Newly discovered antiterminator RNAs in bacteriophage

Isolation and Characterization of Phages That Bypass the Requirement for RNA-Mediated Antitermination

Introduction

The rpoCY75N mutation in the zinc-binding domain of the β' subunit of Escherichia coli RNA polymerase blocks the RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022.

Materials and Methods

Mutant phages that overcome the block imposed by the rpoCY75N mutation are described. These phages, designated "orc" (overcomes rpoC), carry mutations that create new promoters. Promoter activity was assessed by cloning the respective regions from the wild-type and orc phages into a promoterless lacZ reporter vector.

Results

Reporter assays showed that the sequence originating from orc phages had significant promoter activity when compared with the equivalent sequence cloned from the parental phage.

Conclusions

The newly created promoters facilitate the expression of phage genes that are essential for growth on the rpoCY75N strain by bypassing transcription terminators. The small plaque phenotype of orc phages, when grown on the mutant host, suggests that suppression of the rpoCY75N mutation is incomplete.

Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA

Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans-elements like protein factors and/or by cis-elements like specific sequences on the DNA. Lambdoid phage HK022 contains a cis-element, put, which suppresses pausing and termination during transcription of the early phage genes. The putRNA transcript solely performs the anti-pausing/termination activities by interacting directly with the E.coli RNAP elongation complex (EC) by an unknown structural mechanism. In this study, we reconstituted putRNA-associated ECs and determined the structures using cryo-electron microscopy. The determined structures of putRNA-associated EC, putRNA-absent EC, and σ⁷⁰-bound EC suggest that the putRNA interaction with the EC counteracts swiveling, a conformational change previously identified to promote pausing and σ⁷⁰ might modulate putRNA folding via σ⁷⁰-dependent pausing during elongation.

Genomic comparison of 60 completely sequenced bacteriophages that infect Erwinia and/or Pantoea bacteria

Erwinia and Pantoea are closely related bacterial plant pathogens in the Gram negative Enterobacteriales order. Sixty tailed bacteriophages capable of infecting these pathogens have been completely sequenced by investigators around the world and are in the current databases, 30 of which were sequenced by our lab. These 60 were compared to 991 other Enterobacteriales bacteriophage genomes and found to be, on average, just over twice the overall average length. These Erwinia and Pantoea phages comprise 20 clusters based on nucleotide and protein sequences. Five clusters contain only phages that infect the Erwinia and Pantoea genera, the other 15 clusters are closely related to bacteriophages that infect other Enterobacteriales; however, within these clusters the Erwinia and Pantoea phages tend to be distinct, suggesting ecological niche may play a diversification role. The failure of many of their encoded proteins to have predicted functions highlights the need for further study of these phages.