A high-resolution map of bacteriophage ϕX174 transcription.

  title={A high-resolution map of bacteriophage ϕX174 transcription.},
  author={Dominic Y. Logel and Paul R. Jaschke},

Virulent but not temperate bacteriophages display hallmarks of rapid translation initiation

It is shown that phage mRNAs are highly enriched in strong Shine-Dalgarno sequences and have comparatively weaker secondary structures in the start codon region than host-cell m RNAs.

Low-Temperature Adaptation Targets Genome Packing Reactions in an Icosahedral Single-Stranded DNA Virus

The results presented here demonstrate how physical parameters, such as temperature, can directly influence viral diversification and niche determination in a host-independent manner.

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses

A major part of the healthy human gut microbiome is the Microviridae bacteriophage, exemplified by the model φX174 phage, and their E. coli hosts, and this work investigates the host response to infection in detail.

Proteomic and transcriptomic analysis of Microviridae φXI74 infection reveals broad up-regulation of host membrane damage and heat shock responses

The proteomic and transcriptomic pathways differentially regulated during the φX174 infection cycle are revealed, and a coordinated cellular response to membrane damage that results in increased lipoprotein processing and membrane trafficking, likely due to the phage antibiotic-like lysis protein.

Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction.

For the first time comprehensively demonstrated that gene modularization severely perturbs the coordinated functioning of a bacteriophage replication cycle, highlighting the biological importance of gene overlap in natural genomes.

ΦX174 Attenuation by Whole-Genome Codon Deoptimization

The need to better understand how selection acts on patterns of synonymous codon usage across the genome is highlighted and the recoded bacteriophage ΦX174 provides a convenient system to investigate the genetic determinants of virulence.

Generating dynamic gene expression patterns without the need for regulatory circuits

This work demonstrates that varying only the placement and strengths of promoters, terminators, and RNase cleavage sites in a computational model of a bacteriophage genome is sufficient to achieve solutions to a variety of basic gene expression patterns and shows that non-trivial patterns can be evolved.

Generating complex patterns of gene expression without regulatory circuits

This work demonstrates that varying only the placement and strengths of promoters, terminators, and RNase cleavage sites in a computational model of a bacteriophage genome is sufficient to achieve solutions to a variety of basic expression patterns.

When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome

This reanalysis challenges the reported findings as supportive of a prenatal fetal lamb microbiome and proposes genomic independence of separate biological samples, i.e. distinctive profiles at the microbial strain level, as a potential new microbiome marker to increase confidence in metagenomics analyses of controversial low-biomass microbiomes.

Bionanoparticles in cancer imaging, diagnosis, and treatment

This review critically analyzed the use of bionanoparticles in cancer imaging, diagnosis, and treatment and described its unique properties that render it powerful in cancer theranostics compared with synthetic inorganic nanoparticles.



Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis

Interestingly, most of the transcriptional repressed genes were involved in the utilization of specific carbon sources such as ribose and inositol, and many contained promoter binding-sites for the catabolite control protein A (CcpA).

Global analysis of host response to induction of a latent bacteriophage

This study provides the first global dynamic picture of how host processes respond to lambda phage induction, observing that prophage induction has a surprisingly low impact on host physiology.

High-throughput evaluation of T7 promoter variants using biased randomization and DNA barcoding

It is demonstrated that the method enables simple and high-throughput analysis of the effects of various CRE mutations on transcriptional regulation and the bases from −9 to −7 play an important role in the transcriptional activity of the T7 promoter.

Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases

The AR9 transcription strategy and the effect of AR9 infection on the transcription of its host, Bacillus subtilis, are investigated and viral promoters recognized by two virus-encoded RNA polymerases that are a unique feature of the phiKZ-related group of phages to which AR9 belongs are identified.

Control of gene expression in bacteriophage P22 by a small antisense RNA. I. Characterization in vitro of the Psar promoter and the sar RNA transcript.

The location and properties of Psar suggest an important regulatory function for sar RNA as a negative effector of ant expression, and the results of Wu et al. (this issue) support this suggestion.

Positive selection at high temperature reduces gene transcription in the bacteriophage ϕX174

It is suggested that gene transcription plays an important role in influencing fitness in the bacteriophage ϕX174, and different point mutations in a single cis-regulatory region provided the genetic basis for this role in adaptation to high temperature.

The role of the OOP antisense RNA in coliphage λ development

A derivative of bacteriophage λ that makes no OOP antisense RNA is made, and it is found a two‐fold greater phage burst following ultraviolet induction of a λ+ than of aλp o− prophage.

Bacteriophage phi X174-specific mRNA synthesis in cells deficient in termination factor rho activity

The rho mutation relieved polar effects caused by nonsense mutations in the phage genome or by chloramphenicol treatment of the host cells, and polarity was not caused by premature termination of transcription at the site of the polar mutation.