SPLICE SITE SELECTION IN PLANT PRE-mRNA SPLICING

An iterative gene-editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to multiple potyvirus isolates

Resistance to potyviruses in plants has been largely provided by the selection of natural variant alleles of eukaryotic translation initiation factors (eIF) 4E in many crops. However, the sources of such variability for breeding can be limited for certain crop species, while new virus isolates continue to emerge. Different methods of mutagenesis have been applied to inactivate the eIF4E genes to generate virus resistance, but with limited success due to the physiological importance of translation factors and their redundancy. Here, we employed genome editing approaches at the base level to induce non-synonymous mutations in the eIF4E1 gene and create genetic diversity in cherry tomato (Solanum lycopersicum var. cerasiforme). We sequentially edited the genomic sequences coding for two regions of eIF4E1 protein, located around the cap-binding pocket and known to be important for susceptibility to potyviruses. We show that the editing of only one of the two regions, by gene knock-in and base editing, respectively, is not sufficient to provide resistance. However, combining amino acid mutations in both regions resulted in resistance to multiple potyviruses without affecting the functionality in translation initiation. Meanwhile, we report that extensive base editing in exonic region can alter RNA splicing pattern, resulting in gene knockout. Altogether our work demonstrates that precision editing allows to design plant factors based on the knowledge on evolutionarily selected alleles and enlarge the gene pool to potentially provide advantageous phenotypes such as pathogen resistance.

Exon skipping in IspE Gene is associated with abnormal chloroplast development in rice albino leaf 4 mutant

The formation of leaf color largely depends on the components of pigment accumulation in plastids, which are involved in chloroplast development and division. Here, we isolated and characterized the rice albino leaf 4 (al4) mutant, which exhibited an albino phenotype and eventually died at the three-leaf stage. The chloroplasts in al4 mutant were severely damaged and unable to form intact thylakoid structure. Further analysis revealed that the candidate gene encodes 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE), which participates in the methylerythritol phosphate (MEP) pathway of isoprenoid biosynthesis. We further demonstrated that the mutation at the exon-intron junction site cause alternative splicing factors fail to distinguish the origin of the GT-AG intron, leading to exon skipping and producing a truncated OsIspE in the al4 mutant. Notably, disruption of OsIspE led to the reduced expression of chloroplast-associated genes, including chloroplast biosynthetic and translation related genes and photosynthetic associated nuclear genes (PhANGs). In summary, these findings reveal that OsIspE plays a crucial role in chloroplast biogenesis and provides novel insights into the function of CMK during chloroplast development in rice.

Identification of a biomass unaffected pale green mutant gene in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Chlorophyll (Chl) is an essential component of the photosynthetic apparatus and pigments in plant greening. Leaf color is an important agronomic and commercial trait of Chinese cabbage. In this study, we identified a pale green mutant pgm created by ethyl methane sulfonate (EMS) mutagenesis in Chinese cabbage. Compared with wild-type (FT), pgm had a lower Chl content with a higher Chl a/b ratio, imperfect chloroplast structure, and lower non-photochemical quenching. However, its net photosynthetic rate and biomass showed no significant differences. Genetic analysis revealed that the pale green phenotype of pgm was controlled by a recessive nuclear gene, designated as Brpgm. We applied BSR-Seq, linkage analysis, and whole-genome resequencing to map Brpgm and predicted that the target gene was BraA10g007770.3C (BrCAO), which encodes chlorophyllide a oxygenase (CAO). Brcao sequencing results showed that the last nucleotide of its first intron changed from G to A, causing the deletion of the first nucleotide in its second CDS and termination of the protein translation. The expression of BrCAO in pgm was upregulated, and the enzyme activity of CAO in pgm was significantly decreased. These results provide an approach to explore the function of BrCAO and create a pale green variation in Chinese cabbage.

Monoterpene Synthase Genes and Monoterpene Profiles in Pinus nigra subsp. laricio

In the present study, we carried out a quantitative analysis of the monoterpenes composition in different tissues of the non-model conifer Pinus nigra J.F. Arnold subsp. laricio Palib. ex Maire (P. laricio, in short). All the P. laricio tissues examined showed the presence of the same fourteen monoterpenes, among which the most abundant were β-phellandrene, α-pinene, and β-pinene, whose distribution was markedly tissue-specific. In parallel, from the same plant tissues, we isolated seven full-length cDNA transcripts coding for as many monoterpene synthases, each of which was found to be attributable to one of the seven phylogenetic groups in which the d1-clade of the canonical classification of plants' terpene synthases can be subdivided. The amino acid sequences deduced from the above cDNA transcripts allowed to predict their putative involvement in the biosynthesis of five of the monoterpenes identified. Transcripts profiling revealed a differential gene expression across the different tissues examined, and was found to be consistent with the corresponding metabolites profiles. The genomic organization of the seven isolated monoterpene synthase genes was also determined.

Diterpene Resin Acids and Olefins in Calabrian Pine (Pinus nigra subsp. laricio (Poiret) Maire) Oleoresin: GC-MS Profiling of Major Diterpenoids in Different Plant Organs, Molecular Identification and Expression Analysis of Diterpene Synthase Genes

A quali-quantitative analysis of diterpenoid composition in tissues obtained from different organs of Pinus nigra subsp. laricio (Poiret) Maire (Calabrian pine) was carried out. Diterpene resin acids were the most abundant diterpenoids across all the examined tissues. The same nine diterpene resin acids were always found, with the abietane type prevailing on the pimarane type, although their quantitative distribution was found to be remarkably tissue-specific. The scrutiny of the available literature revealed species specificity as well. A phylogeny-based approach allowed us to isolate four cDNAs coding for diterpene synthases in Calabrian pine, each of which belonging to one of the four groups into which the d3 clade of the plants' terpene synthases family can be divided. The deduced amino acid sequences allowed predicting that both monofunctional and bifunctional diterpene synthases are involved in the biosynthesis of diterpene resin acids in Calabrian pine. Transcript profiling revealed differential expression across the different tissues and was found to be consistent with the corresponding diterpenoid profiles. The isolation of the complete genomic sequences and the determination of their exon/intron structures allowed us to place the diterpene synthase genes from Calabrian pine on the background of current ideas on the functional evolution of diterpene synthases in Gymnosperms.

ORF Ι of Mycovirus SsNSRV-1 is Associated with Debilitating Symptoms of Sclerotinia sclerotiorum

We previously identified Sclerotinia sclerotiorum negative-stranded virus 1 (SsNSRV-1), the first (-) ssRNA mycovirus, associated with hypovirulence of its fungal host Sclerotinia sclerotiorum. In this study, functional analysis of Open Reading Frame Ι (ORF Ι) of SsNSRV-1 was performed. The integration and expression of ORF Ι led to defects in hyphal tips, vegetative growth, and virulence of the mutant strains of S. sclerotiorum. Further, differentially expressed genes (DEGs) responding to the expression of ORF Ι were identified by transcriptome analysis. In all, 686 DEGs consisted of 267 up-regulated genes and 419 down-regulated genes. DEGs reprogramed by ORF Ι were relevant to secretory proteins, pathogenicity, transcription, transmembrane transport, protein biosynthesis, modification, and metabolism. Alternative splicing was also detected in all mutant strains, but not in hypovirulent strain AH98, which was co-infected by SsNSRV-1 and Sclerotinia sclerotiorum hypovirus 1 (SsHV-1). Thus, the integrity of SsNSRV-1 genome may be necessary to protect viral mRNA from splicing and inactivation by the host. Taken together, the results suggested that protein ORF Ι could regulate the transcription, translation, and modification of host genes in order to facilitate viral proliferation and reduce the virulence of the host. Therefore, ORF Ι may be a potential gene used for the prevention of S. sclerotiorum.

Comprehensive genomic analyses with 115 plastomes from algae to seed plants: structure, gene contents, GC contents, and introns

BACKGROUND

Chloroplasts are a common character in plants. The chloroplasts in each plant lineage have shaped their own genomes, plastomes, by structural changes and transferring many genes to nuclear genomes during plant evolution. Some plastid genes have introns that are mostly group II introns.

OBJECTIVE

This study aimed to get genomic and evolutionary insights on the plastomes from green algae to flowering plants.

METHODS

Plastomes of 115 species from green algae, bryophytes, pteridophytes (spore bearing vascular plants), gymnosperms, and angiosperms were mined from NCBI organelle genome database. Plastome structure, gene contents and GC contents were analyzed by the in-house developed Phyton code. Intronic features including presence/absence, length, intron phases were analyzed by manually in the annotated information in NCBI.

RESULTS

The canonical quadripartite structures were retained in most plastomes except of a few plastomes that had lost an invert repeat (IR). Expansion or reduction or deletion of IRs resulted in the length variation of the plastomes. The number of protein coding genes ranged from 40 to 92 with an average 79.43 ± 5.84 per plastome and gene losses were apparent in specific lineages. The number of trn genes ranged from 13 to 33 with an average 21.19 ± 2.42 per plastome. Ribosomal RNA genes, rrn, were located in the IRs so that they were present in a duplicate except of the species that had lost one of the IR. GC contents were variable from 24.9 to 51.0% with an average 38.21 ± 3.27%, indicating bias to high AT contents. Plastid introns were present in 18 protein coding genes, six trn genes, and one rrn gene. Intron losses occurred among the orthologous genes in different plant lineages. The plastid introns were long compared with the nuclear introns, which might be related with the spliceosome nuclear introns and self-splicing group II plastid introns. The trnK-UUU intron contained the maturase encoding matK gene except in the chlorophyte algae and monilophyte ferns in which the trnK-UUU was lost, but matK retained. There were many annotation artefacts in the intron positions in the NCBI database. In the analysis of intron phases, phase 0 introns were more frequent than those of phase 2 and 3 introns. Phase polymorphism was observed in the introns of clpP which was derived from nucleotide insertion. Plastid trn introns were long compared to the archaeal or eukaryotic nuclear tRNA introns. Of the six plastid trn introns, one was at the D loop and other five were at the anticodon loop. The insertion sites were conserved among the trn genes in archaea, eukaryotic nuclear and plastid tRNA genes.

CONCLUSIONS

Current study refurbrished the previous findings of structural variations, gene contents, and GC contents of the chloroplast genomes from green algae to flowering plants. The study also included some noble findings and discussions on the plastome introns including their length variations and phase variation. We also presented and corrected some false annotations on the introns in protein coding and tRNA genes in the genome database, which might be confirmed by the chloroplast transcriptome analysis in the future.

Short and narrow flag leaf1, a GATA zinc finger domain-containing protein, regulates flag leaf size in rice (Oryza sativa)

BACKGROUND

The flag leaf of rice (Oryza sativa L.) is an important determinant of plant type characteristics and grain yield. Identification of flag leaf mutants of rice is crucial to elucidate the molecular mechanism of flag-leaf development, and for exploitation of rice germplasm resources.

RESULTS

In this study, we describe a mutant designated short and narrow flag leaf 1 (snfl1). Histological analysis showed that the length of epidermal cells and number of longitudinal veins were decreased in the flag leaf of the snfl1 mutant. Map-based cloning indicated that a member of the GATA family of transcription factors is a candidate gene for SNFL1. A single-nucleotide transition at the last base in the single intron of snfl1 led to variation in alternative splicing and early termination of translation. Complemented transgenic plants harbouring the candidate SNFL1 gene rescued the snfl1 mutant. Analysis of RT-PCR and the SNFL1 promoter by means of a GUS fusion expression assay showed that abundance of SNFL1 transcripts was higher in the culm, leaf sheath, and root. Expression of the SNFL1-GFP fusion protein in rice protoplasts showed that SNFL1 was localized in nucleus.

CONCLUSIONS

We conclude that SNFL1 is an important regulator of leaf development, the identification of which might have important implications for future research on GATA transcription factors.

A single-nucleotide exon found in Arabidopsis

The presence of introns in gene-coding regions is one of the most mysterious evolutionary inventions in eukaryotic organisms. It has been proposed that, although sequences involved in intron recognition and splicing are mainly located in introns, exonic sequences also contribute to intron splicing. The smallest constitutively spliced exon known so far has 6 nucleotides, and the smallest alternatively spliced exon has 3 nucleotides. Here we report that the Anaphase Promoting Complex subunit 11 (APC11) gene in Arabidopsis thaliana carries a constitutive single-nucleotide exon. In vivo transcription and translation assays performed using APC11-Green Fluorescence Protein (GFP) fusion constructs revealed that intron splicing surrounding the single-nucleotide exon is effective in both Arabidopsis and rice. This discovery warrants attention to genome annotations in the future.

Integration of the proteome and transcriptome reveals multiple levels of gene regulation in the rice dl2 mutant

Leaf vascular system differentiation and venation patterns play a key role in transporting nutrients and maintaining the plant shape, which is an important agronomic trait for improving photosynthetic efficiency. However, there is little knowledge about the regulation of leaf vascular specification and development. Here we utilized the rice midribless mutant (dl2) to investigate the molecular changes in transcriptome and proteome profiles during leaf vascular specification and differentiation. Using isobaric tags for relative and absolute quantification (iTRAQ) with digital gene expression (DGE) techniques, a nearly complete catalog of expressed protein and mRNA was acquired. From the catalog, we reliably identified 3172 proteins and 9,865,230 tags mapped to genes, and subsets of 141 proteins and 98 mRNAs, which were differentially expressed between the dl2 mutant and wild type. The correlation analysis between the abundance of differentially expressed mRNA and DEPs (differentially expressed proteins) revealed numerous discordant changes in mRNA/protein pairs and only a modest correlation was observed, indicative of divergent regulation of transcription and translational processes. The DEPs were analyzed for their involvement in biological processes and metabolic pathways. Up- or down- regulation of some key proteins confirmed that the physiological process of vascular differentiation is an active process. These key proteins included those not previously reported to be associated with vascular differentiation processes, and included proteins that are involved in the spliceosome pathway. Together, our results show that the developmental and physiological process of the leaf vascular system is a thoroughly regulated and complicated process and this work has identified potential targets for genetic modification that could be used to regulate the development of the leaf vasculature.

Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa

RNA helicases are enzymes that are thought to unwind double-stranded RNA molecules in an energy-dependent fashion through the hydrolysis of NTP. RNA helicases are associated with all processes involving RNA molecules, including nuclear transcription, editing, splicing, ribosome biogenesis, RNA export, and organelle gene expression. The involvement of RNA helicase in response to stress and in plant growth and development has been reported previously. While their importance in Arabidopsis and Oryza sativa has been partially studied, the function of RNA helicase proteins is poorly understood in Zea mays and Glycine max. In this study, we identified a total of RNA helicase genes in Arabidopsis and other crop species genome by genome-wide comparative in silico analysis. We classified the RNA helicase genes into three subfamilies according to the structural features of the motif II region, such as DEAD-box, DEAH-box and DExD/H-box, and different species showed different patterns of alternative splicing. Secondly, chromosome location analysis showed that the RNA helicase protein genes were distributed across all chromosomes with different densities in the four species. Thirdly, phylogenetic tree analyses identified the relevant homologs of DEAD-box, DEAH-box and DExD/H-box RNA helicase proteins in each of the four species. Fourthly, microarray expression data showed that many of these predicted RNA helicase genes were expressed in different developmental stages and different tissues under normal growth conditions. Finally, real-time quantitative PCR analysis showed that the expression levels of 10 genes in Arabidopsis and 13 genes in Zea mays were in close agreement with the microarray expression data. To our knowledge, this is the first report of a comparative genome-wide analysis of the RNA helicase gene family in Arabidopsis, Oryza sativa, Zea mays and Glycine max. This study provides valuable information for understanding the classification and putative functions of the RNA helicase gene family in crop growth and development.

A biophysical model for identifying splicing regulatory elements and their interactions

Alternative splicing (AS) of precursor mRNA (pre-mRNA) is a crucial step in the expression of most eukaryotic genes. Splicing factors (SFs) play an important role in AS regulation by binding to the cis-regulatory elements on the pre-mRNA. Although many splicing factors (SFs) and their binding sites have been identified, their combinatorial regulatory effects remain to be elucidated. In this paper, we derive a biophysical model for AS regulation that integrates combinatorial signals of cis-acting splicing regulatory elements (SREs) and their interactions. We also develop a systematic framework for model inference. Applying the biophysical model to a human RNA-Seq data set, we demonstrate that our model can explain 49.1%–66.5% variance of the data, which is comparable to the best result achieved by biophysical models for transcription. In total, we identified 119 SRE pairs between different regions of cassette exons that may regulate exon or intron definition in splicing, and 77 SRE pairs from the same region that may arise from a long motif or two different SREs bound by different SFs. Particularly, putative binding sites of polypyrimidine tract-binding protein (PTB), heterogeneous nuclear ribonucleoprotein (hnRNP) F/H and E/K are identified as interacting SRE pairs, and have been shown to be consistent with the interaction models proposed in previous experimental results. These results show that our biophysical model and inference method provide a means of quantitative modeling of splicing regulation and is a useful tool for identifying SREs and their interactions. The software package for model inference is available under an open source license.

Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana

MicroRNAs (miRNAs) have emerged as a class of regulators of gene expression through posttranscriptional degradation or translational repression in living cells. Increasing evidence points to the important relationship between miRNAs and environmental stress responses, but the regulatory mechanisms in plants are poorly understood. Here, we found that Arabidopsis thaliana intronic miR400 was cotranscribed with its host gene (At1g32583) and downregulated by heat treatment. Intriguingly, an alternative splicing (AS) event that occurred in the intron (306 bp) where MIR400 was located was specifically induced by heat stress. A 100 bp fragment was excised, and the remaining 206 bp intron containing MIR400 transcripts was retained in the host gene. The stress-induced AS event thus resulted in greater accumulation of miR400 primary transcripts and a low level of mature miR400. Together, these results provide the direct evidence that AS acts as a regulatory mechanism linking miRNAs and environmental stress in plants.

Natural rules for Arabidopsis thaliana pre-mRNA splicing site selection

The accurate prediction of plant pre-mRNA splicing sites has been studied extensively. The rules for plant pre-mRNA splicing still remain unknown. This study, based on confirmed sequence data, systematically analyzed all expressed genes on Arabidopsis thaliana chromosome IV to quantitatively explore the natural splicing rules. The results indicated that defining Arabidopsis thaliana pre-mRNA splicing sites required a combination of multiple factors including (1) relative conserved consensus sequence at splicing site; (2) individual nucleotide distribution pattern in 50 nucleotides up- and down-stream regions of splicing site; (3) quantitative analysis of individual nucleotide distribution by using the formulations concluded from this study. The combination of all these factors together can bring the accuracy of Arabidopsis thaliana splicing site recognition over 99%. The results provide additional information to the future of plant pre-mRNA splicing research.

Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. As very few genome-wide studies analyzing AS in plants are available, we have performed high-throughput sequencing of a normalized cDNA library which resulted in a high coverage transcriptome map of Arabidopsis. We detect ∼150,000 splice junctions derived mostly from typical plant introns, including an eightfold increase in the number of U12 introns (2069). Around 61% of multiexonic genes are alternatively spliced under normal growth conditions. Moreover, we provide experimental validation of 540 AS transcripts (from 256 genes coding for important regulatory factors) using high-resolution RT-PCR and Sanger sequencing. Intron retention (IR) is the most frequent AS event (∼40%), but many IRs have relatively low read coverage and are less well-represented in assembled transcripts. Additionally, ∼51% of Arabidopsis genes produce AS transcripts which do not involve IR. Therefore, the significance of IR in generating transcript diversity was generally overestimated in previous assessments. IR analysis allowed the identification of a large set of cryptic introns inside annotated coding exons. Importantly, a significant fraction of these cryptic introns are spliced out in frame, indicating a role in protein diversity. Furthermore, we show extensive AS coupled to nonsense-mediated decay in AFC2, encoding a highly conserved LAMMER kinase which phosphorylates splicing factors, thus establishing a complex loop in AS regulation. We provide the most comprehensive analysis of AS to date which will serve as a valuable resource for the plant community to study transcriptome complexity and gene regulation.

The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator

Correct interpretation of the coding capacity of RNA polymerase II transcribed eukaryotic genes is determined by the recognition and removal of intronic sequences of pre-mRNAs by the spliceosome. Our current knowledge on dynamic assembly and subunit interactions of the spliceosome mostly derived from the characterization of yeast, Drosophila, and human spliceosomal complexes formed on model pre-mRNA templates in cell extracts. In addition to sequential structural rearrangements catalyzed by ATP-dependent DExH/D-box RNA helicases, catalytic activation of the spliceosome is critically dependent on its association with the NineTeen Complex (NTC) named after its core E3 ubiquitin ligase subunit PRP19. NTC, isolated recently from Arabidopsis, occurs in a complex with the essential RNA helicase and GTPase subunits of the U5 small nuclear RNA particle that are required for both transesterification reactions of splicing. A compilation of mass spectrometry data available on the composition of NTC and spliceosome complexes purified from different organisms indicates that about half of their conserved homologs are encoded by duplicated genes in Arabidopsis. Thus, while mutations of single genes encoding essential spliceosome and NTC components lead to cell death in other organisms, differential regulation of some of their functionally redundant Arabidopsis homologs permits the isolation of partial loss of function mutations. Non-lethal pleiotropic defects of these mutations provide a unique means for studying the roles of NTC in co-transcriptional assembly of the spliceosome and its crosstalk with DNA repair and cell death signaling pathways.

The modified castor bean catalase intron is incompletely spliced in tobacco and Arabidopsis

In an attempt to insert the modified castor bean catalase intron (mCBC intron) into the coding sequence of the Cre recombinase gene, we found that the mCBC intron was not completely spliced from the resulting iCre gene in tobacco and Arabidopsis. Sequencing and allele-specific PCR analyses indicated that six nucleotides (UUACAG) at the 3' terminus of the mCBC intron were retained in the mature mRNA of the iCre gene. Moreover, the mCBC intron was incompletely spliced from the Gus gene in pCAMBIA vectors. A mutational analysis of the mCBC intron demonstrated that the incomplete splicing was due to an artificial 3' splice site introduced by the insertion of an adenine, which created a TAG (stop) codon near the 3' splice site of the original CBC intron. Deletion of the inserted adenine or the six nucleotides that were retained from the mCBC intron led to the complete removal of the intron from the resulting iCre2 and iCre3 genes. Thus, in this study, we not only characterized the incomplete splicing event of the mCBC intron in tobacco and Arabidopsis, but also reported the construction of two intron-containing Cre recombinase genes that are useful for plant biotechnology applications.

Alternate transcripts of a floral developmental regulator have both distinct and redundant functions in opium poppy

BACKGROUND AND AIMS

The MADS-box transcription factor AGAMOUS (AG) is an important regulator of stamen and fruit identity as well as floral meristem determinacy in a number of core eudicots and monocots. However, its role outside of these groups has not been assessed explicitly. Examining its role in opium poppy, a basal eudicot, could uncover much about the evolution and development of flower and fruit development in the angiosperms.

METHODS

AG orthologues were isolated by degenerate RT-PCR and the gene sequence and structure examined; gene expression was characterized using in situ hybridization and the function assessed using virus-induced gene silencing.

KEY RESULTS

In opium poppy, a basal eudicot, the AGAMOUS orthologue is alternatively spliced to produce encoded products that vary at the C-terminus, termed PapsAG-1 and PapsAG-2. Both transcripts are expressed at high levels in stamens and carpels. The functional implications of this alternative transcription were examined using virus-induced gene silencing and the results show that PapsAG-1 has roles in stamen and carpel identity, reflecting those found for Arabidopsis AG. In contrast, PapsAG-2, while displaying redundancy in these functions, has a distinctive role in aspects of carpel development reflected in septae, ovule and stigma defects seen in the loss-of-function line generated.

CONCLUSIONS

These results describe the first explicit functional analysis of an AG-clade gene in a basal eudicot; illustrate one of the few examples of the functional consequences of alternative splicing in transcription factors and reveal the importance of alternative transcription, as well as gene duplication, as a driving force in evolution.

Knock-out mutations of Arabidopsis SmD3-b induce pleotropic phenotypes through altered transcript splicing

SmD3 is a core protein of small nuclear ribonucleoprotein (snRNP) essential for splicing of primary transcripts. To elucidate function of SmD3 protein in plants, phenotypes and gene expression of SmD3 knock-out and overexpressing mutants in Arabidopsis have been analyzed. smd3-a knock-out mutant or SmD3-a and SmD3-b overexpressors did not show phenotypic alteration. Knock-out of SmD3-b resulted in the pleotropic phenotypes of delayed flowering time and completion of life cycle, reduced root growth, partially defective leaf venation, abnormal numbers of trichome branches, and changed numbers of floral organs. Microarray data revealed that the smd3-b mutant had altered expression of genes related to the above phenotypes, indirectly suggesting that changed splicing of these genes may cause the observed phenotypes. Splicing of selected genes was either totally blocked or reduced in the smd3-b mutant, indicating the important role of SmD3-b in the process. A double knock-out mutant of smd3-a and smd3-b could not be generated, indicating possible redundant function of these two genes. All data indicate that SmD3-b may be major component of the spliceosomal snRNP in Arabidopsis, but the function of SmD3-a may be redundant.

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

Combining translating ribosome affinity purification with RNA-seq for cell-specific profiling of translating RNAs in developing flowers.

Cell type comparisons of cell type-specific hormone responses, promoter motifs, coexpressed cognate binding factor candidates, and splicing isoforms.

Widespread post-transcriptional regulation at both the intron splicing and translational stages.

A new class of noncoding RNAs associated with polysomes.

What constitutes a differentiated cell type? How much do cell types differ in their transcription of genes? The development and functions of tissues rely on constant interactions among distinct and nonequivalent cell types. Answering these questions will require quantitative information on transcriptomes, proteomes, protein–protein interactions, protein–nucleic acid interactions, and metabolomes at cellular resolution. The systems approaches emerging in biology promise to explain properties of biological systems based on genome-wide measurements of expression, interaction, regulation, and metabolism. To facilitate a systems approach, it is essential first to capture such components in a global manner, ideally at cellular resolution.

Recently, microarray analysis of transcriptomes has been extended to a cellular level of resolution by using laser microdissection or fluorescence-activated sorting (for review, see Nelson et al, 2008). These methods have been limited by stresses associated with cellular separation and isolation procedures, and biases associated with mandatory RNA amplification steps. A newly developed method, translating ribosome affinity purification (TRAP; Zanetti et al, 2005; Heiman et al, 2008; Mustroph et al, 2009), circumvents these problems by epitopetagging a ribosomal protein in specific cellular domains to selectively purify polysomes. We combined TRAP with deep sequencing, which we term TRAP-seq, to provide cell-level spatiotemporal maps for Arabidopsis early floral development at single-base resolution.

Flower development in Arabidopsis has been studied extensively and is one of the best understood aspects of plant development (for review, see Krizek and Fletcher, 2005). Genetic analysis of homeotic mutants established the ABC model, in which three classes of regulatory genes, A, B and C, work in a combinatorial manner to confer organ identities of four whorls (Coen and Meyerowitz, 1991). Each class of regulatory gene is expressed in a specific and evolutionarily conserved domain, and the action of the class A, B and C genes is necessary for specification of organ identity (Figure 1A).

Using TRAP-seq, we purified cell-specific translating mRNA populations, which we and others call the translatome, from the A, B and C domains of early developing flowers, in which floral patterning and the specification of floral organs is established. To achieve temporal specificity, we used a floral induction system to facilitate collection of early stage flowers (Wellmer et al, 2006). The combination of TRAP-seq with domain-specific promoters and this floral induction system enabled fine spatiotemporal isolation of translating mRNA in specific cellular domains, and at specific developmental stages.

Multiple lines of evidence confirmed the specificity of this approach, including detecting the expression in expected domains but not in other domains for well-studied flower marker genes and known physiological functions (Figures 1B–D and 2A–C). Furthermore, we provide numerous examples from flower development in which a spatiotemporal map of rigorously comparable cell-specific translatomes makes possible new views of the properties of cell domains not evident in data obtained from whole organs or tissues, including patterns of transcription and cis-regulation, new physiological differences among cell domains and between flower stages, putative hormone-active centers, and splicing events specific for flower domains (Figure 2A–D). Such findings may provide new targets for reverse genetics studies and may aid in the formulation and validation of interaction and pathway networks.

Beside cellular heterogeneity, the transcriptome is regulated at several steps through the life of mRNA molecules, which are not directly available through traditional transcriptome profiling of total mRNA abundance. By comparing the translatome and transcriptome, we integratively profiled two key posttranscriptional control points, intron splicing and translation state. From our translatome-wide profiling, we (i) confirmed that both posttranscriptional regulation control points were used by a large portion of the transcriptome; (ii) identified a number of cis-acting features within the coding or noncoding sequences that correlate with splicing or translation state; and (iii) revealed correlation between each regulation mechanism and gene function. Our transcriptome-wide surveys have highlighted target genes transcripts of which are probably under extensive posttranscriptional regulation during flower development.

Finally, we reported the finding of a large number of polysome-associated ncRNAs. About one-third of all annotated ncRNA in the Arabidopsis genome were observed co-purified with polysomes. Coding capacity analysis confirmed that most of them are real ncRNA without conserved ORFs. The group of polysome-associated ncRNA reported in this study is a potential new addition to the expanding riboregulator catalog; they could have roles in translational regulation during early flower development.

Determining both the expression levels of mRNA and the regulation of its translation is important in understanding specialized cell functions. In this study, we describe both the expression profiles of cells within spatiotemporal domains of the Arabidopsis thaliana flower and the post-transcriptional regulation of these mRNAs, at nucleotide resolution. We express a tagged ribosomal protein under the promoters of three master regulators of flower development. By precipitating tagged polysomes, we isolated cell type-specific mRNAs that are probably translating, and quantified those mRNAs through deep sequencing. Cell type comparisons identified known cell-specific transcripts and uncovered many new ones, from which we inferred cell type-specific hormone responses, promoter motifs and coexpressed cognate binding factor candidates, and splicing isoforms. By comparing translating mRNAs with steady-state overall transcripts, we found evidence for widespread post-transcriptional regulation at both the intron splicing and translational stages. Sequence analyses identified structural features associated with each step. Finally, we identified a new class of noncoding RNAs associated with polysomes. Findings from our profiling lead to new hypotheses in the understanding of flower development.

Preferential repair of the transcribed DNA strand in plants

UV-induced pyrimidine dimers block the progression of both DNA and RNA polymerases. In order to reduce the disruptive effect of these lesions on gene expression, bacteria, yeasts, and animals preferentially repair the transcribed strand of actively expressed genes, essentially employing the stalled polymerase as a detector for bulky lesions. It has been assumed, but not demonstrated, that this prioritization of repair also occurs in plants. Here we demonstrate that in the constitutively expressed gene encoding the RNA polymerase II large subunit cyclobutane pyrimidine dimers are removed from the transcribed strand more rapidly than from the non-transcribed strand.

A SNP associated with alternative splicing of RPT5b causes unequal redundancy between RPT5a and RPT5b among Arabidopsis thaliana natural variation

BACKGROUND

The proteasome subunit RPT5, which is essential for gametophyte development, is encoded by two genes in Arabidopsis thaliana; RPT5a and RPT5b. We showed previously that RPT5a and RPT5b are fully redundant in the Columbia (Col-0) accession, whereas in the Wassilewskia accession (Ws-4), RPT5b does not complement the effect of a strong rpt5a mutation in the male gametophyte, and only partially complements rpt5a mutation in the sporophyte. RPT5bCol-0 and RPT5bWs-4 differ by only two SNPs, one located in the promoter and the other in the seventh intron of the gene.

RESULTS

By exploiting natural variation at RPT5b we determined that the SNP located in RPT5b intron seven, rather than the promoter SNP, is the sole basis of this lack of redundancy. In Ws-4 this SNP is predicted to create a new splicing branchpoint sequence that induces a partial mis-splicing of the pre-mRNA, leading to the introduction of a Premature Termination Codon. We characterized 5 accessions carrying this A-to-T substitution in intron seven and observed a complete correlation between this SNP and both a 10 to 20% level of the RPT5b pre-mRNA mis-splicing and the lack of ability to complement an rpt5a mutant phenotype.

CONCLUSION

The accession-dependent unequal redundancy between RPT5a and RPT5b genes illustrates an example of evolutionary drifting between duplicated genes through alternative splicing.

Ubiquitous aspartic proteinase as an actor in the stress response in buckwheat

The aspartic protease (FeAP9) gene from buckwheat resembles the exon-intron structure characteristic for typical aspartic proteinases, including the presence of the leader intron in the 5'-UTR. RT PCR experiments and gel protein blot analysis indicated that FeAP9 was present in all analyzed organs: developing seeds, seedlings, flowers, leaves, roots and stems. Using Real-time PCR, we found that FeAP9 expression is upregulated in buckwheat leaves under the influence of different abiotic stresses, including dark, drought and UV-B light, as well as wounding and salicylic acid.

Plant SMU-1 and SMU-2 homologues regulate pre-mRNA splicing and multiple aspects of development

In eukaryotes, alternative splicing of pre-mRNAs contributes significantly to the proper expression of the genome. However, the functions of many auxiliary spliceosomal proteins are still unknown. Here, we functionally characterized plant homologues of nematode suppressors of mec-8 and unc-52 (smu). We compared transcript profiles of maize (Zea mays) smu2 endosperm with those of wild-type plants and identified pre-mRNA splicing events that depend on the maize SMU2 protein. Consistent with a conserved role of plant SMU-2 homologues, Arabidopsis (Arabidopsis thaliana) smu2 mutants also show altered splicing of similar target pre-mRNAs. The Atsmu2 mutants occasionally show developmental phenotypes, including abnormal cotyledon numbers and higher seed weights. We identified AtSMU1 as one of the SMU2-interacting proteins, and Atsmu1 mutations cause similar developmental phenotypes with higher penetrance than Atsmu2. The AtSMU2 and AtSMU1 proteins are localized to the nucleus and highly prevalent in actively dividing tissues. Taken together, our data indicated that the plant SMU-1 and SMU-2 homologues appear to be involved in splicing of specific pre-mRNAs that affect multiple aspects of development.

ps-2, the gene responsible for functional sterility in tomato, due to non-dehiscent anthers, is the result of a mutation in a novel polygalacturonase gene

The recessive mutation ps-2, which appeared spontaneously in tomato, confers functional male sterility due to non-dehiscent anthers. In this study, we isolated and characterized the PS-2 gene. A single nucleotide mutation in a novel tomato polygalacturonase gene is responsible for the ps-2 phenotype. The mutation in ps-2 is responsible for an alternative splicing during maturation of the pre-mRNA, which leads to an aberrant mRNA. Differentiation between ps-2 and wild type (PS-2) anthers only appears in the final developmental stage in which the stomium remains closed in the mutant. To our knowledge, this is the first functional sterility gene isolated in the Solanaceae family. The specific expression of the Arabidopsis homolog of PS-2 in the anther dehiscence zone suggests a conserved mode of action over the plant kingdom, which means that the repression of PS-2 homologs may be a potential way to introduce functional sterility in other species.

Whole genome transcriptome polymorphisms in Arabidopsis thaliana

New methods for detecting global patterns of gene expression and splicing variation in natural Arabidopsis thaliana populations.

Whole genome tiling arrays are a key tool for profiling global genetic and expression variation. In this study we present our methods for detecting transcript level variation, splicing variation and allele specific expression in Arabidopsis thaliana. We also developed a generalized hidden Markov model for profiling transcribed fragment variation de novo. Our study demonstrates that whole genome tiling arrays are a powerful platform for dissecting natural transcriptome variation at multi-dimension and high resolution.

U12-dependent intron splicing in plants

U12-dependent (U12) introns have persisted in the genomes of plants since the ancestral divergence between plants and metazoans. These introns, which are rare, are found in a range of genes that include essential functions in DNA replication and RNA metabolism and are implicated in regulating the expression of their host genes. U12 introns are removed from pre-mRNAs by a U12 intron-specific spliceosome. Although this spliceosome shares many properties with the more abundant U2-dependent (U2) intron spliceosome, four of the five small nuclear RNAs (snRNAs) required for splicing are different and specific for the unique splicing of U12 introns. Evidence in plants so far indicates that splicing signals of plant U12 introns and their splicing machinery are similar to U12 intron splicing in other eukaryotes. In addition to the high conservation of splicing signals, plant U12 introns also retain unique characteristic features of plant U2 introns, such as UA-richness, which suggests a requirement for plant-specific components for both the U2 and U12 splicing reaction. This chapter compares U12 and U2 splicing and reviews what is known about plant U12 introns and their possible role in gene expression.

Biochemical and genomic characterization of terpene synthases in Magnolia grandiflora

Magnolia grandiflora (Southern Magnolia) is a primitive evergreen tree that has attracted attention because of its horticultural distinctiveness, the wealth of natural products associated with it, and its evolutionary position as a basal angiosperm. Three cDNAs corresponding to terpene synthase (TPS) genes expressed in young leaves were isolated, and the corresponding enzymes were functionally characterized in vitro. Recombinant Mg25 converted farnesyl diphosphate (C(15)) predominantly to beta-cubebene, while Mg17 converted geranyl diphosphate (C(5)) to alpha-terpineol. Efforts to functionally characterize Mg11 were unsuccessful. Transcript levels for all three genes were prominent in young leaf tissue and significantly elevated for Mg25 and Mg11 messenger RNAs in stamens. A putative amino-terminal signal peptide of Mg17 targeted the reporter green fluorescent protein to both chloroplasts and mitochondria when transiently expressed in epidermal cells of Nicotiana tabacum leaves. Phylogenetic analyses indicated that Mg25 and Mg11 belonged to the angiosperm sesquiterpene synthase subclass TPS-a, while Mg17 aligned more closely to the angiosperm monoterpene synthase subclass TPS-b. Unexpectedly, the intron-exon organizations for the three Magnolia TPS genes were different from one another and from other well-characterized TPS gene sets. The Mg17 gene consists of six introns arranged in a manner similar to many other angiosperm sesquiterpene synthases, but Mg11 contains only four introns, and Mg25 has only a single intron located near the 5' terminus of the gene. Our results suggest that the structural diversity observed in the Magnolia TPS genes could have occurred either by a rapid loss of introns from a common ancestor TPS gene or by a gain of introns into an intron-deficient progenote TPS gene.

Insertion of introns: a strategy to facilitate assembly of infectious full length clones

Some DNA fragments are difficult to clone in Escherichia coli by standard methods. It has been speculated that unintended transcription and translation result in expression of proteins that are toxic to the bacteria. This problem is frequently observed during assembly of infectious full-length virus clones. If the clone is constructed for transcription in vivo, interrupting the virus sequence with an intron can solve the toxicity problem. The AU-rich introns generally contain many stop codons, which interrupt translation in E. coli, while the intron sequence is precisely eliminated from the virus sequence in the plant nucleus. The resulting RNA, which enters the cytoplasm, is identical to the virus sequence and can initiate infection.

Plant SR proteins and their functions

SR proteins are a family of splicing factors important for splice site recognition and spliceosome assembly. Their ability to bind to RNA and to interact with proteins as well identifies them as important players in splice site choice and alternative splicing. Plants possess twice as many SR proteins as animals, and some of the subfamilies are plant specific. Arabidopsis SR proteins are involved in different aspects of plant growth and development as well as in responses to environmental cues. The plant-specific subfamilies have been shown to be regulated by alternative splicing events, which are highly conserved in evolution. The tight regulation of splicing factors by alternative splicing might allow coordinated responses of their target genes.

CsV03-3 is a member of a novel gene family from citrus that encodes a protein with DNA binding activity and whose expression is responsive to defense signals and abiotic stress

We have identified a novel gene designated CsV03-3 from Citrus sinensis (L.) Osbeck that encodes a 50 amino acid polypeptide with a predicted molecular mass of 5.4kDa and a pI of 3.7. CsV03-3 expression is up-regulated by application of methyl jasmonate, salicylic acid, and abscisic acid as well as by abiotic stress and insect herbivory. CsV03-3 belongs to a small gene family consisting of at least three other closely related members (CsV03-1, CsV03-2, and CsV03-4) whose expression is also responsive to phytohormone application and abiotic stress. Sequence similarity searches of the public databases were unsuccessful in finding sequence homologs to CsV03-3 or any CsV03 family member; however, structural prediction models coupled with model comparison to Protein Data Bank folds indicated that the predicted polypeptide encoded by CsV03-3 has structural similarity to proteins with nucleic acid binding activity. Gel mobility shift assays performed on recombinant CsV03-3 protein demonstrated active binding with dsDNA and, to a lesser extent, ssDNA. Based on the phytohormone-inducible expression patterns, the ability to bind nucleic acids, and the lack of significant sequence homology to public databases, we propose that CsV03-3 and its related homologs defines a new class of nucleic acid binding proteins that are responsive to defense and stress signaling in woody perennials.

Structure and alternative splicing of a heat shock transcription factor gene, MsHSF1, in Medicago sativa

Plant heat shock transcription factors (HSF) are highly complex. In this study, we identified an alfalfa HSF gene MsHSF1 that is composed of four exons and three introns in the encoding region. The intron1-exon2-intron2-exon3-intron3 as an intervening sequence was inserted at the conserved position that separates the coding region for the DNA-binding domain by single intron in other known plant HSF genes. Alternative splicing of MsHSF1 has generated five transcript isoforms. Spliced transcript MsHSF1b consisted of exon1 and exon4, encodes a class A1 HSF protein that can specifically bind to the heat shock elements in vitro. Other four spliced transcripts (MsHSF1a-1 to 4) consist of exon1, part of the intervening sequence and exon4. These transcripts carry the premature termination codon and are low-abundant. Apparently these transcripts are the targets of nonsense-mediated mRNA decay (NMD). These results provide new insight into roles in the expression regulation of plant HSF genes.

The M flax rust resistance pre-mRNA is alternatively spliced and contains a complex upstream untranslated region

Alternative splicing is an important step in controlling gene expression and has been shown to occur for a number of plant disease resistance (R) genes. The specific biological role of alternatively spliced transcripts from most R genes is unknown, yet in two cases it is clear that functional disease resistance cannot be activated without them. We report 12 splice isoforms of the M flax rust resistance gene, a TIR-NBS-LRR class of R gene. Collectively, these isoforms are predicted to encode at least nine different polypeptide products, only one of which is a full length peptide believed to confer functional M gene-specific disease resistance. An additional intron to that previously described was found in the 5' untranslated region. Splicing of this leader intron removes an upstream ORF (muORF) sequence. In some transcripts the leader intron is retained and in this case we predict negligible translation initiation of the full length M gene-encoding ORF. The majority of the alternatively spliced isoforms of M would encode truncated TIR and TIR-NBS containing proteins. Although the role of alternative splicing and the existence and function of the products they encode is still unclear, the complexities of the splicing profile, and the 5' UTR of the M gene, are likely to serve in mechanisms to regulate R protein levels.

Alternative splicing of pre-mRNA in plants

Alternative splicing is an important cellular mechanism that increases the diversity of gene products. The study of alternatively spliced genes reported so far in plants is far less documented than that in mammals, but considerable results have been reported, showing the role of these genes in regulating mechanisms, influencing factors, and specificities and function of alternative splicing in plants. This review summarizes briefly the major progress made on alternative splicing in plants.

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana

Background

Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites.

Results

We have developed a new computational technique to identify significantly conserved motifs involved in splice site regulation. First, 84 putative exonic splicing enhancer hexamers are identified in Arabidopsis thaliana. Then a Gibbs sampling program called ELPH was used to locate conserved motifs represented by these hexamers in exonic regions near splice sites in confirmed genes. Oligomers containing 35 of these motifs have been shown experimentally to induce significant inclusion of A. thaliana exons. Second, integration of our regulatory motifs into two different splice site recognition programs significantly improved the ability of the software to correctly predict splice sites in a large database of confirmed genes. We have released GeneSplicerESE, the improved splice site recognition code, as open source software.

Conclusion

Our results show that the use of the ESE motifs consistently improves splice site prediction accuracy.

Alternative splicing expression of U1 snRNP 70K gene is evolutionary conserved between different plant species

A U1-snRNP--specific 70K (U1-70K) protein is intricately involved in both constitutive and alternative splicing of pre-mRNAs. Here, we report cDNA and cognate genomic sequences of the U1-70K gene of maize and rice. The maize and rice U1-70K genes bear strong similarity to the Arabidopsis gene and each encode three transcripts in roots and shoots. Alternative splicing produces two transcripts from each gene in addition to the mRNA encoding the wild type protein. In both cases, selective inclusion of intron 6 or utilization of a cryptic donor site within intron 6 sequence generates the two alternatively spliced transcripts. This evolutionary conservation of splicing patterns between different plant species suggests an important biological function for alternative splicing in the expression of U1-70K gene.

Characterization and expression analysis of the aspartic protease gene family of Cynara cardunculus L

Cardosin A and cardosin B are two aspartic proteases mainly found in the pistils of cardoon Cynara cardunculus L., whose flowers are traditionally used in several Mediterranean countries in the manufacture of ewe's cheese. We have been characterizing cardosins at the biochemical, structural and molecular levels. In this study, we show that the cardoon aspartic proteases are encoded by a multigene family. The genes for cardosin A and cardosin B, as well as those for two new cardoon aspartic proteases, designated cardosin C and cardosin D, were characterized, and their expression in C. cardunculus L. was analyzed by RT-PCR. Together with cardosins, a partial clone of the cyprosin B gene was isolated, revealing that cardosin and cyprosin genes coexist in the genome of the same plant. As a first approach to understanding what dictates the flower-specific pattern of cardosin genes, the respective gene 5' regulatory sequences were fused with the reporter beta-glucuronidase and introduced into Arabidopsis thaliana. A subsequent deletion analysis of the promoter region of the cardosin A gene allowed the identification of a region of approximately 500 bp essential for gene expression in transgenic flowers. Additionally, the relevance of the leader intron of the cardosin A and B genes for gene expression was evaluated. Our data showed that the leader intron is essential for cardosin B gene expression in A. thaliana. In silico analysis revealed the presence of potential regulatory motifs that lay within the aforementioned regions and therefore might be important in the regulation of cardosin expression.

Alternative splicing of pre-messenger RNAs in plants in the genomic era

Primary transcripts (precursor-mRNAs) with introns can undergo alternative splicing to produce multiple transcripts from a single gene by differential use of splice sites, thereby increasing the transcriptome and proteome complexity within and between cells and tissues. Alternative splicing in plants is largely an unexplored area of gene expression, as this phenomenon used to be considered rare. However, recent genome-wide computational analyses have revealed that alternative splicing in flowering plants is far more prevalent than previously thought. Interestingly, pre-mRNAs of many spliceosomal proteins, especially serine/arginine-rich (SR) proteins, are extensively alternatively spliced. Furthermore, stresses have a dramatic effect on alternative splicing of pre-mRNAs including those that encode many spliceosomal proteins. Although the mechanisms that regulate alternative splicing in plants are largely unknown, several reports strongly suggest a key role for SR proteins in spliceosome assembly and regulated splicing. Recent studies suggest that alternative splicing in plants is an important posttranscriptional regulatory mechanism in modulating gene expression and eventually plant form and function.

Structure, expression, and mapping of two nodule-specific genes identified by mining public soybean EST databases

Numerous nodule-specific genes, which are involved in the root nodule development and function, have been known and are still being discovered. Here, we reported the structure, expression, and genetic map location of two novel nodule-specific genes. First, two EST groups, one obtained from a nodule library and the other from all aboveground tissue libraries, were clustered with regard to in silico expression profiles. We compiled a pool of 103 putative nodule-specific sequence clusters. Then, two representative ESTs were selected for further experimental analyses. According to the full-length cDNA sequences, one was an EST of a novel nodule-specific polygalacturonase gene, GmPGN, and the other was an EST of a new short nodule-specific gene, GmEKN. The results of expression analyses of the GmPGN cDNAs indicated that GmPGN expression was not detectable in any of the soybean tissues except in the nodule tissue and may be regulated via alternative splicing. GmEKN expression was the most strongly detected in the nodule. The predicted GmEKN protein is both glutamic acid- and lysine-rich, and is also highly hydrophilic. Genetic mapping located GmPGN near the known quantitative trait locus conferring resistance to soybean cyst nematode on soybean molecular linkage group (MLG) B1, and GmEKN on MLG A2. These results provide useful information for the use of these genes in research on the orchestration of numerous genes in nodule development and function.

Characterization of alternative oxidase (AOX) gene expression in response to methyl salicylate and methyl jasmonate pre-treatment and low temperature in tomatoes

Methyl salicylate (MeSA) vapor increased resistance against chilling injury (CI) in freshly harvested pink tomatoes. The expression patterns of alternative oxidase (AOX) before and during the chilling period demonstrated that pre-treatment of tomato fruit with MeSA vapor increased the transcript levels of AOX. We used 4 EST tomato clones of AOX from the public database that belong to two distinctly related families, 1 and 2 defined in plants. Three clones were designated as LeAOX1a, 1b and 1c and the fourth clone as LeAOX2. Using RT-PCR, 1a and 1b genes were found to be expressed in leaf, root and fruit tissues, but 1c was expressed preferentially in roots. RNA transcript from LeAOX1a of AOX subfamily 1 was present in much greater abundance than 1b or 1c. The presence of longer AOX transcripts detected by RNA gel blot analysis in cold-stored tomato fruit was confirmed to be the un-spliced pre-mRNA transcripts of LeAOX1a and LeAOX1b genes. Intron splicing of LeAOX1c gene was also affected by cold storage when it was detected in roots. This alternative splicing event in AOX pre-mRNAs molecules occurred, preferentially at low temperature, regardless of mRNA abundance. Transcript levels of several key genes involved in RNA processing (splicing factors: 9G8-SR and SF2-SR, fibrillarin and DEAD box RNA helicase) were also affected by changes in storage temperature. The aberrant splicing event in AOX pre-mRNA and its possible association with the change in expression of genes involved in RNA processing in tomato fruit having chilling disorder was discussed.

Stress- and development-induced expression of spliced and unspliced transcripts from two highly similar dehydrin 1 genes in V. riparia and V. vinifera

Dehydrins are proteins that accumulate in vegetative tissues subjected to various dehydrating stress conditions such as cold, drought, and salinity and in seeds at later stages of embryogenesis. Here, we report on two highly identical dehydrin genes, DHN1a and DHN1b, in wild and cultivated grapes, Vitis riparia and Vitis vinifera, and their expression in different tissues and under different environmental conditions. The two genes and their transcripts can easily be distinguished by RT-PCR because DHN1b has an 18 bp deletion compared to DHN1a. V. riparia expressed only DHN1a; V. vinifera expressed both DHN1a and DHN1b. Spliced transcripts, DHN1-S, encoding a putative YSK(2)-type dehydrin were present in low amounts in control leaves, but in high amounts in buds and seeds. Unspliced transcripts, DHN1-U, accumulated to high levels in buds and seeds. Cold, drought, and ABA treatment increased accumulation of both DHN1-S and DHN1-U in leaves, whereas short-day treatment increased only DHN1-S. The possible relation of these results with the difference in freezing stress tolerance between V. riparia and V. vinifera is discussed.

Hard tick calreticulin (CRT) gene coding regions have only one intron with conserved positions and variable sizes

Calreticulin (CRT) is a unique eukaryotic gene. The CRT gene product, calreticulin, was first identified as a calcium binding protein in 1974, but further investigations have indicated that CRT protein performs many functions in cells, including involvement in evading the host's immune system by parasites. Many studies of CRT have been published since the molecule was first discovered; however, the CRT gene exon-intron structure is only known for a limited number of ectoparasite species. In this study, we compared tick CRT genomic sequences to the corresponding cDNA from 28 species and found that 2 exons and 1 intron are present in the tick CRT gene. The intron position is conserved in 28 hard ticks, but intron size and nucleotide sequences vary. Three tick introns possess duplicated fragments and are twice as long as other introns. All tick CRT introns obey the GT-AG rule in the splice-site junctions and are phase 1 introns. By comparing tick CRT introns to those of fruit fly, mouse, and human, we conclude that tick CRT introns belong to the intron-late type. The number and size of CRT introns have increased through the evolution of eukaryotes.

Cloning and characterization of a novel splicing isoform of the iron-superoxide dismutase gene in rice (Oryza sativa L.)

Superoxide dismutases (SODs) are ubiquitous metalloenzymes in aerobic organisms that play a crucial role in protecting organisms against ROS. Here, we report the molecular cloning and functional characterization of a novel alternatively spliced variant of the iron-superoxide dismutase gene, OsFe-SODb, from a rice panicle cDNA library. The alternative splicing event occurred in the fourth exon of the OsFe-SOD gene, and led to the translation of two isoforms of different sizes. The 5' flanking region of the OsFe-SOD was cloned and many cis-acting regulatory elements were found that are involved in light responsiveness, including a G-box and an I-box. RT-PCR analysis showed that the two alternative forms of OsFe-SOD were expressed in both the vegetative and reproductive tissues of Cpslo17. Moreover, accumulation of both isoforms was upregulated by light induction. In addition, the alternative splicing of OsFe-SOD mRNA was sensitive to low temperature. High yield production of the two recombinant OsFe-SOD isoforms was achieved in Escherichia coli. SOD assays showed that C-terminal truncation in OsFe-SODb did not result in a loss of SOD enzyme activity.

A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice

MYB transcription factor genes play important roles in many developmental processes and in various defence responses of plants. Two Arabidopsis R2R3-type MYB genes, AtMYB59 and AtMYB48, were found to undergo similar alternative splicing. Both genes have four distinctively spliced transcripts that encode either MYB-related proteins or R2R3-MYB proteins. An extensive BLAST search of the GenBank database resulted in finding and cloning two rice homologues, both of which were also found to share a similar alternative splicing pattern. In a semi-quantitative study, the expression of one splice variant of AtMYB59 was found to be differentially regulated in treatments with different phytohormones and stresses. GFP fusion protein analysis revealed that both of the two predicted nuclear localization signals (NLSs) in the R3 domain are required for localizing to the nucleus. Promoter-GUS analysis in transgenic plants showed that 5'-UTR is sufficient for the translation initiation of type 3 transcripts (encoding R2R3-MYB proteins), but not for type 2 transcripts (encoding MYB-related proteins). Moreover, a new type of non-canonical intron, with the same nucleotide repeats at the 5' and 3' splice sites, was identified. Thirty-eight Arabidopsis and rice genes were found to have this type of non-canonical intron, most of which undergo alternative splicing. These data suggest that this subgroup of transcription factor genes may be involved in multiple biological processes and may be transcriptionally regulated by alternative splicing.

Low temperature promotes intron retention in two e-cor genes of durum wheat

Following the screening of a suppression subtractive library developed from durum wheat plants exposed to low temperature for 6 h, two early cold-regulated (e-cor) genes have been isolated. These genes, coding putatively for a ribokinase (7H8) and a C3H2C3 RING-finger protein (6G2), were characterized by the stress-induced retention of a subset of introns in the mature mRNA. This feature was dependent on cold for 7H8 and on cold and dehydration for 6G2. When other genes, such as the stress-related gene WCOR410c, coding for a dehydrin (one intron), or a gene coding for a putative ATP binding cassette transporter (16 introns) were analyzed, no cold-dependent intron retention was observed. Cold-induced intron retention was not observed in mutants defective in the chloroplast development; nevertheless treatment with cycloheximide in the absence of cold was able to promote intron retention for the 7H8 e-cor gene. These results suggest that the cold-induced intron retention reflects the response of the spliceosoma to specific environmental signals transduced to the splicing protein factors through a chloroplast-dependent pathway. Notably, when the 7H8 Arabidopsis orthologous gene was analyzed, no stress induction in terms of mRNA abundance and no cold-dependent intron retention was detected. Otherwise, 6G2 Arabidopsis homologous sequences sharing the same genomic structure of the durum wheat 6G2 showed a similar intron retention event although not strictly dependent on stress.

Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events

The extensive mechanistic and regulatory interconnections between the various events of mRNA biogenesis are now recognized as a fundamental principle of eukaryotic gene expression, yet the specific details of the coupling between the various steps of mRNA biogenesis do differ, and sometimes dramatically, between the different kingdoms. In this review, we emphasize examples where plants must differ in this respect from other eukaryotes, and highlight a recurring trend of recruiting the conserved, versatile functional modules, which have evolved to support the general mRNA biogenesis reactions, for plant-specific functions. We also argue that elucidating the inner workings of the plant 'mRNA factory' is essential for accomplishing the ambitious goal of building the 'virtual plant'.