Bacteriophage P4 DNA replication

Ziegelin, Günter

doi:10.1016/0168-6445(94)00080-8

Cited by 9 publications

(11 citation statements)

References 22 publications

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“…Phage- or plasmid-associated DNA primase ( Ziegelin and Lanka 1995 ) have been reported in various green algal lineages, including prasinophytes ( Turmel et al. 1999 ; Turmel, Gagnon, et al 2009 ), Chlorophyceae ( Brouard et al.…”

Section: Resultsmentioning

confidence: 99%

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Cremen

Leliaert

Marcelino

et al. 2018

Genome Biology and Evolution

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Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.

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Section: Resultsmentioning

confidence: 99%

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Cremen

Leliaert

Marcelino

et al. 2018

Genome Biology and Evolution

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“…However, they vary in the direction of translocation: for example, E. coli DnaB and bacteriophage T7 gene 4 translocate in the 5’ to 3’ direction but, bacteriophage P4 helicase and the archaeal and eukaryotic MCM helicases show the opposite polarity 31–34 . To test the polarity of Cch, we compared its activity on substrates with 3’ or 5’ single stranded tails as well as blunt ends.…”

Section: Resultsmentioning

confidence: 99%

Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative

Mir-Sanchis

Roman

Misiura

et al. 2016

Nat Struct Mol Biol

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Methicillin resistant Staphylococcus aureus (MRSA) is a public health threat worldwide. Although the mobile genomic island responsible for this phenotype, called SCC, was labeled non-replicative, we predicted DNA replication-related functions for some of their conserved proteins. We show that one of these, Cch, is homologous to the self-loading initiator helicases of an unrelated family of genomic islands, that it is an active 3’ to 5' helicase, and that the adjacent ORF encodes an ssDNA-binding protein. Our 2.9Å crystal structure of intact Cch shows that it forms a hexameric ring. Cch belongs to the pre-sensor II insert clade of AAA+ ATPases, as do the archaeal and eukaryotic MCM-family replicative helicases. Additionally, we find that SCC elements are part of a broader family of mobile elements that all encode a replication initiator upstream of their recombinases. Replication after excision would enhance the efficiency of horizontal gene transfer.

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“…Family A polymerases fill DNA gaps that arise during DNA repair, recombination and replication, and are found primarily in prokaryotes [ 34 ]. Orf16 showed high similarity to phage/plasmid DNA primases, which are known from phages and plasmids of Bacteria and Archaea [ 35 ]. The presence of these four ORFs indicates that the 7 kp region may be a mobile element of bacterial origin.…”

Section: Resultsmentioning

confidence: 99%

The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin

Leliaert

Lopez-Bautista

2015

BMC Genomics

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BackgroundSpecies of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified).ResultsBoth DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.ConclusionsThe cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1418-3) contains supplementary material, which is available to authorized users.

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Bacteriophage P4 DNA replication

Cited by 9 publications

References 22 publications

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative

The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin

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