HETEROGENEITY OF SENESCENT RIBOSOME COMPLEX AFFECTS THE TRANSLATIONAL EFFICIENCY OF SENESCENCE RELATED MRNAS

The ribosome, a protein factory, has a lateral stalk known as the ribosomal P complex made up of rpLP0, rpLP1, and rpLP2. It plays an important role in translation by recruiting translational factors. One of these proteins, rpLP2, was decreased in translating ribosome when cellular senescence was induced. Additionally, Y-box binding protein-1 (YB-1), a multifunctional protein that regulates the transcription and translation, was also reduced in polysomal fraction of senescent cells. We have discovered that rpLP2 depletion in heterogeneous ribosome causes the detachment of YB-1 in polysomes and link to cellular senescence. Here, we also have found that a decrement of CK2α or GRK2 on senescent cells induced an increment of unphosphorylated rpLP2, resulting in the release of YB-1 from a ribosome complex. The heterogeneous senescent ribosome has different translational efficiency for some senescence related genes such as AHR, RAB27B, FEZ1, and DDIT4. Our results revealed that the decrease of rpLP1/rpLP2 and YB-1 in translating senescent ribosomes is not specific to cell type or stress type. Furthermore, the same phenomenon was observed in aged mouse liver. Taken together, our results suggest that the senescent ribosome complex appears to have low levels of rpLP1/ rpLP2 and YB-1, resulting in the alteration of translational efficiency for senescence related genes. (Journals of Gerontology: Biological Sciences, 2019 in press)

NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated

As the most common RNA cap in eukaryotes, the 7-methylguanosine (m7G) cap impacts nearly all processes that a messenger RNA undergoes, such as splicing, polyadenylation, nuclear export, translation, and degradation. The metabolite and redox agent, nicotinamide adenine diphosphate (NAD+), can be used as an initiating nucleotide in RNA synthesis to result in NAD+-capped RNAs. Such RNAs have been identified in bacteria, yeast, and human cells, but it is not known whether they exist in plant transcriptomes. The functions of the NAD+ cap in RNA metabolism or translation are still poorly understood. Here, through NAD captureSeq, we show that NAD+-capped RNAs are widespread in Arabidopsis thaliana. NAD+-capped RNAs are predominantly messenger RNAs encoded by the nuclear and mitochondrial genomes, but not the chloroplast genome. NAD+-capped transcripts from the nuclear genome appear to be spliced and polyadenylated. Furthermore, although NAD+-capped transcripts constitute a small proportion of the total transcript pool from any gene, they are enriched in the polysomal fraction and associate with translating ribosomes. Our findings implicate the existence of as yet unknown mechanisms whereby the RNA NAD+ cap interfaces with RNA metabolic processes as well as translation initiation. More importantly, our findings suggest that cellular metabolic and/or redox states may influence, or be regulated by, mRNA NAD+ capping.

Gene expression changes after heat shock of procyclic-form Trypanosoma brucei suggest that stress has a role in differentiation to mammalian-infective forms

Trypanosome procyclic forms multiply in the midgut of Tsetse flies, and are routinely cultured at 27°C. Heat shocks of 37°C and above result in general inhibition of translation, and severe heat shock (41°C) results in sequestration of mRNA in granules. The mRNAs that are bound by the zinc-finger protein ZC3H11, including those encoding refolding chaperones, escape heat-induced translation inhibition.a At 27°C, ZC3H11 mRNA is predominantly present as an untranslated cytosolic messenger ribonucleoprotein particle, but after heat shocks of 37°C - 41°C, the ZC3H11 mRNA moves into the polysomal fraction. To investigate the scope and specificities of heat-shock translational regulation and granule formation, we analysed the distributions of mRNAs on polysomes at 27C and after 1 hour at 39°C, and the mRNA content of 41°C heat shocks granules. We found that that mRNAs that bind to ZC3H11 remained in polysomes at 39°C and were protected from sequestration in granules at 41°C. As previously seen for starvation stress granules, the mRNAs that encode ribosomal proteins were excluded from heat-shock granules. Seventy mRNAs moved towards the polysomal fraction after the 39°C heat shock; surprisingly, many of these are also increased when trypanosomes migrate to the Tsetse salivary glands. It therefore seems possible that in the wild, temperature changes due to diurnal variations and periodic intake of warm blood might influence the efficiency with which procyclic forms develop into mammalian-infective formsAuthor summaryWhen trypanosomes are inside tsetse flies, they have to cope with temperature variations from below 20°C up to nearly 40°C, due to diurnal variations and periodic intake of warm blood. The procyclic forms, which usually multiply in the midgut, are routinely cultured at 27°C in the laboratory. When they are heated to temperatures of 37°C and above, they shut down protein production, and at 41°C, mRNAs aggregate into granules. We show here that quite a large number of mRNAs are not included in granules and continue to be used for making proteins. Some of the proteins that continue to be made are needed in order to defend the cells against the effects of heat shock. Interestingly, however, a moderate heat shock stimulates expression of genes needed for the parasites to develop further into forms that can colonise the salivary glands. It thus seems possible that in the field, temperature variations might influence the efficiency with which of trypanosomes in tsetse flies become infective for mammals.

Butyrate increases the efficiency of translation of γ-globin mRNA

Fetal hemoglobin (Hb F) levels increase in most patients with sickle cell disease following intermittent butyrate therapy. Although the full effects of butyrate on Hb F levels usually require multiple treatment cycles, in some patients a peak level is achieved after a few days of butyrate therapy. Our investigation of the mechanism(s) responsible for this rapid induction of Hb F by butyrate showed that reticulocyte γ-globin chain synthesis markedly increased within 24 hours of butyrate exposure, without concomitant changes in reticulocyte γ-globin mRNA levels. This suggests that butyrate might induce Hb F by increasing the efficiency of translation of γ-globin mRNA. This hypothesis was confirmed by ribosome loading studies that demonstrated enrichment of the polysomal fraction of reticulocytes with γ-globin mRNA following butyrate exposure. Thus, the induction of Hb F by butyrate may be mediated by translational effects in addition to its well-known effects on transcription of the γ-globin genes. (Blood. 2005;105:1807-1809)

Mechanical activity in heart regulates translation of α-myosin heavy chain mRNA but not its localization

Mechanical inactivity depresses protein expression in cardiac muscle tissue and results in atrophy. We explore the mechanical transduction mechanism in spontaneously beating neonatal rat cardiomyocytes expressing the α-myosin heavy chain (α-MyHC) isoform by interfering with cross-bridge function [2,3-butanedione monoxime (BDM), 7.5 mM] without affecting cell calcium. The polysome content and α-MyHC mRNA levels in fractions from a sucrose gradient were analyzed. BDM treatment blocked translation at initiation (162 ± 12% in the nonpolysomal RNA fraction and 43 ± 6% in the polysomal fraction, relative to control as 100%; P < 0.05). There was an increase in α-MyHC mRNA from the nonpolysomal fraction (120.5 ± 7.7%; P < 0.05 compared with control) with no significant change in the heavy polysomes. In situ hybridization of α-MyHC mRNA was used to estimate message abundance as a function of the distance from the nucleus. The mRNA was dispersed through the cytoplasm in spontaneously beating cells as well as in BDM-treated cells (no significant difference). We conclude that direct inhibition of contractile machinery, but not calcium, regulates initiation of α-MyHC mRNA translation. However, calcium, not pure mechanical signals, appears to be important for message localization.

Xenopus cyclin E, a nuclear phosphoprotein, accumulates when oocytes gain the ability to initiate DNA replication

The capacity to initiate DNA replication appears during oocyte maturation in Xenopus. Initiation of S phase is driven by several components which include active cyclin/cdk complexes. We have identified three Xenopus cyclin E clones showing 59% amino acid identity with human cyclin E. The recruitment of cyclin E mRNA, like cdk2 mRNA, into the polysomal fraction during oocyte maturation, results in the accumulation of the corresponding proteins in unfertilized eggs. Cyclin E mRNA remains polyadenylated during cleavage and anti-cyclin E antibodies detect Xlcyclin E in embryonic nuclei at this time. Cdk2 protein is necessary for the phosphorylation of radiolabelled cyclin E added to egg extracts. Radiolabelled Xlcyclin E enters interphase nuclei and, though stable through interphase and mitosis, is not associated with condensed mitotic chromatin. In egg extracts, endogenous Xlcyclin E rapidly associates with nuclei before S phase and remains nuclear throughout interphase, becoming nucleoplasmic in G2/prophase. Under conditions where initiation of replication is limiting in extracts, Xlcyclin E associates only with those nuclei that undergo S phase. These features are entirely consistent with the view that Xlcyclin E is required for initiation of S phase.

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.

Increased preproenkephalin A gene expression in the rat heart after induction of a myocardial infarction

The expression of preproenkephalin A (ppENK) gene was investigated in the rat heart, following the onset of myocardial infarction induced by ligation of the left anterior descending coronary artery. The relative abundance of ppENK mRNA and the level of enkephalins were measured by Northern blot analysis and radioimmunoassay, respectively, in the ventricles from control-unoperated, sham-operated, and operated rats. Three hours after the surgery, a comparison between rats with infarction and sham-operated rats revealed that the relative abundance of ppENK mRNA and the level of enkephalins were increased three- to four- and two- to three-fold, respectively, in the ventricles of rats with infarction. No difference was observed between rats with infarction and sham-operated rats 24 h after the surgery, or between rats with infarction compared at time intervals of 3 and 24 h following the surgery. The abundance of the ppENK mRNA in the polysomal fraction of the ventricular septum was also measured 3 h after the surgery and found to be threefold higher in rats with infarction as compared with sham-operated rats. These results indicate that the level of enkephalins rapidly increases in the ventricles of rats following myocardial infarction, and that this higher level may be ascribed to a stimulation of the local synthesis of enkephalins.Key words: preproenkephalin A, enkephalins, gene expression, myocardial infarction.

Utilization of cytoplasmic poly(A)+RNA for protein synthesis in preimplantation mouse embryos

The distribution of cytoplasmic poly(A)+RNA between subribosomal (&lt;80S) and ribosomal/polysomal (≥80S) ribonucleoprotein particles has been investigated in mouse morulae and blastocysts. After labelling for 24h with 3[5,6-3H]undine, late morulae (96h post-hCG), early blastocysts (100h post-hCG), or late blastocysts (120h post-hCG) were homogenized in detergent buffer, and 11000 g supernatants were prepared and centrifuged through 15–40% sucrose gradients. Poly(A)+RNA was isolated from the appropriate gradient fractions by affinity chromatography. In late morulae beginning to undergo cavitation, poly(A)+RNA was evenly distributed between the two types of RNP particles whereas it was almost entirely in the ribosomal/polysomal fraction in early and late blastocysts. The sedimentation profile (in 5–20% sucrose gradients) of poly(A)+RNA from the ribosomal/polysomal fraction of late morulae and blastocysts was the same, with a range of 4S to greater than 28S and a modal peak slightly smaller than 18S. Roughly 75% of this RNA was judged to be functional mRNA based on the EDTA sensitivity of the RNP particles containing it. Poly(A)+RNA from the subribosomal fraction of late morulae displayed a similar range of sedimentation values, but was enriched for a component sedimenting at 6–7S. These results demonstrate that the subcellular distribution of poly(A)+RNA shifts as cavitation begins, with the decline of the non-translating, subribosomal fraction. Although most of this fraction in late morulae is probably too small to constitute translatable mRNA, the remainder may represent a reserve available for recruitment into polyribosomes to support blastocyst expansion. Since little non-translating mRNA exists in blastocysts, the increasing rate of protein synthesis during blastocyst expansion must be driven by mRNA accumulation and/or stabilization.