A screen for LINE retrotransposition host factors

To identify host factors important for LINE retrotransposition, we screened the S. cerevisiae yeast knockout collection [53] for strains unable to support robust Zorro3 retrotransposition. Each strain was transformed with a Zorro3 retrotransposition reporter plasmid (Fig 1C), then assayed for retrotransposition. This assay is based on previously described retrotransposition assays [52,54,55] and depends on the splicing of an artificial intron out of a reporter gene (mMET15AI) placed in the Zorro3 3’ untranslated region. A functional MET15 reporter is reconstituted only after Zorro3 transcription, splicing, and integration. Knockout strains were first qualitatively screened for lack of retrotransposition, then the identified retrotransposition-defective strains were quantitatively assayed for retrotransposition frequency (Fig 1D). Out of 4,819 knockout strains screened, 56 strains had a severe (> = 90%) decrease in retrotransposition as compared to a wild-type control strain (S1 Table). Of these 56 strains, 9 were deleted in a gene encoding an endosome associated protein, and 6 of these proteins belong to the endosomal sorting complex required for transport (ESCRT), a 27-fold enrichment of ESCRT genes as compared to the entire genome. Because our screen only identified 6 out of the 19 ESCRT proteins, we next individually tested deletion strains of all ESCRT genes with the quantitative retrotransposition assay, and found that virtually all ESCRT strains had a defect in retrotransposition (Fig 1E, S2 Table). The two exceptions, IST1Δ and VTA1Δ, have been reported as non-essential for ESCRT function [56,57]. In the early stages of our screen, we also transformed a plasmid expressing the lacZ gene under the control of the GAL1 promoter into selected knockout strains with potentially altered retrotransposition frequency. We assayed β-galactosidase activity in these strains to determine whether the altered retrotransposition frequencies could be explained by effects on the GAL1 promoter (S3 Table). For some knockout strains (e.g. SNO1, NPR1, YML095C-A, CUE1, YNL190W) reduction of β-galactosidase activity tracked closely with retrotransposition activity. In the case of the four ESCRT knockouts examined, β-galactosidase activity was lower, but could not entirely explain the >90% reduction in retrotransposition activity in each case (S3 Table). In sum, our screen suggests that ESCRT is required for efficient LINE retrotransposition in budding yeast.

ESCRT physically interacts with Zorro3

ESCRT has roles in cell abscission, formation of intraluminal vesicles, nuclear envelope reformation, and viral budding from the plasma membrane [58–65]. The commonality between these topologically equivalent processes is membrane fusion, a process ESCRT facilitates by constricting and sealing the membrane “neck” made in each case (Fig 2A). Because LINE RNPs have not been known to traffic through membranes, and ESCRT has multiple important cellular roles, we wondered whether ESCRT and Zorro3 directly interact, or if the retrotransposition defects present in ESCRT deficient strains were simply indirect genetic effects. To test this, we asked whether ESCRT proteins physically associate with Zorro3 proteins.

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Fig 2. Interaction between ESCRT proteins and Zorro3 ORF1p.

A. Known roles of ESCRT in the cell. 1) Formation of multivesicular bodies. 2) Cell abscission. 3) Nuclear membrane reformation after mitosis. 4) Viral budding. B. Immunoprecipitation in Zorro3 containing strains. JHY148 was transformed with plasmids encoding the indicated HA-tagged cDNAs. After galactose induction to express Zorro3 and the transformed cDNAs, cells were lysed and immunoprecipitations performed with anti-HA matrix or anti-Zorro3 ORF1p antibody. Whole lysates (left panels) or immunoprecipitations (right panels) were separated by SDS-PAGE and subjected to western blot with the indicated antibodies. Expected molecular weights of HA-tagged proteins are indicated with asterisks. C. Immunoprecipitation in control strains. JHY146 was transformed and analyzed as described in Fig 2B.

https://doi.org/10.1371/journal.pgen.1006837.g002

We HA-epitope tagged and overexpressed 6 yeast ESCRT proteins (Snf7p, Vps4p, Vps23p, Bro1p, Snf8p, and Vps20p) in the S. cerevisiae strain JHY148 [52], which expresses Zorro3 (Fig 2B). Snf7p, Vps4p, Vps23p, Bro1p, and Snf8p associated with Zorro3 ORF1p in both ORF1p and HA immunoprecipitations (Fig 2B). These associations were not disrupted in the presence of RNase A, suggesting that the interactions were not RNA mediated (S1 Fig). In the strain without a plasmid (JHY148 alone) or with empty vector (pGAL-HA, S1 Fig), HA pulldowns did not co-immunoprecipiate Zorro3 ORF1p, demonstrating that the interactions were dependent on the presence of HA-tagged ESCRT proteins. When the same experiment was performed in JHY146, a Zorro3-free strain isogenic to JHY148, the Zorro3 ORF1p antibody only pulled down Bro1p (Fig 2C), suggesting that while the Bro1p interaction is non-specific, the other ESCRT/ORF1p interactions are Zorro3 specific. Thus, components of the ESCRT complex physically interact with Zorro3.

ESCRT proteins are required for efficient human L1 retrotransposition

ESCRT is a conserved complex in eukaryotes, so we next tested the effects of reduced levels of human ESCRT proteins on human L1 retrotransposition. We chose three human genes (ALIX, CHMP6, and CHMP3) orthologous to yeast ESCRT proteins that 1) had a dramatic effect on Zorro3 retrotransposition in yeast and 2) only have one known human ortholog (Fig 3A). We transfected short interfering RNAs (siRNAs) into HeLa cells, which depleted endogenous ALIX, CHMP6 or CHMP3 protein to levels undetectable by western blot (Fig 3B). Using a standard retrotransposition assay [15,66], these ESCRT-depleted cells were then tested for their ability to support human L1 retrotransposition. In parallel, the cells were also transfected with a control plasmid, pcDNA3, containing the neomycin resistance gene, to determine whether depletion of ESCRT genes limited the ability to form G418 resistant colonies. To take into account possible effects of ESCRT knockdown on cell growth and/or viability, retrotransposition induced G418 resistant colonies were normalized to pcDNA3 induced G418 colonies. Knocking down ALIX, CHMP6, or CHMP3 led to a 67%, 94%, and 81% reduction, respectively, in normalized L1 activity (Fig 3C, S4 Table). ESCRT knockdown does not reduce steady state L1 ORF1p levels (S2 Fig), suggesting that the retrotransposition defects are not due to alteration of L1 expression. To ensure that the reduction in L1 activity was not caused by siRNA off target effects, we designed ALIX, CHMP6, and CHMP3 cDNAs with synonomous mutations conferring resistance to their respective siRNA used in Fig 3C. When empty vector was cotransfected in the L1 assay, siRNA knockdown of ALIX, CHMP6, and CHMP3 led to 82%, 95%, and 87% reduction of L1 retrotransposition (Fig 4D, S5 Table), similar to the results in Fig 3C. However, cotransfection of the appropriate siRNA-resistant cDNA in the L1 assay mitigated the effects of ESCRT siRNAs (Fig 3D, S5 Table). In the presence of resistant ALIX cDNA, siALIX reduced relative L1 activity to 54% from 70%, a reduction of only 23%. In the presence of resistant CHMP6 cDNA, siCHMP6 reduced relative L1 activity to 7% from 32%, a reduction of 78%. In the presence of resistant CHMP3 cDNA, siCHMP3 increased relative L1 activity to 69% from 61%. Overexpression of CHMP6 is known to cause cytotoxicity [67], which is consistent with the low levels of G418 colony formation when CHMP6 is overexpressed (Fig 3D, resistant CHMP6 cDNA + scramble siRNA). This makes the results of the CHMP6 rescue ambiguous as compared to the rescue with ALIX and CHMP3 (Fig 3D). In total, our results suggest an important role for ESCRT proteins during human L1 retrotransposition.

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Fig 3. ESCRT proteins are required for efficient human L1 retrotransposition.

A. Human genes (listed with the corresponding yeast ortholog) targeted for knockdown by siRNA in this figure. B. Validation of siRNA knockdown. HeLa cells were co-transfected with pEFALIX-2HA, pEFCHMP6-2HA, or pEFCHMP3-2HA and the indicated siRNAs. Shown are western blots of whole cell lysates. C. Knockdown of ESCRT genes reduces human L1 retrotransposition. HeLa cells were co-transfected with the indicated siRNA and L1 reporter plasmid, then selected with G418 for retrotransposition events. wt = pJM101L1.3. RT^- = pJM105L1.3. Results are relative to the wild type L1, and normalized to pcDNA3 induced colonies to take into account toxicity of ESCRT siRNAs. The ESCRT siRNA toxicity assay is shown in the right panel. Error bars indicate standard deviations. Raw data are shown in S4 Table. D. Rescue of ESCRT phenotypes. HeLa cells were co-transfected with pJM101L1.3 and the indicated plasmids and siRNAs, then selected with G418 for retrotransposition events. For each gene, results are normalized to pJM101L1.3 with scramble siRNA and pEF. Error bars indicate standard deviations. Raw data are shown in S5 Table.

https://doi.org/10.1371/journal.pgen.1006837.g003

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Fig 4. ESCRT/L1 interact via an L1 late domain.

A. Comparison of L1 YPX_nL motif to selected viral late domains. EIAV = equine infectious anemia virus. HIV-1 = human immunodeficiency virus-1. RSV = Rous sarcoma virus. PFV = prototype foamy virus. VACV = vaccinia virus. The Y282 residue of human L1 ORF1p is indicated. B. Conservation of YPX_nL motif in mammals. Alignment of the YPX_nL motif +/- 20 amino acids from indicated species, representing the breadth of mammalian diversity. Phylogenetic relationships are based on [104]. Consensus ORF1 sequences were derived from [105]. The YPX_nL motif is highlighted yellow. Other conserved residues are highlighted gray. C. Expression levels and RNP purification of ORF1p mutants. Shown are western blots of whole cell lysates and RNP preparations from HeLa cells transfected with the indicated vectors. L1 = pJM101L1.3. L1-Y282A = pJM101L1.3-Y282A. L1-AAAALA = pJM110. D. Results of L1 element amplification protocol (LEAP) assays. Shown are western blots of whole cell lysates and RNP preps from transfected HeLa cells, and the resulting LEAP PCRs derived from the RNPs. E. Retrotransposition assays. HeLa cells were co-transfected with the indicated L1 reporter plasmids, then selected with G418 for retrotransposition events. L1 = pJM101L1.3. L1-Y282A = pJM101L1.3-Y282A. RT^- = pJM105L1.3. F. Co-immunoprecipitation of ORF1p and ALIX. tet-293T cells were transfected with pTetPuro (vector), pTetL1.3 (L1), or pTetL1.3–282 (L1-Y282A) and selected with puromycin. Puromycin selected cells were then transfected with pEFALIX-2HA. After ALIX transfection, cells were treated with doxycycline to induce L1 expression. 48 hours after ALIX transfection, cells were lysed and ORF1p immunoprecipitated with the antibody JH74. Shown are western blots of the lysates (left panel) and immunoprecipitations (right panel).

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ESCRT/L1 interact via an L1 “late domain”

Some enveloped viruses encode short amino acid motifs called “late domains”, which recruit ESCRT to the budding virus at the plasma membrane [68]. Without ESCRT, viral buds are not pinched off the membrane, and remain attached to the cell [69]. We recognized that the consensus sequence of a known viral late domain, YPX_nL, corresponds to a motif in human L1 ORF1p (Fig 4A). This motif is conserved among many mammalian L1s (Fig 4B), but the biological function of this L1 motif has not been previously assigned. However, introducing multiple alanine substitutions (YPAKLS->AAAALA) in the motif is known to abolish 99.9% of L1 activity [15]. Although this reduction in retrotransposition activity could be explained, in part, to a disrupted ESCRT/ORF1p interaction, the YPAKLS->AAAALA mutation also leads to poor steady state ORF1p expression and severe defects in L1 RNP formation ([9] and Fig 4C). Thus, the reduction in L1 activity could simply be attributed to the instability of ORF1p and/or the inability to form RNPs.

We took advantage of previous YPX_nL studies to make a separation of function ORF1p mutant that can still form functional L1 RNPs. The known binding partner of the YPX_nL late domain is the human protein ALIX, which serves as an adapter protein to recruit ESCRT [69]. The structures of HIV and EIAV YPX_nL motifs bound to ALIX have been solved and revealed critical interactions required for ALIX/ YPX_nL binding [70]. The YPX_nL tyrosine extends into a hydrophobic pocket in ALIX, and mutating this tyrosine eliminates late domain binding. The corresponding Y282 tyrosine within the L1 ORF1p YPX_nL motif is conserved in mammalian ORF1p, and is present on the external surface of the protein in a position that is presumably accessible for binding to ALIX [11]. We mutated this tyrosine to alanine (Y282A) in L1 ORF1p. In contrast to the YPAKLS->AAAALA mutant, the Y282A mutant produces steady state ORF1p and RNPs indistinguishable from wild type (Fig 4C), suggesting that the Y282A mutant does not alter steady-state levels of L1 RNPs. In addition, we examined RNPs for reverse transcriptase activity using the L1 element amplification protocol (LEAP) assay, the best current biochemical assay for functional L1 RNPs [71]. RNPs isolated from wild type or Y282A transfected cells generated similar LEAP products, whether analyzed by gel electrophoresis or direct DNA sequencing (Fig 4D and S3 Fig). We found no evidence of reverse transcriptase priming upstream of the L1 poly(A) tail (S3 Fig). Thus, based on currently available assays, RNPs produced by a Y282A mutant appear to be functionally “normal”. However, the Y282A mutant exhibited a profound defect (~90% reduction) in retrotransposition (Fig 4E, S6 Table). Co-immunoprecipitation of ALIX with L1 ORF1p was dependent on the YPX_nL motif, as the Y282A mutant abolished the ORF1/ALIX interaction (Fig 4F). These co-IPs were performed in the presence of RNase A, suggesting that this interaction is not RNA dependent. The strength of the wild type ORF1p/ALIX interaction varied from experiment to experiment (S4 Fig). In sum, our data support the importance of the L1 YPX_nL late domain for L1/ESCRT interaction and L1 retrotransposition.

Lysosomal function, glycosylation, and the exocytic pathway are dispensable for L1 retrotransposition

The interaction between ESCRT and L1 proteins strongly suggests that the L1 RNP buds into or interacts with a membrane at some point during L1 replication. Several factors confound our ability to directly pinpoint which membranes, if any, are relevant to L1 biology. L1 retrotransposition is inefficient–even under conditions of massive L1 overexpression over multiple days, typically less than 1% of cells will harbor a retrotransposition event [15,72–75]. In addition, although the L1 mRNA/proteins must enter the nucleus to replicate, most reports suggest that the vast majority of L1 protein is detected in the cytoplasm [18,49,76]. In our hands, we see similar cytoplasmic localization of L1 ORF1p, without obvious co-localization with known cellular organelles (S5 Fig). With the enormous background of L1 particles sequestered in the cytoplasm, it is currently impossible to visually identify the location of the rare “active” RNPs.

We therefore blocked membrane associated functions that we hypothesized could play a role in retrotransposition. ESCRTs are used for budding into endosomes and lysosomes, both of which lead to cargo deposition and degradation in the lysosome. Although it is counterintuitive that lysosome targeting would be required for retrotransposition, the close association of ESCRT with the endosomal membrane system led us to test the requirement of functional lysosomes for L1 activity. We blocked lysosome function using amantadine or chloroquine, drugs that neutralize the acidic lysosome environment [77]. L1 activity was unaffected in amantadine treated cells, and increased in chloroquine treated cells (Fig 5A). Cells treated with amantadine or chloroquine demonstrated the previously described swelling of lysosomes when visualized by confocal microscopy [78–80], indicating that the inhibitors were acting as expected (Fig 5B). This suggests that lysosomal function is not required for L1 retrotransposition. We also reasoned that the L1 RNP might be associated with endoplasmic reticulum (ER) membrane. L1 entry into the ER could be required for glycosylation or transport of the L1 RNP. We treated cells with kifunensine or D-mannojirimycin, inhibitors of N-linked glycosylation [81,82]. These drugs reduced glycosylation and production of the mature, endoglycosidase H resistant form of the normally heavily glycosylated ICAM-1 (Fig 5C), indicating an effective glycosylation block. L1 retrotransposition was not significantly affected by this block (Fig 5A). Finally, we treated cells with Exo1 or golgicide A, potent golgi inhibitors that cause golgi collapse and arrest of soluble and membrane associated protein secretion [83,84]. Neither of these drugs had a dramatic effect on L1 retrotransposition frequency (S5 Fig), suggesting that glycosylation or other pathways downstream of the ER are not essential for L1 replication. However, this does not rule out the possibility that L1 RNPs enter the ER for another purpose, such as formation of a shielded vesicular compartment analogous to viral replication compartments [85], or retrograde L1 RNP transport towards the nucleus, the ultimate destination for successful L1 retrotransposition.

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Fig 5. Membrane associated functions dispensible for L1 retrotransposition.

A. Results of L1 retrotransposition assays. HeLa cells were transfected with pJM101L1.3. 1 hour after transfection, media was replaced with media containing the indicated inhibitors. 24 hours after transfection, cells were selected for G418 resistance. AMT = amantadine. CQ = chloroquine. 1-DMJM = D-mannojirimycin. KIF = kifunensine. B. Confocal imaging of inhibitor-treated cells. HeLa cells were treated with the indicated drugs. 24 hours later, cells were stained with acridine orange and visualized by confocal miscroscopy. C. Confirmation of glycosidase inhibition. HeLa cells were treated with the indicated inhibitors for 24 hours. The cells were lysed and digested with endoglycosidase H. Shown are western blots of undigested (left panel) and digested (right panel) lysates. Black asterisk = mature glycosylated ICAM-1 form. White asterisk = endoH sensitive ICAM-1 form [106].

https://doi.org/10.1371/journal.pgen.1006837.g005

A potential role of ESCRT for L1 nuclear entry

Because of the importance of ESCRT in vesicular traffic, and the assumed requirement of L1 RNPs to traffic to the nucleus to replicate, we wondered whether the ESCRT/L1 interaction is necessary for L1 nuclear entry. In our hands, we detect a very low amount of L1 protein in the nucleus when we induce L1 expression (S6 Fig) in tissue culture cells. The small amount of L1 ORF1 that we detect in the nucleus hinders our ability to identify “active” L1 RNPs from the overwhelming amount of background L1 expression. Thus, we chose to use a functional assay as a proxy for nuclear entry of L1 particles. Expression of full-length, replication competent L1 induces the formation of γ-H2AX foci, a marker for DNA double stranded breaks or replication stress [23]. The L1-induced γ-H2AX foci are dependent on L1 endonuclease activity, suggesting that chromosome cleavage by L1 proteins leads to foci formation. As these are nuclear events, we presume that if γ-H2AX foci are formed, enzymatically active L1 particles have entered the nucleus. We used a tetracycline inducible system [86] to induce L1 expression. In this system, full-length L1 is under the control of a Tet-On promoter, allowing L1 expression upon treatment with doxycycline. When we induced L1 expression in tet-HeLa cells, we found L1-dependent upregulation of γ-H2AX by western blot (Fig 6A). This γ-H2AX upregulation was eliminated when we induced expression of L1 with an endonuclease active site mutation (D145A), suggesting that the γ-H2AX upregulation was dependent on L1 endonuclease activity. In a similar manner, we found that when we induce expression of ORF1 Y282A mutant L1, the γ-H2AX upregulation is reduced (Fig 6B). Because the Y282A mutation presumably disrupts the L1/ESCRT interaction, this result is consistent with the hypothesis that the L1/ESCRT interaction is a prerequisite for nuclear L1 endonuclease activity. This further implies that, in the absence of ESCRT, L1 RNPs are impaired for nuclear entry. Alternatively, it is possible that the Y282A mutant blocks endonuclease activity independent of nuclear entry.

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Fig 6. Effect of disrupting the L1/ESCRT interaction of nuclear L1 endonuclease activity.

A. γH2AX production in response to L1 expression. tet-HeLa cells were transfected with pTetPuro, pTetL1.3, or pTetL1.3-D145A and selected for puromycin resistance. The puromycin resistant populations were treated with doxycycline to induce L1 expression. 72 hours after L1 induction, cell lysates were harvested. Shown are western blots of cell lysates. B. γ-H2AX production when ESCRT/ORF1 interaction is disrupted. tet-HeLa cells were transfected with pTetPuro, pTetL1.3, or pTetL1.3-Y282A then treated with doxycycline for 72 hours. Shown are western blots of cell lysates.

https://doi.org/10.1371/journal.pgen.1006837.g006

Yeast strains

The yeast knockout collection [53] was obtained from the ATCC (GSA-5) and was in the BY4741 background (MATa his3Δ1; leu2Δ0; met15Δ0; ura3Δ0) [97]. Construction of strains JHY146 (MATα his3Δ200 ura3-167 GAL+ lys2::mHIS3AI) and JHY148 (MATα his3Δ200 ura3-167 GAL+ lys2::Zorro3mHIS3AI) have been described previously [52].

Cell culture

HeLa cells were a gift from John Moran [15]. Tet-HeLa cells were from Clontech (Mountain View, CA). Tet-293 cells were a gift from Jef Boeke [51]. All cells were grown in Dulbecco’s Modified Eagle Media (Invitrogen #11965118) supplemented with 10% fetal bovine serum (Invitrogen, #16000069) and 1% Penicillin/Streptomycin (Invitrogen, #15140122). Puromycin resistant plasmids were selected with 1 μg/mL puromycin (Invivogen #ant-pr-1) and maintained with 0.25 μg/mL puromycin. Tet-inducible proteins were induced with 500 ng/mL doxycycline (Fisher Scientific #BP2653). Cells were grown at 37°C unless otherwise specified.

Oligonucleotides

Oligonucleotides used in this study are listed in S9 Table.

Plasmids

All cloned PCR and site directed mutagenesis products described below were completely sequenced. Sequence files of all plasmids are available upon request.

p425Zorro3mMET15AI (Zorro3 retrotransposition plasmid)—The yeast MET15AI retrotransposition marker was made by first PCR amplifying the MET15 gene from the yeast strain BY4742 using primer JH308/JH311, then TOPO cloning the amplicon into pCR2.1 to make pCRMET15. An artificial intron was amplified from pSCZorro3mHIS3AI [52] using the primers JH251/JH255, digested with PvuII/SnaBI, and cloned into the AleI site of pCRMET15 to make pCRMET15AI. The MET15AI marker was removed from pCRMET15AI with XhoI, blunted with T4 DNA polymerase/dNTPs, and cloned into the T4 DNA polymerase blunted SalI site of pSCZorro3 [52] to make pSCZorro3mMET15AI. Oligonucleotides JH28/JH29 were annealed then digested with RsaI/SacI. pRS425 [98] was digested with XhoI, blunted with T4 DNA polymerase, then further digested with SacI. Oligonucleotides JH28/JH29 were annealed then digested with RsaI/SacI, then cloned into the digested pRS425 vector to make pRS425FE. The EagI/FseI GAL1-Zorro3mMET15AI fragment from pSCZorro3mMET15AI was cloned into the EagI/FseI of pRS425FE to make p425Zorro3mMET15AI. Standard site directed mutagenesis techniques were used to make p425Zorro3RTmutmMET15AI, which is identical to p425Zorro3mMET15AI but with D674A, D675A missense mutations in ORF2p.

p415GAL-lacZ was made by cloning the SmaI/HindIII lacZ fragment from pCMV-lacZ (Clontech) into the SmaI/HindIII sites of p415Gal1 [99].

pGAL-HASNF7, pGAL-HAVPS4, pGAL-HAVPS23, pGAL-HABRO1, pGAL-HASNF8, pGAL-HAVPS20 –These plasmids are based on the p426GAL1 vector [99], with a URA3 selection marker, 2 micron replication origin and GAL1 promoter. Using standard PCR cloning procedures, a 3x HA tag was inserted, along with each ORF amplified from BY4741 genomic DNA.

pJM101L1.3, pJM105L1.3, and pJM110 were gifts from John Moran and Haig Kazazian [15,66,100]. These plasmids were derived from a pCEP4 backbone (Invitrogen).

pJM101L1.3Y282A was made site directed mutagenesis of pJM101L1.3 using standard cloning techniques.

pTetPuro was made by digesting pMT302 (gift from Jef Boeke [49]) with NotI/BstZ17I, blunting, and religation.

pTetL1.3 was made by ligating a NotI/BstZ17I fragment from pJM101L1.3 into the NotI/BstZ17I sites of pMT302.

pTetL1.3–282 was made by ligating a NotI/BstZ17I fragment from pJM101L1.3Y282A into the NotI/BstZ17I sites of pMT302.

pTetL1.3–145 was made by ligating a PmlI/BbvCI fragment from pQF288 (a gift from Jef Boeke [16]) and a BbvCI/BamHI fragment from pTetL.13 into the PmlI/BamHI sites of pTetL1.3.

pEF was made by digesting pTracerEF A (Invitrogen) with SphI/BspQI, blunting, and religating.

pEFALIX-2HA was made by filling in annealed JH-IM54/JH-IM55 by PCR, then amplifying this product with JH-IM56/JH-IM57 to make tandem HA tags. ALIX cDNA was amplified from mammalian gene collection clone MGC-17003 using primers JH-IM50/JH-IM61. The amplified ALIX cDNA and tandem HA tags were fused together in a PCR with JH-IM50/JH-IM57. The product was digested with EcoRI and cloned into EcoRI/EcoRV digested pEF. Although this strategy intended to add 3 HA tags, in practice it added 2 HA tags. cDNA expression is under the control of the strong constitutive elongation factor-1α promoter.

pEFCHMP6-2HA was made by filling in annealed JH-IM54/JH-IM55 by PCR, then amplifying this product with JH-IM56/JH-IM57 to make tandem HA tags. CHMP6 cDNA was amplified from mammalian gene collection clone MGC-19477 using primers JH-IM44/JH-IM58. The amplified CHMP6 cDNA and tandem HA tags were fused together in a PCR with JH-IM44/JH-IM57. The product was digested with MfeI/XbaI and cloned into EcoRI/XbaI digested pEF.

pEFCHMP3-2HA was made by filling in annealed JH-IM54/JH-IM55 by PCR, then amplifying this product with JH-IM56/JH-IM57 to make tandem HA tags. CHMP3 cDNA was amplified from mammalian gene collection clone MGC-11028 using primers JH-IM53/JH-IM59. The amplified CHMP3 cDNA and tandem HA tags were fused together in a PCR with JH-IM53/JH-IM57. The product was digested with MfeI/XbaI and cloned into EcoRI/XbaI digested pEF.

pEFALIXs19465mut (cDNA resistant to the s19465 siRNA) was made by amplifying the ALIX cDNA from MGC-17003 using a series of fusion PCRs with primer sets JH-IM50/JH-IM88 and JH-IM87/JH-IM62, digesting with EcoRI/EagI, and cloning into the EcoRI/EagI sites of pEF.

pEFCHMP6s28474mut (cDNA resistant to the s28474 siRNA) was made by amplifying the CHMP6 cDNA from MGC-19477 using a series of fusion PCRs with primer sets JH-IM77/JH-IM81 and JH-IM74/JH-IM67, digesting with EcoRI/XbaI, and cloning into the EcoRI/XbaI sites of pEF.

pEFCHMP3s35990mut (cDNA resistant to the s35990 siRNA) was made by amplifying the CHMP3 cDNA from MGC-11028 using a series of fusion PCRs with primer sets JH-IM78/JH-IM82 and JH-IM75/JH-IM68, digesting with MfeI/XbaI, and cloning into the EcoRI/XbaI sites of pEF.

pGEX6p2Z3ORF1 –Zorro3 ORF1 was amplified with primers JH256/JH257, digested with BamHI/SalI, and ligated into the BamHI/XhoI sites of pGEX-6P-2 (GE Healthcare).

pGEX-3’hORF1 –synthetic human L1 [101] was amplified with primer JH1004/JH1005, digested with EcoRI/BamHI, and ligated into the EcoRI/BamHI sites of pGEX-6P-2.

Antibodies

G01 (rabbit polyclonal anti-Zorro3 ORF1)–The plasmid pGEX6p2Z3ORF1 was transformed into BL(DE3)plysS competent bacteria and GST-Z3ORF1p expression was induced with IPTG. GSTZ3ORF1p was purified with a glutathione sepharose column, followed by FPLC on a Superose 6 10/300 GL column. Fractions of the highest purity and concentration were sent to Proteintech (Chicago, IL) for antibody production. Characterization of G01 is shown in S7 Fig.

JH73 and JH74 (rabbit monoclonal anti-L1 ORF1)–The plasmid pGEX-3’hORF1 was transformed into BL(DE3)plysS bacteria and GST-3’hORF1 was purified as described for GSTZ3ORF1p. Purified GST-3’hORF1 was sent to Epitomics (now Abcam) for rabbit monoclonal antibody production. Hybridoma supernatants were screened by western blot, immunoprecipitation, immunofluorescence, and immunohistochemistry of paraffin embedded samples for the best clones for all applications. Antibody was purified from hybridoma supernatant with Protein A Agarose (Pierce). Characterization of JH73 and JH74 is shown in S8 Fig. Additional characterization is shown in [49].

Commercially available antibodies used: anti-HA affinity matrix (Sigma #11815016001), mouse anti-HA clone 12CA5 (Sigma #11583816001), rat anti-HA clones 3F10 (Sigma #11867423001), rabbit polyclonal anti-ALIX (Bethyl #A302-938A), mouse monoclonal anti-CHMP3 clone F-1 (Santa Cruz #sc-166361), rabbit polyclonal anti-CHMP6 clone FL-201 (Santa Cruz #sc-67231), rabbit polyclonal anti-H3 (Abcam #ab1791), mouse monoclonal anti-γ-H2AX clone JBW301 (EMD Millipore #05-636-I), mouse monoclonal anti-ICAM-1, clone 15.2 (Santa Cruz #sc-107), mouse monoclonal anti-tubulin clone DM1A (Sigma #T6199), rabbit monoclonal anti-EEA1 clone C45B10 (Cell Signaling Technology #3288), rabbit monoclonal anti-Rab7 clone D95F2 (Cell Signaling Technology #9367), mouse monoclonal anti-LAMP2 clone H4B4 (Abcam #ab25631), mouse monoclonal anti-calnexin clone AF18 (ThermoFisher #MA3-027), rabbit monoclonal anti-AIF clone D39D2 (Cell Signaling Technology #5318), mouse monoclonal anti-RCAS1 clone D9 (Santa Cruz #sc-398052), rabbit polyclonal anti-EDC4 (Cell Signaling Technology #2548), rabbit monoclonal anti-eIF3H clone DC91 (Cell Signaling Technology #3413).

Screen for Zorro3 host factors

Lithium acetate transformation was used to transform all strains of the yeast knockout collection with the plasmid p425Zorro3mMET15AI. For controls, BY4741 was transformed with p425Zorro3mMET15AI or p425Zorro3RTmutmMET15AI. Transformants were selected on SC-leu plates. Three clones from each transformation were used to make 1.5 cm² patches on SC-leu+galactose plates. After 6 days at 23°C, the patches were replica plated to SC-met plates. Strains that exhibited a qualitatively noticeable decrease in Zorro3 retrotransposition were selected for quantitative Zorro3 retrotransposition assays [52]. Briefly, transformants were inoculated in 3 mL SC-leu cultures and incubated for 3 days at 23°C on a roller drum. After incubation, 200 μL of each culture was plated on an SC-met plate, and 10 μL of a 1:1000 dilution was plated on a YPD plate. Retrotransposition frequency was calculated as (SC-met colonies)/(YPD colonies x dilution factor).

β-galactosidase assay of yeast lysates

Yeast strains were transformed with p415GAL-lacZ and selected on SC-leu plates. The transformed strains were grown overnight in SC-leu media with glucose, washed with H₂O, then resuspended and incubated overnight in SC-leu with galactose. Cell concentrations of cultures were normalized to a constant OD₆₀₀. 1 mL of each normalized culture was used to assay for β-galactosidase activity using a previous described method [102]. Briefly, the pelleted culture was resuspended in 500 μL of Z buffer. 50 μL of 0.1% SDS and 50 μL chloroform were added and the solution was vortexed. 100 μL of a 4 mg/mL stock of o-nitrophenol-β-D-galactoside (ONPG) was added and incubated at 37 degrees for 15 minutes. The reaction was quenched with 500 μL of 1 M Na₂CO₃. 100 uL of each supernantant was transferred into a 96 well plate, and OD₄₂₀ was measured with a plate reader. Wild-type BY4741 transformed with p415GAL-lacZ and grown in glucose was used as to measure background activity and was subtracted from all other values. β-galactosidase activity of BY4741 transformed with p415GAL-lacZ was set to 1, and for each experiment, the activity of knockout strains were normalized to this value.

Immunoprecipitations from yeast

Strains JHY146 or JHY148 were transformed with pGAL-HASNF7, pGAL-HAVPS4, pGAL-HAVPS23, pGAL-HABRO1, pGAL-HASNF8, or pGAL-HAVPS20 and selected on SC-ura plates. Zorro3 and the respective ESCRT proteins were induced in SC-ura+galactose cultures for 16 hours, and lysed in a BioSpec mini bead beater with 25 mM Tris-Cl pH 7.4, 150 mM NaCl, 0.5% Triton X-100, 0.5% Na-deoxycholate, 1 mM EDTA, 4% glycerol, 1% protease inhibitor cocktail (Sigma #P2714), 1 mM PMSF, 10 mM MgCl2, and acid washed glass beads. Where indicated, 0.5 μg/mL RNase A was added to the IPs. Antibody G01 was used for IP and western blot of Zorro3 ORF1p, anti-HA affinity matrix was used for HA IP, and anti-HA clones 12CA5 or 3F10 were used for HA western blot.

L1 retrotransposition assays

To knockdown expression of ESCRT proteins and test L1 retrotransposition, we modified an established retrotransposition assay [66]. 2 x 10⁵ HeLa cells/well were seeded in 6-well plates. 24 hours after seeding, cells were transfected with 1 μg of L1 reporter plasmid (pJM101L1.3 or pJM105L1.3) and 15 pmol of silencer select siRNA (Ambion—s19465 for ALIX, s29474 for CHMP6, s35990 for CHMP3, or scramble negative control) using Lipofectamine 2000 (Invitrogen) according to the manufacturers protocol. 24 hours post-transfection, G418 selection (600 μg/mL) was started and continued for 11–12 days. G418-resistant colonies were fixed and stained with 250 μl/well of modified Giemsa stain (Sigma #GS500). To assess whether knockdown affected transfection efficiency or viability, we performed parallel co-transfections with 10 ng pcDNA3 (Invitrogen) in place of the L1 reporter plasmid. G418-resistant colonies from the retrotransposition assay were normalized to the respective pcDNA3 colony forming assays to give “normalized L1 activity”. For siRNA rescue retrotransposition experiments, co-transfections were performed as described above with the following amounts of nucleic acids: 0.5 μg L1 reporter construct, 0.5 μg siRNA resistant cDNA or empty vector, and 15 pmol siRNA.

To test the effectiveness of siRNA knockdown, we performed separate experiments where we co-transfected HeLas with pEFALIX-2HA, pEFCHMP6-2HA, or pEFCHMP3-2HA and the relevant siRNA or scramble negative control siRNA. Knockdown was assessed by western blot with anti-HA 12CA5 antibody.

To perform standard L1 retrotransposition assays (in the absence of siRNA knockdown), 2.5 x 10⁵ HeLas/well were seeded in 6-well plates. 24 hours after seeding, cells were transfected with 1 μg L1 reporter plasmid and 3 μL XtremeGENE9 (Roche) according to the manufacturer’s protocol. 24 hours post-transfection, G418 selection (600 μg/mL) was started and continued for 11–12 days. G418-resistant colonies were fixed and stained with 250 μl/well of modified Giemsa stain (Sigma #GS500). To assess transfection efficiency, extra wells were set aside for each condition and analyzed for ORF1p expression by western blot. In cases where inhibitors were added to the retrotransposition assays, the inhibitors were added to the media 1 hour post-transfection. The final concentration of drugs used were as follows: 500 μM amantadine (Sigma #A1260), 10 μM chloroquine (Sigma #C6628), 25 μM kifunensine (Sigma #K1140), 1 mM D-mannojirimycin (Sigma #D9160), 2.5 μM golgicide (Sigma #G0923), 75 μM Exo1 (Sigma #E8280).

L1 RNP isolation and LEAP assays

RNP isolation and LEAP assays were based on previous published work [71]. Briefly, to isolate L1 RNPs, 2 x 10⁶ HeLa cells were plated in a T75 cell culture flask. Cells were transfected 24 hours later with 20 μg of L1 plasmid per flask. Three days post-transfection, medium was replaced by DMEM supplemented with 0.2 mg/mL hygromycin B and exchanged daily. On day 7 post-transfection, one T-75 flask was seeded with 2 x 10⁶ untransfected HeLa cells to be used as a negative control. On day 10 post-transfection, transfected and untransfected cells were harvested and whole-cell lysates were prepared and subjected to ultracentrifugation as described previously [71].

The LEAP reaction was performed as described previously [71] with the following changes: a 1 μL aliquot of the pelleted samples was incubated with 50 mM Tris-HCl (pH 7.5), 50 mM KCl, 5 mM MgCl₂, 10 mM DTT, 0.4 mM LEAP primer, 20 U RNaseOut (Invitrogen), 0.2 mM dNTPs and 0.05% Tween 20 in a final volume of 50 μL for 1 hour at 37°C. After incubation, 1 μL of LEAP reaction was used in a standard 30 μL PCR using AmpliTaq DNA polymerase (Applied Biosystems) and 0.4 mM of each linker PCR primer and L1.3 end primer according to the manufacturer’s protocol. PCR conditions as previously described [71]. The complete reaction was visualized on a 2% agarose gel with Ethidium Bromide.

Immunoprecipitations from human cells

Tet-293 cells were transfected with pTetPuro, pTetL1.3, or pTetL1.3–282. 24 hours post-transfection, cells were selected with puromycin. 100 mm plates of selected cells were transfected with 21 μg of pEFALIX-2HA in N,N-bis(2-hydroxyethyl)-2-amino-ethanesulfonic acid (BES) buffer as previously described [103]. L1 expression was induced with doxycycline, and after 48 hours of induction cells were lysed using a Precellys 24 homogenizer (Bertin Instruments) and acid-washed beads (Sigma #G8772) in 25 mM HEPES pH 7.4, 200 mM NaCl, 1 mM MgCl₂, 1 mM CaCl₂, 1 x protease inhibitor cocktail (Sigma #S8830), 40 units DNase I, 2.5 mg RNaseA, and 10% glycerol. L1 ORF1p was immunoprecipitated with JH74. Western blot analysis was performed with JH73 (ORF1p) and anti-ALIX or 12CA5 (HA).

Confocal microscopy

HeLa cells were seeded at 2 x 10⁵ cells/dish in 35 mm glass bottom dishes (MatTek #P35G-0-10-C). 24 hours after seeding, cells were treated with 10 μM chloroquine or 50 μM amantadine. After 24 hours, fresh media/drug was added along with 1 μM acridine orange, and incubated at 37°C for 1 hour. The media was washed and replace with PBS, then directly imaged on an Olympus FV1000 confocal miscroscope with a FITC filter.

L1 and γ-H2AX induction

Tet-HeLa cells were transfected with pTetPuro, pTetL1.3, pTetL1.3–282, or pTetL1.3–145 and transfected populations were selected with puromycin. In selected cells, L1 expression was induced with doxycycline, and whole cell lysates were analysed by western blot for H3 and γ-H2AX at 72 hours.

Immunofluorescence

10,000 cells containing the plasmid pTetL1.3 were seeded on coverslips treated with 0.01% poly-L-lysine in 24-well plate. Approximatively 16 hours after seeding, L1.3 expression was induced with 0.5 ug/ml doxycycline. Cells were fixed 48 hours after induction with 4% paraformaldehyde in PBS pH 7.4 for 15 minutes at room temperature (RT). After fixation, cells were washed 3 times with PBS pH7 .4. For calnexin, RCAS1, EEA1, RAB7 and AIF staining, cells were permeabilized with PBS pH 7.4 containing 0.1% Triton X-100 for 15 minutes at RT. Nonspecific interactions were blocked with 10% normal donkey serum (NDS) in PBS for 1 hour at RT. Staining with primary antibody, diluted in PBS pH 7.4 and 2% NDS was done overnight at 4°C. The following dilutions for primary antibody were used: anti-ORF1p clone 4H1 (mouse monoclonal antibody) 0.75 μg/ml, anti-ORF1p clone JH74 (rabbit monoclonal antibody) 0.15 μg/ml; anti-calnexin 1:1000; anti-RCAS1 1:200; anti-EEA1 1:200; anti-RAB7 1:100; anti-AIF 1:400. After primary antibody incubation, cells were washed 3 times with PBS pH 7.4. Secondary antibodies were used at 1:1000 dilution in PBS pH7.4 with 2% NDS for 1–2 hours at RT. To detect anti-ORF1p antibodies, we used Alexa Fluor 488 Donkey anti-Mouse IgG (ThermoFisher # A21202) or Alexa Fluor 488 Donkey anti-Rabbit IgG (ThermoFisher # A21206). To detect antibodies against organelle markers, we used Alexa Fluor 594 Donkey anti-Mouse IgG (ThermoFisher # A21203) or Alexa Fluor 594 Donkey anti-Rabbit IgG (ThermoFisher #A21207). After incubation with secondary antibody, cells were washed 2 times with PBS pH 7.4, incubated with 1 μg/ml DAPI in PBS pH 7.4 for 5 minutes and washed once with PBS pH 7.4. Coverslips were mounted on glass slides with ProLong Gold antifade reagent (Life Technologies #P36930). For LAMP2 and eIF3h staining, cells were incubated with PBS pH 7.4 with 0.3% Triton X-100 and 5% NDS for 1 hour at RT to permeabilize cells and block nonspecific protein interactions. Staining with primary antibody was done overnight at 4°C in PBS pH 7.4 with 0.3% Triton X-100 and 1% BSA. Anti-LAMP2 antibody was used at a 1:100 dilution and anti-eIF3h antibody at a 1:400 dilution. Cells were washed 3 times with PBS pH 7.4 and incubated with secondary antibodies diluted to 1:500 in PBS pH 7.4 with 0.3% Triton X-100 and 1% BSA for 1–2 hours at RT. After secondary antibody, cells were washed, DAPI stainied and mounted as described above.