Responding subgenomic wild type gag/gagpol control expression plasmid UTRgpRRE in

Responding subgenomic wild type gag/Autophagy gagpol control expression plasmid UTRgpRRE in theRev-Stimulated Encapsidation of Spliced Vector RNAFigure 1. Construction of lentiviral vectors. A) The HIV-1 provirus NL4.3 and the HIV-1-vector VHgenomic are shown. Large parts of the gag, pol and env genes are deleted in VHgenomic (see white bars in the deleted regions 25033180 marked by shaded areas). The remaining gag sequence contains parts of the encapsidation signal (Psi, Y) and the env fragments contain splicing regulatory elements as well as the RRE. Due to deletions (shaded squares) and frameshift mutations (black asterisks in gag and rev) no viral genes are expressed from VHgenomic. Both vectors are drawn to scale. B) Schematic representation of the lentiviral vectors VHgenomic, VHenv and VHnef. The intron between SD1 and SA5 or the introns between SD1 and SA5 and between SD4 and SA7 were deleted from VHgenomic in VHenv or VHnef, respectively. Unspliced and spliced transcripts with splice sites (59 splice sites in green and 39 splice sites in blue) and cis-acting splicing regulatory elements (in orange) are shown. Please note that the unspliced Msd1-sa5 RNA of VHenv is identical in sequence to the singly-spliced SD1-SA5 RNA of VHgenomic. Furthermore, the unspliced Msd1-sa5+Msd4-sa7 RNA of VHnef is identical to the fully-spliced SD1-SA5+SD4-SA7 RNA of VHgenomic and the singly-spliced Msd1-sa5+SD4-SA7 RNA of VHenv. Arrowheads represent RT-PCR primers. C) and D) After cotransfection of lentiviral vectors with tat and rev expression plasmids into HEK293T cells Epigenetic Reader Domain cytoplasmic RNA was isolated and analyzed by RT-PCR with primer pairs depicted in figure 1B. Agarose gel electrophoretic analyses of PCR products are shown. The amplification products were sequenced to verify splicing between the indicated splice sites. doi:10.1371/journal.pone.0048688.gVHgenomic in this work (figure 3 and 4) are fully consistent with the results we reported previously [13] confirming that the fractionation protocol worked as before. However, a fractionation control was not included in the particular experiments shown here. In contrast 1081537 to observations with lentiviral vector constructs, Rev significantly enhances cytoplasmic RNA levels of wild type genomic HIV RNA. This difference between the genomic wild type and the lentiviral vector RNAs may be due to differences intheir nuclear retention in the absence of Rev, since lentiviral vectors lack large regions of the HIV genome (see figure 1A) that are implicated in nuclear retention of viral RNA (gag, pol and env sequences). Previously, it could be shown that deletion or codonoptimization of these cis-acting sequences can reduce or prevent nuclear retention of the resulting transcripts even in the presence of splice donor and splice acceptor sites [26,27]. In the present study no effect of Rev on cytoplasmic vector RNA levels could beRev-Stimulated Encapsidation of Spliced Vector RNAFigure 2. Rev-dependency of the infectious lentiviral vector titer. A) Cellular lysates and viral particles were harvested two days after transfection of HEK293T cells and were analyzed by an anti-CA Western Blot. The expression plasmid UTRgpRRE contains wild type gag/gagpol gene sequences combined with a part of the viral 59UTR and the RRE. The Rev-independent gag/gagpol expression plasmid Hgpsyn encodes proteins with wild type amino acid sequences but the gene sequence is dramatically altered due to codon-optimization. B) HEK293 cells were infected with s.Responding subgenomic wild type gag/gagpol control expression plasmid UTRgpRRE in theRev-Stimulated Encapsidation of Spliced Vector RNAFigure 1. Construction of lentiviral vectors. A) The HIV-1 provirus NL4.3 and the HIV-1-vector VHgenomic are shown. Large parts of the gag, pol and env genes are deleted in VHgenomic (see white bars in the deleted regions 25033180 marked by shaded areas). The remaining gag sequence contains parts of the encapsidation signal (Psi, Y) and the env fragments contain splicing regulatory elements as well as the RRE. Due to deletions (shaded squares) and frameshift mutations (black asterisks in gag and rev) no viral genes are expressed from VHgenomic. Both vectors are drawn to scale. B) Schematic representation of the lentiviral vectors VHgenomic, VHenv and VHnef. The intron between SD1 and SA5 or the introns between SD1 and SA5 and between SD4 and SA7 were deleted from VHgenomic in VHenv or VHnef, respectively. Unspliced and spliced transcripts with splice sites (59 splice sites in green and 39 splice sites in blue) and cis-acting splicing regulatory elements (in orange) are shown. Please note that the unspliced Msd1-sa5 RNA of VHenv is identical in sequence to the singly-spliced SD1-SA5 RNA of VHgenomic. Furthermore, the unspliced Msd1-sa5+Msd4-sa7 RNA of VHnef is identical to the fully-spliced SD1-SA5+SD4-SA7 RNA of VHgenomic and the singly-spliced Msd1-sa5+SD4-SA7 RNA of VHenv. Arrowheads represent RT-PCR primers. C) and D) After cotransfection of lentiviral vectors with tat and rev expression plasmids into HEK293T cells cytoplasmic RNA was isolated and analyzed by RT-PCR with primer pairs depicted in figure 1B. Agarose gel electrophoretic analyses of PCR products are shown. The amplification products were sequenced to verify splicing between the indicated splice sites. doi:10.1371/journal.pone.0048688.gVHgenomic in this work (figure 3 and 4) are fully consistent with the results we reported previously [13] confirming that the fractionation protocol worked as before. However, a fractionation control was not included in the particular experiments shown here. In contrast 1081537 to observations with lentiviral vector constructs, Rev significantly enhances cytoplasmic RNA levels of wild type genomic HIV RNA. This difference between the genomic wild type and the lentiviral vector RNAs may be due to differences intheir nuclear retention in the absence of Rev, since lentiviral vectors lack large regions of the HIV genome (see figure 1A) that are implicated in nuclear retention of viral RNA (gag, pol and env sequences). Previously, it could be shown that deletion or codonoptimization of these cis-acting sequences can reduce or prevent nuclear retention of the resulting transcripts even in the presence of splice donor and splice acceptor sites [26,27]. In the present study no effect of Rev on cytoplasmic vector RNA levels could beRev-Stimulated Encapsidation of Spliced Vector RNAFigure 2. Rev-dependency of the infectious lentiviral vector titer. A) Cellular lysates and viral particles were harvested two days after transfection of HEK293T cells and were analyzed by an anti-CA Western Blot. The expression plasmid UTRgpRRE contains wild type gag/gagpol gene sequences combined with a part of the viral 59UTR and the RRE. The Rev-independent gag/gagpol expression plasmid Hgpsyn encodes proteins with wild type amino acid sequences but the gene sequence is dramatically altered due to codon-optimization. B) HEK293 cells were infected with s.