Bacteriophage T4 genetic homologies with bacteria and eucaryotes

Bernstein, Harris; Bernstein, Carol

doi:10.1128/jb.171.5.2265-2270.1989

Cited by 40 publications

(20 citation statements)

References 60 publications

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“…T4 encodes almost all of the proteins required for its own DNA transactions, and these proteins more closely resemble their counterparts in archaea and eukaryotes than in eubacteria (40). Despite several decades of vigorous exploration of T4 repair mechanisms, there is a striking absence of any report of the kind of break-reunion recombination repair so well characterized in E. coli.…”

Section: Discussionmentioning

confidence: 98%

UvsX Recombinase and Dda Helicase Rescue Stalled Bacteriophage T4 DNA Replication Forks in Vitro

Kadyrov¹,

Drake

2004

Journal of Biological Chemistry

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The rescue of stalled replication forks via a series of steps that include fork regression, template switching, and fork restoration often has been proposed as a major mechanism for accurately bypassing non-coding DNA lesions. Bacteriophage T4 encodes almost all of the proteins required for its own DNA replication, recombination, and repair. Both recombination and recombination repair in T4 rely on UvsX, a RecA-like recombinase. We show here that UvsX plus the T4-encoded helicase Dda suffice to rescue stalled T4 replication forks in vitro. This rescue is based on two sequential template-switching reactions that allow DNA replication to bypass a non-coding DNA lesion in a non-mutagenic manner.DNA template-strand lesions that prevent the extension of primer strands are usually lethal. Four general mechanisms operate to overcome such lethality: direct repair that regenerates a native structure (e.g. photoreaction and dealkylation), excision repair that replaces damaged bases or deoxyribose residues, translesion synthesis that is usually mutation-prone, and recombination repair that accurately bypasses DNA damage.The essence of recombination repair is that it derives accurate genetic information from the nascent sister chromatid (or from a homologous chromosome when repairing a double strand break); excision repair, on the other hand, derives the requisite genetic information from the complementary strand of the same double helix. Recombination repair was first characterized in Escherichia coli (1-4). The classical E. coli breakreunion model holds that blocked primer extension is followed by downstream reinitiation, leaving a gap that is then filled at least in part by the physical donation of a strand of appropriate polarity cut from the sister chromatid. The donating strand gap is filled by DNA synthesis, whereas the blocking lesion remains as a problem for the future.Recent progress in understanding recombination repair, based mainly on work with E. coli, has highlighted its importance for rescuing replication forks stalled at sites of DNA damage or spontaneous fork collapse (8 -11). One model of recombination repair (Fig. 1) invokes a topological rearrangement in which the fork regresses into a configuration in which the parental strands reanneal and the two daughter strands anneal. This rearrangement generates a structure that constitutes a Holliday junction and that to some resembles a chicken foot (12). In the case of a primer strand whose extension is blocked by a lesion in the template strand, fork regression provides a template that allows limited primer extension. Subsequent reformation of a conventional replication fork then provides a primer strand that has accurately bypassed the template lesion. This pathway was named replication repair and was initially suggested to occur during mammalian DNA replication (5). It was later validated by genetical and enzymological analyses in phage T4 (6, 7).In addition to a DNA polymerase, the canonical model of replication repair (Fig. 1) immediately suggests roles f...

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Section: Discussionmentioning

confidence: 98%

UvsX Recombinase and Dda Helicase Rescue Stalled Bacteriophage T4 DNA Replication Forks in Vitro

Kadyrov¹,

Drake

2004

Journal of Biological Chemistry

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“…By contrast, an SRP-based cotranslational targeting mechanism that promotes rapid association of ribosome-nascent-chain complexes with transport channels appears to be required for effective biogenesis of extremely hydrophobic IMPs that would tend to aggregate if exposed to the cytoplasmic environment. Moreover, recent results suggest that a highly efficient targeting system for IMPs is required partly to protect cells from the toxic effects of mislocalizing hydrophobic proteins in the cytoplasm (36). Nevertheless, a significant fraction of many SRP substrates can be transported across the IM by secondary pathways (6,7,22,27).…”

Section: Discussionmentioning

confidence: 99%

The targeting pathway of Escherichia coli presecretory and integral membrane proteins is specified by the hydrophobicity of the targeting signal

Lee

Bernstein

2001

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

186

176

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Previous studies have demonstrated that presecretory proteins such as maltose binding protein (MBP) and outer membrane protein A (OmpA) are targeted to the Escherichia coli inner membrane by the molecular chaperone SecB, but that integral membrane proteins are targeted by the signal recognition particle (SRP). In vitro studies have suggested that trigger factor binds to a sequence near the N terminus of the mature region of OmpA and shunts the protein into the SecB pathway by blocking an interaction between SRP and the signal peptide. By contrast, we have found that the targeting pathway of a protein under physiological conditions is dictated by the composition of its targeting signal. Replacement of the MBP or OmpA signal peptide with the first transmembrane segment of AcrB abolished the dependence on SecB for transport and rerouted both proteins into the SRP targeting pathway. More modest alterations of the MBP signal peptide that simply increase its hydrophobicity also promoted SRP binding. Furthermore, we obtained evidence that SRP has a low affinity for typical signal peptides in vivo. These results imply that different classes of E. coli proteins are targeted by distinct pathways because bacterial SRP binds to a more restricted range of targeting signals than its eukaryotic counterpart.

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“…The 46 and 47 proteins, acting in a complex, have similarity to the E. coli SbcBC and RecBC proteins and the eukaryotic Rad50/Mre11 complex. The strand invasion UvsX protein is a structural and functional homologue of the E. coli RecA protein and the eukaryotic Rad51, Dmc1, and Rad54 proteins (69,192,739). As expected, if this is the major pathway to initiate T4 replication forks, defective mutants arrest DNA replication after limited origin replication has occurred.…”

Section: Recombination and Recombination-dependent Dna Replicationmentioning

confidence: 99%

“…T4 proteins involved in nucleotide and nucleic acid metabolism typically show sequence similarity to functionally related enzymes of other organisms (69). Proteins that have orthologs in the database are often members of multientry clusters of orthologous groups (COGs) curated at the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih .gov/COG).…”

Section: Orthologous T4 Proteinsmentioning

confidence: 99%

Bacteriophage T4 Genome

Miller

Kutter

Mosig

et al. 2003

Microbiol Mol Biol Rev

701

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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Bacteriophage T4 genetic homologies with bacteria and eucaryotes

Cited by 40 publications

References 60 publications

UvsX Recombinase and Dda Helicase Rescue Stalled Bacteriophage T4 DNA Replication Forks in Vitro

UvsX Recombinase and Dda Helicase Rescue Stalled Bacteriophage T4 DNA Replication Forks in Vitro

The targeting pathway of Escherichia coli presecretory and integral membrane proteins is specified by the hydrophobicity of the targeting signal

Bacteriophage T4 Genome

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