We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V.harveyi ATTC BAA-1116 and V.campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T=12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.

There is currently a handful of genome sequences available for tailed bacteriophages with genomes of more than 200 kbp of DNA, designated here as giant or jumbo phages. The majority of the proteins predicted from the genome sequences of these phages have no matches in the current sequence databases, and the genomes themselves are diverse enough to preclude the sorts of detailed comparative analysis that has benefited study of the smaller phages, for which hundreds of genome sequences are available. However, it is informative to extrapolate the better known genome organizations and mechanisms of evolution seen in the smaller phages to the jumbo phages. In this way, we see that the jumbo phages encode the same functions as the smaller phages, supplemented with large numbers of mostly small genes of mostly undiscovered functions. A case can be made that the jumbo phages evolved from smaller tailed phages, possibly in a process mediated by the constraints imposed on genome size by capsid size.

The bacteriophage HK97 capsid is a molecular machine that exhibits large-scale conformational rearrangements of its 420 identical protein subunits during capsid maturation. Immature empty capsids, termed Prohead II, assemble in vivo in an Escherichia coli expression system. Maturation of these particles may be induced in vitro, converting them into Head II capsids that are indistinguishable in conformation from the capsid of an infectious phage particle. One method of in vitro maturation requires acidification to drive the reaction through two expansion intermediates (EI-I, EI-II) to its penultimate particle state (EI-III), which has 86% more internal volume than Prohead II. Neutralization of EI-III produces the fully mature capsid, Head II. The three expansion intermediates and the acid expansion pathway were characterized by cryo-EM analysis and 3D reconstruction. We now report that, although large-scale structural changes are involved, the electron density maps for these intermediate states are readily interpreted in terms of quasi-atomic models based on subunit structures determined by prior crystallographic analysis of Head II. Progression through the expansion intermediate states primarily represents rigid-body rotations and translations of the subunits, accompanied by refolding of two small regions, the N-terminal arm and a β-hairpin called the E-loop. Movies made with these pseudo-atomic coordinates and the Head II X-ray coordinates illuminate various aspects of the maturation pathway in the course of which the pattern of inter-subunit interactions is sequentially transformed while the integrity of the capsid is maintained.

(Current Biology 16, R11–R13; January 10, 2006) As a result of an oversight during the production of this Correspondence, in two references to bacteriophage λ in the paragraph spanning pages R12 and R13, the Greek symbol λ was replaced by the numeral 1. This error has now been corrected online. Shared architecture of bacteriophage SPO1 and herpesvirus capsidsDuda et al.Current BiologyJanuary 10, 2006In BriefViruses have probably existed for as long as cells. Recent structural studies of viral capsids have revealed similarities that span the domains of life and point to distant evolutionary connections between viruses that pre-date the division of their host organisms into domains [1–3]. Comparisons of adenovirus and phage PRD1 demonstrate this emerging theme: these viruses share a unique T=25 capsid geometry with unusual 'trimeric hexons' and a common core fold for the major capsid proteins [4]. We describe a novel structural link between herpesviruses and the bacteriophage SPO1 revealed by cryo-electron microscopy (cryoEM) data showing that the SPO1 capsid has icosahedral geometry with triangulation number T=16, a value previously associated uniquely with herpesviruses, as well as an asymmetric capsid surface molecule reminiscent of the 'triplex' molecule of HSV-1. Full-Text PDF Open Archive

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

Dynamic shifts between open reading frames and the redefinition of codon meaning at specific sites, programmed by signals in mRNA, permits versatility of gene expression. Such alterations are characteristic of organisms in all domains of life and serve a variety of functional purposes. In this article, we concentrate on programmed ribosomal frameshifting, stop codon read-through and transcriptional slippage in the decoding of phage genes and bacterial mobile elements. Together with their eukaryotic counterparts, the genes encoding these elements are the richest known source of nonstandard decoding. Recent analyses revealed several novel sequences encoding programmed alterations in gene decoding and provide a glimpse of the emerging picture.

A vital part of a virus is its protein shell, called the viral capsid, that encapsulates and hence protects the viral genome. It has been shown in Twarock [2004. A tiling approach to vius capsids assembly explaining a structural puzzle in virology. J. Theor. Biol. 226, 477–482] that the surface structures of viruses with icosahedrally symmetric capsids can be modelled in terms of tilings that encode the locations of the protein subunits. This theory is extended here to multi-level tilings in order to model crosslinking structures. The new framework is demonstrated for the case of bacteriophage HK97, and it is shown, how the theory can be used in general to decide if crosslinking, and what type of crosslinking, is compatible from a mathematical point of view with the geometrical surface structure of a virus.

ABSTRACT The generalized transducing double-stranded DNA bacteriophage ES18 has an icosahedral head and a long noncontractile tail, and it infects both rough and smooth Salmonella enterica strains. We report here the complete 46,900-bp genome nucleotide sequence and provide an analysis of the sequence. Its 79 genes and their organization clearly show that ES18 is a member of the lambda-like (lambdoid) phage group; however, it contains a novel set of genes that program assembly of the virion head. Most of its integration-excision, immunity, Nin region, and lysis genes are nearly identical to those of the short-tailed Salmonella phage P22, while other early genes are nearly identical to Escherichia coli phages λ and HK97, S. enterica phage ST64T, or a Shigella flexneri prophage. Some of the ES18 late genes are novel, while others are most closely related to phages HK97, lambda, or N15. Thus, the ES18 genome is mosaically related to other lambdoid phages, as is typical for all group members. Analysis of virion DNA showed that it is circularly permuted and about 10% terminally redundant and that initiation of DNA packaging series occurs across an approximately 1-kbp region rather than at a precise location on the genome. This supports a model in which ES18 terminase can move substantial distances along the DNA between recognition and cleavage of DNA destined to be packaged. Bioinformatic analysis of large terminase subunits shows that the different functional classes of phage-encoded terminases can usually be predicted from their amino acid sequence.

Bacteriophage HK97 illustrates a number of assembly mechanisms, among them mechanisms that appear to be shared widely with other tailed phages under study and others that are at least unusual. Comparisons of capsid protein sequences argue, moreover, that HK97 is a member of an evolutionarily related family of phages that may encompass the entirety of the tailed phages. HK97 provides a rich source of head assembly mechanisms, spanning from the overall organization of the pathway to atomic level details of the motions of the capsid subunits during capsid maturation. Many of the features of the pathway resemble those of other tailed phages for which capsid assembly has been studied in detail, despite the lack of detectable sequence similarity in the respective proteins. Some specific details of the HK97 pathway, such as the chain-mail cross-linking and the use of an attached scaffolding protein, are unique to HK97 among the well-studied systems. The bacterial hosts associated with the HK97 capsid protein sequences span a wide phylogenetic range, and the strength of sequence matches vary from identity to barely detectable. It is plausible (although not yet proved) that the common ancestor of the HK97-like sequences may be the common ancestor of all tailed phage capsid genes, some of which have drifted too far in sequence to be recognizably related.

In HK97 capsid maturation, structural change (‘expansion’) is accompanied by formation of covalent crosslinks, connecting residue K169 in the ‘E‐loop’ of each subunit with N356 on another subunit. We show by complementation experiments with the K169Y mutant, which cannot crosslink, that crosslinking is an essential function. The precursor Prohead‐II passes through three expansion intermediate (EI) states en route to the end state, Head‐II. We investigated the effects of expansion and crosslinking on stability by differential scanning calorimetry of wild‐type and K169Y capsids. After expansion, the denaturation temperature (Tp) of K169Y capsids is slightly reduced, indicating that their thermal stability is not enhanced, but crosslinking effects a major stabilization (ΔTp, +11°C). EI‐II is the earliest capsid to form crosslinks. Cryo‐electron microscopy shows that for both wild‐type and K169Y EI‐II, most E‐loops are in the ‘up’ position, 30 Å from the nearest N356: thus, crosslinking in EI‐II represents capture of mobile E‐loops in ‘down’ positions. At pH 4, most K169Y capsids remain as EI‐II, whereas wild‐type capsids proceed to EI‐III, suggesting that crosslink formation drives maturation by a Brownian ratchet mechanism.

The capsid of Escherichia coli bacteriophage HK97 assembles as a 420 subunit icosahedral shell called Prohead I which undergoes a series of maturation steps, including proteolytic cleavage, conformational rearrangements, and covalent cross-linking among all the subunits to yield the highly stable mature Head II shell. Prohead I have been shown to assemble from pre-formed hexamers and pentamers of the capsid protein subunit. We report here the properties of a mutant of the capsid protein, E219K, which illuminate the assembly of Prohead I. The mutant capsid protein is capable of going through all of the biochemically and morphologically defined steps of capsid maturation, and when it is expressed by itself from a plasmid it assembles efficiently into a Prohead I that is morphologically indistinguishable from the wild-type Prohead I, with a full complement of both hexamers and pentamers. Unlike the wild-type Prohead I, when the mutant structure is dissociated into capsomers in vitro, only hexamers are found. When such preparations are put under assembly conditions, these mutant hexamers assemble into "Whiffleballs", particles that are identical with Prohead I except that they are missing the 12 pentamers. These Whiffleballs can even be converted to Prohead I by specifically binding wild-type pentamers. We argue that the ability of the mutant hexamers to assemble in the absence of pentamers implies that they retain a memory of their earlier assembled state, most likely as a conformational difference relative to assembly-naive hexamers. The data therefore favor a model in which Prohead I assembly is regulated by conformational switching of the hexamer.

We report the complete genome sequence of enterobacteriophage SP6, which infects Salmonella enterica serovar Typhimurium. The genome contains 43,769 bp, including a 174-bp direct terminal repeat. The gene content and organization clearly place SP6 in the coliphage T7 group of phages, but there is approximately 5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes 1.3 through 3 appear to have undergone an unusual reorganization. Sequence analysis identified 10 putative promoters for the SP6-encoded RNA polymerase and seven putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provided clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcated exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggested that DNA replication occurs in large part through a bidirectional mechanism, possibly with circular intermediates.