Multiple pathways of RNA processing and decay for the major leftward N- independent RNA transcript of coliphage lambda

Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage lambda

The gene regulatory circuitry of phage lambda is among the best-understood circuits. Much of the circuitry centres around the immunity region, which includes genes for two repressors, CI and Cro, and their cis-acting sites. Related phages, termed lambdoid phages, have different immunity regions, but similar regulatory circuitry and genome organization to that of lambda, and show a mosaic organization, arising by recombination between lambdoid phages. We sequenced the immunity regions of several wild phages with the immunity specificity of lambda, both to determine whether natural variation exists in regulation, and to analyse conservation and variability in a region rich in well-studied regulatory elements. CI, Cro and their cis-acting sites are almost identical to those in lambda, implying that regulatory mechanisms controlled by the immunity region are conserved. A segment adjacent to one of the operator regions is also conserved, and may be a novel regulatory element. In most isolates, different alleles of two regulatory proteins (N and CII) flank the immunity region; possibly the lysis-lysogeny decision is more variable among isolates. Extensive mosaicism was observed for several elements flanking the immunity region. Very short sequence elements or microhomologies were also identified. Our findings suggest mechanisms by which fine-scale mosaicism arises.

The global regulator RNase III modulates translation repression by the transcription elongation factor N

Efficient expression of most bacteriophage lambda early genes depends upon the formation of an antiterminating transcription complex to overcome transcription terminators in the early operons, p(L) and p(R). Formation of this complex requires the phage-encoded protein N, the first gene product expressed from the p(L) operon. The N leader RNA contains, in this order: the NUTL site, an RNase III-sensitive hairpin and the N ribosome-binding site. N bound to NUTL RNA is part of both the antitermination complex and an autoregulatory complex that represses the translation of the N gene. In this study, we show that cleavage of the N leader by RNase III does not inhibit antitermination but prevents N-mediated translation repression of N gene expression. In fact, by preventing N autoregulation, RNase III activates N gene translation at least 200-fold. N-mediated translation repression is extremely sensitive to growth rate, reflecting the growth rate regulation of RNase III expression itself. Given N protein's critical role in lambda development, the level of RNase III activity therefore serves as an important sensor of physiological conditions for the bacteriophage.

Use of a gene encoding a suppressor tRNA as a reporter of transcription: analyzing the action of the Nun protein of bacteriophage HK022

The Nun protein of phage HK022 blocks the expression of genes that lie downstream of the nut sites of phage lambda. Nun is believed to act by promoting premature termination of transcription at or near these sites. To test this hypothesis and to facilitate mapping the sites of termination, we inserted a gene encoding a suppressor tRNA immediately downstream of the lambda nutL site and determined the effect of Nun on tRNA level. We found that Nun severely reduced the accumulation of mature, biologically active tRNA and promoted the accumulation of short, promoter-proximal transcripts whose 3' ends were dispersed over a 100-nucleotide region downstream of nutL. These results are consistent with the hypothesis that Nun terminates transcription within the region immediately downstream of nutL and are inconsistent with the hypothesis that the only action of Nun is to prevent translation of genes located downstream of the nut site. The stability, small size, and easily assayable biological function of suppressor tRNA recommend it as a reporter of transcription in other systems.

RNaselll activation of bacteriophage lambda N synthesis

The bacteriophage lambda N gene product is one of the first genes expressed during phage development. N protein allows the expression of other phage genes by altering the transcription elongation process so as to prevent transcription termination. We have found that N levels may be modulated soon after induction or infection. Using N-lacZ fusions, we determined that cells containing RNaselll have at least a fourfold greater expression than cells defective for RNaselll. This effect is exerted at the post-transcriptional level. RNaselll processes an RNA stem structure in the N-leader RNA. Removal of the stem structure by deletion increases N expression and prevents further stimulation by RNaselll. The base of this stable stem is adjacent to the N ribosome binding site. We present a model for control of N synthesis in which this stable stem inhibits ribosome access to the N mRNA.

RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression

The primary transcripts of the rpsO-pnp, rnc-era-recO and metY-nusA-infB operons of E coli are each processed by RNase III, upstream of the first translated gene, in hair-pin structures formed by the 5' non-coding leader. The mRNAs of the 3 operons, of which the 5' terminal motifs have been removed by RNase III, decay significantly more rapidly than the uncut transcripts which accumulate in the RNase III deficient strain. The rapid decay of a primary transcript of the metY-nusA-infB operon, initiated at a secondary promoter in the vicinity of the RNase III sites, suggests that the 5' features upstream of the RNase III cutting sites are responsible for the stability of the uncut RNAs. RNase III autocontrols its own expression by removing the 5' motif which stabilizes its mRNA. Similarly, the synthesis of polynucleotide phosphorylase and of protein Era are also controlled by RNase III cleavages which trigger the degradation of their messengers. The role of RNase III in the regulation of gene expression and the possible mechanisms of mRNA stabilization and of 5' to 3' decay initiated by RNase III processing are discussed.

An antitermination protein engages the elongating transcription apparatus at a promoter-proximal recognition site

As a transcriptional activator, the N protein of phage lambda acts to suppress transcription termination by recognizing a promoter-proximal site, nut, which is separated from the terminators by thousands of base pairs. We demonstrate here that N interacts with the elongating RNA polymerase in transit through the boxB domain of nut. This interaction leads to the stable association of N as an integral component of the transcription apparatus. During subsequent elongation, N translocates along with polymerase through several defined terminators positioned beyond nut. Therefore, by being an operon-specific subunit of the transcription apparatus, N presumably prevents the interaction of polymerase with termination signals.

Transcription termination and processing sites in the bacteriophage lambda pL operon

S1 nuclease mapping was performed on transcripts from the major leftward operon of the bacteriophage lambda in order to locate the 3' ends of stable RNA species produced in vivo. The analysis was carried out on RNA purified from either an induced lambda prophage or bacteria carrying a plasmid containing a large segment of lambda including the intact PL operon through the bet gene. The S1 nuclease mapping was performed on transcripts produced in the presence and the absence of the N antitermination function, and in the presence and the absence of either the RNase III processing enzyme or the Rho factor. The results of this work indicate that the intercistronic region between the N and ral genes of lambda contains three sites at which transcripts end under N-Rho+ conditions (positions on the lambda sequence: 34,826, 34,558 and 34,393). The distal two correspond to the two sites previously described in this region as tL1 (on both sides of the BamHI site). In the region between ral and Ea10, we mapped the 3' ends of three species of RNA. The 3' end of one species was found to be located 90 nucleotides proximal to tL2a, at 34,000 in the lambda sequence. The terminator at this site may be partially N-resistant. In an RNase III deficient host, an additional RNA species is formed. The 3' end of this RNA species is located at tL2a (33,910 on the lambda sequence). In the presence of the antitermination N gene product, the readthrough transcripts are processed to form a 3' end at position 33,980 on the lambda sequence. These results suggest that elongation of transcription of the lambda PL operon is reduced gradually by clusters of termination located between genes and that the expression of the terminated products is further controlled by processing of the mRNA.

Conservation of genome form but not sequence in the transcription antitermination determinants of bacteriophages lambda, phi 21 and P22

Comparisons are made among DNA sequences upstream from terminators in both leftwards and rightwards early operons of related coliphages lambda, phi 21 and P22. These sequences include both left and right determinants of response to phage-coded antitermination proteins, "N", as well as the N structural genes themselves. Despite almost total disparity of DNA sequence, the three genomes can be discerned to include the same elements in the same order and spacing: downstream from the early left promoter are sequentially a site of recognition for host nusA protein, a dyad symmetry "nut" essential for N function in lambda, overlapping sites for processing of the transcript by RNAase III and then the N structural genes; downstream from the cro gene on the right are sites of nusA recognition and nut dyad symmetries homologous to those on the left. Because the N proteins of lambda, phi 21 and P22 do not for the most part complement each other, a specific site of N recognition has been postulated for each N-responding operon. The nut dyad symmetry qualifies as such a site, since the loop of the left dyad in lambda is marked by mutations that block N function leftwards, and since DNA sequences here show close homology between the loops of left and right dyads for each phage, but less if not little homology for different phages.

Characterization of cytochrome P2-450 (20-S) mRNA. Association with the P1-450 genomic gene and differential response to the inducers 3-methylcholanthrene and isosafrole

Mouse liver cytochrome P2-450 is defined as the major isosafrole-inducible form of P-450 which is most specific for isosafrole metabolism. lambda AhP-1 represents a 15.5 X 10(3)-base-pair segment of mouse genomic DNA having the cytochrome P1-450 gene (approximately equal to 4600 base pairs) located in the middle portion. Using various subclones as probes, we investigated the differential expression of P1-450 mRNA and P2-450 mRNA induction as a function of association with the Ah locus, 3-methylcholanthrene or isosafrole dosage, tissue specificity, and developmental age. Both P1-450 (23-S) mRNA and P2-450 (20-S) mRNA induction processes are regulated by the Ah receptor. P2-450 mRNA is about 10-fold more sensitive than P1-450 mRNA to induction by either 3-methylcholanthrene or isosafrole. Phenobarbital pretreatment has no effect at all on either P1-450 mRNA or P2-450 mRNA. Whereas both P1-450 mRNA and P2-450 mRNA are induced by 3-methylcholanthrene in C57BL/6N liver, P1-450 (23-S) mRNA but not P2-450 (20-S) mRNA is induced by 3-methylcholanthrene in C57BL/6N kidney. P1-450 mRNA induction by 3-methylcholanthrene is measurable in C57BL/6N liver at day 15 of gestation, and the expression becomes enhanced with increasing age. P2-450 mRNA induction by 3-methylcholanthrene in C57BL/6N liver appears about 7 days later during development than 3-methylcholanthrene-inducible P1-450 mRNA. Both 3-methylcholanthrene-induced P1-450 mRNA and P2-450 mRNA are detectable in DBA/2N liver; their appearance is later in development, however, and at lower concentrations than that seen with C57BL/6N liver. P1-450 (23-S) mRNA and P2-450 (20-S) mRNA appear to hybridize to a common 5' fragment of the P1-450 gene.

Regulation of transcription and DNA replication of bacteriophage phi 80

Transcriptional mapping and DNA replication measurements have been used to characterize a series of phi 80 suppressor-sensitive mutants which are defective in genes 15, 14, 16, and 17. These genes are localized within the inner right arm of the vegetative phi 80 DNA genome. The sus326 mutation in gene 15 leads to a decrease in major leftward (pL-att80) RNA levels and to a marked pleiotropic reduction in major rightward RNA synthesis; however, phi 80 DNA synthesis is reduced only moderately (about two-fold). These findings are consistent with the gene 15 product being a positive control regulator that is essential for normal transcriptional development, in particular, beyond a termination signal(s) (tR) located between genes 16 and 17. The sus8 and sus258 mutations (in genes 14 and 16, respectively) lead to severe blockage of both major rightward RNA transcription and phi 80 DNA synthesis. The products of genes 14 and 16 appear to be required for both autonomous phi 80 DNA replication and the "late" transcriptional development. The sus121 mutation in gene 17 reduces the level of "late" major rightward transcription (gene 17-1-13-att'80 segment) by about 10-fold but does not have any apparent effect on the levels of phi 80 DNA synthesis. These profiles identify the product of gene 17 as a "Q-type" positive control regulator for the "late" major rightward RNA. These studies reveal the functional characterization of four genes, the products of which are necessary for the efficient expression of the "early" RNA transcribed segments, autonomous DNA replication, and the production of normal levels of "late" (17-1-13-att'80) RNA synthesis.