scholarly journals Bacteriophage P4 sut1: a mutation suppressing transcription termination

2007 ◽  
Vol 88 (3) ◽  
pp. 1041-1047
Author(s):  
Susanna Terzano ◽  
Ilaria Oliva ◽  
Francesca Forti ◽  
Claudia Sala ◽  
Francesca Magnoni ◽  
...  
Keyword(s):  
Stop Codon ◽  
Transcription Termination ◽  
Spontaneous Mutation ◽  
Wild Type ◽  
Stem Loop ◽  
Reading Frame ◽  
E Coli ◽  
Stem Loop Structure ◽  
Bacteriophage P4 ◽  
Sense Codon

In the Escherichia coli satellite phage P4, transcription starting from PLE is prevalently controlled via premature termination at several termination sites. We identified a spontaneous mutation, P4 sut1 (suppression of termination), in the natural stop codon of P4 orf151 that, by elongating translation, suppresses transcription termination at the downstream t151 site. Both the translational and the transcriptional profile of P4 sut1 differed from those of P4 wild-type. First of all, P4 sut1 did not express Orf151, but a higher molecular mass protein, compatible with the 303 codon open reading frame generated by the fusion of orf151, cnr and the intervening 138 nt. Moreover, after infection of E. coli, the mutant expressed a very low amount of the 1.3 and 1.7 kb transcripts originating at PLE and PLL promoters, respectively, and terminating at the intracistronic t151 site, whereas correspondingly higher amounts of the 4.1 and 4.5 kb RNAs arising from the same promoters and covering the entire operon were detected. Thus the sut1 mutation converts a natural stop codon into a sense codon, suppresses a natural intracistronic termination site and leads to overexpression of the downstream cnr and α genes. This correlates with the inability of P4 sut1 to propagate in the plasmid state. By cloning different P4 DNA fragments, we mapped the t151 transcription termination site within the 7633–7361 region between orf151 and gene cnr. A potential stem–loop structure, resembling the structure of a Rho-independent termination site, was predicted by mfold sequence analysis at 7414–7385.

scholarly journals The Bulged Nucleotide in the Escherichia coli Minimal Selenocysteine Insertion Sequence Participates in Interaction with SelB: a Genetic Approach

2000 ◽  
Vol 182 (22) ◽  
pp. 6302-6307 ◽  
Author(s):  
Chuang Li ◽  
Myriam Reches ◽  
Hanna Engelberg-Kulka
Keyword(s):  
Escherichia Coli ◽  
Insertion Sequence ◽  
Stop Codon ◽  
Loop Structure ◽  
Genetic Approach ◽  
Stem Loop ◽  
E Coli ◽  
Stem Loop Structure ◽  
Suppressor Mutations

ABSTRACT The UGA codon, which usually acts as a stop codon, can also direct the incorporation into a protein of the amino acid selenocysteine. This UGA decoding process requires acis-acting mRNA element called the selenocysteine insertion sequence (SECIS), which can form a stem-loop structure. InEscherichia coli, selenocysteine incorporation requires only the 17-nucleotide-long upper stem-loop structure of thefdhF SECIS. This structure carries a bulged nucleotide U at position 17. Here we asked whether the single bulged nucleotide located in the upper stem-loop structure of the E. coli fdhF SECIS is involved in the in vivo interaction with SelB. We used a genetic approach, generating and characterizingselB mutations that suppress mutations of the bulged nucleotide in the SECIS. All the selB suppressor mutations isolated were clustered in a region corresponding to 28 amino acids in the SelB C-terminal subdomain 4b. These selBsuppressor mutations were also found to suppress mutations in either the loop or the upper stem of the E. coli SECIS. Thus, the E. coli SECIS upper stem-loop structure can be considered a “single suppressible unit,” suggesting that there is some flexibility to the nature of the interaction between this element and SelB.

scholarly journals Widespread Distribution of a Group I Intron and Its Three Deletion Derivatives in the Lysin Gene of Streptococcus thermophilus Bacteriophages

2000 ◽  
Vol 74 (2) ◽  
pp. 611-618 ◽  
Author(s):  
Sophie Foley ◽  
Anne Bruttin ◽  
Harald Brüssow
Keyword(s):  
Stop Codon ◽  
Sequence Similarity ◽  
Consensus Sequence ◽  
Gc Content ◽  
Streptococcus Thermophilus ◽  
Variant Form ◽  
Bacterial Genomes ◽  
Stem Loop ◽  
Reading Frame ◽  
Group I

ABSTRACT Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes revealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S. thermophilusbacterial genomes. Folding of the intron RNA revealed secondary structure elements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two stem-loop structures (shared with introns from Bacillusphage SPO1 and relatives); second, a conserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns fromLactococcus, Lactobacillus, andBacillus phages.

scholarly journals Expression of Different-Size Transcripts from theclpP-clpX Operon of Escherichia coli during Carbon Deprivation

2000 ◽  
Vol 182 (23) ◽  
pp. 6630-6637 ◽  
Author(s):  
Chin Li ◽  
Yi Ping Tao ◽  
Lee D. Simon
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Type Strain ◽  
Wild Type Strain ◽  
Transcription Termination ◽  
Carbon Starvation ◽  
Lower Percentage ◽  
Wild Type ◽  
Lower Efficiency ◽  
E Coli

ABSTRACT Transcription of the clpP-clpX operon ofEscherichia coli leads to the production of two different sizes of transcripts. In log phase, the level of the longer transcript is higher than the level of the shorter transcript. Soon after the onset of carbon starvation, the level of the shorter transcript increases significantly, and the level of the longer transcript decreases. The longer transcript consists of the entireclpP-clpX operon, whereas the shorter transcript contains the entire clpP gene but none of the clpXcoding sequence. The RpoH protein is required for the increase in the level of the shorter transcript during carbon starvation. Primer extension experiments suggest that there is increased usage of the ς32-dependent promoter of the clpP-clpXoperon within 15 min after the start of carbon starvation. Expression of the clpP-clpX operon from the promoters upstream of theclpP gene decreases to a very low level by 20 min after the onset of carbon starvation. Various pieces of evidence suggest, though they do not conclusively prove, that production of the shorter transcript may involve premature termination of the longer transcript. The half-life of the shorter transcript is much less than that of the longer transcript during carbon starvation. E. coli rpoBmutations that affect transcription termination efficiency alter the ratio of the shorter clpP-clpX transcript to the longer transcript. The E. coli rpoB3595 mutant, with an RNA polymerase that terminates transcription with lower efficiency than the wild type, accumulates a lower percentage of the shorter transcript during carbon starvation than does the isogenic wild-type strain. In contrast, the rpoB8 mutant, with an RNA polymerase that terminates transcription with higher efficiency than the wild type, produces a higher percentage of the shorter clpP-clpXtranscript when E. coli is in log phase. These and other data are consistent with the hypothesis that the shorter transcript results from premature transcription termination during production of the longer transcript.

scholarly journals Ribosomal Pausing at a Frameshifter RNA Pseudoknot Is Sensitive to Reading Phase but Shows Little Correlation with Frameshift Efficiency

2001 ◽  
Vol 21 (24) ◽  
pp. 8657-8670 ◽  
Author(s):  
Harry Kontos ◽  
Sawsan Napthine ◽  
Ian Brierley
Keyword(s):  
Rna Structure ◽  
Phase Dependence ◽  
Stem Loop ◽  
Reading Frame ◽  
Stem Loop Structure ◽  
Rna Pseudoknot ◽  
Ribosomal P ◽  
Slippery Sequence ◽  
The Impact ◽  
Ribosomal Pausing

ABSTRACT Here we investigated ribosomal pausing at sites of programmed −1 ribosomal frameshifting, using translational elongation and ribosome heelprint assays. The site of pausing at the frameshift signal of infectious bronchitis virus (IBV) was determined and was consistent with an RNA pseudoknot-induced pause that placed the ribosomal P- and A-sites over the slippery sequence. Similarly, pausing at the simian retrovirus 1 gag/pol signal, which contains a different kind of frameshifter pseudoknot, also placed the ribosome over the slippery sequence, supporting a role for pausing in frameshifting. However, a simple correlation between pausing and frameshifting was lacking. Firstly, a stem-loop structure closely related to the IBV pseudoknot, although unable to stimulate efficient frameshifting, paused ribosomes to a similar extent and at the same place on the mRNA as a parental pseudoknot. Secondly, an identical pausing pattern was induced by two pseudoknots differing only by a single loop 2 nucleotide yet with different functionalities in frameshifting. The final observation arose from an assessment of the impact of reading phase on pausing. Given that ribosomes advance in triplet fashion, we tested whether the reading frame in which ribosomes encounter an RNA structure (the reading phase) would influence pausing. We found that the reading phase did influence pausing but unexpectedly, the mRNA with the pseudoknot in the phase which gave the least pausing was found to promote frameshifting more efficiently than the other variants. Overall, these experiments support the view that pausing alone is insufficient to mediate frameshifting and additional events are required. The phase dependence of pausing may be indicative of an activity in the ribosome that requires an optimal contact with mRNA secondary structures for efficient unwinding.

scholarly journals A potential stem-loop structure and the sequence CAAUCAA in the transcript are insufficient to signal ϱ-dependent transcription termination at λtR1

1984 ◽  
Vol 12 (2) ◽  
pp. 1287-1299 ◽  
Author(s):  
Lester F. Lau ◽  
Jeffrey W. Roberts ◽  
Ray WU ◽  
Fawzy Georges ◽  
Saran A. Narang
Keyword(s):  
Transcription Termination ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure

scholarly journals HuR Uses AUF1 as a Cofactor To Promote p16INK4 mRNA Decay

2010 ◽  
Vol 30 (15) ◽  
pp. 3875-3886 ◽  
Author(s):  
Na Chang ◽  
Jie Yi ◽  
Gaier Guo ◽  
Xinwen Liu ◽  
Yongfeng Shang ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Untranslated Region ◽  
Mrna Decay ◽  
Loop Structure ◽  
Wild Type ◽  
Stem Loop ◽  
Human Diploid Fibroblasts ◽  
Stem Loop Structure ◽  
Chimeric Transcripts ◽  
P16 Expression

ABSTRACT In this study, we show that HuR destabilizes p16INK4 mRNA. Although the knockdown of HuR or AUF1 increased p16 expression, concomitant AUF1 and HuR knockdown had a much weaker effect. The knockdown of Ago2, a component of the RNA-induced silencing complex (RISC), stabilized p16 mRNA. The knockdown of HuR diminished the association of the p16 3′ untranslated region (3′UTR) with AUF1 and vice versa. While the knockdown of HuR or AUF1 reduced the association of Ago2 with the p16 3′UTR, Ago2 knockdown had no influence on HuR or AUF1 binding to the p16 3′UTR. The use of EGFP-p16 chimeric reporter transcripts revealed that p16 mRNA decay depended on a stem-loop structure present in the p16 3′UTR, as HuR and AUF1 destabilized EGFP-derived chimeric transcripts bearing wild-type sequences but not transcripts with mutations in the stem-loop structure. In senescent and HuR-silenced IDH4 human diploid fibroblasts, the EGFP-p16 3′UTR transcript was more stable. Our results suggest that HuR destabilizes p16 mRNA by recruiting the RISC, an effect that depends on the secondary structure of the p16 3′UTR and requires AUF1 as a cofactor.

Reversion analysis of dynein intermediate chain function

1993 ◽  
Vol 105 (4) ◽  
pp. 1069-1078 ◽  
Author(s):  
D.R. Mitchell ◽  
Y. Kang
Keyword(s):  
Sequence Analysis ◽  
Stop Codon ◽  
Function Analysis ◽  
Beat Frequency ◽  
Immunoblot Analysis ◽  
Wild Type ◽  
Direct Role ◽  
Reading Frame ◽  
Frame Shift ◽  
Intermediate Chain

The ODA6 locus of Chlamydomonas reinhardtii encodes a 70 kDa intermediate chain protein of the flagellar outer row dynein ATPase, and mutations at this locus prevent assembly of the entire outer row dynein arm complex. To initiate a structure-function analysis of the 70 kDa protein, we used transformation with chimeric mutant/wild-type genes to localize the defect in one assembly mutation, oda6-95. Sequence analysis revealed a frame-shift mutation in codon 53, which is followed by a stop codon after 13 amino acids in the new reading frame. By selecting intragenic pseudorevertants of this mutation we obtained 11 new oda6 alleles. Many of these pseudorevertants encode intermediate chain proteins that permit assembly of outer row arms but do not restore full wild-type motility. Revertant strains fall into two phenotypic classes, one with average beat frequencies of 54 Hz (similar to wild type) and one with average frequencies of 27 Hz (compared with 24 Hz for oda6-95) during normal forward swimming. Low beat frequency strains also display abnormalities during photophobic reversal (symmetric waveform). Amplification and sequence analysis of revertant alleles indicated that each reversion caused a second frame-shift, within a 115 nt interval, which restored the original reading frame, and that phenotypic severity was related to both direction (5′ or 3′) and distance between the original mutation and the reversion event. On the basis of immunoblot analysis of outer arm proteins, we conclude that revertant motility defects do not correlate with deficits in assembly of a specific dynein heavy chain or intermediate chain polypeptide, and electron microscopy confirms that revertants have normal outer arm structures. These results suggest that the 70 kDa intermediate chain plays a direct role in outer arm function distinct from its role in the assembly process.

scholarly journals Moraxella catarrhalis Expresses an Unusual Hfq Protein

2008 ◽  
Vol 76 (6) ◽  
pp. 2520-2530 ◽  
Author(s):  
Ahmed S. Attia ◽  
Jennifer L. Sedillo ◽  
Wei Wang ◽  
Wei Liu ◽  
Chad A. Brautigam ◽  
...  
Keyword(s):  
Moraxella Catarrhalis ◽  
Cell Envelope ◽  
Stress Sensitivity ◽  
Wild Type ◽  
Mobility Shift ◽  
Altered Expression ◽  
Reading Frame ◽  
E Coli ◽  
Different Types

ABSTRACT The Hfq protein is recognized as a global regulatory molecule that facilitates certain RNA-RNA interactions in bacteria. BLAST analysis identified a 630-nucleotide open reading frame in the genome of Moraxella catarrhalis ATCC 43617 that was highly conserved among M. catarrhalis strains and which encoded a predicted protein with significant homology to the Hfq protein of Escherichia coli. This protein, containing 210 amino acids, was more than twice as large as the Hfq proteins previously described for other bacteria. The C-terminal half of the M. catarrhalis Hfq protein was very hydrophilic and contained two different types of amino acid repeats. A mutation in the M. catarrhalis hfq gene affected both the growth rate of this organism and its sensitivity to at least two different types of stress in vitro. Provision of the wild-type M. catarrhalis hfq gene in trans eliminated these phenotypic differences in the hfq mutant. This M. catarrhalis hfq mutant exhibited altered expression of some cell envelope proteins relative to the wild-type parent strain and also had a growth advantage in a continuous flow biofilm system. The presence of the wild-type M. catarrhalis hfq gene in trans in an E. coli hfq mutant fully reversed the modest growth deficiency of this E. coli mutant and partially reversed the stress sensitivity of this E. coli mutant to methyl viologen. The use of an electrophoretic mobility shift assay showed that this M. catarrhalis Hfq protein could bind RNA derived from a gene whose expression was altered in the M. catarrhalis hfq mutant.

scholarly journals Three new dominant C1 suppressor alleles in Zea mays

1998 ◽  
Vol 71 (2) ◽  
pp. 127-132 ◽  
Author(s):  
TATJANA SINGER ◽  
ALFONS GIERL ◽  
PETER A. PETERSON
Keyword(s):  
Amino Acids ◽  
Transcriptional Activation ◽  
Stop Codon ◽  
Suppressive Effect ◽  
Wild Type ◽  
Activation Domain ◽  
Reading Frame ◽  
Transcriptional Activation Domain ◽  
Imprecise Excision ◽  
Carboxy Terminal

Three new dominant suppressor mutations of the C1 transcription regulator gene in maize – C1-IΔ1, C1-IΔ2 and C1-IΔ3 – are described that suppress anthocyanin colouration in kernels similar to the function of the C1-I standard inhibitor. The C1-IΔ mutations were induced by imprecise excision of an En/Spm transposon in the third exon of the C1 gene. These transposon footprints cause a frameshift in the C1 open reading frame that leads to truncated proteins due to an early stop codon 30 amino acids upstream of the wild-type C1 protein. Therefore, the C1-IΔ gene products lack the carboxy-terminal transcriptional activation domain of C1. The C1-I standard allele also lacks this domain and in addition differs in 17 amino acids from the wild-type C1 allele. The new C1-IΔ alleles provide evidence that deletion of the carboxy-terminal activation domain alone is sufficient to generate a dominant suppressive effect on the function of wild-type C1.

scholarly journals Role of the E1∧E4 Protein in the Differentiation-Dependent Life Cycle of Human Papillomavirus Type 31

2005 ◽  
Vol 79 (11) ◽  
pp. 6732-6740 ◽  
Author(s):  
Regina Wilson ◽  
Frauke Fehrmann ◽  
Laimonis A. Laimins
Keyword(s):  
Life Cycle ◽  
Stop Codon ◽  
S Phase ◽  
Human Papillomaviruses ◽  
Wild Type ◽  
Late Gene Expression ◽  
Semisolid Medium ◽  
Genome Amplification ◽  
Reading Frame

ABSTRACT The most highly expressed protein in the productive life cycle of human papillomaviruses (HPVs) is E1∧E4, but its function is not well understood. To investigate the role of E1∧E4, we undertook a genetic analysis in the context of the complete HPV type 31 (HPV31) genome. A mutant HPV31 genome (E4M9) was constructed that contained a stop codon in the E4 open reading frame at amino acid 9 and was silent in the overlapping E2 coding sequence. Wild-type and mutant genomes were transfected into normal human foreskin keratinocytes (HFKs) and selected for drug resistance, and pooled cultures were examined for effects of E1∧E4 on viral functions. Southern blot analyses of transfected HFKs demonstrated that cells carrying the E4M9 mutant genomes were maintained as episomes at copy numbers similar to those in keratinocytes transfected with wild-type HPV31. Both sets of cells grew at similar rates, exhibited comparable extensions of life spans, and had equivalent levels of early transcripts. Following suspension of the cells in a semisolid medium, differentiation-dependent genome amplification and late gene expression were significantly decreased in cells maintaining the E4M9 mutant genome compared to those with wild-type HPV31. One explanation for these effects could be a reduction in the number of cells harboring mutant genomes that enter S phase upon differentiation. An analysis of cells containing E4M9 mutant genomes in organotypic raft cultures indicated a reduction in bromodeoxyuridine incorporation in differentiated suprabasal cells compared to that seen in wild-type rafts. Our results indicate that the HPV31 E1∧E4 protein plays a significant role in promoting HPV genome amplification and S phase maintenance during differentiation.

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