Retroelement and Retrovirus Universal Classification
- Pat Heslop-Harrison

Retroelements and Related Viruses - A Classification

Here, we give a classification of retroelements and related viruses (presented in C Hansen and JS Heslop-Harrison, 2004. Sequences and phylogenies of plant pararetroviruses, viruses and transposable elements. Advances in Botanical Research 41: 165-193: see this link for text including colour figures and supplementary information; and based on work by Hull, 1999a, 2001; and ICTV International Committee for the Taxonomy of Viruses) 2003. 

Nuclear DNA elements that include the gene for reverse transcriptase, RT, (‘retroelements’, also known as class I transposable elements) can be integrated into a unified classification for reverse transcribing elements that includes viruses and transposable elements (Hull 1999). The elements can be divided into retroviruses, pararetroviruses and the abundant group of nuclear sequences, the retrotransposons, including the long terminal repeat (LTR) retrotransposons, non-LTR retroposons and group II mitochondrial introns (Hull, 1999a, 2001). Another important enzyme, telomerase, which adds the telomere sequences to most eukaryotic chromosomes, also incorporates a RT function

The diagram below shows the relationship of all these elements. At the bottom of the page, an alignment of the reverse transcriptase domain of representatives of most of these suborders shows how all the amino acid sequences has conserved active sites..

Abbreviations: CaMV, Cauliflower mosaic caulimovirus; BSV, Banana streak badnavirus; SbCMV, Soybean chlorotic mottle soymovirus; PVCV, Petunia vein clearing petuvirus; CsVMV, Cassava vein mosaic cavemovirus; RTBV, Rice tungro bacilliform tungrovirus; TVCV, Tobacco vein clearing cavemovirus. The taxonomic endings follow the ICTV nomenclature: order - virales; suborder (after Hull) - ineae; family - viridae; subfamily (not shown) - virinae; genus - virus. Mis-spelling: retorelements, retrorelements, retroelments, retrelements, retroelemnts

(Link to Universal protocols for isolation of retroelement fragment from genomic DNA by PCR)

After Figure 1. Celia Hansen and J.S. Heslop-Harrison. 2004. www.molcyt.com After. Advances in Botanical Research 41: 165-193.

(Diagram above); for Indexing programmes, lines are as follows in text:

CLASS: Retroelementopsida (Retroelements)
ORDERS: Retrovirales (includes DNA and RNA reverse transcribing viruses) AND Retrales (non-viral)

ORDER Retrales
            Suborder Retroposineae (LINE, SINE) Non-LTR retrotransposons
            Suborder Retronineae (e.g. Group II mitochondrial introns)

ORDER Retrovirales
            Suborder Orthoretrovirineae (RNA; Retroviruses Nuclear integration part of replication cycle Example family Retroviridae Examples   HeRV, SFV-1)

            Suborder Pararetrovirineae (DNA; Pararetroviruses, No integrase function)
            Family: Hepadnaviridae (infect animals, e.g. HBV)
            Family: Caulimoviridae (infect plants)
            (Caulimoviridae genera are Caulimovirus, Badnavirus, Petuvirus, Soymovirus, Cavemovirus, Tungrovirus, an example virus in each genus is CaMV, BSV, PVCV, SbCMV, CsVMV, RTBV)

Suborder Retrotransposineae (DNALTR-Retrotransposons)
            Family: Pseudoviridae (e.g. Ty1, copia)
            Family: Metaviridae (e.g. Ty3, gypsy)

An alignment of amino acid sequences from a range of different nuclear elements containing reverse transcriptase. Conserved residues are marked in red, and the domains relate to known and postulated functional regions of the sequence. Sorry – you will need to drag out your browser window to show the full lines of the alignment and then use the scroll bar at the bottom of the screen.

<    domain 3    >             <   domain 4   >             < domain 5 >        <     domain 6     >             < domain 7 >
 
Eap123
MDIEKCYDSVNREKLSTFLKTTK103FYKQTKGIPQGLCVSSILSSFYY·······NVNLLMRLTDDYLLITTQ··FIEKLINVSRENGFKFNMK KLQTSF······ NIVQDYCDWIGISIDMKTLAL
BLIN                                             
LDLARAFDSVSWPFLFEVLRCHG27PAIWHRRGLHQGDPVSPQLLVLAV········IPAISLYADDVILLCHP··AVKEILQLFGRASGLHVNFQKSAAAL······  IVDFPLTYLGIPLKLRRPTAGQLQ
Ty1                                             
LDISSAYLYADIKEELYIRPPPH·NDKLIRLKKSLYGLKQSGANWYETI········QVTICLFVDDMVLFSKN           LNSNKRIIEKLKMQYDTKIINLGESDEEIQYDILGLEIKYQRGKYMKLGMENS
Copia                        
MDVKTAFLNGTLKEEIYMRLPQG·· NVCKLNKAIYGLKQAARCWFEVF··········YVLLYVDDVVIATGD               MTRMNNFKRYLME   KFRMTDLNEIKHFIGIRIEMQEDKIYLSQSAYVKKILSKFNM
BARE-1      
MDVKAAFLNGLLKEELYMMQPEG··· ACKLQGSIYGLVQASRSWNKRF·········AFLILYVDDILLIGNG               VEFLENIKDYLNK   SFSMKDLGEAAYILGIKIYRDRSRVIGLSQSTYLDKVLKRFK
Gypsy            
LDLKSGYHQIY··EKTSFSV··        FCRLPFGLRNASSIFQRALDDVLREQIGKICYVYVDDVIIFSEN··HIDTVLKCLIDANMRVSQE KTRFFK              EYLGFIVSKDGTKS····EPDCVYKVRSFLG
BAGY-1            
MDLRLGYHQIK··PKKAFVT··        YTVMSFGLTNAPATFSRLMNSIFMEYLDKFVVVYLDDILIYSMN··HLRLVLMKLREHRLYAKFS KCEFWY           HKVTYLGHVISGKGIAV····QPESVKQVRSFLG
Cyclops           
LDGYSGYNQIA··*KTAFTC··        YRKMSFGLCNAPTTFQRCVQAIFADLNEKTMEVFMDDFSVFGVS··NLKTVLERCVKTNLVLNW* KCHFMV           TEGIVLGHKVSSRGLEV····PPVNVKGIRSFLG
Athila        
LDGYSGFFQIP··EKTTFTC··        YKRMPFGLCNAPATFQRCMTSIFSDLIEEMVEVFMDDFSVYGPS··NLGRVLTRCEETNLVLNWE KCHFMV           KEGIVLDHKISEKGIEV····PPKTVKDIRSFLG
CaMV                   
FDCKSGFWQVL··PLTAFTC··        WNVVPFGLKQAPSIFQRHMDE AFRVFRKFCCVYVDDILVFSNN··HVAMILQKCNQHGIILSKK KAQLFK           KKINFLGLEIDEGTHKPQGHILEHINK
tprv                    
FDCKSGFYHLK··KLTAFTV··        WNVLPFGYKNAPGRYQHFMDN  YFNQLENCIIYIDDILLYSRT··LLEKFIHIVEISGISLSKK KAEVMK           NQIEFLGIQIDKNGIKMQTHVVQKI
BSV                    
FDLKSGFHQVA··PWTAFWA··        WLVMPFGLKNAPAIFQRKMDN CFRGTEDFIAVYIDDILVFSET··HLKKFMTICEKNGLVLSPT KMKIGT           RQIDFLGATIGNSKIKLQPHII
HBV                                  
LDVSAAFYHIP58FGRKLHLYSHPIILGFRKIPMGVGLSPFL LAQFTS·· RRAFPHCVAFSYMDDVVLGAKS··LFTSITNFLLSLGIHLNPN KTKRWG           YSLNFMGYVIGSWGTLPQEHI
HERV-K              
IDLKDCFFTIP··EKFAFTI·· EPATRFQWKVLPQGMLNSPTICQTFV··VREKFSDCYIIHYIDDILCAAET··CYTFLQAEVANAGLAIASD KIQTST            PFHYLGMQI
SFV            
LDLSNGFWAHS··WLTAFTWLGQQYCW    TRLPQGFLNSPALFTADV  VDLLKEVPNVQVYVDIYISHDDP··LEKVFSLLLNAGYVVSLK  KSEIAQ           HEVEFLGFNITKEG