Group II Intron Retroelements: Function and Diversity

Total Page:16

File Type:pdf, Size:1020Kb

Group II Intron Retroelements: Function and Diversity Diversity of Retrotransposable Elements Cytogenet Genome Res 110:589–597 (2005) DOI: 10.1159/000084992 Group II intron retroelements: function and diversity A.R. Robart, S. Zimmerly Department of Biological Sciences, University of Calgary, Calgary, Alberta (Canada) Manuscript received 16 October 2003; accepted in revised form for publication by J.-N. Volff 8 December 2003. Abstract. Group II introns are a class of retroelements capa- and bacterial introns with regard to structures, insertion pat- ble of carrying out both self-splicing and retromobility reac- terns and inferred behaviors. We also discuss the evolution of tions. In recent years, the number of known group II introns has group II introns, as they are the putative ancestors of spliceoso- increased dramatically, particularly in bacteria, and the new mal introns and possibly non-LTR retroelements, and may information is altering our understanding of these intriguing have played an important role in the development of eukaryote elements. Here we review the basic properties of group II genomes. introns, and summarize the differences between the organellar Copyright © 2005 S. Karger AG, Basel Group II introns are a unique type of genetic element with catalytic core of the ribozyme (Fig. 1A) (Michel and Ferat, two remarkable properties. They are catalytic RNAs, or ribo- 1995; Qin and Pyle, 1998). Domain I is the largest domain and zymes, that can excise themselves from pre-mRNA without the is also important for catalysis, while domain VI contains the aid of proteins. They are also retroelements that encode reverse bulged A that forms the branch site in the spliced product. transcriptases (RTs) and can insert themselves into new loca- RNA structures are divided into two major classes, IIA and IIB, tions. Group II introns are present in mitochondria and chloro- with class IIC being a minor class of bacterial introns. plasts of plants and fungi, where they are relatively abundant The ORF is encoded within the loop of domain IV (Fig. 1A) (Michel et al., 1989), and they are also found in about 25% of and has four functionally defined domains: RT (reverse trans- eubacterial genomes, in either full-length or truncated forms criptase activity, with sub-domains 0–7), X (maturase activity (Ferat and Michel, 1993; Dai and Zimmerly, 2002). Recently, associated with intron splicing), D (non-conserved DNA-bind- they were found even in some archaebacterial species (Dai and ing domain) and En (endonuclease activity) (Fig. 1B) (Zimmer- Zimmerly, 2003; Rest and Mindell, 2003; Toro, 2003). Due to ly et al., 2001; Belfort et al., 2002; San Filippo and Lambowitz, the burgeoning information from the genome projects, our 2002). The protein serves two functions for the intron. It assists knowledge about the introns has increased significantly in the intron splicing in vivo through an activity associated with the X past few years, and this review emphasizes this new genomic domain (maturase activity), and it also allows the intron to act and comparative perspective. as a mobile element and invade intronless sites, a process which The typical group II intron consists of a conserved intron involves all four of the ORF domains, as well as the catalytic RNA structure and an RT ORF. The RNA structure is com- RNA activity. prised of six domains, of which domain V is believed to be the Self-splicing reaction Ribozyme activity was the first property assigned to group Supported by the Canadian Institutes of Health Research (CIHR) and by Alberta II introns (van der Veen et al., 1986; Peebles et al., 1987). Self- Heritage Foundation for Medical Research (AHFMR). splicing is accomplished by two transesterifications (Fig. 2A). Request reprints from Dr. Steven Zimmerly In the first step, the 5) exon is defined through two base-pairing Department of Biological Sciences, University of Calgary 2500 University Dr. NW, Calgary, AB T2N 1N4 (Canada) interactions, in which the intron binding sequences (IBS) 1 and telephone: (403) 220-7933; fax: (403) 289-9311; e-mail: [email protected] 2 pair to their corresponding exon binding sequences (EBS) Fax + 41 61 306 12 34 © 2005 S. Karger AG, Basel Accessible online at: ABC E-mail [email protected] 1424–8581/05/1104–0589$22.00/0 www.karger.com/cgr www.karger.com Fig. 1. Basic group II intron structure. (A) Simplified secondary structure of IIB introns, composed of six structural domains, with the ORF located in domain IV. The intron is shown by black lines, exons by thick gray lines, and the ORF by a dotted black line. Black dots indicate individual nucleotides involved in base pairing tertiary interactions. The most important tertiary interactions are IBS1,2,3/EBS1,2,3, Á–Á) and ‰–‰), which are indicated by gray lines and arrows. For IIA introns, ‰) is located at the first nucleotide of Fig. 2. Reactions performed by group II introns. (A) Self-splicing reac- the 3) exon rather than in domain I, and there is no IBS3/EBS3 pairing. See tion. Self-splicing is catalyzed by the intron RNA structure through two Toor et al. (2001) for detailed information about RNA structural subclasses. transesterification reactions, yielding spliced exons and intron lariat. The (B) Intron-encoded ORF domains. The ORF consists of an RT domain (out- bulged A branch site that attacks the 5)-splice site is shown in domain VI of lined gray boxes; reverse transcriptase with sub-domains 0–7), domain X Fig. 1A. (B) Basic mechanism of group II intron mobility. The intron lariat in (solid box; maturase domain), domain D (hatched box; DNA binding an RNP particle (lariat+RT) reverse splices into the top strand of the DNA domain, not conserved in sequence among different ORFs), and the En target site. The bottom strand is cleaved by the En domain, and the intron is domain (double-hatched box; endonuclease domain). Exons are dark gray, reverse transcribed. Recombination and repair activities complete the inser- and intron RNA structure light gray. tion. 1 and 2 (Fig. 1A). The two interactions position the 5) splice site bond of the 3) junction, resulting in exon ligation and release of in proximity to the bulged adenosine in DVI (Jacquier and the intron lariat (Fig. 2A). Because the number of phosphate Michel, 1987). The 2)-OH of the adenosine acts as a nucleo- bonds broken and created during the reaction is equal, splicing phile, attacking the phosphodiester bond of the 5) junction to is energetically neutral and reversible, and does not require break the bond and form a lariat intermediate with a 2)–5) link- energy sources such as ATP. age (Fig. 2A). The self-splicing reaction in vitro requires relatively ex- In the second splicing step, the 3) exon is defined by two, treme reaction conditions of salt, magnesium and sometimes single-base-pair interactions, which vary for the RNA structur- temperature (e.g., 500 mM KCl, 100 mM MgCl2, 45°C) (Jarrell al classes. For IIA introns, the base pairs are Á–Á) and ‰–‰), et al., 1988), and it is known that protein factors are required while for IIB and IIC introns, they are Á–Á) and IBS3-EBS3 for splicing of introns in vivo. For many introns, the most (Fig. 1A) (Jacquier and Michel, 1990; Costa et al., 2000). The important splicing factor is the intron-encoded protein. Upon second transesterification is similar to the first, but with the transcription, the protein is translated from unspliced mRNA, now free 3)-OH of the 5) exon attacking the phosphodiester and binds to a high affinity binding site in domain IVA in un- 590 Cytogenet Genome Res 110:589–597 (2005) spliced intron (Fig. 1A) (Wank et al., 1999). Combined with markers (Eskes et al., 2000). The pathways differ with regard to contacts with other regions of the intron RNA, the protein the role of double-strand break repair (DSBR) activities that induces structural changes that stimulate self-splicing (Matsuu- complete the insertion event. In bacteria, group II introns have ra et al., 2001; Noah and Lambowitz, 2003), to yield spliced not been observed to coconvert exon markers, and mobility exons and a ribonucleoprotein (RNP) particle consisting of a occurs in RecA– strains, indicating independence from a gener- lariat with the protein still attached. This RNP is the entry mol- al DSBR system during retrohoming (Mills et al., 1997; Cousi- ecule to the mobility pathway. neau et al., 1998; Martı´nez-Abarca and Toro, 2000). Interestingly, many bacterial introns do not encode En domains (Fig. 3B), yet appear to be mobile. The best studied of The basic intron mobility reaction these is the Sinorhizobium intron RmInt1 (Martı´nez-Abarca et al., 2000; Muñoz-Adelantado et al., 2003), which is efficiently Mobility of group II introns occurs through a simple yet spe- mobile in vivo even though it does not have an En domain. A cialized mechanism. In the predominant event, retrohoming, similar process was characterized for an Ll.ltrB intron with a the introns invade double-stranded DNA targets with high site mutated En domain (Zhong and Lambowitz, 2003). The data specificity (Moran et al., 1995). Non-site-specific mobility, or suggested a mechanism in which the intron reverse splices into retrotransposition, also occurs (see below) (Mueller et al., 1993; the double-stranded DNA target, and cDNA synthesis is Sellem et al., 1993; Cousineau et al., 2000; Martı´nez-Abarca primed by the 3) end of a DNA at the replication fork, rather and Toro, 2000), but the majority of characterized introns than priming by cleaved target DNA. home to consistent and predictable locations. A final variation of mobility is insertion into noncognate Homing is initiated by recognition of the DNA target site by sites, known as retrotransposition.
Recommended publications
  • Mobile Genetic Elements in Streptococci
    Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G.
    [Show full text]
  • Exploring the Structure of Long Non-Coding Rnas, J
    IMF YJMBI-63988; No. of pages: 15; 4C: 3, 4, 7, 8, 10 1 2 Rise of the RNA Machines: Exploring the Structure of 3 Long Non-Coding RNAs 4 Irina V. Novikova, Scott P. Hennelly, Chang-Shung Tung and Karissa Y. Sanbonmatsu Q15 6 Los Alamos National Laboratory, Los Alamos, NM 87545, USA 7 Correspondence to Karissa Y. Sanbonmatsu: [email protected] 8 http://dx.doi.org/10.1016/j.jmb.2013.02.030 9 Edited by A. Pyle 1011 12 Abstract 13 Novel, profound and unexpected roles of long non-coding RNAs (lncRNAs) are emerging in critical aspects of 14 gene regulation. Thousands of lncRNAs have been recently discovered in a wide range of mammalian 15 systems, related to development, epigenetics, cancer, brain function and hereditary disease. The structural 16 biology of these lncRNAs presents a brave new RNA world, which may contain a diverse zoo of new 17 architectures and mechanisms. While structural studies of lncRNAs are in their infancy, we describe existing 18 structural data for lncRNAs, as well as crystallographic studies of other RNA machines and their implications 19 for lncRNAs. We also discuss the importance of dynamics in RNA machine mechanism. Determining 20 commonalities between lncRNA systems will help elucidate the evolution and mechanistic role of lncRNAs in 21 disease, creating a structural framework necessary to pursue lncRNA-based therapeutics. 22 © 2013 Published by Elsevier Ltd. 24 23 25 Introduction rather than the exception in the case of eukaryotic 50 organisms. 51 26 RNA is primarily known as an intermediary in gene LncRNAs are defined by the following: (i) lack of 52 11 27 expression between DNA and proteins.
    [Show full text]
  • The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
    PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA.
    [Show full text]
  • A Group Ill Twintron Encoding a Maturase-Like Gene Excises Through Lariat Intermediates
    I.=) 1994 Oxford University Press Nucleic Acids Research, 1994, Vol. 22, No. 6 1029-1036 A group Ill twintron encoding a maturase-like gene excises through lariat intermediates Donald W.Copertino1 2+, Edina T.Hall2,§, Fredrick W.Van Hook2, Kristin P.Jenkins2 and Richard B.Hallick1,2* 1Departments of Biochemistry and 2Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA Received December 9, 1993; Revised and Accepted February 10, 1994 ABSTRACT The 1605 bp intron 4 of the Euglena gracilis chloroplast the closely related nonphotosynthetic euglenoid Astasia longa psbC gene was characterized as a group Ill twintron (8, 9). composed of an internal 1503 nt group Ill intron with Euglena chloroplast genes also contain 15 twintrons, introns- an open reading frame of 1374 nt (ycfl3, 458 amino within-introns, that are sequentially spliced (3). There are acids), and an external group Ill intron of 102 nt. twintrons with one intron internal to another intron (2, 6, 10), Twintron excision proceeds by a sequential splicing and complex twintrons with multiple internal introns (11; for pathway. The splicing of the internal and external group review, see 3). Group II and group III introns can occur as Ill introns occurs via lariat intermediates. Branch sites internal and/or external introns of twintrons. Excision of internal were mapped by primer extension RNA sequencing. introns occurs prior to excision of external introns. The excision The unpaired adenosines in domains VI of the internal of internal group IH introns of twintrons can proceed from and external introns are covalently linked to the 5' multiple 5' and 3' splice sites (6, 1 1).
    [Show full text]
  • Comprehensive Analysis of Mobile Genetic Elements in the Gut Microbiome Reveals Phylum-Level Niche-Adaptive Gene Pools
    bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Comprehensive analysis of mobile genetic elements in the gut microbiome 2 reveals phylum-level niche-adaptive gene pools 3 Xiaofang Jiang1,2,†, Andrew Brantley Hall2,3,†, Ramnik J. Xavier1,2,3,4, and Eric Alm1,2,5,* 4 1 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, 5 Cambridge, MA 02139, USA 6 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 7 3 Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard 8 Medical School, Boston, MA 02114, USA 9 4 Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General 10 Hospital and Harvard Medical School, Boston, MA 02114, USA 11 5 MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 12 02142, USA 13 † Co-first Authors 14 * Corresponding Author bioRxiv preprint doi: https://doi.org/10.1101/214213; this version posted December 22, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 15 Abstract 16 Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer 17 could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could 18 threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological 19 importance and medical relevance, MGEs from the gut microbiome have not been systematically 20 characterized.
    [Show full text]
  • The Association of Group IIB Intron with Integrons in Hypersaline Environments Sarah Sonbol1 and Rania Siam1,2*
    Sonbol and Siam Mobile DNA (2021) 12:8 https://doi.org/10.1186/s13100-021-00234-2 RESEARCH Open Access The association of group IIB intron with integrons in hypersaline environments Sarah Sonbol1 and Rania Siam1,2* Abstract Background: Group II introns are mobile genetic elements used as efficient gene targeting tools. They function as both ribozymes and retroelements. Group IIC introns are the only class reported so far to be associated with integrons. In order to identify group II introns linked with integrons and CALINS (cluster of attC sites lacking a neighboring integron integrase) within halophiles, we mined for integrons in 28 assembled metagenomes from hypersaline environments and publically available 104 halophilic genomes using Integron Finder followed by blast search for group II intron reverse transcriptases (RT)s. Results: We report the presence of different group II introns associated with integrons and integron-related sequences denoted by UHB.F1, UHB.I2, H.ha.F1 and H.ha.F2. The first two were identified within putative integrons in the metagenome of Tanatar-5 hypersaline soda lake, belonging to IIC and IIB intron classes, respectively at which the first was a truncated intron. Other truncated introns H.ha.F1 and H.ha.F2 were also detected in a CALIN within the extreme halophile Halorhodospira halochloris, both belonging to group IIB introns. The intron-encoded proteins (IEP) s identified within group IIB introns belonged to different classes: CL1 class in UHB.I2 and bacterial class E in H.ha.Fa1 and H.ha.F2. A newly identified insertion sequence (ISHahl1)ofIS200/605 superfamily was also identified adjacent to H.
    [Show full text]
  • The Obscure World of Integrative and Mobilizable Elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget
    The obscure world of integrative and mobilizable elements Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget To cite this version: Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot-Lacroix, Nathalie Leblond-Bourget. The obscure world of integrative and mobilizable elements: Highly widespread elements that pirate bacterial conjugative systems. Genes, MDPI, 2017, 8 (11), pp.337. 10.3390/genes8110337. hal- 01686871 HAL Id: hal-01686871 https://hal.archives-ouvertes.fr/hal-01686871 Submitted on 26 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License G C A T T A C G G C A T genes Review The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems Gérard Guédon *, Virginie Libante, Charles Coluzzi, Sophie Payot and Nathalie Leblond-Bourget * ID DynAMic, Université de Lorraine, INRA, 54506 Vandœuvre-lès-Nancy, France; [email protected] (V.L.); [email protected] (C.C.); [email protected] (S.P.) * Correspondence: [email protected] (G.G.); [email protected] (N.L.-B.); Tel.: +33-037-274-5142 (G.G.); +33-037-274-5146 (N.L.-B.) Received: 12 October 2017; Accepted: 15 November 2017; Published: 22 November 2017 Abstract: Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements.
    [Show full text]
  • Virology Is That the Study of Viruses ? Submicroscopic, Parasitic Particles
    Current research in Virology & Retrovirology 2021, Vol.4, Issue 3 Editorial Bahman Khalilidehkordi Shahrekord University of Medical Sciences, Iran mobile genetic elements of cells (such as transposons, Editorial retrotransposons or plasmids) that became encapsulated in protein capsids, acquired the power to “break free” from Virology is that the study of viruses – submicroscopic, the host cell and infect other cells. Of particular interest parasitic particles of genetic material contained during a here is mimivirus, a huge virus that infects amoebae and protein coat – and virus-like agents. It focuses on the sub- encodes much of the molecular machinery traditionally sequent aspects of viruses: their structure, classification associated with bacteria. Two possibilities are that it’s a and evolution, their ways to infect and exploit host cells for simplified version of a parasitic prokaryote or it originated copy , their interaction with host organism physiology and as an easier virus that acquired genes from its host. The immunity, the diseases they cause, the techniques to iso- evolution of viruses, which frequently occurs together with late and culture them, and their use in research and ther- the evolution of their hosts, is studied within the field of apy. Virology is a subfield of microbiology.Structure and viral evolution. While viruses reproduce and evolve, they’re classification of Virus: A major branch of virology is virus doing not engage in metabolism, don’t move, and depend classification. Viruses are often classified consistent with on variety cell for copy . The often-debated question of the host cell they infect: animal viruses, plant viruses, fun- whether or not they’re alive or not could also be a matter gal viruses, and bacteriophages (viruses infecting bacte- of definition that does not affect the biological reality of vi- ria, which include the foremost complex viruses).
    [Show full text]
  • Mutualism Between Self‑Splicing Introns and Their Hosts David R Edgell1*, Venkata R Chalamcharla2,3 and Marlene Belfort2*
    Edgell DR et al. BMC Biology 2011, 9:22 http://www.biomedcentral.com/1741-7007/9/22 review Open Access Learning to live together: mutualism between self‑splicing introns and their hosts David R Edgell1*, Venkata R Chalamcharla2,3 and Marlene Belfort2* Abstract data argue that the relationship is more elaborate than previously appreciated. Group I and II introns can be considered as molecular parasites that interrupt protein-coding and structural Mobile introns: ribozymes with baggage RNA genes in all domains of life. They function as self- One group of mobile genetic elements comprises the group I splicing ribozymes and thereby limit the phenotypic and II introns. These sequences interrupt protein-coding and costs associated with disruption of a host gene while structural RNA genes in all domains of life and can be con­ they act as mobile DNA elements to promote their sidered as molecular parasites. When the gene is trans­cribed spread within and between genomes. Once considered into RNA, the intron sequence acts as a ribozyme (an RNA purely selfish DNA elements, they now seem, in the with enzymatic activity), which removes the intron sequence light of recent work on the molecular mechanisms from the primary RNA transcript, thus limiting the regulating bacterial and phage group I and II intron phenotypic cost associated with insertion of the element into dynamics, to show evidence of co-evolution with their a host gene and promoting their maintenance in the genome. hosts. These previously underappreciated relationships In the case of group I and II introns, the host-parasite serve the co-evolving entities particularly well in times relationship is enriched by the fact that the introns of environmental stress.
    [Show full text]
  • Pathological and Evolutionary Implications of Retroviruses As Mobile Genetic Elements
    Genes 2013, 4, 573-582; doi:10.3390/genes4040573 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Review Pathological and Evolutionary Implications of Retroviruses as Mobile Genetic Elements 1 2 Madeline Hayes , Mackenzie Whitesell and Mark A. Brown 3,* 1 Department of Biology, Colorado State University, 801 Oval Drive, Fort Collins, CO 80523, USA; E-Mail: [email protected] 2 Department of Environmental and Radiological Health Sciences, Colorado State University, 801 Oval Drive, Fort Collins, CO 80523, USA; E-Mail: [email protected] 3 Department of Clinical Sciences, Colorado State University, Colorado State University, 801 Oval Drive, Fort Collins, CO 80523, USA * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-970-491-5782. Received: 15 July 2013; in revised form: 27 September 2013 / Accepted: 8 October 2013 / Published: 24 October 2013 Abstract: Retroviruses, a form of mobile genetic elements, have important roles in disease and primate evolution. Exogenous retroviruses, such as human immunodeficiency virus (HIV), have significant pathological implications that have created a massive public health challenge in recent years. Endogenous retroviruses (ERVs), which are the primary focus of this review, can also be pathogenic, as well as being beneficial to a host in some cases. Furthermore, retroviruses may have played a key role in primate evolution that resulted in the incorporation of these elements into the human genome. Retroviruses are mobile genetic elements that have important roles in disease and primate evolution. We will further discuss the pathogenic potential of retroviruses, including their role in cancer biology, and will briefly summarize their evolutionary implications.
    [Show full text]
  • Group II Intron Rnps and Reverse Transcriptases: from Retroelements to Research Tools
    Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools Marlene Belfort1 and Alan M. Lambowitz2 1Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, New York 12222 2Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 Correspondence: [email protected]; [email protected] SUMMARY Group II introns, self-splicing retrotransposons, serve as both targets of investigation into their structure, splicing, and retromobility and a source of tools for genome editing and RNA anal- ysis. Here, we describe the first cryo-electron microscopy (cryo-EM) structure determination, at 3.8–4.5 Å, of a group II intron ribozyme complexed with its encoded protein, containing a reverse transcriptase (RT), required for RNA splicing and retromobility. We also describe a method called RIG-seq using a retrotransposon indicator gene for high-throughput integration profiling of group II introns and other retrotransposons. Targetrons, RNA-guided gene targeting agents widely used for bacterial genome engineering, are described next. Finally, we detail thermostable group II intron RTs, which synthesize cDNAs with high accuracy and processiv- ity, for use in various RNA-seq applications and relate their properties to a 3.0-Å crystal structure of the protein poised for reverse transcription. Biological insights from these group II intron revelations are discussed. Outline 1 Introduction 5 Technique 4. RTs with novel enzymatic properties as potent research tools 2 Technique 1.
    [Show full text]
  • Comparative Genomics Shows That Viral Integrations Are Abundant And
    Palatini et al. BMC Genomics (2017) 18:512 DOI 10.1186/s12864-017-3903-3 RESEARCH ARTICLE Open Access Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus Umberto Palatini1†, Pascal Miesen2†, Rebeca Carballar-Lejarazu1, Lino Ometto3, Ettore Rizzo4, Zhijian Tu5, Ronald P. van Rij2 and Mariangela Bonizzoni1* Abstract Background: Arthropod-borne viruses (arboviruses) transmitted by mosquito vectors cause many important emerging or resurging infectious diseases in humans including dengue, chikungunya and Zika. Understanding the co-evolutionary processes among viruses and vectors is essential for the development of novel transmission-blocking strategies. Episomal viral DNA fragments are produced from arboviral RNA upon infection of mosquito cells and adults. Additionally, sequences from insect-specific viruses and arboviruses have been found integrated into mosquito genomes. Results: We used a bioinformatic approach to analyse the presence, abundance, distribution, and transcriptional activity of integrations from 425 non-retroviral viruses, including 133 arboviruses, across the presentlyavailable22mosquito genome sequences. Large differences in abundance and types of viral integrations were observed in mosquito species from the same region. Viral integrations are unexpectedly abundant in the arboviral vector species Aedes aegypti and Ae. albopictus, in which they are approximately ~10-fold more abundant than in other mosquito species analysed. Additionally, viral integrations are enriched in piRNA clusters of both the Ae. aegypti and Ae. albopictus genomes and, accordingly, they express piRNAs, but not siRNAs. Conclusions: Differences in the number of viral integrations in the genomes of mosquito species from the same geographic area support the conclusion that integrations of viral sequences is not dependent on viral exposure, but that lineage-specific interactions exist.
    [Show full text]