Cncrnas: Rnas with Both Coding and Non-Coding Roles in Development Karuna Sampath1,* and Anne Ephrussi2,*
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Molecular Analysis of Small Rna and Small Protein Regulation of Escherichia Coli Stress Responses
MOLECULAR ANALYSIS OF SMALL RNA AND SMALL PROTEIN REGULATION OF ESCHERICHIA COLI STRESS RESPONSES BY CHELSEA R. LLOYD DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate College of the University of Illinois at Urbana-Champaign, 2018 Urbana, Illinois Doctoral Committee: Associate Professor Carin K. Vanderpool, Chair Professor John E. Cronan Professor William W. Metcalf Professor Peter A. B. Orlean Abstract Small RNA (sRNA) regulators control gene expression throughout all domains of life. In bacteria, they typically affect virulence, metabolism, and stress response genes posttranscriptionally through imperfect antisense pairing with their mRNAs. While most sRNAs are non-coding, a small number act as mRNAs themselves by encoding functional proteins. This study examines the regulatory and physiological effects of both a non-coding sRNA, DicF, and the protein product of a dual-function sRNA, SgrS in Eschericha coli. The sRNA SgrS encodes the small 43-amino acid protein SgrT. Both molecules are expressed during glucose-phosphate stress - a bacteriostatic condition in which phosphosugars accumulate in the cell either because of mutations in glycolysis or because of the transport of non-metabolizable glucose analogs such as αMG or 2DG. While both SgrT and SgrS base pairing can independently mitigate glucose-phosphate stress, they do so through distinct mechanisms. SgrS base pairing destabilizes the mRNA of the respective major and minor glucose transporters PtsG and ManXYZ, thereby inhibiting synthesis of additional glucose permeases and restricting further influx of non- metabolizable sugars. In this study we demonstrate that SgrT acts to specifically inhibit the transport activity of preexisting PtsG transporters, but does not affect ManXYZ. -
Determinants of Target Prioritization and Regulatory Hierarchy for the Bacterial Small RNA Sgrs
Molecular Microbiology (2019) 112(4), 1199–1218 doi:10.1111/mmi.14355 First published online 6 August 2019 Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS Maksym Bobrovskyy,1,† Muhammad S. Azam,1 of regulation of SgrS targets. The RNA chaperone Jane K. Frandsen,2,3,‡ Jichuan Zhang,4 Hfq uses distinct modes of binding to different SgrS Anustup Poddar,4 Xiangqian Ma,1 Tina M. Henkin,2 mRNA targets, which differentially influences posi- Taekjip Ha4,5 and Carin K. Vanderpool 1* tive and negative regulation. The RNA degradosome 1 Department of Microbiology, University of Illinois at plays a larger role in regulation of some SgrS targets Urbana-Champaign, 601 S. Goodwin Ave., Urbana, compared to others. Collectively, our results sug- IL 61801, USA. gest that sRNA selection of target mRNAs and regu- 2 Department of Microbiology and Center for RNA latory hierarchy are influenced by several molecular Biology, The Ohio State University, Columbus, features and that the combination of these features OH 43210, USA. precisely tunes the efficiency of regulation of multi- 3 Biochemistry Program, The Ohio State University, target sRNA regulons. Columbus, OH 43210, USA. 4 Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA. Introduction 5 Howard Hughes Medical Institute, Baltimore, Bacteria live in diverse niches, often encountering rapidly MD 21205, USA. changing and stressful environments. Bacterial stress responses can mitigate the negative effects of stress on cell structure and function. Stress responses are usually coordinated by regulators, either RNAs or proteins, that Summary alter expression of a regulon comprised of multiple genes. -
Genome-Wide Investigation of Micrornas and Their Targets in Response to Freezing Stress in Medicago Sativa L., Based on High-Throughput Sequencing
INVESTIGATION Genome-Wide Investigation of MicroRNAs and Their Targets in Response to Freezing Stress in Medicago sativa L., Based on High-Throughput Sequencing Yongjun Shu,1 Ying Liu, Wei Li, Lili Song, Jun Zhang, and Changhong Guo1 Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, 150025, China ABSTRACT Winter damage, especially in northern climates, is a major limitation of the utilization of perennial KEYWORDS forages such as alfalfa. Therefore, improving freezing tolerance is imperative in alfalfa genetic breeding. However, Medicago sativa freezing tolerance is a complex trait that is determined by many genes. To understand the complex regulation cold acclimation mechanisms of freezing tolerance in alfalfa, we performed small RNA sequencing analysis under cold (4°)and freezing stress freezing (28°) stress. The sequencing results revealed that 173 known, and 24 novel miRNAs were microRNA expressed, and that the expression of 35 miRNAs was affected by cold and/or freezing stress. Meanwhile, degradome 105 target genes cleaved by these miRNAs were characterized by degradome sequencing. These targets sequencing were associated with biological regulation, cellular processes, metabolic processes, and response to stress. Interestingly, most of them were characterized as transcription factors (TFs), including auxin response factors, SBP, NAC, AP2/ERF, and GRF, which play important roles in plant abiotic responses. In addition, important miRNAs and mRNAs involved in nodulation were also identified, for example, the relationship between miR169 and the TF CCAAT (also named as NF-YA/HAP2), which suggested that nodulation has an important function in freezing tolerance in alfalfa. -
Or Drought-Responsive Lncrnas in Cassava
www.nature.com/scientificreports OPEN Genome-wide identification and functional prediction of cold and/ or drought-responsive lncRNAs in Received: 06 December 2016 Accepted: 07 March 2017 cassava Published: 07 April 2017 Shuxia Li1,*, Xiang Yu2,3,*, Ning Lei1, Zhihao Cheng4, Pingjuan Zhao1, Yuke He2, Wenquan Wang1 & Ming Peng1 Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava. Plants are sessile organisms and are constantly exposed to a wide range of environmental stresses during their life cycle. Cold and drought are the most severe abiotic stresses that seriously influence plant growth and develop- ment, and are major limiters of crop productivity worldwide1. -
Computational Methods for the Identification and Characterization
Computational Methods for the Identification and Characterization of Non-Coding RNAs in Bacteria Dissertation der Mathematisch-Naturwissenschaftlichen Fakult¨at der Eberhard Karls Universit¨atT¨ubingen zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Alexander Herbig aus Altenkirchen T¨ubingen 2014 Tag der m¨undlichenQualifikation: 30.01.2015 Dekan: Prof. Dr. Wolfgang Rosenstiel 1. Berichterstatterin: PD Dr. Kay Nieselt 2. Berichterstatter: Prof. Dr. Daniel Huson 3. Berichterstatter: Prof. Dr. Rolf Backofen Zusammenfassung Forschungsergebnisse vergangener Jahre konnten zeigen wie komplex die Struktur und Regulation selbst bakterieller Transkriptome sein kann. Auch die wichtige Rolle nicht-kodierender RNAs (ncRNA), die nicht in Proteine translatiert werden, wird dabei immer deutlicher. Diese Molek¨uleerf¨ullen in der Zelle verschiedenste Aufgaben wie zum Beispiel die Regulation von Stoffwechselprozessen. Daher ist die Charakter- isierung der ncRNA-Gene eines Organismus immer mehr zu einem unverzichtbaren Teil von Systembiologie-Projekten geworden. Hierbei erlauben moderne Hochdurch- satzverfahren im Bereich der DNA- und RNA-Sequenzierung das im hohen Maße detaillierte Studium von Genomen und Transkriptomen. Die daraus resultierenden Daten m¨usseneiner vergleichenden Analyse unterzogen werden, um Variationen des Transkriptoms zwischen verschiedenen Organismen und Umweltbedingungen untersuchen zu k¨onnen.Hierf¨urwerden effiziente Computerprogramme ben¨otigt, die in der Lage sind genomische und transkriptomische Daten zu kombinieren und entsprechende Analysen automatisiert und reproduzierbar durchzuf¨uhren.Zu- dem m¨ussendiese Ans¨atzenicht-kodierende Elemente im genomischen Kontext lokalisieren und annotieren k¨onnen. In dieser Dissertation pr¨asentiere ich Computerprogramme zur L¨osungdieser Aufgaben. So wurde das Programm nocoRNAc entwickelt, welches ncRNAs in bakteriellen Genomen detektiert und diese bez¨uglich verschiedener Eigenschaften charakterisiert. -
The Ancestral Sgrs RNA Discriminates Horizontally Acquired Salmonella Mrnas Through a Single G-U Wobble Pair
The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair Kai Papenforta, Dimitri Podkaminskia, Jay C. D. Hintonb, and Jörg Vogela,1 aRNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; and bDepartment of Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland AUTHOR SUMMARY Small noncoding RNAs A characteristic of HGT (sRNAs) constitute a vital group genes is that they are more likely of so-called posttranscriptional to undergo duplication than so- SgrS RNA regulators that shape the gene Core genome Horizontally acquired called core genes. Gene dupli- expression of eukaryotic and elements pathogenicity genes cation is a well-studied phe- prokaryotic organisms. In bac- nomenon accelerating evolu- teria, sRNAs generally act duplication tionary change in bacterial through base pairing to reduce pathogens (4). For example, the Hfq or increase the translation of ptsG/manXYZ mRNAs sopD mRNA sopD2 mRNA sopD gene has been duplicated target mRNAs into protein. target (G-C base-pair) pseudotarget (G-U base-pair) to generate sopD2 throughout Most of our current knowledge the S. enterica species, except in of sRNA numbers and functions the ancestral S. bongori (1). A Fig. P1. Posttranscriptional interaction between the core and stems from two species, Escher- horizontally acquired genome through Hfq and sRNAs. The SgrS sRNA bioinformatic comparison of the ichia coli and Salmonella enterica is encoded by the Salmonella core genome and conserved in many sopD and sopD2 sequences serovar Typhimurium. Both bacterial species, including E. coli and Salmonella. Aided by the RNA showed that the SgrS targeting organisms display a high degree chaperone Hfq, SgrS reduces the expression of mRNAs encoding for region is well-conserved be- of sequence conservation across sugar transport proteins (ptsG and manXYZ), both of which are core tween both genes; in other about three-quarters of the genomic elements. -
Evolution of the Small Family of Alternative Splicing Modulators Nuclear Speckle RNA-Binding Proteins in Plants
G C A T T A C G G C A T genes Article Evolution of the Small Family of Alternative Splicing Modulators Nuclear Speckle RNA-Binding Proteins in Plants Leandro Lucero 1, Jeremie Bazin 2, Johan Rodriguez Melo 3, Fernando Ibañez 3 , Martín D. Crespi 2,* and Federico Ariel 1,* 1 Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina; [email protected] 2 CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Universite Paris Sud, Universite Evry, Universite Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, 91405 Orsay, France; [email protected] 3 Instituto de Investigaciones Agrobiotecnológicas, CONICET, Universidad Nacional de Río Cuarto, Río Cuarto 5800, Argentina; [email protected] (J.R.M.); fi[email protected] (F.I.) * Correspondence: [email protected] (M.D.C.); [email protected] (F.A.); Tel./Fax: +54-342-4511-370 (ext. 5017) (F.A.) Received: 5 December 2019; Accepted: 30 January 2020; Published: 18 February 2020 Abstract: RNA-Binding Protein 1 (RBP1) was first identified as a protein partner of the long noncoding RNA (lncRNA) ENOD40 in Medicago truncatula, involved in symbiotic nodule development. RBP1 is localized in nuclear speckles and can be relocalized to the cytoplasm by the interaction with ENOD40. The two closest homologs to RBP1 in Arabidopsis thaliana were called Nuclear Speckle RNA-binding proteins (NSRs) and characterized as alternative splicing modulators of specific mRNAs. -
Small RNA-Mediated Activation of Sugar Phosphatase Mrna Regulates Glucose Homeostasis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Small RNA-Mediated Activation of Sugar Phosphatase mRNA Regulates Glucose Homeostasis Kai Papenfort,1,2 Yan Sun,3 Masatoshi Miyakoshi,1 Carin K. Vanderpool,3,* and Jo¨ rg Vogel1,* 1Institute for Molecular Infection Biology, University of Wu¨ rzburg, Wu¨ rzburg 97070, Germany 2Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA 3Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA *Correspondence: [email protected] (C.K.V.), [email protected] (J.V.) http://dx.doi.org/10.1016/j.cell.2013.03.003 SUMMARY glycolytic flux, their intracellular levels must be tightly regulated since high levels are toxic and strongly impair cell growth (Irani Glucose homeostasis is strictly controlled in all and Maitra, 1977; Kadner et al., 1992) and cause DNA damage domains of life. Bacteria that are unable to balance (Bucala et al., 1985; Lee and Cerami, 1987). Similarly, many non- intracellular sugar levels and deal with potentially metabolizable sugars can cause phosphosugar stress. For toxic phosphosugars cease growth and risk being example, the glucose analog a-methyl-glucoside (a-MG) is outcompeted. Here, we identify the conserved haloa- efficiently imported by PtsG, the major glucose transporter of a cid dehalogenase (HAD)-like enzyme YigL as the pre- Escherichia coli and Salmonella (Jahreis et al., 2008). -MG-6- phosphate accumulates in the cytoplasm and can terminate viously hypothesized phosphatase for detoxification bacterial growth (Pikis et al., 2006; Rogers and Yu, 1962). -
Long Non-Coding Rnas, the Dark Matter: an Emerging Regulatory Component in Plants
International Journal of Molecular Sciences Review Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants Muhammad Waseem 1,2,3 , Yuanlong Liu 1,2,3 and Rui Xia 1,2,3,* 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510640, China; [email protected] (M.W.); [email protected] (Y.L.) 2 Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510640, China 3 Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510640, China * Correspondence: [email protected] Abstract: Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Ad- vances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. -
Beta Version
Beta Version Zentrum für Infektionsforschung Research Centre for Infectious Diseases Wissenschaftlicher Bericht Josef-Schneider-Str. 2/D15 Scientific Report 2014–2015 97080 Würzburg Germany T +49-931-3182575 F +49-931-3182578 zentrum für M [email protected] infektionsforschung research centre for infectious diseases research centre for infectious diseases 2014–2015 zentrum für infektionsforschung – scientific report 2014-2015 content 1. general remarks 3.6 Department of Internal Medicine II 98 3.6.1 Hermann Einsele – Interaction of Immune Effector Cells with Aspergillus fumigatus 100 1.1 Speaker‘s Report 2014 – 2015 / Sprecherbericht für den Zeitraum 2014 – 2015 6 3.6.2 Andreas Beilhack – Experimental Stem Cell Transplantation 102 1.2 Directory of People Associated with the ZINF 12 3.6.3 Hartwig Klinker – Division of Infectious Diseases 104 1.3 Structure of the ZINF 18 3.6.4 Jürgen Löffl er – Immunity against Aspergillus spp. 106 1.4 News from the ZINF 20 3.6.5 Andrew Ullmann – Clinical Infectious Diseases 108 2. young investigator groups of the zinf 4. zinf members associated with other institutes 2.1 Cynthia Sharma (ZINF) – Deep Sequencing Approaches to Pathogenesis 28 4.1 Gerhard Bringmann – Natural Products Chemistry 112 2.2 Daniel Lopez (ZINF) – Cell-Cell Communication and Signal Transduction 30 4.2 Thomas Dandekar – Bioinformatics 114 2.3 Nicolai Siegel (ZINF) – Trypanosoma Gene Regulation 32 4.3 Markus Engstler – Molecular and Physical Parasitology 116 2.4 Ana Eulalio (BioSysNet) – Host RNA Metabolism 34 4.4 Ute Hentschel-Humeida – Marine Sponge-Microbe Interactions 118 2.5 Christian Perez (IZKF) – Regulatory Networks in Pathogenesis 36 4.5 Ulrike Holzgrabe – Medicinal Chemistry 120 2.6 Sebastian Geibel (Elite Network Bavaria) – Structural Biology of Mycobacteria 38 4.6 Caroline Kisker – Structure Based Drug Design 122 2.7 Sina Bartfeld (ZINF) – Organoids as Host Model 40 4.7 Gabriela Krasteva-Christ – Pulmonary Neurobiology 124 4.8 August Stich – Tropical Medicine 126 4.9 Heike Walles – Tissue Engineering 128 3. -
An E. Coli Small Rna Inhibits Translation Initiation from a Distance
AN E. COLI SMALL RNA INHIBITS TRANSLATION INITIATION FROM A DISTANCE BY MUHAMMAD SHAFIUL AZAM DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate College of the University of Illinois at Urbana-Champaign, 2019 Urbana, Illinois Doctoral Committee: Professor Carin K. Vanderpool, Chair Professor Rachel J. Whitaker Professor James M. Slauch Professor Gary J. Olsen ABSTRACT In bacterial systems, small RNA (sRNA)-dependent translational repression is commonly carried out via sRNA-mRNA base pairing interactions near the Shine- Dalgarno (SD) region. In this so-called “canonical” mechanism, the sRNA is the direct regulator; it competes with the initiating ribosomes while the chaperone protein Hfq plays a supporting role. Contrary to this widely accepted model, there are a few examples in the literature where the sRNA base pairs far from the SD region, yet translation of the target mRNA is still inhibited. Mechanistically, non-canonical translation regulation is one of the least understood aspects of sRNA biology. In the targetome of an E. coli sRNA SgrS, manXYZ is a non-canonical target where SgrS base pairs at two distinct sites that are far from the SD regions of manX and manY , yet translation of these two cistrons are repressed by SgrS. We found that manX translation is controlled by a molecular role- reversal mechanism where an Hfq binding site is directly adjacent to the manX ribosome binding site. In this regulatory mechanism, SgrS plays the role of a guide to recruit Hfq to the appropriate binding site to form the silencing complex. -
Soybean ENOD40 Encodes Two Peptides That Bind to Sucrose Synthase
Soybean ENOD40 encodes two peptides that bind to sucrose synthase Horst Ro¨ hrig*, Ju¨ rgen Schmidt, Edvins Miklashevichs, Jeff Schell, and Michael John Max-Planck-Institut fu¨rZu¨ chtungsforschung, Carl-von-Linne´-Weg 10, 50829 Cologne, Germany Contributed by Jeff Schell, December 12, 2001 ENOD40 is expressed at an early stage in root nodule organogen- tion and identification of a protein from nodules that specifically esis in legumes. Identification of ENOD40 homologs in nonlegu- binds both peptides. minous plants suggests that this gene may have a more general biological function. In vitro translation of soybean ENOD40 mRNA Materials and Methods in wheat germ extracts revealed that the conserved nucleotide Plant Materials. Soybean plants (Glycine max cv. Jutro) were sequence at the 5 end (region I) encodes two peptides of 12 and grown in nitrogen-free medium in a growth chamber at 26°C 24 aa residues (peptides A and B). These peptides are synthesized under a photoperiod of 16 h. Inoculation of plants with Brady- de novo from very short, overlapping ORFs. Appropriate ORFs are rhizobium japonicum USDA 110 was performed directly upon present in all legume ENOD40s studied thus far. In this case small sowing, and nodules were collected 4 wk after inoculation. peptides are directly translated from polycistronic eukaryotic Uninfected soybean plants were cultured in the same way. mRNA. The 24-aa peptide B was detected in nodules by Western Nodules and uninfected roots were frozen in liquid nitrogen blotting. Both peptides specifically bind to the same 93-kDa pro- immediately after harvesting and stored at Ϫ70°C.