Identification and characterization of domesticated bacterial transposases

Bertels, Frederic; Gallie, Jenna; Rainey, Paul B.

doi:10.1101/119735

Cited by 2 publications

(14 citation statements)

References 55 publications

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“…Gene annotation, sequence alignments, and phylogenetic tree construction. Prochlorosin annotations were taken from [1] , and TnpA REP from [18], [24] . Prediction of procA and tnpA REP genes was expanded to new strains using BLASTP (E value of 1e-5) with ProcA or TnpA REP protein sequence query.…”

Section: Methodsmentioning

confidence: 99%

“…In the process of our detailed exploration of prochlorosin genomic structure and context, however, we observed the association of prochlorosin genes with a single-stranded DNA transposase from the TnpA REP family [15]- [18] (Fig. 1).…”

Section: Observationmentioning

confidence: 99%

“…1). TnpA REP transposases are single-stranded DNA recombinases that -unlike the closely-related IS200-like transposasesare considered domesticated in the sense that they do not move across genomes in a typical transposon structure, but rather are involved in creating large repeat regions containing 'REPs' (Repetitive Extragenic Palindromes, motifs that form DNA hairpin structures) [15], [18]- [20] . For example, there are 600 REP repeats in E. coli , representing ~1% of its genome [21] .…”

Section: Observationmentioning

confidence: 99%

“…We found a number of TnpA REP family transposase homologs in marine picocyanobacteria, all of them forming a monophyletic group that appears to be descended from TnpA REP in other cyanobacteria such as Trichodesmium erythraeum (Sup Fig 1, 2). They belong to a subclass of TnpA REP (RAYT group 1 in [18] , or subclass 2.1 in [24] ) which possess an additional conserved domain in the C-terminal region, likely involved in DNA-binding [24] . In marine picocyanobacteria, the tnpA REP genes tend to co-localize with clusters or individual procA genes, which encode for the peptides that are cyclized by ProcM to become the final product: prochlorosins ( Fig.…”

Section: Observationmentioning

confidence: 99%

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Association of lanthipeptide genes with TnpA_REPtransposases in marine picocyanobacteria

Laurenceau

Raho

Cariani

et al. 2020

Preprint

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Lanthipeptides are a family of ribosomally synthesized, post-translationally modified peptides that are widespread among bacteria, typically functioning as antibacterials. The marine picocyanobacteria Prochlorococcus and Synechococcus produce an unusual and diverse set of lanthipeptides of unknown function called prochlorosins. While well-studied model bacteria produce one or two different molecules of this type, a single picocyanobacterium can produce as many as 80; the community of picocyanobacteria in a single milliliter of seawater can collectively encode up to 10,000 prochlorosins. The molecular events that led to this expansion and diversification of the lanthipeptide repertoire in picocyanobacteria -the numerically dominant photosynthesizers in the oceans -is unknown.We present evidence for an unusual association between prochlorosin genes with a single-stranded DNA transposase belonging to the TnpA REP family. The genes co-occur and co-localize across the phylogeny of marine picocyanobacteria forming a distinct association pattern within genomes, most likely resulting from the transposase activity. Given the role of TnpA REP homologs in other bacteria, we propose -based on genomic structures -that they contribute to the creation of the prochlorosin structural diversity through a diversifying recombination mechanism. IMPORTANCEOnly a few mechanisms have been described that promote the diversification of a targeted gene region in bacteria. We present indirect evidence that the TnpA REP transposases associated with

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Section: Methodsmentioning

confidence: 99%

Section: Observationmentioning

confidence: 99%

Section: Observationmentioning

confidence: 99%

Section: Observationmentioning

confidence: 99%

See 2 more Smart Citations

Association of lanthipeptide genes with TnpA_REPtransposases in marine picocyanobacteria

Laurenceau

Raho

Cariani

et al. 2020

Preprint

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“…The apparent stability of tnpA REP genes raises the question of how and why they are maintained in their host bacterial genomes. This was recently addressed through an analysis of tnpA REP properties and a comparison to transposases of IS families (IS 200 /IS 605 and the entirely unrelated IS 110 ) and two housekeeping genes [38]. The observations that tnpA REP share more characteristics with housekeeping genes than with insertion sequences and that tnpA REP are predominantly vertically transmitted, at the subgenus level, suggest that they have a yet uncharacterized function(s) that benefit their host cell and hence insure their maintenance [38].…”

Section: Introductionmentioning

confidence: 99%

Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

Quentin

Siguier

Chandler

et al. 2018

Preprint

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BackgroundSome mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-stranded circular DNA intermediates for excision and insertion and encode a transposase, TnpAIS200, which recognizes subterminal secondary structures at the insertion sequence ends. Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes. TnpAIS200-related proteins, TnpAREP, have been identified and could be responsible for REP sequence proliferation. These proteins share a conserved HuH/Tyrosine core domain responsible for catalysis and are involved in processes of ssDNA cleavage and ligation. Our goal is to characterize the diversity of these proteins collectively referred as the TnpAY1 family.ResultsA genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles.ConclusionsWe established a detailed classification of TnpAY1 proteins, consolidated by the analysis of the conserved core domains and the characterization of additional domains. The data obtained illustrate the unexpected diversity of the TnpAY1 family and provide a strong framework for future evolutionary and functional studies. By their potential function in ssDNA edition, they may confer adaptive responses to host cell physiology and metabolism.

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Identification and characterization of domesticated bacterial transposases

Abstract: IntroductionMechanisms for the maintenance of selfish genetic elements (SGEs) have been discussed for over 40 years

Cited by 2 publications

References 55 publications

Association of lanthipeptide genes with TnpA_REPtransposases in marine picocyanobacteria

Association of lanthipeptide genes with TnpA_REPtransposases in marine picocyanobacteria

Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

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Identification and characterization of domesticated bacterial transposases

Abstract: IntroductionMechanisms for the maintenance of selfish genetic elements (SGEs) have been discussed for over 40 years

Cited by 2 publications

References 55 publications

Association of lanthipeptide genes with TnpAREPtransposases in marine picocyanobacteria

Association of lanthipeptide genes with TnpAREPtransposases in marine picocyanobacteria

Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases

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Association of lanthipeptide genes with TnpA_REPtransposases in marine picocyanobacteria

Association of lanthipeptide genes with TnpA_REPtransposases in marine picocyanobacteria