Life Sciences Commons^™

Most Caenorhabditis Elegans Micrornas Are Individually Not Essential For Development Or Viability, Eric A. Miska, Ezequiel Alvarez-Saavedra, Allison L. Abbott, Nelson C. Lau, Andrew B. Hellman, Shannon M. Mcgonagle, David P. Bartel, Victor R. Ambros, H. Robert Horvitz

Biological Sciences Faculty Research and Publications

MicroRNAs (miRNAs), a large class of short noncoding RNAs found in many plants and animals, often act to post-transcriptionally inhibit gene expression. We report the generation of deletion mutations in 87 miRNA genes in Caenorhabditis elegans, expanding the number of mutated miRNA genes to 95, or 83% of known C. elegans miRNAs. We find that the majority of miRNAs are not essential for the viability or development of C. elegans, and mutations in most miRNA genes do not result in grossly abnormal phenotypes. These observations are consistent with the hypothesis that there is significant functional redundancy among miRNAs …

Cold Responsive Earli1 Type Hyprps Improve Freezing Survival Of Yeast Cells And Form Higher Order Complexes In Plants, Yi Zhang, Michael Schläppi

Biological Sciences Faculty Research and Publications

Plants have large families of proteins sharing a conserved eight-cysteine-motif (8CM) domain. The biological functions of these proteins are largely unknown. EARLI1 is a cold responsive Arabidopsis gene that encodes a hybrid proline-rich protein (HyPRP) with a three-domain architecture: a putative signal peptide at the N-terminus, a proline-rich domain (PRD) in the middle, and an 8CM domain at the C-terminus. We report here that yeast cells expressing different EARLI1 genes had significantly higher rates of freezing survival than empty-vector transformed controls. Arabidopsis plants with knocked down EARLI1 genes had an increased tendency for freezing-induced cellular damage. EARLI1-GFP Fluorescence in …

A Mutant Dec-1 Transgene Induces Dominant Female Sterility In Drosophila Melanogaster, Daniel K. Spangenberg, Gail L. Waring

Biological Sciences Faculty Research and Publications

The Drosophila dec-1 gene produces three proproteins required for female fertility and eggshell assembly. The three proproteins are distinguished by their C termini. Fc106, the most abundant proprotein, is cleaved within the vitelline membrane to three mature derivatives in a developmentally regulated manner. To define sequences within fc106 that are critical for its function, we created wild-type and mutant versions of an fc106 cDNA transgene. The functional consequences of the mutations were assessed in dec-1⁴, a female-sterile splicing mutant that does not produce the fc106 isoform. The fertility of dec-1⁴ females was restored by the introduction of …

The Chlamydomonas Genome Reveals The Evolution Of Key Animal And Plant Functions, Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Maréchal-Drouard, Wallace F. Marshall, Liang-Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Pierre Cardol, Heriberto Cerutti, Guillaume Chanfreau, Chun-Long Chen, Valerie Cognat, Martin T. Croft, Rachel Dent, Susan Dutcher, Emilio Fernández, Hideya Fukuzawa, David González-Ballester, Diego González-Halphen, Armin Hallmann, Marc Hanikenne, Michael Hippler, William Inwood, Kamel Jabbari, Ming Kalanon, Richard Kuras, Paul A. Lefebvre, Stéphane D. Lemaire, Alexey V. Lobanov, Martin Lohr, Andrea Manuell, Iris Meier, Laurens Mets, Maria Mittag, Telsa Mittelmeier, James V. Moroney, Jeffrey Moseley, Carolyn Napoli, Aurora M. Nedelcu, Krishna Niyogi, Sergey V. Novoselov, Ian T. Paulsen, Greg Pazour, Saul Purton, Jean-Philippe Ral, Diego Mauricio Riaño-Pachón, Wayne Riekhof, Linda Rymarquis, Michael Schroda, David Stern, James Umen, Robert Willows, Nedra Wilson, Sara Lana Zimmer, Jens Allmer, Janneke Balk, Katerina Bisova, Chong-Jian Chen, Mark Elias, Karla Gendler, Charles Hauser, Mary Rose Lamb, Heidi Ledford, Joanne C. Long, Jun Minagawa, M. Dudley Page, Junmin Pan, Wirulda Pootakham, Sanja Roje, Annkatrin Rose, Eric Stahlberg, Aimee M. Terauchi, Pinfen Yang, Steven Ball, Chris Bowler, Carol L. Dieckmann, Vadim N. Gladyshev, Pamela Green, Richard Jorgensen, Stephen Mayfield, Bernd Mueller-Roeber, Sathish Rajamani, Richard T. Sayre, Peter Brokstein, Inna Dubchak, David Goodstein, Leila Hornick, Y. Wayne Huang, Jinal Jhaveri, Yigong Luo, Diego Martinez, Wing Chi Abby Ngau, Bobby Otillar, Alexander Poliakov, Aaron Porter, Lukasz Szajkowski, Gregory Werner, Kemin Zhou, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman

Biological Sciences Faculty Research and Publications

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, …

Evidence For Gondwanan Vicariance In An Ancient Clade Of Gecko Lizards, Tony Gamble, Aaron M. Bauer, E. Greenbaum, Todd R. Jackman

Biological Sciences Faculty Research and Publications

Aim

Geckos (Reptilia: Squamata), due to their great age and global distribution, are excellent candidates to test hypotheses of Gondwanan vicariance against post‐Gondwanan dispersal. Our aims are: to generate a phylogeny of the sphaerodactyl geckos and their closest relatives; evaluate previous phylogenetic hypotheses of the sphaerodactyl geckos with regard to the other major gecko lineages; and to use divergence date estimates to inform a biogeographical scenario regarding Gondwanan relationships and assess the roles of vicariance and dispersal in shaping the current distributions of the New World sphaerodactyl geckos and their closest Old World relatives.

Location

Africa, Asia, Europe, South America, …

The Exosome Subunit Rrp44 Plays A Direct Role In Rna Substrate Recognition, Claudia Schneider, James T. Anderson, David Tollervey

Biological Sciences Faculty Research and Publications

The exosome plays key roles in RNA maturation and surveillance, but it is unclear how target RNAs are identified. We report the functional characterization of the yeast exosome component Rrp44, a member of the RNase II family. Recombinant Rrp44 and the purified TRAMP polyadenylation complex each specifically recognized tRNA_i^Met lacking a single m¹A₅₈ modification, even in the presence of a large excess of total tRNA. This tRNA is otherwise mature and functional in translation in vivo but is presumably subtly misfolded. Complete degradation of the hypomodified tRNA required both Rrp44 and the poly(A) polymerase activity …

Change In Nutritional Status Modulates The Abundance Of Critical Pre-Initiation Intermediate Complexes During Translation Initiation In Vivo, Chingakham Ranjit Singh, Tsuyoshi Udagawa, Bumjun Lee, Sarah Wassink, Hei He, Yasufumi Yamamoto, James T. Anderson, Graham D. Pavitt, Katsura Asano

Biological Sciences Faculty Research and Publications

In eukaryotic translation initiation, eIF2∙GTP–Met-tRNA_i^Met ternary complex (TC) interacts with eIF3–eIF1–eIF5 complex to form the multifactor complex (MFC), while eIF2∙GDP associates with eIF2B for guanine nucleotide exchange. Gcn2p phosphorylates eIF2 to inhibit eIF2B. Here we evaluate the abundance of eIFs and their pre-initiation intermediate complexes in gcn2 deletion mutant grown under different conditions. We show that ribosomes are three times as abundant as eIF1, eIF2 and eIF5, while eIF3 is half as abundant as the latter three and hence, the limiting component in MFC formation. By quantitative immunoprecipitation, we estimate that ∼ 15% of …

Rhizobium Etli Ce3 Bacteroid Lipopolysaccharides Are Structurally Similar But Not Identical To Those Produced By Cultured Ce3 Bacteria, Wim D'Haeze, Christine Leoff, Glenn Freshour, K. Dale Noel, Russell W. Carlson

Biological Sciences Faculty Research and Publications

Rhizobium etli CE3 bacteroids were isolated from Phaseolus vulgaris root nodules. The lipopolysaccharide (LPS) from the bacteroids was purified and compared with the LPS from laboratory-cultured R. etli CE3and from cultures grown in the presence of anthocyanin. Comparisons were made of the O-chain polysaccharide, the core oligosaccharide, and the lipid A. Although LPS from CE3 bacteria and bacteroids are structurally similar, it was found that bacteroid LPS had specific modifications to both the O-chain polysaccharide and lipid A portions of their LPS. Cultures grown with anthocyanin contained modifications only to the O-chain polysaccharide. The changes to the O-chain polysaccharide consisted …

Preferential Myosin Heavy Chain Isoform B Expression May Contribute To The Faster Velocity Of Contraction In Veins Versus Arteries, Catherine M. Rondelli, Irina T. Szasz, Anas Kayal, Keshari Thakali, Ralph E. Watson, Arthur S. Rovner, Thomas Eddinger, Gregory D. Fink, Stephanie W. Watts

Biological Sciences Faculty Research and Publications

Smooth muscle myosin heavy chains occur in 2 isoforms, SMA (slow) and SMB (fast). We hypothesized that the SMB isoform is predominant in the faster-contracting rat vena cava compared to thoracic aorta. We compared the time to half maximal contraction in response to a maximal concentration of endothelin-1 (ET-1; 100 nM), potassium chloride (KCl; 100 mM) and norepinephrine (NE; 10 µM). The time to half maximal contraction was shorter in the vena cava compared to aorta (aorta: ET-1 = 235.8 ± 13.8 s, KCl = 140.0 ± 33.3 s, NE = 19.8 ± 2.7 s; vena cava: ET-1 = 121.8 …

Ras Transformation Of Rie-1 Cells Activates Cap-Independent Translation Of Ornithine Decarboxylase: Regulation By The Raf/Mek/Erk And Phosphatidylinositol 3-Kinase Pathways, Sofia Origanti, Lisa M. Shantz

Biological Sciences Faculty Research and Publications

Ornithine decarboxylase (ODC) is the first and generally rate-limiting enzyme in polyamine biosynthesis. Deregulation of ODC is critical for oncogenic growth, and ODC is a target of Ras. These experiments examine translational regulation of ODC in RIE-1 cells, comparing untransformed cells with those transformed by an activated Ras12V mutant. Analysis of the ODC 5′ untranslated region (5′UTR) revealed four splice variants with the presence or absence of two intronic sequences. All four 5′UTR species were found in both cell lines; however, variants containing intronic sequences were more abundant in Ras-transformed cells. All splice variants support internal ribosome entry site …

Oxa1 Directly Interacts With Atp9 And Mediates Its Assembly Into The Mitochondrial F1FO-Atp Synthase Complex, Lixia Jia, Mary Kathryn Dienhart, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

The yeast Oxa1 protein is involved in the biogenesis of the mitochondrial oxidative phosphorylation (OXPHOS) machinery. The involvement of Oxa1 in the assembly of the cytochrome oxidase (COX) complex, where it facilitates the cotranslational membrane insertion of mitochondrially encoded COX subunits, is well documented. In this study we have addressed the role of Oxa1, and its sequence-related protein Cox18/Oxa2, in the biogenesis of the F₁F_o-ATP synthase complex. We demonstrate that Oxa1, but not Cox18/Oxa2, directly supports the assembly of the membrane embedded F_o-sector of the ATP synthase. Oxa1 was found to physically interact with …

Is Oak Establishment In Old‐Fields And Savanna Openings Context Dependent?, Ian A. Dickie, Stefan A. Schnitzer, P. B. Reich, S. E. Hobbie

Biological Sciences Faculty Research and Publications

1. Multiple factors are known to influence tree seedling establishment, yet the degree to which these factors depend on each other and on spatial context is largely unknown. We examined the influence of herbaceous competition and water and nitrogen limitations on tree seedling establishment as functions of distance from trees (within‐site spatial context) and site history (between‐site spatial context; as old‐fields vs. savanna openings).
2. We grew Quercus ellipsoidalis E.J. Hill (pin oak) and Q. macrocarpa Michx. (bur oak) seedlings for 3 years in abandoned agricultural fields and savannas in central Minnesota, USA, near and distant from adult oak trees, with and …