Medicine and Health Sciences Commons^™

Initiator Trna Genes Template The 3' Cca End At High Frequencies In Bacteria., David H. Ardell, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

BACKGROUND: While the CCA sequence at the mature 3' end of tRNAs is conserved and critical for translational function, a genetic template for this sequence is not always contained in tRNA genes. In eukaryotes and Archaea, the CCA ends of tRNAs are synthesized post-transcriptionally by CCA-adding enzymes. In Bacteria, tRNA genes template CCA sporadically.

RESULTS: In order to understand the variation in how prokaryotic tRNA genes template CCA, we re-annotated tRNA genes in tRNAdb-CE database version 0.8. Among 132,129 prokaryotic tRNA genes, initiator tRNA genes template CCA at the highest average frequency (74.1%) over all functional classes except selenocysteine and …

The Yersinia Pestis Effector Yopm Inhibits Pyrin Inflammasome Activation., Dmitry Ratner, M Pontus A Orning, Megan K. Proulx, Donghai Wang, Mikhail A. Gavrilin, Mark D. Wewers, Emad S. Alnemri, Peter F. Johnson, Bettina Lee, Joan Mecsas, Nobuhiko Kayagaki, Jon D. Goguen, Egil Lien

Department of Biochemistry and Molecular Biology Faculty Papers

Type III secretion systems (T3SS) are central virulence factors for many pathogenic Gram-negative bacteria, and secreted T3SS effectors can block key aspects of host cell signaling. To counter this, innate immune responses can also sense some T3SS components to initiate anti-bacterial mechanisms. The Yersinia pestis T3SS is particularly effective and sophisticated in manipulating the production of pro-inflammatory cytokines IL-1β and IL-18, which are typically processed into their mature forms by active caspase-1 following inflammasome formation. Some effectors, like Y. pestis YopM, may block inflammasome activation. Here we show that YopM prevents Y. pestis induced activation of the Pyrin inflammasome induced …

Potent And Broad Inhibition Of Hiv-1 By A Peptide From The Gp41 Heptad Repeat-2 Domain Conjugated To The Cxcr4 Amino Terminus., George J. Leslie, Jianbin Wang, Max W. Richardson, Beth S. Haggarty, Kevin L. Hua, Jennifer Duong, Anthony J. Secreto, Andrea P.O. Jordon, Josephine Romano, Kritika E. Kumar, Joshua J. Declercq, Philip D. Gregory, Carl H. June, Michael J. Root, James L. Riley, Michael C. Holmes, James A. Hoxie

Department of Biochemistry and Molecular Biology Faculty Papers

HIV-1 entry can be inhibited by soluble peptides from the gp41 heptad repeat-2 (HR2) domain that interfere with formation of the 6-helix bundle during fusion. Inhibition has also been seen when these peptides are conjugated to anchoring molecules and over-expressed on the cell surface. We hypothesized that potent anti-HIV activity could be achieved if a 34 amino acid peptide from HR2 (C34) were brought to the site of virus-cell interactions by conjugation to the amino termini of HIV-1 coreceptors CCR5 or CXCR4. C34-conjugated coreceptors were expressed on the surface of T cell lines and primary CD4 T cells, retained the …

Chromatin Proteins And Rna Are Associated With Dna During All Phases Of Mitosis., Kathryn L Black, Svetlana Petruk, Tyler K Fenstermaker, Jacob W Hodgson, Jeffrey L Caplan, Hugh W Brock, Alexander Mazo

Department of Biochemistry and Molecular Biology Faculty Papers

Mitosis brings about major changes to chromosome and nuclear structure. We used recently developed proximity ligation assay-based techniques to investigate the association with DNA of chromatin-associated proteins and RNAs in Drosophila embryos during mitosis. All groups of tested proteins, histone-modifying and chromatin-remodeling proteins and methylated histones remained in close proximity to DNA during all phases of mitosis. We also found that RNA transcripts are associated with DNA during all stages of mitosis. Reduction of H3K27me3 levels or elimination of RNAs had no effect on the association of the components of PcG and TrxG complexes to DNA. Using a combination of …

The Α-Arrestin Arrdc3 Regulates The Endosomal Residence Time And Intracellular Signaling Of The Β2-Adrenergic Receptor., Xufan Tian, Roshanak Irannejad, Shanna L. Bowman, Yang Du, Manojkumar A. Puthenveedu, Mark Von Zastrow, Jeffrey L. Benovic

Department of Biochemistry and Molecular Biology Faculty Papers

Arrestin domain-containing protein 3 (ARRDC3) is a member of the mammalian α-arrestin family, which is predicted to share similar tertiary structure with visual-/β-arrestins and also contains C-terminal PPXY motifs that mediate interaction with E3 ubiquitin ligases. Recently, ARRDC3 has been proposed to play a role in regulating the trafficking of G protein-coupled receptors, although mechanistic insight into this process is lacking. Here, we focused on characterizing the role of ARRDC3 in regulating the trafficking of the β2-adrenergic receptor (β2AR). We find that ARRDC3 primarily localizes to EEA1-positive early endosomes and directly interacts with the β2AR in a ligand-independent manner. Although …

Molecular Basis And Consequences Of The Cytochrome C-Trna Interaction., Cuiping Liu, Aaron J Stonestrom, Thomas Christian, Jeongsik Yong, Ryuichi Takase, Ya-Ming Hou, Xiaolu Yang

Department of Biochemistry and Molecular Biology Faculty Papers

The intrinsic apoptosis pathway occurs through the release of mitochondrial cytochrome c to the cytosol, where it promotes activation of the caspase family of proteases. The observation that tRNA binds to cytochrome c revealed a previously unexpected mode of apoptotic regulation. However, the molecular characteristics of this interaction, and its impact on each interaction partner, are not well understood. Using a novel fluorescence assay, we show here that cytochrome c binds to tRNA with an affinity comparable with other tRNA-protein binding interactions and with a molecular ratio of ∼3:1. Cytochrome c recognizes the tertiary structural features of tRNA, particularly in …

A Parp1-Erk2 Synergism Is Required For The Induction Of Ltp., L Visochek, G Grigoryan, A Kalal, H Milshtein-Parush, N Gazit, I Slutsky, A Yeheskel, A Shainberg, A Castiel, R Seger, Marie-France Langelier, F Dantzer, Pascal Jabbour Md, M Segal, M Cohen-Armon

Department of Biochemistry and Molecular Biology Faculty Papers

Unexpectedly, a post-translational modification of DNA-binding proteins, initiating the cell response to single-strand DNA damage, was also required for long-term memory acquisition in a variety of learning paradigms. Our findings disclose a molecular mechanism based on PARP1-Erk synergism, which may underlie this phenomenon. A stimulation induced PARP1 binding to phosphorylated Erk2 in the chromatin of cerebral neurons caused Erk-induced PARP1 activation, rendering transcription factors and promoters of immediate early genes (IEG) accessible to PARP1-bound phosphorylated Erk2. Thus, Erk-induced PARP1 activation mediated IEG expression implicated in long-term memory. PARP1 inhibition, silencing, or genetic deletion abrogated stimulation-induced Erk-recruitment to IEG promoters, gene …

Parp-2 Domain Requirements For Dna Damage-Dependent Activation And Localization To Sites Of Dna Damage., Amanda A Riccio, Gino Cingolani, John M Pascal

Department of Biochemistry and Molecular Biology Faculty Papers

Poly(ADP-ribose) polymerase-2 (PARP-2) is one of three human PARP enzymes that are potently activated during the cellular DNA damage response (DDR). DDR-PARPs detect DNA strand breaks, leading to a dramatic increase in their catalytic production of the posttranslational modification poly(ADP-ribose) (PAR) to facilitate repair. There are limited biochemical and structural insights into the functional domains of PARP-2, which has restricted our understanding of how PARP-2 is specialized toward specific repair pathways. PARP-2 has a modular architecture composed of a C-terminal catalytic domain (CAT), a central Trp-Gly-Arg (WGR) domain and an N-terminal region (NTR). Although the NTR is generally considered the …

The Eff-1a Cytoplasmic Domain Influences Hypodermal Cell Fusions In C. Elegans But Is Not Dependent On 14-3-3 Proteins., Jessica H Shinn-Thomas, Jacob J Del Campo, Jianjun Wang, William A Mohler

Department of Biochemistry and Molecular Biology Faculty Papers

BACKGROUND: Regulatory and biophysical mechanisms of cell-cell fusion are largely unknown despite the fundamental requirement for fused cells in eukaryotic development. Only two cellular fusogens that are not of clear recent viral origin have been identified to date, both in nematodes. One of these, EFF-1, is necessary for most cell fusions in Caenorhabditis elegans. Unregulated EFF-1 expression causes lethality due to ectopic fusion between cells not developmentally programmed to fuse, highlighting the necessity of tight fusogen regulation for proper development. Identifying factors that regulate EFF-1 and its paralog AFF-1 could lead to discovery of molecular mechanisms that control cell fusion …