Within target T lymphocytes, human immunodeficiency virus type I (HIV-1) encounters the retroviral restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), which is counteracted by the HIV-1 accessory protein Vif. Vif is encoded by intron-containing viral RNAs that are generated by splicing at 3= splice site (3=ss) A1 but lack splicing at 5=ss D2, which results in the retention of a large downstream intron. Hence, the extents of activation of 3=ss A1 and repression of D2, respectively, determine the levels of vif mRNA and thus the ability to evade A3G-mediated antiviral effects. The use of 3=ss A1 can be enhanced or repressed by splicing regulatory elements that control the recognition of downstream 5=ss D2. Here we show that an intronic G run (G I2 -1) represses the use of a second 5=ss, termed D2b, that is embedded within intron 2 and, as determined by RNA deep-sequencing analysis, is normally inefficiently used. Mutations of G I2 -1 and activation of D2b led to the generation of transcripts coding for Gp41 and Rev protein isoforms but primarily led to considerable upregulation of vif mRNA expression. We further demonstrate, however, that higher levels of Vif protein are actually detrimental to viral replication in A3G-expressing T cell lines but not in A3G-deficient cells. These observations suggest that an appropriate ratio of Vifto-A3G protein levels is required for optimal virus replication and that part of Vif level regulation is effected by the novel G run identified here. R eplication of human immunodeficiency virus type 1 (HIV-1) is counteracted by four major classes of host-encoded restriction factors: APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), TRIM5␣ (tripartite motif 5␣), tetherin (BST-2, CD317, or HM1.24), and SAMHD1 (1-4). A3G (5) belongs to a family of cytidine deaminases that includes seven members (A3A to A3D and A3F to A3H) located in a gene cluster on chromosome 22 (6-8). It is encapsidated into newly assembled virions and introduces C-to-U substitutions during minus-strand synthesis, resulting in G-to-A hypermutations and aberrant DNA ends in the HIV-1 genome. Furthermore, A3G, independent of its deaminase activity, inhibits reverse transcriptase-mediated minus-strand elongation by direct binding to the viral RNA (9). This leads to massive impairment of viral replication (10). However, the HIV-1-encoded accessory protein Vif counteracts A3G by direct interaction, by inducing proteasomal degradation, and by repression of mRNA synthesis (10). Whereas HIV-1 is able to replicate efficiently in A3G-expressing cells, Vifdeficient virus strains are completely suppressed (5). Nevertheless, a narrowly restricted level of Vif is crucial for optimal HIV-1 replication since proteolytic processing of the Gag precursor at the p2/nucleocapsid processing site is inhibited by high levels of Vif (11).During the course of infection, the HIV-1 9-kb single-sense pre-mRNA is processed into more than 40 alternatively spliced m...

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Mitochondrial topoisomerase I is a genetically distinct mitochondria-dedicated enzyme with a crucial but so far unknown role in the homeostasis of mitochondrial DNA metabolism. Here, we present data suggesting a negative regulatory function in mitochondrial transcription or transcript stability. Deficiency or depletion of mitochondrial topoisomerase I increased mitochondrial transcripts, whereas overexpression lowered mitochondrial transcripts, depleted respiratory complexes I, III and IV, decreased cell respiration and raised superoxide levels. Acute depletion of mitochondrial topoisomerase I triggered neither a nuclear mito-biogenic stress response nor compensatory topoisomerase IIβ upregulation, suggesting the concomitant increase in mitochondrial transcripts was due to release of a local inhibitory effect. Mitochondrial topoisomerase I was co-immunoprecipitated with mitochondrial RNA polymerase. It selectively accumulated and rapidly exchanged at a subset of nucleoids distinguished by the presence of newly synthesized RNA and/or mitochondrial RNA polymerase. The inactive Y559F-mutant behaved similarly without affecting mitochondrial transcripts. In conclusion, mitochondrial topoisomerase I dampens mitochondrial transcription and thereby alters respiratory capacity. The mechanism involves selective association of the active enzyme with transcriptionally active nucleoids and a direct interaction with mitochondrial RNA polymerase. The inhibitory role of topoisomerase I in mitochondrial transcription is strikingly different from the stimulatory role of topoisomerase I in nuclear transcription.