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

Retroelement and Retrovirus Universal Classification - Pat Heslop-Harrison

Retroelement and Retrovirus Universal Classification
- Pat Heslop-Harrison