Degradation products of the mRNA encoding the small subunit of ribulose-1,5-bisphosphate carboxylase in soybean and transgenic petunia

Posttranscriptional control of photosynthetic mRNA decay under stress conditions requires 3' and 5' untranslated regions and correlates with differential polysome association in rice

Abiotic stress, including drought, salinity, and temperature extremes, regulates gene expression at the transcriptional and posttranscriptional levels. Expression profiling of total messenger RNAs (mRNAs) from rice (Oryza sativa) leaves grown under stress conditions revealed that the transcript levels of photosynthetic genes are reduced more rapidly than others, a phenomenon referred to as stress-induced mRNA decay (SMD). By comparing RNA polymerase II engagement with the steady-state mRNA level, we show here that SMD is a posttranscriptional event. The SMD of photosynthetic genes was further verified by measuring the half-lives of the small subunit of Rubisco (RbcS1) and Chlorophyll a/b-Binding Protein1 (Cab1) mRNAs during stress conditions in the presence of the transcription inhibitor cordycepin. To discern any correlation between SMD and the process of translation, changes in total and polysome-associated mRNA levels after stress were measured. Total and polysome-associated mRNA levels of two photosynthetic (RbcS1 and Cab1) and two stress-inducible (Dehydration Stress-Inducible Protein1 and Salt-Induced Protein) genes were found to be markedly similar. This demonstrated the importance of polysome association for transcript stability under stress conditions. Microarray experiments performed on total and polysomal mRNAs indicate that approximately half of all mRNAs that undergo SMD remain polysome associated during stress treatments. To delineate the functional determinant(s) of mRNAs responsible for SMD, the RbcS1 and Cab1 transcripts were dissected into several components. The expressions of different combinations of the mRNA components were analyzed under stress conditions, revealing that both 3' and 5' untranslated regions are necessary for SMD. Our results, therefore, suggest that the posttranscriptional control of photosynthetic mRNA decay under stress conditions requires both 3' and 5' untranslated regions and correlates with differential polysome association.

Transcriptome analysis reveals season-specific rbcS gene expression profiles in diploid perennial ryegrass (Lolium perenne L.)

Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972) The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24-31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159,002 14-mer SAGE tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher) and expressed sequence tag (EST) sequences. The analysis of 14,559 unique SAGE tags, which were present more than once in our SAGE library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level.

Empty pericarp2 encodes a negative regulator of the heat shock response and is required for maize embryogenesis

The heat shock response (HSR) is an evolutionarily conserved molecular/biochemical reaction to thermal stress that is essential to the survival of eukaryotic organisms. Recessive Mutator transposon mutations at the maize empty pericarp2 (emp2) locus led to dramatically increased expression of heat shock genes, retarded embryo development, and early-stage abortion of embryogenesis. The developmental timing of emp2 mutant embryo lethality was correlated with the initial competence of maize kernels to invoke the HSR. Cloning and sequence analyses revealed that the emp2 gene encoded a predicted protein with high similarity to HEAT SHOCK BINDING PROTEIN1, which was first described in animals as a negative regulator of the HSR. emp2 is a loss-of-function mutation of an HSR-negative regulator in plants. Despite the recessive emp2 phenotype, steady state levels of emp2 transcripts were abundant in mutant kernels, and the predicted coding region was unaffected. These expression data suggest that emp2 transcription is feedback regulated, whereas S1 nuclease mapping suggests that emp2 mutant transcripts are 5' truncated and nontranslatable. In support of this model, immunoblot assays revealed that EMP2 protein did not accumulate in mutant kernels. These data support a model whereby an unattenuated HSR results in the early abortion of emp2 mutant embryos. Furthermore, the developmental retardation of emp2 mutant kernels before the HSR suggests an additional role for EMP2 during embryo development distinct from the HSR.

Sequence-, tissue-, and delivery-specific targeting of RNA during post-transcriptional gene silencing

Transgenic Nicotiana benthamiana plants expressing an untranslatable version of the coat protein (CP) gene from the Tamarillo mosaic virus (TaMV) were either resistant to TaMV infection or recovered from infection. These phenotypes were the result of a post-transcriptional gene silencing (PTGS) mechanism that targeted TaMV-CP sequences for degradation. The TaMV-CP sequences were degraded when present in the wild-type TaMV potyvirus, in transgene mRNA, or in chimeric viral vectors based on White clover mosaic virus. The more efficiently targeted region was mapped to a 134-nt segment. Differences were observed in the efficiency of targeting during cell-to-cell and long-distance movement of the chimeric viruses. However, the TaMV-CP sequences do not appear to be targeted for degradation when delivered by biolistics.

Degradation of oat mRNAs during seed development

The genes AV1, AV10, and Z1 encode proteins that accumulate during oat seed development. In developing endosperm of Avena sativa (cultivated oat), AV1, AV10 and Z1 mRNAs reach maximal levels midway through seed development but fall to very low levels in mature seeds. Similarly, mRNAs for these proteins peak during endosperm development of Avena fatua (wild oat) and are later degraded. However, during late maturation of A. fatua seeds, populations of mRNA fragments shorter than the intact transcripts accumulate as the full-length transcripts decline in abundance. The smaller RNA molecules, which are apparently long-lived decay intermediates, are derived randomly from the entire transcripts and are most likely not generated by cleavage at precisely defined sites. Other A. fatua endosperm mRNAs that are degraded during late seed development, such as those for ADP glucose pyrophosphorylase and starch synthase, do not produce detectable decay intermediates. Decay intermediates of AV1 and Z1 mRNAs persist at high levels during late seed development of two other undomesticated oat species, Avena strigosa and Avena barbata. The persistence of decay intermediates for these endosperm mRNAs in wild grass species may represent a model system for studying RNA decay process in plant tissues.

Silencing of beta-1,3-glucanase genes in tobacco correlates with an increased abundance of RNA degradation intermediates

Post-transcriptional gene silencing of beta-1,3 glucanase genes in the transgenic tobacco line T17 is characterised by an increased turnover and, as a consequence, reduced levels of gn1 transgene and endogenous beta-1,3 glucanase mRNAs. Here, additional gn1 RNAs, both larger and smaller than the full-length messenger, are shown to accumulate in silenced plants of the transgenic tobacco line T17. The longer-than-full-length gn1 RNAs are the result of cryptic processing of the gn1 messenger. The small gn1 RNAs in silenced plants correspond to distal and proximal parts of the mature gn1 messenger. The proximal RNA products are intact at their 5' extremity, but terminate at different positions at the 3'-end. The distal RNA products contain a poly(A) tail and are truncated to various positions at the 5'-end. These observations indicate that degradation of the mature gn1 transcript does not start at the 5'- or 3'-end, but rather are consistent with degradation of the gn1 transcript starting with an endonucleolytic cleavage followed by internal exonuclease digestion. Importantly, the truncated products are more abundant in silenced plants than in expressing plants. This suggests, together with the previously reported silencing-related increased gn1 mRNA turnover and the similar rates of gn1 transcription in silenced and expressing T17 plants, that the predominant decay route for the gn1 transcripts differs between silenced and expressing conditions.

RNase Activities Are Reduced Concomitantly with Conservation of Total Cellular RNA and Ribosomes in O2-Deprived Seedling Roots of Maize

The effect of O2 deprivation on the activities of RNases and levels of total cellular RNA and ribosomes in seedling roots of maize (Zea mays L.) was investigated. Sodium dodecyl sulfate-polyacrylamide gels containing RNA were used to distinguish RNase isoenzymes by apparent molecular mass. Since O2 deprivation causes a decrease in cytosolic pH from approximately pH 7.4 to 6.4 and an elevation in cytosolic Ca2+, RNase levels were examined in the physiological range of cytosolic pH and in the presence of Ca2+, Mg2+, Zn2+, ethylenediaminetetracetate, or ethyleneglycol-bis([beta]-aminoethyl ether)-N,N[prime]-tetraacetic acid. The activity of a number of RNases present in aerobic roots was reduced in response to O2 deprivation. Several RNases with a pH optimum of 6.4 were rapidly down-regulated by O2 deprivation. Spectrophotometric assay of extracts revealed that RNase activity was higher at pH 6.4 than at 7.2, and ethylenediaminetetracetate-insensitive RNase activity decreased in response to O2 deprivation. The decrease in RNase activity was correlated with no loss of total cellular RNA or ribosomes, despite a 4-fold decrease in run-on transcription of rRNA in isolated nuclei. Regulation of RNase activity may facilitate the conservation of nontranslating ribosomes and poorly translated mRNAs during O2 deprivation.

Characterization of Post-Transcriptionally Suppressed Transgene Expression That Confers Resistance to Tobacco Etch Virus Infection in Tobacco

Tobacco lines expressing transgenes that encode tobacco etch virus (TEV) coat protein (CP) mRNA with or without nonsense codons give rise to TEV-resistant tissues that have reduced levels of TEV CP mRNA while maintaining high levels of transgene transcriptional activity. Two phenotypes for virus resistance in the lines containing the transgene have been described: immune (no virus infection) and recovery (initial systemic symptoms followed by gradual recovery over several weeks). Here, we show that at early times in development, immune lines are susceptible to TEV infection and accumulate full-length CP mRNA. Therefore, immune lines also exhibit meiotic resetting, as is seen in the recovery lines, providing molecular evidence for a common mechanism of gene silencing and virus resistance in both cases. We also investigated the characteristics of two sets of low molecular weight RNAs that appear only in silenced tissue. One set has nearly intact 5[prime] ends, lacks poly(A) tails, and is associated with polyribosomes; the second set contains the 3[prime] end of the mRNA. Treating silenced leaf tissue with cycloheximide resulted in decreased levels of full-length mRNA and an increase in the levels of the low molecular weight RNAs, supporting a cytoplasmic decay mechanism that does not require ongoing translation. Surprisingly, mRNA from the transgene containing nonsense codons was associated with more ribosomes than expected, possibly resulting from translation from a start codon downstream of the introduced translational stop codons. We present a hypothesis for transgene/viral RNA degradation in which RNA degradation occurs in the cytoplasm while in association with polyribosomes.

Absolute quantification of five phytochrome transcripts in seedlings and mature plants of tomato (Solanum lycopersicum L.)

Described here are the first quantitative measurements of absolute amounts of mRNAs transcribed from individual members of a phytochrome gene (PHY) family. The abundances of PHY mRNAs were determined for dry seed and for selected organs of green-house-grown tomato (Solanum lycopersicum L.) seedlings and mature plants. With a Phosphoimager, absolute amounts of PHYA, PHYB1, PHYB2, PHYE and PHYF transcripts were measured with reference to standard curves prepared from mRNA fragments synthesized in vivo. Methodology was developed permitting the use of polymerase chain reaction (PCR)-generated probes derived from a highly conserved region of PHY, obviating the necessity to clone cDNAs and to isolate probes derived from their 3' non-coding regions. In dry seeds, PHYB1 mRNA appeared to be most abundant (4-5 mumol/mol mRNA) while in all other instances PHYA mRNA predominated. In seedlings, PHYB1, PHYB2, PHYE, and PHYF mRNAs were most abundant in the shoot (25-87 mumol/mol mRNA) while PHYA mRNA was most abundant in the root (325 mumol/mol mRNA). In adult plants, the levels of PHYA. PHYB1 and PHYE mRNAs were relatively uniform among different organs (approx. 100, 75, and 10 mumol/mol mRNA, respectively). In contrast, PHYB2 and PHYF were expressed preferentially in ripening fruits (35 and 47 mumol/mol mRNA, respectively), indicative of a possible role in fruit ripening for the phytochromes they encode. In general, the order of decreasing abundance of the five mRNAs for both seedlings and mature plants was PHYA, PHYB1, PHYE, PHYB2 and PHYF. Based upon observations that relatively modest changes in the extent of PHY expression result in changes in phenotype, the differential expression of each of the five tomato PHY described here is predicted to impact upon the spatial expression of biological activity of each phytochrome.

Control of mRNA stability in higher plants

The degradation rates of different mRNAs in higher plants can vary over a broad range and are regulated by a variety of endogenous and exogenous stimuli. During the past several years, efforts to better understand the control of mRNA stability in plants have increased considerably and this has led to improved methodologies and important mechanistic insights. In this review, we highlight some of the most interesting examples of plant transcripts that are controlled at the level of mRNA decay and discuss what has been learned from their study. Experiments that implicate or demonstrate the involvement of particular cis- and trans-acting factors in mRNA decay pathways are a major focus, as are those experiments that have led to mechanistic models. Emphasis is also placed on studies that address the relationship between translation and mRNA stability. Our current knowledge indicates that some of the determinants and pathways for mRNA decay may differ in plants compared to other eukaryotes, whereas others appear to be similar. This knowledge, coupled with the availability of biochemical, molecular and genetic approaches to elucidate plant mRNA decay mechanisms, should continue to lead to findings of novel and general significance.

Light-dependent developmental control of rbcS gene expression in epidermal cells of maize leaves

Regulatory elements of the maize rbcS-m3 gene (a member of the family of genes encoding the small subunit of ribulose bisphosphate carboxylase) that are sufficient for expression of the beta-glucuronidase (gusA) gene in photosynthetic tissue lead to relatively weak expression of the reporter gene in epidermal cells of green maize leaves when delivered by ballistic gene transfer methods. However, epidermal cells of white, immature segments of maize leaf bases express the same reporter gene strongly. Morphologically, these epidermal cells look undifferentiated and are uniform in size and shape. When cultured for seven days on Murashige-Skoog medium [18], exised leaf base segments expand two-to threefold, and epidermal and guard cells differentiate and mature, regardless of whether or not the tissue is illuminated. Epidermal cells that differentiate in darkness continue to have the capacity to express the rbcS-m3::gusA reporter gene strongly. However, if the leaf base segments are illuminated after four to five days of expansion in darkness, but not before, these more mature epidermal cells are largely unable to express the same gene. That is, they acquire the characteristics of epidermal cells of green maize leaves with regard to expressing the rbcS-m3 reporter gene after undergoing a developmental program (in light or darkness) in vitro and after being exposed to light. White light but not red is effective. Suppression of expression in maize epidermal cells requires different rbcS-m3 sequences than in mesophyll cells [31].

The arabidopsis ACT7 actin gene is expressed in rapidly developing tissues and responds to several external stimuli

ACT7 encodes one of the six distinct and ancient subclasses of actin protein in the complex Arabidopsis actin gene family. We determined the sequence and structure of the Arabidopsis thaliana ACT7 actin gene and investigated its tissue-specific expression and regulation. The ACT7 mRNA levels varied by 128-fold among several different tissues and organs. The highest levels of aCT7 mRNA were found in rapidly expanding vegetative organs, the lowest in pollen. A translational fusion with the 5' end of ACT 7 (1.9 kb) joined to the beta-glucuronidase reporter gene was strongly and preferentially expressed in all young, developing vegetative tissues of transgenic Arabidopsis plants. ACT7 was the only Arabidopsis actin gene strongly expressed in the hypocotyl and seed coat. Although no beta-glucuronidase expression was seen in developing ovules or immature seeds, strong expression was seen in dry seeds and immediately after imbibition in the entire seedling. ACT7 was the only Arabidopsis actin gene to respond strongly to auxin, other hormone treatments, light regime, and wounding, and may be the primary actin gene responding to external stimuli. The ACT7 promoter sequence contains a remarkable number of motifs with sequence similarity to putative phytohormone response elements.

The Arabidopsis profilin gene family. Evidence for an ancient split between constitutive and pollen-specific profilin genes

Profilin is a ubiquitous eukaryotic protein that regulates the actin cytoskeleton and recently has been identified as a potent allergen in pollen. We examined the profilin gene family in the model plant, Arabidopsis thaliana, and found that it contained approximately 8 to 10 members. Four distinct profilin sequences, three cDNAs, PRF1, PRF2, and PRF3, and two genomic clones, PRF1 and PRF4, were isolated and characterized. These genes encoded four distinct profilin isoforms of 131 to 134 amino acids. Northern and reverse-transcriptase polymerase chain reaction analyses demonstrated that Arabidopsis PRF1 was expressed in all major plant organs, whereas PRF4 was specifically expressed in mature pollen. Gene trees constructed from amino acid sequence data revealed the presence of two ancient, distinct profilin gene classes in plants. PRF4 was in a class with previously identified pollen-specific profilins from monocot and dicot species. PRF1, PRF2, PRF3, and a distant dicot sequence formed a separate novel class, suggesting an ancient separation of plant profilins based on regulation and perhaps function. The coevolution of plant actin and profilin classes with similar patterns of expression is discussed. The similarity of plant, fungal, protist, insect, and nematode profilins and their extreme divergence from the vertebrate profilins has striking implications for the evolution of fungal-spore- and plant-pollen-profilins as allergens.

Conserved expression of the Arabidopsis ACT1 and ACT 3 actin subclass in organ primordia and mature pollen

We have proposed that ancient and divergent classes of plant actin genes have been preserved throughout vascular plant evolution, because they have distinct patterns of gene regulation. The hypothesis was explored for ACT1 and ACT3, which represent one of the six ancient subclasses in the Arabidopsis actin gene family. Comparison of ACT1 and ACT3 cDNA and genomic sequences revealed highly divergent flaking and intron sequences, whereas they encoded nearly identical proteins. Quantification of their level of divergence suggests that they have not shared a common ancestor for 30 to 60 million years. Gene-specific RNA gel blot hybridization and reverse transcriptase-polymerase chain reaction analyses demonstrated that the distribution of ACT1 and ACT3 mRNAs was very similar: both preferentially accumulated at high levels in mature pollen and at very low levels in the other major organs. The 5' flanking regions of both genes, including the promoter, leader exon and intron, and the first 19 condons, were fused to the beta-glucuronidase (GUS) reporter gene. The expression of these reporter fusions was examined in a large number of transgenic Arabidopsis plants. Histochemical assays demonstrated that both ACT1-GUS and ACT3-GUS constructs were expressed preferentially in pollen, pollen tubes, and in all organ primordia, including those in roots shoots, and the inflorescence. Comparison of the 5' flanking regions of ACT1 and ACT3 revealed a number of short conserved sequences, which may direct their common transcriptional and post-transcriptional regulation. The expression patterns observed were distinct from those of any other other Arabidopsis actin subclass. The conservation of their expression pattern and amino acid sequences suggests that this actin subclass plays a distinct and required role in the plant cytoskeleton.

Degradation of the soybean ribulose-1,5-bisphosphate carboxylase small-subunit mRNA, SRS4, initiates with endonucleolytic cleavage

The degradation of the soybean SRS4 mRNA, which encodes the small subunit of ribulose-1,5-bisphosphate carboxylase, yields a set of proximal (5' intact) and distal (3' intact) products both in vivo and in vitro. These products are generated by endonucleolytic cleavages that occur essentially in a random order, although some products are produced more rapidly than others. Comparison of sizes of products on Northern (RNA) blots showed that the combined sizes of pairs of proximal and distal products form contiguous full-length SRS4 mRNAs. When the 3' ends of the proximal products and the 5' ends of the distal products were mapped by S1 nuclease and primer extension assays, respectively, both sets of ends mapped to the same sequences within the SRS4 mRNA. A small in vitro-synthesized RNA fragment containing one cleavage site inhibited cleavage of all major sites, equivalently consistent with one enzymatic activity generating the endonucleolytic cleavage products. These products were rich in GU nucleotides, but no obvious consensus sequence was found among several cleavage sites. Preliminary evidence suggested that secondary structure could play a role in site selection. The structures of the 5' ends of the proximal products and the 3' ends of the distal products were examined. Proximal products were found with approximately equal frequency in both m7G cap(+) and m7G cap(-) fractions, suggesting that the endonucleolytic cleavage events occurred independently of the removal of the 5' cap structure. Distal products were distributed among fractions with poly(A) tails ranging from undetectable to greater than 100 nucleotides in length, suggesting that the endonucleolytic cleavage events occurred independently of poly(A) tail shortening. Together, these data support a stochastic endonuclease model in which an endonucleolytic cleavage event is the initial step in SRS4 mRNA degradation.

Organ-Specific Stability of Two Lemna rbcS mRNAs Is Determined Primarily in the Nuclear Compartment

It has previously been shown that the organ-specific expression of two members of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene family is post-transcriptionally regulated in Lemna gibba. While both small subunit genes encoding SSU1 and SSU5B were transcribed at comparable levels in root and frond nuclei, SSU1 mRNA accumulated to high levels in both roots and fronds in contrast to SSU5B mRNA, which was of very low abundance in the roots compared with the fronds. In this study, we have used two approaches to pinpoint the step(s) at which SSU1 and SSU5B mRNAs are differentially accumulated in these organs. In the first approach, total nuclear steady state mRNA was isolated from roots and fronds, and the amount of each transcript was measured by RNase protection assays and compared with the transcription rates in isolated nuclei. In the second approach, cordycepin was used to inhibit mRNA synthesis in Lemna fronds or roots, and the rate of decay of each mRNA was measured by RNA gel blot analysis or RNase protection assays. Our findings indicate that the differential accumulation of SSU1 and SSU5B mRNAs in the fronds versus the roots is determined primarily in the nuclear compartment. In addition, SSU1 was found to have a longer half-life in total steady state mRNA than SSU5B had in both organs. This feature probably accounts for SSU1 being the predominantly expressed family member.

Light-regulated expression of the Arabidopsis thaliana ferredoxin gene requires sequences upstream and downstream of the transcription initiation site

The effect of light on the expression of the Arabidopsis thaliana ferredoxin gene (fedA) was studied in mature tobacco plants. In light-treated leaves of tobacco plants transformed with a full-length ferredoxin gene, fedA-specific mRNA levels were more than twenty fold higher than in dark-treated controls. This indicates that all components for regulation of the Arabidopsis ferredoxin gene are present in tobacco. To identify light-regulatory elements in the fedA gene, we have tested a set of chimeric genes containing various parts of the fedA gene for light-dependent expression in mature tobacco plants. A fedA promoter-GUS fusion gene was not light-responsive, indicating that the 5'-upstream promoter region is not sufficient for light regulation. Fusion genes in which different transcribed regions of the fedA gene were expressed from the CaMV 35S promoter showed only limited light regulation, if any at all. This indicates that, like the fedA upstream region, the region downstream of the transcription start site is also not sufficient for full light regulation. The combined results suggest that for full light-regulated expression of the fedA gene, both the promoter region and sequences downstream of the transcription start site are required.

Oat phytochrome A mRNA degradation appears to occur via two distinct pathways

We have identified possible mechanisms for the degradation of oat phytochrome A (PHYA) mRNA. The majority of PHYA mRNA molecules appeared to be degraded prior to removal of the poly(A) tail, a pathway that differs from that reported for the degradation of other eukaryotic mRNAs. Polyadenylated PHYA mRNA contained a pattern of putative degradation products that is consistent with a 5'-->3' exoribonuclease, although the participation of a stochastic endoribonuclease cannot be excluded. The poly(A) tail of PHYA mRNA was heterogeneous in size and ranged from approximately 14 to 220 nucleotides. Early PHYA mRNA degradation events did not appear to involve site-specific endoribonucleases. Approximately 25% of the apparently full-length PHYA mRNA was poly(A) deficient. Oat H4 histone, beta-tubulin, and actin mRNA populations had lower amounts of apparently full-length mRNAs that were poly(A) deficient. Degradation of the poly(A)-deficient PHYA mRNA, a second pathway, appeared to be initiated by a 3'-->5' exoribonucleolytic removal of the poly(A) tail followed by both 5'-->3' and 3'-->5' exoribonuclease activities. Polysome-associated RNA contained putative PHYA mRNA degradation products and was a mixture of polyadenylated and deadenylated PHYA messages, suggesting that the two distinct degradation pathways are polysome associated.

Faithful degradation of soybean rbcS mRNA in vitro

The mRNA encoding the soybean rbcS gene, SRS4, is degraded into a set of discrete lower-molecular-weight products in light-grown soybean seedlings and in transgenic petunia leaves. The 5'-proximal products have intact 5' ends, lack poly(A) tails, lack various amounts of 3'-end sequences, and are found at higher concentrations in the polysomal fraction. To study the mechanisms of SRS4 mRNA decay more closely, we developed a cell-free RNA degradation system based on a polysomal fraction isolated from soybean seedlings or mature petunia leaves. In the soybean in vitro degradation system, endogenous SRS4 mRNA and proximal product levels decreased over a 6-h time course. When full-length in vitro-synthesized SRS4 RNAs were added to either in vitro degradation system, the RNAs were degraded into the expected set of proximal products, such as those observed for total endogenous RNA samples. When exogenously added SRS4 RNAs already truncated at their 3' ends were added to either system, they too were degraded into the expected subset of proximal products. A set of distal fragments containing intact 3' ends and lacking various portions of 5'-end sequences were identified in vivo when the heterogeneous 3' ends of the SRS4 RNAs were removed by oligonucleotide-directed RNase H cleavage. Significant amounts of distal fragments which comigrated with the in vivo products were also observed when exogenous SRS4 RNAs were degraded in either in vitro system. These proximal and distal products lacking various portions of their 3' and 5' sequences, respectively, were generated in essentially a random order, a result supporting a nonprocessive mechanism. Tagging of the in vitro-synthesized RNAs on their 5' and 3' ends with plasmid vector sequences or truncation of the 3' end had no apparent effect on the degradation pattern. Therefore, RNA sequences and/or structures in the immediate vicinity of each 3' end point may be important in the degradation machinery. Together, these data suggest that SRS4 mRNA is degraded by a stochastic mechanism and that endonucleolytic cleavage may be the initial event. These plant in vitro systems should be useful in identifying the cis- and trans-acting factors involved in the degradation of mRNAs.

Faithful degradation of soybean rbcS mRNA in vitro

The mRNA encoding the soybean rbcS gene, SRS4, is degraded into a set of discrete lower-molecular-weight products in light-grown soybean seedlings and in transgenic petunia leaves. The 5'-proximal products have intact 5' ends, lack poly(A) tails, lack various amounts of 3'-end sequences, and are found at higher concentrations in the polysomal fraction. To study the mechanisms of SRS4 mRNA decay more closely, we developed a cell-free RNA degradation system based on a polysomal fraction isolated from soybean seedlings or mature petunia leaves. In the soybean in vitro degradation system, endogenous SRS4 mRNA and proximal product levels decreased over a 6-h time course. When full-length in vitro-synthesized SRS4 RNAs were added to either in vitro degradation system, the RNAs were degraded into the expected set of proximal products, such as those observed for total endogenous RNA samples. When exogenously added SRS4 RNAs already truncated at their 3' ends were added to either system, they too were degraded into the expected subset of proximal products. A set of distal fragments containing intact 3' ends and lacking various portions of 5'-end sequences were identified in vivo when the heterogeneous 3' ends of the SRS4 RNAs were removed by oligonucleotide-directed RNase H cleavage. Significant amounts of distal fragments which comigrated with the in vivo products were also observed when exogenous SRS4 RNAs were degraded in either in vitro system. These proximal and distal products lacking various portions of their 3' and 5' sequences, respectively, were generated in essentially a random order, a result supporting a nonprocessive mechanism. Tagging of the in vitro-synthesized RNAs on their 5' and 3' ends with plasmid vector sequences or truncation of the 3' end had no apparent effect on the degradation pattern. Therefore, RNA sequences and/or structures in the immediate vicinity of each 3' end point may be important in the degradation machinery. Together, these data suggest that SRS4 mRNA is degraded by a stochastic mechanism and that endonucleolytic cleavage may be the initial event. These plant in vitro systems should be useful in identifying the cis- and trans-acting factors involved in the degradation of mRNAs.

Development and Environmental Stress Employ Different Mechanisms in the Expression of a Plant Gene Family

Ribulose bisphosphate carboxylase small subunit (RbcS) genes in the common ice plant, as in all higher plants, constitute a multigene family. We have measured transcription activity and steady state mRNA levels of individual members of the family, six RbcS genes, in the ice plant with emphasis on the transition from C3 photosynthesis to Crassulacean acid metabolism (CAM), which this plant undergoes during development and under environmental stress. Four RbcS genes are differentially expressed in leaves but are regulated in a coordinate fashion. A developmentally engrained, sharp decline in the steady state mRNA levels, which is observed during the juvenile-to-adult growth phase transition, coincides with the time interval when the C3-to-CAM switch occurs. Developmental down regulation of RbcS is due to down regulation of transcription. In contrast, NaCl stress specifically affected RbcS transcript accumulation post-transcriptionally, resulting in decreased RbcS mRNA levels. Antagonistic regulatory programs are apparent in stress/stress relief experiments. The results indicate complex controls, affecting both transcriptional and post-transcriptional processes, that act differentially during plant development, stress, and recovery from stress.

Fungal Elicitor-Induced Bean Proline-Rich Protein mRNA Down-Regulation Is Due to Destabilization That Is Transcription and Translation Dependent

In bean cells treated with fungal elicitor, the transcripts of PvPRP1, a gene encoding a proline-rich protein, decreased to ~6% of the original level within 4 hr. The apparent mRNA half-life during the period of rapid degradation was ~45 min. The rate of PvPRP1 gene transcription remained constant over this period, as determined by nuclear run-off assays, indicating a decrease in mRNA stability. By using actinomycin D to block transcription, the half-life of PvPRP1 mRNA in unelicited cells was estimated to be ~60 hr. In cells treated with actinomycin D followed by the addition of elicitor, the PvPRP1 mRNA half-life was ~18 hr, whereas cells treated with these reagents in reciprocal order exhibited a half-life of ~6 hr. The protein synthesis inhibitors emetine and anisomycin also inhibited the rate of PvPRP1 mRNA degradation in elicited cells. Based on these data, we concluded that the rapid decrease in the PvPRP1 mRNA level in elicited cells is due to destabilization, which is dependent on new RNA and protein synthesis.