish regulatory versus functional changes within the LcrLFY locus, reciprocal chimeric transgenes between LcrLFY and LFY were constructed. These lines implicate divergence of LcrLFY cis-regulation as the primary cause of both novel transgenic phenotypes but implicate divergence of LcrLFY protein function as the primary cause of elevated TFL1 levels. Taken together these results show that LcrLFY has diverged from A. thaliana in both the cis-regulatory and protein-coding regions and imply that molecular coevolution of LcrLFY and the L. crassa TFL1 ortholog, LcrTFL1, contributed to the evolution of rosette flowering.

Wrinkled petals and stamens 1, is required for the morphogenesis of petals and stamens in Lotus japonicus

Although much progress has been made in understanding how floral organ identity is determined during the floral development, less is known about how floral organ is elaborated in the late floral developmental stages. Here we describe a novel floral mutant, wrinkled petals and stamens1 (wps1), which shows defects in the development of petals and stamens. Genetic analysis indicates that wps1 mutant is corresponding to a single recessive locus at the long arm of chromosome 3. The early development of floral organs in wps1 mutant is similar to that in wild type, and the malfunction of the mutant commences in late developmental stages, displaying a defect on the appearance of petals and stamens. In the mature flower, petals and stamen filaments in the mutant are wrinkled or folded, and the cellular morphology under L1 layer of petals and stamen filaments is abnormal. It is found that the expression patterns of floral organ identity genes are not affected in wps1 mutants compared with that of wild type, consistent with the unaltered development of all floral organs. Furthermore, the identities of epidermal cells in different type of petals are maintained. The histological analysis shows that in wps1 flowers all petals are irregularly folded, and there are knotted structures in the petals, while the shape and arrangement of inner cells are malformed and unorganized. Based on these results, we propose that Wps1 acts downstream to the class B floral organ identity genes, and functions to modulate the cellular differentiation during the late flower developmental stages.

BIGPETALp, a bHLH transcription factor is involved in the control of Arabidopsis petal size

In Arabidopsis, APETALA1, PISTILLATA, APETALA3 and SEPALLATA interact to form multimeric protein complexes required to specify petal identity. However, the downstream events that lead to petal specific shape and size remain largely unknown. Organ final size can be influenced by cell number or cell expansion or both. To date, no gene that specifically limits petal size by controlling postmitotic cell expansion has been identified. Here we have identified a novel petal-expressed, basic helix-loop-helix encoding gene (BIGPETAL, BPE) that is involved in the control of petal size. BPE is expressed via two mRNAs derived from an alternative splicing event. The BPEub transcript is expressed ubiquitously, whereas the BPEp transcript is preferentially expressed in petals. We demonstrate that BPEp is positively regulated downstream of APETALA3, PISTILLATA, APETALA1 and PISTILLATA3 and is negatively regulated downstream of AGAMOUS. Plants that lack the petal-expressed variant BPEp have larger petals as a result of increased cell size, showing that BPEp interferes with postmitotic cell expansion. BPEp is therefore a part of the network that links the patterning genes to final morphogenesis.

Molecular analysis of early rice stamen development using organ-specific gene expression profiling

Elucidating the regulatory mechanisms of plant organ formation is an important component of plant developmental biology and will be useful for crop improvement applications. Plant organ formation, or organogenesis, occurs when a group of primordial cells differentiates into an organ, through a well-orchestrated series of events, with a given shape, structure and function. Research over the past two decades has elucidated the molecular mechanisms of organ identity and dorsalventral axis determinations. However, little is known about the molecular mechanisms underlying the successive processes. To develop an effective approach for studying organ formation at the molecular level, we generated organ-specific gene expression profiles (GEPs) reflecting early development in rice stamen. In this study, we demonstrated that the GEPs are highly correlated with early stamen development, suggesting that this analysis is useful for dissecting stamen development regulation. Based on the molecular and morphological correlation, we found that over 26 genes, that were preferentially up-regulated during early stamen development, may participate in stamen development regulation. In addition, we found that differentially expressed genes during early stamen development are clustered into two clades, suggesting that stamen development may comprise of two distinct phases of pattern formation and cellular differentiation. Moreover, the organ-specific quantitative changes in gene expression levels may play a critical role for regulating plant organ formation.

Functional characterization of gibberellin-regulated genes in rice using microarray system

Gibberellin (GA) is collectively referred to a group of diterpenoid acids, some of which act as plant hormones and are essential for normal plant growth and development. DNA microarray technology has become the standard tool for the parallel quantification of large numbers of messenger RNA transcripts. The power of this approach has been demonstrated in dissecting plant physiology and development, and in unraveling the underlying cellular signaling pathways. To understand the molecular mechanism by which GA regulates the growth and development of plants, with reference to the monocot model plant-rice, it is essential to identify and analyze more genes and their products at the transcription and translation levels that are regulated by GA. With the availability of draft sequences of two major rice types, indica and japonica rice, it has become possible to analyze global expression profiles of genes on a genome scale. In this review, the progress made in finding new genes in rice leaf sheath using microarray system and their characterization is discussed. It is believed that the findings made in this regard have important implications for understanding the mechanism by which GA regulates the growth and development of rice.

Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling

In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 genes were repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are probably upregulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild-type, but production of a myb21myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.

Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis

Stem cell function during organogenesis is a key issue in developmental biology. The transcription factor SHORT-ROOT (SHR) is a critical component in a developmental pathway regulating both the specification of the root stem cell niche and the differentiation potential of a subset of stem cells in the Arabidopsis root. To obtain a comprehensive view of the SHR pathway, we used a statistical method called meta-analysis to combine the results of several microarray experiments measuring the changes in global expression profiles after modulating SHR activity. Meta-analysis was first used to identify the direct targets of SHR by combining results from an inducible form of SHR driven by its endogenous promoter, ectopic expression, followed by cell sorting and comparisons of mutant to wild-type roots. Eight putative direct targets of SHR were identified, all with expression patterns encompassing subsets of the native SHR expression domain. Further evidence for direct regulation by SHR came from binding of SHR in vivo to the promoter regions of four of the eight putative targets. A new role for SHR in the vascular cylinder was predicted from the expression pattern of several direct targets and confirmed with independent markers. The meta-analysis approach was then used to perform a global survey of the SHR indirect targets. Our analysis suggests that the SHR pathway regulates root development not only through a large transcription regulatory network but also through hormonal pathways and signaling pathways using receptor-like kinases. Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway.

Meta-analysis to combine the results of several microarray experiments reveals a new function for the transcription factor SHORT-ROOT in the development of vascular tissue.

Genome-wide analysis of spatial and temporal gene expression in rice panicle development

The basic structure of a rice inflorescence (the panicle) is determined by the pattern of branch formation, which is established at the early stages of panicle development. In this study we conducted global transcriptome profiling of the early stages of rice panicle development from phase transition to floral organ differentiation. To generate a meristem-specific gene-expression profile, shoot apical meristems (SAMs) and subsequently formed, very young panicles were collected manually and used for cDNA microarray analysis. We identified 357 out of 22,000 genes that are expressed differentially in the early stages of panicle development, and the 357 genes were classified into seven groups based on their temporal expression patterns. The most noticeable feature is that a fairly small number of genes, which are extensively enriched in transcription factors, are upregulated in the SAM immediately after phase transition. In situ hybridization analysis showed that each gene analysed exhibits a unique and interesting localization of mRNA. Remarkably, one of the transcription factors was proven to be a close downstream component of the pathway in which LAX, a major regulator of panicle branching, acts. These results suggest that our strategy--careful collection of meristems, global transcriptome analysis and subsequent in situ hybridization analysis--is useful not only to obtain a genome-wide view of gene expression, but also to reveal genetic networks controlling rice panicle development.

trans meets cis in MADS science

The interaction between a transcription factor and its binding site at the DNA is an integral part of transcriptional regulatory networks, which is fundamental for an understanding of biological processes. An example is the family of MADS domain transcription factors, which represent key regulators of processes in yeast, animals and plants. However, despite our extensive knowledge of these transcription factors, limited information is available on the cis-elements to which these proteins bind or how these elements are defined. Here, we discuss the current understanding of MADS protein binding sites and compare data from various organisms. This information can help us in developing algorithms to predict binding sites for MADS domain transcription factors, which would be a significant step forward in the identification of "down-stream" target genes and the elucidation of transcriptional networks.

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks

Gene regulatory pathways converge at the level of transcription, where interactions among regulatory genes and between regulators and target genes result in the establishment of spatiotemporal patterns of gene expression. The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the elucidation of regulatory networks at the genome level. To integrate this information into a Web-based knowledgebase, we have developed the Arabidopsis Gene Regulatory Information Server (AGRIS). AGRIS, which contains all Arabidopsis (Arabidopsis thaliana) promoter sequences, TFs, and their target genes and functions, provides the scientific community with a platform to establish regulatory networks. AGRIS currently houses three linked databases: AtcisDB (Arabidopsis thaliana cis-regulatory database), AtTFDB (Arabidopsis thaliana transcription factor database), and AtRegNet (Arabidopsis thaliana regulatory network). AtTFDB contains 1,690 Arabidopsis TFs and their sequences (protein and DNA) grouped into 50 (October 2005) families with information on available mutants in the corresponding genes. AtcisDB consists of 25,806 (September 2005) promoter sequences of annotated Arabidopsis genes with a description of putative cis-regulatory elements. AtRegNet links, in direct interactions, several hundred genes with the TFs that control their expression. The current release of AtRegNet contains a total of 187 (September 2005) direct targets for 66 TFs. AGRIS can be accessed at http://Arabidopsis.med.ohio-state.edu.

Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives

DNA microarrays have been used to characterize plant transcriptomes to answer various biological questions. While many studies have provided significant insights, there has been great debate about the general reliability of the technology and data analysis. When compared to well-established transcript analysis technologies, such as RNA blot analysis or quantitative reverse transcription-PCR, discrepancies have frequently been observed. The reasons for these discrepancies often relate to the technical and experimental systems. This review-tutorial addresses common problems in microarray analysis and describes: (i) methods to maximize extraction of valuable biological information from the vast amount of microarray data and (ii) approaches to balance resource availability with high scientific standards and technological innovation with peer acceptability.

Molecular mechanisms of flower development: an armchair guide

An afternoon stroll through an English garden reveals the breathtaking beauty and enormous diversity of flowering plants. The extreme variation of flower morphologies, combined with the relative simplicity of floral structures and the wealth of floral mutants available, has made the flower an excellent model for studying developmental cell-fate specification, morphogenesis and tissue patterning. Recent molecular genetic studies have begun to reveal the transcriptional regulatory cascades that control early patterning events during flower formation, the dynamics of the gene-regulatory interactions, and the complex combinatorial mechanisms that create a distinct final floral architecture and form.

Flower proteome: changes in protein spectrum during the advanced stages of rose petal development

Flowering is a unique and highly programmed process, but hardly anything is known about the developmentally regulated proteome changes in petals. Here, we employed proteomic technologies to study petal development in rose (Rosa hybrida). Using two-dimensional polyacrylamide gel electrophoresis, we generated stage-specific (closed bud, mature flower and flower at anthesis) petal protein maps with ca. 1,000 unique protein spots. Expression analyses of all resolved protein spots revealed that almost 30% of them were stage-specific, with ca. 90 protein spots for each stage. Most of the proteins exhibited differential expression during petal development, whereas only ca. 6% were constitutively expressed. Eighty-two of the resolved proteins were identified by mass spectrometry and annotated. Classification of the annotated proteins into functional groups revealed energy, cell rescue, unknown function (including novel sequences) and metabolism to be the largest classes, together comprising ca. 90% of all identified proteins. Interestingly, a large number of stress-related proteins were identified in developing petals. Analyses of the expression patterns of annotated proteins and their corresponding RNAs confirmed the importance of proteome characterization.

Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens

To identify genes involved in Arabidopsis thaliana petal and stamen organogenesis, we used a gene trap approach to examine the patterns of reporter expression at each stage of flower development of 1765 gene trap lines. In 80 lines, the reporter gene showed petal- and/or stamen-specific expression or lack of expression, or expression in distinct patterns within the petals and/or the stamens, including distinct suborgan domains of expression, such as tissue-specific lines marking epidermis and vasculature, as well as lines demarcating the proximodistal or abaxial/adaxial axes of the organs. Interestingly, reporter gene expression was typically restricted along the proximodistal axis of petals and stamens, indicating the importance of this developmental axis in patterning of gene expression domains in these organs. We identified novel domains of gene expression along the axis marking the midregion of the petals and apical and basal parts of the anthers. Most of the genes tagged in these 80 lines were identified, and their possible functions in petal and/or stamen differentiation are discussed. We also scored the floral phenotypes of the 1765 gene trap lines and recovered two mutants affecting previously uncharacterized genes. In addition to revealing common domains of gene expression, the gene trap lines reported here provide both useful markers and valuable starting points for reverse genetic analyses of the differentiation pathways in petal and stamen development.

Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars

Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P<0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon- and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the down-regulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.

Genome-wide identification of genes expressed in Arabidopsis pistils specifically along the path of pollen tube growth

Plant reproductive development is dependent on successful pollen-pistil interactions. In crucifers, the pollen tube must breach the stigma surface and burrow through the extracellular matrix of the stigma epidermal cells and transmitting tract cells before reaching its ovule targets. The high degree of specificity in pollen-pistil interactions and the precision of directional pollen tube growth suggest that signals are continually being exchanged between pollen/pollen tubes and cells of the pistil that line their path. However, with few exceptions, little is known about the genes that control these interactions. The specialized functions of stigma epidermal cells and transmitting tract cells are likely to depend on the activity of genes expressed specifically in these cells. In order to identify these genes, we used the Arabidopsis (Arabidopsis thaliana) ATH1 microarray to compare the whole-genome transcriptional profiles of stigmas and ovaries isolated from wild-type Arabidopsis and from transgenic plants in which cells of the stigma epidermis and transmitting tract were specifically ablated by expression of a cellular toxin. Among the 23,000 genes represented on the array, we identified 115 and 34 genes predicted to be expressed specifically in the stigma epidermis and transmitting tract, respectively. Both gene sets were significantly enriched in predicted secreted proteins, including potential signaling components and proteins that might contribute to reinforcing, modifying, or remodeling the structure of the extracellular matrix during pollination. The possible role of these genes in compatible and incompatible pollen-pistil interactions is discussed.

Characterization of SpAPETALA3 and SpPISTILLATA, B class floral identity genes in Spinacia oleracea, and their relationship to sexual dimorphism

Floral organ identity B class genes are generally recognized as being required for development of petals and stamens in angiosperm flowers. Spinach flowers are distinguished in their complete absence of petals in both sexes, and the absence of a developed stamen whorl in female flowers. As such, we hypothesized that differential expression of B class floral identity genes is integral to the sexual dimorphism in spinach flowers. We isolated two spinach orthologs of Arabidopsis B class genes by 3' and 5' RACE. Homology assignments were tested by comparisons of percent amino acid identities, searches for diagnostic consensus amino acid residues, conserved motifs, and phylogenetic groupings. In situ hybridization studies demonstrate that both spinach B class genes are expressed throughout the male floral meristem in early stages, and continue to be expressed in sepal primordia in reduced amounts at later stages of development. They are also highly expressed in the third whorl primordia when they arise and continue to be expressed in these tissues through the development of mature anthers. In contrast, neither gene can be detected in any stage in female flowers by in situ analyses, although northern blot experiments indicate low levels of SpAP3 within the inflorescence. The early, strong expressions of both B class floral identity genes in male floral primordia and their absence in female flowers demonstrate that B class gene expression precedes the origination of third whorl primordia (stamen) in males and is associated with the establishment of sexual floral dimorphism as it initiates in the first (sepal) whorl. These observations suggest that regulation of B class floral identity genes has a role in the development of sexual dimorphism and dioecy in spinach rather than being a secondary result of organ abortion.

Evolutionary dynamics of genes controlling floral development

Advances in the understanding of floral developmental genetics in model species such as Arabidopsis continue to provide an important foundation for comparative studies in other flowering plants. In particular, floral organ identity genes are the focus of many projects that are addressing both ancient and recent evolutionary questions. Expanded analyses of the evolution of these gene lineages have highlighted the dynamic nature of the gene birth-and-death process, and may have significant implications for the evolution of genetic pathways. Crucial functional studies of floral organ identity genes in diverse taxa are allowing the first real insight into the conservation of gene function, while findings on the genetic control of organ elaboration offer to open up new avenues for investigation. Taken together, these trends show that the field of floral developmental evolution continues to make significant progress towards elucidating the processes that have shaped the evolution of flower development and morphology.

Cell-specific regulation of a Brassica napus CMS-associated gene by a nuclear restorer with related effects on a floral homeotic gene promoter

Cytoplasmic male sterility (CMS) is a maternally inherited defect in pollen production specified by novel mitochondrial genes. It can be suppressed by nuclear restorer (Rf) genes which normally downregulate expression of a CMS-associated novel mitochondrial gene. Two forms of Brassica napus CMS, nap and pol, are associated with related chimeric genes, orf222 and orf224, respectively. We show that in pol and nap CMS, anther locule development is asynchronous and asymmetric, that one or more locules within each anther may fail to develop entirely and that CMS anthers display polarity in locule development. We show, by in situ hybridization, that orf222 transcripts accumulate in sterile anthers prior to development of morphological differences between CMS and restored stamens, and remain preferentially localized to microsporangia. In fertility-restored anthers, however, orf222 transcript levels remain low throughout development. Some sporogenous and meiotic cells differentiate within CMS anthers and form functional pollen despite retaining high orf222 transcript levels, suggesting that the effect of orf222 expression in blocking pollen development is limited to an early and specific stage. Transcripts of other mitochondrial genes, exemplified by atp6 and cob, and of the nuclear-encoded ATP synthase gamma subunit, accumulate preferentially in the microsporangia of both sterile and fertile anthers. Thus nuclear fertility restoration reduces orf222 transcript levels in a gene and tissue-specific manner. We observe differences between CMS and fertile plants in the timing and patterning of APETALA3 promoter activity that suggest a possible basis for the developmental abnormalities of CMS flowers.

Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis

Floral organs, whose identity is determined by specific combinations of homeotic genes, originate from a group of undifferentiated cells called the floral meristem. In Arabidopsis, the homeotic gene AGAMOUS (AG) terminates meristem activity and promotes development of stamens and carpels. To understand the program of gene expression activated by AG, we followed genome-wide expression during early stamen and carpel development. The AG target genes included most genes for which mutant screens revealed a function downstream of AG. Novel targets were validated by in situ hybridisation and binding to AG in vitro and in vivo. Transcription factors formed a large fraction of AG targets, suggesting that during early organogenesis, much of the genetic program is concerned with elaborating gene expression patterns. The results also suggest that AG and other homeotic proteins with which it interacts (SEPALLATA3, APETALA3, PISTILLATA) are coordinately regulated in a positive-feedback loop to maintain their own expression, and that AG activates biosynthesis of gibberellin, which has been proposed to promote the shift from meristem identity to differentiation.

Conservation of B-class floral homeotic gene function between maize andArabidopsis

The ABC model of flower development, established through studies in eudicot model species, proposes that petal and stamen identity are under the control of B-class genes. Analysis of B- and C-class genes in the grass species rice and maize suggests that the C- and B-class functions are conserved between monocots and eudicots, with B-class genes controlling stamen and lodicule development. We have undertaken a further analysis of the maize B-class genes Silky1, the putative AP3 ortholog, and Zmm16, a putative PI ortholog, in order to compare their function with the Arabidopsis B-class genes. Our results show that maize B-class proteins interact in vitro to bind DNA as an obligate heterodimer, as do Arabidopsis B-class proteins. The maize proteins also interact with the appropriate Arabidopsis B-class partner proteins to bind DNA. Furthermore, we show that maize B-class genes are capable of rescuing the corresponding Arabidopsis B-class mutant phenotypes. This demonstrates B-class activity of the maize gene Zmm16, and provides compelling evidence that B-class gene function is conserved between monocots and eudicots.

Characterization of antirrhinum petal development and identification of target genes of the class B MADS box gene DEFICIENS

The class B MADS box transcription factors DEFICIENS (DEF) and GLOBOSA (GLO) of Antirrhinum majus together control the organogenesis of petals and stamens. Toward an understanding of how the downstream molecular mechanisms controlled by DEF contribute to petal organogenesis, we conducted expression profiling experiments using macroarrays comprising >11,600 annotated Antirrhinum unigenes. First, four late petal developmental stages were compared with sepals. More than 500 ESTs were identified that comprise a large number of stage-specifically regulated genes and reveal a highly dynamic transcriptional regulation. For identification of DEF target genes that might be directly controlled by DEF, we took advantage of the temperature-sensitive def-101 mutant. To enhance the sensitivity of the profiling experiments, one petal developmental stage was selected, characterized by increased transcriptome changes that reflect the onset of cell elongation processes replacing cell division processes. Upon reduction of the DEF function, 49 upregulated and 52 downregulated petal target genes were recovered. Eight target genes were further characterized in detail by RT-PCR and in situ studies. Expression of genes responding rapidly toward an altered DEF activity is confined to different petal tissues, demonstrating the complexity of the DEF function regulating diverse basic processes throughout petal morphogenesis.

Identification and expression profiling of tomato genes differentially regulated during a resistance response to Xanthomonas campestris pv. vesicatoria

The gram-negative bacterium Xanthomonas campestris pv. vesicatoria is the causal agent of spot disease in tomato and pepper. Plants of the tomato line Hawaii 7981 are resistant to race T3 of X. campestris pv. vesicatoria expressing the type III effector protein AvrXv3 and develop a typical hypersensitive response upon bacterial challenge. A combination of suppression subtractive hybridization and microarray analysis identified a large set of cDNAs that are induced or repressed during the resistance response of Hawaii 7981 plants to X. campestris pv. vesicatoria T3 bacteria. Sequence analysis of the isolated cDNAs revealed that they correspond to 426 nonredundant genes, which were designated as XRE (Xanthomonas-regulated) genes and were classified into more than 20 functional classes. The largest functional groups contain genes involved in defense, stress responses, protein synthesis, signaling, and photosynthesis. Analysis of XRE expression kinetics during the tomato resistance response to X. campestris pv. vesicatoria T3 revealed six clusters of genes with coordinate expression. In addition, by using isogenic X. campestris pv. vesicatoria T2 strains differing only by the avrXv3 avirulence gene, we found that 77% of the identified XRE genes were directly modulated by expression of the AvrXv3 effector protein. Interestingly, 64% of the XRE genes were also induced in tomato during an incompatible interaction with an avirulent strain of Pseudomonas syringae pv. tomato. The identification and expression analysis of X. campestris pv. vesicatoria T3-modulated genes, which may be involved in the control or in the execution of plant defense responses, set the stage for the dissection of signaling and cellular responses activated in tomato plants during the onset of spot disease resistance.

Transcript profiling of transcription factor genes during silique development in Arabidopsis

Flower development is a key process for all angiosperms and is essential for sexual reproduction. The last phase in flower development is fertilization of the ovules and formation of the fruits, which are both biologically and economically of importance. Here, we report the expression profiles of over 1100 unique Arabidopsis genes coding for known and putative transcription factors (TFs) during silique development using high-density filter array hybridizations. Hierarchical cluster analyses revealed distinct expression profiles for the different silique developmental stages. This allowed a functional classification of these expression profiles in groups, namely pistil development, embryogenesis, seed maturation, fruit maturation, and fruit development. A further focus was made on the MADS-box family, which contains many members that are functionally well-characterized. The expression profiles of these MADS-box genes during silique development give additional clues on their functions and evolutionary relationship.

Genome-wide analysis of spatial gene expression in Arabidopsis flowers

We have compared the gene expression profiles of inflorescences of the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous with that of wild-type plants using a flower-specific cDNA microarray and a whole genome oligonucleotide array. By combining the data sets from the individual mutant/wild type comparisons, we were able to identify a large number of genes that are, within flowers, predicted to be specifically or at least predominantly expressed in one type of floral organ. We have analyzed the expression patterns of several of these genes by in situ hybridization and found that they match the predictions that were made based on the microarray experiments. Moreover, genes with known floral organ-specific expression patterns were correctly assigned by our analysis. The vast majority of the identified transcripts are found in stamens or carpels, whereas few genes are predicted to be expressed specifically or predominantly in sepals or petals. These findings indicate that spatially limited expression of a large number of genes is part of flower development and that its extent differs significantly between the reproductive organs and the organs of the perianth.

Flower development: initiation, differentiation, and diversification

Flowering is one of the most intensively studied processes in plant development. Despite the wide diversity in floral forms, flowers have a simple stereotypical architecture. Flowers develop from florally determined meristems. These small populations of cells proliferate to form the floral organs, including the sterile outer organs, the sepals and petals, and the inner reproductive organs, the stamens and carpels. In the past decade, analyses of key flowering genes have been carried out primarily in Arabidopsis and have provided a foundation for understanding the underlying molecular genetic mechanisms controlling different aspects of floral development. Such studies have illuminated the transcriptional cascades responsible for the regulation of these key genes, as well as how these genes effect their functions. In turn, these studies have resulted in the refinement of the original ideas of how flowers develop and have indicated the gaps in our knowledge that need to be addressed.

Global expression profiling applied to plant development

Plant development is controlled by both endogenous genetic programs and responses to exogenous signals. Microarray experiments are being used to identify the genes involved in these developmental processes. Most of the analyses conducted to date have been conducted on whole organs. Although these studies have provided valuable information, they are limited by the composite nature of plant organs that consist of multiple cell types. Technical advances that have made it possible to study global patterns of gene expression in individual cell types promise to increase greatly the information revealed by microarray experiments.

Dissection of floral induction pathways using global expression analysis

Flowering of the reference plant Arabidopsis thaliana is controlled by several signaling pathways, which converge on a small set of genes that function as pathway integrators. We have analyzed the genomic response to one type of floral inductive signal, photoperiod, to dissect the function of several genes transducing this stimulus, including CONSTANS, thought to be the major output of the photoperiod pathway. Comparing the effects of CONSTANS with those of FLOWERING LOCUS T, which integrates inputs from CONSTANS and other floral inductive pathways, we find that expression profiles of shoot apices from plants with mutations in either gene are very similar. In contrast, a mutation in LEAFY, which also acts downstream of CONSTANS, has much more limited effects. Another pathway integrator, SUPPRESSOR OF OVEREXPRESSION OF CO 1, is responsive to acute induction by photoperiod even in the presence of the floral repressor encoded by FLOWERING LOCUS C. We have discovered a large group of potential floral repressors that are down-regulated upon photoperiodic induction. These include two AP2 domain-encoding genes that can repress flowering. The two paralogous genes, SCHLAFMÜTZE and SCHNARCHZAPFEN, share a signature with partial complementarity to the miR172 microRNA, whose precursor we show to be induced upon flowering. These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering.

A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development

A microarray based on PCR amplicons of 1864 confirmed and predicted Arabidopsis transcription factor genes was produced and used to profile the global expression pattern in seedlings, specifically their light regulation. We detected expression of 1371 and 1241 genes in white-light- and dark-grown 6-d-old seedlings, respectively. Together they account for 84% of the transcription factor genes examined. This array was further used to study the kinetics of transcription factor gene expression change of dark-grown seedlings in response to blue light and the role of specific photoreceptors in this blue-light regulation. The expression of about 20% of those transcription factor genes are responsive to blue-light exposure, with 249 and 115 genes up or down-regulated, respectively. A large portion of blue-light-responsive transcription factor genes exhibited very rapid expression changes in response to blue light, earlier than the bulk of blue-light-regulated genes. This result suggests the involvement of transcription cascades in blue-light control of genome expression. Comparative analysis of the expression profiles of wild type and various photoreceptor mutants demonstrated that during early seedling development cryptochromes are the major photoreceptors for blue-light control of transcription factor gene expression, whereas phytochrome A and phototropins play rather limited roles.

Isolation, sequence analysis, and expression studies of florally expressed cDNAs in Arabidopsis

Molecular genetics has identified dozens of genes that regulate flower development in Arabidopsis. However, the complexity of flower development suggests that many other genes are yet to be uncovered. To identify floral genes that are expressed at low levels in the flower, we have sequenced 1587 cDNA fragments from a subtractive floral cDNA library. A total of 1222 unique genes represented by these ESTs are distributed on all five chromosomes with similar frequencies as all predicted genes in the genome. Among these, 17 genes were shown to be expressed anywhere for the first time because they were not found in previous EST and full-length cDNA datasets. Furthermore, 724 of the genes revealed by this library were not definitively shown to be expressed in the flower by previous floral EST datasets. In addition, 49 transcriptional regulators, 31 protein kinases, 12 zinc-finger proteins and other signaling proteins were found to be present in floral buds. Moreover, the EST sequences likely extended the transcribed regions of 26 previously annotated genes, and may have uncovered several previously unrecognized genes. To obtain additional clues about possible gene function, we hybridized cDNA microarray with probes derived from wild-type Arabidopsis rosette leaves and floral buds. We estimated that over 50% of genes were expressed at levels lower than 1/30 of the highest detectable signal intensity, indicating that many floral genes are expressed at low levels. Furthermore, 97 genes were found to be expressed at a higher level in the flower than the leaf by the Significance Analysis of Microarray (SAM) method with a 1.0% false discovery rate (FDR). Further RT-PCR analyses of selected genes support the microarray results. We suggest that the genes encoding putative regulatory proteins and at least some proteins with currently unknown functions might play important roles during flowering.

Global analysis of gene expression using GeneChip microarrays

DNA microarray technology, especially the use of GeneChip microarrays, has become a standard tool for parallel gene expression analysis. Recent improvements in GeneChip microarrays enable whole-genome expression analysis, and thus open a new avenue for studies of the composition, dynamics, and regulation of the transcriptome in plants.

And then there were many: MADS goes genomic

During the past decade, MADS-box genes have become known as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by bioinformatics, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Therefore, the recent advances in comparative and functional genomics should enable researchers to identify the full range of MADS-box gene functions, which should help us significantly in developing a better understanding of plant development and evolution.

Alternative splicing modulation by a LAMMER kinase impinges on developmental and transcriptome expression

Alternative splicing is a major contributor to genome complexity, playing a significant role in various cellular functions, including signal transduction, immunity, and development. The spliceosomal machinery is responsible for the processing of nuclear RNA. Several splicing factors associated with this complex are phosphorylated by kinases that possess a conserved LAMMER motif. We demonstrate in BY-2 tobacco cells a novel role for the LAMMER motif in the maintenance of proper subnuclear localization. Furthermore, high expression of the LAMMER kinase in Arabidopsis plants modulated the alternative splicing of specific endogenous genes and resulted in abnormal plant development and a novel transcriptome profile. A prominent feature was the upregulation of genes that play a role in protein turnover, suggesting a moderating function for these gene products in the control of alternative splicing events. Together, these results demonstrate alternative splicing modulation as a result of phosphorylation activity, providing an opportunity to study its global effect on the plasticity of plant development and gene expression at the organism level.

Expression profiling of plant development

Microarrays have been used to study the response of plants to many signals, including light, hormones and transcription factors. The results in each case can give an overall view of the global response to the signal or identify direct targets of the signal, and can reveal new links between different signaling pathways.