DOE Energy Biosciences Projects Supported in FY 2002 (NOTE: Dollar Amounts Are for a Twelve-Month Period Using FY 2002 Funds Unless Otherwise Stated)
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Family Proteins Are Required for RNA Editing in Mitochondria and Plastids of Plants
Correction PLANT BIOLOGY Correction for “Multiple organellar RNA editing factor issue 13, March 27, 2012, of Proc Natl Acad Sci USA (109: (MORF) family proteins are required for RNA editing in 5104–5109; first published March 12, 2012; 10.1073/pnas. mitochondria and plastids of plants,” by Mizuki Takenaka, 1202452109). Anja Zehrmann, Daniil Verbitskiy, Matthias Kugelmann, The authors note that Fig. 2 appeared incorrectly. The cor- Barbara Härtel, and Axel Brennicke, which appeared in rected Fig. 2 and its legend appear below. Fig. 2. The MORF family of proteins contains nine genes and a potential pseudogene in A. thaliana.(A) The cladogram of similarities between the MORF proteins shows that the plastid editing factors MORF2 and MORF9 are rather distant from each other and more similar to the mitochondrial proteins MORF3 and MORF1, respectively. Predictions (marked mt or cp) and experi- mental data obtained by GFP-fusion protein localization (only MORF2) or proteomics MS data (marked with an asterisk) for the respective organellar locations are indicated. The MORF8 protein encoded by At3g15000 has been found in mitochondria in three independent assays. Proteins investigated here for their function are boxed. The conserved ∼100-amino acids domain is shaded; the other sequences show much less conservation (SI Appendix, Fig. S2). The potential pseudogene (At1g53260) contains only the C-terminal part of this conserved region. (B) Exon structures of the MORF3, MORF4 and MORF6 genes are similar to the MORF1 locus and contribute similar frag- ments but differ in their C-terminal extensions. MORF3 is a mitochondrial editing factor involved at more than 40 sites. -
Kaic Cii Ring Flexibility Governs the Rhythm of The
KAIC CII RING FLEXIBILITY GOVERNS THE RHYTHM OF THE CIRCADIAN CLOCK OF CYANOBACTERIA A Dissertation by NAI-WEI KUO Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2011 Major Subject: Biochemistry KAIC CII RING FLEXIBILITY GOVERNS THE RHYTHM OF THE CIRCADIAN CLOCK OF CYANOBACTERIA A Dissertation by NAI-WEI KUO Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Co-Chairs of Committee, Andy LiWang Pingwei Li Committee Members, Deborah Bell-Pedersen Frank Raushel Head of Department, Gregory Reinhart May 2011 Major Subject: Biochemistry iii ABSTRACT KaiC CII Ring Flexibility Governs the Rhythm of the Circadian Clock of Cyanobacteria. (May 2011) Nai-Wei Kuo, B.S.; M.S., National Tsing Hua University, Taiwan Co-Chairs of Advisory Committee: Dr. Andy LiWang, Dr. Pingwei Li The circadian clock orchestrates metabolism and cell division and imposes important consequences to health and diseases, such as obesity, diabetes, and cancer. It is well established that phosphorylation-dependent circadian rhythms are the result of circadian clock protein interactions, which regulate many intercellular processes according to time of day. The phosphorylation-dependent circadian rhythm undergoes a succession of phases: Phosphorylation Phase → Transition Phase → Dephosphorylation Phase. Each phase induces the next phase. However, the mechanism of each phase and how the phosphorylation and dephosphorylation phases are prevented from interfering with each other remain elusive. In this research, we used a newly developed isotopic labeling strategy in combination with a new type of nuclear magnetic resornance (NMR) experiment to obtain the structural and dynamic information of the cyanobacterial KaiABC oscillator system. -
Two CRM Protein Subfamilies Cooperate in the Splicing of Group IIB Introns in Chloroplasts
JOBNAME: RNA 14#11 2008 PAGE: 1 OUTPUT: Wednesday September 17 14:17:18 2008 csh/RNA/170257/rna12237 Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts YUKARI ASAKURA, OMER ALI BAYRAKTAR, and ALICE BARKAN Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA ABSTRACT Chloroplast genomes in angiosperms encode ;20 group II introns, approximately half of which are classified as subgroup IIB. The splicing of all but one of the subgroup IIB introns requires a heterodimer containing the peptidyl-tRNA hydrolase homolog CRS2 and one of two closely related proteins, CAF1 or CAF2, that harbor a recently recognized RNA binding domain called the CRM domain. Two CRS2/CAF-dependent introns require, in addition, a CRM domain protein called CFM2 that is only distantly related to CAF1 and CAF2. Here, we show that CFM3, a close relative of CFM2, associates in vivo with those CRS2/CAF- dependent introns that are not CFM2 ligands. Mutant phenotypes in rice and Arabidopsis support a role for CFM3 in the splicing of most of the introns with which it associates. These results show that either CAF1 or CAF2 and either CFM2 or CFM3 simultaneously bind most chloroplast subgroup IIB introns in vivo, and that the CAF and CFM subunits play nonredundant roles in splicing. These results suggest that the expansion of the CRM protein family in plants resulted in two subfamilies that play different roles in group II intron splicing, with further diversification within a subfamily to accommodate multiple intron ligands. -
Molecular and Genetic Characterization of Rf2, A
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2001 Molecular and genetic characterization of rf2, a mitochondrial aldehyde dehydrogenase gene required for male fertility in maize (Zea mays L) Xiangqin Cui Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Genetics Commons, Molecular Biology Commons, and the Plant Sciences Commons Recommended Citation Cui, Xiangqin, "Molecular and genetic characterization of rf2, a mitochondrial aldehyde dehydrogenase gene required for male fertility in maize (Zea mays L) " (2001). Retrospective Theses and Dissertations. 1037. https://lib.dr.iastate.edu/rtd/1037 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. -
Profile of Susan S. Golden
PROFILE Profile of Susan S. Golden Sujata Gupta Science Writer Susan Golden did not set out to become Golden pursued other passions. She loved an expert in biological clocks, the internal literature, she says, an interest gleaned timepieces that keep life on Earth adjusted from her mother, an avid reader. And she to a 24-hour cycle. Instead, Golden, elected played the bassoon in the school band— in 2010 to the National Academy of Sci- where she made most of her friends. “That ences, wanted to identify the genes that un- turned out to be a social bifurcation. I did derpin photosynthesis. However, her focus not realize that the band route is the nerd changed in 1986 with the discovery of route. You can’t break over into the other biological clocks in cyanobacteria (1). [cool] group,” Golden says. She also worked Because cyanobacteria are among Earth’s on the school newspaper as a photographer, earliest living organisms, the discovery made one, she is quick to note, without any formal clear that biological clocks are evolutionarily training. By the time she graduated high ancient. Golden had been studying photosyn- school in 1976 as salutatorian of her 600- thesis in cyanobacteria since graduate school. student class, Golden harbored dreams of Her reason was simple: Cyanobacteria are becoming a photojournalist for Life maga- single-celled, and thus they are much easier zine or National Geographic. to manipulate in a laboratory than plants. Golden’s main consideration in selecting a With her expertise in cyanobacteria, Golden college, though, was not prestige or program found herself well-positioned to identify the of study but money. -
Light-Induced Psba Translation in Plants Is Triggered by Photosystem II Damage Via an Assembly-Linked Autoregulatory Circuit
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.061879; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Light-induced psbA translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit Prakitchai Chotewutmontri and Alice Barkan* Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA * Corresponding Author. Email: [email protected] Alice Barkan ORCID 0000-0003-3049-2838 Prakitchai Chotewutmontri ORCID 0000-0002-8672-2973 Classification: Biological Sciences/ Plant Biology Keywords: translational control / photosystem II / chloroplast / psbA / Arabidopsis / maize / Author Contributions: Both authors conceived the study, designed experiments, interpreted data, and wrote the manuscript. This PDF file includes: Main Text Figures 1 to 6 SI Appendix: Figures S1 to S4 and SI Materials and Methods 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.061879; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The D1 reaction center protein of Photosystem II (PSII) is subject to light-induced damage. Degradation of damaged D1 and its replacement by nascent D1 are at the heart of a PSII repair cycle, without which photosynthesis is inhibited. In mature plant chloroplasts, light stimulates the recruitment of ribosomes specifically to psbA mRNA to provide nascent D1 for PSII repair, and also triggers a global increase in translation elongation rate. -
CCB Annual Report 2010–2011
Report http://research.ucsd.edu/orureporting/revandsub.aspx?ReportID=825&rep... CCB Annual Review of the Organized Research Unit Fiscal Year 2011 The University of California, San Diego Center for Chronobiology 1 of 33 11/30/2011 3:44 PM Report http://research.ucsd.edu/orureporting/revandsub.aspx?ReportID=825&rep... 825 Director's Statement Director’s Statement During our second year as an ORU, the Center for Chronobiology had immediate goals of increasing the visibility of CCB on campus and around the world as a premier center for chronobiology research and facilitating interactions among members. We met these goals by: hosting local activities and outfitting facilities to engage our members and encourage interaction; expanding the content on an attractive and informative website; and hosting a symposium with top chronobiologist speakers from within CCB and around the world. Staffing section ‐ We have merged the External Advisory Committee and Executive Committee members into the Advisory Committee section since this report does not have a field for Executive Committee Members. All people included in the staffing section participate and contribute to the Center for Chronobiology. The Facilities section lists 12,568 square feet for CCB. Most of this space belongs to the Division of Biological Sciences. The actual space allocation for CCB is 551 square feet. This includes two administrative offices and one small conference room. Goals Met: · Expanded the membership of the Center for Chronobiology ORU to 32 UCSD faculty members as of June 30, 2011. · Hosted subgroups of members for research collaboration meetings · Held monthly meetings of the CCB Executive Committee · Recruited outstanding external academic and business professionals to serve as member of a CCB External Advisory Committee, which will meet on February 15, 2012. -
Precise Circadian Clocks in Prokaryotic Cyanobacteria
Curr. Issues Mol. Biol. (2004) 6: 103-110. Circadian ClocksOnline in journal Cyanobacteria at www.cimb.org 103 Precise Circadian Clocks in Prokaryotic Cyanobacteria Carl Hirschie Johnson* was a stroke of luck. Subsequent experiments using other strains/species of cyanobacteria have found rhythms (Aoki Department of Biological Sciences, Vanderbilt University, et al., 1997), but the reporters in those strains are not Nashville, TN 37235, USA bright. And even in S. elongatus, other promoters do not show such a robust rhythm of luminescence (see Class 3-5 rhythms in Figure 1– psbAIp is a strong Class 1 promoter; Abstract Liu et al., 1995). The combination of the psbAIp::luxAB reporter and the S. elongatus strain remains one of the Prokaryotic cyanobacteria express robust circadian most robustly rhythmic combinations in cyanobacteria, (daily) rhythms under the control of a timing even after ten years of intensive research. Dr. Kondo was mechanism that is independent of the cell division able to exploit the bright and robust luminescence rhythm cycle. This biological clock orchestrates global by designing clever apparatuses to monitor the rhythms. regulation of gene expression and controls the timing For liquid cultures, Dr. Kondo enlisted and modifi ed the of cell division. Proteins that may be involved in input automated photomultiplier apparatus that was originally pathways have been identifi ed. Mutational screening designed for endogenously bioluminescent algae (Kondo et has identifi ed three clock genes that are organized al., 1993). For monitoring colonies, Drs. Kondo and Ishiura as a gene cluster. The structure of cyanobacterial discovered that the rhythms of single colonies could be clock proteins, their phosphorylation, and regulation tracked with a CCD camera (Kondo and Ishiura, 1994). -
Cellular Function and Localization of Circadian Clock Proteins in Cyanobacteria
CELLULAR FUNCTION AND LOCALIZATION OF CIRCADIAN CLOCK PROTEINS IN CYANOBACTERIA A Dissertation by GUOGANG DONG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2008 Major Subject: Microbiology ii CELLULAR FUNCTION AND LOCALIZATION OF CIRCADIAN CLOCK PROTEINS IN CYANOBACTERIA A Dissertation by GUOGANG DONG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Susan S. Golden Committee Members, Deborah Bell-Pedersen Andy LiWang Deborah Siegele Head of Department, Thomas D. McKnight December 2008 Major Subject: Microbiology iii ABSTRACT Cellular Function and Localization of Circadian Clock Proteins in Cyanobacteria. (December 2008) Guogang Dong, B.S., Peking University Chair of Advisory Committee: Dr. Susan S. Golden The cyanobacterium Synechococcus elongatus builds a circadian clock on an oscillator comprised of three proteins, KaiA, KaiB, and KaiC, which can recapitulate a circadian rhythm of KaiC phosphorylation in vitro. The molecular structures of all three proteins are known, and the phosphorylation steps of KaiC, the interaction dynamics among the three Kai proteins, and a weak ATPase activity of KaiC have all been characterized. A mutant of a clock gene in the input pathway, cikA , has a cell division defect, and the circadian clock inhibits the cell cycle for a short period of time during each cycle. However, the interaction between the circadian cycle and the cell cycle and the molecular mechanisms underlying it have been poorly understood. -
UCSD Center for Chronobiology
Center for Chronobiology CCB 5 year Review of the Organized Research Unit Fiscal Year 2010 thru 2013 The University of California, San Diego Center for Chronobiology Director’s Statement Center for Chronobiology (CCB) The UCSD Center for Chronobiology (CCB) was established as an Organized Research Unit in 2009 to leverage the exceptional strength and breadth of circadian biology research that is conducted at UCSD. The Center brings together faculty from diverse disciplinary areas of the campus, including the Biological, Physical, and Social Sciences, Engineering, and the Schools of Medicine and Pharmacy. CCB focuses on questions in chronobiology - the study of biological timing – found at all levels of biological complexity and central to the organization of life, with an emphasis on circadian (~24 h) biological rhythms. With 34 members at UCSD, and affiliate members at the Scripps Research Institute, UC Santa Cruz, and UC Merced, CCB is the largest aggregate of circadian rhythms researchers in the world. CCB members span an exceptional range of research approaches and organisms, from in vitro rhythms and synthetic biology in micro-organisms, through plant and animal model organisms, to human clinical research. Moreover, members are, as individuals, leaders in their specific areas. Since the establishment of CCB, three members have been elected to the National Academy of Sciences (Golden, Sejnowski, and Spitzer). The establishment of this ORU in 2009 had the immediate effect of focusing both internal and international attention on our unique concentration of strength in circadian biology and placing UCSD on the map as a major center of research in this broad field. -
Exploring the Link Between Photosystem II Assembly and Translation of the Chloroplast Psba Mrna
plants Article Exploring the Link between Photosystem II Assembly and Translation of the Chloroplast psbA mRNA Prakitchai Chotewutmontri y, Rosalind Williams-Carrier y and Alice Barkan * Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; [email protected] (P.C.); [email protected] (R.W.-C.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 20 December 2019; Accepted: 21 January 2020; Published: 25 January 2020 Abstract: Photosystem II (PSII) in chloroplasts and cyanobacteria contains approximately fifteen core proteins, which organize numerous pigments and prosthetic groups that mediate the light-driven water-splitting activity that drives oxygenic photosynthesis. The PSII reaction center protein D1 is subject to photodamage, whose repair requires degradation of damaged D1 and its replacement with nascent D1. Mechanisms that couple D1 synthesis with PSII assembly and repair are poorly understood. We address this question by using ribosome profiling to analyze the translation of chloroplast mRNAs in maize and Arabidopsis mutants with defects in PSII assembly. We found that OHP1, OHP2, and HCF244, which comprise a recently elucidated complex involved in PSII assembly and repair, are each required for the recruitment of ribosomes to psbA mRNA, which encodes D1. By contrast, HCF136, which acts upstream of the OHP1/OHP2/HCF244 complex during PSII assembly, does not have this effect. The fact that the OHP1/OHP2/HCF244 complex brings D1 into proximity with three proteins with dual roles in PSII assembly and psbA ribosome recruitment suggests that this complex is the hub of a translational autoregulatory mechanism that coordinates D1 synthesis with need for nascent D1 during PSII biogenesis and repair. -
Multilevel Effects of Light on Ribosome Dynamics in Chloroplasts Program Genome- Wide and Psba-Specific Changes in Translation
RESEARCH ARTICLE Multilevel effects of light on ribosome dynamics in chloroplasts program genome- wide and psbA-specific changes in translation Prakitchai Chotewutmontri, Alice Barkan* Institute of Molecular Biology, University of Oregon, Eugene, OR, United States of America * [email protected] a1111111111 a1111111111 Abstract a1111111111 a1111111111 Plants and algae adapt to fluctuating light conditions to optimize photosynthesis, minimize a1111111111 photodamage, and prioritize energy investments. Changes in the translation of chloroplast mRNAs are known to contribute to these adaptations, but the scope and magnitude of these responses are unclear. To clarify the phenomenology, we used ribosome profiling to ana- lyze chloroplast translation in maize seedlings following dark-to-light and light-to-dark shifts. OPEN ACCESS The results resolved several layers of regulation. (i) The psbA mRNA exhibits a dramatic Citation: Chotewutmontri P, Barkan A (2018) gain of ribosomes within minutes after shifting plants to the light and reverts to low ribosome Multilevel effects of light on ribosome dynamics in occupancy within one hour in the dark, correlating with the need to replace damaged PsbA chloroplasts program genome-wide and psbA- in Photosystem II. (ii) Ribosome occupancy on all other chloroplast mRNAs remains similar specific changes in translation. PLoS Genet 14(8): to that at midday even after 12 hours in the dark. (iii) Analysis of ribosome dynamics in the e1007555. https://doi.org/10.1371/journal. pgen.1007555 presence of lincomycin revealed a global decrease in the translation elongation rate shortly after shifting plants to the dark. The pausing of chloroplast ribosomes at specific sites Editor: Tessa Burch-Smith, University of Tennessee at Knoxville, UNITED STATES changed very little during these light-shift regimes.