Senescence and stomatal aperture as affected by antibiotics in darkness and light

In leaves of barley (Hordeum vulgare), as previously found with oats (Avena sativa), a group of six antibiotics that interfere in different ways with the sequence DNA → mRNA → protein all delay senescence in the dark, acting to conserve chlorophyll (Chl) and protein and also to open the stomata. Among the active compounds is chloramphenicol, which had previously been reported to act only on procaryotes. It is now shown that all these compounds with senescence-delaying action in darkness have the opposite effect in light, accelerating Chl destruction and partially or completely closing the stomata. Leaves of the dicot Tropaeolum majus show most of the same responses, though the changes in protein and amino acids are more variable. The data as a whole support the previous conclusion that the synthesis of one or more proteins controls both the opening and the closing of the stomata. An additional compound, kanamycin, acts in the same way as the other six compounds on oats and barley, though its action on proteolysis is unclear. On Tropaeolum, however, it opens the stomata in both light and darkness. Anisomycin and ethidium bromide have comparably atypical effects. Thus, although changes in stomatal opening or closing in the majority of cases are closely linked to the breakdown or preservation of Chl, the occasional exception shows that the biochemical phenomena of senescence cannot be under the direct control of changes in stomatal aperture.     

Characteristics of the process of enzyme release from secretory plant cells

Secretion—the outward movement of molecules across the plasmalemma—of α-amylase by barley (Hordeum vulgare L. cv. Himalaya) aleurone layers is an energy-dependent process that is not directly dependent upon protein synthesis or RNA synthesis and does not appear to be under the direct control of gibberellic acid or abscisic acid. Release—the movement of the secreted α-amylase molecules through the walls into the surrounding medium—is apparently diffusion limited and is markedly dependent upon the presence of ions.     

RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins

Biomolecular condensates formed via liquid–liquid phase separation (LLPS) play a crucial role in the spatiotemporal organization of the cell material. Nucleic acids can act as critical modulators in the stability of these protein condensates. To unveil the role of RNA length in regulating the stability of RNA binding protein (RBP) condensates, we present a multiscale computational strategy that exploits the advantages of a sequence-dependent coarse-grained representation of proteins and a minimal coarse-grained model wherein proteins are described as patchy colloids. We find that for a constant nucleotide/protein ratio, the protein fused in sarcoma (FUS), which can phase separate on its own—i.e., via homotypic interactions—only exhibits a mild dependency on the RNA strand length. In contrast, the 25-repeat proline-arginine peptide (PR₂₅), which does not undergo LLPS on its own at physiological conditions but instead exhibits complex coacervation with RNA—i.e., via heterotypic interactions—shows a strong dependence on the length of the RNA strands. Our minimal patchy particle simulations suggest that the strikingly different effect of RNA length on homotypic LLPS versus RBP–RNA complex coacervation is general. Phase separation is RNA-length dependent whenever the relative contribution of heterotypic interactions sustaining LLPS is comparable or higher than those stemming from protein homotypic interactions. Taken together, our results contribute to illuminate the intricate physicochemical mechanisms that influence the stability of RBP condensates through RNA inclusion.     

Stomatal diffusion resistance of snap beans. I. Influence of leaf-water potential

Concurrent measurements of abaxial and adaxial stomatal resistance and leaf-water potentials of snap beans (Phaseolus vulgaris L.) in the field and growth chamber show that the stomata on the 2 surfaces of the leaflet react differently to water deficit. The stomata on the abaxial surface, which are about 7 times more numerous than on the adaxial surface, are not significantly affected at leaf-water potentials greater than —11 bars, but with further decrease in leaf-water potential, the resistance rapidly increases. On the other hand, the resistance of the adaxial stomata increases sharply at a leaf-water potential of about —8 bars and is constant at higher water potentials. The average stomatal resistance for both surfaces of the leaf, which is the major diffusive resistance to water vapor, to a first approximation acts as an on-off switch and helps prevent further decline in leaf-water potential. The relation between the leaf-water potential and the stomatal resistance links the soil-water potential to the transpiration stream as needed for soil-plant-atmosphere models.     

The Synthesis of Ribosomes in E. coli: IV. The Synthesis of Ribosomal Protein and the Assembly of Ribosomes

The incorporation of C¹⁴ leucine into the protein moiety of ribosomes has been studied as a sequel to the studies of ribosomal RNA synthesis. In contrast to the latter studies, labeled leucine is incorporated directly into 50S and 30S ribosomes without measurable delay by precursor stages. There is, however, evidence of some transfer of radioactivity from the 43S group of particles to the 50S. The inhibition of protein synthesis by chloramphenicol results in the accumulation of material similar to the eosome—the primary precursor in ribosome synthesis. There is also evidence for the synthesis of some neosome. The results of the studies of ribosomal RNA and protein synthesis are combined into a model of ribosome synthesis. Finally, consideration is made of the significance of these studies of ribosome synthesis for general problems of protein synthesis and information transfer.     

The senescence of detached leaves of tropaeolum

The senescence of detached Tropaeolum majus leaves was compared with that described earlier for Avena. Tropaeolum was chosen as being not only a dicot but also as having a nearly circular leaf, thus needing only the smallest minimum of wounding, since wounding delays the loss of chlorophyll and protein in darkness. Tropaeolum resembles Avena in that closing the stomata osmotically or with ABA causes rapid senescence in light. As in Avena also, n-hexanol and α,α′-dipyridyl delay senescence in darkness but cause `bleaching' of chlorophyll in light. Unlike Avena, however, kinetin and gibberellic acid, which delay senescence in the dark in both species, do so in Tropaeolum without causing any significant stomatal opening. The senescence of Tropaeolum leaves is actually promoted by fusicoccin, which powerfully delays senescence in Avena, although fusicoccin does cause stomatal opening in darkness in both species. Thus, many of the phenomena of senescence are alike in the monocot and dicot, but there are several significantly different responses to the senescence-modifying reagents. It is concluded that while stomatal closure accelerates senescence in both species, stomatal opening is not directly linked to the prevention of leaf senescence.     

The role of protein synthesis in the senescence of leaves: I. The formation of protease

The senescence of oat leaves has been studied by following the loss of chlorophyll and protein and the increase of α-amino nitrogen, after detachment and darkening. Protein synthesis and the amounts of proteolytic enzymes in the leaves have been determined directly. The process of senescence is shown to be a sequential one in which protein synthesis,most probably the formation of a proteolytic enzyme with l-serine in its active center, is of prime importance. The evidence is as follows. Firstly, l-serine specifically enhances senescence, especially in presence of kinetin. Secondly, cycloheximide, which inhibits protein synthesis in other systems, delays senescence and prevents the serine enhancement. Although requiring higher concentrations, cycloheximide can be as effective as kinetin in inhibiting senescence. It is shown directly that cycloheximide prevents protein synthesis in oat leaves under the same conditions as when it prevents senescence. Thirdly, leaves have been shown to contain two proteinases, with pH optima at 3 and 7.5, whose activity increases during senescence, even though the total leaf protein is decreasing. The amounts of both these enzymes present after 3 days are clearly increased by serine, and are greatly decreased by cycloheximide or by kinetin. The role of kinetin in delaying senescence thus may rest on its ability to suppress protease formation.     

The role of spartin and its novel ubiquitin binding region in DALIS occurrence

Troyer syndrome is an autosomal recessive hereditary spastic paraplegia (HSP) caused by frameshift mutations in the SPG20 gene that results in a lack of expression of the truncated protein. Spartin is a multifunctional protein, yet only two conserved domains—a microtubule-interacting and trafficking domain and a plant-related senescence domain involved in cytokinesis and mitochondrial physiology, respectively—have been defined. We have shown that overexpressed spartin binds to the Ile44 hydrophobic pocket of ubiquitin, suggesting spartin might contain a ubiquitin-binding domain. In the present study, we demonstrate that spartin contributes to the formation of dendritic aggresome-like induced structures (DALIS) through a unique ubiquitin-binding region (UBR). Using short hairpin RNA, we knocked down spartin in RAW264.7 cells and found that DALIS frequency decreased; conversely, overexpression of spartin increased the percentage of cells containing DALIS. Using nuclear magnetic resonance spectroscopy, we characterized spartin''s UBR and defined the UBR''s amino acids that are key for ubiquitin binding. We also found that spartin, via the UBR, binds Lys-63–linked ubiquitin chains but does not bind Lys-48–linked ubiquitin chains. Finally, we demonstrate that spartin''s role in DALIS formation depends on key residues within its UBR.     

Nucleolar Integrity Is Required for the Maintenance of Long-Term Synaptic Plasticity

Long-term memory (LTM) formation requires new protein synthesis and new gene expression. Based on our work in Aplysia, we hypothesized that the rRNA genes, stimulation-dependent targets of the enzyme Poly(ADP-ribose) polymerase-1 (PARP-1), are primary effectors of the activity-dependent changes in synaptic function that maintain synaptic plasticity and memory. Using electrophysiology, immunohistochemistry, pharmacology and molecular biology techniques, we show here, for the first time, that the maintenance of forskolin-induced late-phase long-term potentiation (L-LTP) in mouse hippocampal slices requires nucleolar integrity and the expression of new rRNAs. The activity-dependent upregulation of rRNA, as well as L-LTP expression, are poly(ADP-ribosyl)ation (PAR) dependent and accompanied by an increase in nuclear PARP-1 and Poly(ADP) ribose molecules (pADPr) after forskolin stimulation. The upregulation of PARP-1 and pADPr is regulated by Protein kinase A (PKA) and extracellular signal-regulated kinase (ERK)—two kinases strongly associated with long-term plasticity and learning and memory. Selective inhibition of RNA Polymerase I (Pol I), responsible for the synthesis of precursor rRNA, results in the segmentation of nucleoli, the exclusion of PARP-1 from functional nucleolar compartments and disrupted L-LTP maintenance. Taken as a whole, these results suggest that new rRNAs (28S, 18S, and 5.8S ribosomal components)—hence, new ribosomes and nucleoli integrity—are required for the maintenance of long-term synaptic plasticity. This provides a mechanistic link between stimulation-dependent gene expression and the new protein synthesis known to be required for memory consolidation.     

Photo- and Metabolite Regulation of the Synthesis of Ribulose Bisphosphate Carboxylase/Oxygenase and the Phycobiliproteins in the Alga Cyanidium caldarium

In the eukaryotic and unicellular alga Cyanidium caldarium the synthesis of the plastid enzyme ribulose bisphosphate carboxylase/oxygenase (RuBPCase) and the light gathering proteins phycocyanin (PC) and allophycocyanin (APC) is under the control of light and glucose, which is a metabolizable carbon source for this organism. Light promotes the synthesis of these proteins while glucose has a strong inhibitory effect on this process. All subunits of the proteins mentioned above are in vitro translation products of poly (A)⁻-RNA (Steinmüller, Kaling, Zetsche 1983 Planta 159: 308-313). Both factors—light and glucose—exert their effects mainly by modulation of the level of translatable messenger RNA for these proteins. Under autotrophic growth conditions the level of translatable RuBPCase-, PC-, and APC-messenger RNA is high, whereas in the presence of glucose the level of these mRNAs is low or not detectable at all.     

Separation of Chlorophyll Degradation from Other Senescence Processes in Leaves of a Mutant Genotype of Meadow Fescue (Festuca pratensis L.)

Chlorophyll levels in l-cm sections of the youngest fully expanded leaves of normal (Y) Festuca pratensis L. declined almost to zero over a period of 6 days after excision. Chlorophyll in a mutant genotype (NY) remained near the initial level for the whole of this period. Abscisic acid promoted pigment loss in Y but had no significant effect on chlorophyll in NY. Kinetin retarded pigment loss in Y but was ineffective in NY. Other biochemical changes associated with leaf senescence—reduction in protein content and the appearance of novel isoenzymes of α-naphthyl acetate esterases—occurred in both genotypes. Abscisic acid accelerated protein breakdown, whereas kinetin inhibited the loss of protein in both genotypes. The mutation thus appears to be expressed as a highly specific lesion in pigment metabolism. We concluded that pigment breakdown, which is widely used as an index of leaf senescence, may not be an inevitable part of the aging process.     

Insights into RNA binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome

Cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. Among cisplatin targets, cellular RNAs remain the most poorly characterized molecules. Although cisplatin was shown to inactivate essential RNAs, including ribosomal, spliceosomal and telomeric RNAs, cisplatin binding sites in most RNA molecules are unknown, and therefore it remains challenging to study how modifications of RNA by cisplatin contributes to its toxicity. Here we report a 2.6Å-resolution X-ray structure of cisplatin-modified 70S ribosome, which describes cisplatin binding to the ribosome and provides the first nearly atomic model of cisplatin–RNA complex. We observe nine cisplatin molecules bound to the ribosome and reveal consensus structural features of the cisplatin-binding sites. Two of the cisplatin molecules modify conserved functional centers of the ribosome—the mRNA-channel and the GTPase center. In the mRNA-channel, cisplatin intercalates between the ribosome and the messenger RNA, suggesting that the observed inhibition of protein synthesis by cisplatin is caused by impaired mRNA-translocation. Our structure provides an insight into RNA targeting and inhibition by cisplatin, which can help predict cisplatin-binding sites in other cellular RNAs and design studies to elucidate a link between RNA modifications by cisplatin and cisplatin toxicity.     

Altered protein synthesis during in situ oat leaf senescence

Quantitative and qualitative changes in protein synthesis during in situ senescence of oat ( Avena saliva L. cv. Victory) leaf have been examined. The rate of protein synthesis shows a transitory increase during early stages of senescence. This increase is not accompanied by a corresponding increase in amino acid uptake and is smaller when expressed on a dry weight rather than a protein basis. Total protein, total RNA and poly(A)⁺-RNA decline rapidly during senescence. Analysis of protein populations with 2-D SDS-PAGE shows that while some proteins decline sharply during leaf senescence, the synthesis of several others is induced or enhanced. Synthesis of new proteins shown in this study may explain the reported requriement for protein synthesis in leaf senescence.     

Engineering the elongation factor Tu for efficient selenoprotein synthesis

Selenocysteine (Sec) is naturally co-translationally incorporated into proteins by recoding the UGA opal codon with a specialized elongation factor (SelB in bacteria) and an RNA structural signal (SECIS element). We have recently developed a SECIS-free selenoprotein synthesis system that site-specifically—using the UAG amber codon—inserts Sec depending on the elongation factor Tu (EF-Tu). Here, we describe the engineering of EF-Tu for improved selenoprotein synthesis. A Sec-specific selection system was established by expression of human protein O⁶-alkylguanine-DNA alkyltransferase (hAGT), in which the active site cysteine codon has been replaced by the UAG amber codon. The formed hAGT selenoprotein repairs the DNA damage caused by the methylating agent N-methyl-N′-nitro-N-nitrosoguanidine, and thereby enables Escherichia coli to grow in the presence of this mutagen. An EF-Tu library was created in which codons specifying the amino acid binding pocket were randomized. Selection was carried out for enhanced Sec incorporation into hAGT; the resulting EF-Tu variants contained highly conserved amino acid changes within members of the library. The improved UTu-system with EF-Sel1 raises the efficiency of UAG-specific Sec incorporation to >90%, and also doubles the yield of selenoprotein production.     

Black beetle virus: messenger for protein B is a subgenomic viral RNA

Black beetle virus induces the synthesis of three new proteins, protein A (molecular weight, 104,000), protein α (molecular weight, 47,000), and protein B (molecular weight, 10,000), in infected Drosophila cells. Two of these proteins, A and α, are known to be encoded by black beetle virus RNAs 1 and 2, respectively, extracted from virions. We found that RNA extracted from infected cells directed the synthesis of all three proteins when it was added to a cell-free protein-synthesizing system. When polysomal RNA was fractionated on a sucrose density gradient, the messengers for proteins A and α cosedimented with viral RNAs 1 (22S) and 2 (15S), respectively. However, the messenger for protein B was a 9S RNA (RNA 3) not found in purified virions. Like the synthesis of viral RNAs 1 and 2, intracellular synthesis of RNA 3 was not affected by the drug actinomycin D at concentrations which blocked synthesis of host cell RNA. This indicated that RNA 3 is a virus-specific subgenomic RNA and, therefore, that protein B is a virus-encoded protein.     

SENESCENCE: HORMONAL CONTROL OF RNA AND PROTEIN SYNTHESIS IN EXCISED BEAN POD TISSUE

The kinetics of degradation of RNA, total protein, ribosomal and soluble (R-S) protein and DNA were followed over 24 hours in excised segments of Kentucky Wonder pole beans (Phaseolus vulgaris). In absence of exogenous auxin, RNA degradation proceeded from about zero time. By 15 hours, after about 20% of the RNA had degraded, the degradation of DNA, total protein and R-S protein was initiated. Exogenous auxin (25 ppm α-napthaleneacetic acid) prevented these degradations. The addition of kinetin had little or no effect. Auxin enhanced incorporation of orotic acid into RNA two to several times more than it did amino acids into protein. Actinomycin D repressed RNA synthesis about 75% including a repression of auxin-induced synthesis. It had no effect on the basal level of protein synthesis but did repress auxin-induced synthesis. The results indicate that the primary action of auxin in preventing senescence of bean endocarp tissue is at the site of RNA synthesis, and the effect of auxin on DNA and protein is a consequence of the effect of auxin on RNA metabolism.