Alignment of eubacterial pre-tRNA group I intron sequences
Note: This alignment complements the paper entitled "Origin and Evolution of Group I
Introns in Cyanobacterial tRNA Genes." (submitted). The phylogeny presented in figure 7 of
the cited paper is based on this alignment. Sources of the sequences are also mentioned in
the legend of figure 7. Helices (Pn-Pn') are indicated on top of the alignment. Stars
point to peripheral regions that were excluded (see figure 6). Legend at the end of the
alignment.
P1 P1'
|------------------------| |----------
- Anabaena AG-------------------------AAAA------------------
| Calothrix AG-------------------------ACAA------------------
| Chloroglo AA-------------------------GTAA------------------
| Cylindros AG-------------------------ATAA------------------
| Fischerel AA-------------------------GTAA------------------
| Nos 7120 AA-------------------------ATAA------------------
| Nostoc sp AG-------------------------ATAA------------------
| Osc 6304 AG-------------------------AAAA------------------
Leu | Phormidiu AG-------------------------AAAA------------------
| Prochloro AG-------------------------ATAAA-----------------
| Pseudanab AA-------------------------GCAAA-----------------
| Scytonema AG-------------------------AAAA------------------
| Synechoco AG-------------------------AAAA------------------
| Marcha cp AA-------------------------TTTAA-----------------
| Nicoti cp AA-------------------------TTGGA-----------------
| Chlore cp AA-------------------------ATT-------------------
-
- Cylindros CTCAATGGTGAAA-TTAACT-------AAACGCTTATC-----------
| Dermocarp CAACA--TGCAAGATTAACT-------AAGTGCTTAGC-----------
| Gloeobact CGAACAGCAGGTTCAGGGGTTCAGCGTTACGTCAGG--CGCTAGACCAC
fMet | Osc 6304 CTCAATACGCAAG-TTAACT-------AAACGCTTAAT-----------
| Osc 7105 CTCAAAGGCT-GGCTTAATC-------AAACGCTTAGC-----------
| Scytonema CAACGAGT--AAGATTGACT-------AAACGCTTAAA-----------
| Synechocy CA-GGT-CGCAAGATG----------TAAACCATGT-------------
Arg Agrobacte AA------------------------GGTAAA-----------------
Ile Azoarcus AT-------------------------TTCG------------------
P1' P2 P2'
------------------------| |----------| |--------|
Anabaena --------------------CTGAGCCTTG-ATA--GAGAAATC-TTTCAAG
Calothrix --------------------CTGAGCCTTGCTGT--GAGAAATC-CTTCAAG
Chloroglo --------------------TTGAGCCTTG-AAG--GAGAAATC-CTTTAAG
Cylindros --------------------CTGAGCCTTG-ATA--GAGAAATC-TTTCAAG
Fischerel --------------------TTGAGCCTTA-AAG--AAGAAACT-CTTTAAG
Nos 7120 --------------------TTGAGCCTTA-GAG--AAGAAATT-CTTTAAG
Nostoc sp --------------------CTGAGCCTTG-AAG--GAGAAATC-CCTCAAG
Osc 6304 --------------------CTGAGCCTTA-TTG--GAGAAATC-CATTAAG
Phormidiu --------------------CTGAGCCTTA-GTG--GAGAAATC-TGCTAAG
Prochloro --------------------CTGGGCCTTG-GTG--GAGAAATC-CGCGAAG
Pseudanab --------------------TTGAGCCTTA-GCA--AAGAAATT-TGTTAAG
Scytonema --------------------CTGAGCCTTG-ATA--GAGAAATC-TTTCAAG
Synechoco --------------------CTGGGCCTCG-ATC--GCGAAAGG-GATCGAG
Marcha cp --------------------TTGAGCTTTA-GTT--GAGAAATT-TACTAAA
Nicoti cp --------------------TTGAGCCTTG-GTA--TGGAAACT-TACTAAG
Chlore cp --------------------TTGAGCCTTT-AAA--GGGAAACT-TTTAAAG
Cylindros ------AGTTAACTTCACAGTGGGCGGCAT-ATA--AAGAAACT-TATATGC
Dermocarp ------AGTTAGTTTTGCTATGGGCGGTAC-GTA--AAGAAATT-TGCGTGC
Gloeobact ATCAAACCTGGGTCTGCATATGGGCTGTAC-AGG--GAGTAACC-CTTGTAC
Osc 6304 ------AGTTAGCATTGCGATGGGCTGCAT-ACTA-AGGAAACT-GGTATGC
Osc 7105 ------GGTTGAGTCAGCA--GGGCTGTAA-GGC--AGGAAACT-GCTTTGC
Scytonema ------AGTTATTCTTACTATGGGCGGTAC-GTA--AAGAAACT-TACGTAT
Synechocy -------CATCTTGCAAAAAGGGGCTGCGC-AAA--AGGAAACT-TCTGCGT
Agrobacte --------------------TTGGG-GGTT-GCGCCCGGAAACGACGCAATC
Azoarcus --------------------ATGTG-CCTT-GCGCCGGGAAACCACGCAAGG
P3 P4 P5 P5a P5a'
|----| |----| || |--| |--|
Anabaena TGGAAGCTCTCAAATTCAGGGAAACCT--AAA--TCTG*CAGA--TA
Calothrix TGTAAGCTCTCAAATTCAGGGAAACCT--AAT--TCTA*TAGA--TA
Chloroglo TGTCCGCTCTCAAATTCAGGGAAACCT--AAA--TCTG*CAGA--CA
Cylindros TGGAAGCTCTCAAACTCAGGGAAACCT--AAA--TCTG*CAGA--CA
Fischerel TGAATGCTCTCAAATTCAGGGAAACCT--AAA--TCTG*CAGA--CA
Nos 7120 TGGATGCTCTCAAACTCAGGGAAACCT--AAA--TCTA*TAGA--CA
Nostoc sp TGGAAGCTCTCAAACTCAGGGAAACCT--AAA--TCTG*CAGA--CA
Osc 6304 TGACCGCTCTCAAATTCAGGGAAACCT--AAC--TCTG*CAGA--CA
Phormidiu TGGAAGCTCTCAAACTCAGGGAAACCT--AAG--TCAG*GAGA--TA
Prochloro TGTAAGCTCTCAAATTCAGGGAAACCT--AAG--GCC-*-GGC--TA
Pseudanab TGGACGCTCTCAAACTCAGGGAAACCT--AAA--TTTG*TAGA--CA
Scytonema TGACTGCTCTCAAACTCAGGGAAACCT--AAA--TCTG*CAGA--CA
Synechoco TGGCAGCTCTCAAACTCAGGGAAACCT--AAA--ACTT*AAGT--CA
Marcha cp TGATTGTTTTCAAATTCAGGGAAACCTAG-GTTG----*-----AAA
Nicoti cp TGATCACTTTCAAATTCAGAGAAACCC---TGGA----*----AAAA
Chlore cp TGAATGCTTTCAAATTCAGGGAAACTCT---T--GAAA*TTTC--TA
Cylindros GTTTATCTGTCAAACTCGGGGAAGCC------------*--------
Dermocarp GTTTACCTGTCAAACTCGGGGAAGCC------------*--------
Gloeobact GAACTCCTGCCAAATTCGGGGAAGCC------------*--------
Osc 6304 GATAGCCTCTCAAATTCGGGGAAGCC------------*--------
Osc 7105 GACAACTTCCCAAACTCGGGGAAGCC------------*--------
Scytonema GTTTACCTGTCAAACTCGGGGAAGCC------------*--------
Synechocy GATTATCTCTCAAATTCGGGGAAGCC------------*--------
Agrobacte GAT--CTGCTCAAAGTCGGGGAAAGC---TTC--GCTG*CAGT---A
Azoarcus GAT--GGTGTCAAATTCGGCGAAACC---TAA--GCGC*GCGT---A
P5' P4' P6 P6a P6a' P6' P7
|| |----||-| |--| |--| |-| |-----|
Anabaena --TGGCAATCCTGAGCCAAGCCCG*AGGGAAGGTGCAGAGACTCG
Calothrix --TGGCAATCCTGAGCCAAGCCAA*TTGGAAGGTGCAGAGACTCG
Chloroglo --AGGCAATCCTGAGCCAAGCCAA*TTGGAAGGTGCAGAGACCCG
Cylindros --TGGCAATCCTGAGCCAAGCCCA*AGGGAAGGTGCAGAGACCCG
Fischerel --AGGCAATCCTGAGCCAAGCCAA*TTGGAAGGTGCAGAGACCCG
Nos 7120 --AGGCAATCCTGAGCCAAGCCGA*ACGGAAGGTGCAGAGACTCG
Nostoc sp --TGGCAATCCTGAGCCAAGCCCG*AGGGAAGGTGCAGAGACCCG
Osc 6304 --AGGCAATCCTGAGCCAAGCCGA*TCGGAAGGTGCAGAGACTCG
Phormidiu --TGGCAATCCTGAGCCAAGCCGT*GCGGAAGGTGCAGAGGCCCG
Prochloro --GGGCAATCCTGAGCCAAGCTGA*TCGGAAGGTGCAGAGACTCG
Pseudanab --AGGCAATCCTGAGCCAAGCCTA*AAGGAAGGTGCAGAGACTCG
Scytonema --TGGCAATCCTGAGCCAAGCCAA*TAGGAAGGTGCAGAGGCCCG
Synechoco --TGGCAATCCTGAGCCAAGCTAA*TTAGAAGGTGCAGAGACTAG
Marcha cp TTAGGTAATCCTGAGCCAAATTTT*AAAAGAGGTGCAGAGACTCA
Nicoti cp T-GGGCAATCCTGAGCCAAATCCT*AGGATAGGTGCAGAGACTCA
Chlore cp TAGAGTAATCCTGAGTCAA-TTCA*TGAAGAGGTGCAGAGACTCA
Cylindros ---GGTAATCCCGAACCAAGCCTC*GAGGAAGGTGTAGAGACTGG
Dermocarp ---GGTAATCCCGAACCAAGCTCT*AGAGAAGGTGTAGAGACTGG
Gloeobact ---GGTAATCCCGAGCCAAGCTCC*GGAGAAGGTGTAGAGACTGG
Osc 6304 ---GGTAATCCCGAGCCAAGCTCT*GAACAAGGTGTAGAGACTCG
Osc 7105 ---GGTAATCCCGAGCCAAGCTCC*GGAGAAGGTGTAGAGACTCG
Scytonema ---GGTAATCCCGAACCAAGCTCC*GGAGAAGGTGTAGAGACTGG
Synechocy ---GGTAATCCCGAGCCAAACCTA*TGGGAAGGTGTAGAGACTTA
Agrobacte --TGCCAATCCCGAGCCAAGCTCC*GGTGAAGGTGTAGAGACTGG
Azoarcus --TGGCAACGCCGAGCCAAGCTTC*GATGAAGGTGTAGAGACTAG
P3' P8 P8a P8a' P8' P7'
|----||----| || || |----| |------|
Anabaena ACGGGAGCTACCCTAA-CGT*GCG--AGGGTAAAGGGAGAGTCCA----
Calothrix ACGGGAGCTACCCTAA-CGT*GCG--AGGGTAAAGGGAGAGTCCA----
Chloroglo ACGGGAGCTACCCTAA-CGT*TCG--AGGGTAAAGGGAGAGTCCA----
Cylindros ACGGGAGCTACCCTAA-CGT*TCG--AGGGTAAAGGGAGAGTCCA----
Fischerel ACGGGAGCTACCCTAA-CGT*TCG--AGGGTAAAGGGAGAGTCCA----
Nos 7120 ACGGGAGCTACCCTAA-CGT*ACG--AGGGTAAAGAGAGAGTCCA----
Nostoc sp ACGGGAGCTACCCTAA-CGT*TCG--AGGGTAAAGGGAGAGTCCA----
Osc 6304 ACGGGAGCTACCCTAA-CGT*CCG--AGGGTAAAGGGAGAGTCCA----
Phormidiu ACGGGAGCTACCCTAA-CGT*TCG--AGGGTAAAGGGAGGGTCCA----
Prochloro ACGGGAGCTACCCTAA-CAG*CTG--AGGGTAAAGGGAGAGTCCA----
Pseudanab ACGGGAGCTACCCTAA-CGT*ACG--AGGGTAAAGAGAGAGTCCA----
Scytonema ACGGGAGCTACCCTAA-CGT*TCG--AGGGTAAAGGGAGGGTCCG----
Synechoco ACGGGAGCTACCCTAA-CGG*CCG--AGGGTAAAGGGATAGTCCA----
Marcha cp AAGAAAACTATCCTAA-CGA*ACG--AGGATAAAGATAGAGTCCGT---
Nicoti cp ATGGAAGCTATTCTAA-CAA*ACG--AGAATAAAGATAGAGTCCCG---
Chlore cp ACGGGAGCTATCCTAA-CAA*TTG--AGGATAAAGAGAGAGTCC-----
Cylindros AAGGCAGACACCCTAA-CGC*ACG--AGGGTGAAGGGACAGTCCAG---
Dermocarp AAGGCAGGCATCCTAA-CGT*CCG--AGGATGAAGGGACAGTCCAG---
Gloeobact ATGGCAGGCACCCTAA-CGG*CCG--AGGGTGAAGGGACAGTCCAG---
Osc 6304 ATGGGAGGCACCCTAA-CAG*TTA--AGGGTGAAGGGAGAGTCCAG---
Osc 7105 ATGGGAAGCACCCTAA-CAG*CTG--AGGGTGAAGGGAGAGTCCAG---
Scytonema AAGGCAGGTACCCTAA-CAG*CTG--AGGGTAAAGGGACAGTCCAG---
Synechocy ATGGGAGACACCCTAA-CAG*CTG--AGGGTGAAGAGAAAGTCCAG---
Agrobacte ATGGGCAGCAC-CTAAAGGC*GTCCACG-GTGAAGGGACAGTCCAG---
Azoarcus ACGGCACCCAC-CTAA-GGC*GCTA-TG-GTGAAGGCATAGTCCAGGGA
P9 P9a P9a' P9b P9b' P9'
|----| |--| |--| |---| |---| |----|
Anabaena ATTCTT-AAAGCCT*AGGCAACAGTGAAAGCTGTGG--AAGAAT--------G
Calothrix ATCCTT-AAAACCT*TGGTAGTAGTGAAAGCTACAA--AAGGAT--------G
Chloroglo ATTCTC-AAAGCCT*AGGCAGTGGCGAAAGCTGCGG--GAGAAT--------G
Cylindros ATTTTC-AAAGCCT*AGGCAGCAGTGAAAACTGCGG--GAAAAT--------G
Fischerel ATTCTC-AAAGCC-*-GGCAGTAGTGAAAACTGCGG--GAGAAT--------G
Nos 7120 ATTCTC-AAAGCC-*-GGCAGTAGCGAAAGCTGCGG--GAGAAT--------G
Nostoc sp ATTCTC-AAAATCT*AGGTAGCAGTGAAAACTGCGG--GAGGAT--------G
Osc 6304 ATTCTC-AAAACCA*TGGCAGCAGCGAAAGTTGCGG--GAGAAT--------G
Phormidiu ATCCTC-AAAGCCC*TGGCAGCAACGAAAGTTGTGG--GAGGGT--------G
Prochloro ATTCTC-AAAACCT*GGGCAACAGTGAAAGCTGTGG--GAGAAT--------G
Pseudanab ATTCTT-AAAGCC-*-GGCAGTGATGAAAGTCACAG--AAGAAT--------G
Scytonema ATTCTC-AAAACCT*AGGCAGTAGCGAAAGCTGCAG--GAGAAT--------G
Synechoco ATTCTC-AACATCG*TGATGGCAGCGAAAGTTGCAGA-GAGAAT--------G
Marcha cp -TTTTACAA-GTTA*TAACAACAATGCAAATTGTA--GTAAAA--------TG
Nicoti cp -TTCTACAT-GTCA*CGGCAACAATGAAATTTATC--GTAAGA--------GG
Chlore cp AGT-----------*--------------------------ACT--------G
Cylindros ACCA--CAAACTGG*CCAG-GCAACGAAAGTTGTAGT---TGGT------AAG
Dermocarp ACCA--CAAACTGG*TCAG-GCAGTGAAAGCTGTAGA---TGGT------AAG
Gloeobact ACCC--CAAACTGC*GCAG-GCAGCGGAAGCTGTAG----TGGT------ACG
Osc 6304 ACCA--CAAACTGG*CCGG-GCAGCGAAAGCTGTAGA---TGGT------ACG
Osc 7105 ACTA--CAAACTGA*TCAG-GCAGTGAAAACTGTAG----TAGT------ACG
Scytonema ACCA--CAAACTGG*CCAG-GCAGTGAAAACTGTAGA---TGGT------AAG
Synechocy ACCA--CAAACTGA*TCAG-GCAGTGAAAACTGTAGT---TGGT------AAG
Agrobacte ACCAC--GAACGCC*GGCG-GCGGCGAAAGCCGA-A---GCGGT------ATG
Azoarcus --------------------GTGGCGAAAGTCAC----------ACAAACCGG
Legend:
Insertion site of the introns, indicated by a star along with the anticodon: Leu, tRNALeu
(U*AA); fMet, tRNAfMet (*CAU); Arg, tRNA Arg (CCU*); Ile, tRNAIle (CAU*)
Species nomenclature: Agrobacte, Agrobacterium tumefasciens A136; Anabaena, Anabaena
cylindrica; Azoarcus, Azoarcus BH72; Calothrix, Calothrix desertica PCC7102; Chlore cp,
Chlorella vulgaris chloroplast; Chloroglo, Chlorogloeopsis fritschii; Cylindros,
Cylindrospermum PCC7417; Dermocarp, Dermocarpa PCC7437; Fischerel, Fischerella ambigua
UTEX1903; Gloeobact, Gloeobacter violaceus PCC7421; Marcha cp, Marchantia polymorpha
chloroplast; Nicoti cp, Nicotiana tabacum chloroplast; Nos 7120, Nostoc PCC7120; Nostoc
sp, Nostoc PCC 73102; Osc 6304, Oscillatoria PCC6304; Osc 7105, Oscillatoria PCC7105;
Phormidiu, Phormidium ectocarpi PCC7375; Prochloro, Prochlorothrix hollandica; Pseudanab,
Pseudanabaena PCC7403; Scytonema, Scytonema PCC7110; Synechoco, Synechococcus PCC7942;
Synechocy, Synechocystis PCC6308.