Plant Ribosomes Research Articles

Variation in transcript abundance among the four members of the Arabidopsis thaliana RIBOSOMAL PROTEIN S15a gene family

As a ribonucleoprotein complex, the plant ribosome consists of four ribosomal RNAs (rRNAs) and 75–92 ribosomal proteins (r-proteins), depending on the species. Arabidopsis thaliana r-protein genes exist in multi-gene families ranging in size from two to seven transcriptionally active members. The cytosolic RPS15a gene family consists of four members that, at the amino acid level, share 87–100% identity. The 5′ regulatory regions of the four genes contain many of the same putative regulatory elements but share only 46–49% nucleotide sequence identity. Semi-quantitative RT-PCR (sqRT-PCR) was used to determine RPS15a transcript abundance patterns and identify possible regulatory differences among the four genes. RPS15aC expression was not detected in any tissue under any treatment while transcript abundance for RPS15aA, - D and - F was highest in mitotically active tissues e.g. bud and flower. Seedlings showed increased transcript abundance following treatment with the cytokinin 6-benzylaminopurine (BAP) while the auxin indole acetic acid (IAA) induced an increase in RPS15aF abundance only. Abscisic acid (ABA) treatment resulted in decreased transcript abundance while gibberellic acid (GA 3) had little effect on all four genes. Similar trends were established for RPS15aA, -D and - F transcript abundance as a result of temperature mechanical stress. This study reports the differences in transcript abundance of the four cytosolic RPS15a genes in Arabidopsis and we suggest that RPS15a genes should no longer be considered ‘housekeeping’ genes.

The ribosomal subunit assembly line

Recent proteomic studies in in yeast and plants have identified nearly 200 yeast proteins that participate in the assembly of ribosomal subunits and their transport from the nucleus, and revealed considerable variability in the protein composition of individual plant ribosomes.

Silencing of ribosomal protein L3 genes in N. tabacum reveals coordinate expression and significant alterations in plant growth, development and ribosome biogenesis.

The expression of ribosomal protein genes is coordinately regulated in bacteria, yeast, and vertebrates, so that equimolar amounts of ribosomal proteins accumulate for assembly into ribosomes. To understand how expression of ribosomal protein genes is regulated in plants, we altered expression of the large subunit ribosomal protein L3 (RPL3) genes in Nicotiana tabacum using post-transcriptional gene silencing (PTGS). L3 is encoded by two genes, RPL3A and RPL3B, with 80.2% amino acid sequence identity in tobacco. Two types of 'hairpin' RNA (hpRNA) vectors carrying the RPL3A or RPL3B sequences in both sense and antisense orientation were generated in order to alter the expression level of both RPL3 genes. Tobacco plants transformed with a vector containing a 5'-terminal fragment of RPL3A gene displayed decreased RPL3A mRNA levels and a marked increase in the abundance of RPL3B mRNA. These results indicated that expression of the RPL3 genes is coordinately regulated in tobacco. The transgenic plants that contained higher levels of RPL3B mRNA exhibited leaf overgrowth and mottling. Epidermal cells of these plants were increased in number and decreased in size. The precursor rRNA (pre-rRNA) and the mature rRNAs accumulated in these plants, suggesting that ribosome biogenesis is upregulated. Tobacco plants transformed with an hpRNA vector harboring the full-length RPL3B cDNA exhibited efficient silencing of both RPL3A and RPL3B genes, reduced L3 levels, and an abnormal phenotype characterized by a delay in development, stunting, and inhibition of lateral root growth. L3 deficiency led to a reduction in cell number and an increase in cell size, suggesting that L3 positively regulates cell division. Decreasing RPL3 gene expression resulted in a decrease in accumulation of the pre-rRNA, establishing a prominent role for L3 in ribosome biogenesis in plants.

Analysis of the in planta antiviral activity of elderberry ribosome-inactivating proteins.

Although the type-2 ribosome-inactivating proteins (SNA-I, SNA-V, SNLRP) from elderberry (Sambucus nigra L.) are all devoid of rRNA N-glycosylase activity towards plant ribosomes, some of them clearly show polynucleotide-adenosine glycosylase activity towards tobacco mosaic virus RNA. This particular substrate specificity was exploited to further unravel the mechanism underlying the in planta antiviral activity of ribosome-inactivating proteins. Transgenic tobacco (Nicotiana tabacum L. cv Samsun NN) plants expressing the elderberry ribosome-inactivating proteins were generated and challenged with tobacco mosaic virus in order to analyze their antiviral properties. Although some transgenic plants clearly showed antiviral activity, no clear correlation was observed between in planta antiviral activity of transgenic tobacco lines expressing the different ribosome-inactivating proteins and the in vitro polynucleotide-adenosine glycosylase activity of the respective proteins towards tobacco mosaic virus genomic RNA. However, our results suggest that the in planta antiviral activity of some ribosome-inactivating proteins may rely on a direct mechanism on the virus. In addition, it is evident that the working mechanism proposed for pokeweed antiviral protein cannot be extrapolated to elderberry ribosome-inactivating proteins because the expression of SNA-V is not accompanied by induction of pathogenesis-related proteins.

A nascent polypeptide domain that can regulate translation elongation.

The evolutionarily conserved fungal arginine attenuator peptide (AAP), as a nascent peptide, stalls the translating ribosome in response to the presence of a high concentration of the amino acid arginine. Here we examine whether the AAP maintains regulatory function in fungal, plant, and animal cell-free translation systems when placed as a domain near the N terminus or internally within a large polypeptide. Pulse-chase analyses of the radiolabeled polypeptides synthesized in these systems indicated that wild-type AAP functions at either position to stall polypeptide synthesis in response to arginine. Toeprint analyses performed to map the positions of stalled ribosomes on transcripts introduced into the fungal system revealed that ribosome stalling required translation of the AAP coding sequence. The positions of the stalled ribosomes were consistent with the sizes of the radiolabeled polypeptide intermediates. These findings demonstrate that an internal polypeptide domain in a nascent chain can regulate eukaryotic translational elongation in response to a small molecule. Apparently the peptide-sensing features are conserved in fungal, plant, and animal ribosomes. These data provide precedents for translational strategies that would allow domains within nascent polypeptide chains to modulate gene expression.

Isolation and characterization of velutin, a novel low-molecular-weight ribosome-inactivating protein from winter mushroom ( Flammulina velutipes) fruiting bodies

From the fruiting bodies of the edible mushroom Flammulina velutipes a single-chained ribosome inactivating protein with a molecular weight of 13.8 kDa was isolated with a procedure involving ion exchange chromatography on DEAE-cellulose and SP-Sepharose and affinity chromatography on Affi-gel blue gel. The protein was novel in that it possessed a molecular weight lower than those of previously reported RIPs and that it was capable of inhibiting human immunodeficiency virus (HIV-1) reverse transcriptase, β-glucosidase and β-glucuronidase. Its N-terminal sequence exhibited a certain degree of similarity to those of plant ribosome inactivating proteins.

Panaxagin, a new protein from Chinese ginseng possesses anti-fungal, anti-viral, translation-inhibiting and ribonuclease activities

From the roots of the Chinese ginseng Panax ginseng a protein designated panaxagin with ribonuclease activity, but possessing a sequence distinct from ribonucleases previously reported from ginseng calluses, was isolated. The purification protocol employed comprised extraction with cold saline, (NH 4) 2SO 4 precipitation, ion exchange chromatography on DEAE-cellulose, affinity chromatography on Affi-gel blue gel, ion exchange chromatography on SP-Sepharose, and gel filtration on Superdex 75 by fast protein liquid chromatography. The purified protein was composed of two identical subunits each with a molecular weight of 26 kDa. Its N-terminal amino acid sequence exhibits sites of similarity with the sequences of plant ribosome inactivating proteins and fungal ribonucleases. The spectrum of biological activities of panaxagin encompassed ribonuclease activity toward yeast transfer RNA, translation-inhibitory activity in a rabbit reticulocyte lysate system, and antifungal activity against fungi including Coprinus comatus and Fusarium oxysporum, but not against Rhizoctonia solani. In addition it displayed an inhibitory activity against human immunodeficiency virus reverse transcriptase and succinylation augmented this activity.

Gelonin Is an Unusual DNA Glycosylase That Removes Adenine from Single-stranded DNA, Normal Base Pairs and Mismatches

We reported that plant ribosome inactivating proteins (RIP) have a unique DNA glycosylase activity that removes adenine from single-stranded DNA (Nicolas, E., Beggs, J. M., Haltiwanger, B. M., and Taraschi, T. F. (1998) J. Biol. Chem. 273, 17216-17220). In this investigation, we further characterized the interaction of the RIP gelonin with single-stranded oligonucleotides and investigated its activity on double-stranded oligonucleotides. At physiological pH, zinc and beta-mercaptoethanol stimulated the adenine DNA glycosylase activity of gelonin. Under these conditions, gelonin catalytically removed adenine from single-stranded DNA and, albeit to a lesser extent, from normal base pairs and mismatches in duplex DNA. Also unprecedented was the finding that activity on single-stranded and double-stranded oligonucleotides containing multiple adenines generated unstable products with several abasic sites, producing strand breakage and duplex melting, respectively. The results from competition experiments suggested similar interactions between gelonin's DNA-binding domain and oligonucleotides with and without adenine. A re-examination of the classification of gelonin as a DNA glycosylase/AP lyase using the borohydride trapping assay revealed that gelonin was similar to the DNA glycosylase MutY: both enzymes are monofunctional glycosylases, which are trappable to their DNA substrates. The k(cat) for the removal of adenine from single-stranded DNA was close to the values observed with multisubstrate DNA glycosylases, suggesting that the activity of RIPs on DNA may be physiologically relevant.

The plant ribosome inactivating proteins luffin and saporin are potent inhibitors of HIV-1 integrase

The ribosome inactivating proteins (RIPs) are a group of proteins that are able to inactivate eukaryotic protein synthesis by attacking the 28S ribosomal RNA. Recent studies have shown that some RIPs possess strong anti-human immunodeficiency virus (HIV) activity. In this study, several common plant RIPs including agrostin, gelonin, luffin, α-momorcharin, β-momorcharin, saporin and trichosanthin were examined for the ability to interfere with HIV-1 replication in a variety of mechanistic assays in vitro. These assays included the CD4/gp120 interaction assay, HIV-1 reverse transcriptase (RT) assay, HIV-1 protease assay and HIV-1 integrase assay. At the concentration of 100 nM, all RIPs appeared to enhance the CD4/gp120 interaction by about 50%. These RIPs exhibited a very weak suppressive effect on HIV-1 RT and on HIV-1 protease. In contrast, with the exception of agrostin, all the RIPs tested could strongly inhibit HIV-1 integrase, the extent of inhibition ranging from 26.1 to 96.3% in an ELISA-based assay. Two RIPs, saporin and luffin, which licited over 90% inhibition in the ELISA-based assay, were further characterized in a radiometric assay. Both of these two RIPs evoked a strong dose-dependent inhibition in the 3′-end processing and strand-transfer activities of integrase. The results from this study suggest that the anti-HIV property of RIPs may be due to inhibition of HIV-1 integrase.

Quinqueginsin, a Novel Protein with Anti-Human Immunodeficiency Virus, Antifungal, Ribonuclease and Cell-Free Translation-Inhibitory Activities from American Ginseng Roots

A homodimeric protein designated quinqueginsin, with a molecular weight of 53 kDa, has been isolated from the roots of American ginseng Panax quinquefolium. It was unadsorbed on DEAE cellulose in low ionic strength and neutral pH, and adsorbed on Affigel blue gel and SP-Sepharose under similar conditions. Its N-terminal sequence bore similarity to those of plant ribosome inactivating proteins and fungal ribonucleases. The protein displayed a variety of biological activities. It possessed ribonucleolytic activity toward yeast tRNA and specific activity toward poly C. It inhibited cell-free translation in a rabbit reticulocyte lysate system with an IC50 of 0.26 nM, and exerted antifungal action against Fusarium oxysporum, Rhizoctonia solani, and Coprinus comatus. An inhibitory action was expressed toward human immunodeficiency virus-1 reverse transcriptase. This action was potentiated after chemical modification with succinic anhydride.

Plant ribosome recycling factor homologue is a chloroplastic protein and is bactericidal in escherichia coli carrying temperature-sensitive ribosome recycling factor.

We have isolated a protein, mature RRFHCP, from chloroplasts of spinach (Spinacia oleracea L.) that shows 46% sequence identity and 66% sequence homology with ribosome recycling factor (RRF) of Escherichia coli. RRF recycles ribosomes through disassembly of the posttermination complex. From the cDNA analysis and from the amino-terminal sequencing of the isolated protein, the mature RRFHCP was deduced to have a Mr of 21,838 with 193 aa. It lacks the 78-aa chloroplast targeting sequence encoded by the RRFHCP cDNA sequence. The RRFHCP synthesized in vitro was imported into isolated chloroplasts with simultaneous conversion to the mature RRFHCP. Transcription of the gene coding for RRFHCP was not dependent on light, yet it was limited mostly to photosynthetic tissues in which only one transcript size was detected. Mature RRFHCP exerted a bactericidal effect on E. coli carrying temperature-sensitive RRF at the permissive temperature whereas wild-type E. coli was not affected.

RIP-JIP60 Alters Conformation of Ribosomesin Vivo

Recently it has been demonstrated that expression putative ribosome-inactivating protein JIP 60 in transgenic tobacco plants leads to the depurination of large rRNA and inactivation of plant ribosomes. Treatment of ribosomes from transgenic tobacco plants with low concentration of α-sarcin resulted in the appearance of an rRNA specific fragment. No fragment was observed under the same conditions for ribosomes from wild type plants. The alteration of the comformation of ribosomes in transgenic tobacco due to the expression of JIP60 is assumed.

The plant ribosome inactivating protein saporin induces micronucleus formation in peripheral human lymphocytes in vitro

Saporin belongs to the family of plant enzymes known as ribosome inactivating proteins (RIPs) for their property to depurinate the major rRNA, thus leading to inactivation of ribosomes. In this work we analyzed the genotoxic effects of saporin, purified from root cultures of Saponaria officinalis, by evaluating micronucleus formation and by the quantitative determination of cytosolic histone-associated DNA fragments. Saporin induces micronuclei formation in cultured human lymphocytes in a dose dependent manner; treated lymphocytes show a decrease in cell viability and a concomitant increase in the apoptotic response evidenced by the appearance of cytosolic oligonucleosomes. On the other hand saporin treatment failed to induce sister-chromatid exchange (SCE) at any of the doses tested.

Constitutive and inducible type 1 ribosome-inactivating proteins (RIPs) in elderberry ( Sambucus nigra L.)

Two novel highly basic type 1 (single chain) ribosome-inactivating proteins (RIPs) with N-glycosidase activity have been found in elderberries (the fruits of Sambucus nigra L.). Mass spectrometry of these RIPs, which we named nigritins f1 and f2, gave M r values of 24 095 and 23 565, respectively. Both proteins strongly inhibited protein synthesis in rabbit reticulocyte lysates but were inactive against plant ribosomes. Both nigritins have a similar topological activity on pBlueScript SK + DNA as that displayed by dianthin 30. Nigritin f1 is a constitutive RIP since it is present in both green and mature intact elderberries at nearly the same proportion with respect to total fruit protein. By contrast, nigritin f2 is inducible and only appeared in mature intact elderberries. Elderberries also contain two isoforms of a basic nigrin equivalent to the recently found basic nigrin b in elder bark (De Benito et al., FEBS Letters 413 (1997) 85–91). Our results indicate that probably not all plant RIPs exert the same biological function and that this may be determined by the physiological state of the tissue.

Evolutionary analyses of the 12-kDa acidic ribosomal P-proteins reveal a distinct protein of higher plant ribosomes.

The P-protein complex of eukaryotic ribosomes forms a lateral stalk structure in the active site of the large ribosomal subunit and is thought to assist in the elongation phase of translation by stimulating GTPase activity of elongation factor-2 and removal of deacylated tRNA. The complex in animals, fungi, and protozoans is composed of the acidic phosphoproteins P0 (35 kDa), P1 (11-12 kDa), and P2 (11-12 kDa). Previously we demonstrated by protein purification and microsequencing that ribosomes of maize (Zea mays L.) contain P0, one type of P1, two types of P2, and a distinct P1/P2 type protein designated P3. Here we implemented distance matrices, maximum parsimony, and neighbor-joining analyses to assess the evolutionary relationships between the 12 kDa P-proteins of maize and representative eukaryotic species. The analyses identify P3, found to date only in mono- and dicotyledonous plants, as an evolutionarily distinct P-protein. Plants possess three distinct groups of 12 kDa P-proteins (P1, P2, and P3), whereas animals, fungi, and protozoans possess only two distinct groups (P1 and P2). These findings demonstrate that the P-protein complex has evolved into a highly divergent complex with respect to protein composition despite its critical position within the active site of the ribosome.

Targeted inactivation of a tobacco intron-containing open reading frame reveals a novel chloroplast-encoded photosystem I-related gene.

The chloroplast genome of all higher plants encodes, in its large single-copy region, a conserved open reading frame of unknown function (ycf3), which is split by two group II introns and undergoes RNA editing in monocotyledonous plants. To elucidate the function of ycf3 we have deleted the reading frame from the tobacco plastid genome by biolistic transformation. We show here that homoplasmic Deltaycf3 plants display a photosynthetically incompetent phenotype. Molecular analyses indicate that this phenotype is not due to a defect in any of the general functions of the plastid genetic apparatus. Instead, the mutant plants specifically lack detectable amounts of all photosystem I (PSI) subunits analyzed. In contrast, at least under low light conditions, photosystem II subunits are still present and assemble into a physiologically active complex. Faithful transcription of photosystem I genes as well as correct mRNA processing and efficient transcript loading with ribosomes in the Deltaycf3 plants suggest a posttranslational cause of the PSI-defective phenotype. We therefore propose that ycf3 encodes an essential protein for the assembly and/or stability of functional PSI units. This study provides a first example for the suitability of reverse genetics approaches to complete our picture of the coding capacity of higher plant chloroplast genomes.

A plant ribosome inactivating protein, Viscum album Agglutinin-I (VAA-I) induces cytokine gene expression and apoptosis in cultures of peripheral blood mononuclear cells

A plant ribosome inactivating protein, Viscum album Agglutinin-I (VAA-I) induces cytokine gene expression and apoptosis in cultures of peripheral blood mononuclear cells

A plant ribosome inactivating protein, Viscum album Agglutinin-I (VAA-I) induces cytokine gene expression and apoptosis in cultures of peripheral blood mononuclear cells

A plant ribosome inactivating protein, Viscum album Agglutinin-I (VAA-I) induces cytokine gene expression and apoptosis in cultures of peripheral blood mononuclear cells

Direct evidence for the deoxyribonuclease activity of the plant ribosome inactivating protein gelonin

Several plant ribotoxins, including gelonin, were reported to have additional weak nuclease activities on supercoiled DNA. The potential contribution of this activity to their cytotoxicity has not been given serious consideration due to concerns about contaminating nucleases in the protein preparations. We now report the degradation of single-stranded DNA by preparations of native plant gelonin and recombinant gelonin produced in E. coli. The DNase activity of both preparations is similarly modulated by zinc. An SDS-PAGE DNase assay identifies gelonin as the polypeptide responsible for deoxyribonuclease activity.

Induction of a ribosome-inactivating protein upon environmental stress.

Transcripts of altered abundance in RNA from unstressed and 500 mm salt-shocked Mesembryanthemum crystallinum (common ice plant) were detected by reverse-transcription differential display (RT-DD). One transcript, Rip1, was of very low abundance in unstressed plants and was strongly induced by stress. RNA blot hybridizations showed strong induction and a diurnal rhythm of transcript abundance with a maximum each day around the middle of the light phase. Rip1 encodes a reading frame of 289 amino acids (molecular mass 32,652), RIP1, with homology to single-chain ribosome inactivating proteins (rRNA N-glycosidases). The deduced amino acid sequence is 31.7% identical to pokeweed antiviral protein RIP-C (overall similarity 66.5%) with highest identity in domains of documented functional importance. RT-DD also detected mRNA for pyruvate, orthophosphate dikinase (PPDK) which has already been shown to be stress-induced in the ice plant [16]. RIP1, expressed in Escherichia coli, showed rRNA N-glycosidase activity against ice plant and rabbit reticulocyte ribosomes. The induction of Rip1 coincides with the transition period during which global changes in translation lead to adaptation of the ice plant to salt stress.