Transcriptional and post-transcriptional regulation of ribulose 1,5-bisphosphate carboxylase gene expression in light- and dark-grown amaranth cotyledons

Synthesis of pathogenesis-related proteins in tobacco is regulated at the level of mRNA accumulation and occurs on membrane-bound polysomes

The pathogenesis-related (PR) proteins of tobacco plants are induced in response to a variety of pathogenic and chemical agents. Although the function of these proteins is unknown, they are associated with resistance to multiplication and/or spread of tobacco mosaic virus. We report that functional mRNAs encoding PR proteins are present only when synthesis of these proteins has been induced, suggesting that their synthesis is controlled in part at the level of mRNA accumulation. In addition PR proteins appear to be synthesized and processed in a manner analogous to proteins destined for the endoplasmic reticulum since (i) the in vitro translation products synthesized in the wheat-germ cell-free system are slightly larger than the in vivo products, (ii) translation of PR mRNAs in the rabbit reticulocyte lysate system is blocked unless that system is supplemented with dog pancreas microsomes, and (iii) mRNAs for PR proteins are associated predominantly with membrane-bound polysomes in vivo. This pathway of synthesis and posttranslational modification suggests possible sites of action of these proteins.

mRNAs encoding ribulose-1,5-bisphosphate carboxylase remain bound to polysomes but are not translated in amaranth seedlings transferred to darkness

When light-grown seedlings of amaranth are transferred to total darkness, synthesis of the large subunit (LS) and small subunit (SS) of ribulose-1,5-bisphosphate carboxylase [RbuP(2)Case; 3-phospho-D-glycerate carboxylase (dimerizing), EC 4.1.1.39] is rapidly depressed. This reduction in RbuP(2)Case synthesis occurs in the absence of any corresponding changes in levels of functional mRNA for either subunit. Four hours after light-to-dark transition little, if any, changes in the distribution of LS and SS mRNAs on polysomes could be detected. The association of these mRNAs with polysomes was authenticated by treatment with RNase A or puromycin. Furthermore, polysomes were able to synthesize LS and SS precursor in cell-free translation systems supplemented with inhibitors of initiation. Therefore, during a light-to-dark transition LS and SS mRNAs remained bound to polysomes but were not translated in vivo, suggesting that control is exercised, in part, at the translational elongation step.

Genetic modification of alternative respiration has differential effects on antimycin A-induced versus salicylic acid-induced resistance to Tobacco mosaic virus

Salicylic acid (SA), a natural defensive signal chemical, and antimycin A, a cytochrome pathway inhibitor, induce resistance to Tobacco mosaic virus (TMV). Pharmacological evidence suggested signaling during resistance induction by both chemicals involved alternative oxidase (AOX), sole component of the alternative respiratory pathway (AP). Roles of the AP include regulation of intramitochondrial reactive oxygen species and maintenance of metabolic homeostasis. Transgenic tobacco (Nicotiana tabacum) with modified AP capacities (2- to 3-fold increased or decreased) showed no alteration in phenotype with respect to basal susceptibility to TMV or the ability to display SA-induced resistance to systemic viral disease. However, in directly inoculated tissue, antimycin A-induced TMV resistance was inhibited in plants with increased AP capacities, whereas SA and antimycin A-induced resistance was transiently enhanced in plant lines with decreased AP capacities. We conclude that SA-induced TMV resistance results from activation of multiple mechanisms, a subset of which are inducible by antimycin A and influenced by AOX. Other antiviral factors, potentially including the SA-inducible RNA-dependent RNA polymerase, are regulated by AOX-independent mechanisms.

Essential role of a kinesin-like protein in Arabidopsis trichome morphogenesis

Little is known about how cell shape is controlled. We are using the morphogenesis of trichomes (plant hairs) on the plant Arabidopsis thaliana as a model to study how cell shape is controlled. Wild-type Arabidopsis trichomes are large, single epidermal cells with a stalk and three or four branches, whereas in zwichel (zwi) mutants the trichomes have a shortened stalk and only two branches. To further understand the role of the ZWI gene in trichome morphogenesis we have cloned the wild-type ZWICHEL (ZWI) gene by T-DNA tagging, and report here that it encodes a member of the kinesin superfamily of microtubule motor proteins. Kinesin proteins transport diverse cellular materials in a directional manner along microtubules. Kinesin-like proteins are characterized by a highly conserved "head" region that comprises the motor domain, and a nonconserved "tail" region that is thought to participate in recognition and binding of the appropriate cargo.

Detection of Gene Expression in Genetically Engineered Microorganisms and Natural Phytoplankton Populations in the Marine Environment by mRNA Analysis

A simple method that combines guanidinium isothiocyanate RNA extraction and probing with antisense and sense RNA probes is described for analysis of microbial gene expression in planktonic populations. Probing of RNA sample extracts with sense-strand RNA probes was used as a control for nonspecific hybridization or contamination of mRNA with target DNA. This method enabled detection of expression of a plasmid-encoded neomycin phosphotransferase gene (nptII) in as few as 10Vibrio cells per ml in 100 ml of seawater. We have used this method to detect expression of the ribulose-1,5-bisphosphate carboxylase large-subunit gene (rbcL) in Synechococcus cultures and natural phytoplankton populations in the Dry Tortugas, Florida. During a 36-h diel study, rbcL expression of the indigenous phytoplankton was greatest in the day, least at night (1100, 0300, and 0100 h), and variable at dawn or dusk (0700 and 1900 h). These results are the first report of gene expression in natural populations by mRNA isolation and probing. This methodology should be useful for the study of gene expression in microorganisms released into the environment for agricultural or bioremediation purposes and indigenous populations containing highly conserved target gene sequences.

Plants transformed with a tobacco mosaic virus nonstructural gene sequence are resistant to the virus

Nicotiana tabacum cv. Xanthi nn plants were transformed with nucleotides 3472-4916 of tobacco mosaic virus (TMV) strain U1. This sequence contains all but the three 3 terminal nucleotides of the TMV 54-kDa gene, which encodes a putative component of the replicase complex. These plants were resistant to infection when challenged with either TMV U1 virions or TMV U1 RNA at concentrations of up to 500 micrograms/ml or 300 micrograms/ml, respectively, the highest concentrations tested. Resistance was also exhibited when plants were inoculated at 100 micrograms/ml with the closely related TMV mutant YSI/1 but was not shown in plants challenged at the same concentrations with the more distantly related TMV strains U2 or L or cucumber mosaic virus. Although the copy number of the 54-kDa gene sequence varied in individual transformants from 1 to approximately 5, the level of resistance in plants was not dependent on the number of copies of the 54-kDa gene sequence integrated. The transformed plants accumulated a 54-kDa gene sequence-specific RNA transcript of the expected size, but no protein product was detected.

A potential role for RNA turnover in the light regulation of plant gene expression: ribulose-1,5-bisphosphate carboxylase small subunit in soybean

Post-transcriptional regulation of the genes encoding the small subunit (rbcS) of ribulose-1,5-bisphosphate carboxylase was examined in soybean seedlings. Substantial discrepancies were detected between relative in vitro transcription rates and steady-state RNA levels in light- and dark-grown seedling leaves, indicating that rbcS RNA may be degraded more rapidly in light than in darkness. Additional data imply that the turnover mechanism is rapidly induced by light, maintained for some time in darkness, and that it may be negatively controlled by far-red light. The proposed RNA turnover system does not affect all RNAs equally since a soybean actin gene showed equivalent in vitro transcription rates and RNA levels in light and darkness. Soybean rbcS genes may be subject to a novel mode of control in which light-induced expression is accompanied by an increased rate of RNA degradation. Models for the specific regulation of rbcS RNA stability in response to light are presented.

Transcriptional regulation and DNA methylation of nuclear genes for photosynthesis in nongreen plant cells

The transcripts of nuclear genes for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcS), chlorophyll a/b-binding protein (cab), and extrinsic 33-kDa protein involved in photosystem II water oxidation (woxA) were not detectable in the white wild cultured cells of sycamore (Acer pseudoplatanus), in contrast to their high levels in the sibling green mutant cells and the constitutive expression of actin genes (act) in both cell types. We have examined the template activities of nuclear DNAs using the HeLa cell in vitro transcription system. All of the three photosynthesis genes from the green cell line and act from both cell types were well transcribed in vitro, but these photosynthesis genes from the white cell line were not, indicating that the transcriptional regulation is ascribable to DNA templates. Digestion of nuclear DNA with methyl-sensitive and -insensitive isoschizomeric endonucleases and the subsequent Southern hybridization showed that each gene has the identical recognition sites of restriction enzymes in the green and white cell lines, but some of the sites were methylated only in the photosynthesis genes in the white cells. There was observed a clear inverse relationship between the level of expressed transcripts and the extent of DNA methylation. Thus, it is inferred that the selective methylation of DNA is a likely mechanism for suppressing transcription of nuclear genes for photosynthesis in the nonphotosynthetic plant cells.

Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms

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Allelic variation and differential expression at the 27-kilodalton zein locus in maize

Allelic variation between inbred lines at the 27-kilodalton zein gene locus in maize has been used to study gene expression in developing endosperm. The inbred lines W22 and W23 contain two genes for this protein within two tandem repeats; the individual genes are virtually identical, with 99.9% homology in the 5'-flanking regions. Using gene-specific oligonucleotide probes, we have shown that transcripts of the downstream gene are found at a 2.5-fold-higher level than those of the upstream gene. Another inbred line, BSSS53, has one copy of the gene which is a recombinant of the duplicated genes at the 3'-flanking region. This line has been used in reciprocal crosses to demonstrate dosage effects for the overexpression of the downstream gene and to show that the overexpression of mRNA is reflected in a corresponding increase in the protein level. The accumulation of the protein through development does not, however, always correspond to the difference in mRNA levels.

Differential expression of a gene for a methionine-rich storage protein in maize

A methionine-rich 10 kDa zein storage protein from maize was isolated and the sequence of the N-terminal 30 amino acids was determined. Based on the amino acid sequence, two mixed oligonucleotides were synthesized and used to probe a maize endosperm cDNA library. A full-length cDNA clone encoding the 10 kDa zein was isolated by this procedure. The nucleotide sequence of the cDNA clone predicts a polypeptide of 129 amino acids, preceded by a signal peptide of 21 amino acids. The predicted polypeptide is unique in its extremely high content of methionine (22.5%). The maize inbred line BSSS-53, which has increased seed methionine due to overproduction of this protein, was compared to W23, a standard inbred line. Northern blot analysis showed that the relative RNA levels for the 10 kDa zein were enhanced in developing seeds of BSSS-53, providing a molecular basis for the overproduction of the protein. Southern blot analysis indicated that there are one or two 10 kDa zein genes in the maize genome.

Allelic variation and differential expression at the 27-kilodalton zein locus in maize

Allelic variation between inbred lines at the 27-kilodalton zein gene locus in maize has been used to study gene expression in developing endosperm. The inbred lines W22 and W23 contain two genes for this protein within two tandem repeats; the individual genes are virtually identical, with 99.9% homology in the 5'-flanking regions. Using gene-specific oligonucleotide probes, we have shown that transcripts of the downstream gene are found at a 2.5-fold-higher level than those of the upstream gene. Another inbred line, BSSS53, has one copy of the gene which is a recombinant of the duplicated genes at the 3'-flanking region. This line has been used in reciprocal crosses to demonstrate dosage effects for the overexpression of the downstream gene and to show that the overexpression of mRNA is reflected in a corresponding increase in the protein level. The accumulation of the protein through development does not, however, always correspond to the difference in mRNA levels.

Developmental, organ-specific, and light-dependent expression of the tomato ribulose-1,5-bisphosphate carboxylase small subunit gene family

The tomato gene family for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase [3-phospho-D-glycerate carboxy-lyase (dimerizing); EC 4.1.1.39] has five genes, designated Rbcs-1, -2, -3A, -3B, and -3C. We have measured the steady-state mRNA levels for each of the five genes in various tomato organs using gene-specific oligonucleotides. All five genes are highly expressed in leaves, and transcripts of two genes, Rbcs-3B and Rbcs-3C, account for approximately equal to 60% of the total leaf transcripts. The relative transcript levels in the stem, in nature fruits, and etiolated seedlings (plants germinated and grown in the dark) correspond to 3.2%, 6.5%, and 4.6%, respectively, of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit mRNA level in leaves, and no transcripts have been detected in roots and ripe tomato fruits. Only Rbcs-1 and Rbcs-2 are expressed during the photosynthetically active phase of fruit development. Transcripts from these genes and from the Rbcs-3A locus are also present in etiolated seedlings. Rbcs-3B and Rbcs-3C transcripts, which are the most abundant mRNAs of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene family in the leaf, are undetectable in dark-grown seedlings and immature fruit. The selective expression of Rbcs-1 and Rbcs-2 in the dark and in the pericarp of green fruit and the induction and rapid mRNA accumulation for Rbcs-3B and Rbcs-3C after illumination may reflect different regulatory mechanism(s) that control the expression of individual members in the tomato ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene family.

Genomic organization, sequence analysis and expression of all five genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from tomato

We have cloned and sequenced all five members of the gene family for the small subunit (rbcS) of ribulose-1,5-bisphosphate carboxylase/oxygenase from tomato, Lycopersicon esculentum cv. VFNT LA 1221 cherry line. Two of the five genes, designated Rbcs-1 and Rbcs-2, are present as single genes at individual loci. Three genes, designated Rbcs-3A, Rbcs-3B and Rbcs-3C, are organized in a tandem array within 10 kb at a third independent locus. The Rbcs-2 gene contains three introns; all the other members of the tomato gene family contain two introns. The coding sequence of Rbcs-1 differs by 14.0% from that of Rbcs-2 and by 13.3% from that of Rbcs-3 genes. Rbcs-2 shows 10.4% divergence from Rbcs-3. The exon and intron sequences of Rbcs-3A are identical to those of Rbcs-3C, and differ by 1.9% from those of Rbcs-3B. Nucleotide sequence analysis suggests that the five rbcS genes encode four different precursors, and three different mature polypeptides. S1 nuclease mapping of the 5' end of rbcS mRNAs revealed that the mRNA leader sequences vary in length from 8 to 75 nucleotides. Northern analysis using gene-specific oligonucleotide probes from the 3' non-coding region of each gene reveals a four to five-fold difference among the five genes in maximal steady-state mRNA levels in leaves.

Characterization of the alpha-tubulin gene family of Arabidopsis thaliana

The genome of Arabidopsis thaliana (Linnaeus) Heynhold was shown to contain an alpha-tubulin gene family consisting of at least four genes and/or pseudogenes. The primary structure of a transcribed alpha-tubulin gene was determined. A comparison of the predicted amino acid sequence of the A. thaliana alpha-tubulin with the predicted amino acid sequences of alpha-tubulins of Chlamydomonas reinhardtii, Stylonychia lemnae, and Homo spaiens reveals a high degree of homology; 90%, 87%, and 83% identity, respectively. Thus, a plant alpha-tubulin exhibits a high degree of homology to the alpha-tubulins of protists and animals. The coding sequence of the A. thaliana alpha-tubulin gene is interrupted by four introns, which occur at positions different from those of the less numerous introns of C. reinhardtii and rat alpha-tubulin genes. S1 nuclease mapping data showed that transcription is initiated 99 +/- 1 base pairs upstream from the translation initiation codon. Both 5' and 3' noncoding gene-specific probes were used to examine the expression of the alpha-tubulin gene in leaves, roots, and flowers by hybridization to total RNA isolated from these tissues. The results showed that the alpha-tubulin gene was transcribed in all three tissues.

Synthesis and localization of pathogenesis-related proteins in tobacco

The PR1 family of pathogenesis-related proteins from tobacco (Nicotiana tabacum L.) leaves is induced by a variety of pathogenic and chemical agents and is associated with resistance to tobacco mosaic virus. The majority of the PR1 proteins did not copurify with mesophyll protoplasts (the major cell type of the leaf) isolated from tobacco mosaic virus-infected N. tabacum cv. Xanthi-nc leaves. However, these isolated protoplasts were capable of synthesizing and selectively secreting the PR1 proteins. Using monoclonal antibodies for immunofluorescence microscopy, we localized these proteins to the extracellular spaces predominantly in regions adjacent to viral lesions as well as in xylem elements of infected leaves.

Synthesis and localization of pathogenesis-related proteins in tobacco

The PR1 family of pathogenesis-related proteins from tobacco (Nicotiana tabacum L.) leaves is induced by a variety of pathogenic and chemical agents and is associated with resistance to tobacco mosaic virus. The majority of the PR1 proteins did not copurify with mesophyll protoplasts (the major cell type of the leaf) isolated from tobacco mosaic virus-infected N. tabacum cv. Xanthi-nc leaves. However, these isolated protoplasts were capable of synthesizing and selectively secreting the PR1 proteins. Using monoclonal antibodies for immunofluorescence microscopy, we localized these proteins to the extracellular spaces predominantly in regions adjacent to viral lesions as well as in xylem elements of infected leaves.

Product of Saccharomyces cerevisiae nuclear gene PET494 activates translation of a specific mitochondrial mRNA

The product of Saccharomyces cerevisiae nuclear gene PET494 is known to be required for a posttranscriptional step in the accumulation of one mitochondrial gene product, subunit III of cytochrome c oxidase (coxIII). Here we show that the PET494 protein probably acts in mitochondria by demonstrating that both a PET494-beta-galactosidase fusion protein and unmodified PET494 are specifically associated with mitochondria. To define the PET494 site of action, we isolated mutations that suppress a pet494 deletion. These mutations were rearrangements of the mitochondrial gene oxi2 that encodes coxIII. The suppressor oxi2 genes had acquired the 5'-flanking sequences of other mitochondrial genes and gave rise to oxi2 transcripts carrying the 5'-untranslated leaders of their mRNAs. These results demonstrate that in wild-type cells PET494 specifically promotes coxIII translation, probably by interacting with the 5'-untranslated leader of the oxi2 mRNA.

Translational regulation of light-induced ribulose 1,5-bisphosphate carboxylase gene expression in amaranth

The regulation of the genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase was examined in amaranth cotyledons in response to changes in illumination. When dark-grown cotyledons were transferred into light, synthesis of the large- and small-subunit polypeptides was initiated very rapidly, before any increase in the levels of their corresponding mRNAs. Similarly, when light-grown cotyledons were transferred to total darkness, synthesis of the large- and small-subunit proteins was rapidly depressed without changes in mRNA levels for either subunit. In vitro translation or in vivo pulse-chase experiments indicated that these apparent changes in protein synthesis were not due to alterations in the functionality of the mRNAs or to protein turnover, respectively. These results, in combination with our previous studies, suggest that the expression of ribulose 1,5-bisphosphate carboxylase genes can be adjusted rapidly at the translational level and over a longer period through changes in mRNA accumulation.

Regulation of genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase and the photosystem II polypeptides D-1 and D-2 during the cell cycle of Chlamydomonas reinhardtii

Synthesis of the major chloroplast proteins is temporally regulated in light-dark-synchronized Chlamydomonas cells. We have used cloned chloroplast DNA probes, and in vitro and in vivo protein synthesis to examine the cell cycle regulation of photosystem II polypeptides D-1 and D-2, and the large subunit of ribulose-1,5-bisphosphate carboxylase (RuBPCase LS). Synthesis and accumulation of D-1 and D-2 mRNAs occurs during the first half of the light period (G1), correlating with increasing synthesis of the polypeptides. Rifampicin, added immediately before the light period, inhibited the normal increase in D-1, D-2 polypeptide synthesis. During the dark period D-1, D-2 mRNAs persist at high levels despite reduced rates of mRNA synthesis and translation during this period. Cell-free translation analyses indicate that the D-1 mRNA present during the dark period is efficient at directing synthesis of the D-1 precursor in vitro. We conclude that expression of the psbA (D-1) and psbD (D-2) genes are regulated primarily at the transcriptional level during the light-induction period but at the translational level for the remainder of the cell cycle. Transcripts of the RuBPCase LS gene (rbcL) are also found at high levels during the light and dark periods but, unlike D-1 and D-2, LS mRNA levels do not increase until the last half of the light period and measurable synthesis and accumulation of this mRNA occurs during the dark. Furthermore, induction of LS polypeptide synthesis during the light period is insensitive to rifampicin. We conclude that LS production is regulated primarily at the translational level during the cell cycle.

Product of Saccharomyces cerevisiae nuclear gene PET494 activates translation of a specific mitochondrial mRNA

The product of Saccharomyces cerevisiae nuclear gene PET494 is known to be required for a posttranscriptional step in the accumulation of one mitochondrial gene product, subunit III of cytochrome c oxidase (coxIII). Here we show that the PET494 protein probably acts in mitochondria by demonstrating that both a PET494-beta-galactosidase fusion protein and unmodified PET494 are specifically associated with mitochondria. To define the PET494 site of action, we isolated mutations that suppress a pet494 deletion. These mutations were rearrangements of the mitochondrial gene oxi2 that encodes coxIII. The suppressor oxi2 genes had acquired the 5'-flanking sequences of other mitochondrial genes and gave rise to oxi2 transcripts carrying the 5'-untranslated leaders of their mRNAs. These results demonstrate that in wild-type cells PET494 specifically promotes coxIII translation, probably by interacting with the 5'-untranslated leader of the oxi2 mRNA.

Biogenesis of photosystem II complexes: transcriptional, translational, and posttranslational regulation

The integral membrane proteins of photosystem II (PS II) reaction center complexes are encoded by chloroplast genomes. These proteins are absent from thylakoids of PS II mutants of algae and vascular plants as a result of either chloroplast or nuclear gene mutations. To resolve the molecular basis for the concurrent absence of the PS II polypeptides, protein synthesis rates and mRNA levels were measured in mutants of Chlamydomonas reinhardtii that lack PS II. The analyses show that one nuclear gene product regulates the levels of transcripts from the chloroplast gene encoding the 51-kD chlorophyll a-binding polypeptide (polypeptide 5) but is not involved in the synthesis of other chloroplast mRNAs. Another nuclear product is specifically required for translation of mRNA encoding the 32-34-kD polypeptide, D1. The absence of either D1 or polypeptide 5 does not eliminate the synthesis and thylakoid insertion of two other integral membrane proteins of PS II, the chlorophyll a-binding polypeptide of 46 kD (polypeptide 6) and the 30-kD "D1-like" protein, D2. However, these two unassembled subunits cannot be properly processed and/or are degraded in the mutants even though they reside in the membrane. In addition, pulse labeling of the nuclear mutants and a chloroplast mutant that does not synthesize D1 mRNA indicates that synthesis of polypeptide 5 and D1 is coordinated at the translational level. A model is presented to explain how absence of one of the two proteins could lead to translational arrest of the other.

Translational regulation of light-induced ribulose 1,5-bisphosphate carboxylase gene expression in amaranth

The regulation of the genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase was examined in amaranth cotyledons in response to changes in illumination. When dark-grown cotyledons were transferred into light, synthesis of the large- and small-subunit polypeptides was initiated very rapidly, before any increase in the levels of their corresponding mRNAs. Similarly, when light-grown cotyledons were transferred to total darkness, synthesis of the large- and small-subunit proteins was rapidly depressed without changes in mRNA levels for either subunit. In vitro translation or in vivo pulse-chase experiments indicated that these apparent changes in protein synthesis were not due to alterations in the functionality of the mRNAs or to protein turnover, respectively. These results, in combination with our previous studies, suggest that the expression of ribulose 1,5-bisphosphate carboxylase genes can be adjusted rapidly at the translational level and over a longer period through changes in mRNA accumulation.