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PubMed1983

The lethal effect of a plasmid resulting from transcriptional readthrough of rplJ from the rplKA operon in Escherichia coli.

A high-copy plasmid, pGA217, which carries a deletion (lacking the carboxy-terminal 20 amino acids) of the structural gene for ribosomal protein L10 (rplJ) is lethal to the cell in the absence of the gene (rplL) for r-proteins L7/L12, but only if the upstream operon for r-proteins L11 (rplK) and L1 (rplA) is present on the same plasmid. Measurements of beta-galactosidase activity of a hybrid protein expressed by a rplL-lacZ fusion indicated that the L10 fragment peptide which lacks the carboxy-terminal 20 amino acids is capable of exerting feedback regulation. Double transformation experiments with two compatible plasmids showed that the detrimental effect of the rplJ deletion on pGA217 can be reversed by the addition of a second plasmid which carries a functional gene for L7/L12. These two pieces of evidence suggest that the lethal effect of pGA217 is due to its property of feeding back on L7/L12 production from the chromosomal rplK gene. The upstream rplKA operon was inferred to have a cis-acting, stimulating effect on rplJ expression from the following evidence: (1) donor plasmids carrying the genes for L11 and/or L1 fail to exert a trans-acting effect, (2) deletion mutants which removed portions of rplK and/or rplA, but maintained the rplKA promoter, rplKp, still retained a severe growth-inhibiting effect. We suggest that these results can be explained by assuming that there is transcription from the rplKA promoter through rplJ and perhaps beyond.

Chromosome Deletion↗

PubMed1997

A conditional-lethal translation termination defect in a sup45 mutant of the yeast Saccharomyces cerevisiae.

Genetic studies have indicated that the product of the yeast SUP45 gene encodes a component of the translational-termination machinery. In higher eukaryotes, genes similar to SUP45 encode eukaryote release factor 1 (eRF1), which has a stop-codon-dependent peptidyl-release activity. Using a conditional-lethal mutant allele of SUP45 (sup45-2) and a combination of in vivo and in vitro approaches, we demonstrate that the product of the SUP45 gene (Sup45p or eRF1) is a factor required for translation termination in yeast. A homologous in vitro assay based on suppressor-tRNA-mediated readthrough of stop codons is used to show that a translating lysate from a sup45-2 mutant strain exhibits a termination defect when heated for short periods to greater than the non-permissive temperature (37 degrees C). This defect can be complemented with a purified preparation of Sup45p (eRF1) expressed in Eschericha coli. The termination defect in this strain appears to be due to an inability of the Sup45p protein to bind the ribosome, resulting in vivo in a reduced ability of Sup45p to release nascent polypeptides from the ribosome at the non-permissive temperature. Cell-free translation lysates from the sup45-2 strain do not show a defect in sense-codon translation at the non-permissive temperature. These data demonstrate that yeast eRF1 plays a role in translation termination and is functionally equivalent to its higher eukaryotic homologues.

Fungal Proteins↗

PubMed1997

Pheromone cCF10 and plasmid pCF10-encoded regulatory molecules act post-transcriptionally to activate expression of downstream conjugation functions.

Expression of aggregation protein Asc10 from the prgB gene of conjugative plasmid pCF10 in Enterococcus faecalis is induced by the peptide pheromone cCF10. Genes required for Asc10 production, prgQ and prgS, lie 3-5 kb upstream, but can function at much greater distances. The prgQ transcripts encode a pheromone inhibitor peptide (iCF10) at the extreme 5' end. Neither production of this peptide nor translation of the 5' end of prgQ transcripts was found to be necessary for prgB expression. Pheromone cCF10 is required to activate prgB expression, even in the absence of iCF10 production, and does not affect initiation of transcription. The prgS gene encodes a 10.5 kDa protein that appears to be required for translation of prgB, and a non-coding RNA at the 3' end of prgS may be required for readthrough of transcription to prgB from the prgQ promoter. Although the entire positive control region is transcribed constitutively from the prgQ promoter, translation of PrgS and transcriptional readthrough to prgB occur only after induction with pheromone. The combined data are consistent with a model in which the positive regulatory molecules and pheromone cCF10 activate prgB expression post-transcriptionally.

Bacterial Proteins↗

PubMed1988

Promoter occlusion during ribosomal RNA transcription.

The ability of RNA polymerase I to read through a promoter-bound transcription initiation factor (TIF) was assessed using a dimeric ribosomal RNA gene promoter. Transcription from the upstream promoter is unaffected by TIF bound to the downstream promoter; RNA polymerase I is freely able to read through DNA-bound TIF. In contrast, transcription from the downstream promoter is inhibited by the passage of RNA polymerase I. Readthrough by RNA polymerase I disrupts the downstream TIF-DNA complex, and alters the TIF footprint. A general function for sequences leading to transcription termination upstream of rRNA or other promoters may be the prevention of promoter occlusion in tandem arrays of genes.

Acanthamoeba↗

PubMed2004

Alternative polyadenylation of adeno-associated virus type 5 RNA within an internal intron is governed by both a downstream element within the intron 3' splice acceptor and an element upstream of the P41 initiation site.

Adeno-associated virus type 5 (AAV5) has a linear, single-stranded DNA genome of ca. 5 kb and an overlapping transcription profile featuring multiple promoters and a single intron in the center of the genome. Unlike the situation for the prototype AAV2, AAV5 RNAs transcribed from upstream promoters at map units 7 (P7) and 19 (P19), which encode the viral Rep proteins, are predominantly polyadenylated at a site within the intron [(pA)p]. RNAs generated from the AAV5 capsid gene promoter P41, which is only 78 nucleotides (nt) upstream of the intron donor, and 281 nt upstream of (pA)p, primarily readthrough (pA)p, are polyadenylated at a more distal site at the 3' end of the genome [(pA)d] and ultimately spliced. The intron contains the core sequences sufficient for polyadenylation at (pA)p, which is governed by a G/U-rich downstream element that overlaps with the intron 3' A2 splice acceptor. In addition, polyadenylation of P7- and P19-generated RNAs at (pA)p is influenced by an upstream element that lies 5' to the start of the P41 transcript. Our results also suggest that splicing and polyadenylation of P41-generated RNA can compete for the same pool of precursor pre-mRNA molecules. The cis-acting signals within the A2 3' splice site that govern polyadenylation and splicing of AAV5 RNAs must be optimized to program both (i) the levels of polyadenylation of P7- and P19-generated RNA at (pA)p required to generate the proper levels of the essential Rep proteins and (ii) the splicing of P41-generated RNAs to generate the proper ratio of capsid proteins during AAV5 infection.

3' Untranslated Regions↗

PubMed1998

Effect of cellular level of FliK on flagellar hook and filament assembly in Salmonella typhimurium.

Frameshift mutations in the fliK gene of Salmonella result in abnormal elongation of the hook and the failure to assemble filament (polyhook phenotype). Second-site suppressor mutations restore filament assembly, but the cells often remain defective in hook-length control (polyhook-filament phenotype). Where the suppressor mutations are intragenic, the second mutation restores the original frame, generating a region of frameshifted sequence, but restoring the natural C terminus. Some of these frameshifted sequences contain a UGA (opal) termination codon. These cells have few flagella and swarm poorly. We suspected that readthrough of UGA by tRNATrp might be the reason for the partial function. When the UGA codon was changed to the Trp codon UGG, flagellar assembly and function were restored to wild-type levels. Conversely, underexpression of the wild-type fliK gene, achieved by changing the sole Trp codon in the sequence (Trp271) to UGA, decreased both the number of flagella and the ability to swarm. These results validate the readthrough hypothesis and indicate that low levels of FliK sustain some degree of flagellation and motility. At low levels of FliK, most flagella had polyhooks. With increasing amounts, the morphology progressively changed to polyhook-filament, and eventually to wild-type hook-filament. When FliK was overproduced, the hook length was slightly shorter (46(+/-7) nm) than that of the wild-type strain (55(+/-9) nm). FliK levels were measured by immunoblotting. Wild-type levels were about 40 to 80 molecules/cell. FliK synthesized by UGA readthrough could be detected when overproduced from plasmid fliK-W271opal, and the levels indicated a probability of readthrough of 0.002 to 0.01. This value was used to estimate the cellular level of underexpressed FliK, which could partly restore function to a fliK mutant, at about 0.07 to 0.8 molecule/cell. These results suggest that FliK does not form a large structure in the cytoplasm and may function as a regulatory protein for protein export. A model for hook-length control is presented that involves feedback from the assembly point to the export apparatus.

Bacterial Proteins↗

PubMed1994

Immunodetection of the 33 K/92 K polymerase proteins in cymbidium ringspot virus-infected and in transgenic plant tissue extracts.

An antiserum was raised against the 33 K protein encoded by the 5' proximal gene of cymbidium ringspot tombusvirus RNA. This antiserum reacts specifically with the 33 K and 92 K proteins, which constitute the viral replicase, in CyRSV-infected Nicotiana benthamiana plants and in transgenic plants transformed with the full-length replicase gene. In inoculated leaves of infected plants, synthesis of the 33 K/92 K proteins stops ten days after inoculation, whereas in newly produced systemically infected leaves there was continuous production of these proteins. In transgenic plants, both proteins were detected showing that readthrough of the termination codon of the 33 K protein does not depend on the presence of the replicating virus. The subcellular localization of the 33 K/92 K proteins is similar in infected and transgenic plants. No correlation was found between the level of expression of integrated virus gene and level of resistance to the challenging virus.

Amino Acid Sequence↗

PubMed2000

Life in protein-rich environments: the relA-independent response of Streptococcus pyogenes to amino acid starvation.

Considering that group A streptococci are multiple auxotrophs that may encounter shortage of amino acids during specific stages of the infectious process, we studied their adaptive response to amino acid deprivation. We found that, in addition to the (p)ppGpp-mediated stringent response characterized previously, Streptococcus pyogenes exhibits a relA-independent response comprising transcriptional modulation of a specific subset of genes involved in pathogenesis. Genes/operons transcriptionally upregulated during starvation of both wild type and relA mutants included the two-component signal transduction system covRS, the positive regulator (ropB) of the pyrogenic exotoxin B gene, speB, the oligopeptide (opp) and dipeptide (dpp) permease systems and the pepB gene putatively involved in the intracellular processing of oligopeptides. Upregulation of covRS was accompanied by downregulation of ska, one of the target genes of the negative CovR regulator, and the net effect of amino acid starvation also favoured repression of speB. A significant feature of upregulated opp expression was stimulated readthrough transcription of the operon-internal oppA terminator, leading to increased mRNA levels for synthesis of the translocator complex relative to the substrate-binding protein. Based on these and previous results, a stimulus-response network is proposed that counteracts the stringent response and may enable the pathogen to mount a dynamic response to the protein-rich environment provided by its human host.

Amino Acids↗

PubMed1994

Cruciform structure of a DNA motif of parvovirus minute virus of mice (prototype strain) involved in the attenuation of gene expression.

It has previously been reported that the region between nucleotides 259 and 383 immediately downstream from the P4 early promoter of parvovirus minute virus of mice, prototype strain (MVMp) is responsible for transcriptional attenuation. Attenuation results from the premature pausing of RNA polymerase II within this sequence (designated to as att) and seems to depend on potential RNA secondary structure. To assess the attenuation capacity of att under near physiological conditions, the early transcription unit of MVMp was replaced by the chloramphenicol acetyltransferase reporter gene under control of the early P4 promoter, in the presence or absence of att. The resulting recombinant vectors were encapsidated in parvovirus particles and replicated in cells after co-infection with the wild-type virus. The att fragment reduced the rate of expression of the reporter gene by approximately threefold, confirming previously reported data from transfection experiments performed in the same cellular system. This attenuation factor is unexpectedly high, considering that the 'readthrough' fold of the nascent viral transcript is thermodynamically more stable than the 'attenuation' configuration. In an attempt to elucidate this point, we sought for the presence of secondary structures in the template DNA molecule. In vitro nuclease probing of viral dsDNA revealed that the att fragment had a cruciform configuration with both complementary strands folding into the computer-predicted stem-loop 'attenuation' structure. These observations lead us to propose that the secondary structure of the DNA template may prompt the formation of the 'attenuation' stem-loop in nascent mRNAs by bringing corresponding self-complementary sequences into close proximity.

Base Sequence↗

PubMed1983

Attenuation and modulation of mRNA secondary structure in a feedback control system regulating SV40 gene expression.

Alternative secondary structures can be predicted for the initial 94 nucleotides synthesized from the major transcription initiation site of SV40 late RNA: a transcription-termination conformation results in the production of aborted RNA and a readthrough conformation leads to the synthesis of the primary SV40 late RNA. In the cytoplasm similar alternative conformations can be predicted for the initial nucleotides at the 5' ends o both the major 16S and 19S late mRNAs. In one of these alternative conformations the AUG initiation codon of the leader protein (agnoprotein) is sequestered and not available for ribosome binding. In the alternative conformation the same AUG is accessible for ribosome binding. We suggest that these mutually exclusive conformations are fundamental elements in a transcription and translation feedback control mechanism regulating the synthesis of 16S and 19S mRNA in the nucleus and the translation of their encoded proteins in the cytoplasm.

Feedback↗

PubMed1990

pheAo mutants of Escherichia coli have a defective pheA attenuator.

Two classes of mutants affecting the regulation of pheA expression in Escherichia coli have been reported previously: trans-acting mutants involving the locus pheR, and cis-acting mutants involving the locus pheAo. The effects of these mutants have been found to be mediated through one regulatory mechanism. The gene pheR has been shown to encode tRNA(Phe) (Gavini, N., and Davidson, B. E. (1990) J. Biol. Chem. 265, 21527-21531). In this paper we report the cloning and nucleotide sequencing of the promoter-attenuator regions from two of the cis-acting mutants pheAo351 and pheAo352. Both pheAo351 and pheAo352 contained a G:C to A:T base pair transition, at different positions in the 3:4 stem of the pheA attenuator terminator. Since these changes would destabilize the G:C stem of the attenuator terminator we propose that the enhanced expression of pheA observed in the pheAo mutants is due to increased transcription readthrough at the defective attenuator terminator.

Amino Acid Sequence↗

PubMed1984

Topological repression of gene activity by a transposable element.

The ebgA (evolved beta-galactosidase) gene of Escherichia coli was isolated as part of a 9.6-kilobase (kb) sequence cloned into plasmid pBR322. The position of the ebgA gene within that 9.6-kilobase sequence was identified by insertional inactivation by means of the transposon gamma-delta. In addition to the gamma-delta insertions that inactivate ebgA by disrupting the coding sequence, seven additional gamma-delta insertions reduce expression of the gene by a factor of greater than 200 by insertions elsewhere into the replicon. One of these insertions is into the pBR322 sequence itself. This action at a distance to reduce expression requires that gamma-delta is cis with respect to the ebgA gene. The effect is independent of the orientation or position of gamma-delta within the replicon, but it does depend both upon the orientation of the ebgA-bearing sequence within the replicon and upon the total size of the replicon. Transcription readthrough (promoter occlusion) does not explain this phenomenon, and we suggest that the presence of gamma-delta may alter the local supercoiling in the region of the ebgA promoter in such a way as to inhibit transcription. This repression by a transposable element appears to represent a novel mechanism for altering gene expression.

DNA Restriction Enzymes↗

PubMed1989

Transcription of human ribosomal DNA may terminate at multiple sites.

The termination of human pre-rRNA transcription has been investigated. The most abundant possible termination site was detected 360 bp downstream from the 28S gene, in front of the first SalI box of the rDNA spacer. This site, however, is partially bypassed during transcription, and three additional termination points were detected inside the heterogeneous region of the rDNA spacer. Later sites were mapped about 930, 1030 and 1110 bp downstream from the 3' end of the 28S rRNA gene. The authors suggest that the T clusters and pyrimidine-rich regions play an important role in the termination processes. They either may influence the efficiency of the SalI boxes in terminating the synthesis of pre-rRNAs or may serve as independent signals for the fail-safe termination of readthrough transcripts. In both cases transcription of human rDNA ceases at multiple sites.

Animals↗

PubMed2005

Muscarinic modulations of neuronal anticholinesterase responses.

Anticholinesterases (antiChEs) are increasingly used for treating patients with neurodegenerative diseases, but the dependence of their effects on the integrity of cholinergic functions has not yet been analyzed at the molecular level. Here, we report that manipulation of muscarinic neurotransmission confers drastic changes on antiChE responses in the rat brain. In the brains of naïve, un-stressed rats, the irreversible organophosphate antiChE, diisopropylfluorophosphonate (DFP) induced post-treatment accumulation of catalytically active G1 monomers of acetylcholinesterase (AChE). Pre-treatment with the selective M1 muscarinic antagonist, pirenzepine, but not the general muscarinic antagonist, scopolamine, attenuated this G1 increase. DFP-enhanced AChE gene expression was accompanied by diverted splicing from the primary AChE-S mRNA variant, encoding G4 synaptic membrane AChE-S tetramers, to "readthrough" AChE-R mRNA, which encodes soluble G1 monomers. Both the mRNA increase and the shifted splicing were long lasting (>24 h) and common to the parietal cortex and hippocampal CA1 and CA3 neurons. Importantly, the splicing shift was maximal under DFP alone, as compared with sham-injected rats, and virtually preventable by pre-treatment with pirenzepine. In contrast, induction of AChE transcription was less dependent on muscarinic function, resulting in AChE-S but not AChE-R increases. Our findings demonstrate distinct regulation of the enhanced transcription and the alternative splicing reactions to antiChE treatment and shed new light on the differential responses to antiChEs of demented patients with increasingly impaired cholinergic neurotransmission.

Acetylcholinesterase↗

PubMed2000

Generation of a non-sporulating strain of Streptomyces coelicolor A3(2) by the manipulation of a developmentally controlled ftsZ promoter.

The differentiation of Streptomyces aerial hyphae into chains of unigenomic spores occurs through the synchronous formation of multiple FtsZ rings, leading to sporulation septa. We show here that developmental control of ftsZ transcription is required for sporulation in Streptomyces coelicolor A3(2). Three putative ftsZ promoters were detected in the ftsQ-ftsZ intergenic region. In addition, some readthrough from upstream promoter(s) contributed to ftsZ transcription. S1 nuclease protection assays and transcriptional fusions of the ftsZ promoter region to the egfp gene (for green fluorescent protein) provided evidence that ftsZ2p is a developmentally controlled promoter that is specifically upregulated in sporulating aerial hyphae. This upregulation required all the six early regulatory sporulation genes that were tested: whiA, B, G, H, I and J. The DNA sequence of the promoter indicated that it is not part of the developmental regulon that is controlled by the RNA polymerase sigma factor sigma(WhiG). A strain in which the ftsZ2p promoter was inactivated grew normally during vegetative growth and formed aerial mycelium, but was deficient in sporulation septation. Thus, ftsZ2p was dispensable for vegetative growth, but was required for the strain to make sufficient FtsZ to support developmentally controlled multiple cell divisions in aerial hyphae.

Bacterial Proteins↗

PubMed2002

Molecular biology of Borna disease virus and persistence.

Borna disease virus (BDV) causes central nervous system (CNS) disease that is frequently manifested by behavioral abnormalities. Recent evidence indicates that the natural host range and geographic distribution of BDV is wider than originally thought BDV has been molecularly characterized as a non-segmented, negative single-stranded (NNS) RNA virus. Its genome (ca 8.9 kb), the smallest among known NNS RNA viruses, has an organization similar to that of other members of the order Mononegavirales. BDV has the property, unique among known animal NNS RNA viruses, of a nuclear site for the replication and transcription of its genome. The nucleocytoplasmic transport of BDV macromolecules is an essential component of the life cycle of BDV. An overlap of transcription units and transcriptive signals, overlap of ORFs, transcriptional readthrough and RNA splicing regulate expression of the BDV compact genome. The concurrent use of such diversity of strategies for the regulation of virus gene expression is unique among known NNS RNA viruses. Moreover, BDV appears to have also an unusual assembly process. Based on its unique genetic and biological features, BDV is considered to be the prototypic member of a new virus family, Bornaviridae, within the order Mononegavirales. Therefore, the investigation of the molecular biology of BDV may provide new insights about the biology of mononegaviruses, which include important human pathogens.

Animals↗

PubMed2003

recX, a new SOS gene that is co-transcribed with the recA gene in Escherichia coli.

recX is a small open reading frame located downstream of recA that is conserved in many bacteria. In Escherichia coli, the recX gene (also named oraA) is a 501 bp open reading frame that encodes a predicted basic protein. Transcriptional analysis by Northern blots showed that in E. coli the recX gene is SOS-regulated. Primer extension data and transcriptional fusions indicate that recX transcription is down regulated with respect to recA by an intrinsic transcription terminator that is located between the recA and recX coding sequences. Despite the presence of this terminator, a recA-recX message resulting from transcriptional readthrough is detected at a level of 5-10% of the recA message. In addition, transcriptional/translational fusion experiments show that recX expression is further down regulated at the translational level reaching an estimated protein level about 500-fold lower than RecA. Strains in which the recX gene was disrupted were constructed by insertion of an antibiotic resistance cassette. The survival after UV irradiation, the spontaneous and UV-induced mutation rates were not significantly different in these recX strains compared to the corresponding wild type strain. Overexpression of RecA was shown to be lethal in a recX deletion strain in Pseudomonas aeruginosa [J. Bacteriol. 175 (1993) 2451], Mycobacterium tuberculosis [Mol. Microbiol. 30 (1998) 525] and Streptomyces lividans [J. Bacteriol. 182 (2000) 4005] suggesting that the recX gene may act as a regulator of recA. In contrast in E. coli, in a recX deletion strain, RecA overexpression is neither toxic nor is the expression of the recA(+) gene affected in a recX deletion strain at the basal level or after UV induction.

Bacterial Proteins↗

PubMed2006

Adaptive changes in acetylcholinesterase gene expression as mediators of recovery from chemical and biological insults.

Both organophosphate (OP) exposure and bacterial infection notably induce short- and long-term cholinergic responses. These span the central and peripheral nervous system, neuromuscular pathway and hematopoietic cells and involve over-expression of the "readthrough" variant of acetylcholinesterase, AChE-R, and its naturally cleavable C-terminal peptide ARP. However, the causal involvement of these changes with post-exposure recovery as opposed to apoptotic events remained to be demonstrated. Here, we report the establishment of stably transfected cell lines expressing catalytically active human "synaptic" AChE-S or AChE-R which are fully viable and non-apoptotic. In addition, intraperitoneally injected synthetic mouse ARP (mARP) elevated serum AChE levels post-paraoxon exposure. Moreover, mARP treatment ameliorated post-exposure increases in corticosterone and decreases in AChE gene expression and facilitated earlier retrieval of motor activity following both paraoxon and lipopolysaccharide (LPS) exposures. Our findings suggest a potential physiological role for overproduction of AChE-R and the ARP peptide following exposure to both chemical warfare agents and bacterial LPS.

Adaptation, Physiological↗