Phage λ—New Insights into Regulatory Circuits

Węgrzyn, Grzegorz; Licznerska, Katarzyna; Węgrzyn, Alicja

doi:10.1016/b978-0-12-394621-8.00016-9

Cited by 59 publications

(73 citation statements)

References 109 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While this mode of replication has been demonstrated for pG0400 (27), CNPX shares the genetic organization of the lambda phage, with extensive homology in the region encoding genes involved in DNA replication (7). Therefore, we believe that CNPX most likely has a replication cycle similar to the lambda replication cycle, which undergoes about six rounds of theta replication before switching to rolling circle replication (37).…”

Section: Discussionmentioning

confidence: 82%

Impact of Different Target Sequences on Type III CRISPR-Cas Immunity

et al. 2016

View full text Add to dashboard Cite

Clustered regularly interspaced short palindromic repeat (CRISPR) loci encode an adaptive immune system of prokaryotes. Within these loci, sequences intercalated between repeats known as "spacers" specify the targets of CRISPR immunity. The majority of spacers match sequences present in phages and plasmids; however, it is not known whether there are differences in the immunity provided against these diverse invaders. We studied this issue using the Staphylococcus epidermidis CRISPR system, which harbors spacers matching both phages and plasmids. We determined that this CRISPR system provides similar levels of defense against the conjugative plasmid pG0400 and the bacteriophage CNPX. However, whereas antiplasmid immunity was very sensitive to the introduction of mismatches in the target sequence, mutations in the phage target were largely tolerated. Placing the phage and plasmid targets into a vector that can be both conjugated and transduced, we demonstrated that the route of entry of the target has no impact on the effect of the mismatches on immunity. Instead, we established that the specific sequences of each spacer/target determine the susceptibility of the S. epidermidis CRISPR system to mutations. Therefore, spacers that are more resistant to mismatches would provide long-term immunity against phages and plasmids that otherwise would escape CRISPR targeting through the accumulation of mutations in the target sequence. These results uncover an unexpected complexity in the arms race between CRISPR-Cas systems and prokaryotic infectious genetic elements. IMPORTANCECRISPR-Cas loci protect bacteria and archaea from both phage infection and plasmid invasion. These loci harbor short sequences of phage and plasmid origin known as "spacers" that specify the targets of CRISPR-Cas immunity. The presence of a spacer sequence matching a phage or plasmid ensures host immunity against infection by these genetic elements. In turn, phages and plasmids constantly mutate their targets to avoid recognition by the spacers of the CRISPR-Cas immune system. In this study, we demonstrated that different spacer sequences vary in their ability to tolerate target mutations that allow phages and plasmids to escape from CRISPR-Cas immunity. These results uncover an unexpected complexity in the arms race between CRISPR-Cas systems and prokaryotic infectious genetic elements. C lustered regularly interspaced short palindromic repeat (CRISPR) loci and their CRISPR-associated (Cas) proteins encode an adaptive immune system that defends prokaryotes from bacteriophage (1) and plasmid (2) infection. Within these loci, sequences intercalated between repeats known as "spacers" specify the targets of CRISPR immunity. Spacer sequences are acquired during infection (1), when a subset of Cas proteins insert a short sequence of the invader's genome upstream of the first repeat of the CRISPR cluster (3). Spacers are transcribed and processed into short antisense RNAs, the CRISPR RNAs (crRNAs), that are used by RNA-guided Cas nucleases to reco...

show abstract

Section: Discussionmentioning

confidence: 82%

Impact of Different Target Sequences on Type III CRISPR-Cas Immunity

et al. 2016

View full text Add to dashboard Cite

show abstract

“…In fact, negative effects of ppGpp on p Rinitiated transcription were demonstrated previously for two such phages, ST2-8624 and 933W (24). Transcription from this promoter provides mRNA for proteins necessary during early stages of the phage lytic development, and in phage such a transcription is in addition required to activate initiation of phage DNA replication (20). An alternative hypothesis that inhibition of replication of Shiga toxin-converting bacteriophages by ppGpp results from impaired priming reactions seems to be less likely.…”

Section: Discussionmentioning

confidence: 92%

ppGpp-Dependent Negative Control of DNA Replication of Shiga Toxin-Converting Bacteriophages in Escherichia coli

et al. 2013

Self Cite

View full text Add to dashboard Cite

bThe pathogenicity of enterohemorrhagic Escherichia coli (EHEC) strains depends on the production of Shiga toxins that are encoded on lambdoid prophages. Effective production of these toxins requires prophage induction and subsequent phage replication. Previous reports indicated that lytic development of Shiga toxin-converting bacteriophages is inhibited in amino acidstarved bacteria. However, those studies demonstrated that inhibition of both phage-derived plasmid replication and production of progeny virions occurred during the stringent as well as the relaxed response to amino acid starvation, i.e., in the presence as well as the absence of high levels of ppGpp, an alarmone of the stringent response. Therefore, we asked whether ppGpp influences DNA replication and lytic development of Shiga toxin-converting bacteriophages. Lytic development of 5 such bacteriophages was tested in an E. coli wild-type strain and an isogenic mutant that does not produce ppGpp (ppGpp 0 ). In the absence of ppGpp, production of progeny phages was significantly (in the range of an order of magnitude) more efficient than in wild-type cells. Such effects were observed in infected bacteria as well as after prophage induction. All tested bacteriophages formed considerably larger plaques on lawns formed by ppGpp 0 bacteria than on those formed by wild-type E. coli. The efficiency of synthesis of phage DNA and relative amount of lambdoid plasmid DNA were increased in cells devoid of ppGpp relative to bacteria containing a basal level of this nucleotide. We conclude that ppGpp negatively influences the lytic development of Shiga toxin-converting bacteriophages and that phage DNA replication efficiency is limited by the stringent control alarmone.

show abstract

“…In general, phage integration into and excision from the host chromosome requires a site-specific recombinase or integrase, which mediates the homologous recombination between the phage attP site and the bacterial attB site [40]. Within the pp3 cluster, gene PA1S_06780 ( int3 ), located adjacent to the attL site, is predicted to encode an integrase with 98% identity to the integrase of LES prophage 3 of P .…”

Section: Resultsmentioning

confidence: 99%

Characterization and interstrain transfer of prophage pp3 of Pseudomonas aeruginosa

Shen

et al. 2017

PLoS ONE

View full text Add to dashboard Cite

Prophages are major contributors to horizontal gene transfer and drive the evolution and diversification of bacteria. Here, we describe the characterization of a prophage element designated pp3 in the clinical Pseudomonas aeruginosa isolate PA1. pp3 spontaneously excises from the PA1 genome and circularizes at a very high frequency of 25%. pp3 is likely to be a defective prophage due to its inability to form plaques on P. aeruginosa indicator strains, and no phage particles could be detected in PA1 supernatants. The pp3-encoded integrase is essential for excision by mediating site-specific recombination at the 26-bp attachment sequence. Using a filter mating experiment, we demonstrated that pp3 can transfer into P. aeruginosa recipient strains that do not possess this element naturally. Upon transfer, pp3 integrates into the same attachment site as in PA1 and maintains the ability to excise and circularize. Furthermore, pp3 significantly promotes biofilm formation in the recipient. Sequence alignment reveals that the 26-bp attachment site recognized by pp3 is conserved in all P. aeruginosa strains sequenced to date, making it possible that pp3 could be extensively disseminated in P. aeruginosa. This work improves our understanding of the ways in which prophages influence bacterial behavior and evolution.

show abstract

Phage λ—New Insights into Regulatory Circuits

Cited by 59 publications

References 109 publications

Impact of Different Target Sequences on Type III CRISPR-Cas Immunity

Impact of Different Target Sequences on Type III CRISPR-Cas Immunity

ppGpp-Dependent Negative Control of DNA Replication of Shiga Toxin-Converting Bacteriophages in Escherichia coli

Characterization and interstrain transfer of prophage pp3 of Pseudomonas aeruginosa

Contact Info

Product

Resources

About