Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements

Redrejo-Rodríguez, Modesto; Ordóñez, Carlos D.; Berjón-Otero, Mónica; Moreno-González, Juan; Aparicio-Maldonado, Cristian; Forterre, Patrick; Salas, Margarita; Krupovìč, Mart

doi:10.1016/j.celrep.2017.10.039

Cited by 31 publications

(65 citation statements)

References 74 publications

(90 reference statements)

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“…In some genomes, three att-repeats were detected, as those pipolins seem to share the integration site and mechanism with some prophage, as previously detected for the enterotoxigenic Escherichia coli H10407 strain [3]. Indeed, comparison of the genetic structure of all pipolins ( Figure S5), confirmed that a similar myovirus enterophage is present next to pipolins from eight strains, spanning phylogroups A (H10407, 2014EL-1346-6 and 99-3165), C (LREC239 and LREC246) and D (112648, 122715, 2015C-3125 and FWSEC0002).…”

Section: Mapping and Extraction Of New Pipolins From Lrec And Genbanksupporting

confidence: 63%

“…This analysis showed that an important proportion of pipolins from phylogroups C and D, but Overall, we can conclude that the pipolins diversity is poorly congruent with the strains phylogeny and their distribution is rather indicative of a patchy distribution amongst a wide variety of pathogenic E. coli strains, as expected from horizontally transferred MGEs. This pattern may reflect the wide distribution of pipolins beyond E. coli, dispersed among major bacterial phyla, namely Actinobacteria, Firmicutes, and Proteobacteria, as well as in mitochondria [3]. Tanglegram representation of maximum-likelihood comparative phylogenies of piPolB and host strains core genome as hallmark of pipolins.…”

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confidence: 99%

“…cassettes and antibiotic resistance genes, which are usually carried by MGEs, such as 99 pathogenicity islands (PAIs), plasmids, integrons, etc [9][10][11]. However, the annotation 100 of pipolins from E. coli as well as from proteobacteria did not lead to the identification of 101 any antibiotic resistance genes or virulence factors [3].…”

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confidence: 99%

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High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains

Flament-Simon¹,

Toro

Chuprikova

et al. 2020

Preprint

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31 32 Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that 33 encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they 34 are proposed as key players in the evolution of several groups of DNA viruses and 35 virus-host interaction machinery. Pipolins are the most recent addition to the group, are 36 integrated in the genomes of bacteria from diverse phyla and also present as circular 37 plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA 38 polymerases endowed with DNA priming capacity, hence the name, primer-

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Section: Mapping and Extraction Of New Pipolins From Lrec And Genbanksupporting

confidence: 63%

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confidence: 99%

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High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains

Flament-Simon¹,

Toro

Chuprikova

et al. 2020

Preprint

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“…This might be due to insufficient sampling or to genuine lack of these elements in this archaeal phylum. By contrast, bacteria are known to (Nicolas et al, 2015); various pathogenicity islands and phage-inducible chromosomal islands that are induced upon phage infection and hijack the virus particle for intercellular transmission (Novick and Ram, 2016;; mobile integrons, complex genetic platforms that allow bacteria to evolve rapidly through the acquisition, excision and shuffling of genes found in mobile elements known as cassettes (Escudero et al, 2015); or pipolins, a recently characterized group of bacterial iMGE encoding primer-independent DNA polymerases (Redrejo-Rodríguez et al, 2017). However, given our limited understanding on the archaeal mobilome and especially the diversity of iMGE, it cannot be ruled out that counterparts to some of these bacterial iMGE classes in thaumarchaea are awaiting discovery.…”

Section: Discussionmentioning

confidence: 99%

Integrated mobile genetic elements in Thaumarchaeota

Krupovìč

Makarova

Wolf

et al. 2019

Environmental Microbiology

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Summary To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence‐like transposons, (iv) integrative‐conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly‐roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I‐B CRISPR‐Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.

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“…This complexity may be reduced by exploiting more minimal replisomes, for example those of infective viruses or phages. [141] Bacteriophage Phi29 from B. subtilis initiates replication by a protein-priming mechanism enabling a minimal set of four Phi29 replication proteins to suffice for in vitro amplification of heterologous DNA. [139] The T7 phage, infecting E. coli, uses a host component for processivity and can carry out the replication of duplex DNA with a minimum of four core components.…”

Section: Self-encoded Dna Replicationmentioning

confidence: 99%

Templated Self‐Replication in Biomimetic Systems

et al. 2019

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nanostructures and nanopatterns. [13][14][15] The specificity of the molecular recognitions between replicative units is concomitant with the encoding and transmission of information, with the degree of specificity determining the fidelty and capacity of information transfer against competing background interactions in noisy "chemical" environments. [16] However, the ability to replicate in this manner does not imply the ability to transmit additional heritable information-simple replicators can only replicate information related to recognition and template directed autocatalysis as this information is intrinsically linked to phenotype. In contrast to most artificial autocatalytic replicators, living systems (including viruses) store the key instructions for replication on an inheritable genetic system rather than in the native structures of the individual sub-components. This decoupling of phenotype and genotype enables heredity and open-ended evolution, the possibility of an indefinite increase in complexity, as evolutionary innovations aquired by natural selection are anchored in the genotype only. [17,18] The most prominent self-replicating molecules are nucleic acids, which form the fundamental basis for information storage and propagation in biological systems. The ability of polynucleic acids to store information is self-evident, and based upon the ability to form cognate Watson-Crick base pair interactions. Nucleic acid systems may have also formed the first genetic replicators in biology. The RNA world hypothesis postulates a stage in the origin of life in which RNA proliferated before the emergence of DNA and proteins. To do this, RNA must be able to carry out several key roles: information storage, catalysis, and (self-) replication. Multiple examples of catalytic RNAs (ribozymes) are known both from nature and in vitro selection experiments, [19][20][21][22] but there is no fossil evidence of an RNA capable of (self-)replication without the involvement of proteins.While minimal nucleic acid-only systems with replicationlike properties have been identified by directed evolution and engineering, limitations such as low activity, lack of generality, and poor information capacity limit their usefulness in bottomup synthetic biology, except in origin of life research. For the creation of more complex biological in vitro systems, RNA or DNA replication mechanisms involving more powerful protein enzymes are likely to be necessary. Even so, the achievement of self-sustained in vitro self-replication inspired by the central dogma of molecular biology is currently hampered by the requirement to encode and efficiently express the enormous A key characteristic of living systems is the storage and replication of information, and as such the development of self-replicating systems capable of heredity is of great importance to the fields of synthetic biology and origin of life research. In this review, the design and implementation of self-replicating systems in the context of bottom-up synthetic biology is discusse...

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Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements

Cited by 31 publications

References 74 publications

High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains

High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains

Integrated mobile genetic elements in Thaumarchaeota

Templated Self‐Replication in Biomimetic Systems

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