ADP-Ribosylation and Early Transcription Regulation by Bacteriophage T4

K, Wilkens; Tiemann, Bernd; Bazán, Fernando; Rüger, Wolfgang

doi:10.1007/978-1-4419-8632-0_8

Cited by 34 publications

(30 citation statements)

References 29 publications

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“…In T4, these enzymes ADP-ribosylate many proteins, including the RNA polymerase ␣ subunits (59,60). Compared to most 70 promoters, T4 early promoters have an extended Ϫ10 region, a Ϫ35 region (GTT TAC) that differs from the generalized 70 Ϫ35 (TTGACa), and an A-rich upstream (Ϫ42) region (reviewed in reference 44).…”

Section: Resultsmentioning

confidence: 99%

Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

Miller

Heidelberg²,

Eisen³

et al. 2003

J Bacteriol

214

197

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The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G؉C content of 42.6%. It encodes 386 putative proteinencoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early-or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.Bacteriophage KVP40 and similar Vibrio phages were isolated from polluted seawater off the coast of Japan with a strain of Vibrio parahaemolyticus as the host (41). KVP40 differs from many described vibriophages in having a broad host range; it has been reported to infect eight Vibrio species, including Vibrio cholerae and Vibrio parahaemolyticus, the nonpathogenic species Vibrio natriegens, and Photobacterium leiognathi (41). Additional studies have implicated the Vibrio OmpK outer membrane protein as the phage receptor (23).Vibriophage KVP40, like the well-studied phage T4 (27, 44), belongs to the Myoviridae family of viruses. This family is characterized by having a double-stranded DNA genome, a prolate icosahedral capsid, and a contractile tail with associated baseplate and extended tail fibers (1). However, there are morphological differences between phage T4 and KVP40. For example, the head of KVP40 is longer (140 nm long and 70 nm wide) than that of T4. Due to the constraints of head size on DNA packaging, this observation suggested that the genome of KVP40 is larger than the 168,903-bp genome of T4.Beyond morphological similarities, major and minor capsid genes of KVP40 have been sequenced and are related to and functionally conserved with those of T4 (39). However, phylogenetic analysis of Myoviridae capsid genes suggests that the vibriophages, along with ...

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Section: Resultsmentioning

confidence: 99%

Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

Miller

Heidelberg²,

Eisen³

et al. 2003

J Bacteriol

214

197

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“…All the paralogs to gp93 in KZ and members of PF12699 in other phages have a cleavage-like motif close to their N terminus. The T4 CTStargeted proteins have important roles in host takeover, such as Alt, which ribosylates the host RNA polymerase, altering its promoter specificity to increase transcription of T4 promoters (44), and IPI*, a restriction endonuclease inhibitor (45).…”

Section: Discussionmentioning

confidence: 99%

Mutational Analysis of the Pseudomonas aeruginosa Myovirus ϕKZ Morphogenetic Protease gp175

Thomas

Black

2013

J Virol

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Pseudomonas aeruginosa myovirus KZ has a 270-kb genome within a T‫72؍‬ icosahedral capsid that contains a large, unusual, and structurally well-defined protein cylindrical inner body (IB) spanning its interior. Proteolysis forms a pivotal stage in KZ head and IB morphogenesis, with the protease gp175 cleaving at least 19 of 49 different head proteins, including the major capsid protein and five major structural IB proteins. Here we show that the purified mature form of gp175 is active and cleaves purified IB structural proteins gp93 and gp89. Expression vector synthesis and purification of the zymogen/precursor yielded an active, mature-length protease, showing independent C-terminal gp175 self-cleavage autoactivation. Mutation of either the predicted catalytic serine or histidine inactivated mature gp175, supporting its classification as a serine protease and representing the first such direct biochemical demonstration with purified protease and substrate proteins for any phage protease. These mutations also blocked self-cleavage of the precursor while allowing intermolecular gp175 processing. To confirm the cleavage specificity of gp175, we mutated three cleavage sites in gp93, which blocked proteolysis at these sites. The N-terminal propeptide of gp93 was shown to undergo more extensive proteolysis than previously identified. We found that proteolysis in gp93 progressed from the N to C terminus, while blocking cleavage sites slowed but did not eliminate downstream proteolysis. These findings were shown by informatics to be relevant to the head morphogenesis of numbers of other related IB-containing giant phages as well as to T4 and herpesviruses, which have homologous proteases.T he giant myovirus KZ, which is infective for Pseudomonas aeruginosa, is a member of the KZ-related phages that currently incorporate two genera, the KZ-like phages (KZ, PA3, and 2012-1) and the more distantly related EL-like phages (EL and OBP) (1-3). These phages are distributed widely geographically and are of interest because those infective for pathogens have been used for phage therapy (4) and/or have potential for further biocontrol applications (5-8). These phages are also a curiosity, as they are remarkably complex, both at the genome and structural levels, with large virions comprised of a Tϭ27 capsid or head (9) and contractile tail that ends in an elaborate baseplate (10, 11). The complexity of the virion is reflected in the numbers of different proteins, Ͼ60 different proteins, with nearly 50 different proteins present in the head alone, possibly the highest number for any known group of viruses (12)(13)(14). A remarkable feature of the KZ-related phages is that within the head there is a large, protein cylinder called an inner body (IB) around which the DNA is tightly spooled (15). The structure of the KZ IB was recently solved, revealing it to be approximately 24 by 105 nm and tilted at an angle of approximately 22°relative to the portal axis (16). Its structure is also regular, with an apparent 6-fold symmetry in some ...

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“…In particular, base position Ϫ33 of the T4 promoter and the A-rich UP element at position Ϫ42 contribute to the strong interactions with ADP-ribosylated RNAP of T4-infected cells (1026). Therefore, Alt presumably contributes to the preferential transcription from T4 promoters after infection (1168,1170).…”

Section: Early Transcriptionmentioning

confidence: 99%

Bacteriophage T4 Genome

Miller

Kutter

Mosig

et al. 2003

Microbiol Mol Biol Rev

688

801

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SUMMARY Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the “cell-puncturing device,” combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages—the most abundant and among the most ancient biological entities on Earth.

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ADP-Ribosylation and Early Transcription Regulation by Bacteriophage T4

Cited by 34 publications

References 29 publications

Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

Mutational Analysis of the Pseudomonas aeruginosa Myovirus ϕKZ Morphogenetic Protease gp175

Bacteriophage T4 Genome

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