cyanobacteria’s repeat sequences … where did they come from?
DESCRIPTION
Cyanobacteria’s Repeat Sequences … where did they come from?. Molly Sergio. Overview of Presentation. unique DNA repeats Cyanobacteria genomes Similarities? Research !. Eureaka! Repeated Sequences!. Dispersed Repeats. Tandem Repeats. CRISPRs. - PowerPoint PPT PresentationTRANSCRIPT
Cyanobacteria’s
Repeat Sequences… where did they come from?
Molly Sergio
Overview of Presentation
unique DNA repeats
Cyanobacteria genomes
Similarities?
Research !
Eureaka! Repeated Sequences!
Tandem Repeats
CRISPRs
Dispersed Repeats
Dispersed Repeats
Jumping Genes
Transposons!
Barbara McClintock
Tandem Repeats
“Slippage”
CRISPRs CClustered lustered SShort hort RRegularly egularly SSpaced paced PPalindromic alindromic RRepeatepeat
Exact count of nuclotides
Non-CRISPR sequence would be duplicated
~ 35 to 37
nucleotides
Jump?
Slippage?
Where do CRISPRs come from?
Picture credit: James Godde
Example of CRISPRs in Npun
28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16 GTTTTAACTAACAAAAATCCCTATCAGGGATTGAAAC13 GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9 GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4 GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4 GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
Nostoc PCC 7120
58 ATTGCAATTTCTCAAAATCCCTATTAGGGATTGAAAC42 ATTGCAATTCATCAAAATCCCTATCAGGGATTGAAAC19 ATTGCAATTCATCAAAATCCCTATTAGGGATTGAAAC 9 ATTGCAATTTATCAAAATCCCTATTAGGGATTGAAAC12 GTGGCAACAACCCTCCAGGTACTGGGTGGGTTGAAAG
Nostoc punctiforme
2-4 CGGTTTATCCCCG GCGGG-GAACAC CTGGC
Escherichia coli
CRISPR Sequences Found In CyanobacteriaCopy
#
28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16 GTTTTAACTAACAAAAATCCCTATCAGGGATTGAAAC13 GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9 GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4 GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4 GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
Nostoc PCC 7120
58 ATTGCAATTTCTCAAAATCCCTATTAGGGATTGAAAC42 ATTGCAATTCATCAAAATCCCTATCAGGGATTGAAAC19 ATTGCAATTCATCAAAATCCCTATTAGGGATTGAAAC 9 ATTGCAATTTATCAAAATCCCTATTAGGGATTGAAAC12 GTGGCAACAACCCTCCAGGTACTGGGTGGGTTGAAAG
Nostoc punctiforme
CGGTTTATCCCCG GCGGG—GAACAC
CTGGC
Escherichia coli 2-4
Similarity Between CRISPRs
How did CRISPRS arise in cyanobacteria genomes?
com
pare
Any matching CRISPR in Anabaena variabilis?Anabaena 7120
Anabaena variabilis
? ? ? ? ? ?
Any non-CRISPR sequences match?
?? ? ? ?
Locating a CRISPR in a7120 (SEQUENCE-SIMILAR-TO "CTTTCCGATCACATCACCCCGAAAGGGGATGGAAAC" IN a7120)
Query Q-start Q-end Subject S-start S-end ID value
1. "Seq1" 1 36 #$A7120.CHROMOSOME 5647145 5647110 100% 2. "Seq1" 1 36 #$A7120.CHROMOSOME 5647076 5647041 100% 3. "Seq1" 1 36 #$A7120.CHROMOSOME 5646995 5646960 100% 4. "Seq1" 1 36 #$A7120.CHROMOSOME 5646922 5646887 100% 5. "Seq1" 1 36 #$A7120.CHROMOSOME 5646849 5646814 100% 6. "Seq1" 1 36 #$A7120.CHROMOSOME 5646774 5646739 100% 7. "Seq1" 1 36 #$A7120.CHROMOSOME 5646703 5646668 100% 8. "Seq1" 1 36 #$A7120.CHROMOSOME 5646635 5646600 100% 9. "Seq1" 1 36 #$A7120.CHROMOSOME 5646562 5646527 100% 10."Seq1" 1 36 #$A7120.CHROMOSOME 5646490 5646455 100%
1 36
Locating in between an a7120 CRISPR
(FOR-EACH coord-pair IN * AS left-coord = (+ (FIRST coord-pair) 1) AS right-coord = (- (SECOND coord-pair) 1) AS seq = (SEQUENCE-OF A7120.chromosome FROM left-coord TO right-coord) COLLECT seq)
Non-coding sequences (in between CRISPRs)1-2. "GAGAGACTGGAAACAATTTCTATAGCGATGTCGGAT" 2-3. "TCAATCATCTTTGCATTATATCCTGAAATTACAAGAT" 3-4. "CTCCCTTAGCCACTCTAGGATTTGTGACTGTT" 4-5. "ATGATTATCGAGGAATCTCGAAAATAGGACGTCGA" 5-6. "AAGCGACCATCGCTTTTTGCACGAACAGCAGATGGAACG" 6-7. "TCCTGCTCCAAGCATTAGTCCTTCGGAGATTAAAAAC" 7-8. "TAACTACTGCAAGCGTTGTGCAAGCAGCAATACCTGC" 8-9. "TGCACATTGATATAAACGAAGCTAAAAAAGCCTCTACCAATATAA" 9-10."TCTTGCATACAAAGCTGCATTTCTAGATGACAA"
How did CRISPRS arise in cyanobacteria genomes?
Anabaena 7120CTTTCCGATCACATCACCCCGAAAGGGGATGGAAAC
GAGAGACTGGAAACAATTTCTATAGCGATGTCGGAT
Compare CRISPR similarity
Compare similarity
Anabaena variabilis
28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16 GTTTTAACTAACAAAAATCCCTATCAGGGATTGAAAC13 GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9 GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4 GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4 GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
Nostoc PCC 7120
CRISPR Sequences Found In CyanobacteriaCopy #
1
2
3
4
5
6
?Anabaena variabilisBlast
How did CRISPRS arise in cyanobacteria genomes?
(SEQUENCE-SIMILAR-TO "CTTTCCGATCACATCACCCCGAAAGGGGATGGAAAC" IN avar) Nil
(SEQUENCE-SIMILAR-TO "**********************************************" IN avar) Nil
(SEQUENCE-SIMILAR-TO "GTTTTAATTCCTTTACCCCTCACGGGGATGGAAAC" IN avar)
Query Q-start Q-end Subject S-start S-end E-value
1. "Seq1" 1 35 #$A29413.Contig256 360180 360074 1.0d-13 2. "Seq1" 1 35 #$A29413.Contig256 360039 360005 1.0d-13
(SEQUENCE-SIMILAR-TO "**********************************************" IN avar) Nil
Use a different CRISPR and its non-CRISPR sequences from a7120…
28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16 GTTTTAATTCCTTTACCCCTCACGGGGATGGAAAC13 GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9 GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4 GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4 GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
Nostoc PCC 7120
Sequences Found In CyanobacteriaCopy
#
1
2
3
4
5
6
Anabaena variabilisBlast ?
28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16 GTTTTAATTCCTTTACCCCTCACGGGGATGGAAAC13 GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9 GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4 GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4 GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
Nostoc PCC 7120
Sequences Found In CyanobacteriaCopy
#
1
2
3
4
5
6
Anabaena variabilisBlast ?
02 14735 1460
000 000
What conclusions can be drawn?
• Anabaena 7120 has at least four unique CRISPRs that were found in Anabaena variabilis
common ancestor of cyanobacteria
Anabaena variabilisAnabaena 7120
Six matching CRISPRs inserted
retained all six CRISPRs
lost two CRISPRs
What conclusions can be drawn?
• Anabaena 7120 has at least four unique CRISPRs that were found in Anabaena variabilis
Anabaena variabilis
common ancestor of cyanobacteria
Anabaena 7120
six CRISPRs insertedfour CRISPRs inserted into A.var
The End
Special thanks to Dr. James Godde• Assistant Professor at Monmouth, Illinois • Contact number: 309-457-2350• Email: [email protected]
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