A novel family of tyrosine integrases encoded by the temperate pleolipovirus SNJ2

Wang, Jiao; Liu, Yingchun; Liu, Ying; Du, Kun; Xu, Shuqi; Wang, Yuchen; Krupovìč, Mart; Chen, Xiangdong

doi:10.1093/nar/gky005

Cited by 30 publications

(50 citation statements)

References 87 publications

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“…All plasmids of the pT26‐2 family encode an integrase of the tyrosine recombinase superfamily. So far, several families of tyrosine recombinases encoded by viruses and plasmids have been described in archaea (She et al ., ; Erauso et al ., ; Cossu et al ., ; Wang et al ., ). They are divided in two major types based on the strategy of integration (She et al ., ): for type I integrases, recombination of the circular element with the host chromosome leads to division of the integrase gene into two fragments, a longer Int(C) fragment and a shorter Int(N) fragment; in contrast, the type II integrases maintain an intact integrase‐encoding gene after recombination.…”

Section: Resultsmentioning

confidence: 97%

“…SiLiX (Miele et al ., ) is a programme developed to cluster homologous proteins into families based on blastp results. All‐against‐all blastp analyses were performed on all encoded pT26‐2 integrases with the addition of related integrases found in Thermococcales and Methanococcales and of an integrase and a part of the dataset recently used for the analysis of the SNJ2 integrase family (Wang et al ., ). The all‐against‐all integrases blastp results were grouped using the SiLiX package v1.2.8 (http://lbbe.univ-lyon1.fr/SiLiX; Miele et al ., ).…”

Section: Methodsmentioning

confidence: 97%

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The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Badel

Erauso

Gomez

et al. 2019

Environmental Microbiology

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Summary Although plasmids play an important role in biological evolution, the number of plasmid families well‐characterized in terms of geographical distribution and evolution remains limited, especially in archaea. Here, we describe the first systematic study of an archaeal plasmid family, the pT26‐2 plasmid family. The in‐depth analysis of the distribution, biogeography and host–plasmid co‐evolution patterns of 26 integrated and 3 extrachromosomal plasmids of this plasmid family shows that they are widespread in Thermococcales and Methanococcales isolated from around the globe but are restricted to these two orders. All members of the family share seven core genes but employ different integration and replication strategies. Phylogenetic analysis of the core genes and CRISPR spacer distribution suggests that plasmids of the pT26‐2 family evolved with their hosts independently in Thermococcales and Methanococcales, despite these hosts exhibiting similar geographic distribution. Remarkably, core genes are conserved even in integrated plasmids that have lost replication genes and/or replication origins suggesting that they may be beneficial for their hosts. We hypothesize that the core proteins encode for a novel type of DNA/protein transfer mechanism, explaining the widespread oceanic distribution of the pT26‐2 plasmid family.

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Section: Resultsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 97%

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Badel

Erauso

Gomez

et al. 2019

Environmental Microbiology

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“…By contrast, the att sites characterized for MGEs integrated in crenarchaeal genomes ranged from 29 to 69 bp (median length of 45 bp) (She et al, 2002). Similarly to the case of bacteria, archaeal MGEs often integrate into tRNA genes (Williams, 2002;She et al, 2004;Krupovic et al, 2010b;Béguin et al, 2016;Cossu et al, 2017;Wang et al, 2018a). However, other integration targets, including protein-coding genes and intergenic regions, have also been reported (Krupovic et al, 2010a;Shah et al, 2012;Anderson et al, 2017).…”

Section: Targets and Molecular Features Of Mge Integrationmentioning

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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“…For YR, we added the sequences found in kinetoplastids, the related proteins found by blastp searches and several known related proteins representatives of distinct groups {Flippase, Phage integrase, Resolvase (XerC and XerD) and Prokaryotic Transposase [also used by Lorenzi et al (2006)]}. We also included one representative sequence of each of the major clades recovered by Wang et al (2018) [90] (see Additional file 15).…”

Section: Evolution Of Dirs Elementsmentioning

confidence: 99%

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

et al. 2019

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Background Kinetoplastids are a flagellated group of protists, including some parasites, such as Trypanosoma and Leishmania species, that can cause diseases in humans and other animals. The genomes of these species enclose a fraction of retrotransposons including VIPER and TATE , two poorly studied transposable elements that encode a tyrosine recombinase (YR) and were previously classified as DIRS elements. This study investigated the distribution and evolution of VIPER and TATE in kinetoplastids to understand the relationships of these elements with other retrotransposons. Results We observed that VIPER and TATE have a discontinuous distribution among Trypanosomatidae, with several events of loss and degeneration occurring during a vertical transfer evolution. We were able to identify the terminal repeats of these elements for the first time, and we showed that these elements are potentially active in some species, including T. cruzi copies of VIPER . We found that VIPER and TATE are strictly related elements, which were named in this study as VIPER-like . The reverse transcriptase (RT) tree presented a low resolution, and the origin and relationships among YR groups remain uncertain. Conversely, for RH, VIPER-like grouped with Hepadnavirus , whereas for YR, VIPER-like sequences constituted two different clades that are closely allied to Crypton . Distinct topologies among RT, RH and YR trees suggest ancient rearrangements/exchanges in domains and a modular pattern of evolution with putative independent origins for each ORF. Conclusions Due to the presence of both elements in Bodo saltans, a nontrypanosomatid species, we suggested that VIPER and TATE have survived and remained active for more than 400 million years or were reactivated during the evolution of the host species. We did not find clear evidence of independent origins of VIPER-like from the other YR retroelements, supporting the maintenance of the DIRS group of retrotransposons. Nevertheless, according to phylogenetic findings and sequence structure obtained by this study and other works, we proposed separating DIRS elements into four subgroups: DIRS-like, PAT-like, Ngaro-like, and VIPER-like. Electronic supplementary material The online version of this article (10.1186/s13100-019-0175-2) contains supplementary material, which is available to authori...

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A novel family of tyrosine integrases encoded by the temperate pleolipovirus SNJ2

Cited by 30 publications

References 87 publications

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Integrated mobile genetic elements in Thaumarchaeota

Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

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