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Conformational heterogeneity in the Salmonella typhimurium pyrC and pyrD leader mRNAs produced in vivo.

In Salmonella typhimurium, different conformations of the pyrC and pyrD leader transcripts are produced as a result of nucleotide sensitive selection of the transcriptional start site. The CTP-initiated transcripts, synthesized at high intracellular CTP/GTP pool ratios (repressing conditions), have the potential of forming a stable secondary structure at the 5' end, thereby sequestering the site for translational initiation. At low CTP/GTP pool ratios (derepressing conditions), transcription starts 2-3 bp further downstream, resulting in transcripts with limited potential for stem-loop formation and therefore open for translational initiation. The conformation of the leader regions of wild type pyrC and pyrD mRNA has been investigated by chemical and enzymatic probing of RNA isolated from cultures grown in repressing and derepressing conditions. As controls and to obtain further information on the relation between the leader RNA conformation and the regulatory mechanism, the probing experiments also included pyrC and pyrD mRNA from mutants that contain a base substitution at a position that destabilizes the putative hairpin. In accordance with predictions based on the nucleotide sequence, the results showed that the 5' end of pyrC and pyrD leader mRNA isolated from repressed cultures is folded into a secondary structure, whereas it is largely unstructured in mRNA isolated from derepressed cultures.

Base Sequence↗

Cryptococcus neoformans gene expression during murine macrophage infection.

The fungal pathogen Cryptococcus neoformans survives phagocytosis by macrophages and proliferates within, ultimately establishing latent infection as a facultative intracellular pathogen that can escape macrophage control to cause disseminated disease. This process is hypothesized to be important for C. neoformans pathogenesis; however, it is poorly understood how C. neoformans adapts to and overcomes the hostile intracellular environment of the macrophage. Using DNA microarray technology, we have investigated the transcriptional response of C. neoformans to phagocytosis by murine macrophages. The expression profiles of several genes were verified using quantitative reverse transcription-PCR and a green fluorescent protein reporter strain. Multiple membrane transporters for hexoses, amino acids, and iron were up-regulated, as well as genes involved in responses to oxidative stress. Genes involved in autophagy, peroxisome function, and lipid metabolism were also induced. Interestingly, almost the entire mating type locus displayed increased expression 24 h after internalization, suggesting an intrinsic connection between infection and the MAT locus. Genes in the Gpa1-cyclic AMP-protein kinase A pathway were also up-regulated. Both gpa1 and pka1 mutants were found to be compromised in macrophage infection, confirming the important role of this virulence pathway. A large proportion of the repressed genes are involved in ribosome-related functions, rRNA processing, and translation initiation/elongation, implicating a reduction in translation as a central response to phagocytosis. In summary, this gene expression profile allows us to interpret the adaptation of C. neoformans to the intracellular infection process and informs the search for genes encoding novel virulence attributes.

Animals↗

Toxicological implications of enzymatic control of reactive metabolites.

Many foreign compounds are transformed into reactive metabolites, which may produce genotoxic effects by chemically altering critical biomolecules. Reactive metabolites are under the control of activating, inactivating and precursor sequestering enzymes. Such enzymes are under the long-term control of induction and repression, as well as the short-term control of post-translational modification and low molecular weight activators or inhibitors. In addition, the efficiency of these enzyme systems in preventing reactive metabolite-mediated toxicity is directed by their subcellular compartmentalization and isoenzymic multiplicity. Extrapolation from toxicological test systems to the human requires information of these variables in the system in question and in man. Differences in susceptibility to toxic challenges between species and individuals are often causally linked to differences in these control factors.

Base Sequence↗

Dynamical principles of two-component genetic oscillators.

Genetic oscillators based on the interaction of a small set of molecular components have been shown to be involved in the regulation of the cell cycle, the circadian rhythms, or the response of several signaling pathways. Uncovering the functional properties of such oscillators then becomes important for the understanding of these cellular processes and for the characterization of fundamental properties of more complex clocks. Here, we show how the dynamics of a minimal two-component oscillator is drastically affected by its genetic implementation. We consider a repressor and activator element combined in a simple logical motif. While activation is always exerted at the transcriptional level, repression is alternatively operating at the transcriptional (Design I) or post-translational (Design II) level. These designs display differences on basic oscillatory features and on their behavior with respect to molecular noise or entrainment by periodic signals. In particular, Design I induces oscillations with large activator amplitudes and arbitrarily small frequencies, and acts as an "integrator" of external stimuli, while Design II shows emergence of oscillations with finite, and less variable, frequencies and smaller amplitudes, and detects better frequency-encoded signals ("resonator"). Similar types of stimulus response are observed in neurons, and thus this work enables us to connect very different biological contexts. These dynamical principles are relevant for the characterization of the physiological roles of simple oscillator motifs, the understanding of core machineries of complex clocks, and the bio-engineering of synthetic oscillatory circuits.

Animals↗

Plasticity in the entorhinal cortex suppresses memory for contextual fear.

Several studies have delineated a role for the hippocampus in fear conditioning. However, in this task, the role of the entorhinal cortex (EC), the main input-output structure for the hippocampus, is uncertain. The extracellular signal-regulated kinase (ERK) cascade has been shown to be a molecular correlate for long-term memory, and its activity is required for various types of memory storage, including fear memory. In this study, we show that ERK activity in the EC increased 90 min after fear conditioning. Post-training intra-EC infusion of ERK cascade inhibitors (PD098059, UO126) at 40 min, but not at 10 min, resulted in increased freezing to the context, but not to the tone, during a 48 hr retention test. Interestingly, both PD098059- and UO126-infused animals also demonstrated anticipatory freezing in the context, freezing maximally at the time the shock was given during training. This anticipatory behavior was also seen in naive animals receiving additional training. Together, these results suggest that ERK-mediated plasticity in the EC normally suppresses context-specific fear memory, especially the temporal nature of the freezing response, and that blocking this plasticity mimics the effects of additional training.

Animals↗

Actual targets in cytodifferentiation cancer therapy.

Transformation of a normal cell into a tumor cell results from six essential alterations in cell physiology. There is a complex relationship that exists between growth, differentiation, neoplastic transformation, and the expression of genes and tumor suppressor genes. The knowledge of these mechanisms demonstrates that it is possible to pharmacologically modulate the growth and differentiation of tumor cells. The differentiation therapy focuses on demonstrating that cancer is a reversible state with altered maturation in which the transformed phenotype may be suppressed by cytostatic agents and by the pharmacological differentiation towards benign forms with no proliferative potential. One of the mechanisms determining the activity of target genes is the post-translational modification of the N-terminal tails of core histones. Inappropriate repression of genes required for cell differentiation has been linked to several forms of cancer. Histone deacetylase inhibitors modulate transcription, and are endowed with cytodifferentiating, antiproliferative and apoptogenic properties. Retinoids modulate cell differentiation, proliferation, apoptosis and morphogenesis in vertebrates, and have proved to be clinically useful. Their biological effects are mediated by the activation of retinoic acid receptors, which are ligand-dependent gene transcription factors. Checkpoints during cell cycle allow the cell to respond to proliferation signals or decide between the alternate pathways leading to cytokinesis, differentiation, quiescence, and cell death. Abrogation of normal cell cycle controls in tumor cells contributes to their inability to differentiate and the restoration of such controls in G1 can lead to the resumption of differentiation and terminal cell division. Chemical inhibitors of cyclin-dependent kinases have been reported to stimulate differentiation of tumor-cell lines.

Animals↗

UCN-01 suppresses E2F-1 mediated by ubiquitin-proteasome-dependent degradation.

E2F-1 regulates the transcription of genes required for DNA synthesis. Previously, we have reported that UCN-01 suppresses E2F-1 protein expression without any noticeable effect on its mRNA level in gastric cancer cell line SK-GT5 (Clin. Cancer Res., 4: 2201-2206, 1998). In this study, we investigated the mechanism responsible for the suppression of E2F-1 expression by UCN-01 in SK-GT5 cells. After 24-h exposure to 1 microM UCN-01, E2F-1 protein expression was decreased by >99%. The suppressive effect of UCN-01 could be reversed by ubiquitin-dependent proteasome inhibitors such as calpain inhibitor I and lactacystin. Transfection experiments using expression plasmids encoding full-length E2F-1 or truncated E2F-1 with deletion of the COOH-terminal region (which is required for eliciting ubiquitination and protein degradation) revealed that the expression of truncated E2F-1 was not affected by UCN-01. Other cell-cycle-related and ubiquitin-proteasome-regulated proteins such as p21, p27, and cyclin B1 were not repressed by UCN-01 in E2F-1-overexpressing cells. In vitro-translated, full-length E2F-1 degraded more rapidly upon incubation with extracts from UCN-01-treated cells when compared with truncated E2F-1. Taken together, these data indicate that UCN-01 suppresses E2F-1 protein expression mediated by the ubiquitin-proteasome pathway in a specific manner.

Acetylcysteine↗

Oxi4503, a novel vascular targeting agent: effects on blood flow and antitumor activity in comparison to combretastatin A-4 phosphate.

Oxi4503, which is the diphosphate prodrug of combretastatin A1, is a novel vascular targeting agent from the combretastatin family. Another member of this family, Combretastatin A-4 phosphate (CA4P), is a well-characterized vascular targeting agent already being evaluated in clinical trials. The potential for tumor vascular targeting by Oxi4503 was assessed in a mouse system. This approach aims to shut down the established tumor vasculature, leading to the development of extensive tumor cell necrosis. The vascular effects of Oxi4503 were assessed in the s.c. implanted MDA-MB-231 adenocarcinoma and the MHEC5-T hemangio-endothelioma in SCID mice and in a range of normal tissues. Blood flow was measured by i.v. injection of fluorescence beads, while quantitative fluorescence microscopy was used to measure the spatial heterogeneity of blood flow in tumor sections. Oxi4503 induced the shutdown of tumor blood vessels in a dose-dependent pattern with an ED50 at 3 mg/kg in contrast to 43 mg/kg of CA4P. Quantitative fluorescence microscopy showed that Oxi4503 increased the spatial heterogeneity in tumor blood flow. Oxi4503 affected peripheral tumor regions less than central regions, although this was not as pronounced as seen with CA4P, where only central regions were affected. The vascular shutdown induced by administration of Oxi4503 at a dose of 6 mg/kg resulted in extensive cell loss 24 hours following treatment, which translated into a significant effect on tumor growth. Tumor growth was completely repressed at doses above 12.5 mg/kg of Oxi4503, while doses above 25 mg/kg showed tumor regression and even complete regression in some animals. These results are promising for the use of Oxi4503 as a tumor vascular targeting agent. Moreover the potent antitumor effect when administered as a single agent suggests a different activity profile than CA4P.

Adenocarcinoma↗

Transcriptional mapping of a DNA replication gene cluster in bacteriophage T4. Sites for initiation, termination, and mRNA processing.

A phage T4 genetic cluster that encodes DNA polymerase, several other DNA replication proteins, transcriptional factors, and the translation repressor RegA has been shown to be controlled by overlapping modes of transcription which initiate at several promoters. The promoters were mapped by using a combination of assays including Northern blotting, S1-mapping, RNA sequencing, and analysis of products of radioactive labeling of 5' ends on T4-induced RNA in vitro via the reaction catalyzed by eukaryotic guanylyl transferase (RNA capping assay). The most proximal in the cluster are two promoters that do not require any phage-induced factors for activation, i.e. they are T4 early promoters. Initiation at these promoters yields several RNA species having overlapping 5'-terminal sequences, the largest of which is estimated to be about 15,000 nucleotides long and to include all the cistrons of the cluster. A third early promoter maps inside the protein encoding segment of one of the cistrons (T4 gene 47), while at least five additional promoters map in intercistronic regions and are T4 middle promoters, i.e. they require the T4-induced DNA-binding transcription factor MotA. Transcriptional readthrough at a termination site within the T4 gene 45-44 intercistronic region is required for synthesis of gp44 and gp62, two essential T4 DNA-polymerase (gp43) accessory proteins. In contrast, transcription of T4 gene 43 is serviced by readthrough across a termination site in the regA-43 intercistronic region as well as by a MotA-dependent promoter that maps downstream of the termination site, and the region contains a site for processing by a T4-induced enzyme that also cleaves elsewhere in the polycistronic mRNA from the cluster (i.e. in the Shine-Dalgarno sequence of the gene 45.2 mRNA). The termination events in the gene 45-44 and regA-43 intercistronic regions both occur downstream of RNA stem-loop structures containing the sequence 5'CUUCGG3' in the loop segments. Transcription termination in the 78-base-pair regA-43 intercistronic region occurs about 60 nucleotides away from the gp43 initiator AUG, transcription initiation occurs at 38-40 nucleotides upstream from the AUG, and T4-dependent RNA processing occurs at several sites (including a GGAG sequence) between the transcription termination and initiation sites. Thus, all gp43-encoding mRNAs contain the translational operator (residues -40 to -1 relative to the AUG) for autogenous repression by this DNA polymerase (Andrake et al., 1988).(ABSTRACT TRUNCATED AT 400 WORDS)

Base Sequence↗

Translational regulation of the synthesis of a major heat shock protein in HeLa cells.

The synthesis of a major heat shock protein (HSP 70) was measured in HeLa cells incubated at 42.5 degrees C and then transferred to 37 degrees C or 30 degrees C. After 90 min, synthesis of HSP 70 decreased by 54 and 85%, respectively, whereas HSP 70 mRNA was reduced at most by 20%. Therefore, the reduced synthesis of HSP 70 could not be accounted for by mRNA turnover. HSP 70 was associated with large polyribosomes (6-10 ribosomes) in cells kept at 42.5 degrees C, but with medium or small polyribosomes in cells transferred to 37 degrees C or 30 degrees C (5-6 or 2-3 ribosomes, respectively). Addition of puromycin to these cells resulted in the release of all ribosomes from HSP 70 mRNA, indicating that they were translationally active. The regulation of HSP 70 synthesis was investigated in cell-free systems prepared from heat-shocked or control cells and incubated at 30 degrees C and 42 degrees C. After 5 min at 42 degrees C, the cell-free system from heat-shocked cells synthesized protein at 3 times the rate of the control cell-free system. This difference was in large part due to synthesis of HSP 70. Addition of HSP mRNA to the control cell-free system stimulated protein synthesis at 42 degrees C, but not at 30 degrees C. These findings suggest that translation of HSP 70 mRNA is specifically promoted at high temperature and repressed during recovery from heat shock by regulatory mechanisms active at the level of initiation.

Cell-Free System↗

General control of arginine biosynthetic enzymes in Neurospora crassa.

The response of six amino acid synthetic enzymes, including four concerned with arginine synthesis, one with histidine synthesis and one with lysine synthesis, to conditions of histidine and arginine limitation and to exogenously provided amino acids is described in Neurospora crassa. The activities of all these enzymes increased in response to lowered levels of histidine or arginine, but showed little or no repression in wild-type cultures supplemented with casein hydrolysate. The activity of glucose-6-phosphate dehydrogenase (an enzyme not concerned with amino acid synthesis) remained unaffected by any of these conditions. In the case of the four arginine synthetic enzymes evidence is presented that suggests the "general' system implicated in the 'cross-pathway' response to histidine is also entirely responsible for the derepression occurring under conditions of arginine limitation. Further investigations into the control of one enzyme, ornithine carbamoyltransferase, are also reported. These show that the enzyme is stable, and suggest that its derepression in response to histidine limitation entails new protein synthesis and involves control at a stage prior to translation.

Arginine↗

The regulation of the Drosophila msl-2 gene reveals a function for Sex-lethal in translational control.

In Drosophila, dosage compensation occurs by increasing the transcription of the single male X chromosome. Four trans-acting factors encoded by the male-specific lethal genes are required for this process. Dosage compensation is restricted to males by the splicing regulator Sex-lethal, which functions to prevent the production of the MSL-2 protein in females by an unknown mechanism. In this report, we provide evidence that Sex-lethal acts synergistically through sequences in both the 5' and 3' untranslated regions of MSL-2 to mediate repression. We also provide evidence that the repression of MSL-2 is directly regulated by Sex-lethal at the level of translation.

Animals↗

Regulated phosphorylation and low abundance of HeLa cell initiation factor eIF-4F suggest a role in translational control. Heat shock effects on eIF-4F.

Initiation factor eIF-4F, a multiprotein cap binding protein complex, was purified from HeLa cells by m7G affinity chromatography and independently by phosphocellulose column chromatography. The m7G affinity-purified sample contains three major proteins, p220, eIF-4A, and p28 (also known as CBP-I or eIF-4E). The abundancies of these proteins are roughly 2, 10, and 0.8 X 10(6) molecules/cell, respectively. Two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the eIF-4F samples shows that p28 comprises two isoelectric variants, one of which labels with phosphate and disappears when samples are treated with alkaline phosphatase. The 45,000-dalton protein in eIF-4F appears to be identical to eIF-4A. The p220 subunit rarely produces discrete spots on two-dimensional gel electrophoresis; in purified samples it usually forms 3 closely spaced streaks. eIF-4F fractionated by phosphocellulose chromatography separates into forms containing either phosphorylated or unphosphorylated p28. However, both fractions possess similar specific activities in in vitro translation assays for eIF-4F activity. The phosphorylation of p28 decreases upon heat shock when protein synthesis is repressed. The correlation of dephosphorylation of p28 with the inhibition of protein synthesis and the relatively low abundance of the eIF-4F complex suggest that eIF-4F plays a role in the translational control of mRNA binding. Limitations of the in vitro assay system may account for the failure to detect phosphorylation-dependent activity differences.

Chromatography↗

The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene.

Expression of thrS, the gene encoding Escherichia coli threonyl-tRNA synthetase, is negatively autoregulated at the translational level. Regulation is due to the binding of threonyl-tRNA synthetase to its own mRNA at a site called the operator, located immediately upstream of the initiation codon. The present work investigates the relationship between regulation and mRNA degradation. We show that two regulatory mutations, which increase thrS expression, cause an increase in the steady-state mRNA concentration. Unexpectedly, however, the half-life of thrS mRNA in the derepressed mutants is equal to that of the wild-type, indicating that mRNA stability is independent of the repression level. All our results can be explained if one assumes that thrS mRNA is either fully translated or immediately degraded. The immediately degraded RNAs are never detected due to their extremely short half-lives, while the fully translated messengers share the same half-lives, irrespective of the mutations. The increase in the steady-state level of thrS mRNA in the derepressed mutants is simply explained by an increase in the population of translated molecules, i.e. those never bound by the repressor, ThrRS. Despite this peculiarity, thrS mRNA degradation seems to follow the classical degradation pathway. Its stability is increased in a strain defective for RNase E, indicating that an endonucleolytic cleavage by this enzyme is the rate-limiting process in degradation. We also observe an accumulation of small fragments corresponding to the 5' end of the message in a strain defective for polynucleotide phosphorylase, indicating that, following the endonucleolytic cleavages, fragments are normally degraded by 3' to 5' exonucleolytic trimming. Although mRNA degradation was suspected to increase the efficiency of translational control based on several considerations, our results indicate that inhibition of mRNA degradation has no effect on the level of repression by ThrRS.

Endoribonucleases↗

Effect of inhibitors of S-adenosylmethionine decarboxylase on the contents of ornithine decarboxylase and S-adenosylmethionine decarboxylase in L1210 cells.

Treatment of L1210 cells with either of two inhibitors of S-adenosylmethionine decarboxylase (AdoMetDC), namely 5'-deoxy-5'-[N-methyl-N-[2-(amino-oxy)ethyl])aminoadenosine or 5'-deoxy-5'-[N-methyl-N-(3-hydrazinopropyl)]aminoadenosine, produced a large increase in the amount of ornithine decarboxylase (ODC) protein. The increased enzyme content was due to a decreased rate of degradation of the protein and to an increased rate of synthesis, but there was no change in its mRNA content. The inhibitors led to a substantial decline in the amounts of intracellular spermidine and spermine, but to a big increase in the amount of putrescine. These results indicate that the content of ODC is negatively regulated by spermidine and spermine at the levels of protein translation and turnover, but that putrescine is much less effective in bringing about this repression. Addition of either spermidine or spermine to the cells treated with the AdoMetDC inhibitors led to a decrease in ODC activity, indicating that either polyamine can bring about this effect, but spermidine produced effects at concentrations similar to those found in the control cells and appears to be the physiologically important regulator. The content of AdoMetDC protein (measured by radioimmunoassay) was also increased by these inhibitors, and a small increase in its mRNA content was observed, but this was insufficient to account for the increase in protein. A substantial stabilization of AdoMetDC occurred in these cells, contributing to the increased enzyme content, but an increase in the rate of translation cannot be ruled out.

Adenosine↗

Actin and creatine kinase mRNAs in rat levator ani and vastus muscles as a function of androgen status.

The plasticity of two selected mRNAs was studied in two typical fast-twitch muscles at different time intervals after orchiectomy (GDX). The levator ani muscle of the rat (LA) is exquisitely sensitive to androgens, whereas the superficial vastus lateralis (SVL) lacks such sensitivity. In vitro translation of RNA isolated from both tissues indicated that actin was among the most repressed proteins of the LA at day 10 postsurgery (GDX-10 days), whereas the template activity of the SVL mRNAs remains virtually unmodified. We used an available actin cDNA and demonstrated that the expression of the LA actin message is reduced by 85% in GDX-10 days and can be recovered after testosterone propionate (TP) injections (GDX + TP). In contrast, the actin expression in SVL remains constant up to day 20 postsurgery. In the LA, the expression of creatine kinase (CK) mRNA was increased 140% in GDX-5 days and decreased 34 and 17% in GDX-10 days and GDX-20 days, respectively, although the measured CK activity, as well as the in vitro translation of the message, remained elevated in those two latter groups. Control level of the CK mRNA expression was recovered in the GDX + TP group. Again, the expression of the message was unchanged in SVL, suggesting that the protein synthesis of this skeletal muscle is far less sensitive to androgen deprivation than that of the LA muscle.

Actins↗

Regulation of the nuclear-coded peptides of yeast cytochrome c oxidase.

We have analyzed the catabolite regulation of cytochrome oxidase by assaying changes in the synthesis of precursors of the nuclear-coded peptides (IV--VII) of cytochrome c oxidase in an in vitro reticulocyte cell-free system programmed with RNA isolated from cells grown in either glucose or raffinose. As a first step, we have characterized antibodies which bind to the precursors of subunits V and VI. Initial translation products for subunits IV and VII have also been tentatively identified by utilizing these antibodies. The messenger RNAs coding for the precursors of the nuclear-coded subunits fall in the expected size range of 8--15 S. Catabolite repression of the nuclear-coded oxidase peptides appears to be regulated by the abundance of their messenger RNAs. Translation of messenger RNA isolated from yeast cells grown on glucose indicates a coordinate and uniform increase in precursor synthesis during glucose derepression. In contrast, when RNA isolated from raffinose (derepressed) grown cells is used to direct cell-free translation, precursor abundance is high throughout growth, although the synthesis of some of the species changes in a complex pattern of ratio and abundance. These data indicate that the abundance of the messengers for the nuclear-coded precursors is regulated in a fashion dependent on the physiologic state of the cell.

Electron Transport Complex IV↗

Small cytoplasmic RNAs from human placental free mRNPs. Structure and their effect on in vitro protein synthesis.

A new family of small cytoplasmic RNA species (scRNAs) was found to be associated with human term-placental free messenger ribonucleoprotein particles (mRNPs). Placental scRNAs strongly inhibit translation of both homologous and heterologous mRNAs in a cell-free rabbit reticulocyte system. scRNAs could be resolved into at least four different RNA species. One of the RNA molecules, scRNA species 1, was the most potent protein synthesis inhibitor found among the placental scRNAs. The nucleotide sequence of the scRNA species 1 was determined. In spite of its short length, scRNA species 1 still exhibited a very strong inhibitory effect on the in vitro protein synthesis. scRNAs were found to be complexed with proteins in the form of scRNPs. Proteins of these complexes enhanced the inhibitory effect of scRNAs on in vitro translation. Experiments provided evidence that inhibition of in vitro protein synthesis by the scRNAs is not dependent upon mRNA concentration. However, inhibition can be overcome by increasing the ratio lysate/scRNAs, thus suggesting that scRNAs act on some essential component of the cell-free system. The degree of inhibition is decreased when scRNAs are added after the start of translation, suggesting that scRNAs (or scRNPs) interfere with the initiation stage of translation, probably acting on an initiation factor(s). Placental scRNAs are unique in their size, being smaller than other known scRNAs. Their association with free cytoplasmic repressed mRNPs in human placenta suggests that scRNAs play a role in the regulation of mRNP metabolism and, consequently, in the control of mRNA translation.

Base Sequence↗