http://precedings.nature.com/tags/HIV-1 Recently posted documents tagged with 'HIV-1' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/2041/version/1 A compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1 predominantly targets rich-clubs, human proteins that are not only well connected but also strongly intertwined among each other. These assemblies of proteins putatively serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. In particular, HIV-1 utilizes its small number of proteins in a combinatorial manner, exerting a significant influence on pathways that deal with transcriptional, translational and degradation processes. Surprisingly, the small repertoire of HIV proteins also interferes loosely with many signaling and regulation pathways, suggesting that a widespread involvement in such pathways secures the control of the host cell. Such insights offer novel perspectives to investigate the progression of HIV infection and potentially can contribute to our abilities to fight this virus. http://precedings.nature.com/documents/2041/version/1 Wed, 09 Jul 2008 17:18:11 UTC Viral organization of human proteins hdl:10101/npre.2008.2041.1 2008-07-09 Stefan Wuchty Nature Precedings 2008-07-09T17:18:11Z Manuscript Microbiology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1248/version/1 The search for mechanisms of translational regulation has yielded many experimentally identified internal ribosome entry sites (IRES). Because of the lack of sequence similarity among the experimentally IRESs, it is widely assumed that IRESs posses stable secondary structure allowing them to interact with the components of the translation machinery. Contrary to this view, here we show that IRES activity in nine yeast IRESs, mapped to 60 nt immediately upstream of the initiation AUG, is strongly associated with the lack of secondary structure of IRESs. Furthermore, the reverse complements of these IRESs, with their secondary structure more stable than those of the IRESs, exhibit little IRES activity. The generality of this association is exemplified by the observation that, in the natural vpu-env bicistronic mRNA in HIV-1, the mRNA segment (60 nt) immediately upstream of the initiation AUG of env has the weakest secondary structure among all dominant HIV-1 mRNA species. These results suggest a unified model of alternative translation initiation. http://precedings.nature.com/documents/1248/version/1 Tue, 23 Oct 2007 15:17:56 UTC Internal ribosomal entry site lacks secondary structure hdl:10101/npre.2007.1248.1 2007-10-23 Xuhua Xia Nature Precedings 2007-10-23T15:17:56Z Manuscript Microbiology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.1212.1 Human immunodeficiency virus type 1 (HIV-1) is a human retrovirus and the causative agent of the acquired immunodeficiency syndrome. Genetic analysis has revealed that the HIV-1 LTR contains a potential negative regulatory element (NRE) with an E box, the recognition sequence for the helix-loop-helix (HLH) family of transcription factors. Furthermore, the upstream stimulatory factor (USF) has been implicated as a negative regulator of HIV-1 expression. Here, we report that the NRE is a composite element and that both C/EBPδ and USF can specifically bind to the NRE. The recognition sequence for C/EBPδ overlaps with the E box in the NRE of HIV-1. Competition experiments showed that either USF or C/EBPδ binds to this NRE but not both together. http://dx.doi.org/10.1038/npre.2007.1212.1 Tue, 09 Oct 2007 08:34:15 UTC Upstream Stimulatory Factor (USF) and CCAAT/Enhancer Binding Protein δ (C/EBPδ) Compete for overlapping Sites in the Negative Regulatory Region of the HIV-1 LTR doi:10.1038/npre.2007.1212.1 2007-10-09 Torik T. A. Ayoubi Nature Precedings 2007-10-09T08:34:15Z Manuscript Immunology Molecular Cell Biology http://creativecommons.org/licenses/by/2.5/