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Gillis A, Fayad N, Makart L, Bolotin A, Sorokin A, Kallassy M, Mahillon J. Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensis. FEMS Microbiol Rev 2018; 42:829-856. [PMID: 30203090 PMCID: PMC6199540 DOI: 10.1093/femsre/fuy034] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Bacillus thuringiensis is a well-known biopesticide that has been used for more than 80 years. This spore-forming bacterium belongs to the group of Bacillus cereus that also includes, among others, emetic and diarrheic pathotypes of B. cereus, the animal pathogen Bacillus anthracis and the psychrotolerant Bacillus weihenstephanensis. Bacillus thuringiensis is rather unique since it has adapted its lifestyle as an efficient pathogen of specific insect larvae. One of the peculiarities of B. thuringiensis strains is the extent of their extrachromosomal pool, with strains harbouring more than 10 distinct plasmid molecules. Among the numerous serovars of B. thuringiensis, 'israelensis' is certainly emblematic since its host spectrum is apparently restricted to dipteran insects like mosquitoes and black flies, vectors of human and animal diseases such as malaria, yellow fever, or river blindness. In this review, the putative role of the mobile gene pool of B. thuringiensis serovar israelensis in its pathogenicity and dedicated lifestyle is reviewed, with specific emphasis on the nature, diversity, and potential mobility of its constituents. Variations among the few related strains of B. thuringiensis serovar israelensis will also be reported and discussed in the scope of this specialised insect pathogen, whose lifestyle in the environment remains largely unknown.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Nancy Fayad
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
- Laboratory of Biodiversity and Functional Genomics (BGF), Faculty of Sciences, Université Saint-Joseph, 1107 2050 Beirut, Lebanon
| | - Lionel Makart
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Alexander Bolotin
- UMR1319 Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Alexei Sorokin
- UMR1319 Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - Mireille Kallassy
- Laboratory of Biodiversity and Functional Genomics (BGF), Faculty of Sciences, Université Saint-Joseph, 1107 2050 Beirut, Lebanon
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
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52
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Guillory WX, Onyshchenko A, Ruck EC, Parks M, Nakov T, Wickett NJ, Alverson AJ. Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta). Genome Biol Evol 2018; 10:1504-1515. [PMID: 29850800 PMCID: PMC6007386 DOI: 10.1093/gbe/evy103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 01/23/2023] Open
Abstract
We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.
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Affiliation(s)
- Wilson X Guillory
- Department of Biological Sciences, University of Arkansas
- Department of Zoology, Southern Illinois University, Carbondale, IL
| | | | | | - Matthew Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, Illinois
| | - Teofil Nakov
- Department of Biological Sciences, University of Arkansas
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, Illinois
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53
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Wu B, Macielog AI, Hao W. Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria. Genome Biol Evol 2018; 9:2658-2667. [PMID: 29048531 PMCID: PMC5647799 DOI: 10.1093/gbe/evx211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species. Within the genome, spliceosomal introns can proliferate in unrelated genes and intergenic regions. Among conspecific strains, spliceosomal introns undergo rapid turnover (gains and losses) and frequent sequence exchange between geographically distinct strains. Furthermore, spliceosomal introns could undergo introgression between distinct species, which can further promote intron invasion and proliferation. The dynamic invasion and proliferation processes of spliceosomal introns resemble the life cycles of mobile selfish (group I/II) introns, and these intron movements, at least in part, account for the dramatic processes of intron gain and intron loss during eukaryotic evolution.
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Affiliation(s)
- Baojun Wu
- Department of Biology, Clark University, Worcester, MA, USA
| | | | - Weilong Hao
- Department of Biological Sciences, Wayne State University
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54
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Toro N, Martínez-Abarca F, Molina-Sánchez MD, García-Rodríguez FM, Nisa-Martínez R. Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution. Front Microbiol 2018; 9:627. [PMID: 29670598 PMCID: PMC5894124 DOI: 10.3389/fmicb.2018.00627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/19/2018] [Indexed: 12/26/2022] Open
Abstract
Mobile group II introns are ribozymes and retroelements that probably originate from bacteria. Sinorhizobium meliloti, the nitrogen-fixing endosymbiont of legumes of genus Medicago, harbors a large number of these retroelements. One of these elements, RmInt1, has been particularly successful at colonizing this multipartite genome. Many studies have improved our understanding of RmInt1 and phylogenetically related group II introns, their mobility mechanisms, spread and dynamics within S. meliloti and closely related species. Although RmInt1 conserves the ancient retroelement behavior, its evolutionary history suggests that this group II intron has played a role in the short- and long-term evolution of the S. meliloti genome. We will discuss its proposed role in genome evolution by controlling the spread and coexistence of potentially harmful mobile genetic elements, by ectopic transposition to different genetic loci as a source of early genomic variation and by generating sequence variation after a very slow degradation process, through intron remnants that may have continued to evolve, contributing to bacterial speciation.
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Affiliation(s)
- Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - María D Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Fernando M García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Rafael Nisa-Martínez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
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55
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Pogoda CS, Keepers KG, Hamsher SE, Stepanek JG, Kane NC, Kociolek JP. Comparative analysis of the mitochondrial genomes of six newly sequenced diatoms reveals group II introns in the barcoding region of cox1. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [PMID: 29527965 DOI: 10.1080/24701394.2018.1450397] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Diatoms are the most diverse lineage of algae and at the base of most aquatic food webs, but only 11 of their mitochondrial genomes have been described. Herein, we present the mitochondrial genomes of six diatom species, including: Melosira undulata, Nitzschia alba, Surirella sp., Entomoneis sp., Halamphora coffeaeformis, and Halamphora calidilacuna. Comparison of these six genomes to the 11 currently published diatom mitochondrial genomes revealed a novel ubiquitous feature block consisting of tatC-orf157-rps11. The presence of intronic retrotransposable elements in the barcoding region of cox1 in the Halamphora genomes may explain historic difficulty (especially PCR) with cox1 as a universal barcode for diatoms. Our analysis suggests that high rates of variability in number and position of introns, in many commonly used coding sequences, prevent these from being universally viable as barcodes for diatoms. Therefore, we suggest researchers examine the chloroplast and/or nuclear genomes for universal barcoding markers.
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Affiliation(s)
- Cloe S Pogoda
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Kyle G Keepers
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Sarah E Hamsher
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Joshua G Stepanek
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - Nolan C Kane
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
| | - J Patrick Kociolek
- a Department of Ecology and Evolutionary Biology, and Museum of Natural History , University of Colorado , Boulder , CO , USA
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56
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Abstract
MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and were inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jumping genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes. When a transposon is inserted in the intron, it becomes an intronic miRNA, taking advantage of the protein synthesis machinery, i.e., mRNA transcription and splicing, as a means for processing and maturation. MiRNAs have been found to play an important, but not life-threatening, role in embryonic development. They might play a pivotal role in diverse biological systems in various organisms, facilitating a quick response and accurate plotting of body physiology and structures. Based on these unique properties, manufactured intronic miRNAs have been developed for in vitro evaluation of gene function, in vivo gene therapy, and generation of transgenic animal models. The biogenesis of miRNAs, circulating miRNAs, miRNAs and cancer, iPSCs, and heart disease are presented in this chapter, highlighting some recent studies on these topics.
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Affiliation(s)
- Shao-Yao Ying
- Department of Integrative Anatomical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Donald C Chang
- WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA, USA
| | - Shi-Lung Lin
- Division of Regenerative Medicine, WJWU & LYNN Institute for Stem Cell Research, Santa Fe Springs, CA, USA
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57
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Qu Y, Legen J, Arndt J, Henkel S, Hoppe G, Thieme C, Ranzini G, Muino JM, Weihe A, Ohler U, Weber G, Ostersetzer O, Schmitz-Linneweber C. Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation. FRONTIERS IN PLANT SCIENCE 2018; 9:1453. [PMID: 30337934 PMCID: PMC6180158 DOI: 10.3389/fpls.2018.01453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
Chloroplasts (and other plastids) harbor their own genetic material, with a bacterial-like gene-expression systems. Chloroplast RNA metabolism is complex and is predominantly mediated by nuclear-encoded RNA-binding proteins. In addition to these nuclear factors, the chloroplast-encoded intron maturase MatK has been suggested to perform as a splicing factor for a subset of chloroplast introns. MatK is essential for plant cell survival in tobacco, and thus null mutants have not yet been isolated. We therefore attempted to over-express MatK from a neutral site in the chloroplast, placing it under the control of a theophylline-inducible riboswitch. This ectopic insertion of MatK lead to a variegated cotyledons phenotype. The addition of the inducer theophylline exacerbated the phenotype in a concentration-dependent manner. The extent of variegation was further modulated by light, sucrose and spectinomycin, suggesting that the function of MatK is intertwined with photosynthesis and plastid translation. Inhibiting translation in the transplastomic lines has a profound effect on the accumulation of several chloroplast mRNAs, including the accumulation of an RNA antisense to rpl33, a gene coding for an essential chloroplast ribosomal protein. Our study further supports the idea that MatK expression needs to be tightly regulated to prevent detrimental effects and establishes another link between leaf variegation and chloroplast translation.
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Affiliation(s)
- Yujiao Qu
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia Legen
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jürgen Arndt
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stephanie Henkel
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Galina Hoppe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Giovanna Ranzini
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jose M. Muino
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Weihe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gert Weber
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Joint Research Group Macromolecular Crystallography, Berlin, Germany
| | - Oren Ostersetzer
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christian Schmitz-Linneweber
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- *Correspondence: Christian Schmitz-Linneweber,
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58
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Studying Parasite Gene Function and Interaction Through Ribozymes and Riboswitches Design Mechanism. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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59
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Sulo P, Szabóová D, Bielik P, Poláková S, Šoltys K, Jatzová K, Szemes T. The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'. DNA Res 2017; 24:571-583. [PMID: 28992063 PMCID: PMC5726470 DOI: 10.1093/dnares/dsx026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/23/2017] [Indexed: 11/24/2022] Open
Abstract
The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters. Their most profound feature is species-specific alteration in gene order. The genetic code slightly differs from well-established yeast mitochondrial code as GUG is used rarely as the translation start and CGA and CGC code for arginine. The multilocus phylogeny, inferred from mtDNA, does not correlate with the trees derived from nuclear genes. mtDNA data demonstrate that Saccharomyces cariocanus should be assigned as a separate species and Saccharomyces bayanus CBS 380T should not be considered as a distinct species due to mtDNA nearly identical to Saccharomyces uvarum mtDNA. Apparently, comparison of mtDNAs should not be neglected in genomic studies as it is an important tool to understand the origin and evolutionary history of some yeast species.
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Affiliation(s)
- Pavol Sulo
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava 842 15, Slovakia
| | - Dana Szabóová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava 842 15, Slovakia
| | - Peter Bielik
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava 842 15, Slovakia
| | - Silvia Poláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava 842 15, Slovakia
| | - Katarína Šoltys
- Comenius University Science Park, Bratislava 841 04, Slovakia
| | - Katarína Jatzová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava 842 15, Slovakia
| | - Tomáš Szemes
- Comenius University Science Park, Bratislava 841 04, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 842 15, Slovakia
- Geneton s.r.o., Galvaniho 7, Bratislava 821 04, Slovakia
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60
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Moelling K, Broecker F, Russo G, Sunagawa S. RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense. Front Microbiol 2017; 8:1745. [PMID: 28959243 PMCID: PMC5603734 DOI: 10.3389/fmicb.2017.01745] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/28/2017] [Indexed: 12/21/2022] Open
Abstract
Retroviral infections are 'mini-symbiotic' events supplying recipient cells with sequences for viral replication, including the reverse transcriptase (RT) and ribonuclease H (RNase H). These proteins and other viral or cellular sequences can provide novel cellular functions including immune defense mechanisms. Their high error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and the related transposable elements (TEs) have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes. Endogenous retroviruses regulate host genes, have provided novel genes including the syncytins that mediate maternal-fetal immune tolerance and can be experimentally rendered infectious again. The RT and the RNase H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of TEs. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses. These enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. The retroviral replication components share striking similarities with the RNA-induced silencing complex (RISC), the prokaryotic CRISPR-Cas machinery, eukaryotic V(D)J recombination and interferon systems. Viruses supply antiviral defense tools to cellular organisms. TEs are the evolutionary origin of siRNA and miRNA genes that, through RISC, counteract detrimental activities of TEs and chromosomal instability. Moreover, piRNAs, implicated in transgenerational inheritance, suppress TEs in germ cells. Thus, virtually all known immune defense mechanisms against viruses, phages, TEs, and extracellular pathogens require RNase H-like enzymes. Analogous to the prokaryotic CRISPR-Cas anti-phage defense possibly originating from TEs termed casposons, endogenized retroviruses ERVs and amplified TEs can be regarded as related forms of inheritable immunity in eukaryotes. This survey suggests that RNase H-like activities of retroviruses, TEs, and phages, have built up innate and adaptive immune systems throughout all domains of life.
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Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of ZurichZurich, Switzerland
- Max Planck Institute for Molecular GeneticsBerlin, Germany
| | - Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New YorkNY, United States
| | - Giancarlo Russo
- Functional Genomics Center Zurich, ETH Zurich/University of ZurichZurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH ZurichZurich, Switzerland
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61
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Abstract
Group II introns are large, autocatalytic ribozymes that catalyze RNA splicing and retrotransposition. Splicing by group II introns plays a major role in the metabolism of plants, fungi, and yeast and contributes to genetic variation in many bacteria. Group II introns have played a major role in genome evolution, as they are likely progenitors of spliceosomal introns, retroelements, and other machinery that controls genetic variation and stability. The structure and catalytic mechanism of group II introns have recently been elucidated through a combination of genetics, chemical biology, solution biochemistry, and crystallography. These studies reveal a dynamic machine that cycles progressively through multiple conformations as it stimulates the various stages of splicing. A central active site, containing a reactive metal ion cluster, catalyzes both steps of self-splicing. These studies provide insights into RNA structure, folding, and catalysis, as they raise new questions about the behavior of RNA machines.
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Affiliation(s)
- Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, Howard Hughes Medical Institute, New Haven, Connecticut 06520.,Department of Chemistry, Yale University, Howard Hughes Medical Institute, New Haven, Connecticut 06520;
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62
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On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires. mBio 2017; 8:mBio.00897-17. [PMID: 28698278 PMCID: PMC5513706 DOI: 10.1128/mbio.00897-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium—Arthrospira platensis. Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis, a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.
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63
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Cai M, Li S, Sun F, Sun Q, Zhao H, Ren X, Zhao Y, Tan BC, Zhang Z, Qiu F. Emp10 encodes a mitochondrial PPR protein that affects the cis-splicing of nad2 intron 1 and seed development in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:132-144. [PMID: 28346745 DOI: 10.1111/tpj.13551] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 03/15/2017] [Accepted: 03/22/2017] [Indexed: 05/20/2023]
Abstract
In higher plants, many mitochondrial genes contain group II-type introns that are removed from RNAs by splicing to produce mature transcripts that are then translated into functional proteins. However, the factors involved in the splicing of mitochondrial introns and their biological functions are not well understood in maize. Here, we isolated an empty pericarp 10 (emp10) mutant and identified the underlying gene by map-based cloning. Emp10 encodes a P-type mitochondria-targeted pentatricopeptide repeat (PPR) protein with 10 PPR motifs. Loss of Emp10 function results in splicing defect of the first intron of nad2, a gene encoding subunit 2 of NADH dehydrogenase (also called complex I). The emp10 mutant has undetectable activity of complex I and has arrested development of embryo and endosperm, and thus defective seeds with empty pericarp. Additionally, the basal endosperm transfer layer cells were severely affected, indicating the deficiency of cell wall ingrowths in the emp10 kernels. Moreover, the alternative respiratory pathway involving alternative oxidase was significantly induced in the emp10 mutant. These results suggest that EMP10 is specifically required for the cis-splicing of mitochondrial nad2 intron 1, embryogenesis and endosperm development in maize.
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Affiliation(s)
- Manjun Cai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuzhen Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Sun
- School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuemei Ren
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanxin Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bao-Cai Tan
- School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Filyushin MA, Boris KV. Polymorphism and the secondary structure of the mitochondrial nad1 gene b/c intron in Malus species and related Rosaceae species. BIOL BULL+ 2017. [DOI: 10.1134/s1062359017040033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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65
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Heijstra BD, Leang C, Juminaga A. Gas fermentation: cellular engineering possibilities and scale up. Microb Cell Fact 2017; 16:60. [PMID: 28403896 PMCID: PMC5389167 DOI: 10.1186/s12934-017-0676-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/04/2017] [Indexed: 12/11/2022] Open
Abstract
Low carbon fuels and chemicals can be sourced from renewable materials such as biomass or from industrial and municipal waste streams. Gasification of these materials allows all of the carbon to become available for product generation, a clear advantage over partial biomass conversion into fermentable sugars. Gasification results into a synthesis stream (syngas) containing carbon monoxide (CO), carbon dioxide (CO2), hydrogen (H2) and nitrogen (N2). Autotrophy-the ability to fix carbon such as CO2 is present in all domains of life but photosynthesis alone is not keeping up with anthropogenic CO2 output. One strategy is to curtail the gaseous atmospheric release by developing waste and syngas conversion technologies. Historically microorganisms have contributed to major, albeit slow, atmospheric composition changes. The current status and future potential of anaerobic gas-fermenting bacteria with special focus on acetogens are the focus of this review.
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Affiliation(s)
| | - Ching Leang
- LanzaTech, Inc., 8045 Lamon Ave, Suite 400, Skokie, IL USA
| | - Alex Juminaga
- LanzaTech, Inc., 8045 Lamon Ave, Suite 400, Skokie, IL USA
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Guha TK, Hausner G. Insertion of Group II Intron-Based Ribozyme Switches into Homing Endonuclease Genes. Methods Mol Biol 2017; 1498:135-152. [PMID: 27709573 DOI: 10.1007/978-1-4939-6472-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fungal mitochondrial genomes act as "reservoirs" for homing endonucleases. These enzymes with their DNA site-specific cleavage activities are attractive tools for genome editing, targeted mutagenesis and gene therapy applications. Herein, we present strategies where homing endonuclease open reading frames (HEases ORFs) are interrupted with group II intron sequences. The ultimate goal is to achieve in vivo expression of HEases that can be regulated by manipulating the splicing efficiency of the HEase ORF-embedded group II introns. That addition of exogenous magnesium chloride (MgCl2) appears to stimulate splicing of nonnative group II introns in Escherichia coli and the addition of cobalt chloride (CoCl2) to the growth medium antagonizes the expression of HEase activity (i.e., splicing). Group II introns are potentially autocatalytic self-splicing elements and thus can be used as molecular switches that allow for temporal regulated HEase expression. This should be useful in precision genome engineering, mutagenesis, and minimizing off-target activities.
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Affiliation(s)
- Tuhin Kumar Guha
- Department of Microbiology, 401 University of Manitoba, Buller Building 213, Winnipeg, MB, Canada, R3T 2N2
| | - Georg Hausner
- Department of Microbiology, 401 University of Manitoba, Buller Building 213, Winnipeg, MB, Canada, R3T 2N2.
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67
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Menéndez-Arias L, Sebastián-Martín A, Álvarez M. Viral reverse transcriptases. Virus Res 2016; 234:153-176. [PMID: 28043823 DOI: 10.1016/j.virusres.2016.12.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/19/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
Reverse transcriptases (RTs) play a major role in the replication of Retroviridae, Metaviridae, Pseudoviridae, Hepadnaviridae and Caulimoviridae. RTs are enzymes that are able to synthesize DNA using RNA or DNA as templates (DNA polymerase activity), and degrade RNA when forming RNA/DNA hybrids (ribonuclease H activity). In retroviruses and LTR retrotransposons (Metaviridae and Pseudoviridae), the coordinated action of both enzymatic activities converts single-stranded RNA into a double-stranded DNA that is flanked by identical sequences known as long terminal repeats (LTRs). RTs of retroviruses and LTR retrotransposons are active as monomers (e.g. murine leukemia virus RT), homodimers (e.g. Ty3 RT) or heterodimers (e.g. human immunodeficiency virus type 1 (HIV-1) RT). RTs lack proofreading activity and display high intrinsic error rates. Besides, high recombination rates observed in retroviruses are promoted by poor processivity that causes template switching, a hallmark of reverse transcription. HIV-1 RT inhibitors acting on its polymerase activity constitute the backbone of current antiretroviral therapies, although novel drugs, including ribonuclease H inhibitors, are still necessary to fight HIV infections. In Hepadnaviridae and Caulimoviridae, reverse transcription leads to the formation of nicked circular DNAs that will be converted into episomal DNA in the host cell nucleus. Structural and biochemical information on their polymerases is limited, although several drugs inhibiting HIV-1 RT are known to be effective against the human hepatitis B virus polymerase. In this review, we summarize current knowledge on reverse transcription in the five virus families and discuss available biochemical and structural information on RTs, including their biosynthesis, enzymatic activities, and potential inhibition.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Alba Sebastián-Martín
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mar Álvarez
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
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Krishnamurthy M, Moore RT, Rajamani S, Panchal RG. Bacterial genome engineering and synthetic biology: combating pathogens. BMC Microbiol 2016; 16:258. [PMID: 27814687 PMCID: PMC5097395 DOI: 10.1186/s12866-016-0876-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of MDR pathogenic bacteria. According to recent reports by the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC), there is an unprecedented increase in the occurrence of MDR infections worldwide. The rise in these infections has generated an economic strain worldwide, prompting the WHO to endorse a global action plan to improve awareness and understanding of antimicrobial resistance. This health crisis necessitates an immediate action to target the underlying mechanisms of drug resistance in bacteria. RESEARCH The advent of new bacterial genome engineering and synthetic biology (SB) tools is providing promising diagnostic and treatment plans to monitor and treat widespread recalcitrant bacterial infections. Key advances in genetic engineering approaches can successfully aid in targeting and editing pathogenic bacterial genomes for understanding and mitigating drug resistance mechanisms. In this review, we discuss the application of specific genome engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats (CRISPR), and bacterial cell-cell signaling mechanisms for pathogen targeting. The utility of these tools in developing antibacterial strategies such as novel antibiotic production, phage therapy, diagnostics and vaccine production to name a few, are also highlighted. CONCLUSIONS The prevalent use of antibiotics and the spread of MDR bacteria raise the prospect of a post-antibiotic era, which underscores the need for developing novel therapeutics to target MDR pathogens. The development of enabling SB technologies offers promising solutions to deliver safe and effective antibacterial therapies.
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Affiliation(s)
- Malathy Krishnamurthy
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Richard T. Moore
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Sathish Rajamani
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
| | - Rekha G. Panchal
- Department of Target Discovery and Experimental Microbiology, Division of Molecular and Translational Sciences, U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702 USA
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69
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Molina-Sánchez MD, García-Rodríguez FM, Toro N. Functionality of In vitro Reconstituted Group II Intron RmInt1-Derived Ribonucleoprotein Particles. Front Mol Biosci 2016; 3:58. [PMID: 27730127 PMCID: PMC5037169 DOI: 10.3389/fmolb.2016.00058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/12/2016] [Indexed: 01/22/2023] Open
Abstract
The functional unit of mobile group II introns is a ribonucleoprotein particle (RNP) consisting of the intron-encoded protein (IEP) and the excised intron RNA. The IEP has reverse transcriptase activity but also promotes RNA splicing, and the RNA-protein complex triggers site-specific DNA insertion by reverse splicing, in a process called retrohoming. In vitro reconstituted ribonucleoprotein complexes from the Lactococcus lactis group II intron Ll.LtrB, which produce a double strand break, have recently been studied as a means of developing group II intron-based gene targeting methods for higher organisms. The Sinorhizobium meliloti group II intron RmInt1 is an efficient mobile retroelement, the dispersal of which appears to be linked to transient single-stranded DNA during replication. The RmInt1IEP lacks the endonuclease domain (En) and cannot cut the bottom strand to generate the 3' end to initiate reverse transcription. We used an Escherichia coli expression system to produce soluble and active RmInt1 IEP and reconstituted RNPs with purified components in vitro. The RNPs generated were functional and reverse-spliced into a single-stranded DNA target. This work constitutes the starting point for the use of group II introns lacking DNA endonuclease domain-derived RNPs for highly specific gene targeting methods.
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Affiliation(s)
- Maria D Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Fernando M García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
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70
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Bilto IM, Hausner G. The diversity of mtDNA rns introns among strains of Ophiostoma piliferum, Ophiostoma pluriannulatum and related species. SPRINGERPLUS 2016; 5:1408. [PMID: 27610327 PMCID: PMC4995192 DOI: 10.1186/s40064-016-3076-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/15/2016] [Indexed: 02/08/2023]
Abstract
Background Based on previous studies, it was suspected that the mitochondrial rns gene within the Ophiostomatales is rich in introns. This study focused on a collection of strains representing Ophiostoma piliferum, Ophiostoma pluriannulatum and related species that cause blue-stain; these fungi colonize the sapwood of trees and impart a dark stain. This reduces the value of the lumber. The goal was to examine the mtDNA rns intron landscape for these important blue stain fungi in order to facilitate future annotation of mitochondrial genomes (mtDNA) and to potentially identify mtDNA introns that can encode homing endonucleases which may have applications in biotechnology. Results Comparative sequence analysis identified five intron insertion sites among the ophiostomatoid fungi examined. Positions mS379 and mS952 harbor group II introns, the mS379 intron encodes a reverse transcriptase, and the mS952 intron encodes a potential homing endonuclease. Positions mS569, mS1224, and mS1247 have group I introns inserted and these encode intact or eroded homing endonuclease open reading frames (ORF). Phylogenetic analysis of the intron ORFs showed that they can be found in the same insertion site in closely and distantly related species. Conclusions Based on the molecular markers examined (rDNA internal transcribed spacers and rns introns), strains representing O. pilifera, O. pluriannulatum and Ophiostoma novae-zelandiae could not be resolved. Phylogenetic studies suggest that introns are gained and lost and that horizontal transfer could explain the presence of related intron in distantly related fungi. With regard to the mS379 group II intron, this study shows that mitochondrial group II introns and their reverse transcriptases may also follow the life cycle previously proposed for group I introns and their homing endonucleases. This consists of intron invasion, decay of intron ORF, loss of intron, and possible reinvasion. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-3076-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iman M Bilto
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
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71
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Nisa-Martínez R, Molina-Sánchez MD, Toro N. Host Factors Influencing the Retrohoming Pathway of Group II Intron RmInt1, Which Has an Intron-Encoded Protein Naturally Devoid of Endonuclease Activity. PLoS One 2016; 11:e0162275. [PMID: 27588750 PMCID: PMC5010178 DOI: 10.1371/journal.pone.0162275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 08/21/2016] [Indexed: 11/21/2022] Open
Abstract
Bacterial group II introns are self-splicing catalytic RNAs and mobile retroelements that have an open reading frame encoding an intron-encoded protein (IEP) with reverse transcriptase (RT) and RNA splicing or maturase activity. Some IEPs carry a DNA endonuclease (En) domain, which is required to cleave the bottom strand downstream from the intron-insertion site for target DNA-primed reverse transcription (TPRT) of the inserted intron RNA. Host factors complete the insertion of the intron. By contrast, the major retrohoming pathway of introns with IEPs naturally lacking endonuclease activity, like the Sinorhizobium meliloti intron RmInt1, is thought to involve insertion of the intron RNA into the template for lagging strand DNA synthesis ahead of the replication fork, with possible use of the nascent strand to prime reverse transcription of the intron RNA. The host factors influencing the retrohoming pathway of such introns have not yet been described. Here, we identify key candidates likely to be involved in early and late steps of RmInt1 retrohoming. Some of these host factors are common to En+ group II intron retrohoming, but some have different functions. Our results also suggest that the retrohoming process of RmInt1 may be less dependent on the intracellular free Mg2+ concentration than those of other group II introns.
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Affiliation(s)
- Rafael Nisa-Martínez
- Structure, Dynamics and Function of Rhizobacterial Genomes, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Calle Profesor Albareda 1, 18008, Granada, Spain
| | - María Dolores Molina-Sánchez
- Structure, Dynamics and Function of Rhizobacterial Genomes, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Calle Profesor Albareda 1, 18008, Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Calle Profesor Albareda 1, 18008, Granada, Spain
- * E-mail:
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Zumkeller SM, Knoop V, Knie N. Convergent Evolution of Fern-Specific Mitochondrial Group II Intron atp1i361g2 and Its Ancient Source Paralogue rps3i249g2 and Independent Losses of Intron and RNA Editing among Pteridaceae. Genome Biol Evol 2016; 8:2505-19. [PMID: 27492234 PMCID: PMC5010907 DOI: 10.1093/gbe/evw173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2016] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial intron patterns are highly divergent between the major land plant clades. An intron in the atp1 gene, atp1i361g2, is an example for a group II intron specific to monilophytes (ferns). Here, we report that atp1i361g2 is lost independently at least 4 times in the fern family Pteridaceae. Such plant organelle intron losses have previously been found to be accompanied by loss of RNA editing sites in the flanking exon regions as a consequence of genomic recombination of mature cDNA. Instead, we now observe that RNA editing events in both directions of pyrimidine exchange (C-to-U and U-to-C) are retained in atp1 exons after loss of the intron in Pteris argyraea/biaurita and in Actiniopteris and Onychium We find that atp1i361g2 has significant similarity with intron rps3i249g2 present in lycophytes and gymnosperms, which we now also find highly conserved in ferns. We conclude that atp1i361g2 may have originated from the more ancestral rps3i249g2 paralogue by a reverse splicing copy event early in the evolution of monilophytes. Secondary structure elements of the two introns, most characteristically their domains III, show strikingly convergent evolution in the monilophytes. Moreover, the intron paralogue rps3i249g2 reveals relaxed evolution in taxa where the atp1i361g2 paralogue is lost. Our findings may reflect convergent evolution of the two related mitochondrial introns exerted by co-evolution with an intron-binding protein simultaneously acting on the two paralogues.
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Affiliation(s)
- Simon Maria Zumkeller
- Abteilung Molekulare Evolution, IZMB-Institut Für Zelluläre Und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, IZMB-Institut Für Zelluläre Und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Nils Knie
- Abteilung Molekulare Evolution, IZMB-Institut Für Zelluläre Und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115 Bonn, Germany
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73
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Singh J, Sikand K, Conrad H, Will CL, Komar AA, Shukla GC. U6atac snRNA stem-loop interacts with U12 p65 RNA binding protein and is functionally interchangeable with the U12 apical stem-loop III. Sci Rep 2016; 6:31393. [PMID: 27510544 PMCID: PMC4980772 DOI: 10.1038/srep31393] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 06/06/2016] [Indexed: 12/11/2022] Open
Abstract
Formation of catalytic core of the U12-dependent spliceosome involves U6atac and U12 interaction with the 5′ splice site and branch site regions of a U12-dependent intron, respectively. Beyond the formation of intermolecular helix I region between U6atac and U12 snRNAs, several other regions within these RNA molecules are predicted to form stem-loop structures. Our previous work demonstrated that the 3′ stem-loop region of U6atac snRNA contains a U12-dependent spliceosome-specific targeting activity. Here, we show a detailed structure-function analysis and requirement of a substructure of U6atac 3′ stem-loop in U12-dependent in vivo splicing. We show that the C-terminal RNA recognition motif of p65, a U12 snRNA binding protein, also binds to the distal 3′ stem-loop of U6atac. By using a binary splice site mutation suppressor assay we demonstrate that p65 protein-binding apical stem-loop of U12 snRNA can be replaced by this U6atac distal 3′ stem-loop. Furthermore, we tested the compatibility of the U6atac 3′ end from phylogenetically distant species in a human U6atac background, to establish the evolutionary relatedness of these structures and in vivo function. In summary, we demonstrate that RNA-RNA and RNA-protein interactions in the minor spliceosome are highly plastic as compared to the major spliceosome.
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Affiliation(s)
- Jagjit Singh
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Kavleen Sikand
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Heike Conrad
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Girish C Shukla
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.,Department of Biological Sciences, Cleveland State University, Cleveland, OH 44115, USA
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Cuenca A, Ross TG, Graham SW, Barrett CF, Davis JI, Seberg O, Petersen G. Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome. Genome Biol Evol 2016; 8:2176-89. [PMID: 27435795 PMCID: PMC4987113 DOI: 10.1093/gbe/evw148] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 12/23/2022] Open
Abstract
Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.
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Affiliation(s)
- Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - T Gregory Ross
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W Graham
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig F Barrett
- Department of Biological Sciences, California State University, Los Angeles, California
| | - Jerrold I Davis
- L.H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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75
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Slijepcevic P. Mechanisms of the Evolutionary Chromosome Plasticity: Integrating the 'Centromere-from-Telomere' Hypothesis with Telomere Length Regulation. Cytogenet Genome Res 2016; 148:268-78. [PMID: 27398800 DOI: 10.1159/000447415] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
The 'centromere-from-telomere' hypothesis proposed by Villasante et al. [2007a] aims to explain the evolutionary origin of the eukaryotic chromosome. The hypothesis is based on the notion that the process of eukaryogenesis was initiated by adaptive responses of the symbiont eubacterium and its archaeal host to their new conditions. The adaptive responses included fragmentation of the circular genome of the host into multiple linear fragments with free DNA ends. The action of mobile genetic elements stabilized the free DNA ends resulting in the formation of proto-telomeres. Sequences next to the proto-telomeres, the subtelomeric sequences, were immediately targeted as the new cargo by the tubulin-based cytoskeleton, thus becoming proto-centromeres. A period of genomic instability followed. Eventually, functioning centromeres and telomeres emerged heralding the arrival of the eukaryotic chromosome in the evolution. This paper expands the 'centromere-from-telomere' hypothesis by integrating it with 2 sets of data: chromosome-specific telomere length distribution and chromomere size gradient. The integration adds a new dimension to the hypothesis but also provides an insight into the mechanisms of chromosome plasticity underlying karyotype evolution.
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Affiliation(s)
- Predrag Slijepcevic
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
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76
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Garg SG, Martin WF. Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor. Genome Biol Evol 2016; 8:1950-70. [PMID: 27345956 PMCID: PMC5390555 DOI: 10.1093/gbe/evw136] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2016] [Indexed: 02/07/2023] Open
Abstract
Theories for the origin of sex traditionally start with an asexual mitosing cell and add recombination, thereby deriving meiosis from mitosis. Though sex was clearly present in the eukaryote common ancestor, the order of events linking the origin of sex and the origin of mitosis is unknown. Here, we present an evolutionary inference for the origin of sex starting with a bacterial ancestor of mitochondria in the cytosol of its archaeal host. We posit that symbiotic association led to the origin of mitochondria and gene transfer to host's genome, generating a nucleus and a dedicated translational compartment, the eukaryotic cytosol, in which-by virtue of mitochondria-metabolic energy was not limiting. Spontaneous protein aggregation (monomer polymerization) and Adenosine Tri-phosphate (ATP)-dependent macromolecular movement in the cytosol thereby became selectable, giving rise to continuous microtubule-dependent chromosome separation (reduction division). We propose that eukaryotic chromosome division arose in a filamentous, syncytial, multinucleated ancestor, in which nuclei with insufficient chromosome numbers could complement each other through mRNA in the cytosol and generate new chromosome combinations through karyogamy. A syncytial (or coenocytic, a synonym) eukaryote ancestor, or Coeca, would account for the observation that the process of eukaryotic chromosome separation is more conserved than the process of eukaryotic cell division. The first progeny of such a syncytial ancestor were likely equivalent to meiospores, released into the environment by the host's vesicle secretion machinery. The natural ability of archaea (the host) to fuse and recombine brought forth reciprocal recombination among fusing (syngamy and karyogamy) progeny-sex-in an ancestrally meiotic cell cycle, from which the simpler haploid and diploid mitotic cell cycles arose. The origin of eukaryotes was the origin of vertical lineage inheritance, and sex was required to keep vertically evolving lineages viable by rescuing the incipient eukaryotic lineage from Muller's ratchet. The origin of mitochondria was, in this view, the decisive incident that precipitated symbiosis-specific cell biological problems, the solutions to which were the salient features that distinguish eukaryotes from prokaryotes: A nuclear membrane, energetically affordable ATP-dependent protein-protein interactions in the cytosol, and a cell cycle involving reduction division and reciprocal recombination (sex).
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Affiliation(s)
- Sriram G Garg
- Institute of Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine Universität Düsseldorf, Düsseldorf 40225, Germany
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Suzuki S, Hirakawa Y, Kofuji R, Sugita M, Ishida KI. Plastid genome sequences of Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia reveal remarkable structural conservation among chlorarachniophyte species. JOURNAL OF PLANT RESEARCH 2016; 129:581-590. [PMID: 26920842 DOI: 10.1007/s10265-016-0804-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
Chlorarachniophyte algae have complex plastids acquired by the uptake of a green algal endosymbiont, and this event is called secondary endosymbiosis. Interestingly, the plastids possess a relict endosymbiont nucleus, referred to as the nucleomorph, in the intermembrane space, and the nucleomorphs contain an extremely reduced and compacted genome in comparison with green algal nuclear genomes. Therefore, chlorarachniophyte plastids consist of two endosymbiotically derived genomes, i.e., the plastid and nucleomorph genomes. To date, complete nucleomorph genomes have been sequenced in four different species, whereas plastid genomes have been reported in only two species in chlorarachniophytes. To gain further insight into the evolution of endosymbiotic genomes in chlorarachniophytes, we newly sequenced the plastid genomes of three species, Gymnochlora stellata, Lotharella vacuolata, and Partenskyella glossopodia. Our findings reveal that chlorarachniophyte plastid genomes are highly conserved in size, gene content, and gene order among species, but their nucleomorph genomes are divergent in such features. Accordingly, the current architecture of the plastid genomes of chlorarachniophytes evolved in a common ancestor, and changed very little during their subsequent diversification. Furthermore, our phylogenetic analyses using multiple plastid genes suggest that chlorarachniophyte plastids are derived from a green algal lineage that is closely related to Bryopsidales in the Ulvophyceae group.
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Affiliation(s)
- Shigekatsu Suzuki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Rumiko Kofuji
- Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Aichi, Japan
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan.
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78
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Intron Derived Size Polymorphism in the Mitochondrial Genomes of Closely Related Chrysoporthe Species. PLoS One 2016; 11:e0156104. [PMID: 27272523 PMCID: PMC4894602 DOI: 10.1371/journal.pone.0156104] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/08/2016] [Indexed: 01/21/2023] Open
Abstract
In this study, the complete mitochondrial (mt) genomes of Chrysoporthe austroafricana (190,834 bp), C. cubensis (89,084 bp) and C. deuterocubensis (124,412 bp) were determined. Additionally, the mitochondrial genome of another member of the Cryphonectriaceae, namely Cryphonectria parasitica (158,902 bp), was retrieved and annotated for comparative purposes. These genomes showed high levels of synteny, especially in regions including genes involved in oxidative phosphorylation and electron transfer, unique open reading frames (uORFs), ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as intron positions. Comparative analyses revealed signatures of duplication events, intron number and length variation, and varying intronic ORFs which highlighted the genetic diversity of mt genomes among the Cryphonectriaceae. These mt genomes showed remarkable size polymorphism. The size polymorphism in the mt genomes of these closely related Chrysoporthe species was attributed to the varying number and length of introns, coding sequences and to a lesser extent, intergenic sequences. Compared to publicly available fungal mt genomes, the C. austroafricana mt genome is the second largest in the Ascomycetes thus far.
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79
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Zhao C, Pyle AM. Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution. Nat Struct Mol Biol 2016; 23:558-65. [PMID: 27136328 PMCID: PMC4899126 DOI: 10.1038/nsmb.3224] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/06/2016] [Indexed: 12/17/2022]
Abstract
Group II introns are self-splicing ribozymes that are essential in many organisms, and they have been hypothesized to share a common evolutionary ancestor with the spliceosome. Although structural similarity of RNA components supports this connection, it is of interest to determine whether associated protein factors also share an evolutionary heritage. Here we present the crystal structures of reverse transcriptase (RT) domains from two group II intron-encoded proteins (maturases) from Roseburia intestinalis and Eubacterium rectale, obtained at 1.2-Å and 2.1-Å resolution, respectively. These domains are more similar in architecture to the spliceosomal Prp8 RT-like domain than to any other RTs, and they share substantial similarity with flaviviral RNA polymerases. The RT domain itself is sufficient for binding intron RNA with high affinity and specificity, and it is contained within an active RT enzyme. These studies provide a foundation for understanding structure-function relationships within group II intron-maturase complexes.
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Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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80
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Sasikumar P, Paul E, Gomathi S, Abhishek A, Sasikumar S, Selvam GS. Mobile group II intron based gene targeting in Lactobacillus plantarum WCFS1. J Basic Microbiol 2016; 56:1107-1116. [PMID: 27119622 DOI: 10.1002/jobm.201500746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/11/2016] [Indexed: 11/09/2022]
Abstract
The usage of recombinant lactic acid bacteria for delivery of therapeutic proteins to the mucosa has been emerging. In the present study, an attempt was made to engineer a thyA mutant of Lactobacillus plantarum (L. plantarum) using lactococcal group II intron Ll.LtrB for the development of biologically contained recombinant L. plantarum for prevention of calcium oxalate stone disease. The 3 kb Ll.LtrB intron donor cassettes from the source vector pACD4C was PCR amplified, ligated into pSIP series of lactobacillus vector pLp_3050sAmyA, yielding a novel vector pLpACD4C (8.6 kb). The quantitative real-time PCR experiment shows 94-fold increased expression of Ll.LtrB intron and 14-fold increased expression of ltrA gene in recombinant L. plantarum containing pLpACD4C. In order to target the thyA gene, the potential intron RNA binding sites in the thyA gene of L. plantarum was predicted with help of computer algorithm. The insertion location 188|189s of thyA gene (lowest E-0.134) was chosen and the wild type intron Ll.LtrB was PCR modified, yielding a retargeted intron of pLpACDthyA. The retargeted intron was expressed by using induction peptide (sppIP), subsequently the integration of intron in thyA gene was identified by PCR screening and finally ThyA- mutant of L. plantarum (ThyA18) was detected. In vitro growth curve result showed that in the absence of thymidine, colony forming units of mutant ThyA18 was decreased, whereas high thymidine concentration (10 μM) supported the growth of the culture until saturation. In conclusion, ThyA- mutant of L. plantarum (ThyA18) constructed in this study will be used as a biologically contained recombinant probiotic to deliver oxalate decarboxylase into the lumen for treatment of hyperoxaluria and calcium oxalate stone deposition.
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Affiliation(s)
- Ponnusamy Sasikumar
- Department of Biochemistry, Centre for Advanced Studies in Functional Genomics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | - Eldho Paul
- Department of Biochemistry, Centre for Advanced Studies in Functional Genomics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | - Sivasamy Gomathi
- Department of Biochemistry, Centre for Advanced Studies in Functional Genomics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | - Albert Abhishek
- Department of Biochemistry, Centre for Advanced Studies in Functional Genomics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | - Sundaresan Sasikumar
- Department of Biochemistry, Centre for Advanced Studies in Functional Genomics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India
| | - Govindan Sadasivam Selvam
- Department of Biochemistry, Centre for Advanced Studies in Functional Genomics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625 021, India.
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81
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Vicente CSL, Nascimento FX, Ikuyo Y, Cock PJA, Mota M, Hasegawa K. The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus. BMC Genomics 2016; 17:301. [PMID: 27108223 PMCID: PMC4841953 DOI: 10.1186/s12864-016-2626-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/16/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pine wilt disease (PWD) is a worldwide threat to pine forests, and is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus. Bacteria are known to be associated with PWN and may have an important role in PWD. Serratia sp. LCN16 is a PWN-associated bacterium, highly resistant to oxidative stress in vitro, and which beneficially contributes to the PWN survival under these conditions. Oxidative stress is generated as a part of the basal defense mechanism used by plants to combat pathogenic invasion. Here, we studied the biology of Serratia sp. LCN16 through genome analyses, and further investigated, using reverse genetics, the role of two genes directly involved in the neutralization of H2O2, namely the H2O2 transcriptional factor oxyR; and the H2O2-targeting enzyme, catalase katA. RESULTS Serratia sp. LCN16 is phylogenetically most closely related to the phytosphere group of Serratia, which includes S. proteamaculans, S. grimessi and S. liquefaciens. Likewise, Serratia sp. LCN16 shares many features with endophytes (plant-associated bacteria), such as genes coding for plant polymer degrading enzymes, iron uptake/transport, siderophore and phytohormone synthesis, aromatic compound degradation and detoxification enzymes. OxyR and KatA are directly involved in the high tolerance to H2O2 of Serratia sp. LCN16. Under oxidative stress, Serratia sp. LCN16 expresses katA independently of OxyR in contrast with katG which is under positive regulation of OxyR. Serratia sp. LCN16 mutants for oxyR (oxyR::int(614)) and katA (katA::int(808)) were sensitive to H2O2 in relation with wild-type, and both failed to protect the PWN from H2O2-stress exposure. Moreover, both mutants showed different phenotypes in terms of biofilm production and swimming/swarming behaviors. CONCLUSIONS This study provides new insights into the biology of PWN-associated bacteria Serratia sp. LCN16 and its extreme resistance to oxidative stress conditions, encouraging further research on the potential role of this bacterium in interaction with PWN in planta environment.
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Affiliation(s)
- Claudia S L Vicente
- NemaLab/ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554, Évora, Portugal.,Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto, Kasugai, Aichi, 487-8501, Japan
| | - Francisco X Nascimento
- NemaLab/ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554, Évora, Portugal
| | - Yoriko Ikuyo
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto, Kasugai, Aichi, 487-8501, Japan
| | - Peter J A Cock
- Information and Computational Sciences group (PJAC), The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Manuel Mota
- NemaLab/ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Ap. 94, 7002-554, Évora, Portugal.,Departamento de Ciências da Vida, Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal
| | - Koichi Hasegawa
- Department of Environmental Biology, College of Bioscience & Biotechnology, Chubu University, 1200 Matsumoto, Kasugai, Aichi, 487-8501, Japan.
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82
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Abstract
Reverse transcriptases (RTs) are usually thought of as eukaryotic enzymes, but they are also present in bacteria and likely originated in bacteria and migrated to eukaryotes. Only three types of bacterial retroelements have been substantially characterized: group II introns, diversity-generating retroelements, and retrons. Recent work, however, has identified a myriad of uncharacterized RTs and RT-related sequences in bacterial genomes, which exhibit great sequence diversity and a range of domain structures. Apart from group II introns, none of these putative RTs show evidence of active retromobility. Instead, available information suggests that they are involved in useful processes, sometimes related to phages or phage resistance. This article reviews our knowledge of both characterized and uncharacterized RTs in bacteria. The range of their sequences and genomic contexts promises the discovery of new biochemical reactions and biological phenomena.
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83
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Abstract
This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. Their profound similarities include splicing chemistry extending to RNA catalysis, reaction stereochemistry, and the position of two divalent metals that perform catalysis at the RNA active site. There are also sequence and structural similarities between group II introns and the spliceosome's small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns.
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84
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Silas S, Mohr G, Sidote DJ, Markham LM, Sanchez-Amat A, Bhaya D, Lambowitz AM, Fire AZ. Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein. Science 2016; 351:aad4234. [PMID: 26917774 DOI: 10.1126/science.aad4234] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CRISPR systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats in type I and II CRISPR systems by the acquisition of short segments of DNA (spacers) from invasive elements. In several type III CRISPR systems, Cas1 is naturally fused to a reverse transcriptase (RT). In the marine bacterium Marinomonas mediterranea (MMB-1), we showed that a RT-Cas1 fusion protein enables the acquisition of RNA spacers in vivo in a RT-dependent manner. In vitro, the MMB-1 RT-Cas1 and Cas2 proteins catalyze the ligation of RNA segments into the CRISPR array, which is followed by reverse transcription. These observations outline a host-mediated mechanism for reverse information flow from RNA to DNA.
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Affiliation(s)
- Sukrit Silas
- Department of Pathology, Stanford University, Stanford CA 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford CA 94305, USA
| | - Georg Mohr
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, USA
| | - David J Sidote
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, USA
| | - Laura M Markham
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, USA
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, Universidad de Murcia, Murcia 30100, Spain
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford CA 94305, USA
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford CA 94305, USA
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85
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Multiple splicing pathways of group II trans-splicing introns in wheat mitochondria. Mitochondrion 2016; 28:23-32. [PMID: 26970277 DOI: 10.1016/j.mito.2016.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/06/2016] [Accepted: 03/08/2016] [Indexed: 11/23/2022]
Abstract
Trans-splicing of discontinuous introns in plant mitochondria requires the assembly of independently-transcribed precursor RNAs into splicing-competent structures, and they are expected to be excised as Y-branched molecules ("broken lariats") because these introns belong to the group II ribozyme family. We now demonstrate that this is just one of several trans-splicing pathways for wheat mitochondrial nad1 intron 4 and nad5 intron 2; they also use a hydrolytic pathway and the liberated 5'-half-intron linear molecules are unexpectedly abundant in the RNA population. We also observe a third productive splicing pathway for nad5 intron 2 that yields full-length excised introns in which the termini are joined in vivo and possess non-encoded nucleotides. In the case of trans-splicing nad1 intron 1, which has a weakly-structured and poorly-conserved core sequence, excision appears to be solely through a hydrolytic pathway. When wheat embryos are germinated in the cold rather than at room temperature, an increased complexity in trans-splicing products is seen for nad1 intron 4, suggesting that there can be environmental effects on the RNA folding of bipartite introns. Our observations provide insights into intron evolution and the complexity of RNA processing events in plant mitochondria.
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86
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Guha TK, Hausner G. Using Group II Introns for Attenuating the In Vitro and In Vivo Expression of a Homing Endonuclease. PLoS One 2016; 11:e0150097. [PMID: 26909494 PMCID: PMC4801052 DOI: 10.1371/journal.pone.0150097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/09/2016] [Indexed: 01/09/2023] Open
Abstract
In Chaetomium thermophilum (DSM 1495) within the mitochondrial DNA (mtDNA) small ribosomal subunit (rns) gene a group IIA1 intron interrupts an open reading frame (ORF) encoded within a group I intron (mS1247). This arrangement offers the opportunity to examine if the nested group II intron could be utilized as a regulatory element for the expression of the homing endonuclease (HEase). Constructs were generated where the codon-optimized ORF was interrupted with either the native group IIA1 intron or a group IIB type intron. This study showed that the expression of the HEase (in vivo) in Escherichia coli can be regulated by manipulating the splicing efficiency of the HEase ORF-embedded group II introns. Exogenous magnesium chloride (MgCl2) stimulated the expression of a functional HEase but the addition of cobalt chloride (CoCl2) to growth media antagonized the expression of HEase activity. Ultimately the ability to attenuate HEase activity might be useful in precision genome engineering, minimizing off target activities, or where pathways have to be altered during a specific growth phase.
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Affiliation(s)
- Tuhin Kumar Guha
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
- * E-mail:
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87
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McNeil BA, Semper C, Zimmerly S. Group II introns: versatile ribozymes and retroelements. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:341-55. [PMID: 26876278 DOI: 10.1002/wrna.1339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/10/2015] [Accepted: 12/22/2015] [Indexed: 01/10/2023]
Abstract
Group II introns are catalytic RNAs (ribozymes) and retroelements found in the genomes of bacteria, archaebacteria, and organelles of some eukaryotes. The prototypical retroelement form consists of a structurally conserved RNA and a multidomain reverse transcriptase protein, which interact with each other to mediate splicing and mobility reactions. A wealth of biochemical, cross-linking, and X-ray crystal structure studies have helped to reveal how the two components cooperate to carry out the splicing and mobility reactions. In addition to the standard retroelement form, group II introns have evolved into derivative forms by either losing specific splicing or mobility characteristics, or becoming functionally specialized. Of particular interest are the eukaryotic derivatives-the spliceosome, spliceosomal introns, and non-LTR retroelements-which together make up approximately half of the human genome. On a practical level, the properties of group II introns have been exploited to develop group II intron-based biotechnological tools. WIREs RNA 2016, 7:341-355. doi: 10.1002/wrna.1339 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bonnie A McNeil
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Cameron Semper
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Steven Zimmerly
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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88
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Xiu Z, Sun F, Shen Y, Zhang X, Jiang R, Bonnard G, Zhang J, Tan BC. EMPTY PERICARP16 is required for mitochondrial nad2 intron 4 cis-splicing, complex I assembly and seed development in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:507-19. [PMID: 26764126 DOI: 10.1111/tpj.13122] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 01/05/2016] [Indexed: 05/02/2023]
Abstract
In higher plants, chloroplast and mitochondrial transcripts contain a number of group II introns that need to be precisely spliced before translation into functional proteins. However, the mechanism of splicing and the factors involved in this process are not well understood. By analysing a seed mutant in maize, we report here the identification of Empty pericarp16 (Emp16) that is required for splicing of nad2 intron 4 in mitochondria. Disruption of Emp16 function causes developmental arrest in the embryo and endosperm, giving rise to an empty pericarp phenotype in maize. Differentiation of the basal endosperm transfer layer cells is severely affected. Molecular cloning indicates that Emp16 encodes a P-type pentatricopeptide repeat (PPR) protein with 11 PPR motifs and is localized in the mitochondrion. Transcript analysis revealed that mitochondrial nad2 intron 4 splicing is abolished in the emp16 mutants, leading to severely reduced assembly and activity of complex I. In response, the mutant dramatically increases the accumulation of mitochondrial complex III and the expression of alternative oxidase AOX2. These results imply that EMP16 is specifically required for mitochondrial nad2 intron 4 cis-splicing and is essential for complex I assembly and embryogenesis and development endosperm in maize.
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Affiliation(s)
- Zhihui Xiu
- State Key Lab of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, NT, Hong Kong, China
| | - Feng Sun
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Yun Shen
- State Key Lab of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, NT, Hong Kong, China
| | - Xiaoyan Zhang
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Ruicheng Jiang
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Géraldine Bonnard
- Institut de Biologie Moléculaire des Plantes CNRS, Associé à l'Université de Strasbourg, 12 Rue du Général Zimmer, 67084, Strasbourg, France
| | - Jianhua Zhang
- State Key Lab of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, NT, Hong Kong, China
| | - Bao-Cai Tan
- Key Lab of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
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89
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Lin CL, Taggart AJ, Lim KH, Cygan KJ, Ferraris L, Creton R, Huang YT, Fairbrother WG. RNA structure replaces the need for U2AF2 in splicing. Genome Res 2016; 26:12-23. [PMID: 26566657 PMCID: PMC4691745 DOI: 10.1101/gr.181008.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 11/10/2015] [Indexed: 01/21/2023]
Abstract
RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.
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Affiliation(s)
- Chien-Ling Lin
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Allison J Taggart
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kian Huat Lim
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kamil J Cygan
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
| | - Luciana Ferraris
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Robbert Creton
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Yen-Tsung Huang
- Departments of Epidemiology and Biostatistics, Brown University, Providence, Rhode Island 02912, USA
| | - William G Fairbrother
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
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90
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Martin WF, Garg S, Zimorski V. Endosymbiotic theories for eukaryote origin. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140330. [PMID: 26323761 PMCID: PMC4571569 DOI: 10.1098/rstb.2014.0330] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 11/12/2022] Open
Abstract
For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, Universität Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Sriram Garg
- Institute for Molecular Evolution, Universität Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Verena Zimorski
- Institute for Molecular Evolution, Universität Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
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91
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Localization of a bacterial group II intron-encoded protein in human cells. Sci Rep 2015; 5:12716. [PMID: 26244523 PMCID: PMC4525487 DOI: 10.1038/srep12716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/07/2015] [Indexed: 01/06/2023] Open
Abstract
Group II introns are mobile retroelements that self-splice from precursor RNAs to form ribonucleoparticles (RNP), which can invade new specific genomic DNA sites. This specificity can be reprogrammed, for insertion into any desired DNA site, making these introns useful tools for bacterial genetic engineering. However, previous studies have suggested that these elements may function inefficiently in eukaryotes. We investigated the subcellular distribution, in cultured human cells, of the protein encoded by the group II intron RmInt1 (IEP) and several mutants. We created fusions with yellow fluorescent protein (YFP) and with a FLAG epitope. We found that the IEP was localized in the nucleus and nucleolus of the cells. Remarkably, it also accumulated at the periphery of the nuclear matrix. We were also able to identify spliced lariat intron RNA, which co-immunoprecipitated with the IEP, suggesting that functional RmInt1 RNPs can be assembled in cultured human cells.
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92
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Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes. J Mol Evol 2015. [PMID: 26208881 DOI: 10.1007/s00239-015-9688-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The evolution of life from the simplest, original form to complex, intelligent animal life occurred through a number of key innovations. Here we present a new tool to analyze these key innovations by proposing that the process of evolutionary innovation may follow one of three underlying processes, namely a Random Walk, a Critical Path, or a Many Paths process, and in some instances may also constitute a "Pull-up the Ladder" event. Our analysis is based on the occurrence of function in modern biology, rather than specific structure or mechanism. A function in modern biology may be classified in this way either on the basis of its evolution or the basis of its modern mechanism. Characterizing key innovations in this way helps identify the likelihood that an innovation could arise. In this paper, we describe the classification, and methods to classify functional features of modern organisms into these three classes based on the analysis of how a function is implemented in modern biology. We present the application of our categorization to the evolution of eukaryotic gene control. We use this approach to support the argument that there are few, and possibly no basic chemical differences between the functional constituents of the machinery of gene control between eukaryotes, bacteria and archaea. This suggests that the difference between eukaryotes and prokaryotes that allows the former to develop the complex genetic architecture seen in animals and plants is something other than their chemistry. We tentatively identify the difference as a difference in control logic, that prokaryotic genes are by default 'on' and eukaryotic genes are by default 'off.' The Many Paths evolutionary process suggests that, from a 'default off' starting point, the evolution of the genetic complexity of higher eukaryotes is a high probability event.
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93
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Inactivation of group II intron RmInt1 in the Sinorhizobium meliloti genome. Sci Rep 2015; 5:12036. [PMID: 26156864 PMCID: PMC4496777 DOI: 10.1038/srep12036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 06/15/2015] [Indexed: 11/10/2022] Open
Abstract
Group II introns are self-splicing catalytic RNAs that probably originated in bacteria and act as mobile retroelements. The dispersal and dynamics of group II intron spread within a bacterial genome are thought to follow a selection-driven extinction model. Likewise, various studies on the evolution of group II introns have suggested that they are evolving toward an inactive form by fragmentation, with the loss of the intron 3′-terminus, but with some intron fragments remaining and continuing to evolve in the genome. RmInt1 is a mobile group II intron that is widespread in natural populations of Sinorhizobium meliloti, but some strains of this species have no RmInt1 introns. We studied the splicing ability and mobility of the three full-length RmInt1 copies harbored by S. meliloti 1021, and obtained evidence suggesting that specific mutations may lead to the impairment of intron splicing and retrohoming. Our data suggest that the RmInt1 copies in this strain are undergoing a process of inactivation.
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94
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Monat C, Quiroga C, Laroche-Johnston F, Cousineau B. The Ll.LtrB intron from Lactococcus lactis excises as circles in vivo: insights into the group II intron circularization pathway. RNA (NEW YORK, N.Y.) 2015; 21:1286-1293. [PMID: 25956521 PMCID: PMC4478347 DOI: 10.1261/rna.046367.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/31/2015] [Indexed: 06/04/2023]
Abstract
Group II introns are large ribozymes that require the assistance of intron-encoded or free-standing maturases to splice from their pre-mRNAs in vivo. They mainly splice through the classical branching pathway, being released as RNA lariats. However, group II introns can also splice through secondary pathways like hydrolysis and circularization leading to the release of linear and circular introns, respectively. Here, we assessed in vivo splicing of various constructs of the Ll.LtrB group II intron from the Gram-positive bacterium Lactococcus lactis. The study of excised intron junctions revealed, in addition to branched intron lariats, the presence of perfect end-to-end intron circles and alternatively circularized introns. Removal of the branch point A residue prevented Ll.LtrB excision through the branching pathway but did not hinder intron circle formation. Complete intron RNA circles were found associated with the intron-encoded protein LtrA forming nevertheless inactive RNPs. Traces of double-stranded head-to-tail intron DNA junctions were also detected in L. lactis RNA and nucleic acid extracts. Some intron circles and alternatively circularized introns harbored variable number of non-encoded nucleotides at their splice junction. The presence of mRNA fragments at the splice junction of some intron RNA circles provides insights into the group II intron circularization pathway in bacteria.
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Affiliation(s)
- Caroline Monat
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre (MDTC), McGill University, Montréal, Québec, Canada H3A 2B4
| | - Cecilia Quiroga
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre (MDTC), McGill University, Montréal, Québec, Canada H3A 2B4
| | - Felix Laroche-Johnston
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre (MDTC), McGill University, Montréal, Québec, Canada H3A 2B4
| | - Benoit Cousineau
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre (MDTC), McGill University, Montréal, Québec, Canada H3A 2B4
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95
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Abstract
This article describes my early life and the chance events leading to my becoming a microbiologist and then my embarking on a career developing the plasmid biology and genetics of lactococci used in milk fermentations.
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Affiliation(s)
- Larry McKay
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota 55108
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96
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Kamikawa R, Tanifuji G, Kawachi M, Miyashita H, Hashimoto T, Inagaki Y. Plastid genome-based phylogeny pinpointed the origin of the green-colored plastid in the dinoflagellate Lepidodinium chlorophorum. Genome Biol Evol 2015; 7:1133-40. [PMID: 25840416 PMCID: PMC4419806 DOI: 10.1093/gbe/evv060] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Unlike many other photosynthetic dinoflagellates, whose plastids contain a characteristic carotenoid peridinin, members of the genus Lepidodinium are the only known dinoflagellate species possessing green alga-derived plastids. However, the precise origin of Lepidodinium plastids has hitherto remained uncertain. In this study, we completely sequenced the plastid genome of Lepidodinium chlorophorum NIES-1868. Our phylogenetic analyses of 52 plastid-encoded proteins unite L. chlorophorum exclusively with a pedinophyte, Pedinomonas minor, indicating that the green-colored plastids in Lepidodinium spp. were derived from an endosymbiotic pedinophyte or a green alga closely related to pedinophytes. Our genome comparison incorporating the origin of the Lepidodinium plastids strongly suggests that the endosymbiont plastid genome acquired by the ancestral Lepidodinium species has lost genes encoding proteins involved in metabolism and biosynthesis, protein/metabolite transport, and plastid division during the endosymbiosis. We further discuss the commonalities and idiosyncrasies in genome evolution between the L. chlorophorum plastid and other plastids acquired through endosymbiosis of eukaryotic photoautotrophs.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan
| | - Goro Tanifuji
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Masanobu Kawachi
- The National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Hideaki Miyashita
- Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
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97
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Abstract
Present in the genomes of bacteria and eukaryotic organelles, group II introns are an ancient class of ribozymes and retroelements that are believed to have been the ancestors of nuclear pre-mRNA introns. Despite long-standing speculation, there is limited understanding about the actual pathway by which group II introns evolved into eukaryotic introns. In this review, we focus on the evolution of group II introns themselves. We describe the different forms of group II introns known to exist in nature and then address how these forms may have evolved to give rise to spliceosomal introns and other genetic elements. Finally, we summarize the structural and biochemical parallels between group II introns and the spliceosome, including recent data that strongly support their hypothesized evolutionary relationship.
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Affiliation(s)
- Steven Zimmerly
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4 Canada
| | - Cameron Semper
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4 Canada
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98
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Koonin EV, Dolja VV, Krupovic M. Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology 2015; 479-480:2-25. [PMID: 25771806 PMCID: PMC5898234 DOI: 10.1016/j.virol.2015.02.039] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 01/04/2023]
Abstract
Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order "Megavirales" that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015, France.
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99
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Liu YJ, Zhang J, Cui GZ, Cui Q. Current progress of targetron technology: Development, improvement and application in metabolic engineering. Biotechnol J 2015; 10:855-65. [DOI: 10.1002/biot.201400716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/22/2015] [Accepted: 01/29/2015] [Indexed: 01/10/2023]
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100
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Moelling K, Broecker F. The reverse transcriptase-RNase H: from viruses to antiviral defense. Ann N Y Acad Sci 2015; 1341:126-35. [PMID: 25703292 DOI: 10.1111/nyas.12668] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ubiquitous, reverse transcriptase may have contributed to the transition from the RNA to the DNA world, a transition that also involved RNase H-like activities. Both enzymes shaped various genomes and antiviral defense systems as endogenous retroviruses (ERVs) and transposable elements (TEs). A close relationship between a dozen components of retroviruses and the small interfering RNA (siRNA) antiviral-defense machinery has been characterized. Most antiviral-defense systems involve RNase H-like enzymes destroying invading nucleic acids, RNA, or DNA. Such enzymes include RNases H, Argonaute, Dicer, Cas9, transposases, integrases, and enzymes for immunoglobulin rearrangement and splicing. Even in mammalian cells, where protein-based defense dominates, the siRNA machinery remains active, demonstrated by increased virus production and apoptosis after Dicer knockdown. We have noticed a surprising homology between the siRNA silencing system and the interferon response, as well as to siDNA and the CRISPR system. Further, ERVs serve in defense, in addition to having roles in gene regulation and cancer.
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Affiliation(s)
- Karin Moelling
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Heinrich Pette Institute, Hamburg, Germany
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