SURVEY and SUMMARY Retrons and Their Applications in Genome

Total Page:16

File Type:pdf, Size:1020Kb

SURVEY and SUMMARY Retrons and Their Applications in Genome Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gkz865 SURVEY AND SUMMARY Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz865/5584520 by Unitversity of Texas Libraries user on 01 November 2019 Retrons and their applications in genome engineering Anna J. Simon *, Andrew D. Ellington and Ilya J. Finkelstein * Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA Received April 23, 2019; Revised September 19, 2019; Editorial Decision September 23, 2019; Accepted October 02, 2019 ABSTRACT plex Automated Genome Engineering (‘MAGE’) (8), Yeast Oligo-mediated Genome Engineering (‘YOGE’) (9), and it- Precision genome editing technologies have trans- erative CRISPR EnAbled Trackable genome Engineering formed modern biology. These technologies have (‘iCREATE’) (10). arisen from the redirection of natural biological ma- Retrons are a potentially useful tool for targeted genomic chinery, such as bacteriophage lambda proteins for engineering because they produce intracellular DNAs recombineering and CRISPR nucleases for eliciting via reverse transcription of noncoding structural RNAs site-specific double-strand breaks. Less well-known (11,12). While the natural biology of these widespread is a widely distributed class of bacterial retroele- retroelements is largely unknown, retrons have recently ments, retrons, that employ specialized reverse tran- been repurposed as in situ sources of donor DNA for both scriptases to produce noncoding intracellular DNAs. recombineering- and CRISPR-based genome editing ap- Retrons’ natural function and mechanism of genetic plications (13–15). This production of intracellular DNA has so far enabled recording of cellular states (13), high- transmission have remained enigmatic. However, re- throughput genetic editing (14), and targeted genome muta- cent studies have harnessed their ability to produce tion (15). Here, we review retron biology and retron-enabled DNA in situ for genome editing and evolution. This genome engineering applications. We conclude with a dis- review describes retron biology and function in both cussion of future prospects and challenges in retron-based natural and synthetic contexts. We also highlight genome editing. areas that require further study to advance retron- based precision genome editing platforms. RETRON BIOLOGY Retron discovery and biochemistry INTRODUCTION Retrons were initially discovered in 1984 from the presence The ability to precisely edit genomic loci has been a long- of short satellite RNA–DNA molecules in bacterial DNA standing goal of biotechnology. Targeted genome editing preparations (16). Gel electrophoresis of phenol-extracted is being exploited to probe genotype-phenotype relation- chromosomal DNA from Myxobacteria xanthus and Stig- ships, repair disease-causing alleles, develop designer or- matella aurantica indicated a secondary satellite band with ganisms with modified genomes, and to biologically record a mobility of ∼120–190 base pairs (bp) (16). Subsequent intra- and extracellular conditions. Classically, strain im- studies revealed that these bands, termed multicopy single- provement has been achieved either via non-specific mu- stranded DNAs (msDNAs), are comprised of one strand tagenesis of genomes (1,2) or via targeted modifications of structured RNA, the ‘msr,’ connected to one strand of of specific genes expressed on plasmids (3,4). Recombi- DNA, the ‘msd.’ The msr and msd molecules are joined by neering (5) and CRISPR-based genome editing (6,7)have a2-5 phosphodiester bond between a priming guanosine dramatically increased the ease and throughput of tar- within a conserved AGC sequence in the msr and the phos- geting individual genomic loci. Multiplexing and iterating phate of the 5 end of the msd that covalently links the RNA recombineering- and CRISPR-based editing technologies and DNA strands into a single branched molecule (Figure have enabled high-throughput exploration of genotype– 1). The msr and msd are encoded in a compact, contiguous phenotype relationships and continuous evolution of syn- transcriptional cassette that also includes a specialized re- thetic genomes with novel properties, for example in Multi- verse transcriptase (RT); we refer to this cassette as a whole *To whom correspondence should be addressed. Tel: +1 512 475 6172; Email: [email protected] Correspondence may also be addressed to Anna J. Simon. Email: [email protected] C The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Nucleic Acids Research, 2019 A Priming Reverse transcriptase as the retron. The discovery of retron RTs was particularly msr guanosine msd (RT) notable because they were the first discovered bacterially- encoded RTs (17). In vitro studies demonstrated that Es- Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz865/5584520 by Unitversity of Texas Libraries user on 01 November 2019 5’ cherichia coli retron RTs and their paired msrs were both repeat 3’ repeat 2 necessary and sufficient to produce msDNA with the char- bits Reverse transcription 1 acteristic 2 -5 linkage (18,19). To date, 38 distinct retrons 0 have been identified experimentally by their production of B msDNA; 16 of these, which we subsequently refer to as the G ‘experimentally validated retrons’, contain fully annotated A C U G G U C U U C C U A A G and experimentally-validated msr-msd-RT cassettes. Table A msd transcript G C A U C A G T A A G C G U G C U 1 summarizes all experimentally-characterized retrons re- A C G U U G A C C G G ported to date, along with their host organisms. Bioinfor- U U U G A C U U C G A G A C U C U U A matic approaches have also identified hundreds of puta- U C G C C G G U C GC U U G A C U G A U U G U U A tive retrons that have not been characterized experimentally U G C C A U A Reverse A G C G C C G transcription (20–22). U U U C U C C A G C A The rapid discovery of hundreds of putative retrons has A G U C A G A C G G U G G U G U U A U U prompted us to develop a systematic naming convention A G C U A A U U A U C U U A U A U C G Beginning of for these retroelements. Currently, retrons are named by Priming C G C G reverse the first letters of their genus name, species name, and the guanosine A U C G transcription G C length of reverse-transcribed DNA in their native msDNA C G G C sequence. This convention was initially developed by In- 5’ repeat U A A 3’ repeat 5’ 3’ ouye et al. in 1989, who termed a retron isolated from E. coli that contained 86 bases of reverse-transcribed DNA ‘Ec86’ U A (23). However, this nomenclature is not easy to adapt for C U A A G large-scale, systematic retron discovery for three reasons: (i) C G U U U U U A the length of the msd of most experimentally validated and C G C U A U U G putative retrons is unknown; (ii) two letters are insufficient A U U G Priming C G C msr G U to uniquely identify the genus and species of many retron- G C A A guanosine A U U G A U encoding bacteria; and (iii) the convention does not distin- G C C C U G U G G A A C U A UUGGC AAUUU C 5’ G AUGGCCCCAA CU U G C A G A C TTC AAG A guish the entire retron from the RT. Therefore, we propose C G A G T C C A a more general naming convention that is adapted from the A G A A A O A A A A A A C G G G A 5’ T T T C G restriction enzyme literature (Table 1)(24). N G msr (5’) NH C Reverse T A GA N N NH O 2 transcription G C I. Retrons are named as the first letter of their genus, first T A T A two letters of their species, and an Arabic numeral cor- 2’ G C msr (3’) G C responding to the order with which they were discov- O O C T O T T C G ered relative to other retrons from the same species or a O P O N G C NH G C msd different species with the same first genus and first two O A T N G C species letters, respectively. N NH2 reverse O A T 5’ G C transcript II. The prefix ‘Retron-” is added to signify that this object C G A T is a retron, and the prefixes ‘RT-’, ‘msr’, ‘msd’ and ‘ms- T A O C G A DNA’are added when referring to the reverse transcrip- msd C G G tase enzyme, msr, msd and msDNA, respectively. Figure 1. Retron structure and organization. (A) Retrons are encoded as Under the new convention, ‘Ec86’ is re-named ‘Retron- a single polycistronic transcriptional cassette containing a promoter, an Eco1’ and the corresponding RT is ‘RT-Eco1.’ For clarity msr (blue) including a conserved priming guanosine residue (green), an and continuity, the rest of this review will use the new con- msd (red), self-complementary regions (yellow), and a reverse transcrip- tase (purple, not to scale) (12). The black arrow shows the direction of the vention and will also include the historical names in paren- coding strand for the retron cassette; the red arrow shows the direction thesis (e.g.
Recommended publications
  • Two Independent Retrons with Highly Diverse Reverse Transcriptases In
    Proc. Natl. Acad. Sci. USA Vol. 87, pp. 942-945, February 1990 Biochemistry Two independent retrons with highly diverse reverse transcriptases in Myxococcus xanthus (multicopy single-stranded DNA/2',5'-phosphodiester/codon usage/myxobacteria) SUMIKO INOUYE, PETER J. HERZER, AND MASAYORI INOUYE Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854 Communicated by Russell F. Doolittle, November 27, 1989 (received for review September 29, 1989) ABSTRACT A reverse transcriptase (RT) was recently found that the Mx65 retron is highly diverse and independent found in Myxococcus xanthus, a Gram-negative soil bacterium. from the Mx162 retron and that RT associated with the Mx65 This RT has been shown to be associated with a chromosomal retron has only 47% identity with RT for the Mx162 retron. region designated a retron responsible for the synthesis of a peculiar extrachromosomal DNA called msDNA (multicopy single-stranded DNA). We demonstrate that M. xanthus con- MATERIALS AND METHODS tains two independent, unlinked retrons, one for the synthesis Materials. The clone of the 9.0-kilobase (kb) Pst I fragment of msDNA-Mxl62 and the other for msDNA-Mx65. The struc- containing the Mx65 retron was obtained (8). Restriction tural analysis of the retron for msDNA-Mx65 revealed that the enzymes were purchased from New England Biolabs and coding regions for msdRNA (msr) and msDNA (msd), and an Boehringer Mannheim. open reading frame (ORF) downstream of msr are arranged in A deletion mutant strain ofthe Mx162 retron, AmsSX, was the same manner as found for the Mx162 retron.
    [Show full text]
  • Isolation, Antimicrobial Activity of Myxobacterial Crude Extracts and Identification of the Most Potent Strains
    Arch Biol Sci. 2017;69(3):561-568 https://doi.org/10.2298/ABS161011132C Isolation, antimicrobial activity of myxobacterial crude extracts and identification of the most potent strains Ivana Charousová*, Juraj Medo and Soňa Javoreková Department of Microbiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia *Corresponding author: [email protected] Received: October 11, 2016; Revised: November 14, 2016; Accepted: November 18, 2016; Published online: December 14, 2016 Abstract: Broad spectrum antimicrobial agents are urgently needed to fight frequently occurring multidrug-resistant pathogens. Myxobacteria have been regarded as “microbe factories” for active secondary metabolites, and therefore, this study was performed to isolate two bacteriolytic genera of myxobacteria, Myxococcus sp. and Corallococcus sp., from 10 soil/sand samples using two conventional methods followed by purification with the aim of determining the antimicrobial activity of methanol extracts against 11 test microorganisms (four Gram-positive, four Gram-negative, two yeasts and one fungus). Out of thirty-nine directly observed strains, 23 were purified and analyzed for antimicrobial activities. Based on the broth microdilution method, a total of 19 crude extracts showed antimicrobial activity. The range of inhibited wells was more important in the case of anti-Gram-positive-bacterial activity in comparison with the anti-Gram-negative-bacterial and antifungal activity. In light of the established degree and range of antimicrobial activity, two of the most active isolates (BNEM1 and SFEC2) were selected for further characterization. Morphological parameters and a sequence similarity search by BLAST revealed that they showed 99% sequence similarity to Myxococcus xanthus − BNEM1 (accession no.
    [Show full text]
  • 723874V1.Full.Pdf
    bioRxiv preprint doi: https://doi.org/10.1101/723874; this version posted August 5, 2019. 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-NC-ND 4.0 International license. 1 Discovery of a polybrominated aromatic 2 secondary metabolite from a planctomycete 3 points at an ambivalent interaction with its 4 macroalgae host 5 6 7 8 9 10 11 Fabian Panter[a,b], Ronald Garcia[a,b], Angela Thewes[a,b], Nestor Zaburannyi [a,b], Boyke Bunk [b,c], Jörg 12 Overmann[b,c], Mary Victory Gutierrez [d], Daniel Krug[a,b] and Rolf Müller*[a,b] 13 14 15 * Corresponding author, rolf.mü[email protected] 16 17 18 19 20 [a] Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz 21 Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, 22 Germany 23 [b] German Centre for Infection Research (DZIF), Partner Site Hannover–Braunschweig, Germany 24 [c] Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 3814 Braunschweig, 25 Germany 26 [d] Biology Department, Far Eastern University, Nicanor Reyes St., Sampaloc, Manila, 1008 Metro Manila, Philippines 27 28 29 30 31 1 bioRxiv preprint doi: https://doi.org/10.1101/723874; this version posted August 5, 2019. 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.
    [Show full text]
  • Novel Myxobacteria As a Potential Source of Natural Products and Description of Inter-Species Nature of C-Signal
    Novel myxobacteria as a potential source of natural products and description of inter-species nature of C-signal Dissertation zur Erlangung des Grades des Doktors der Naturwissenschaften der Naturwissenschaftlich-Technischen Fakultät III Chemie, Pharmazie, Bio- und Werkstoffwissenschaften der Universität des Saarlandes von Ram Prasad Awal (M. Sc. in Medical Microbiology) Saarbrücken 2016 Tag des Kolloquiums: ......19.12.2016....................................... Dekan: ......Prof. Dr. Guido Kickelbick.............. Berichterstatter: ......Prof. Dr. Rolf Müller...................... ......Prof. Dr. Manfred J. Schmitt........... ............................................................... Vositz: ......Prof. Dr. Uli Kazmaier..................... Akad. Mitarbeiter: ......Dr. Jessica Stolzenberger.................. iii Diese Arbeit entstand unter der Anleitung von Prof. Dr. Rolf Müller in der Fachrichtung 8.2, Pharmazeutische Biotechnologie der Naturwissenschaftlich-Technischen Fakultät III der Universität des Saarlandes von Oktober 2012 bis September 2016. iv Acknowledgement Above all, I would like to express my special appreciation and thanks to my advisor Professor Dr. Rolf Müller. It has been an honor to be his Ph.D. student and work in his esteemed laboratory. I appreciate for his supervision, inspiration and for allowing me to grow as a research scientist. Your guidance on both research as well as on my career have been invaluable. I would also like to thank Professor Dr. Manfred J. Schmitt for his scientific support and suggestions to my research work. I am thankful for my funding sources that made my Ph.D. work possible. I was funded by Deutscher Akademischer Austauschdienst (DAAD) for 3 and half years and later on by Helmholtz-Institute. Many thanks to my co-advisors: Dr. Carsten Volz, who supported and guided me through the challenging research and Dr. Ronald Garcia for introducing me to the wonderful world of myxobacteria.
    [Show full text]
  • Perspectives
    Copvright 0 1999 bv the Genetics Society of Anlerica Perspectives Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove ROLANDTHAXTER’S Legacy and the Origins of Multicellular Development Dale Kaiser Departments of Biochemistry and of Developmental Biology, Stanford University, Stanford, Calijornia 94305 OLAND THAXTER published a bombshell in R December,1892. He reported that Chondro- myces crocatus, before then considered an imperfect fungus because of its complex fruiting bodv, was ac- tually a bacterium (Figure 1). THAXTERhad discov- ered theunicellular vegetative stage of C. crocatus; the cells he found were relatively short and they divided by binary fission. C. crocatus was, heconcluded, a “communal bacterium.” THAXTERdescribed the lo- comotion, swarming, aggregation and process of fruit- ing body formation of C. crocatus and its relatives, which are collectively called myxobacteria, with an accuracy that has survived 100 years of scrutiny. He recognized the behavioral similarity to the myxomv- cetes and the cellular slime molds, drawing attention in all three to the transition from single cells to an integrated multicellular state. He described the be- havior of myxobacteria in fructification in terms of a “course of development” because it was “a definitely recurring aggregation of individuals capable of con- certed action toward a definiteend” (THAXI‘ER1892). This essay will emphasize some implications of THAX- TER’S demonstrations, often apparently unrecognized. The striking similarities to cellular slime mold de- velopment probably led JOHN TYLERBONNER and KENNETHB. RAPER,50 years after THAXTER’Sdiscov- ery, to take independent forays into myxobacterial development. RAPER,an eminent mycologist, had in FIGURE1 .“Chondromyces crocatus fruiting bodv.
    [Show full text]
  • A Quantitative Assay to Study Cell Movement in the Myxobacteria
    jf. Cell Sci. 25, 173-178 (i977) 173 Printed in Great Britain A QUANTITATIVE ASSAY TO STUDY CELL MOVEMENT IN THE MYXOBACTERIA JOSEPH LONSKI, RONALD HEROMIN AND DAVID INGRAHAM Department of Biology, Bucknell University, Lezvisburg, Pennsylvania, U.S.A. SUMMARY A simple quantitative assay has been developed to test the rate of cell movement of myxo- bacteria. The assay employs an agar surface and at no time are the cells cultured in a liquid environment. Isolation of a rate-increasing substance(s) from fruiting Myxococcus xartthus is reported. The understanding of the aggregative process in these bacteria will be aided by characterization of the chemotactic system. INTRODUCTION The myxobacteria represent a unique group of procaryotes which interact with each other throughout their life cycle. These interactions play a role both in the swarming and feeding process, as well as in fruiting body formation. The general properties of the myxobacteria have been reviewed several times (Dworkin, 1966; 1972). A distinctive feature of the myxobacteria is that when cells on the surface of a solid medium are deprived of specific nutrients, they shift from growth to development and begin to migrate, by means of a gliding motility, into aggregation centres (Dworkin, 1963). A number of investigations (Lev, 1954; Jennings, 1961; McVittie & Zahler, 1962; Fleugel, 1963) have suggested that this aggregation is in response to a chemo- tactic substance but this has not yet been carefully examined. Having aggregated, the cells then construct a macroscopic fruiting body. For Myxococcus xanthus this is a simple mound of myxospores encased in a slime sheath. This research was initiated to aid in the search for the mechanism of aggregation of these procaryotes.
    [Show full text]
  • The Soil Microbial Food Web Revisited: Predatory Myxobacteria As Keystone Taxa?
    The ISME Journal https://doi.org/10.1038/s41396-021-00958-2 ARTICLE The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? 1 1 1,2 1 1 Sebastian Petters ● Verena Groß ● Andrea Söllinger ● Michelle Pichler ● Anne Reinhard ● 1 1 Mia Maria Bengtsson ● Tim Urich Received: 4 October 2018 / Revised: 24 February 2021 / Accepted: 4 March 2021 © The Author(s) 2021. This article is published with open access Abstract Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized fi 1234567890();,: 1234567890();,: predatory bacteria af liated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition.
    [Show full text]
  • The Correlation Between Morphological and Phylogenetic Classification of Myxobacteria
    International Journal of Systematic Bacteriology (1 999), 49, 1255-1 262 Printed in Great Britain The correlation between morphological and phylogenetic classification of myxobacteria Cathrin Sproer,’ Hans Reichenbach’ and Erko Stackebrandtl Author for correspondence: Erko Stackebrandt.Tel: +49 531 2616 352. Fax: +49 531 2616 418. e-mail : [email protected] DSMZ-Deutsche Sammlung In order to determine whether morphological criteria are suitable to affiliate von Mikroorganismen und myxobacterial strains to species, a phylogenetic analysis of 16s rDNAs was Zellkulturen GmbH1 and G BF-Gesel Isc haft fur performed on 54 myxobacterial strains that represented morphologically 21 Biotechnologische species of the genera Angiococcus, Archangium, Chondromyces, Cystobacter, Forschung mbH*, 381 24 Melittangium, Myxococcus, Polyangium and Stigmatella, five invalid species Braunschweig, Germany and three unclassified isolates. The analysis included 12 previously published sequences. The branching pattern confirmed the deep trifurcation of the order Myxococcales. One lineage is defined by the genera Cystobacter, Angiococcus, Archangium, Melittangium, Myxococcus and Stigmatella. The study confirms the genus status of Corallococcus’, previously ‘Chondrococcus’,within the family Myxococcaceae. The second lineage contains the genus Chondromyces and the species Polyangium (‘Sorangium’) cellulosum, while the third lineage is comprised of Nannocystis and a strain identified as Polyangium vitellinum. With the exception of a small number of strains that did not cluster phylogenetically with members of the genus to which they were assigned by morphological criteria (‘Polyangium thaxteri’ PI t3, Polyangium cellulosum ATCC 25531T, Melittangium lichenicola ATCC 25947Tand Angiococcus disciformis An dl), the phenotypic classification should provide a sound basis for the description of neotype species in those cases where original strain material is not available or is listed as reference material.
    [Show full text]
  • Planctomycetes Attached to Algal Surfaces: Insight Into Their Genomes
    MSc 2.º CICLO FCUP 2015 into Planctomycetes their Planctomycetes genomes attached attached to algal surfaces: Insight into to algal their genomes surfaces Mafalda Seabra Faria : Insight : Dissertação de Mestrado apresentada à Faculdade de Ciências da Universidade do Porto Laboratório de Ecofisiologia Microbiana da Universidade do Porto Biologia Celular e Molecular 2014/2015 Mafalda Seabra Faria Seabra Mafalda I FCUP Planctomycetes attached to algal surfaces: Insight into their genomes Planctomycetes attached to algal surfaces: Insight into their genomes Mafalda Seabra Faria Mestrado em Biologia Celular e Molecular Biologia 2015 Orientador Olga Maria Oliveira da Silva Lage, Professora Auxiliar, Faculdade de Ciências da Universidade do Porto Co-orientador Jens Harder, Senior Scientist and Professor, Max Planck Institute for Marine Microbiology FCUP II Planctomycetes attached to algal surfaces: Insight into their genomes Todas as correções determinadas pelo júri, e só essas, foram efetuadas. O Presidente do Júri, Porto, ______/______/_________ FCUP III Planctomycetes attached to algal surfaces: Insight into their genomes FCUP IV Planctomycetes attached to algal surfaces: Insight into their genomes “Tell me and I forget, teach me and I may remember, involve me and I learn.” Benjamin Franklin FCUP V Planctomycetes attached to algal surfaces: Insight into their genomes FCUP VI Planctomycetes attached to algal surfaces: Insight into their genomes Acknowledgements Foremost, I would like to express my sincere gratitude to my supervisor Professor
    [Show full text]
  • Myxobacteria-Derived Outer Membrane Vesicles: Potential Applicability Against Intracellular Infections
    cells Article Myxobacteria-Derived Outer Membrane Vesicles: Potential Applicability Against Intracellular Infections Adriely Goes 1,2 , Philipp Lapuhs 1,2 , Thomas Kuhn 1,2, Eilien Schulz 1,2 , Robert Richter 2,3 , Fabian Panter 4 , Charlotte Dahlem 5, Marcus Koch 6, Ronald Garcia 4, Alexandra K. Kiemer 5 , Rolf Müller 2,4,7 and Gregor Fuhrmann 1,2,* 1 Helmholtz Centre for Infection Research (HZI), Biogenic Nanotherapeutics Group (BION), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123 Saarbrücken, Germany; [email protected] (A.G.); [email protected] (P.L.); [email protected] (T.K.); [email protected] (E.S.) 2 Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany; [email protected] (R.R.); [email protected] (R.M.) 3 Helmholtz Centre for Infection Research (HZI), Department of Drug Delivery (DDEL), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123 Saarbrücken, Germany 4 Helmholtz Centre for Infection Research (HZI), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123 Saarbrücken, Germany; [email protected] (F.P.); [email protected] (R.G.) 5 Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany; [email protected] (C.D.); [email protected] (A.K.K.) 6 INM-Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany; [email protected] 7 German Center for Infection Research (DZIF), 38124 Braunschweig, Germany * Correspondence: [email protected]; Tel.: +49-68-198-806 (ext.
    [Show full text]
  • A Genomic Survey of Signalling in the Myxococcaceae
    microorganisms Article A Genomic Survey of Signalling in the Myxococcaceae David E. Whitworth * and Allison Zwarycz Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY19 7DL, UK; [email protected] * Correspondence: [email protected] Received: 14 October 2020; Accepted: 3 November 2020; Published: 6 November 2020 Abstract: As prokaryotes diverge by evolution, essential ‘core’ genes required for conserved phenotypes are preferentially retained, while inessential ‘accessory’ genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera (Myxococcus and Corallococcus), and on a species within each genus (Myxococcus xanthus and Corallococcus exiguus). Four new C. exiguus genome sequences are also described here. Despite accessory genes accounting for substantial proportions of each myxobacterial genome, signalling proteins were found to be enriched in the core genome, with two-component system genes almost exclusively so. We also investigated the conservation of signalling proteins in three myxobacterial behaviours. The linear carotenogenesis pathway was entirely conserved, with no gene gain/loss observed. However, the modular fruiting body formation network was found to be evolutionarily plastic, with dispensable components in all modules (including components required for fruiting in the model myxobacterium M. xanthus DK1622). Quorum signalling (QS) is thought to be absent from most myxobacteria, however, they generally appear to be able to produce CAI-I (cholerae autoinducer-1), to sense other QS molecules, and to disrupt the QS of other organisms, potentially important abilities during predation of other prokaryotes. Keywords: carotenoids; comparative genomics; development; fruiting body formation; one-component systems; quorum signalling; two-component systems; myxobacteria; Myxococcales 1.
    [Show full text]
  • Absolute Chemical Structure of the Myxobacterial Pheromone Of
    FEMS Microbiology Letters 165 (1998) 29^34 Absolute chemical structure of the myxobacterial pheromone of Stigmatella aurantiaca that induces the formation of its fruiting body Downloaded from https://academic.oup.com/femsle/article/165/1/29/623856 by guest on 24 September 2021 Yuka Morikawa a, Seiji Takayama a, Ryosuke Fudo b, Shigeru Yamanaka b, Kenji Mori c, Akira Isogai a;* a Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara 630-0101, Japan b Central Research Laboratories, Ajinomoto Co. Ltd., Suzuki 1-1, Kawasaki, Kanagawa 210-0801, Japan c Department of Chemistry, Science University of Tokyo, Kagurazaka 1-3, Shinjuku, Tokyo 162-8601, Japan Received 6 May 1998; revised 3 June 1998; accepted 4 June 1998 Abstract Stigmatella aurantiaca, a species of myxobacteria, produces a novel extracellular signaling molecule, 8-hydroxy-2,5,8- trimethyl-4-nonanone, which promotes its developmental cycle. To determine the absolute configuration of this pheromone, which contains one asymmetric carbon, we prepared the R- and S-enantiomers by stereoselective synthesis. The synthesized R- and S-enantiomers each showed nearly the same fruiting body-inducing activities as the natural pheromone. Gas chromatography-mass spectrometry (GC-MS) analysis using a chiral capillary column revealed that the naturally-produced pheromone is a mixture of both enantiomers. z 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved. Keywords: Myxobacterium; Stigmatella aurantiaca; Fruiting body; Pheromone; Absolute structure 1. Introduction ing body formation process of S. aurantiaca may be regarded as a model of photomorphogenesis. Myxobacteria are a class of Gram-negative bacte- In addition to environmental factors, an extracel- ria which show a social behavior and complex devel- lular signaling molecule, or pheromone, is known to opmental cycle [1,2].
    [Show full text]