The Chromosome of Shigella flexneri Bacteriophage Sf6: Complete Nucleotide Sequence, Genetic Mosaicism, and DNA Packaging

Casjens, Sherwood; Winn-Stapley, Danella A.; Gilcrease, Eddie B.; Morona, Renato; Kühlewein, Christiane; Chua, James E. H.; Manning, Paul A.; Inwood, William; Clark, Alvin J.

doi:10.1016/j.jmb.2004.03.068

Cited by 130 publications

(167 citation statements)

References 76 publications

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“…Nucleotide sugars are the building blocks for peptidoglycan and lipopolysaccharides, required for cell growth and division. Multiple examples exist of phage proteins that inhibit cell division or cell wall biosynthesis, such as lysis protein E of phiX174 (Bernhardt et al, 2001) or the kil proteins in phages Mu (Waggoner et al, 1989), P22 (Semerjian et al, 1989), lambda (Sergueev et al, 2001) and Sf6 (Casjens et al, 2004). Homologs of these proteins share only low levels of sequence similarity (Sau et al, 2008), and have not yet been identified in these Pseudomonas phages.…”

Section: Resultsmentioning

confidence: 99%

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

et al. 2016

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Phage-mediated metabolic changes in bacteria are hypothesized to markedly alter global nutrient and biogeochemical cycles. Despite their theoretic importance, experimental data on the net metabolic impact of phage infection on the bacterial metabolism remains scarce. In this study, we tracked the dynamics of intracellular metabolites using untargeted high coverage metabolomics in Pseudomonas aeruginosa cells infected with lytic bacteriophages from six distinct phage genera. Analysis of the metabolomics data indicates an active interference in the host metabolism. In general, phages elicit an increase in pyrimidine and nucleotide sugar metabolism. Furthermore, clear phage-specific and infection stage-specific responses are observed, ranging from extreme metabolite depletion (for example, phage YuA) to complete reorganization of the metabolism (for example, phage phiKZ). As expected, pathways targeted by the phage-encoded auxiliary metabolic genes (AMGs) were enriched among the metabolites changing during infection. The effect on pyrimidine metabolism of phages encoding AMGs capable of host genome degradation (for example, YuA and LUZ19) was distinct from those lacking nuclease-encoding genes (for example, phiKZ), which demonstrates the link between the encoded set of AMGs of a phage and its impact on host physiology. However, a large fraction of the profound effect on host metabolism could not be attributed to the phage-encoded AMGs. We suggest a potentially crucial role for small, 'non-enzymatic' peptides in metabolism take-over and hypothesize on potential biotechnical applications for such peptides. The highly phage-specific nature of the metabolic impact emphasizes the potential importance of the 'phage diversity' parameter when studying metabolic interactions in complex communities.

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Section: Resultsmentioning

confidence: 99%

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

et al. 2016

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“…A large region of ∼1; 800 bp in Sf6 genomic DNA that encompasses gp1-and a part of gp2-coding sequences was implicated to harbor the packaging signal (19). To characterize the binding of gp1 to the viral genomic DNA, we performed electrophoretic mobility shifting assay using the DNA corresponding to the region in the Sf6 genome that encodes gp1 and gp2 (the gp1-gp2 coding DNA).…”

Section: Resultsmentioning

confidence: 99%

“…Bacteriophage Sf6 is a member of the Podoviridae family of tailed dsDNA bacteriophage and an evolutionarily close relative of bacteriophage P22 (19,20). Sf6 infects Shigella flexneri, an important human pathogen that can cause acute diarrhoea and bacillary dysentery.…”

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confidence: 99%

“…Sf6 is of particular interest because of its ability to alter the host's serotype and virulence by changing host lipopolysaccharide structure via horizontal gene transfer (21). The Sf6 terminase consists of the DNA-recognition component gp1 and the catalytic component gp2 (19). Here we present the atomic structure of the terminase DNA-recognition component gp1 of bacteriophage Sf6 at 1.65 Å resolution.…”

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confidence: 99%

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Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine

Zhao

Finch

Sequeira

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

101

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In herpesviruses and many bacterial viruses, genome-packaging is a precisely mediated process fulfilled by a virally encoded molecular machine called terminase that consists of two protein components: A DNA-recognition component that defines the specificity for packaged DNA, and a catalytic component that provides energy for the packaging reaction by hydrolyzing ATP. The terminase docks onto the portal protein complex embedded in a single vertex of a preformed viral protein shell called procapsid, and pumps the viral DNA into the procapsid through a conduit formed by the portal. Here we report the 1.65 Å resolution structure of the DNA-recognition component gp1 of the Shigella bacteriophage Sf6 genomepackaging machine. The structure reveals a ring-like octamer formed by interweaved protein monomers with a highly extended fold, embracing a tunnel through which DNA may be translocated. The N-terminal DNA-binding domains form the peripheral appendages surrounding the octamer. The central domain contributes to oligomerization through interactions of bundled helices. The C-terminal domain forms a barrel with parallel beta-strands. The structure reveals a common scheme for oligomerization of terminase DNA-recognition components, and provides insights into the role of gp1 in formation of the packaging-competent terminase complex and assembly of the terminase with the portal, in which ring-like protein oligomers stack together to form a continuous channel for viral DNA translocation.terminase | DNA-packaging | oligomer | bacteriophage | protein:DNA interaction I n many tailed double-stranded DNA (dsDNA) bacteriophages and herpesvirus, the newly synthesized viral DNA in the infected host cell is present as a concatemer that is comprised of multiple copies of unit-length genome. The concatemeric DNA is packaged into a preformed capsid precursor termed procapsid through a channel formed by a portal protein complex embedded in a unique vertex of the procapsid (1-5). The DNApackaging process involves a precisely coordinated sequence of molecular events, driven by a molecular machine called terminase consisting of two proteins: A DNA-recognition component and a catalytic component, also known as the "small" and "large" subunit, respectively. The terminase specifically binds to concatemeric viral DNA through the DNA-recognition component and cleaves it using the catalytic component, generating a new terminus for the DNA. This terminus is threaded through the portal protein channel embedded in the procapsid, and the catalytic component pumps the DNA into the procapsid in an ATP-dependent manner. When an appropriate amount of DNA is inserted, the terminase cuts the DNA again, dissociates from the procapsid, and can start the next cycle of DNA-packaging. Many of these features in DNA-packaging are also shared by adenoviruses (6). The x-ray structures of the catalytic component from bacteriophage T4 and the portals from various phages were previously described (7-10). However, it is not known how the terminases are assembled and h...

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“…Cloning and Protein Expression of Needle Protein Knob-The gene-encoding phage Sf6 tail needle was PCR-amplified from genomic DNA (23) and ligated between the XbaI and HindIII restriction sites of the vector pMal-c2e (New England Biolabs), fusing the Sf6 tail needle to an N-terminal maltose binding protein (MBP) (12). A PreScission Protease cleavage site was engineered between the MBP and the tail needle gene.…”

Section: Methodsmentioning

confidence: 99%

Atomic Structure of Bacteriophage Sf6 Tail Needle Knob

Bhardwaj

Molineux

Casjens

et al. 2011

Journal of Biological Chemistry

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Podoviridae are double-stranded DNA bacteriophages that use short, non-contractile tails to adsorb to the host cell surface. Within the tail apparatus of P22-like phages, a dedicated fiber known as the "tail needle" likely functions as a cell envelopepenetrating device to promote ejection of viral DNA inside the host. In Sf6, a P22-like phage that infects Shigella flexneri, the tail needle presents a C-terminal globular knob. This knob, absent in phage P22 but shared in other members of the P22-like genus, represents the outermost exposed tip of the virion that contacts the host cell surface. Here, we report a crystal structure of the Sf6 tail needle knob determined at 1.0 Å resolution. The structure reveals a trimeric globular domain of the TNF fold structurally superimposable with that of the tail-less phage PRD1 spike protein P5 and the adenovirus knob, domains that in both viruses function in receptor binding. However, P22-like phages are not known to utilize a protein receptor and are thought to directly penetrate the host surface. At 1.0 Å resolution, we identified three equivalents of L-glutamic acid (L-Glu) bound to each subunit interface. Although intimately bound to the protein, L-Glu does not increase the structural stability of the trimer nor it affects its ability to self-trimerize in vitro. In analogy to P22 gp26, we suggest the tail needle of phage Sf6 is ejected through the bacterial cell envelope during infection and its C-terminal knob is threaded through peptidoglycan pores formed by glycan strands.

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The Chromosome of Shigella flexneri Bacteriophage Sf6: Complete Nucleotide Sequence, Genetic Mosaicism, and DNA Packaging

Cited by 130 publications

References 76 publications

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine

Atomic Structure of Bacteriophage Sf6 Tail Needle Knob

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