Chapter 2 RNA Processing and Decay in Bacteriophage T4

Uzan, Marc

doi:10.1016/s0079-6603(08)00802-7

Cited by 26 publications

(29 citation statements)

References 228 publications

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“…The common presence of genes encoding CARF fused with diverse nucleases in CRISPR- cas loci (102) (Figure 2) implies that the CARF domain functions as a sensor of the imminent defeat of the immune system in the battle against the virus, in response to a hypothetical alarmone (most likely, a nucleotide derivative) that remains to be identified (88). Although the immunity-suicide coupling hypothesis was conjured largely on indirect evidence, an experimentally well-characterized case of such coupling is presented by a bacterial antiphage system which includes two HEPN domain–containing RNases, RloC and PrrC, that exert a toxic effect through tRNA cleavage (13, 73, 75, 165). …”

Section: Interactions Between Defense Strategies: Coupling Between Immentioning

confidence: 99%

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Koonin

Makarova²,

Wolf³

2017

Annu. Rev. Microbiol.

275

235

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Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.

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Section: Interactions Between Defense Strategies: Coupling Between Immentioning

confidence: 99%

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Koonin

Makarova²,

Wolf³

2017

Annu. Rev. Microbiol.

275

235

View full text Add to dashboard Cite

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“…The temporal transcriptional events during phage infection of a single host are known to be highly reproducible (Pène and Uzan, 2000;Uzan, 2009). However, it is currently not known whether the transcriptional program of broad host-range phages is differentially tailored for infection of distinct hosts or whether the same program is maintained irrespective of the host infected.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome dynamics of a broad host-range cyanophage and its hosts

et al. 2015

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Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host-ranges relative to other cyanophages. It is currently unknown whether broad host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH7803, WH8102 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early-gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad hostrange phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage.

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“…In addition to nrdAB and nrdD , more enzymes are involved in pyrimidine metabolism; a dCMP deaminase (ALP47131 for φ Grn1 and ALP47515 for φ St2), a thymidine kinase (ALP47080 for φ Grn1 and ALP47460 for φ St2), and a thymidylate synthase ( thyA ; ALP47026 for φ Grn1 and ALP47405 for φ St2) are also present, enhancing dTTP biosynthesis from dCTP, and dUTP, a well-established fact during phage infection. Host and viral RNA decay could potentially be a source of free nucleoside diphosphates during T4-like phage infection (Carpousis et al, 1989, 1994; Ueno and Yonesaki, 2004; Uzan, 2009) and along with the presence of viral nrdAB and nrdD ATP-dependent ribonucleotidases, the phage might be able to enhance the much needed deoxyribonucleotide biosynthesis for DNA replication (Chevallereau et al, 2016). These enzymes reach their transcript levels plateau in 20 min p.i.…”

Section: Resultsmentioning

confidence: 99%

Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell

et al. 2016

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Sequencing and annotation was performed for two large double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage–host metabolic interactions and exploitation was studied by transcript profiling of selected viral and host genes. Comparative genomic analysis with other large Vibrio phages was also performed to establish the presence and location of homing endonucleases highlighting distinct features for both phages. Phylogenetic analysis revealed that they belong to the “schizoT4like” clade. Although many reports of newly sequenced viruses have provided a large set of information, basic research related to the shift of the bacterial metabolism during infection remains stagnant. The function of many viral protein products in the process of infection is still unknown. Genome annotation identified the presence of several viral open reading frames (ORFs) participating in metabolism, including a Sir2/cobB (sirtuin) protein and a number of genes involved in auxiliary NAD+ and nucleotide biosynthesis, necessary for phage DNA replication. Key genes were subsequently selected for detail study of their expression levels during infection. This work suggests a complex metabolic interaction and exploitation of the host metabolic pathways and biochemical processes, including a possible post-translational protein modification, by the virus during infection.

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Chapter 2 RNA Processing and Decay in Bacteriophage T4

Cited by 26 publications

References 228 publications

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Transcriptome dynamics of a broad host-range cyanophage and its hosts

Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell

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