The four members of the gene family encoding the Arabidopsis thaliana translation elongation factor EF-1 alpha are actively transcribed

Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo

Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically to telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human shelterin proteins TRF1 or TRF2, also possess a histone-like domain which is involved in protein-protein interactions e.g., with POT1b. Here we set out to investigate the genome-wide localization pattern of TRB1 to reveal its preferential sites of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Our results demonstrate that TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis, in addition to its roles at telomeres. This preference coincides with the frequent occurrence of telobox motifs in the upstream regions of genes in this category, but it is not restricted to the presence of a telobox. We conclude that TRB1 shows a specific genome-wide distribution pattern which suggests its role in regulation of genes involved in biogenesis of the translational machinery, in addition to its preferential telomeric localization.

Regulation of AtSUS2 and AtSUS3 by glucose and the transcription factor LEC2 in different tissues and at different stages of Arabidopsis seed development

Sucrose synthase (SUS) is a key enzyme of carbon metabolism in heterotrophic tissues of plants. The Arabidopsis genome contains six SUS genes. Two members of this family, namely AtSUS2 (At5g49190) and AtSUS3 (At4g02280) are strongly and differentially expressed in Arabidopsis seed. Expression analysis was carried out using SUS:promoter-GUS fusion lines in a wild-type genetic background or in a mutant carrying a lesion in the transcription factor LEAFY COTYLEDON 2 (LEC2; At1g28300). The accumulation patterns of mRNA, protein, and SUS activity were altered in the lec2 mutant during seed development 9-18 days after flowering. This indicates that LEC2 acts epistatically on the expression of AtSUS2 and AtSUS3. It appears that LEC2 is required for cotyledon-specific expression of both SUS genes but it is not responsible for expression in the radicle tip during embryo development. The AtSUS2 promoter was induced in planta by feeding of glucose but less so by sucrose and trehalose. Non-phosphorylable glucose analogs such as 3-O-methyl-glucose and 2-deoxyglucose also caused an induction, suggesting that sugar signaling proceeds by a hexokinase-independent pathway, possibly involving hexose sensing. Analysis of transgenic lines carrying of truncated versions of the AtSUS2:promoter fused to Beta-glucuronidase activity revealed an internal 421 bp region that was responsible for expression in seeds. Bioinformatic sequence analysis revealed regulatory cis-elements putatively responsible for the spatio-temporal pattern of AtSUS2 expression such as the SEF3 (aaccca) and W-box (ttgact) motifs. These findings are discussed in relation to the roles played by AtSUS2, AtSUS3 and LEC2 in the biosynthesis of seed storage products in Arabidopsis.

Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment

Background

Chloroplasts and mitochondria evolved from the endosymbionts of once free-living eubacteria, and they transferred most of their genes to the host nuclear genome during evolution. The mechanisms used by plants to coordinate the expression of such transferred genes, as well as other genes in the host nuclear genome, are still poorly understood.

Results

In this paper, we use nuclear-encoded chloroplast (cpRPGs), as well as mitochondrial (mtRPGs) and cytoplasmic (euRPGs) ribosomal protein genes to study the coordination of gene expression between organelles and the host. Results show that the mtRPGs, but not the cpRPGs, exhibit strongly synchronized expression with euRPGs in all investigated land plants and that this phenomenon is linked to the presence of a telo-box DNA motif in the promoter regions of mtRPGs and euRPGs. This motif is also enriched in the promoter regions of genes involved in DNA replication. Sequence analysis further indicates that mtRPGs, in contrast to cpRPGs, acquired telo-box from the host nuclear genome.

Conclusions

Based on our results, we propose a model of plant nuclear genome evolution where coordination of activities in mitochondria and chloroplast and other cellular functions, including cell cycle, might have served as a strong selection pressure for the differential acquisition of telo-box between mtRPGs and cpRPGs. This research also highlights the significance of physiological needs in shaping transcriptional regulatory evolution.

Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function

BACKGROUND

Short interstitial telomere motifs (telo boxes) are short sequences identical to plant telomere repeat units. They are observed within the 5' region of several genes over-expressed in cycling cells. In synergy with various cis-acting elements, these motifs participate in the activation of expression. Here, we have analysed the distribution of telo boxes within Arabidopsis thaliana and Oryza sativa genomes and their association with genes involved in the biogenesis of the translational apparatus.

RESULTS

Our analysis showed that the distribution of the telo box (AAACCCTA) in different genomic regions of A. thaliana and O. sativa is not random. As is also the case for plant microsatellites, they are preferentially located in the 5' flanking regions of genes, mainly within the 5' UTR, and distributed as a gradient along the direction of transcription. As previously reported in Arabidopsis, a conserved topological association of telo boxes with site II or TEF cis-acting elements is observed in almost all promoters of genes encoding ribosomal proteins in O. sativa. Such a conserved promoter organization can be found in other genes involved in the biogenesis of the translational machinery including rRNA processing proteins and snoRNAs. Strikingly, the association of telo boxes with site II motifs or TEF boxes is conserved in promoters of genes harbouring snoRNA clusters nested within an intron as well as in the 5' flanking regions of non-intronic snoRNA genes. Thus, the search for associations between telo boxes and site II motifs or TEF box in plant genomes could provide a useful tool for characterizing new cryptic RNA pol II promoters.

CONCLUSIONS

The data reported in this work support the model previously proposed for the spreading of telo boxes within plant genomes and provide new insights into a putative process for the acquisition of microsatellites in plants. The association of telo boxes with site II or TEF cis-acting elements appears to be an essential feature of plant genes involved in the biogenesis of ribosomes and clearly indicates that most plant snoRNAs are RNA pol II products.

HvPG1 and ECA1: two genes activated transcriptionally in the transition of barley microspores from the gametophytic to the embryogenic pathway

Microspores genetically programmed to produce male gametes can be switched to the embryogenic pathway to give rise to haploid embryos. Microspore embryogenesis is usually induced in barley by stress pre-treatment applied to vacuolated microspores. We studied the expression of two genes during the early stages of microspore embryogenesis to gain further insight into the microspore transition from the gametophytic to the embryogenic pathway. RT-PCR together with in situ hybridization on sections (ISH) and whole-mount in situ hybridization (WISH) were used to analyse the expression of the early-culture abundant gene (ECA1), which is expressed in barley during microspore embryogenesis, and a polygalacturonase gene (HvPG1), a late pollen gene expressed during gametogenesis only after microspore division. Both ECA1 and HvPG1 genes were transcriptionally active after stress pre-treatment in the same populations of microspore-derived structures, representing the sporophytically induced ones. ECA1 transcripts were also detected after 3 days' culture. Our results point to the possibility of using ECA1 gene expression as a marker for the induction of microspore embryogenesis and the earliest stages of this process. Finally, we demonstrate that WISH is a suitable technique for studying gene expression in embryogenic microspore populations and, because different structures can be examined individually, is an appropriate complement to transcriptomic profile analyses in the study of early microspore embryogenesis.

The role of AtMUS81 in interference-insensitive crossovers in A. thaliana

MUS81 is conserved among plants, animals, and fungi and is known to be involved in mitotic DNA damage repair and meiotic recombination. Here we present a functional characterization of the Arabidopsis thaliana homolog AtMUS81, which has a role in both mitotic and meiotic cells. The AtMUS81 transcript is produced in all tissues, but is elevated greater than 9-fold in the anthers and its levels are increased in response to gamma radiation and methyl methanesulfonate treatment. An Atmus81 transfer-DNA insertion mutant shows increased sensitivity to a wide range of DNA-damaging agents, confirming its role in mitotically proliferating cells. To examine its role in meiosis, we employed a pollen tetrad–based visual assay. Data from genetic intervals on Chromosomes 1 and 3 show that Atmus81 mutants have a moderate decrease in meiotic recombination. Importantly, measurements of recombination in a pair of adjacent intervals on Chromosome 5 demonstrate that the remaining crossovers in Atmus81 are interference sensitive, and that interference levels in the Atmus81 mutant are significantly greater than those in wild type. These data are consistent with the hypothesis that AtMUS81 is involved in a secondary subset of meiotic crossovers that are interference insensitive.

Meiosis is a specialized type of cell division in which one diploid progenitor cell divides into four haploid cells that are subsequently used for fertilization during sexual reproduction. During meiosis, chromosomes pair, synapse, and exchange genetic information, all of which are required for proper chromosome segregation during subsequent stages. Failure to properly segregate meiotic chromosomes often leads to genetic defects such as aneuploidy. Using the model plant A. thaliana, we have developed a powerful system for the visual analysis of meiotic recombination directly in the pollen, in which the four products of individual meioses are fused together in a tetrad. We have used this system to characterize the gene AtMUS81 and show that Atmus81 mutants have a moderate reduction in meiotic crossovers and are sensitive to a wide range of DNA-damaging agents. Importantly, the remaining crossovers in Atmus81still exhibit crossover interference, a phenomenon whereby one crossover inhibits the occurrence of other nearby crossovers. Our results suggest that AtMUS81 mediates a subset of meiotic recombination events in Arabidopsis that are insensitive to crossover interference.

A putative role for fusaric acid in biocontrol of the parasitic angiosperm Orobanche ramosa

Fusarium spp. are ubiquitous fungi found in soil worldwide as both pathogenic and nonpathogenic strains. The signals leading to disease or the absence of disease are poorly understood. We recently showed that fusaric acid (FA), a nonspecific toxin produced by most Fusarium spp., could elicit various plant defense responses at 100 nM without toxic effect. In this study, we checked for the effect of FA on root and root hairs, probable first site of contact between the fungi and the host. Large FA concentrations reduce root and root-hair growth and induce a rapid transient membrane hyperpolarization, followed by a large depolarization, due to the inhibition of H(+)-ATPase currents. Nanomolar concentrations of FA induced only an early transient membrane hyperpolarization of root hairs compatible with the induction of a signal transduction pathway. FA at 10(-7) M failed to induce salicylic acid- and jasmonic acid/ethylene-dependent defense-related genes but inhibited the germination of the angiosperm parasite Orobanche ramosa in contact of FA-pretreated Arabidopsis thaliana seedlings. These data suggest that FA at nontoxic concentrations could activate signal transduction components necessary for plant-defense responses that could contribute to biocontrol activity of Fusarium spp.

Physiological characterisation of Arabidopsis mutants affected in the expression of the putative regulatory protein PII

The PII signal transducing protein is involved in carbon/nitrogen (C/N) sensing in bacteria and cyanobacteria. In higher plants the function of the PII homolog GLB1 is not known. GLB1 transcripts were found in all plant organs tested, while in Arabidopsis leaves GLB1 expression and PII protein levels were not significantly affected by either the day/night cycle or N-nutrition. Its putative regulatory role in plants has been studied by analysing Arabidopsis thaliana T-DNA insertion lines in the GLB1 gene. These PII mutants showed an 80% (PIIV1 mutant) and 100% (PIIS2 mutant) reduced AtGLB1 transcript level and no detectable PII protein. They did not display an altered growth or developmental phenotype when grown under non-limiting conditions suggesting that the PII protein does not play a crucial role in plants. However, in vitro grown PII mutants did show a higher sensitivity to nitrite (NO (2) (-) ) compared to the wild-type plants. This observation is reminiscent of the role of PII in the regulation of NO (2) (-) metabolism in cyanobacteria. Furthermore, when grown hydroponically, the PII mutants displayed a slight increase in carbohydrate (starch and sugars) levels in response to N starvation and a slight decrease in the levels of ammonium (NH (4) (+) ) and amino acids (mainly Gln) in response to NH (4) (+) resupply. Although the phenotypic changes are rather small in the mutant lines, these data support the hypothesis of a subtle involvement of the PII protein in the regulation of some steps of primary C and N metabolism.

The AtSUC5 sucrose transporter specifically expressed in the endosperm is involved in early seed development in Arabidopsis

The sucrose transporter gene AtSUC5 was studied as part of a programme aimed at identifying and studying the genes involved in seed maturation in Arabidopsis. Expression profiling of AtSUC5 using the technique of real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR) showed that the gene was specifically and highly induced during seed development between 4 and 9 days after flowering (DAF). Analysis of the activity of the AtSUC5 promoter in planta was consistent with this timing, and suggested that AtSUC5 expression is endosperm specific, spreading from the micropylar to the chalazal pole of the filial tissue. To demonstrate the function of AtSUC5, the corresponding cDNA was used to complement a sucrose uptake-deficient yeast mutant, thus confirming its sucrose transport capacity. To investigate the function in planta, three allelic mutants disrupted in the AtSUC5 gene were isolated and characterized. A strong but transient reduction in fatty acid concentration was observed in mutant seeds 8 DAF. This biochemical phenotype was associated with a slight delay in embryo development. Taken together, these data demonstrated the role of the AtSUC5 carrier in the nutrition of the filial tissues during early seed development. However, additional sugar uptake systems, which remain to be characterized, must be functional in developing seeds, especially during maturation of the embryo.

Inducible Expression of a Phytolacca heterotepala Ribosome-Inactivating Protein Leads to Enhanced Resistance Against Major Fungal Pathogens in Tobacco

ABSTRACT Plant genetic engineering has long been considered a valuable tool to fight fungal pathogens because it would limit the economically costly and environmentally undesirable chemical methods of disease control. Ribosome-inactivating proteins (RIPs) are potentially useful for plant defense considering their antiviral and antimicrobial activities but their use is limited by their cytotoxic activity. A new gene coding for an RIP isolated from leaves of Phytolacca heterotepala was expressed in tobacco under the control of the wound-inducible promoter of the bean polygalacturonase-inhibiting protein I gene to increase resistance against different fungal pathogens, because an individual RIP isolated from P. heterotepala showed direct antifungal toxicity. Phenotypically normal transgenic lines infected with Alternaria alternata and Botrytis cinerea showed a significant reduction of leaf damage while reverse transcription-polymerase chain reaction and western analysis indicated the expression of the RIP transgene upon wounding and pathogen attack. This work demonstrates that use of a wound-inducible promoter is useful to limit the accumulation of antimicrobial phytotoxic proteins only in infected areas and that the controlled expression of the PhRIP I gene can be very effective to control fungal pathogens with different phytopathogenic actions.

Structure and expression profile of the sucrose synthase multigene family in Arabidopsis

The release of the complete genome sequence of Arabidopsis enabled the largest sucrose synthase family described to date, comprising six distinct members, for which expression profiles were not yet available, to be identified. Aimed at understanding the precise function of each AtSUS member among the family, a comparative study of protein structure was performed, together with an expression profiling of the whole gene family using the technique of real-time quantitative reverse transcriptase-polymerase chain reaction. Transcript levels were analysed in several plant organs, including both developing and germinating seeds. A series of treatments such as oxygen deprivation, dehydration, cold treatment, or various sugar feedings were then carried out to characterize the members of the family further. The AtSUS genes exhibit distinct but partially redundant expression profiles. Under anaerobic conditions, for instance, both AtSUS1 and AtSUS4 mRNA levels increase, but in a distinct manner. AtSUS2 is specifically and highly induced in seeds at 12 d after flowering and appears as a marker of seed maturation. AtSUS3 seems to be induced in various organs under dehydration conditions including leaves deprived of water or submitted to osmotic stress as well as late-maturing seeds. AtSUS5 and AtSUS6 are expressed in nearly all plant organs and do not exhibit any transcriptional response to stresses. These results add new insights on the expression of SUS genes and are discussed in relation to distinct functions for each member of the AtSUS family.

Hormonal control of cell proliferation requires PASTICCINO genes

PASTICCINO (PAS) genes are required for coordinated cell division and differentiation during plant development. In loss-of-function pas mutants, plant aerial tissues showed ectopic cell division that was specifically enhanced by cytokinins, leading to disorganized tumor-like tissue. To determine the role of the PAS genes in controlling cell proliferation, we first analyzed the expression profiles of several genes involved in cell division and meristem function. Differentiated and meristematic cells of the pas mutants were more competent for cell division as illustrated by the ectopic and enlarged expression profiles of CYCLIN-DEPENDENT KINASE A and CYCLIN B1. The expression of meristematic homeobox genes KNOTTED-LIKE IN ARABIDOPSIS (KNAT2, KNAT6), and SHOOT MERISTEMLESS was also increased in pas mutants. Moreover, the loss of meristem function caused by shoot meristemless mutation can be suppressed by pas2. The KNAT2 expression pattern defines an enlarged meristematic zone in pas mutants that can be mimicked in wild type by cytokinin treatment. Cytokinin induction of the primary cytokinin response markers, ARABIDOPSIS RESPONSE REGULATOR (ARR5 and ARR6), was enhanced and lasted longer in pas mutants, suggesting that PAS genes in wild type repress cytokinin responses. The expression of the cytokinin-regulated cyclin D, cyclin D3.1, was nonetheless not modified in pas mutants. However, primary auxin response genes were down-regulated in pas mutants, as shown by a lower auxin induction of IAA4 and IAA1 genes, demonstrating that the auxin response was also modified. Altogether, our results suggest that PAS genes are involved in the hormonal control of cell division and differentiation.

Defense Gene Expression Analysis of Arabidopsis thaliana Parasitized by Orobanche ramosa

ABSTRACT The infection of Arabidopsis thaliana roots with the obligate parasite Orobanche ramosa represents a useful model for a study of the molecular events involved in the host plant response to a parasitic plant attack. To avoid analysis problems due to the subterranean development of O. ramosa, we developed two in vitro co-culture systems: O. ramosa seedlings infesting Arabidopsis plantlet roots and callus tissues. We were then able to investigate the expression patterns of some host plant genes selected among genes known to be involved in metabolic pathways and resistance mechanisms activated during several plant-pathogen interactions including ethylene, isoprenoid, phenylpropanoid, and jasmonate biosynthesis pathways, oxidative stress responses, and pathogenesis-related proteins. Molecular analyses were carried out using polymerase chain reaction amplification methods allowing semiquantitative evaluation of transcript accumulation during early (first hours) and late (15 days) stages of infestation, in whole roots or parts close to the parasite attachment site. In A. thaliana, O. ramosa induced most of the general response signaling pathways in a transient manner even before its attachment to A. thaliana roots. However, no salicylic acid-dependent defense is observed because no activation of systemic acquired resistance markers is detectable, whereas genes, co-regulated by jasmonate and ethylene, do display enhanced expression.

Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells

We have focused our interest on two cis-regulatory elements, named site II motif and telo box, identified within the promoter of plant proliferating cellular nuclear antigen (PCNA) and putatively involved in meristematic expression of the gene. A conserved topological association between site II motifs and telo boxes is observed in the promoter of numerous genes expressed in cycling cells, including several cell cycle-related genes and 153 Arabidopsis genes encoding ribosomal proteins. Meristematic expression of a GUS reporter gene was observed in plants under the control of Arabidopsis site II motif within a minimal promoter. This expression is strongly enhanced by addition of a telo box within this chimaeric promoter. We showed by gel retardation experiments that the site II motif is a target for several DNA-binding activities present in Arabidopsis crude cell extract and can bind a transcription factor, At-TCP20, from the Teosinte branched 1, Cycloidea, PCF (TCP)-domain protein family. In yeast two-hybrid experiments, At-TCP20 appears to be a potential partner of AtPuralpha, which was previously shown to bind telo boxes. An important consequence of this analysis is to reveal new and conserved regulatory processes concerning the regulation of plant ribosomal gene expression in cycling cells. The implication of these observations in plant-specific developmental pathways is discussed.

Multifunctional acetyl-CoA carboxylase 1 is essential for very long chain fatty acid elongation and embryo development in Arabidopsis

Acetyl-CoA carboxylase (ACCase) catalyses the carboxylation of acetyl-CoA, forming malonyl-CoA, which is used in the plastid for fatty acid synthesis and in the cytosol in various biosynthetic pathways including fatty acid elongation. In Arabidopsis thaliana, ACC1 and ACC2, two genes located in a tandem repeat within a 25-kbp genomic region near the centromere of chromosome 1, encode two multifunctional ACCase isoforms. Both genes, ACC1 and ACC2, appear to be ubiquitously expressed, but little is known about their respective function and importance. Here, we report the isolation and characterisation of two allelic mutants disrupted in the ACC1 gene. Both acc1-1 and acc1-2 mutations are recessive and embryo lethal. Embryo morphogenesis is impaired and both alleles lead to cucumber-like structures lacking in cotyledons, while the shortened hypocotyl and root exhibit a normal radial pattern organisation of the body axis. In this abnormal embryo, the maturation process still occurs. Storage proteins accumulate normally, while triacylglycerides (TAG) are synthesised at a lower concentration than in the wild-type seed. However, these TAG are totally devoid of very long chain fatty acids (VLCFA) and consequently enriched in C18:1, like all lipid fractions analysed in the mutant seed. These data demonstrate, in planta, the role of ACCase 1 in VLCFA elongation. Furthermore, this multifunctional enzyme also plays an unexpected and central function in embryo morphogenesis, especially in apical meristem development.

Cell numbers and leaf development in Arabidopsis: a functional analysis of the STRUWWELPETER gene

The struwwelpeter (swp) mutant in Arabidopsis shows reduced cell numbers in all aerial organs. In certain cases, this defect is partially compensated by an increase in final cell size. Although the mutation does not affect cell cycle duration in the young primordia, it does influence the window of cell proliferation, as cell number is reduced during the very early stages of primordium initiation and a precocious arrest of cell proliferation occurs. In addition, the mutation also perturbs the shoot apical meristem (SAM), which becomes gradually disorganized. SWP encodes a protein with similarities to subunits of the Mediator complex, required for RNA polymerase II recruitment at target promoters in response to specific activators. To gain further insight into its function, we overexpressed the gene under the control of a constitutive promoter. This interfered again with the moment of cell cycle arrest in the young leaf. Our results suggest that the levels of SWP, besides their role in pattern formation at the meristem, play an important role in defining the duration of cell proliferation.

The cell morphogenesis gene ANGUSTIFOLIA encodes a CtBP/BARS-like protein and is involved in the control of the microtubule cytoskeleton

The ANGUSTIFOLIA (AN) gene is required for leaf hair (trichome) branching and is also involved in polarized expansion underlying organ shape. Here we show that the AN gene encodes a C-terminal binding proteins/brefeldin A ADP-ribosylated substrates (CtBP/BARS) related protein. AN is expressed at low levels in all organs and the AN protein is localized in the cytoplasm. In an mutant trichomes, the organization of the actin cytoskeleton is normal but the distribution of microtubules is aberrant. A role of AN in the control of the microtubule cytoskeleton is further supported by the finding that AN genetically and physically interacts with ZWICHEL, a kinesin motor molecule involved in trichome branching. Our data suggest that CtBP/BARS-like protein function in plants is directly associated with the microtubule cytoskeleton.

Arabidopsis glucosidase I mutants reveal a critical role of N-glycan trimming in seed development

Glycoproteins with asparagine-linked (N-linked) glycans occur in all eukaryotic cells. The function of their glycan moieties is one of the central problems in contemporary cell biology. N-glycosylation may modify physicochemical and biological protein properties such as conformation, degradation, intracellular sorting or secretion. We have isolated and characterized two allelic Arabidopsis mutants, gcs1-1 and gcs1-2, which produce abnormal shrunken seeds, blocked at the heart stage of development. The mutant seeds accumulate a low level of storage proteins, have no typical protein bodies, display abnormal cell enlargement and show occasional cell wall disruptions. The mutated gene has been cloned by T-DNA tagging. It codes for a protein homologous to animal and yeast alpha-glucosidase I, an enzyme that controls the first committed step for N-glycan trimming. Biochemical analyses have confirmed that trimming of the alpha1,2- linked glucosyl residue constitutive of the N-glycan precursor is blocked in this mutant. These results demonstrate the importance of N-glycan trimming for the accumulation of seed storage proteins, the formation of protein bodies, cell differentiation and embryo development.

Plant interstitial telomere motifs participate in the control of gene expression in root meristems

The promoters of Arabidopsis eEF1A genes contain a telomere motif, the telo-box, associated with an activating sequence, the tef-box. Database searches indicated the presence of telo-boxes in the 5' region of numerous genes encoding components of the translational apparatus. By using several promoter constructs we demonstrate that the telo-box is required for the expression of a beta-glucoronidase gene in root primordia of transgenic Arabidopsis. This effect was observed when a telo-box was inserted upstream or downstream from the transcription initiation site, and occurred in synergy with the tef-box. These results clearly indicate that interstitial telomere motifs in plants are involved in control of gene expression. South-western screening of a lambdaZAP library with a double-stranded Arabidopsis telomere motif resulted in characterization of a protein related to the conserved animal protein Puralpha. The possibility of a regulation process similar to that achieved by the Rap1p in Saccharomyces cerevisiae is discussed.

Barley elongation factor 1 alpha: genomic organization, DNA sequence, and phylogenetic implications

A full length cDNA clone encoding the 447 amino acid long barley (Hordeum vulgare cv. Bomi) endosperm elongation factor 1 alpha (eF-1 alpha) was isolated by a differential screening procedure. RFLP mapping of eF-1 alpha showed that the barley genome contains a small eF-1 alpha gene family of 4 copies, with 1 copy of the gene being located on each of chromosomes 2, 4, 6, and 7. Analysis of barley endosperm total proteins by Western blot with antibodies directed towards wheat eF-1 alpha and the sea urchin 51 kDa proteins gave a single band of the expected molecular weight. Amino acid sequence comparison with other plant eF-1 alpha sequences showed that the isolated barley endosperm eF-1 alpha is more similar to the published wheat eF-1 alpha sequence than to eF-1 alpha sequences previously published for the barley cultivars Igri and Dicktoo. The phylogenetic analysis suggests that the barley eF-1 alpha gene family can be divided into two subfamilies and that two ancestral genes existed before the divergence of monocotyledonous and dicotyledonous plants.

Genome DNA sequencing around the EF-1 alpha multigene locus of Arabidopsis thaliana indicates a high gene density and a shuffling of noncoding regions

In Arabidopsis thaliana, EF-1 alpha proteins are encoded by a multigene family of four members. Three of them are clustered at the same locus, which was positioned 24 cM from the top of chromosome 1. A region of DNA spanning 63 kb around these locus was sequenced and analyzed. One main characteristic of the locus is the mosaic organization of both genes and intergenic regions. Fourteen genes were identified, among which only four were already described, and other unidentified are most likely present. Functionally diverse genes are found at close intervals. Exon and intron distribution is highly variable at this locus, one gene being split into at least 20 introns. Several duplications were found within the sequenced segment both in coding and noncoding regions, including two gene families. Moreover, a sequence corresponding to the 5' noncoding region of the EF-1 alpha genes and harboring a 5' intervening sequence is duplicated and found upstream of several genes, suggesting that noncoding regions can be shuffled during evolution.

The plant translational apparatus

Protein synthesis in both eukaryotic and prokaryotic cells is a complex process requiring a large number of macromolecules: initiation factors, elongation factors, termination factors, ribosomes, mRNA, amino-acylsynthetases and tRNAs. This review focuses on our current knowledge of protein synthesis in higher plants.

Elongation factor 1 alpha genes of the red alga Porphyra purpurea include a novel, developmentally specialized variant

The life cycle of the red alga Porphyra purpurea alternates between two morphologically distinct phases: a shell-boring, filamentous sporophyte and a free-living, foliose gametophyte. From a subtracted cDNA library enriched for sporophyte-specific sequences, we isolated a cDNA encoding an unusual elongation factor 1 alpha (EF-1 alpha) that is expressed only in the sporophyte. A second EF-1 alpha gene that is expressed equally in the sporophyte and the gametophyte was isolated from a genomic library. These are the only EF-1 alpha genes detectable in P. purpurea. The constitutively expressed gene encodes an EF-1 alpha very similar to those of most eukaryotes. However, the sporophyte-specific EF-1 alpha is one of the most divergent yet described, with nine insertions or deletions ranging in size from 1 to 26 amino acids. This is the first report of a developmental stage-specific EF-1 alpha outside of the animal kingdom and suggests a fundamental role for EF-1 alpha in the developmental process.

Organization and expression of the gene coding for the potassium transport system AKT1 of Arabidopsis thaliana

We have isolated and sequenced the genomic clone coding for the potassium transport system AKT1 of Arabidopsis thaliana. Southern blot analysis indicated that the gene is present in one copy in the Arabidopsis genome. The coding sequence is interrupted by ten introns. Sequence comparisons of AKT1 polypeptide with the voltage-gated inward rectifying Arabidopsis K+ channel KAT1, and with voltage- or cyclic nucleotide-gated channels from insects and mammals, revealed a highly conserved domain found specifically in both plant polypeptides, and corresponding to about the last 50 amino acids of their C-terminal region. Northern blot analysis of AKT1 expression in Arabidopsis seedlings indicated that AKT1 is preferentially expressed in roots. No transcript was detected in extracts from heterotrophic suspension culture cells. Depleting K+ in the Arabidopsis seedling culture medium for 4 days led to a strong decrease in K+ tissue content (ca. 50%), but did not affect AKT1 transcript level.

The tef1 box, a ubiquitous cis-acting element involved in the activation of plant genes that are highly expressed in cycling cells

In Arabidopsis thaliana, the tef1 box is a cis-acting promoter element of the EF-1 alpha A1 gene involved in the activation of transcription in meristematic tissues. The initiation of root calli in transgenic Arabidopsis by 2,4-D shows that the tef1-dependent expression of the GUS reporter gene is not restricted to meristematic regions but involves all of the cycling cells. Hybridization experiments conducted using Arabidopsis cDNA clones organized in a dense array on filters, and cDNA probes prepared from cells in various states of growth, or blocked at different steps of the cell cycle, indicate that the enhanced expression of EF-1 alpha genes occurs in cycling cells at the point of entry into the cell cycle and remains constant during transit through the cycle. The analysis of several promoters of genes, other than EF-1 alpha, which are overexpressed in growing cells and involved in the processes of translation or redox regulation, reveals the presence of sequences showing partial homologies with the tef1 box. The Arabidopsis ribosomal gene srp18 and the tobacco gene thioh2, encoding a thioredoxin h, contain such sequences. Gel retardation experiments suggest that these sequences are targets for the same proteins as those that interact with the tef1 box of the Arabidopsis EF-1 alpha A1 gene. In transfected Arabidopsis protoplasts, the putative tef1 sequence thioh2 partially restores the activity of a tef1 box-less EF-1 alpha A1 promoter. These data demonstrate that the tef1 box is a ubiquitous cis-acting element involved in the transcriptional activation of plant genes that are overexpressed in cycling cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of the gene for the elongation factor 1 alpha from the zygomycete Absidia glauca. Use of the promoter region for constructions of transformation vectors

The complete genomic DNA sequence was determined for one of the gene for the elongation factor 1 alpha (TEF), isolated from the zygomycete Absidia glauca. Sequence comparison with TEF genes from other fungi show the highest similarity to TEF-genes of the closely related zygomycete Mucor racemosus (Sundstrom et al. 1987). Southern-blot analysis of genomic DNA from A. glauca with the TEF gene reveals six chromosomal copies in the genome. In transformation experiments of A. glauca, vector constructions were used which allow targeting of one of the TEF loci. Several transformants of A. glauca were analyzed at the DNA level. In most cases, rearranged forms of autonomously replicated plasmids could be found in these isolates. However, some transformants show a different restriction pattern of the TEF loci if compared with the parental strains. From Southern-blot data it could be concluded that in one case the rearrangement lies downstream of one TEF locus. In a second case genetic parts following the 3'-end of the TEF gene are moved towards the 5'-end of the gene.

Gene density and organization in a small region of the Arabidopsis thaliana genome

We have characterized a 6.4 kb genomic fragment from Arabidopsis thaliana ecotype Columbia overlapping the 5' end of the AKin10 gene which encodes a protein Ser/Thr kinase. Using, as probes, various restriction fragments located upstream of AKin10, two cDNA clones have been isolated from a cDNA library prepared from young shoot tissue. A comparison between the cDNA and the above genomic sequences allowed us to locate two novel genes, Atcys1 and Athyp1 (for Arabidopsis thaliana cystathionine gamma-synthase 1 and hypothetical protein 1). The coding sequences of both genes are interrupted by introns and the exons match the sequences of the corresponding cDNAs. Further analysis of the genomic fragment revealed the presence of an open reading frame (ORF) of 609 nucleotides situated between the two genes. Atcys1, Athyp1, AKin10 and the ORF are very close to each other and organized in the same polarity; hence, the intergenic regions probably contain, within less than 0.5 kb, all the regulatory elements necessary to govern initiation and termination of transcription. The deduced protein sequence of Atcys1 shows a high degree of similarity with the cystathionine gamma-synthase from Escherichia coli. The putative product of the Athyp1 gene contains seven hydrophobic regions flanked by hydrophilic domains, reminiscent of membrane-spanning proteins. Southern blot hybridization experiments suggest the presence of one copy of Atcys1, Athyp1 and AKin10 per haploid genome, and Northern blot analysis demonstrates that the three genes are differentially expressed in roots, shoots and leaves.

Complex duplications in maize lines

Rp1 is a disease resistance complex and is the terminal morphological marker on the short arm of maize chromosome 10. Several restriction fragment length polymorphisms (RFLPs), which map within 5 map units of Rp1, were examined to determine if they are also complex in structure. Two RFLP loci, which mapped distally to Rp1, BNL3.04 and PIO200075, existed in a single copy in all maize lines examined. These two loci cosegregated perfectly in 130 test cross progeny. Two RFLP loci that map proximally to Rp1 had unusual structures, which have not yet been reported for maize RFLPs; the loci were complex, with variable numbers of copies in different maize lines. One of the loci, NP1285, occasionally recombined in meiosis to yield changes in the number of copies of sequences homologous to the probe. The other proximal locus, detected by the probes NPI422, KSU3, and KSU4, was relatively stable in meiosis and no changes in the number of restriction fragments were observed. The similarity in map position between Rp1 and the complex RFLP loci indicate there may be genomic areas where variable numbers of repeated sequences are common. The structure of these complex loci may provide insight into the structure and evolution of Rp1.

Modular organization and development activity of an Arabidopsis thaliana EF-1 alpha gene promoter

The activity of the Arabidopsis thalana A1 EF-1 alpha gene promoter was analyzed in transgenic Arabidopsis plants. The 5' upstream sequence of the A1 gene and several promoter deletions were fused to the beta-glucuronidase (GUS) coding region. Promoter activity was monitored by quantitative and histochemical assays of GUS activity. The results show that the A1 promoter exhibits a modular organization. Sequences both upstream and downstream relative to the transcription initiation site are involved in quantitative and tissue-specific expression during vegetative growth. One upstream element may be involved in the activation of expression in meristematic tissues; the downstream region, corresponding to an intron within the 5' non-coding region (5'IVS), is important for expression in roots; both upstream and downstream sequences are required for expression in leaves, suggesting combinatorial properties of EF-1 alpha cis-regulatory elements. This notion of specific combinatorial regulation is reinforced by the results of transient expression experiments in transfected Arabidopsis protoplasts. The deletion of the 5'IVS has much more effect on expression when the promoter activity is under the control of A1 EF-1 alpha upstream sequences than when these upstream sequences were replaced by the 35S enhancer. Similarly, a synthetic oligonucleotide corresponding to an A1 EF-1 alpha upstream cis-acting element (the TEF1 box), is able to restore partially the original activity when fused to a TEF1-less EF1-alpha promoter but has no significant effect when fused to an enhancer-less 35S promoter.

Sequence of a cDNA encoding the alpha-subunit of wheat translation elongation factor 1

A cDNA encoding the alpha-subunit of wheat protein synthesis elongation factor 1 (EF-1 alpha) was isolated from a wheat cDNA expression library and sequenced. The deduced amino acid sequence is compared to EF-1 alpha from other species and to elongation factor Tu (EF-Tu) from Escherichia coli. Putative GTP-binding sites are identified.

Two genes encoding the soybean translation elongation factor eEF-1 alpha are transcribed in seedling leaves

A cDNA and a genomic DNA library from soybean (Glycine max L.) were used to identify and sequence two genes coding for the alpha-subunit of the translation elongation factor eEF-1. Within the coding part, the two genes (tefS1 and tefS2) diverge in 80 wobble positions thus yielding an identical protein composed of 447 amino acids. The soybean protein has about 95% similarity with eEF-1 alpha proteins of Arabidopsis thaliana and tomato. Both genes S1 and S2 contain, within the coding part at a site seemingly unique to higher plants, a single short intron of 86 and 116 nucleotides, respectively. The untranslated leader part of both genes is interrupted by a large intron (partially sequenced). Genes S1 and S2 are transcribed in young leaves. cDNA and gene-specific oligonucleotide probes interact with a unique transcript of close to 1.9 kb. Northern hybridization studies using RNAs from dark- and light-grown seedlings show that light sharply increases the level of stable transcripts (1.9 kb). A peak value is measured after about 3 h of illumination, afterwards the transcript concentration drops to about 10% of the peak value. Genes S1 and S2 follow a similar transcription pattern in developing seedling leaves, which is distinct from that of the rbcS genes measured in parallel experiments. According to northern results, S1 transcripts are more abundant in leaves at all measured stages of development than S2 transcripts.

Cis and trans-acting elements involved in the activation of Arabidopsis thaliana A1 gene encoding the translation elongation factor EF-1 alpha

In A. thaliana the translation elongation factor EF-1 alpha is encoded by a small multigenic family of four members (A1-A4). The A1 gene promoter has been dissected and examined in a transient expression system using the GUS reporter gene. Deletion analysis has shown that several elements are involved in the activation process. One cis-acting domain, the TEF 1 box, has been accurately mapped 100 bp upstream of the transcription initiation site. This domain is the target for trans-acting factors identified in nuclear extracts prepared from A. thaliana. Homologies are found between the TEF 1 box and sequences present at the same location within the A2, A3 and A4 promoters. This observation, together with those obtained from gel retardation assays performed using DNA fragments from the A4 promoter, suggest that the activation process mediated by the TEF 1 element is conserved among the A. thaliana EF-1 alpha genes. Analysis of nearly full length cDNA clones has shown that in addition to a single intron located within the coding region, the A1 gene contains a second intron located within the 5' non coding region. Such an intron is also present within the A2, A3 and A4 genes. This 5' intervening sequence appears to be essential to obtain a maximum GUS activity driven by the A1 gene promoter.