Acquisition of Full-Length Viral Helicase Domains by Insect Retrotransposon-Encoded Polypeptides

Lazareva, Ekaterina A.; Lezzhov, Alexander A.; Vassetzky, Nikita S.; Solovyev, Andrey G.; Morozov, Sergey Y.

doi:10.3389/fmicb.2015.01447

Cited by 10 publications

(38 citation statements)

References 47 publications

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“…e R1 3′UTR stem-loop from silkworm experimentally reported as recognized by LINE-encoded RT [28]. f L1 3′UTR stem-loop from rat [49]. g L1 3′UTR stem-loop from maize (Malik, Burke et al [45]).…”

Section: Resultsmentioning

confidence: 99%

“…However, horizontal transfer was reported for a minor fraction of LINE clades; these include transfer of jockey elements within Drosophila [46], Bov-B transfer from Squamata to the ancestor of Ruminantia [47, 48], insertion of additional C-terminal domain into ORF2 of insect R1 from plant viruses [49], and L1 transfer from humans to bacteria Neisseria gonorrhoeae [50]. Phylogenetic analysis made on the entire LINE ORF2 sequences, for which corresponding SINE partner is known [51], confirmed 11 clades reported by [45] and further enlarged the number of clades to 15 [51].…”

Section: Introductionmentioning

confidence: 99%

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Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition

Grechishnikova

Poptsova

2016

BMC Genomics

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BackgroundIn the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3′UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA. However polyadenylation is a property of any messenger RNA, and how the LINE RT recognizes transposon and non-transposon RNAs remains an open question. It is likely that RNA secondary structures play an important role in RNA recognition by LINE encoded proteins.ResultsHere we selected a set of L1 and Alu elements from the human genome and investigated their sequences for the presence of position-specific stem-loop structures. We found highly conserved stem-loop positions at the 3′UTR. Comparative structural analyses of a human L1 3′UTR stem-loop showed a similarity to 3′UTR stem-loops of the stringent-type LINEs, which were experimentally shown to be recognized by LINE RT. The consensus stem-loop structure consists of 5–7 bp loop, 8–10 bp stem with a bulge at a distance of 4–6 bp from the loop. The results show that a stem loop with a bulge exists at the 3′-end of Alu. We also found conserved stem-loop positions at 5′UTR and at the end of ORF2 and discuss their possible role.ConclusionsHere we presented an evidence for the presence of a highly conserved 3′UTR stem-loop structure in L1 and Alu retrotransposons in the human genome. Both stem-loops show structural similarity to the stem-loops of the stringent-type LINEs experimentally confirmed as essential for retrotransposition. Here we hypothesize that both L1 and Alu RNA are recognized by L1 RT via the 3′-end RNA stem-loop structure. Other conserved stem-loop positions in L1 suggest their possible functions in protein-RNA interactions but to date no experimental evidence has been reported.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3344-4) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition

Grechishnikova

Poptsova

2016

BMC Genomics

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“…VSRs were first identified in plant viruses and later found in viruses infecting other higher eukaryotes (Axtell, 2013;Csorba et al, 2015). The LINEs described in our recent paper (Lazareva et al, 2015) carry a sequence encoding SF1H domain significantly related to the VSR domain of replicases of plant positive-stranded RNA viruses belonging to the genus Tobamovirus of the family Virgaviridae. Our experimental data demonstrated that the predicted P. xylostella LINE VSR domain exhibits a weak, compared to the potent plant virus VSR p19, but detectable ability to suppress RNA silencing in the Nicotiana benthamiana leaves (Lazareva et al, 2015).…”

Section: Introductionmentioning

confidence: 84%

“…Thus our previous conclusion on the closest relationship between TRAS ORF2 SF1H and replicative helicases of plant tobamoviruses (Lazareva et al, 2015) is explained by incompleteness of sequence data available at that time.…”

Section: Retrotransposonmentioning

confidence: 94%

“…Interestingly, the genome of Plutella xylostella (Plutellidae) contains the highest number (several dozens) of SF1H-encoding LINEs, showing that in specific lepidopteran lineages they underwent a transpositional burst, while in some other genera these elements were subjected to complete or partial deletions (Lazareva et al, 2015). To counteract the RNA silencing, most viruses have evolved viral suppressors of RNA silencing (VSRs), proteins that block one or more steps in the RNA silencing pathway.…”

Section: Introductionmentioning

confidence: 99%

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Supplemental Information 3: Multiple Sequence Alignment of the Analyzed SF1H Proteins Encoded by Lepidoptera TRAS-like LINEs An

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Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress posttranscriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.

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A new nodavirus‐negative Trichoplusia ni cell line for baculovirus‐mediated protein production

Maghodia¹,

Geisler²,

Jarvis

2020

Biotech & Bioengineering

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Cell lines derived from Trichoplusia ni (Tn) are widely used as hosts in the baculovirus-insect cell system (BICS). One advantage of Tn cell lines is they can produce recombinant proteins at higher levels than cell lines derived from other insects. However, Tn cell lines are persistently infected with an alphanodavirus, Tn5 cell-line virus (TnCLV), which reduces their utility as a host for the BICS. Several groups have isolated TnCLV-negative Tn cell lines, but none were thoroughly characterized and shown to be free of other adventitious viruses. Thus, we isolated and extensively characterized a new TnCLV-negative line, Tn-nodavirus-negative (Tn-NVN). Tn-NVN cells have no detectable TnCLV, no other previously identified viral contaminants of lepidopteran insect cell lines, and no sequences associated with any replicating virus or other viral adventitious agents. Tn-NVN cells tested negative for >60 species of Mycoplasma, Acholeplasma, Spiroplasma, and Ureaplasma. Finally, Tn-NVN cells grow well as a single-cell suspension culture in serum-free medium, produce recombinant proteins at levels similar to High Five™ cells, and do not produce recombinant glycoproteins with immunogenic core α1,3fucosylation. Thus, Tn-NVN is a new, well-characterized TnCLV-negative cell line with several other features enhancing its utility as a host for the BICS.

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Acquisition of Full-Length Viral Helicase Domains by Insect Retrotransposon-Encoded Polypeptides

Cited by 10 publications

References 47 publications

Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition

Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition

Untitled

A new nodavirus‐negative Trichoplusia ni cell line for baculovirus‐mediated protein production

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