500 1000 1500 Four ribosomal
Y37E3.8 Y37E3.7 protein gene-containing rpl-27a rpa-1 operons from 500 1000 1500 2000 Caenorhabditis elegans
F25H2.10 F25H2.11 rpa-0 tph-1 500 1000 1500 2000 2500
T01C3.7 T01C3.6 fib-1 rps-16 500 1000 1500 2000 2500
F37C12.9 F37C12.4 F37C12.3 rps-14 rpl-36 ayc-1 500 1000 1500 Conserved operons
Y37E3.8 Y37E3.7 identified in rpl-27a rpa-1 Brugia malayi 500 1000 1500 2000 Oscheius tipulae Pristionchus pacificus F25H2.10 F25H2.11 rpa-0 tph-1 Strongyloides ratti 500 1000 1500 2000 2500 Ascaris suum
T01C3.7 T01C3.6 fib-1 rps-16 500 1000 1500 2000 2500
new intron in some taxa F37C12.9 F37C12.4 F37C12.3 rps-14 rpl-36 ayc-1 intron absent in some taxa Operon sizes in sequenced nematode genomes
10000
1000
MI 100 BM CE
Number of operons
10
1 2 3 4 5 6 7 8 9 10 Size of operon (genes)
B. malayi C. elegans Number of M. incognita genes with 14503 8098 orthologues Number of genes with orthologues in M. 3083 (21%) 1879 (23%) incognita operons Number of M. incognita operonic genes 336 516 with orthologues also in operons Number of operons conserved with M. 3 9 incognita
exon intron exon intron exon intron exon x
transcripton ATG STOP POLYA start 5’ UTR 3’ UTR
exon intron exon intron exon intron exon pre-mRNA x transcripton ATG gt ag gt ag gt ag STOP POLYA start 5’ UTR 3’ UTR
exon exon exon exon mRNA CAP AAAAAAAAAAAAAAAAA ATG STOP
5’ UTR open reading frame 3’ UTR cis-splicing of introns exon intron exon intron exon intron exon x
transcripton ATG STOP POLYA start 5’ UTR 3’ UTR
outron exon intron exon intron exon intron exon pre-mRNA x tttcag ATG gt gt ag gt ag STOP POLYA
5’ UTR 3’ UTR donatron SL1 *CAP gt
exon exon exon exon mRNA *CAP SL1 AAAAAAAAAAAAAAAAA ATG STOP
5’ UTR open reading frame 3’ UTR trans-splicing of leader sequence gene 1 gene 2 x
transcripton start
gene 1 gene 2 polycistronic x pre-mRNA tttcag
*CAP SL1 *CAP SL2
mRNA(gene1) *CAP SL1 AAAAAAAAAAAAAAAAA mRNA(gene2) *CAP SL2 AAAAAAAAAAAAAAAAA trans-splicing of operonic genes A L S L Brugia malayi OP1032 248 bp behaves like an operon BUT the downstream gene B + - M is trans-spliced rpl-27a rpa-1 3054 2036 to SL1 1 1636
2 1018 3
506 gene 1 gene 2 x
gene 1 gene 2
C. elegans *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL2-like AAAAAAAAAAAAAAAAA
C. briggsae *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL2-like AAAAAAAAAAAAAAAAA
B. malayi *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL1 AAAAAAAAAAAAAAAAA gene 1 gene 2 x
gene 1 gene 2
C. elegans *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL2-like AAAAAAAAAAAAAAAAA
C. briggsae *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL2-like AAAAAAAAAAAAAAAAA
N. brasiliensis *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL2-like AAAAAAAAAAAAAAAAA
P. pacificus *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL2-like AAAAAAAAAAAAAAAAA
S. ratti *CAP SL1-like AAAAAAAAAAAAAAAAA *CAP SL1-like AAAAAAAAAAAAAAAAA
A. suum *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL1 AAAAAAAAAAAAAAAAA
B. malayi *CAP SL1 AAAAAAAAAAAAAAAAA *CAP SL1 AAAAAAAAAAAAAAAAA SL2 The nematode Strongylida Rhabditida operonic transcription V Diplogasterida & trans-splicing variant SL1 Strongyloididae system appears IVa Steinernematidae to have been operons Panagrolaimidae assembled piecemeal ??? Cephalobidae Aphelenchida through IVb Tylenchida evolutionary time. SL1 Oxyurida Spirurida III Ascaridida Rhigonematida C Chromadorida Enoplida II Triplonchida Dorylaimida The C. elegans system Mermithida (SL2-like spliced leaders) I Trichocephalida Mononchida is highly derived. Outgroups Mark Blaxter – Comparative Nematode Genomics - 2008
Trichinella spiralis trans-spliced leaders Sr_SL1s GGTTT—-AAAAAACCCA-GTT----TAAG Ts_SL14 GAATT--AAAAAGAAGACGCT----GAAG Ce_SL2 GGTTT-----TAACCCA-GTT-ACTCAAG Ts_SL11 AACCTTT-----GAACCCA-CTT----CAAG Ts_SL1 CAGGTATTT------ACCAG-ATCTA--AAAG TS_SL2 AGGTATTT------ACCGA-ATTAA--AAAG Ts_SL3 GGTTATTT------ACCGA-ACTTA--AAAG Ts_SL4 GCGAATTG------TTCGAATTTACTTGAAG Ts_SL5 AAATACCTTT-----CAATTTG-TTT----GAAG Ts_SL6 AACCTTT-----GCGCATC-GTTT---AAAG Ts_SL7 AACCTGC-----ACGACTT-GTTC---GAAG Ts_SL8 ATCTG------TCGGT-ATTCCTGAAAG Ts_SL9 AGACG------TGGTT-ATTTATTGAAG Ts_SL10 GGTAATATTT------ACTGA-ATT----CAAG Ts_SL12 ACGAATTT------ACCGT-ATTTGT-CAAG Ts_SL13 TACCATT-----CAATTTA-TTTT---GAAG Ts_SLZ GCTA-----TGACCATGATTACGCCAAG Ts_SLY T-----TGACACTGATTACGCCAAG Ts_SLX AGC-----TTGACCTGATTACGCCAAG
Pettitt et al. 2008 RNA 14:760-770 SL2 The nematode Strongylida Rhabditida operonic transcription V Diplogasterida & trans-splicing variant SL1 Strongyloididae system appears IVa Steinernematidae to have been operons Panagrolaimidae assembled piecemeal ??? Cephalobidae Aphelenchida through IVb Tylenchida evolutionary time. SL1 Oxyurida Spirurida While SL1 is a III Ascaridida synapomorphy for Rhigonematida Rhabditida, other facets tSL Chromadorida C of the system Enoplida have limited distribution. II Triplonchida Dorylaimida The C. elegans system Mermithida (SL2-like spliced leaders) I Trichocephalida variant SLs Mononchida is highly derived. Outgroups EXON
INTRON
SPLICED LEADER
EXON +
INTRON trans-splicing
pre-mRNA SL RNA mRNA
EXON +
A
A
A
A
A
A
INTRON A
EXON
A
A A
A
A A SL trans-splicing Rotifers (Philodina spp.) Platyhelminthes ATG
Cnidaria
Trans-spliced leader addition to mRNAs in a cnidarian. Stover N & Steele RE. Proc Natl Acad Sci U S A. 2001 98:5693-8
Surprising diversity and distribution of spliced leader RNAs in flatworms. Davis RE. Mol Biochem Parasitol 1997 90:395-7. Oikopleura dioica Ascidians (sea squirts)
Ciona intestinalis
ATTCTATTTGAATAAG TTCTATTTGAATAAG TCTATTTGAATAAG CTATTTGAATAAG ATTTCTATTTGAATAAG AATTCTATTTGAATAAG GTATTCTATTTGAATAAG ATTCTAATTGAATAAG ATTCTATTAGAATAAG ATTCTA-TTGAATAAG ATTCTATTTCAATAAG ATTCTATTTGAAAAAG ATTCTATTTGAACAAG ATTCTATTTGAAGAAG ATTCTATTTAAATAAG ATTCTATTTGA----- ATTCTGTTTGAATAAG
Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis. Satou Y, et al., Nucleic Acids Res. 2006 34:3378-88.
Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Ganot P, et al., Mol Cell Biol. 2004 24:7795-805. Choanoflagellida Porifera Placozoa Cnidaria Metazoa Ctenophora Acoelomorpha Rhombozoa Orthonectida Multiple, Myxozoa Mollusca Echiura Pogonophora independent Annelida Entoprocta Brachiopoda Bryozoa events of Sipuncula L Rotifera Acanthocephala Platyhelminthes gain of Cycliophora Gnathostomulida Nemertea SL trans- ? Gastrotricha Micrognathozoa Tardigrada E Arthropoda splicing Onychophora Priapulida Kinorhyncha Loricifera and operons D Nematomorpha ? Nematoda Chaetognatha Xenoturbellida Echinodermata Hemichordata Chordata Choanoflagellida Porifera Placozoa Cnidaria Metazoa Ctenophora Acoelomorpha Rhombozoa Orthonectida Multiple, Myxozoa Mollusca Echiura Pogonophora independent Annelida Entoprocta Brachiopoda Bryozoa events of Sipuncula L Rotifera Acanthocephala Platyhelminthes loss of Cycliophora Gnathostomulida Nemertea SL trans- Gastrotricha ? Micrognathozoa Tardigrada E Arthropoda splicing Onychophora Priapulida Kinorhyncha Loricifera and operons D Nematomorpha ? Nematoda Chaetognatha Xenoturbellida Echinodermata Hemichordata Chordata Choanoflagellida Porifera Placozoa Cnidaria Ctenophora Acoelomorpha Rhombozoa Orthonectida Myxozoa Nematoda Nematomorpha Loricifera Kinorhyncha Priapulida Onychophora Arthropoda Tardigrada Micrognathozoa E Gastrotricha E Nemertea Gnathostomulida Cycliophora Platyhelminthes Acanthocephala Rotifera Sipuncula L Bryozoa L Brachiopoda Entoprocta Annelida Pogonophora Echiura D Mollusca D Chaetognatha Xenoturbellida Echinodermata Hemichordata Chordata