Sequence analysis and transcriptional regulation by heat shock of polyubiquitin transcripts from maize

ECPUB5 Polyubiquitin Gene in Euphorbia characias: Molecular Characterization and Seasonal Expression Analysis

The spurge Euphorbia characias is known for its latex, which is rich in antioxidant enzymes and anti-phytopathogen molecules. In this study, we identified a novel polyubiquitin protein in the latex and leaves, leading to the first molecular characterization of its coding gene and expressed protein in E. characias. Using consensus-degenerate hybrid oligonucleotide primers (CODEHOP) and rapid amplification of cDNA ends (5'/3'-RACE), we reconstructed the entire open reading frame (ORF) and noncoding regions. Our analysis revealed that the polyubiquitin gene encodes five tandemly repeated sequences, each coding for a ubiquitin monomer with amino acid variations in four of the five repeats. In silico studies have suggested functional differences among monomers. Gene expression peaked during the summer, correlating with high temperatures and suggesting a role in heat stress response. Western blotting confirmed the presence of polyubiquitin in the latex and leaf tissues, indicating active ubiquitination processes. These findings enhance our understanding of polyubiquitin's regulatory mechanisms and functions in E. characias, highlighting its unique structural and functional features.

Stress induces cell dedifferentiation in plants

Accumulating evidence lends support to the proposal that a major theme in plant responses to stresses is dedifferentiation, whereby mature cells acquire stem cell features (e.g. open chromatin conformation) prior to acquisition of a new cell fate. In this review, we discuss data addressing plant cell plasticity and provide evidence linking stress, dedifferentiation and a switch in cell fate. We emphasize the epigenetic modifications associated with stress-induced global changes in chromatin structure and conclude with the implications for genetic variation and for induced pluripotent stem cells in animals. It appears that stress is perceived as a signal that directs plant cells to undergo reprogramming (dedifferentiation) as a means for adaptation and in preparation for a stimulus-based acquisition of a new cell fate. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.

Microarray analysis of vegetative phase change in maize

Vegetative phase change is the developmental transition from the juvenile phase to the adult phase in which a plant becomes competent for sexual reproduction. The gain of ability to flower is often accompanied by changes in patterns of differentiation in newly forming vegetative organs. In maize, juvenile leaves differ from adult leaves in morphology, anatomy and cell wall composition. Whereas the normal sequence of juvenile followed by adult is repeated with every sexual generation, this sequence can be altered in maize by the isolation and culture of the shoot apex from an adult phase plant: an 'adult' meristem so treated reverts to forming juvenile vegetative organs. To begin to unravel the as-yet poorly understood molecular mechanisms underlying phase change in maize, we compared gene expression in two juvenile sample types, leaf 4 and culture-derived leaves 3 or 4, with an adult sample type (leaf 9) using cDNA microarrays. All samples were leaf primordia at plastochron 6. A gene was scored as 'phase induced' if it was up- or downregulated in both juvenile sample types, compared with the adult sample type, with at least a twofold change in gene expression at a P-value of < or =0.005. Some 221 expressed sequence tags (ESTs) were upregulated in juveniles, and 28 ESTs were upregulated in adults. The largest class of juvenile-induced genes was comprised of those involved in photosynthesis, suggesting that maize plants are primed for energy production early in vegetative growth by the developmental induction of photosynthetic genes.

Induction of a polyubiquitin gene promoter by dehydration stresses in transformed rice cells

The expression of the maize polyubiquitin gene promoter UBI1 in rice cells has been used to study the involvement of ubiquitin in cell protection responses to dehydration caused by osmotic, saline or freezing stress. The effect of these stresses on UBI1 activity was investigated by the use of stably transformed rice calli (UBI1:GUS), as well as by transient expression experiments performed with cell lines with high or low tolerance to each type of stress. The theoretical analysis of the UBI1 promoter shows several putative stress-regulated boxes that could account for the stress-related UBI1 induction pattern described in this work. We suggest that the study of the differential UBI1 promoter-driven expression in rice cell lines with different level of tolerance to stress might be useful to elucidate complex signal transduction pathways in response to dehydration stresses in monocots.

Expression enhancement of a rice polyubiquitin gene promoter

An 808 bp promoter from a rice polyubiquitin gene, rubi3, has been isolated. The rubi3 gene contained an open reading frame of 1,140 bp encoding a pentameric polyubiquitin arranged as five tandem, head-to-tail repeats of 76 aa. The 1,140 bp 5' UTR intron of the gene enhanced its promoter activity in transient expression assays by 20-fold. Translational fusion of the GUS reporter gene to the coding sequence of the ubiquitin monomer enhanced GUS enzyme activity in transient expression assays by 4.3-fold over the construct containing the original rubi3 promoter (including the 5' UTR intron) construct. The enhancing effect residing in the ubiquitin monomer coding sequence has been narrowed down to the first 9 nt coding for the first three amino acid residues of the ubiquitin protein. Mutagenesis at the third nucleotide of this 9 nt sequence still maintains the enhancing effect, but leads to translation of the native GUS protein rather than a fusion protein. The resultant 5' regulatory sequence, consisting of the rubi3 promoter, 5' UTR exon and intron, and the mutated first 9 nt coding sequence, has an activity nearly 90-fold greater than the rubi3 promoter only (without the 5' UTR intron), and 2.2-fold greater than the maize Ubi1 gene promoter (including its 5' UTR intron). The newly created expression vector is expected to enhance transgene expression in monocot plants. Considering the high conservation of the polyubiquitin gene structure in higher plants, the observed enhancement in gene expression may apply to 5' regulatory sequences of other plant polyubiquitin genes.

Duplicate FLORICAULA/LEAFY homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize

The homologous transcription factors FLORICAULA of Antirrhinum and LEAFY of Arabidopsis share conserved roles in flower meristem identity and floral patterning. While roles for FLORICAULA/LEAFY homologs in flower development have been demonstrated in numerous dicots, little is known about the function of these meristem identity genes in the more distantly related flowering plants, the monocots. We used reverse genetics to investigate the role of two duplicate FLORICAULA/LEAFY homologs in maize (Zea mays L. ssp. mays) - a monocot species with dramatically different flower and inflorescence morphology from that of dicot species. Transposon insertions into the maize genes, zfl1 and zfl2, led to a disruption of floral organ identity and patterning, as well as to defects in inflorescence architecture and in the vegetative to reproductive phase transition. Our results demonstrate that these genes share conserved roles with their dicot counterparts in flower and inflorescence patterning. The phenotype of zfl1; zfl2 double mutants suggests that these maize FLORICAULA/LEAFY homologs act as upstream regulators of the ABC floral organ identity genes, and this along with previously published work, indicates that the transcriptional network regulating flower development is at least partially conserved between monocots and dicots. Our data also suggest that the zfl genes may play a novel role in controlling quantitative aspects of inflorescence phyllotaxy in maize, consistent with their candidacy for quantitative trait loci that control differences in inflorescence structure between maize and its progenitor, teosinte.

Changes in three types of ubiquitin mRNA and ubiquitin-protein conjugate levels during lens development

Ubiquitin is a small, highly conserved protein that covalently attaches to other proteins to form a unique branched protein structure. The best characterized function of this post-translational modification is to mark the modified protein for degradation by the proteasome. To investigate whether ubiquitin genes are regulated in lens development, the authors analyzed the levels of three ubiquitin mRNAs (UbA(52), UbB and UbC) in freshly dissected fiber and epithelial cells, and in epithelial explants induced to differentiate ex vivo. Explants, comprising the capsule and adherent epithelial cells, were dissected from lenses of 3 day old Sprague Dawley rats and cultured +/-bFGF to induce differentiation. Quantitative competitive RT-PCR was used to determine the mRNA levels in fresh and cultured cells. UbA(52), UbB and UbC mRNAs were 3.2 (P < 0.0001), 5.0 (P < 0.0001) and 6.8 (P < 0.0001) fold higher, respectively, in freshly dissected epithelial cells than in differentiated fiber cells. Immunological spot assays showed that ubiquitin protein is over two fold as high in rat pup lens epithelial cells as in fiber cells. The ubiquitin protein in fiber cells of adult rat is lower than that in adult epithelium and in pup fiber cells, indicating that ubiquitin content further decreased during lens fiber maturation. Western blots showed a greater amount of protein-conjugated ubiquitin (MW > 81 kD) in epithelial cells than in fiber cells, demonstrating a parallel pattern between the expression of ubiquitin mRNA, the level of ubiquitin protein and the level of conjugates in the cells. Epithelial cell explant cultures permit study of cells initiating differentiation. In contrast to fully differentiated fiber cells, explant cultures induced to initiate differentiation underwent differential up-regulation of ubiquitin gene expression. UbA(52) and UbB mRNA levels in +bFGF (differentiating) explant cultures were 2.6 (P < 0.001) and 1.4 (P < 0.001) fold higher, respectively, than those of -bFGF cultures. UbC mRNA content was similar in explants cultured with or without bFGF. Dissection of the isolated epithelial cells into regions representing distinct populations gave results consistent with this observation of the explant results. UbA(52), UbB and UbC mRNAs are 2.0, 2.2 and 1.76 fold higher, respectively, in the peripheral (initiating differentiation) than in the central (undifferentiated) region of epithelial cells. These results together indicate that UbA(52) and UbB mRNAs are transiently increased during the initiation and early stages of differentiation. However, UbC mRNA appears to be relatively unaffected at the earliest stage in this differentiation model and may have a different distribution than UbA(52) and UbB in the anterior lens cells. These data are consistent with an important role for ubiquitin during the early stages of lens differentiation. The selective expression indicates that the three genes have specific differentiation related functions.

Differential regulation of transcripts encoding cytosolic NADP-malic enzyme in C3 and C4 Flaveria species

A cytosolic NADP-malic enzyme (CYTME) has been described previously in several plants, all C3 species. CYTME is distinct from the chloroplastic NADP-malic enzyme (CHLME) that is highly active in C4 species. We show that at least one CytMe gene is present in all Flaveria spp., including C3, C4, and C3-C4 intermediate types. Based on the CytMe expression patterns in Flaveria pringlei (C3) and Flaveria trinervia (C4), we suggest CYTME has several distinct roles, including the supplying of NADPH for cytosolic metabolism, the supporting of wound response or repair, and the balancing of cellular pH in illuminated leaves. These three roles are likely correlated with CytMe mRNAs of apparent sizes 2.0, 2.2, and 2.4 kb, respectively, which differ in the length of the 5' untranslated regions. Various regulatory mechanisms involving RNA processing and translational efficiency are discussed.

Four mutant alleles elucidate the role of the G2 protein in the development of C(4) and C(3) photosynthesizing maize tissues

Maize leaf blades differentiate dimorphic photosynthetic cell types, the bundle sheath and mesophyll, between which the reactions of C(4) photosynthesis are partitioned. Leaf-like organs of maize such as husk leaves, however, develop a C(3) pattern of differentiation whereby ribulose bisphosphate carboxylase (RuBPCase) accumulates in all photosynthetic cell types. The Golden2 (G2) gene has previously been shown to play a role in bundle sheath cell differentiation in C(4) leaf blades and to play a less well-defined role in C(3) maize tissues. To further analyze G2 gene function in maize, four g2 mutations have been characterized. Three of these mutations were induced by the transposable element Spm. In g2-bsd1-m1 and g2-bsd1-s1, the element is inserted in the second intron and in g2-pg14 the element is inserted in the promoter. In the fourth case, g2-R, four amino acid changes and premature polyadenylation of the G2 transcript are observed. The phenotypes conditioned by these four mutations demonstrate that the primary role of G2 in C(4) leaf blades is to promote bundle sheath cell chloroplast development. C(4) photosynthetic enzymes can accumulate in both bundle sheath and mesophyll cells in the absence of G2. In C(3) tissue, however, G2 influences both chloroplast differentiation and photosynthetic enzyme accumulation patterns. On the basis of the phenotypic data obtained, a model that postulates how G2 acts to facilitate C(4) and C(3) patterns of tissue development is proposed.

A maize glycine-rich protein is synthesized in the lateral root cap and accumulates in the mucilage

The root cap functions in the perception of gravity, the protection of the root apical meristem, and facilitation of the passage of roots through the soil, but the genes involved in these functions are poorly understood. Here we report the isolation of a root-specific gene from the cap of maize (Zea mays L.) primary root by cDNA subtraction and differential screening. The gene zmGRP4 (Z. mays glycine rich protein 4) encodes a member of the glycine-rich proteins with a putative signal peptide at the amino terminus. The deduced molecular mass of mature zmGRP4 is 14.4 kD. In situ-hybridization analysis has shown zmGRP4 to be strongly expressed in the lateral root cap and weakly expressed in the root epidermis. A polyclonal antibody raised against recombinant zmGRP4 detected a protein of 36 kD in the insoluble protein fraction extracted from the root tip and the root proper, indicating posttranslational modification(s) of zmGRP4. Immunohistochemical analysis showed the accumulation of zmGRP4 in the mucilage that covers the root tip. These results indicate that lateral root-cap cells secrete modified zmGRP4 into the mucilage to which the protein may contribute to its characteristic physical properties.

Posttranscriptional gene silencing in transgenic sugarcane. Dissection Of homology-dependent virus resistance in a monocot that has a complex polyploid genome

RNA-mediated, posttranscriptional gene silencing has been determined as the molecular mechanism underlying transgenic virus resistance in many plant virus-dicot host plant systems. In this paper we show that transgenic virus resistance in sugarcane (Saccharum spp. hybrid) is based on posttranscriptional gene silencing. The resistance is derived from an untranslatable form of the sorghum mosaic potyvirus strain SCH coat protein (CP) gene. Transgenic sugarcane plants challenged with sorghum mosaic potyvirus strain SCH had phenotypes that ranged from fully susceptible to completely resistant, and a recovery phenotype was also observed. Clones derived from the same transformation event or obtained after vegetative propagation could display different levels of virus resistance, suggesting the involvement of a quantitative component in the resistance response. Most resistant plants displayed low or undetectable steady-state CP transgene mRNA levels, although nuclear transcription rates were high. Increased DNA methylation was observed in the transcribed region of the CP transgenes in most of these plants. Collectively, these characteristics indicate that an RNA-mediated, homology-dependent mechanism is at the base of the virus resistance. This work extends posttranscriptional gene silencing and homology-dependent virus resistance, so far observed only in dicots, to an agronomically important, polyploid monocot.

Tissue-specific and light-dependent expression within a family of nuclear-encoded sigma-like factors from Zea mays

The principal transcription machinery functioning in chloroplasts of higher plants is encoded in two subcellular compartments. Subunits of the RNA polymerase catalytic core are plastid encoded, while sigma factors required for promoter recognition are encoded in the nucleus. We have isolated nuclear-encoded cDNAs, sig1, sig2, and sig3, specifying three sigma factors from maize (Zea mays). The three deduced polypeptides have extensive sequence identity with the principal sigma factors of eubacteria. Two of the maize cDNAs, sig1 and sig3, encode NH2-terminal transit peptides which direct the uptake of a heterologous protein into chloroplasts in vitro. Transcripts for the sig3 gene were more abundant in green leaves than in roots and in light-treated seedlings than in dark-grown seedlings. In contrast, sig1 transcripts were readily detectable in all tissues examined. Thus, at least two promoter-selectivity factors function with the maize chloroplast RNA polymerase, one of which is constitutively expressed and the other is light activated.

Pea polyubiquitin genes: (I) structure and genomic organization

Four polyubiquitin genes, PUB1, PUB2, PUB3 and PUB4, were isolated from a pea (Pisum sativum L. cv Alaska) genomic library and completely sequenced. They represent all of the four polyubiquitin genes of the ubiquitin gene family in pea. The coding regions of the genes contain five or six coding units arranged as tandem repeats. The different coding repeats of the four genes share homologies between 75 and 97%, encoding the same protein of 76 amino acids identical to those from other higher plants. The open reading frames of PUB1, PUB2 and PUB4 terminate in the additional amino acid, phenylalanine (F), and PUB3 terminates in isoleucine (I). The polyubiquitin genes all contain intron sequences ranging from 584 to 1114 bp immediately 5' to the ATG initiation codon of the first coding sequence. Of the four genes, three are associated with long AT-rich (85.4-89.4% A+T) sequences ranging from about 331 to 478 bp at their 5' or 3' ends. The PUB4 gene was found to be linked to a moderate to highly repetitive DNA at its 5' flanking sequence. The greater sequence homology between different genes than among individual repeating units of a gene suggests that the polyubiquitin genes may have arisen by gene duplication of a single gene sequence.

A maize zinc-finger protein binds the prolamin box in zein gene promoters and interacts with the basic leucine zipper transcriptional activator Opaque2

The prolamin box (P-box) is a highly conserved 7-bp sequence element (5'-TGTAAAG-3') found in the promoters of many cereal seed storage protein genes. Nuclear factors from maize endosperm specifically interact with the P-box present in maize prolamin genes (zeins). The presence of the P-box in all zein gene promoters suggests that interactions between endosperm DNA binding proteins and the P-box may play an important role in the coordinate activation of zein gene expression during endosperm development. We have cloned an endosperm-specific maize cDNA, named prolamin-box binding factor (PBF), that encodes a member of the recently described Dof class of plant Cys2-Cys2 zinc-finger DNA binding proteins. When tested in gel shift assays, PBF exhibits the same sequence-specific binding to the P-box as factors present in maize endosperm nuclei. Additionally, PBF interacts in vitro with the basic leucine zipper protein Opaque2, a known transcriptional activator of zein gene expression whose target site lies 20 bp downstream of the P-box in the 22-kDa zein gene promoter. The isolation of the PBF gene provides an essential tool to further investigate the functional role of the highly conserved P-box in regulating cereal storage protein gene expression.

The evolution of apical dominance in maize

The domestication of crop plants has often involved an increase in apical dominance (the concentration of resources in the main stem of the plant and a corresponding suppression of axillary branches). A striking example of this phenomenon is seen in maize (Zea mays spp. mays), which exhibits a profound increase in apical dominance compared with its probable wild ancestor, teosinte (Zea mays ssp. parviglumis). Previous research has identified the teosinte branched1 (tb1) gene as a major contributor to this evolutionary change in maize. We have cloned tb1 by transposon tagging and show here that it encodes a protein with homology to the cycloidea gene of snapdragon. The pattern of tb1 expression and the morphology of tb1 mutant plants suggest that tb1 acts both to repress the growth of axillary organs and to enable the formation of female inflorescences. The maize allele of tb1 is expressed at twice the level of the teosinte allele, suggesting that gene regulatory changes underlie the evolutionary divergence of maize from teosinte.

Characterization, chromosomal mapping, and expression of different polyubiquitin genes in tissues from control and heat-shocked maize seedlings

Polyubiquitin transcripts accumulate in plant and animal cells following a heat shock. Most species have a few to several polyubiquitin genes; within a species, the genes may differ in nucleotide (nt) sequence and (or) the number of 228-nt repeats encoding the ubiquitin monomer. This study examines three maize (inbred Oh43) polyubiquitin genes. Two of the genes, MubG9 and MubG5, possess five repeats; the third, MubG1 possesses seven repeats. Sequence analyses of the genomic clones, MubG9 and MubG1 and a cDNA clone, MubG5, reveal that they differ primarily from each other in their nt sequences 5' and 3' to their open reading frames. MubG1 contains a 1004-base pair (bp) intron in its 5' untranslated region. Using gene-specific probes, we show that the amount of polyribosome-associated mRNA transcripts from MubG9 isolated from 2- and 5-day old plumules and radicles is unchanged by heat shock. While the amount of transcript from MubG1 and MubG5 on the polyribosomes in plumules and radicles of 2-day-old seedlings is also unchanged by heat shock, the levels of these transcripts are elevated considerably in similar tissues from heat-shocked 5-day-old seedlings. Similar or identical gene-specific probes were employed to map the genes using the recombinant inbred method. MubG9 maps to chromosome 4L position 186; MubG1 maps to 5L104 and MubG5 to 4L188. The opportunity to use gene-specific probes extends the evidence for distinct modulation (time and tissue) of polyubiquitin gene expression in maize and provides the basis for locus assignment within the genome.

Structure and promoter activity of a stress and developmentally regulated polyubiquitin-encoding gene of Nicotiana tabacum

A polyubiquitin-encoding gene was identified from a Nicotiana tabacum genomic library using a specific probe spanning the 3' untranslated region of the corresponding cDNA. The gene, Ubi.U4, is expressed in various amounts in the whole plant, except in just-fully-expanded leaves. Genomic blots indicate that it originates from N. tomentosiformis. Sequence analyses reveal that the gene consists of four ubiquitin monomers extended by a fifth truncated subunit. It is disrupted by a single 457-bp intron in close proximity to the start codon of translation. Primer extension experiments localized the transcription start point (tsp). Transient gene expression in N. tabacum protoplasts indicates that the deletion of the intron has no significant influence on gene expression. Mutagenesis on putative cis-regulatory elements indicates at least three important motifs in the proximal promoter: an 'ACGT' core element, an A + T-rich sequence and a less clearly defined cis-element located between bp -162 and -113.

Functional dissection of a rice high-pI alpha-amylase gene promoter

Deletion analysis has previously shown that a 260 bp fragment, located between positions -230 and +29 of the 5' end of a rice high-pI alpha--amylase gene, OSamy-c, is required for gibberellic acid (GA3)-dependent transcriptional activation. We have since established a quantitative transient assay based on expression of a luciferase reporter gene in rice aleurone cells and continued to characterize the OSamy-c promoter for GA3-dependent regulatory sequences. Using this method, we have shown that the DNA sequence between -158 and -46 (sequence I) is sufficient to confer GA3-responsive activation on OSamy-c. We have also shown that this sequence is capable of directing GA3-dependent expression from a heterologous minimal promoter. Our results also showed that sequence I confers GA3 regulatory control in an orientation-dependent manner and interacts with two further upstream DNA sequences, II and III, in a combination which mildly enhances the level of the GA3 response exhibited by sequence I. Thus, we propose that sequence I confers the fundamental GA3-responsive character on OSamy-c, and that regulatory proteins that bind sequences II and III interact with each other and with regulatory proteins that bind sequence I, effectively to modulate the GA3 response.

Cloning and characterization of two ubiquitin::79-amino-acid extension protein-encoding fusion genes from Lupinus albus

Two different ubiquitin::79-amino-acid (aa) extension protein-encoding fusion genes were isolated from a Lupinus albus nuclear DNA library and sequenced. Both genes have 465-nucleotide open reading frames encoding a single ubiquitin (Ub) monomer fused in frame to a 79-aa extension (Ext) protein. The deduced aa sequences of the encoded Ub are identical to the aa sequences of Ub from other plants. The encoded Ext proteins are putative ribosomal proteins, highly basic, differing by 2 aa from each other, and have a high degree of similarity to Ext proteins from other plants.

Activity of a maize ubiquitin promoter in transgenic rice

We have used the maize ubiquitin 1 promoter, first exon and first intron (UBI) for rice (Oryza sativa L. cv. Taipei 309) transformation experiments and studied its expression in transgenic calli and plants. UBI directed significantly higher levels of transient gene expression than other promoter/intron combinations used for rice transformation. We exploited these high levels of expression to identify stable transformants obtained from callus-derived protoplasts co-transfected with two chimeric genes. The genes consisted of UBI fused to the coding regions of the uidA and bar marker genes (UBI:GUS and UBI:BAR). UBI:GUS expression increased in response to thermal stress in both transfected protoplasts and transgenic rice calli. Histochemical localization of GUS activity revealed that UBI was most active in rapidly dividing cells. This promoter is expressed in many, but not all, rice tissues and undergoes important changes in activity during the development of transgenic rice plants.

Polyubiquitin gene expression and structural properties of the ubi4-2 gene in Petroselinum crispum

Ubiquitin is an omnipresent protein found in all eukaryotes so far analysed. It is involved in several important processes, including protein turnover, chromosome structure and stress response. Parsley (Petroselinum crispum) contains at least two active polyubiquitin (ubi4) genes encoding hexameric precursor proteins. The deduced amino acid sequences of the ubiquitin monomers are identical to one another and to ubiquitin sequences from several other plant species. Analysis of the promoter region of one ubi4 gene revealed putative regulatory elements. In parsley plants, the ubi4 mRNAs were the predominant ubiquitin mRNAs and were present at comparable levels in all plant organs tested. In cultured parsley cells, high levels of ubiquitin gene expression remained unaffected by heat shock, elicitor or light treatment.

Ubiquitin genes are differentially regulated in protoplast-derived cultures of Nicotiana sylvestris and in response to various stresses

Four ubiquitin mRNA size classes were found to be differentially regulated in mesophyll protoplast-derived cultures of Nicotiana sylvestris. Three mRNA families of 1.9, 1.6 and 1.35 kb were expressed as soon as protoplasts were isolated. The 1.9 and 1.6 kb size classes were transiently expressed during the first hours of culture, whereas the level of expression of the 1.35 kb size class was maintained as long as cells kept dividing. A 0.7 kb mRNA size class started to be expressed just before the first divisions were observed. cDNAs corresponding to each of these families were isolated from a 6-h-old protoplast cDNA library and characterized. The 1.9, 1.6 and 1.35 kb mRNAs thus encode 7- or more, 6- and 5-mers, respectively, of ubiquitin whereas the 0.7 kb mRNAs encode a monomer of ubiquitin fused to a carboxyl extension protein of 52 amino acids. The expression of ubiquitin genes was studied, using probes specific for each of these transcript families, during protoplast culture and, for comparison, after various stresses including heat shock, HgCl2 treatment, a viral infection giving rise to a hypersensitive reaction, and an Agrobacterium tumefaciens infection which resulted in tumour formation. The 1.9 and 1.6 kb mRNA size classes were found to be stress-regulated, the 0.7 kb mRNA size class developmentally regulated and the 1.35 kb size class both stress- and developmentally regulated.

Maize polyubiquitin genes: structure, thermal perturbation of expression and transcript splicing, and promoter activity following transfer to protoplasts by electroporation

Two genomic clones (lambda Ubi-1 and lambda Ubi-2) encoding the highly conserved 76 amino acid protein ubiquitin have been isolated from maize. Sequence analysis shows that both genes contain seven contiguous direct repeats of the protein coding region in a polyprotein conformation. The deduced amino acid sequence of all 14 repeats is identical and is the same as for other plant ubiquitins. The use of transcript-specific oligonucleotide probes shows that Ubi-1 and Ubi-2 are expressed constitutively at 25 degrees C but are inducible to higher levels at elevated temperatures in maize seedlings. Both genes contain an intron in the 5' untranslated region which is inefficiently processed following a brief, severe heat shock. The transcription start site of Ubi-1 has been determined and a transcriptional fusion of 0.9 kb of the 5' flanking region and the entire 5' untranslated sequence of Ubi-1 with the coding sequence of the gene encoding the reporter molecule chloramphenicol acetyl transferase (CAT) has been constructed (pUBI-CAT). CAT assays of extracts of protoplasts electroporated with this construct show that the ubiquitin gene fragment confers a high level of CAT expression in maize and other monocot protoplasts but not in protoplasts of the dicot tobacco. Expression from the Ubi-1 promoter of pUBI-CAT yields more than a 10-fold higher level of CAT activity in maize protoplasts than expression from the widely used cauliflower mosaic virus 35S promoter of a 35S-CAT construct. Conversely, in tobacco protoplasts CAT activity from transcription of pUBI-CAT is less than one tenth of the level from p35S-CAT.

Characterization of the structure and transcription of an ubiquitin fusion gene from maize

We have identified a maize ubiquitin (Ubi) fusion gene (UBF9) by screening a maize W22 genomic phage lambda library with a short (16-nucleotide) oligodeoxyribonucleotide probe derived from the sequence for the extension sequence of a yeast UB13 fusion gene. UBF9 consists of an UB monomer sequence (228 bp long) joined to an extension sequence (237 bp long). The extension sequence encodes a protein of 79 amino acids which shares extensive identity with similar extension aa sequences found in yeast, humans, barley and Arabidopsis thaliana. UBF9 encodes a small-size class of Ubi mRNAs in the maize tissues investigated. The UBF9 transcript is present in high levels in maize endosperm tissues 22 days after pollination. Genomic Southern blots of maize inbred W22 DNA indicate that the fusion gene sequences are present in multiple copies in the maize genome. Primer extension experiments indicate that the transcription start point is located at 80 bp upstream from the translation start codon of UBF9. Two 37-bp tandem repeated A + T-rich sequences are found in the 5'-flanking region of UBF9. The A + T-rich sequences share the motif, AATATTTTATT, which is present in a diverse set of plant genes.

Two ubiquitin-long-tail fusion genes arranged as closely spaced direct repeats in barley

Ubiquitin (Ubi) genes encode two types of fusion proteins: polyUbi with a varying number of direct repeats of Ubi, and Ubi-tail fusions with long or short basic C-terminal extensions. A barley (Hordeum vulgare) genomic clone has been isolated with two very similar, intronless genes encoding monoUbi-long-tail fusion peptides. The genes are arranged as direct repeats separated by 3 kb of DNA and account for two of the probable three long-tail genes in the haploid barley genome. Both genes are active and give rise to messengers about 800 nt long. The sequence of the encoded Ubi moieties is identical to the sequence of Ubi repeats of polyUbi precursors from barley and other plants. The basic tails of the peptides are 79 aa long and 71-72% homologous to corresponding sequences from yeast and man. Recently, it was found that the long and short tails are ribosomal proteins in yeast [Finley et al., Nature 338 (1989) 394-401] and the evolutionary conservation of the structure of the Ubi-tail fusion genes suggests that they serve the same function in plants. The similarity between yeast and barley Ubi-long-tail fusion genes may extend to the regulatory regions, since upstream activating sites characteristic of ribosomal protein-encoding genes in yeast (UASrpg) were found in the barley genes.