Tnlo-Encoded Tet Repressor Can Regulate an Operator-Containing

Total Page:16

File Type:pdf, Size:1020Kb

Tnlo-Encoded Tet Repressor Can Regulate an Operator-Containing Proc. Nati. Acad. Sci. USA Vol. 85, pp. 1394-1397, March 1988 Biochemistry TnlO-encoded tet repressor can regulate an operator-containing plant promoter (cauliflower mosaic virus 35S promoter/electroporation/transient chloramphenicol acetyltransferase assays) CHRISTIANE GATZ* AND PETER H. QUAILt Departments of Botany and Genetics, University of Wisconsin, Madison, WI 53706 Communicated by Folke Skoog, October 26, 1987 (receivedfor review July S, 1987) ABSTRACT The TnlO-encoded tet repressor-operator The TnlO-encoded tet repressor regulates the expression system was used to regulate transcription from the cauliflower of the Tc resistance operon by binding to nearly identical mosaic virus (CaMV) 35S promoter. Expression was moni- operator sequences that overlap with three divergent pro- tored in a transient assay system by using electric field- moters (14, 15). The genes of the tet operon are only mediated gene transfer ("electroporation") into tobacco pro- transcribed in the presence of the inducer Tc, which pre- toplasts. The tet repressor, being expressed in the plant cells vents the repressor from binding to its operator sequences. under the control of eukaryotic transcription signals, blocks The tet repressor was chosen for regulating a plant promoter transcription of a CaMV 35S promoter chloramphenicol ace- for two reasons. (i) With a native molecular mass of 48 kDa, tyltransferase (cat) fusion gene when the two tet operators diffusion into the nucleus seemed likely (16). (ii) The high flank the "TATA" box. In the presence of the inducer equilibrium association constant of the repressor-inducer tetracycline, expression is restored to full activity. Location of complex ensures efficient induction at sublethal Tc concen- the operators 21 base pairs downstream of the transcription trations (17), thus making the system useful as an on/off start site does not significantly affect transcription in the switch for the specific regulation of transferred genes. presence of the repressor. These experiments show that a prokaryotic regulatory protein can function in plant cells. The MATERIALS AND METHODS tet repressor-operator complex may be useful for specifically inducing transferred genes at different stages of plant devel- Electric Field-Mediated Gene Transfer ("Electroporation") and Transient Assay Conditions. Expression was measured in opment. electroporated Nicotiana tabacum (gift from T. Bradshaw, University of Washington, Seattle) protoplasts. For the In prokaryotes as well as in eukaryotes, regulation of tran- preparation of protoplasts, suspension cultured cells were scription initiation is mediated by proteins that recognize taken on the third day after being subcultured. Culture specific DNA sites, thereby influencing RNA polymerase conditions were as follows. Cells were maintained in 4.3 g of activity (1). One of the well-characterized negative control Murashige-Skoog (MS) salts per liter, 30 g of sucrose per mechanisms in Escherichia coli involves repressor proteins liter, 1 mg of thiamine per liter, 1 g of myo-inositol per liter, binding to operator DNA, thus preventing RNA polymerase 2 g of KH2PO4 per liter, and 0.2 mg of 2,4-dichlorophenox- from binding (2). In eukaryotes, however, the position of the yacetic acid (2,4-D) per liter at 280C with shaking at 150 rpm regulatory DNA binding sites is not limited to the region near and were subcultured every week with a 5% inoculum. Cells the start site of transcription. Negative (3-5) as well as were washed twice with the culture medium containing 0.4 positive (6) control sequences function somewhat indepen- M mannitol (MSM medium) and then incubated in this dently of their positions and orientations with respect to the medium with 500 mg of cellulase and 50 mg of macerozyme regulated promoter. In spite of these fundamental differ- per 50 ml of cell culture for 2 hr. Cells were pelleted, washed ences between eukaryotic and prokaryotic control mecha- twice with MSM medium, washed once in electroporation nisms, the E. coli lexA protein is able to repress gene buffer (10 mM Hepes, pH 7.2/150 mM NaCl/4 mM expression in yeast (7). Recently, Hu and Davidson (8) have CaCl2/0.4 M mannitol), and resuspended in the same buffer shown that a suitably engineered lac repressor-operator at 4 x 106 protoplasts per ml. After mixing 0.5 ml of the system is functional in mouse cells. By using the TnlO- protoplast-containing solution with 0.5 ml of the same solu- encoded tet repressor-operator interaction, we have ap- tion containing 200 ,ug of supercoiled plasmid DNA, electro- proached the question of whether the plant eukaryotic poration was done as described (18). The electric pulse was transcription machinery can be inhibited by the same mech- delivered from a 490-,uF capacitor charged to 340 V with a anism as is E. coli RNA polymerase-namely, by steric 3-msec resistance-capacitance time constant. Chloramphen- interference with a repressor protein. Introducing the tet icol acetyltransferase (CAT) activity was measured after 24 regulatory elements that respond to the inducer tetracycline hr of incubation (18). Equal amounts of protein were added (Tc) (9, 10) into plant cells provides a unique tool to in each assay. The amount of acetylated chloramphenicol specifically regulate expression of transferred genes. By was determined by cutting the reaction product from a silica using this system rather than plant promoters regulated by plate and counting the radioactivity in a liquid scintillation light (11), stress (12), or hormones (13), one has the advan- spectrometer. tage that only the expression of the transferred gene will be affected by the inducer. This contrasts with the regulatory Abbreviations: CAT, chloramphenicol acetyltransferase; CaMV, factors mentioned above, where pleiotropic effects on the cauliflower mosaic virus; 2,4-D, 2,4-dichlorophenoxyacetic acid; plant are expected. Tc, tetracycline; 01 and 02, operators 1 and 2. *Present address: Institut fuer Genbiologische Forschung, Ihnestr 33, 1 Berlin 63, F.R.G. The publication costs of this article were defrayed in part by page charge tTo whom reprint requests should be addressed at the present payment. This article must therefore be hereby marked "advertisement" address: Plant Gene Expression Center, 800 Buchanan Street, in accordance with 18 U.S.C. §1734 solely to indicate this fact. Albany, CA 94710. 1394 Downloaded by guest on September 30, 2021 Biochemistry: Gatz and Quail Proc. Natl. Acad. Sci. USA 85 (1988) 1395 Construction of Recombinant Plasmids. For constructing region of the tet repressor (tetR) gene was inserted as an pTET7 the cauliflower mosaic virus (CaMV) 35S promoter EcoRI fragment [from pWH305 (24)] between the CaMV 35S fragment [nucleotides 7017-7437 (19)] was subcloned from promoter and the nos poly(A) signal by replacing the nptII an intermediate construct containing these promoter se- gene of pCaMVNEO (20). pTETO contains the same EcoRI quences between the HindIII and the Pst I sites ofthe PiAN7 fragment in the reverse polarity and was used for control (Biolabs, Northbrook, IL) polylinker inserted into pUC18 experiments. (20). The promoter was fused to the cat gene by cloning the former as a Sma I/Bgl II fragment into pGA582 (21) that had been digested with Hpa I and Bgl II. This construct contains RESULTS nucleotides - 390 to + 1 relative to the start site oftranscrip- We inserted the tet operators (01 02) into selected sites of tion of the CaMV 35S promoter, 50 base pairs (bp) between the CaMV 35S promoter whose functional domains have + 1 and the start site ofcat translation, the cat coding region, been characterized by 5' deletions (25, 26). pTET8 (see Fig. and the nos poly(A) signal site. The promoter-cat-nos con- 1) contains the operators between the transcription start site struct was subsequently inserted as a HindIII/Sal I fragment and the initiation codon, with the first base of the left into pUC19 to yield pTET7. Plasmid pTET8 contains an operator (O1) being base + 22 of the cat-encoded mRNA. 80-bp-long EcoRI fragment with the two tet operator sites The inserted operator fragment contains one ATG initiation (14, 22) cloned into the Bgl II site ofpTET7 after filling in the codon that is in frame with the ATG of the cat gene, so that protruding ends. Plasmid pTET8 contains 3 bp of the TnJO- expression was not reduced by an upstream out-of-frame encoded sequence flanking operator 1 (01) and 20 bp flank- open reading frame (27). In pTET14 (Fig. 1A) 01 is posi- ing operator 2 (02). For constructing pTET14, two comple- tioned between the CAAT box and the TATA box and 02 is mentary oligonucleotides containing the "TATA" box ofthe between the TATA box and the start site of transcription. CaMV 35S promoter between the two operators were syn- We chose the position between the consensus boxes under thesized with Hga I and Sau III ends. The distance between the assumption that the CaMV 35S promoter has the same the "CAAT" box and the TATA box was maintained as in characteristics as the thymidine kinase promoter (28). the wild-type promoter. The spacing between the operators Linker scanning of this promoter has shown that the se- was 11 bp as in the E. coli operon. Because of multiple Hga quences between the CAAT and the TATA boxes can be I sites in pUC19, the plasmid was constructed by ligating an changed without eliminating promoter activity. Taking into isolated promoter fragment from HindIII to Hga I ofpTET7, account that spacing between the TATA box and the up- with the hybridized oligonucleotides and the HindIII/Bgl II stream element (in this case, the CAAT box) is important for vector fragment of pTET7. The correct insertion of the maximal promoter activity, at least in simian virus 40 early operators into pTET8 and pTET14 was confirmed by sub- promoter (29), we maintained the CaMV wild-type spacing.
Recommended publications
  • Galactosidase
    Copyright 0 1988 by the Genetics Society of America Effects of Amino Acid Substitutions atthe Active Site in Escherichia coli @-Galactosidase Claire G. Cupples and Jeffrey H. Miller Molecular Biology Institute and Department of Biology, University of Calqornia, Los Angeles, Calqornia 90024 Manuscript received April 2 1, 1988 Accepted July 23, 1988 ABSTRACT Forty-nine amino acid substitutions were made at four positions in the Escherichia coli enzyme p- galactosidase; three of the four targeted amino acids are thought to be part of the active site. Many of the substitutions were made by converting the appropriate codon in lacZ to an amber codon, and using one of 12 suppressor strains to introduce the replacement amino acid. Glu-461 and Tyr-503 were replaced, independently, with 13 amino acids. All 26 of the strains containing mutant enzymes are Lac-. Enzyme activity is reduced to less than 10% of wild type by substitutions at Glu-461 and to less than 1% of wild type by substitutions at Tyr-503. Many of the mutant enzymes have less than 0.1 % wild-type activity. His-464 and Met-3 were replaced with 1 1and 12 amino acids, respectively. Strains containing any one of these mutant proteins are Lac+. The results support previous evidence that Glu-46 1 and Tyr-503 areessential for catalysis, and suggest that His-464 is not part of the active site. Site-directed mutagenesis was facilitated by construction of an fl bacteriophage containing the complete lacz gene on i single ECORIfragment. -GALACTOSIDASE (EC 3.2.1.23) is produced in and J.
    [Show full text]
  • Preinitiation Complex
    Science Highlight – June 2011 Transcription Starts Here: Structural Models of a “Minimal” Preinitiation Complex RNA polymerase II (pol II) plays a central role in the regulation of gene expression. Pol II is the enzyme responsible for synthesizing all the messenger RNA (mRNA) and most of the small nuclear RNA (snRNA) in eukaryotes. One of the key questions for transcription is how pol II decides where to start on the genomic DNA to specifically and precisely turn on a gene. This is achieved during transcription initiation by concerted actions of the core enzyme pol II and a myriad of transcription factors including five general transcription factors, known as TFIIB, -D, -E, -F, -H, which together form a giant transcription preinitiation complex on a promoter prior to transcription. One of the most prominent core promoter DNA elements is the TATA box, usually directing transcription of tissue-specific genes. TATA-box binding protein (TBP), a key component of TFIID, recognizes the TATA DNA sequence. Based on the previous crystallographic studies, the TATA box DNA is bent by nearly 90 degree through the binding of TBP (1). This striking structural feature is thought to serve as a physical landmark for the location of active genes on the genome. In addition, the location of the TATA box at least in part determines the transcription start site (TSS) in most eukaryotes, including humans. The distance between the TATA box and the TSS is conserved at around 30 base pairs. TBP does not contact pol II directly and the TATA-containing promoter must be directed to the core enzyme through another essential transcription factor TFIIB.
    [Show full text]
  • BMB400 Part Four - II = Chpt
    BMB400 Part Four - II = Chpt. 17. Transcriptional regulation by effects on RNA polymerase B M B 400 Part Four: Gene Regulation Section II = Chapter 17. TRANSCRIPTIONAL REGULATION EXERTED BY EFFECTS ON RNA POLYMERASE [Dr. Tracy Nixon made major contributions to this chapter.] A. The multiple steps in initiation and elongation by RNA polymerase are targets for regulation. 1. RNA Polymerase has to * bind to promoters, * form an open complex, * initiate transcription, * escape from the promoter, * elongate , and * terminate transcription. See Fig. 4.2.1. 2. Summarizing a lot of work, we know that: • strong promoters have high KB, high kf, low kr, and high rates of promoter clearance. • weak promoters have low KB, low kf, high kr, and low rates of promoter clearance. • moderate promoters have one or more "weak" spots. 3. To learn these facts, we need: • genetic data to identify which macromolecules (DNA and proteins) interact in a specific regulation event, and to determine which base pairs and amino acid residues are needed for that regulation event. • biochemical data to describe the binding events and chemical reactions that are affected by the specific regulation event. Ideally, we would determine all forward and reverse rate constants, or equilibrium constants (which are a function of the ratio of rate constants) if rates are inaccessible. Although, in reality, we cannot get either rates or equilibrium constants for many of the steps, some of the steps are amenable to investigation and have proved to be quite informative about the mechanisms of regulation. BMB400 Part Four - II = Chpt. 17. Transcriptional regulation by effects on RNA polymerase Fig.
    [Show full text]
  • Targets TFIID and TFIIA to Prevent Activated Transcription
    Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press The mammalian transcriptional repressor RBP (CBF1) targets TFIID and TFIIA to prevent activated transcription Ivan Olave, Danny Reinberg,1 and Lynne D. Vales2 Department of Biochemistry and 1Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854 USA RBP is a cellular protein that functions as a transcriptional repressor in mammalian cells. RBP has elicited great interest lately because of its established roles in regulating gene expression, in Drosophila and mouse development, and as a component of the Notch signal transduction pathway. This report focuses on the mechanism by which RBP represses transcription and thereby regulates expression of a relatively simple, but natural, promoter. The results show that, irrespective of the close proximity between RBP and other transcription factors bound to the promoter, RBP does not occlude binding by these other transcription factors. Instead, RBP interacts with two transcriptional coactivators: dTAFII110, a subunit of TFIID, and TFIIA to repress transcription. The domain of dTAFII110 targeted by RBP is the same domain that interacts with TFIIA, but is disparate from the domain that interacts with Sp1. Repression can be thwarted when stable transcription preinitiation complexes are formed before RBP addition, suggesting that RBP interaction with TFIIA and TFIID perturbs optimal interactions between these coactivators. Consistent with this, interaction between RBP and TFIIA precludes interaction with dTAFII110. This is the first report of a repressor specifically targeting these two coactivators to subvert activated transcription. [Key Words: RBP; transcriptional repression; TFIIA/TFIID targeting] Received November 17, 1997; revised version accepted April 1, 1998.
    [Show full text]
  • Polycomb Repressor Complex 2 Function in Breast Cancer (Review)
    INTERNATIONAL JOURNAL OF ONCOLOGY 57: 1085-1094, 2020 Polycomb repressor complex 2 function in breast cancer (Review) COURTNEY J. MARTIN and ROGER A. MOOREHEAD Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada Received July 10, 2020; Accepted September 7, 2020 DOI: 10.3892/ijo.2020.5122 Abstract. Epigenetic modifications are important contributors 1. Introduction to the regulation of genes within the chromatin. The poly- comb repressive complex 2 (PRC2) is a multi‑subunit protein Epigenetic modifications, including DNA methylation complex that is involved in silencing gene expression through and histone modifications, play an important role in gene the trimethylation of lysine 27 at histone 3 (H3K27me3). The regulation. The dysregulation of these modifications can dysregulation of this modification has been associated with result in pathogenicity, including tumorigenicity. Research tumorigenicity through the increased repression of tumour has indicated an important influence of the trimethylation suppressor genes via condensing DNA to reduce access to the modification at lysine 27 on histone H3 (H3K27me3) within transcription start site (TSS) within tumor suppressor gene chromatin. This methylation is involved in the repression promoters. In the present review, the core proteins of PRC2, as of multiple genes within the genome by condensing DNA well as key accessory proteins, will be described. In addition, to reduce access to the transcription start site (TSS) within mechanisms controlling the recruitment of the PRC2 complex gene promoter sequences (1). The recruitment of H1.2, an H1 to H3K27 will be outlined. Finally, literature identifying the histone subtype, by the H3K27me3 modification has been a role of PRC2 in breast cancer proliferation, apoptosis and suggested as a mechanism for mediating this compaction (1).
    [Show full text]
  • Molecular Biology and Applied Genetics
    MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included.
    [Show full text]
  • Solutions for Practice Problems for Molecular Biology, Session 5
    Solutions to Practice Problems for Molecular Biology, Session 5: Gene Regulation and the Lac Operon Question 1 a) How does lactose (allolactose) promote transcription of LacZ? 1) Lactose binds to the polymerase and increases efficiency. 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. 3) Lactose binds to an activator protein, which can then help the RNA polymerase bind to the promoter and begin transcription. 4) Lactose prevents premature termination of transcription by directly binding to and bending the DNA. Solution: 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. b) What molecule is used to signal low glucose levels to the Lac operon regulatory system? 1) Cyclic AMP 2) Calcium 3) Lactose 4) Pyruvate Solution: 1) Cyclic AMP. Question 2 You design a summer class where you recreate experiments studying the lac operon in E. coli (see schematic below). In your experiments, the activity of the enzyme b-galactosidase (β -gal) is measured by including X-gal and IPTG in the growth media. X-gal is a lactose analog that turns blue when metabolisize by b-gal, but it does not induce the lac operon. IPTG is an inducer of the lac operon but is not metabolized by b-gal. I O lacZ Plac Binding site for CAP Pi Gene encoding β-gal Promoter for activator protein Repressor (I) a) Which of the following would you expect to bind to β-galactosidase? Circle all that apply.
    [Show full text]
  • Mechanism of Promoter Repression by Lac Repressor–DNA Loops Nicole A
    156–166 Nucleic Acids Research, 2013, Vol. 41, No. 1 Published online 9 November 2012 doi:10.1093/nar/gks1011 Mechanism of promoter repression by Lac repressor–DNA loops Nicole A. Becker1, Justin P. Peters1, Troy A. Lionberger2 and L. James Maher III1,* 1Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street Southwest, Rochester, MN 55905, USA and 2Howard Hughes Medical Institute and Jason L. Choy Laboratory of Single-Molecule Biophysics, Department of Physics, University of California, Berkeley, CA 94720, USA Received June 29, 2012; Revised October 1, 2012; Accepted October 2, 2012 ABSTRACT presence of allolactose or its analog, isopropyl b-D-1- thiogalactopyranoside (IPTG), relieving repression. In the The Escherichia coli lactose (lac) operon encodes absence of glucose, RNA polymerase binds cooperatively the first genetic switch to be discovered, and lac with catabolite activator protein at the lac promoter (positive remains a paradigm for studying negative and control). In simplest terms, the mechanism of negative positive control of gene expression. Negative control involves Lac repressor binding to occlude access control is believed to involve competition of RNA of RNA polymerase holoenzyme to the lac promoter (4). polymerase and Lac repressor for overlapping Of particular significance to the present work is the binding sites. Contributions to the local Lac repres- fascinating observation that two remote auxiliary oper- sor concentration come from free repressor and re- ators (Oaux) exist in the lac operon (5). It has been pressor delivered to the operator from remote proposed and demonstrated (6–13) that bidentate repres- auxiliary operators by DNA looping.
    [Show full text]
  • Transcription in Eukaryotes
    Transcription in eukaryotes Chromatin structure and its effects on transcription RNA polymerases Promoters General Transcription Factors Activators and Repressors Enhancers and ( Silencers ) Order of events leading to transcription initiation in eukaryotes at a specific promoter CRC … and chemical DNA modifications The order of steps on the pathway to transcription initiation appears to be different for different promoters Acção concertada de: -Activadores/ repressores ( proteínas auxiliares acessórias) -Proteínas de remodelação da cromatina -Capacidade de ligação dos factores gerais da transcrição Chromatin Remodeling Complexes (CRC) or Nucleosome remodeling factors ATPase/Helicase activity and DNA binding protein motifs Histone acetylation is one of the Histone histone chemical modifications acetylation characteristic of actively transcribed chromatin Interaction with other histones and with DNA Lys + HAT- histone acetyltransferase HDAC- histone deacetylase DNA chemical modifications affecting transcription initiation in eukaryotes How DNA methylation may help turning off genes? The binding of gene regulatory proteins and the general transcription machinery near an active promoter may prevent DNA methylation by excluding de novo methylases . If most of these proteins dissociate from the DNA, however, as generally occurs when a cell no longer produces the required activator proteins , the DNA becomes methylated , which enables other proteins to bind, and these shut down the gene completely by further altering chromatin structure . DNA
    [Show full text]
  • Constitutive Expression KE YE, CHARLES A
    Proc. Natl. Acad. Sci. USA Vol. 90, pp. 2295-2299, March 1993 Immunology Identification of the promoter region of human interleukin 1 type I receptor gene: Multiple initiation sites, high G+C content, and constitutive expression KE YE, CHARLES A. DINARELLO*, AND BURTON D. CLARK Department of Medicine, Tufts University School of Medicine and New England Medical Center, Boston, MA 02111 Communicated by Anthony S. Fauci, December 10, 1992 (receivedfor review November 10, 1992) ABSTRACT To better understand the role ofinterleukin 1 the regulation of expression of the IL-1RI gene at the (IL-1) and its receptor in disease, we have isolated a genomic molecular level, we cloned, identified, and characterized the clone of the human IL-1 type I receptor and have identified the 5' flanking region of this gene.t promoter region. There are multiple transcriptional initiation sites as demonstrated by primer extension. DNA sequence analysis shows that the promoter region contains neither a MATERIALS AND METHODS TATA nor a CAAT box; however, the 5' upstream regulatory Screening of Human Genomic Library. A human placental elements contain two AP-1-like binding sites. The internal genomic library was purchased from Clontech. This library regulatory sequences found immediately downstream to the 5' was prepared by partial Sau3A digestion and cloned into the transcriptional start site contain four Spl binding domains and BamHI site of EMBL-3 vector. Recombinant phage (106) have a high G+C content of 75%. This portion of the 5' were screened from the library through hybridization with a untranslated region of the mRNA can form stable secondary human IL-1RI cDNA probe (from position 1 to 959, a 5' Xba structure as predicted by computer modeling.
    [Show full text]
  • Dynamics and Function of DNA Methylation in Plants
    REVIEWS Dynamics and function of DNA methylation in plants Huiming Zhang1,2*, Zhaobo Lang1,2 and Jian- Kang Zhu 1,2,3* Abstract | DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so- called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions. DNA methylation at the 5ʹ position of cytosine contrib- and regulatory factors are generally not lethal. However, utes to the epigenetic regulation of nuclear gene expres- DNA methylation appears to be more crucial for devel- sion and to genome stability1,2. Epigenetic changes, opment and environmental- stress responses in plants including DNA methylation, histone modifications and that have more complex genomes. Recent findings histone variants and some non- coding RNA (ncRNA) have uncovered important
    [Show full text]
  • I = Chpt 15. Positive and Negative Transcriptional Control at Lac BMB
    BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac B M B 400 Part Four: Gene Regulation Section I = Chapter 15 POSITIVE AND NEGATIVE CONTROL SHOWN BY THE lac OPERON OF E. COLI A. Definitions and general comments 1. Operons An operon is a cluster of coordinately regulated genes. It includes structural genes (generally encoding enzymes), regulatory genes (encoding, e.g. activators or repressors) and regulatory sites (such as promoters and operators). 2. Negative versus positive control a. The type of control is defined by the response of the operon when no regulatory protein is present. b. In the case of negative control, the genes in the operon are expressed unless they are switched off by a repressor protein. Thus the operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated. c. In the case of positive control, the genes are expressed only when an active regulator protein, e.g. an activator, is present. Thus the operon will be turned off when the positive regulatory protein is absent or inactivated. Table 4.1.1. Positive vs. negative control BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac 3. Catabolic versus biosynthetic operons a. Catabolic pathways catalyze the breakdown of nutrients (the substrate for the pathway) to generate energy, or more precisely ATP, the energy currency of the cell. In the absence of the substrate, there is no reason for the catabolic enzymes to be present, and the operon encoding them is repressed. In the presence of the substrate, when the enzymes are needed, the operon is induced or de-repressed.
    [Show full text]