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Wang H.,University of Texas at Austin | Ma X.,University of Texas at Austin | Yeh Y.-S.,University of Texas at Austin | Zhu Y.,University of Texas at Austin | And 5 more authors.
Biophysical Journal | Year: 2010

We report a comparative study in which a single-molecule fluorescence resonance energy transfer approach was used to examine how the binding of two families of HIV-1 viral proteins to viral RNA hairpins locally changes the RNA secondary structures. The single-molecule fluorescence resonance energy transfer results indicate that the zinc finger protein (nucleocapsid) locally melts the TAR RNA and RRE-IIB RNA hairpins, whereas arginine-rich motif proteins (Tat and Rev) may strengthen the hairpin structures through specific binding interactions. Competition experiments show that Tat and Rev can effectively inhibit the nucleocapsid-chaperoned annealing of complementary DNA oligonucleotides to the TAR and RRE-IIB RNA hairpins, respectively. The competition binding data presented here suggest that the specific nucleic acid binding interactions of Tat and Rev can effectively compete with the general nucleic acid binding/chaperone functions of the nucleocapsid protein, and thus may in principle help regulate critical events during the HIV life cycle. © 2010 by the Biophysical Society.

Li Y.,Covidien | Chia N.,Institute for Genomic Biology | Chia N.,University of Illinois at Urbana - Champaign | Lauria M.,Telethon Institute of Genetics and Medicine | And 2 more authors.
Bioinformatics | Year: 2011

Motivation: Sequence alignment is one of the most popular tools of modern biology. NCBI's PSI-BLAST utilizes iterative model building in order to better detect distant homologs with greater sensitivity than non-iterative BLAST. However, PSI-BLAST's performance is limited by the fact that it relies on deterministic alignments. Using a semi-probabilistic alignment scheme such as Hybrid alignment should allow for better informed model building and improved identification of homologous sequences, particularly remote homologs. Results: We have built a new version of the tool in which the Smith-Waterman alignment algorithm core is replaced by the hybrid alignment algorithm. The favorable statistical properties of the hybrid algorithm allow the introduction of position-specific gap penalties in Hybrid PSI-BLAST. This improves the position-specific modeling of protein families and results in an overall improvement of performance. © The Author 2010. Published by Oxford University Press. All rights reserved.

Butler J.S.,Center for Biology | Butler J.S.,University of Rochester | Mitchell P.,University of Sheffield
Advances in Experimental Medicine and Biology | Year: 2010

This chapter reviews the present state of knowledge on the activity of enzymes that function with the RNA exosome in the nucleus. In this compartment, the exosome interacts physically and functionally with the exoribonuclease Rrp6 and several cofactors, most prominently Rrp47 and the TRAMP complex. These interactions decide the fate of RNA precursors from transcription through the formation of mature ribonucleoprotein particles (RNPs) and the export of the RNPs to the cytoplasm. The nuclear exosome catalyzes the formation of the mature 3′ ends of many of these RNAs, but in other cases degrades the RNAs to mononucleotides. Cofactors such as Mpp6, TRAMP and the Nrd1/Nab3 complex play important roles in determining the outcome of the interaction of RNPs with the nuclear exosome. The details that govern the specificity of these decisions remain a rich source for future investigation. © 2010 Landes Bioscience and Springer Science+Business Media.

Seetin M.G.,Center for Biology | Mathews D.H.,Center for Biology | Mathews D.H.,University of Rochester
Bioinformatics | Year: 2012

Motivation: Many RNA molecules function without being translated into proteins, and function depends on structure. Pseudoknots are motifs in RNA secondary structures that are difficult to predict but are also often functionally important. Results: TurboKnot is a new algorithm for predicting the secondary structure, including pseudoknotted pairs, conserved across multiple sequences. TurboKnot finds 81.6% of all known base pairs in the systems tested, and 75.6% of predicted pairs were found in the known structures. Pseudoknots are found with half or better of the false-positive rate of previous methods. © The Author 2012. Published by Oxford University Press.

Rao B.S.,Center for Biology | Rao B.S.,Ohio State University | Maris E.L.,Center for Biology | Jackman J.E.,Center for Biology | Jackman J.E.,Ohio State University
Nucleic Acids Research | Year: 2011

The tRNAHis guanylyltransferase (Thg1) family comprises a set of unique 3′-5′ nucleotide addition enzymes found ubiquitously in Eukaryotes, where they function in the critical G-1 addition reaction required for tRNAHis maturation. However, in most Bacteria and Archaea, G-1 is genomically encoded; thus post-transcriptional addition of G-1 to tRNA His is not necessarily required. The presence of highly conserved Thg1-like proteins (TLPs) in more than 40 bacteria and archaea therefore suggests unappreciated roles for TLP-catalyzed 3′-5′ nucleotide addition. Here, we report that TLPs from Bacillus thuringiensis (BtTLP) and Methanosarcina acetivorans (MaTLP) display biochemical properties consistent with a prominent role in tRNA 5′-end repair. Unlike yeast Thg1, BtTLP strongly prefers addition of missing N+1 nucleotides to 5′-truncated tRNAs over analogous additions to full-length tRNA (kcat/KM enhanced 5-160-fold). Moreover, unlike for -1 addition, BtTLP-catalyzed additions to truncated tRNAs are not biased toward addition of G, and occur with tRNAs other than tRNA His. Based on these distinct biochemical properties, we propose that rather than functioning solely in tRNAHis maturation, bacterial and archaeal TLPs are well-suited to participate in tRNA quality control pathways. These data support more widespread roles for 3′-5′ nucleotide addition reactions in biology than previously expected. © 2010 The Author(s).

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