Regulation of Phage Gene Expression by Termination and Antitermination of Transcription

AbstractCRISPR-Cas immune systems are widespread in bacteria and archaea, but not ubiquitous. Previous work has demonstrated that CRISPR immunity is associated with an infection-induced fitness cost, which may help explain the patchy distribution observed. However, the mechanistic basis of this cost has remained unclear. Using Pseudomonas aeruginosa PA14 and its phage DMS3vir as a model, we perform a 30-day evolution experiment under phage mediated selection. We demonstrate that although CRISPR is initially selected for, bacteria carrying mutations in the phage receptor rapidly invade the population following subsequent reinfections. We then test three potential mechanisms for the observed cost of CRISPR: (1) autoimmunity from the acquisition of self-targeting spacers, (2) immunopathology or energetic costs from increased cas gene expression and (3) toxicity caused by phage gene expression prior to CRISPR-mediated cleavage. We find that phages can express genes before the immune system clears the infection and that expression of these genes can have a negative effect on host fitness. While infection does not lead to increased expression of cas genes, it does cause differential expression of multiple other host processes that may further contribute to the cost of CRISPR immunity. In contrast, we found little support for infection-induced autoimmunological and immunopathological effects. Phage gene expression prior to cleavage of the genome by the CRISPR-Cas immune system is therefore the most parsimonious explanation for the observed phage-induced fitness cost.

Download Full-text

Better Gene Expression by (-)Gene than by (+)Gene in Phage Gene Delivery Systems

Biotechnology Progress ◽

10.1021/bp050392j ◽

2006 ◽

Vol 22 (3) ◽

pp. 626-630 ◽

Cited By ~ 7

Author(s):

Y. Liang ◽

B. Shi ◽

J. Zhang ◽

H. Jiang ◽

Y. Xu ◽

...

Keyword(s):

Gene Expression ◽

Gene Delivery ◽

Delivery Systems ◽

Phage Gene

Download Full-text

The MarR-type regulator MalR is involved in stress-responsive cell envelope remodeling inCorynebacterium glutamicum

10.1101/544056 ◽

2019 ◽

Author(s):

Max Hünnefeld ◽

Marcus Persicke ◽

Jörn Kalinowski ◽

Julia Frunzke

Keyword(s):

Gene Expression ◽

Antibiotic Treatment ◽

Target Genes ◽

Cell Envelope ◽

Affinity Purification ◽

Stress Protein ◽

Bacterial Cells ◽

Phage Gene ◽

A Genome ◽

Target Promoters

1AbstractIt is the enormous adaptive capacity of microorganisms, which is key to their competitive success in nature, but also challenges antibiotic treatment of human diseases. To deal with a diverse set of stresses, bacteria are able to reprogram gene expression using a wide variety of transcription factors. Here, we focused on the MarR-type regulator MalR conserved in theCorynebacterineae, including the prominent pathogensCorynebacterium diphtheriaeandMycobacterium tuberculosis. In several corynebacterial species, themalRgene forms an operon with a gene encoding a universal stress protein (uspA). Chromatin-affinity purification and sequencing (ChAP-Seq) analysis revealed that MalR binds more than 60 target promoters in theC. glutamicumgenome as well as in the large cryptic prophage CGP3. Overproduction of MalR caused severe growth defects and an elongated cell morphology. ChAP-Seq data combined with a global transcriptome analysis of themalRoverexpression strain emphasized a central role of MalR in cell envelope remodeling in response to environmental stresses. Prominent MalR targets are for example involved in peptidoglycan biosynthesis and synthesis of branched-chain fatty acids. Phenotypic microarrays suggest an altered sensitivity of a ΔmalRmutant towards several β-lactam antibiotics. We furthermore revealed MalR as a repressor of several prophage genes suggesting that MalR may be involved in the control of stress-responsive induction of the large CGP3 element. In conclusion, our results emphasize MalR as a regulator involved in stress-responsive remodeling of the cell envelope ofC. glutamicumand suggest a link between cell envelope stress and the control of phage gene expression.ImportanceBacteria live in changing environments that force the cells to be highly adaptive. The cell envelope represents both, a barrier against harsh external conditions and an interaction interface. The dynamic remodeling of the cell envelope as a response towards, e.g. antibiotic treatment represents a major challenge in the treatment of diseases. Members of the MarR family of regulators are known to contribute to an adaptation of bacterial cells towards antibiotic stress. However, our knowledge on this adaptive response was so far restricted to a small number of well-described target genes. In this study, we performed a genome-wide profiling of DNA-binding of the MarR-type regulator MalR ofC. glutamicum, which is conserved in several coryne- and mycobacterial species. By binding to more than 60 different target promoters, MalR is shaping a global reprogramming of gene expression conferring a remodeling of the cell envelope in response to stress.

Download Full-text

A phage satellite tunes inducing phage gene expression using a domesticated endonuclease to balance inhibition and virion hijacking

10.1101/2020.11.28.402263 ◽

2020 ◽

Author(s):

Zoe Netter ◽

Caroline M. Boyd ◽

Tania V. Silvas ◽

Kimberley D. Seed

Keyword(s):

Gene Expression ◽

Gene Transcription ◽

Dna Binding Protein ◽

Lytic Phage ◽

Homing Endonucleases ◽

Arms Races ◽

Phage Gene ◽

Putative Origin ◽

Phage Production ◽

Bacterial Viruses

AbstractBacteria persist under constant threat of predation by bacterial viruses (phages). Bacteria-phage conflicts result in evolutionary arms races often driven by mobile genetic elements (MGEs). One such MGE, a phage satellite in Vibrio cholerae called PLE, provides specific and robust defense against a pervasive lytic phage, ICP1. The interplay between PLE and ICP1 has revealed strategies for molecular parasitism allowing PLE to hijack ICP1 processes in order to mobilize. Here, we describe the mechanism of PLE-mediated transcriptional manipulation of ICP1 structural gene transcription. PLE encodes a novel DNA binding protein, CapR, that represses ICP1’s capsid morphogenesis operon. Although CapR is sufficient for the degree of capsid repression achieved by PLE, its activity does not hinder the ICP1 lifecycle. We explore the consequences of repression of this operon, demonstrating that more stringent repression achieved through CRISPRi restricts both ICP1 and PLE. We also discover that PLE transduces in modified ICP1-like particles. Examination of CapR homologs led to the identification of a suite of ICP1-encoded homing endonucleases, providing a putative origin for the satellite-encoded repressor. This work unveils a facet of the delicate balance of satellite-mediated inhibition aimed at blocking phage production while successfully mobilizing in a phage-derived particle.

Download Full-text

Correction: Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity

The ISME Journal ◽

10.1038/s41396-020-00846-1 ◽

2021 ◽

Author(s):

Sean Meaden ◽

Loris Capria ◽

Ellinor Alseth ◽

Sylvain Gandon ◽

Ambarish Biswas ◽

...

Keyword(s):

Gene Expression ◽

Host Responses ◽

Phage Gene

Download Full-text

SOS Induction in a Subpopulation of Structural Maintenance of Chromosome (Smc) Mutant Cells in Bacillus subtilis

Journal of Bacteriology ◽

10.1128/jb.00132-07 ◽

2007 ◽

Vol 189 (12) ◽

pp. 4359-4366 ◽

Cited By ~ 10

Author(s):

Robert A. Britton ◽

Elke Küster-Schöck ◽

Thomas A. Auchtung ◽

Alan D. Grossman

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Topoisomerase I ◽

Dna Microarrays ◽

Single Cells ◽

Sos Response ◽

Dna Supercoiling ◽

Phage Gene ◽

Chromosome Partitioning ◽

Structural Maintenance Of Chromosome

ABSTRACT The structural maintenance of chromosome (Smc) protein is highly conserved and involved in chromosome compaction, cohesion, and other DNA-related processes. In Bacillus subtilis, smc null mutations cause defects in DNA supercoiling, chromosome compaction, and chromosome partitioning. We investigated the effects of smc mutations on global gene expression in B. subtilis using DNA microarrays. We found that an smc null mutation caused partial induction of the SOS response, including induction of the defective prophage PBSX. Analysis of SOS and phage gene expression in single cells indicated that approximately 1% of smc mutants have fully induced SOS and PBSX gene expression while the other 99% of cells appear to have little or no expression. We found that induction of PBSX was not responsible for the chromosome partitioning or compaction defects of smc mutants. Similar inductions of the SOS response and PBSX were observed in cells depleted of topoisomerase I, an enzyme that relaxes negatively supercoiled DNA.

Download Full-text

Expression and regulation of Halobacterium halobium phage ΦH genes

Canadian Journal of Microbiology ◽

10.1139/m89-028 ◽

1989 ◽

Vol 35 (1) ◽

pp. 182-188 ◽

Cited By ~ 29

Author(s):

Felix Gropp ◽

Peter Palm ◽

Wolfram Zillig

Keyword(s):

Gene Expression ◽

Rna Polymerase ◽

Large Subunit ◽

Halobacterium Halobium ◽

Host Bacterium ◽

Putative Promoter ◽

Phage Gene ◽

Immune Genes ◽

Promoter Sequences ◽

Ribosomal Protein S12

In this paper we describe five distinct modes of ΦH gene expression: (i) transcription of phage ΦH during lytic growth on the sensitive host bacterium (Halobacterium halobium strain R,); (ii) transcription of the circularized prophage ΦH1 in strain R124; (iii) transcription of the L region of ΦH present as 12-kilobase-plasmid in the immune strain R1L; (iv) transcription during the lytic growth of phage mutants containing an ISH23/50 in the immune strain R1L; (v) transcription during lytic growth of ISH23/50-insertion mutants in the sensitive host bacterium R1 showing enhancement of early transcripts. The sequential expression of the phage genome is described together with a detailed analysis of the transcription of early lytic, constitutive, and immune genes that map in the L region. The putative promoter sequences determined for several phage genes were compared with the upstream sequences of the H. halobium DNA-dependent RNA polymerase large subunit genes and with the gene for the ribosomal protein S12 homolog of H, halobium. The similarity of these putative promoter elements revealed conserved motifs that are discussed in relation to the TATA-box motif recognized by the eukaryotic DNA-dependent RNA polymerase II.Key words: Halobacterium, phage, gene expression, enhancer, promoter.

Download Full-text