A Viral microRNA Down-Regulates Multiple Cell Cycle Genes through mRNA 5′UTRs

Global gene expression data combined with bioinformatic analysis provides strong evidence that mammalian miRNAs mediate repression of gene expression primarily through binding sites within the 3′ untranslated region (UTR). Using RNA induced silencing complex immunoprecipitation (RISC-IP) techniques we have identified multiple cellular targets for a human cytomegalovirus (HCMV) miRNA, miR-US25-1. Strikingly, this miRNA binds target sites primarily within 5′UTRs, mediating significant reduction in gene expression. Intriguingly, many of the genes targeted by miR-US25-1 are associated with cell cycle control, including cyclin E2, BRCC3, EID1, MAPRE2, and CD147, suggesting that miR-US25-1 is targeting genes within a related pathway. Deletion of miR-US25-1 from HCMV results in over expression of cyclin E2 in the context of viral infection. Our studies demonstrate that a viral miRNA mediates translational repression of multiple cellular genes by targeting mRNA 5′UTRs.     

Identification of elements in human long 3′ UTRs that inhibit nonsense-mediated decay

The nonsense-mediated mRNA decay (NMD) pathway serves an important role in gene expression by targeting aberrant mRNAs that have acquired premature termination codons (PTCs) as well as a subset of normally processed endogenous mRNAs. One determinant for the targeting of mRNAs by NMD is the occurrence of translation termination distal to the poly(A) tail. Yet, a large subset of naturally occurring mRNAs contain long 3′ UTRs, many of which, according to global studies, are insensitive to NMD. This raises the possibility that such mRNAs have evolved mechanisms for NMD evasion. Here, we analyzed a set of human long 3′ UTR mRNAs and found that many are indeed resistant to NMD. By dissecting the 3′ UTR of one such mRNA, TRAM1 mRNA, we identified a cis element located within the first 200 nt that inhibits NMD when positioned in downstream proximity of the translation termination codon and is sufficient for repressing NMD of a heterologous reporter mRNA. Investigation of other NMD-evading long 3′ UTR mRNAs revealed a subset that, similar to TRAM1 mRNA, contains NMD-inhibiting cis elements in the first 200 nt. A smaller subset of long 3′ UTR mRNAs evades NMD by a different mechanism that appears to be independent of a termination-proximal cis element. Our study suggests that different mechanisms have evolved to ensure NMD evasion of human mRNAs with long 3′ UTRs.     

Distinct 5′ UTRs regulate XIAP expression under normal growth conditions and during cellular stress

X-chromosome linked inhibitor of apoptosis, XIAP, is cellular caspase inhibitor and a key regulator of apoptosis. We and others have previously shown that XIAP expression is regulated primarily at the level of protein synthesis; the 5′ untranslated region (UTR) of XIAP mRNA contains an Internal Ribosome Entry Site (IRES) that supports cap-independent expression of XIAP protein during conditions of pathophysiological stress, such as serum deprivation or gamma irradiation. Here, we show that XIAP is encoded by two distinct mRNAs that differ in their 5′ UTRs. We further show that the dominant, shorter, 5′ UTR promotes a basal level of XIAP expression under normal growth conditions. In contrast, the less abundant longer 5′ UTR contains an IRES and supports cap-independent translation during stress. Our data suggest that the combination of alternate regulatory regions and distinct translational initiation modes is critical in maintaining XIAP levels in response to cellular stress and may represent a general mechanism of cellular adaptation.     

Single mating type-specific genes and their 3′ UTRs control mating and fertility in Cochliobolus heterostrophus

To determine the number of proteins required for mating type (MAT) locus-regulated control of mating in Cochliobolus heterostrophus, MAT fragments of various sizes were expressed in MAT deletion strains. As little as 1.5?kb of MAT sequence, encoding a single unique protein in each mating type (MAT-1 and MAT-2), conferred mating ability, although an additional 160?bp of 3^′ UTR was needed for production of ascospores. No other mating type-specific genes involved in mating identity or fertility were found. Thus, although homologs of the C. heterostrophus MAT-1 and MAT-2 genes exist in the filamentous ascomycetes Neurospora crassa and Podospora anserina, C. heterostrophus does not appear to have mating type-specific homologs of two additional genes required by both N. crassa and P.?anserina for successful sexual reproduction. Three genes were identified in the common DNA flanking the MAT locus: a gene encoding a GTPase-activating protein and an ORF of unknown function lie 5^′ while a β-glucosidase encoding gene lies found 3^′. None of these genes appears to be involving in the mating process.     

Excretion of 5′-Nucleotides by Bacteria

A Bacillus accumulated 5′-nucleotides in the culture fluid during cultivation. These nucleotides consisted mainly of ribonucleoside 5′-monophosphates and of traces of nucleoside 5′-diphosphates. The composition of the accumulated nucleotides resembled that of the nucleotides of intracellular RNA. Therefore an intimate relationship between the accumulation of nucleotides and the metabolism of endogenous RNA was suggested.

The excretion of 5′-nucleotides into the culture fluid took place in parallel with the reduction of intracellular RNA, and it was presumed that the accumulated nucleotides were products of degradation of intracellular RNA.     

Single mating type-specific genes and their 3′ UTRs control mating and fertility in Cochliobolus heterostrophus

To determine the number of proteins required for mating type (MAT) locus-regulated control of mating in Cochliobolus heterostrophus, MAT fragments of various sizes were expressed in MAT deletion strains. As little as 1.5 kb of MAT sequence, encoding a single unique protein in each mating type (MAT-1 and MAT-2), conferred mating ability, although an additional 160 bp of 3^′ UTR was needed for production of ascospores. No other mating type-specific genes involved in mating identity or fertility were found. Thus, although homologs of the C. heterostrophus MAT-1 and MAT-2 genes exist in the filamentous ascomycetes Neurospora crassa and Podospora anserina, C. heterostrophus does not appear to have mating type-specific homologs of two additional genes required by both N. crassa and P.␣anserina for successful sexual reproduction. Three genes were identified in the common DNA flanking the MAT locus: a gene encoding a GTPase-activating protein and an ORF of unknown function lie 5^′ while a β-glucosidase encoding gene lies found 3^′. None of these genes appears to be involving in the mating process. Received: 21 November 1997 / Accepted: 28 April 1998     

5′-Phosphodiesterase Formation by Cultured Plant Cells

5′-Phosphodiesterase (5′-PDase) which degrades RNA to nucleoside-5′-monophosphates was investigated in various kinds of plant calli, and the calli of Vinca rosea and Phytolacca americana were found to have the high activity. The liquid culture conditions of the cells of V. rosea were examined. Three mg of kinetin and 0.5 mg of 2,4-dichlorophenoxyacetic acid per liter in the Murashige and Skoog medium were optimal for the growth and the 5′-PDase formation. Under the optimal conditions, time courses of the cell growth and the enzyme formation were measured.

The 5′-PDase of the cultured cells of V. rosea in suspension showed the maximal activity at pH 8.0 and 60°C. A comparison of 5′-PDase of the cultured cells and of the mother plant of V. rosea was carried out and it was found that the cultured cells had more than 30 times as much 5′-PDase activity as the mother plant on dry cell weight basis.     

Partial initiation of endomitosis by 3′-deoxyadenosine

3-deoxyadenosine, applied to meristematic populations, proves to be a drug which causes an accumulation of cells in the prophase. Analysing its effects, we find that cells in prophase continue to go through their chromosome cycle and thus that the specific effect of the drug is to block the rupture of the nuclear membrane, giving rise to a process of endomitosis in the cells treated. If the drug is applied to synchronous, labelled cells, analysis of its effects reveals that they occur at the prophase level, while the remaining stages of mitosis, if not arrested in the prophase, proceed normally.The data here brought forward as to the effects of 3-deoxyadenosine, like those relating to the effects of other drugs which block RNA synthesis at the prophase level, suggest that this stage in the cell division cycle is of great importance in the evolution of the mitotic process.     

Inhibition of a novel subspecies of DNA polymerase α by 2′-deoxy-2′-azidoadenosine 5′-triphosphate

DNA polymerase α₁, a subspecies of DNA polymerase α of Ehrlich ascites tumor cells, was associated with a novel RNA polymerase activity and utilized poly(dT) and single-stranded circular fd DNA as a template without added primer in the presence of ribonucleoside triphosphates and a specific stimulating factor. DNA synthesis in the above system was inhibited by the ATP analogue, 2′-deoxy-2′-azidoadenosine 5′-triphosphate more than the DNA synthesis with poly(dT)·oligo(rA) by DNA polymerase α₁ and RNA synthesis by mouse RNA polymerases I and II. Kinetic analysis showed that the analogue inhibited DNA polymerase α₁ activity on poly(dT) competitively with respect to ATP, suggesting that the analogue inhibited RNA synthesis by the associated RNA polymerase activity.     

Metabolism of ribosylzeatin-5′-monophosphate by soybean callus

Using cytokinin dependent soybean callus and HPLC analysis it was shown that soybean callus rapidly metabolises ribosylzeatin-5-monophosphate to biologically active compounds which co-chromatographed with trans-ribosylzeatin and trans-zeatin.Abbreviations Z zeatin - RZ ribosylzeatin - RZMP ribosylzeatin-5-monophosphate     

Gastrodin Attenuates Cognitive Deficits Induced by 3,3′-Iminodipropionitrile

3,3′-Iminodipropionitrile (IDPN), one of the nitrile derivatives, can induce persistent neurotoxicity, and therefore cause dyskinesia and cognitive impairments. Gastrodin, a main bioactive ingredient of Gastrodia elata Blume, is shown to greatly improve cognitive function. The aim of this study was to further determine whether administration of gastrodin can ameliorate IDPN-induced cognitive deficits in the Morris water maze (MWM) and novel object recognition (NOR) task, and to explore the underlying mechanisms. Results showed that exposure to IDPN (100 mg/kg/day, for 8 days) significantly impaired spatial and object recognition memory and that repeated treatment with gastrodin (150 mg/kg/day, for 6 weeks) could effectively alleviate the IDPN-induced cognitive impairments as indicated by increased spatial memory and discrimination ratio in the MWM and NOR tests. Gastrodin treatment also reverted IDPN-induced decreases of γ-aminobutyric acid (GABA) levels and increases of a2 GABA_A receptor protein expression in the prefrontal cortex and hippocampus of IDPN-treated rats. These results suggest that gastrodin treatment may provide a novel pharmacological strategy for IDPN-induced cognitive deficits, which was mediated, at least in part, by normalizing the GABAergic system.

     

3′-modified nucleotides: Substrate recognition by phosphohydrolases

Analogs of thymidine-5′-monophosphate, thymidine-5′-monophosphate-p-nitrophenylester, and adenosine-5′-monophosphate with an amino or azido group in the 3′-position have been synthesized by convenient methods. These compounds were tested as substrates for acid phosphatase from potatoes (EC 3.1.3.27), 5′-nucleotidase from snake venom (EC 3.1.3.5), alkaline phosphatase from calf intestine (EC 3.1.3.1), and phosphodiesterase from snake venom (EC 3.1.4.1). The influence of the modification was found to increase with the higher specificity of the enzymes (thus, e.g., 5′-nucleotidase does not accept the 3′-modified thymidine derivatives).     

Synthesis of 2′-deoxythymidine by an enzymatic transdeoyrinosylation

Summary 2-Deoxythymidine was synthesized by an enzymatic transdeoxyribosylation of thymine using either (i) dGuo, dCyd or dAdo, or (ii) the mixture of the same 2-deoxynucleosides resulting from enzymatic hydrolysis of DNA as donors of 2-deoxyribofuranose moiety.