HIV-1 Nef protein contributes to pathogenesis via multiple functions that include enhancement of viral replication and infectivity, alteration of intracellular trafficking, and modulation of cellular signaling pathways. Nef stimulates formation of tunnelling nanotubes and virological synapses, and is transferred to bystander cells via these intercellular contacts and secreted microvesicles. Nef associates with and activates Pak2, a kinase that regulates T-cell signaling and actin cytoskeleton dynamics, but how Nef promotes nanotube formation is unknown. In this dissertation, we developed and characterized a lentiviral vector-based system to express Nef in T-cell lines and primary human peripheral blood mononuclear cells, and then used this system to perform a proteomic screen to identify Nef-associated host cell factors and better understand how Nef hijacks the T-cell machinery to maximize HIV production and dissemination. Bioinformatic and cell-based analysis of the resulting host factors revealed a mechanism by which Nef enhances nanotube formation. To identify Nef binding partners involved in Pak2-association dependent Nef functions, we employed tandem mass spectrometry analysis of Nef immunocomplexes from Jurkat cells expressing wild-type Nef or Nef mutants defective for the ability to associate with Pak2 (F85L, F89H, H191F and A72P, A75P in NL4-3). Wild-type, but not mutant Nef, was associated with 5 components of the exocyst complex (EXOC1, EXOC2, EXOC3, EXOC4, and EXOC6), an octameric complex that tethers vesicles at the plasma membrane, regulates polarized exocytosis, and recruits membranes and proteins required for nanotube formation. Additionally, Pak2 kinase was associated exclusively with wild-type Nef. Association of EXOC1, EXOC2, EXOC3, and EXOC4 with wild-type, but not mutant Nef, was verified by co-immunoprecipitation assays in Jurkat cells. Furthermore, shRNA-mediated depletion of EXOC2 in Jurkat cells abrogated Nef-mediated enhancement of nanotube formation. Using bioinformatic tools, we visualized protein interaction networks that reveal functional linkages between Nef, the exocyst complex, and the cellular endocytic and exocytic trafficking machinery. Together, our findings identify the exocyst complex as a key effector of Nef-mediated enhancement of nanotube formation, and possibly microvesicle secretion. Furthermore, linkages revealed between Nef and the exocyst complex suggest a new paradigm of exocyst involvement in polarized targeting for intercellular transfer of viral proteins and viruses.

Η πρωτεΐνη Tip60 (Tat-interactive protein, 60 kDa) είναι μέλος της οικογένειας πρωτεϊνών MYST και αρχικά προσδιορίστηκε ως αλληλεπιδρώσα πρωτεΐνη με την HIV-1 ΤΑΤ πρωτεΐνη. Πολλά από τα μέλη της οικογένειας MYST μεταξύ αυτών και η Tip60, δρουν ως ακετυλοτρανσφεράσες ιστονών, γεγονός που υποδηλώνει πιθανούς ρόλους στην αναδιαμόρφωση της χρωματίνης και στην γονιδιακή ρύθμιση. Στη παρούσα διπλωματική, στόχος ήταν η μελέτη του προφίλ έκφρασης της ακετυλοτρανσφεράσης Τip60 σε πληθυσμούς Τ βοηθητικών παρθενικών (CD3+CD4+CD45RA+) και Τ βοηθητικών μνημονικών (CD3+CD4+CD45RO+) λεμφοκυττάρων καθώς και η δράση της στην μεταγραφή του HIV-1 και της IL-2. Οι λόγοι που μας οδήγησαν στην μελέτη της Τip60 προκύπτουν από πρόσφατα αποτελέσματα του εργαστηρίου μας, που δείχνουν ότι υπάρχει μια πιθανή αλληλεπίδραση της Tip60 με τον παράγοντα Εts-2, ο οποίος συμμετέχει στη ρύθμιση της μεταγραφής τόσο του γονιδίου της IL-2 όσο και του HIV-1. Επιπλέον η IL-2 και ο HIV-1 παρουσιάζουν κοινή μεταγραφική ρύθμιση που ελέγχεται από την πρόσδεση μεταγραφικών παραγόντων σε κοινά cis στοιχεία. Επίσης, η Tip60 είναι μια Τat-αλληλεπιδρώσα πρωτεΐνη που κωδικοποιείται από το γονίδιο Tat του HIV-1. Τέλος το γεγονός ότι ο HIV-1 παραμένει σε λανθάνουσα κατάσταση στα εν ηρεμία Τ βοηθητικά λεμφοκύτταρα καθώς και ότι ο παράγοντας Εts-2, που πιθανόν αλληλεπιδρά με την Tip60, συμμετέχει στη καταστολή της έκφρασης του ιού, υποδηλώνει μια πιθανή συμμετοχή της Tip60 σε αυτή τη διαδικασία. Αρχικά ελέγξαμε την έκφραση της Tip60 σε υποπληθυσμούς μονοπύρηνων κυττάρων περιφερικού αίματος (PBMCs). Η υψηλότερη έκφραση παρατηρήθηκε στα Τ βοηθητικά λεμφοκύτταρα (CD4+). Για να εξακριβώσουμε το αν και πώς εκφράζεται στους υποπληθυσμούς των Τ λεμφοκυττάρων, απομονώσαμε Τ βοηθητικά μνημονικά λεμφοκύτταρα (CD3+CD4+CD45RO+) από ολικό αίμα ενηλίκων και Τ βοηθητικά παρθενικά λεμφοκύτταρα (CD3+CD4+CD45RA+) από αίμα νεογνών (ομφαλίου λώρου). Τα αποτελέσματά μας έδειξαν ότι σε συνθήκες μη ενεργοποίησης η Τip60 εκφράζεται περισσότερο στα μνημονικά Τh λεμφοκύτταρα σε σχέση με τα παρθενικά Τh λεμφοκύτταρα (στα οποία η έκφραση του παράγοντα παραμένει ουσιαστικά αμετάβλητη). Μετά από την ενεργοποίηση των κυττάρων με PMA/IONO (P/I) η έκφραση της Tip60 αυξάνεται σημαντικά στα μνημονικά Th λεμφοκύτταρα ενώ στα παρθενικά Th παραμένει ουσιαστικά αμετάβλητη. Για να εντοπίσουμε μια λευχαιμική κυτταρική σειρά κατάλληλη για να χρησιμοποιηθεί για πειράματα διαμολύνσεων και ανοσοφθορισμού, ελέγξαμε την έκφραση της Tip60 σε εννέα λευχαιμικές κυτταρικές σειρές και είδαμε ότι η Τ λεμφοκυτταρική λευχαιμική σειρά Jurkat παρουσίαζε την υψηλότερη έκφραση της Τip60. Η κυτταρική σειρά Jurkat παρουσιάζει επίσης παρόμοιο μοτίβο έκφρασης σε επίπεδο mRNA με τα Τ βοηθητικά παρθενικά λεμφοκύτταρα. Την έκφραση της Tip60 την ελέγξαμε και σε πρωτεϊνικό επίπεδο με τη μέθοδο Western blot σε ολικά πρωτεϊνικά εκχυλίσματα που απομονώσαμε από κύτταρα Jurkat. Για να ελέγξουμε τον εντοπισμό της Τip60 στα Jurkat, προχωρήσαμε σε πειράματα ανοσοφθορισμού. Τα αποτελέσματα έδειξαν, ότι σε συνθήκες μη ενεργοποίησης (CM) και ύστερα από ενεργοποίηση των κυττάρων (P/I) η Τip60 εντοπίζεται στον πυρήνα των κυττάρων Jurkat. Επίσης η ποσότητα της πρωτεΐνης Τip60 δεν αλλάζει ύστερα από την ενεργοποίηση των κυττάρων με μιτογόνα, αποτέλεσμα που συμφωνεί με τα πειράματα Western blot. Προκειμένου να ελέγξουμε τη δράση της Τip60 στη μεταγραφική δραστηριότητα του HIV-1 και της IL-2 προχωρήσαμε σε πειράματα διαμόλυνσης Jurkat κυττάρων. Αρχικά διαμολύναμε τα κύτταρα με αυξανόμενες ποσότητες πλασμιδίου υπερέκφρασης της Τip60 (pCMX-tip60) και ελέγξαμε την έκφραση της IL-2 σε μεταγραφικό επίπεδο. Παρατηρήθηκε ότι αυξανομένης της ποσότητας του pCMX-tip60, αυξανόταν και η έκφραση του IL-2 mRNA. Μέσω πειραμάτων CAT-assays σε κύτταρα Jurkat, τα οποία συνδιαμολύναμε με αυξανόμενες ποσότητες πλασμιδίου pCMX-tip60 και πλασμιδίου αναφοράς CAT, που βρίσκεται κάτω από τον έλεγχο του HIV-1-LTR, διαπιστώσαμε ότι η υπερέκφραση της Τip60 αυξάνει και τη μεταγραφική ενεργότητα του υποκινητή του HIV-1. Προκειμένου να διαπιστώσουμε εάν η Tip60 δρα απευθείας στον υποκινητή του HIV-1 και της IL-2 μέσω της πρόσδεσής της σε αυτόν είτε άμεσα, είτε έμμεσα μέσω συμπλόκου με άλλες πρωτεΐνες, προχωρήσαμε σε πειράματα ανοσοκρατακρήμνισης χρωματίνης (ChIP assays) του υποκινητή της IL-2. Παράλληλα επειδή δεν υπάρχει γνωστή θέση πρόσδεσης της Tip60 απευθείας στην LTR αλληλουχία του HIV-1 και στον υποκινητή της IL-2 αναζητήσαμε την πρωτεΐνη με την οποία θα μπορούσε να αλληλεπιδρά προκειμένου να προσδεθεί στα παραπάνω. Με πειράματα συνανοσοκατακρήμνισης διαπιστώσαμε ότι υπάρχει αλληλεπίδραση ανάμεσα στην Tip60 και στον παράγοντα Ets-2, ο οποίος προσδένεται άμεσα στην LTR αλληλουχία του HIV-1 και στον υποκινητή της IL-2 και έτσι επαληθεύσαμε τις αρχικές υποθέσεις για την αλληλεπίδραση τους. Τα πειράματα που πραγματοποιήσαμε μας οδήγησαν στα παρακάτω συμπεράσματα: Υπάρχει διαφορική έκφραση της Tip60 ανάμεσα στα Τ βοηθητικά παρθενικά και μνημονικά λεμφοκύτταρα, αφού σε συνθήκες μη ενεργοποίησης (CM) η έκφραση της Tip60 είναι μεγαλύτερη στα μνημονικά σε σχέση με τα παρθενικά Τh λεμφοκύτταρα. Η ενεργοποίηση των κυττάρων με μιτογόνα προκαλεί επαγωγή της έκφρασης της Tip60 στα μνημονικά Τh λεμφοκύτταρα, ενώ στα παρθενικά δεν προκαλεί καμία ουσιαστική αλλαγή. Η πρωτεΐνη Tip60 δρα σαν συνενεργοποιητής της μεταγραφής του ιού HIV-1 και της IL-2 μιας και προκαλεί επαγωγή στην μεταγραφική τους δραστηριότητα. Η πρωτεΐνη Tip60 αλληλεπιδρά in vivo με τον παράγοντα Εts-2 και παρουσιάζει το ίδιο πρότυπο πρόσδεσης με αυτόν, στον υποκινητή της IL-2 στην κυτταρική σειρά Jurkat. / Tip60 (Tat-interactive protein, 60 kDa) is a member of the MYST protein family and was initially identified as an interacting protein with the HIV-1 TAT protein. Several members of MYST family, Tip60 among them, act as histone acetyltransferases, suggesting their possible roles in chromatin remodeling and gene regulation. We chose to study Tip60 because it is a Tat-interactive protein and Tat is encoded by the Tat gene of HIV-1. Recent results from our laboratory suggest that there is a possible interaction between Tip60 and Εts-2 proteins, which is involved in the regulation of the transcription of both IL-2 and HIV-1. In addition, the transcription of IL-2 and HIV-1 is regulated by common transcription factors that act through binding to common cis-trans elements. We also know that the HIV-1 virus is transcriptionally active in activated CD4 T cells, and inactive in naïve CD4 T cells and that HIV-1 expression is blocked in naive Th cells by the transcriptional factor Ets-2. So the possible interaction between Tip60 and Εts-2 protein led us to study the Tip60 protein. The main purpose of this study was to determine the expression profile of Tip60 acetyltransferase in naive T helper (CD3+CD4+CD45RA+) and memory T helper (CD3+CD4+CD45RO+) lymphocytes and its effect on the transcription of HIV-1 and IL-2 (due to their common transcriptional regulation in T helper cells). The expression of Tip60 mRNA was measured in subpopulations of peripheral blood mononuclear cells (PBMCs) and the highest levels were observed in Th lymphocytes. We therefore isolated from human peripheral blood and cord blood, CD3+CD4+CD45RO+ and CD3+CD4+CD45RA+ Th lymphocytes and we examined the expression of Tip60 at the transcriptional level by RT-PCR. The results showed that Tip60 mRNA expression levels were higher in CD3+CD4+CD45RO+ compared to CD3+CD4+CD45RA+ Th cells. Following cell activation with PMA/IONO (P/I), the transcriptional expression of Tip60 was increased in memory Th cells, whereas it remained unchanged in naive Th cells. To identify a suitable cell line for transfection and immunofluorescence experiments, we measured Tip60 expression in nine cell lines and we observed that the T lymphocytic leukemia Jurkat presented the highest expression of Tip60 mRNA. Jurkat cells also presented a similar pattern of Tip60 mRNA expression levels with naïve Th lymphocytes. In addition to determine the localization of Tip60 into the cells, we proceeded in immunofluorescence experiments. As a result, we observed that when cells were cultured in CM media +/- P/I, Tip60 was identified in the nucleus of Jurkat cells. The amount of Tip60 protein remained unchanged after cell activation (which was also determined by Western blot experiments). To study the effect of Tip60 in transcription of HIV-1 and IL-2 we transfected Jurkat cells with increasing amounts of a Tip60 overexpressing vector (pCMX-tip60) and measured the expression of IL-2 and HIV-1 at the transcriptional level. Overexpression of Tip60, induced the transcription of IL-2 and also increased the transcriptional activity of HIV-1. Co-transfection experiments in Jurkat cells with increasing amounts of PCMX-tip60, led to a gradual increase of HIV1-LTR-CAT Finally, we studied if Tip60 acts directly on the promoter of HIV-1 and IL-2 exercising its effect directly or through complexing with other proteins. According to the literature there is no Tip60 binding site in the promoter of HIV-1 and IL-2, so we searched for a protein that could interact with Tip60. We performed co-immunoprecipitation experiments that showed that there was an interaction between Tip60 and Ets-2, a factor that binds directly both on the LTR of HIV-1 and the IL-2 promoter. In this work we suggest that Tip60 is expressed differentially in naïve and memory helper T cells and participates in the transcriptional activation of both HIV-1 LTR and IL-2. Also Tip60 protein interacts in vivo with Ets-2 protein and Tip60 binding activity is similar with Ets-2 binding activity to the ARRE-2 element of the IL-2 promoter in Jurkat cell line.

Reverse transcription in HIV-1 (human immunodeficiency virus type 1) is initiated from a tRNA, tRNALys3, that is annealed to the primer binding site (PBS) in the 5' region of viral RNA. This tRNA, along with the other major tRNALys isoacceptors, tRNALys1,2 , is selectively packaged into HIV-1 during its assembly. The formation of a tRNALys packaging/annealing complex is believed to involve the interaction between a Gag/GagPol/viral complex with a lysyl-tRNA synthetase (LysRS)/tRNALys complex, with Gag interacting specifically with LysRS, and GagPol interacting with both Gag and tRNALys. In fact, Gag particles alone will package LysRS, but GagPol, which binds tRNA Lys, is also required for incorporation of the tRNALys. / The model we propose for the tRNALys packaging/annealing complex predicts a possible interaction between LysRS and Pol sequences in GagPol, which might facilitate transfer of tRNALys3 from LysRS to the reverse transcriptase (RT) thumb domain where tRNALys3 binds. In this work, we demonstrate that, in addition to its interaction with Gag, LysRS also interacts with sequences within the connection/RNaseH domains in RT. Since these RT domains are not required for tRNALys packaging into HIV-1, the LysRS/Pol interaction is probably not involved in the transfer of tRNALys3 to RT. The LysRS/Pol interaction may instead be involved in tRNALys3 annealing since the connection domain in RT has been found to be required for this process. Also, since an interaction has been reported between Gag and Pol sequences in GagPol, we also investigated whether the Gag/LysRS/Pol interaction played an important role in stabilizing the Gag/Pol interaction, and found, using siRNA to LysRS, that it did not. / tRNALys3 annealing to viral RNA is promoted by nucleocapsid sequences in Gag and by mature NCp7, and we have examined the roles of Gag and NCp7 in this process. Gag- and NC-facilitated tRNALys3 annealing to HIV-1 RNA were measured both in vivo and in vitro, indirectly by the ability of annealed tRNALys3 to prime reverse transcription, and directly by measuring the occupancy of the PBS by tRNALys3. While tRNALys3 annealing can be carried out by both Gag and NCp7, exposure (in vivo or in vitro) of the tRNALys3/viral RNA complex to NCp7 is required for optimum placement of the tRNALys3. This is indicated by 1) tRNALys3's reduced ability to incorporate the first dNTP, dCTP, and 2) its more ready displacement from the PBS by DNA synthesized from a downstream primer. / It has been previously demonstrated that APOBEC3G (A3G) can inhibit tRNA Lys3 annealing to viral RNA, and we have used A3G to further dissect the roles of Gag and NCp7 in annealing, both in vitro and in vivo. Experiments studying how APOBEC3G (A3G) inhibits tRNA Lys3 annealing indicate that in protease-positive viruses, Gag-facilitated tRNALys3 annealing may only playa minor role. In vivo and in vitro, A3G only inhibits NCp7-facilitated annealing, and not Gag-facilitated annealing. Nevertheless, while Gag is able to show 70-80% of the annealing efficiency of NCp7 in a protease-negative virus, A3G can reduce annealing efficiency in protease-positive viruses to 40%. This appears to be due to the fact that, in vitro, the presence of NCp7 makes prior Gag-facilitated annealing susceptible to A3G. This suggests that in wild type viruses, any Gag-facilitated annealing of tRNALys3 to viral RNA that does occur is altered through an A3G-susceptible re-annealing by NCp7.

In the past three decades, various steps of the human immunodeficiency virus type 1 (HIV-1) life cycle have been thoroughly studied. Many of these steps, such as viral entry, reverse transcription and proteolysis have been targets of antiretroviral therapy. Retroviral genomic RNA (gRNA) dimerization appears essential for viral infectivity and this process appears to be chaperoned by the nucleocapsid (NC) protein of HIV-1. In this dissertation, the role of NC in genome dimerization and other aspects of the viral life cycle have been thoroughly studied. Various positions of the NC protein have been mutated through site-directed mutagenesis and relevant and dispensable positions of NC have been identified through this method. 34 of its 55 residues were mutated, individually or in small groups, in a panel of 40 HIV-1 mutants. It was found that the amino-terminus, the proximal zinc finger, the linker, and the distal zinc finger of NC each contributed roughly equally to efficient HIV-1 gRNA dimerization. The various mutations introduced into NC show the first evidence that gRNA dimerization can be inhibited by: 1) mutations in the N-terminus or the linker of retroviral NC; 2) mutations in the proximal or distal zinc finger of lentiviral NC; 3) mutations in the hydrophobic patch (plateau) or the conserved glycines of the proximal or the distal retroviral zinc finger. Some NC mutations impaired gRNA dimerization more than mutations inactivating the viral protease, indicating that gRNA dimerization may be stimulated by the NC component of the Gag polyprotein (Pr55gag). In the second section of my work, I studied the effect of Pr55gag processing on gRNA dimerization by introducing rate alternating mutants into Pr55gag protein cleavage sites. I showed that Maturation ofNCp15 into NCp9 is essential for fast rates of genomic RNA dimerization and maturation of NCp9 into NCp7 has no incidence on genomic RNA dimerization but is essential for viral replication. In order to delineate the amount of viral protease activity needed to produce mature virus 48 hours post transfection, we also studied, by cotransfection studies, the effect of various ratios of wild-type (BH10) and protease-inactive (PR- ) plasmids and found that HIV-1 reaches its full genomic RNA dimerization despite 75% unprocessed Pr55gag polyproteins. We have also shown that wild type BH10 plasmid can rescue those mutations in NCp7 protein that have an effect on gRNA dimerization through rescue experiments. Overall, this thesis sheds light on the role of NC in HIV-1 genome dimerization and other aspects of the viral life cycle and identifies the importance of each component of NC during these processes.

Heterosexual intercourse now accounts for the majority of HIV transmission within sub-Saharan Africa. The generation of microbicides and vaccines, therefore, requires a better understanding of the mucosal correlates of protection, including the role of HIV-specific IgA. It is now accepted that not all individuals are equally susceptible to HIV-1 infection, as exemplified by the HIV Exposed Seronegative (HESN) women of the Pumwani Cohort in Nairobi, Kenya. To assess whether mucosal IgA responses contribute to this protection, 3 novel IgA variable genes were cloned from HESN cervical B-cell cDNA. Nine monoclonal IgA Abs were produced, two of which were properly produced from cell culture. The HESN-derived A6/30L and A9/30L variants had a greater specificity for gp120IIIB than their A6/4L and A9/4L counterparts, while the A6 variant recognizes a distinct gp120 epitope compared to the broadly neutralizing antibody IgGb12. Further characterization of these IgA chains may suggest their suitability for use in microbicides or mucosal vaccines.

Tat1-72, is an intrinsically disordered protein at pH 4.1 as previously indicated by NMR chemical shifts and coupling constants, and confirmed by 15N-relaxation parameters. The presence of SDS elicits a conformational change to α-helicity in Tat1-72. In the presence of the non-ionic DDM detergent and zinc, Tat was found to be soluble at pH 4 when bound to TAR RNA; TAR binding also elicits a conformational shift to α-helicity in Tat1-72. The β-sheet content of Tat1-72 is increased in the presence of NaCl. In similar conditions, Tat1-72 aggregates stained with Congo Red displayed a yellow-green birefringence and a red-shift in the Congo Red absorbance that is typical of β-amyloid fibril. The web-based algorithm “WALTZ” identifies the majority of the Tat1-72 hydrophobic core region as amyloidogenic. The helical propensity of Tat1-72 in TFE was determined by two-dimensional NMR spectroscopy.

Like all viruses, the replication of HIV-1 relies heavily on host proteins due to its limited genome products. HIV-1 integrase (IN) catalyzes the integration of viral DNA into host genome and also impacts other steps of viral replication cycle, all of which are assisted by various cellular proteins. Among them, LEDGF/p75 acts as the IN-to-chromatin tethering factor. However, whether other cellular cofactors also participate in this process still remains elusive. To gain insight into the mechanism of action of HIV-1 IN during viral integration, we used a previously described IN/yeast lethality system and our results revealed that the HIV-1 IN-induced yeast lethality absolutely required its chromatin binding ability. Since there is no yeast homolog of LEDGF/p75, it raises the possibility that IN may recruit other cellular cofactors for its chromatin targeting. Consistently, further analysis in mammalian cells indicated that HIV-1 IN was able to mediate chromatin binding independent of IN-LEDGF/p75 interaction and that HIV-1 fitness relied more on chromatin binding than LEDGF/p75 binding of IN. These data greatly enrich our current knowledge on the dynamic interplay within the ternary complex IN/LEDGF/chromatin. HIV-1 exploits multiple cellular cofactors not only to facilitate viral replication, but also to evade the host defense system in favor of the virus. IN is known to be an unstable protein, degraded by the host ubiquitin-proteasome pathway. To investigate how IN avoids the host degradation machinery in the context of viral infection, we showed that IN interacted with host protein Ku70 and protected itself from the Lys48-linked polyubiquitination proteasomal pathway. More importantly, Ku70 was shown to be incorporated into the progeny virus in an IN-dependent manner, and both cell- and virus- associated Ku70 were essential for HIV-1 replication. Finally, the data demonstrated that the interactions between HIV-1 IN and host cofactors can be regulated through its SUMO-interacting motifs (SIMs). Three putative SIMs (72VILV75; 200IVDI203 and 257IKII260) in IN were examined and shown to be essential for IN-LEDGF/p75 but not IN-Ku70 interaction. In summary, this study advances our knowledge of the interaction network between IN and its cofactors, which would have important implications for the design of anti-HIV drugs.

Reverse transcription of human immunodeficiency virus type-1 (HIV-1) is primed by cellular tRNALys3, which is selectively packaged into viral particles where it is bound at its 3' terminus to a complementary sequence of viral RNA termed the primer binding site (PBS). In addition to the PBS, other regions within the viral genome also interact with tRNALys3. Initiation of HIV-1 reverse transcription requires specific recognition of the viral genome, tRNA primer, and reverse transcriptase (RT). In this work, we study the important role played by the initiation complex in the initiation of HIV-1 reverse transcription. An "A-rich loop" located upstream of the PBS has been shown to interact with the anticodon loop of tRNALys3 and deletion of this A-rich loop caused diminished viral replication fitness. We have now studied the mechanisms involved in the altered replication capacities of the deletion-containing viruses in the context of both wild type HIV-1 and viruses also containing the M184V substitution in RT. We found that the M184V mutation in RT compromises the ability of deletion-containing viruses to restore wild-type replication. Further biochemical study indicates that both the M184V mutation in RT and deletion of sequences upstream of PBS caused diminished viral replication fitness by compromising the efficiency of reverse transcription initiation. / Since the initiation of DNA synthesis was shown to be a highly specific process, it represents a potential target for the development of novel antiviral agents. We developed strategies for inhibition of the HIV-1 replication via interference with the tRNALys3/viral RNA complex. To target primer tRNALys3, we employed oligodeoxyribonucleotides (ODNs) that are complementary to different parts of the tRNA primer. To target viral RNA, we devised a tRNALys3-like molecule, termed tRNA Lys*, that contained sequence alterations that direct initiation from a region distant from the natural PBS, designated PBS*. PBS* is involved in the formation of the natural tRNA/PBS complex and binding of tRNALys* was shown to interfere specifically with the initiation of reverse transcription. Inhibition of the synthesis of (-) strand strong-stop DNA was achieved successfully with both strategies by interfering with the formation of the initiation complex.

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein.

The HIV-1 transactivator of transcription (Tat) is a protein essential for both viral gene expression and virus replication. Tat is an RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The Tat protein is encoded by two exons and is 101 residues in length. The first exon encodes a 72-residue molecule that activates transcription with the same proficiency as the full-length protein. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven cysteine residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of polyhistidine-tagged and isotopically enriched (in 15N and 15N /13C) recombinant HIV-1 Tat1-72 (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the non-proline backbone resonances using heteronuclear 3-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced and monomeric in aqueous solution at pH 4. NMR chemical shifts and coupling constants suggest that it exists in a disordered conformation. Line broadening and multiple peaks in the cysteine-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analysed by spectral density and model-free approaches both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of the Tat protein to interact with a wide variety of proteins and nucleic acid lending further support to the concept that Tat exists as an intrinsically disordered protein.