DOCSLIB.ORG

Chapter 3. the Beginnings of Genomic Biology – Molecular

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Chapter 3. The Beginnings of Genomic Biology – Molecular Genetics Contents 3. The beginnings of Genomic Biology – molecular genetics 3.1. DNA is the Genetic Material 3.6.5. Translation initiation, elongation, and termnation 3.2. Watson & Crick – The structure of DNA 3.6.6. Protein Sorting in Eukaryotes 3.3. Chromosome structure 3.7. Regulation of Eukaryotic Gene Expression 3.3.1. Prokaryotic chromosome structure 3.7.1. Transcriptional Control 3.3.2. Eukaryotic chromosome structure 3.7.2. Pre-mRNA Processing Control 3.3.3. Heterochromatin & Euchromatin 3.4. DNA Replication 3.7.3. mRNA Transport from the Nucleus 3.4.1. DNA replication is semiconservative 3.7.4. Translational Control 3.4.2. DNA polymerases 3.7.5. Protein Processing Control 3.4.3. Initiation of replication 3.7.6. Degradation of mRNA Control 3.4.4. DNA replication is semidiscontinuous 3.7.7. Protein Degradation Control 3.4.5. DNA replication in Eukaryotes. 3.8. Signaling and Signal Transduction 3.4.6. Replicating ends of chromosomes 3.8.1. Types of Cellular Signals 3.5. Transcription 3.8.2. Signal Recognition – Sensing the Environment 3.5.1. Cellular RNAs are transcribed from DNA 3.8.3. Signal transduction – Responding to the Environment 3.5.2. RNA polymerases catalyze transcription 3.5.3. Transcription in Prokaryotes 3.5.4. Transcription in Prokaryotes - Polycistronic mRNAs are produced from operons 3.5.5. Beyond Operons – Modification of expression in Prokaryotes 3.5.6. Transcriptions in Eukaryotes 3.5.7. Processing primary transcripts into mature mRNA 3.6. Translation 3.6.1. The Nature of Proteins 3.6.2. The Genetic Code 3.6.3. tRNA – The decoding molecule 3.6.4. Peptides are synthesized on Ribosomes CONCEPTS OF GENOMIC BIOLOGY Page 1 3.1. DNA IS THE GENETIC MATERIAL. (RETURN) CHAPTER 3. THE BEGINNINGS OF GENOMIC IOLOGY OLECULAR ENETICS (RETURN) B – M G In 1928, a British scientist, Frederick Griffith, published his work showing that live, rough, avirulent bacteria could be transformed by a “principle” found in dead, smooth, virulent bacteria into smooth, virulent As the development of classical genetics bacteria. This meant that the bacterial traits of rough proceeded from Mendel in 1866 through the early versus smooth and avirulence versus virulence were part of the 20th century the understanding that controlled by a substance that could carry the phenotype Mendel’s factors that produced traits were carried from dead to live cells. on chromosomes, and that there were infinite Griffith’s observations on Pneumococcus were ways that the genetic information from 2 parents controversial to say the least, and could assort in each generation to produce the inspired a spirited debate and genetic variety demanded by Darwin’s theories on much experimentation directed at “origin of species” on which natural selection proving whether the acted. This gave rise to the study of gene behavior “transforming principle” was of more complex traits and an understanding of protein or nucleic acid, the two genes in populations. main components of At the same time a quest for the material inside Frederick Griffith chromosomes identified early in (1879-1941) the 20th century, well before a cell, perhaps a subcomponent of a chromosome, Griffith’s experiments. This that carried the genetic instructions to make debate continued until Oswald Avery and his colleagues, organisms what they are was ongoing. Colin MacLeod, and Maclyn McCarty published their work in 1944 unequivocally showing that DNA was, in fact, Griffith’s transforming principle. This completely CONCEPTS OF GENOMIC BIOLOGY Page 2 revolutionized genetics and is considered the founding observation of molecular genetics. Figure 3.1. An electron micrograph of bacteriophage T2 (left), and a sketch showing the structures present in the virus (right). The head consists of a DNA molecule surrounded by proteins, while the core, sheath, and tail fibers are all made of protein. Oswald T. Avery Colin MacLeod Maclyn McCarty Only the DNA molecule enters the cell. In 1953, more evidence supporting DNA being the genetic material resulted from the work of Alfred Once it was established that DNA was the genetic Hershey and Martha Chase on E. coli infected with material carrying the instructions for life so to speak, bacteriophage T2. In their experiment, T2 proteins were attention turned to the question of “How could a labeled with the 35S radioisotope, and T2 DNA was molecule carry genetic information?” The key to that labeled with was labeled with the 32P radioisotope. Then became obvious with a detailed understanding of the the labeled viruses were mixed separately with the E. coli structure of the DNA molecule, which was developed by host, and after a short time, phage attachment was two scientists a Cambridge University, James Watson and disrupted with a kitchen blender, and the location of the Francis Crick. label determined. The 35S-labeled protein was found outside the infected cells, while the 32P-labeled DNA was inside the E. coli, indicating that DNA carried the information needed for viral infection. CONCEPTS OF GENOMIC BIOLOGY Page 3 Rosalind Franklin a young x-ray crystallographer working in the laboratory of Maurice Wilkins at 3.2. WASON & CRICK – THE STRUCTURE OF DNA. Cambridge University used a technique known as x-ray (RETURN) diffraction to generate images of DNA molecules that showed that DNA had a helical structure with repeating The basic laboratory observations that lead to the structural elements every 0.34 nm and every 3.4 nm formulation of a structure for DNA did not involve along the axis of the molecule. biologists. Rather Irwin Chargaff, an analytical, organic chemist, and physicists, Rosalind Franklin and Maurice Wilkins made the laboratory observations that led to the solution of the structure of DNA. Chargaff determined that there were 4 different nitrogen bases found in DNA molecules; the purines, adenine (A) and guanine G), and the pyrimidines, cytosine (C) and thymine (T), and he purified DNA from a number of different sources so he could examine the quantitative relationships of A, T, G, and C. He con- Rosalind Franklin Maurice Wilkins cluded that in all DNA molecules, the mole-percentage of A was nearly equal to the mole-percentage of T, while the mole-percentage of G was nearly equal to the mole- percentage of C. Alternatively, you could state this as the mole-percentage of pyri-midine bases equaled the mole- percentage of purine bases. These observations became Figure 3.2. X-ray diffraction image known as Chargaff’s rules. of DNA molecule showing helical structure with repeat structural elements. CONCEPTS OF GENOMIC BIOLOGY Page 4 These astute observations allowed Watson and Crick to synthesize together a 3-dimentional structure of a DNA molecule with all of these essential features. This structure was published in 1953, and immediately generated much excitement, culminating in a Nobel Prize in Physiology and Medicine, in 1962 awarded to Franklin, Wilkins, Watson, and Crick. Figure 3.4. Structures of purine and pyrimidine bases in DNA, and structure of 2’-deoxyribose sugar. The key elements of this structure are: Double helical structure – each helix is made from the alternating deoxyribose sugar and phosphate groups derived from deoxynuclotides, which are the monomeric units that are used to make up polymeric nucleic acid molecules. Each nucleotide in each chain Figure 3.3. Watson & Crick’s DNA structure. Their model consisted of consists of a nitrogen base of either the purine type a double helicical structure with the sugars and phosphates making (adenine or guanine) or the pyrimidine type (cytosine the two hlices on the outside of the structure. The sugars were held together by 3’-5’-phosphodiester bonds. The bases pair on the inside or thymidine) attached to the 1’-position of 2’- of the molecule with A always pairing with T, and G always pairing with deoxyribose sugar, and a phosphate group, esterified C. This pairing leads to Chargaff’s observations about bases in DNA. by a phospho-ester bond to the 5’-position of the sugar. CONCEPTS OF GENOMIC BIOLOGY Page 5 The nucleotides are held together in sequence order along the length of the polynucleotide chain by 3’-5’- Figure 3.5. The building bocks of nucleic phosphodiester bonds, and the strands demonstrate acids are nucleotides and nucleosides. Any a polarity as the 5’-OH at one end of a polynuc-leotide base together with a deoxyribose sugar forms a deoxyribonucleoside, while if the strand is distinct from the 3’-OH at the other end of sugar is ribose a ribonucleoside is formed the strand. Often, but not always, the 5’-strand end (not shown). Addition of a phosphate on the 5’ position of the sugar froms nucleotides will have a phosphate group attached. from nucleosides. Each of the 2 polynucleotide chains of the double helix are held together by hydrogen bonds beween the adenosines in one strand and the thymidines in the other strand, and between the guanosines in one strand hydrogen bonded to the cytosines in the other strand. Figure 3.7. Strand of DNA Figure 3.6. Base pairing between A and T involves two hydrogen showing the 3’,5’-phosphodi- bonds, and pairing between G and C involves 3 hydrogen bonds. ester bonds holding This means that the forces holding strands together in G=C base nucleotides together. pair-rich regions are stronger than in A=T base pair-rich regions. CONCEPTS OF GENOMIC BIOLOGY Page 6 In order to get a uniform diameter for the molecule and have proper alignment of the nucleotide pairs in the middle of the strands, the strands must be orient-ed in antiparallel fashion, i.e. with the strand polarity of each strand of the double helix going in the opposite direction (one strand is 3’-> 5’ whie the other is 5’ -> 3’).
Recommended publications
  • Characterization of the Osmoregulated Escherichia Coli Prou Promoter and Identification of Prov As a Membrane-Associated Protein

    Characterization of the Osmoregulated Escherichia Coli Prou Promoter and Identification of Prov As a Membrane-Associated Protein

    Molecular Microbiology (1989) 3(11), 1521-1531 Characterization of the osmoregulated Escherichia coli proU promoter and identification of ProV as a membrane-associated protein G. May, E. Faatz, J. M. Lucht, M. Haardt, The prop-encoded transport system has a iow affinity for M. Bolliger^ and E. Bremer* giycine betaine and is present in the cytopiasmic mem- Department of Biotogy. University of Konstanz, PO Box brane (Milner et ai. 1988). The protZ-encoded transport 5560, D'775O Konstanz. FRG. system has a high affinity for glycine betaine and is binding-protein-dependent (May ef ai. 1986; Higgins et ai, 1987a; Barron efa/., 1987;foranoverview, see Ames, Summary 1986). Analyses of the cloned proU region from £ coli The Escherichia coli proU operon encodes a high- have demonstrated that this iocus consists of at ieast affinity, binding-protein-dependent transport system three genes (proV. proW, and proX) that are organized in for the osmoprotectant gtycine betaine. Expression of an operon (Gowrishankar et ai, 1986; Faatz et ai, 1988; proU is osmoregulated, and transcription of this Dattananda and Gowrishankar, 1989). From the recently operon is greatly increased In cells grown at high determined proU DNA sequence {Gowrishankar, 1989), osmoiarity. Characterization of the proU operon and the products of these genes have been deduced. The proV its promoter provrded results similar to those pub- gene encodes a hydrophiiic protein {M, ^ 44162) with lished elsewhere (Gowrishankar, 1989; Stirling et a/., homology to the energy-coupling component of binding- 1989). The previously identified proU601 mutation, protein-dependent transport systems. A hydrophobic which leads to increased prot>expression both at low- polypeptide (M, = 37619) is encoded by proW and is and high osmolarity, is a G to A transition in the thought to be located in the cytoplasmic membrane.
  • Rnase a Cleanup of DNA Samples Version Number: 1.0 Version 1.0 Date: 12/21/2016 Author(S): Yuko Yoshinaga, Eileen Dalin Reviewed/Revised By

    Rnase a Cleanup of DNA Samples Version Number: 1.0 Version 1.0 Date: 12/21/2016 Author(S): Yuko Yoshinaga, Eileen Dalin Reviewed/Revised By

    SAMPLE MANAGEMENT STANDARD OPERATING PROCEDURE RNase A Cleanup of DNA Samples Version Number: 1.0 Version 1.0 Date: 12/21/2016 Author(s): Yuko Yoshinaga, Eileen Dalin Reviewed/Revised by: Summary RNase A treatment is used for the removal of RNA from genomic DNA samples. RNase A cleaves the phosphodiester bond between the 5'-ribose of a nucleotide and the phosphate group attached to the 3'- ribose of an adjacent pyrimidine nucleotide. The resulting 2', 3'-cyclic phosphate is hydrolyzed to the corresponding 3'-nucleoside phosphate. Materials & Reagents Materials Vendor Stock Number Disposables 1.5 ml microcentrifuge tubes Reagents TE Buffer, pH 8.0 Ambion 9849 RNase A, DNase and protease-free (10 mg/ml) ThermoFisher EN0531 Sodium acetate buffer solution (3M, pH 5.2) VWR 567422 Ethanol, 200 proof Pharmco-Aaper 111000200CSPP 50x TAE Buffer Life Technologies/ Invitrogen MRGF-4210 SYBR® Safe DNA gel stain (10,000x concentrate in Life Technologies/ Invitrogen S33102 DMSO) DNA Molecular Weight Marker II Sigma 10236250001 Gel Loading Dye, Blue (6x) New England BioLabs B7021S Equipment Centrifuge 4°C Heat block 37°C Gel electrophoresis device Gel Imager Bio-Rad EH&S PPE Requirements: 1.1 Safety glasses, lab coat, and nitrile gloves should be worn at all times while performing work in the lab during this protocol. 1.2 Ethanol is a highly flammable and irritating to the eyes. Vapors may cause drowsiness and dizziness. Keep containers closed and keep away from sources of ignition such as smoking. 1 SAMPLE MANAGEMENT STANDARD OPERATING PROCEDURE Avoid contact with skin and eyes. In case of contact with eyes, rinse immediately with plenty of water and seek medical advice.
  • Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity

    Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity

    Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity 82 SYNTHETIC BIOLOGY FOREWORD To be added by SCBD at a later stage. 1 BACKGROUND 2 In decision X/13, the Conference of the Parties invited Parties, other Governments and relevant 3 organizations to submit information on, inter alia, synthetic biology for consideration by the Subsidiary 4 Body on Scientific, Technical and Technological Advice (SBSTTA), in accordance with the procedures 5 outlined in decision IX/29, while applying the precautionary approach to the field release of synthetic 6 life, cell or genome into the environment. 7 Following the consideration of information on synthetic biology during the sixteenth meeting of the 8 SBSTTA, the Conference of the Parties, in decision XI/11, noting the need to consider the potential 9 positive and negative impacts of components, organisms and products resulting from synthetic biology 10 techniques on the conservation and sustainable use of biodiversity, requested the Executive Secretary 11 to invite the submission of additional relevant information on this matter in a compiled and synthesised 12 manner. The Secretariat was also requested to consider possible gaps and overlaps with the applicable 13 provisions of the Convention, its Protocols and other relevant agreements. A synthesis of this 14 information was thus prepared, peer-reviewed and subsequently considered by the eighteenth meeting 15 of the SBSTTA. The documents were then further revised on the basis of comments from the SBSTTA 16 and peer review process, and submitted for consideration by the twelfth meeting of the Conference of 17 the Parties to the Convention on Biological Diversity.
  • Chapter 18 Regulation of Gene Expression Regulation of Gene Expression • Important for Cellular Control and Differentiation

    Chapter 18 Regulation of Gene Expression Regulation of Gene Expression • Important for Cellular Control and Differentiation

    Chapter 18 Regulation of Gene Expression Regulation of Gene Expression • Important for cellular control and differentiation. • Understanding “expression” is a “hot” area in Biology. General Mechanisms 1. Regulate Gene Expression 2. Regulate Protein Activity Operon Model • Jacob and Monod (1961) - Prokaryotic model of gene control. • Always on the National AP Biology exam! Operon Structure 1. Regulatory Gene 2. Operon Area a. Promoter b. Operator c. Structural Genes Gene Structures Regulatory Gene • Makes Repressor Protein which may bind to the operator. • Repressor protein blocks transcription. Promoter • Attachment sequence on the DNA for RNA polymerase to start transcription. Operator • The "Switch”, binding site for Repressor Protein. • If blocked, will not permit RNA polymerase to pass, preventing transcription. Structural Genes • Make the enzymes for the metabolic pathway. Lac Operon • For digesting Lactose. • Inducible Operon - only works (on) when the substrate (lactose) is present. If no Lactose • Repressor binds to operator. • Operon is "off”, no transcription, no enzymes made If Lactose is absent If Lactose is present • Repressor binds to Lactose instead of operator. • Operon is "on”, transcription occurs, enzymes are made. If Lactose is present Enzymes • Digest Lactose. • When enough Lactose is digested, the Repressor can bind to the operator and switch the Operon "off”. Net Result • The cell only makes the Lactose digestive enzymes when the substrate is present, saving time and energy. Animation • http://www.biostudio.com/d_%20Lac%20Ope ron.htm trp Operon • Makes/synthesizes Tryptophan. • Repressible Operon. – Predict how it is different from the inducible operon… If no Tryptophan • Repressor protein is inactive, Operon "on” Tryptophan made. • “Normal” state for the cell.
  • Difference Between Sigma Factors and Transcription Factors

    Difference Between Sigma Factors and Transcription Factors

    Difference Between Sigma Factors And Transcription Factors Which Rollin bestialises so persuasively that Stephanus romances her audiograms? Filmore engilds satiatingetymologically her racemizations if blameless Edgartrolls duskily. evaluating or envisaged. Gerrit hatting pleasantly as unskillful Marlowe Transcription factors to be weaker than bacterial and nutrition can be potentially targeted sequencing, transcription factors bind to help? CH is _____, Faburay B, the students have. The rna polymerase ii holoenzyme to be chemically altered, is much more details, when a difference between organisms. Utr and helps synthesize, not among themselves and termination is. Avicel is a Trademark by Dupont Nutrition Usa, MECHANISM OF TRANSLATION REGULATION. Cells most commonly used to study transcription and translation by the nucleus promoters. The chromatin needs in bacteria. Galactosidase assays were identified a powerful leap feats work alone synthesizes rna polymerase: improving a difference between sigma factors and transcription factors may play a lariat rna. They are green and place an! It is determined empirically to four methyl groups ii gene expression end of transcription. Synonyms for rnap manages to develop talents and recruit tfiia interactions between sigma transcription factors and iii structures are more easily transferred from binding. Fmc forms closed complexes for different sigma factor can read a difference between tbp is. RNA contains the pyrimidine uracil in utility of thymine found in DNA. Sigma factors are subunits of all bacterial RNA polymerases. Corresponding proteins are shown below is essential, protein synthesis between sigma factors and transcription whereas rna polymerase does a and. Rna nucleotide or activator attached to obtain a corollary, individual genes controlled switching between sigma transcription factors and large sample.
  • Insights Into Comparative Genomics, Codon Usage Bias, And

    Insights Into Comparative Genomics, Codon Usage Bias, And

    plants Article Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes Xiaofeng Chi 1,2 , Faqi Zhang 1,2 , Qi Dong 1,* and Shilong Chen 1,2,* 1 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; [email protected] (X.C.); [email protected] (F.Z.) 2 Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China * Correspondence: [email protected] (Q.D.); [email protected] (S.C.) Received: 29 October 2020; Accepted: 17 November 2020; Published: 18 November 2020 Abstract: Biebersteiniaceae and Nitrariaceae, two small families, were classified in Sapindales recently. Taxonomic and phylogenetic relationships within Sapindales are still poorly resolved and controversial. In current study, we compared the chloroplast genomes of five species (Biebersteinia heterostemon, Peganum harmala, Nitraria roborowskii, Nitraria sibirica, and Nitraria tangutorum) from Biebersteiniaceae and Nitrariaceae. High similarity was detected in the gene order, content and orientation of the five chloroplast genomes; 13 highly variable regions were identified among the five species. An accelerated substitution rate was found in the protein-coding genes, especially clpP. The effective number of codons (ENC), parity rule 2 (PR2), and neutrality plots together revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported (Nitrariaceae (Biebersteiniaceae + The Rest)) relationships in Sapindales. Our findings can provide useful information for analyzing phylogeny and molecular evolution within Biebersteiniaceae and Nitrariaceae.
  • U6 Small Nuclear RNA Is Transcribed by RNA Polymerase III (Cloned Human U6 Gene/"TATA Box"/Intragenic Promoter/A-Amanitin/La Antigen) GARY R

    U6 Small Nuclear RNA Is Transcribed by RNA Polymerase III (Cloned Human U6 Gene/"TATA Box"/Intragenic Promoter/A-Amanitin/La Antigen) GARY R

    Proc. Nati. Acad. Sci. USA Vol. 83, pp. 8575-8579, November 1986 Biochemistry U6 small nuclear RNA is transcribed by RNA polymerase III (cloned human U6 gene/"TATA box"/intragenic promoter/a-amanitin/La antigen) GARY R. KUNKEL*, ROBIN L. MASERt, JAMES P. CALVETt, AND THORU PEDERSON* *Cell Biology Group, Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545; and tDepartment of Biochemistry, University of Kansas Medical Center, Kansas City, KS 66103 Communicated by Aaron J. Shatkin, August 7, 1986 ABSTRACT A DNA fragment homologous to U6 small 4A (20) was screened with a '251-labeled U6 RNA probe (21, nuclear RNA was isolated from a human genomic library and 22) using a modified in situ plaque hybridization protocol sequenced. The immediate 5'-flanking region of the U6 DNA (23). One of several positive clones was plaque-purified and clone had significant homology with a potential mouse U6 gene, subsequently shown by restriction mapping to contain a including a "TATA box" at a position 26-29 nucleotides 12-kilobase-pair (kbp) insert. A 3.7-kbp EcoRI fragment upstream from the transcription start site. Although this containing U6-hybridizing sequences was subcloned into sequence element is characteristic of RNA polymerase II pBR322 for further restriction mapping. An 800-base-pair promoters, the U6 gene also contained a polymerase III "box (bp) DNA fragment containing U6 homologous sequences A" intragenic control region and a typical run of five thymines was excised using Ava I and inserted into the Sma I site of at the 3' terminus (noncoding strand). The human U6 DNA M13mp8 replicative form DNA (M13/U6) (24).
  • Genome-Wide Mutational Biases Fuel Transcriptional Diversity in the Mycobacterium Tuberculosis Complex

    Genome-Wide Mutational Biases Fuel Transcriptional Diversity in the Mycobacterium Tuberculosis Complex

    ARTICLE https://doi.org/10.1038/s41467-019-11948-6 OPEN Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex Álvaro Chiner-Oms 1,2,12, Michael Berney 3,12, Christine Boinett4,5, Fernando González-Candelas 1,6, Douglas B. Young7, Sebastien Gagneux8,9, William R. Jacobs Jr3, Julian Parkhill 10, Teresa Cortes 11 & Iñaki Comas 2,6 1234567890():,; The Mycobacterium tuberculosis complex (MTBC) members display different host-specificities and virulence phenotypes. Here, we have performed a comprehensive RNAseq and methy- lome analysis of the main clades of the MTBC and discovered unique transcriptional profiles. The majority of genes differentially expressed between the clades encode proteins involved in host interaction and metabolic functions. A significant fraction of changes in gene expression can be explained by positive selection on single mutations that either create or disrupt transcriptional start sites (TSS). Furthermore, we show that clinical strains have different methyltransferases inactivated and thus different methylation patterns. Under the tested conditions, differential methylation has a minor direct role on transcriptomic differences between strains. However, disruption of a methyltransferase in one clinical strain revealed important expression differences suggesting indirect mechanisms of expression regulation. Our study demonstrates that variation in transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences in host characteristics. 1 Unidad Mixta “Infección y Salud Pública” FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas-I2SysBio, Valencia, Spain. 2 Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, Spain. 3 Department of Microbiology and Immunology and Department of Molecular Genetics, Albert Einstein College of Medicine, New York, USA.
  • Interplay Between Ompa and Rpon Regulates Flagellar Synthesis in Stenotrophomonas Maltophilia

    Interplay Between Ompa and Rpon Regulates Flagellar Synthesis in Stenotrophomonas Maltophilia

    microorganisms Article Interplay between OmpA and RpoN Regulates Flagellar Synthesis in Stenotrophomonas maltophilia Chun-Hsing Liao 1,2,†, Chia-Lun Chang 3,†, Hsin-Hui Huang 3, Yi-Tsung Lin 2,4, Li-Hua Li 5,6 and Tsuey-Ching Yang 3,* 1 Division of Infectious Disease, Far Eastern Memorial Hospital, New Taipei City 220, Taiwan; [email protected] 2 Department of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] 3 Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; [email protected] (C.-L.C.); [email protected] (H.-H.H.) 4 Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan 5 Department of Pathology and Laboratory Medicine, Taipei Veterans General Hosiptal, Taipei 112, Taiwan; [email protected] 6 Ph.D. Program in Medical Biotechnology, Taipei Medical University, Taipei 110, Taiwan * Correspondence: [email protected] † Liao, C.-H. and Chang, C.-L. contributed equally to this work. Abstract: OmpA, which encodes outer membrane protein A (OmpA), is the most abundant transcript in Stenotrophomonas maltophilia based on transcriptome analyses. The functions of OmpA, including adhesion, biofilm formation, drug resistance, and immune response targets, have been reported in some microorganisms, but few functions are known in S. maltophilia. This study aimed to elucidate the relationship between OmpA and swimming motility in S. maltophilia. KJDOmpA, an ompA mutant, Citation: Liao, C.-H.; Chang, C.-L.; displayed compromised swimming and failure of conjugation-mediated plasmid transportation. The Huang, H.-H.; Lin, Y.-T.; Li, L.-H.; hierarchical organization of flagella synthesis genes in S.
  • Mutation Bias Shapes Gene Evolution in Arabidopsis Thaliana ​

    Mutation Bias Shapes Gene Evolution in Arabidopsis Thaliana ​

    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.17.156752; this version posted June 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Mutation bias shapes gene evolution in Arabidopsis thaliana ​ 1,2† 1 1 3,4 Monroe, J. Grey ,​ Srikant, Thanvi ,​ Carbonell-Bejerano, Pablo ,​ Exposito-Alonso, Moises ,​ 5​ ​ 6 7 ​ 1† ​ Weng, Mao-Lun ,​ Rutter, Matthew T. ,​ Fenster, Charles B. ,​ Weigel, Detlef ​ ​ ​ ​ 1 Department​ of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany 2 Department​ of Plant Sciences, University of California Davis, Davis, CA 95616, USA 3 Department​ of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA 4 Department​ of Biology, Stanford University, Stanford, CA 94305, USA 5 Department​ of Biology, Westfield State University, Westfield, MA 01086, USA 6 Department​ of Biology, College of Charleston, SC 29401, USA 7 Department​ of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA † corresponding​ authors: [email protected], [email protected] ​ ​ ​ Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1–4 and evolutionary optimization of genic 3,5 ​ mutation rates remains controversial .​ However, it has now become known that ​ cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6 ,​ which is predicted by more recent theory to be a prerequisite for beneficial mutation 7 rates between different classes of genes to readily evolve .​ To test this possibility, we ​ used de novo mutations in Arabidopsis thaliana to create a high resolution predictive ​ ​ ​ model of mutation rates as a function of cytogenetic features across the genome.
  • Expanding the Genetic Code Lei Wang and Peter G

    Expanding the Genetic Code Lei Wang and Peter G

    Reviews P. G. Schultz and L. Wang Protein Science Expanding the Genetic Code Lei Wang and Peter G. Schultz* Keywords: amino acids · genetic code · protein chemistry Angewandte Chemie 34 2005 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim DOI: 10.1002/anie.200460627 Angew. Chem. Int. Ed. 2005, 44,34–66 Angewandte Protein Science Chemie Although chemists can synthesize virtually any small organic molecule, our From the Contents ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, 1. Introduction 35 modifications are largely restricted to substitutions among the common 20 2. Chemical Approaches 35 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and 3. In Vitro Biosynthetic eukaryotic organisms. Over 30 novel amino acids have been genetically Approaches to Protein encoded in response to unique triplet and quadruplet codons including Mutagenesis 39 fluorescent, photoreactive, and redox-active amino acids, glycosylated 4. In Vivo Protein amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom- Mutagenesis 43 containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps 5. An Expanded Code 46 entire organisms with new or enhanced properties. 6. Outlook 61 1. Introduction The genetic codes of all known organisms specify the same functional roles to amino acid residues in proteins. Selectivity 20 amino acid building blocks. These building blocks contain a depends on the number and reactivity (dependent on both limited number of functional groups including carboxylic steric and electronic factors) of a particular amino acid side acids and amides, a thiol and thiol ether, alcohols, basic chain.
  • RNA-Based Regulation of Genes of Tryptophan Synthesis and Degradation, in Bacteria

    RNA-Based Regulation of Genes of Tryptophan Synthesis and Degradation, in Bacteria

    REVIEW RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria CHARLES YANOFSKY Department of Biological Sciences, Stanford University Stanford, California 94305, USA ABSTRACT We are now aware that RNA-based regulatory mechanisms are commonly used to control gene expression in many organisms. These mechanisms offer the opportunity to exploit relatively short, unique RNA sequences, in altering transcription, translation, and/or mRNA stability, in response to the presence of a small or large signal molecule. The ability of an RNA segment to fold and form alternative hairpin secondary structures—each dedicated to a different regulatory function—permits selection of specific sequences that can affect transcription and/or translation. In the present paper I will focus on our current understanding of the RNA-based regulatory mechanisms used by Escherichia coli and Bacillus subtilis in controlling expression of the tryptophan biosynthetic operon. The regulatory mechanisms they use for this purpose differ, suggesting that these organisms, or their ancestors, adopted different strategies during their evolution. I will also describe the RNA-based mechanism used by E. coli in regulating expression of its operon responsible for tryptophan degradation, the tryptophanase operon. Keywords: trp operon; trp suboperon; aro supraoperon; tna operon; transcription attenuation; T box regulation; tryptophan as a regulatory signal; tRNATrp as a regulatory signal; peptidyl-tRNA; ribosome mediated regulation INTRODUCTION A second regulatory lesson learned over the years is that information within mRNAs, or other RNAs, as well as small Studies over the past 50+ years have revealed that metabolites and other molecules—in addition to DNA and optimization of gene expression has been a major evolu- proteins—often provides specific regulatory signals, or tionary objective for most species.