Cyanobacteria

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Cyanobacterias Repeat Sequences
where did they come from?

• Molly Sergio

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Overview of Presentation

• unique DNA repeats
• Cyanobacteria genomes
• Similarities?
• Research !

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Eureaka! Repeated Sequences!

• Dispersed Repeats

Tandem Repeats
CRISPRs
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Dispersed Repeats
Transposons!
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Tandem Repeats
Slippage
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CRISPRs
Clustered Short Regularly Spaced Palindromic
Repeat
Where do CRISPRs come from?
Picture credit James Godde
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Example of CRISPRs in Npun
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28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16
GTTTTAACTAACAAAAATCCCTATCAGGGATTGAAAC13
GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9
GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4
GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4
GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
CRISPR Sequences Found In Cyanobacteria
Copy
Nostoc PCC 7120
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Similarity Between CRISPRs
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How did CRISPRS arise in cyanobacteria genomes?
Any matching CRISPR in Anabaena variabilis?
Any non-CRISPR sequences match?
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Locating a CRISPR in a7120
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36

• (SEQUENCE-SIMILAR-TO "CTTTCCGATCACATCACCCCGAAAGGGG
  ATGGAAAC" 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

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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. "TGCACATTGATATAAACGAAGCTAAAAAAGCCTCTACCAATATA
  A"
• 9-10."TCTTGCATACAAAGCTGCATTTCTAGATGACAA"

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How did CRISPRS arise in cyanobacteria genomes?
GAGAGACTGGAAACAATTTCTATAGCGATGTCGGAT
Anabaena 7120
CTTTCCGATCACATCACCCCGAAAGGGGATGGAAAC
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28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16
GTTTTAACTAACAAAAATCCCTATCAGGGATTGAAAC13
GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9
GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4
GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4
GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
CRISPR Sequences Found In Cyanobacteria
Copy
Nostoc PCC 7120
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How did CRISPRS arise in cyanobacteria genomes?

• (SEQUENCE-SIMILAR-TO "CTTTCCGATCACATCACCCCGAAAGGGG
  ATGGAAAC" IN avar)
• Nil
• (SEQUENCE-SIMILAR-TO "
  " IN avar)
• Nil

Use a different CRISPR and its non-CRISPR
sequences from a7120

• (SEQUENCE-SIMILAR-TO "GTTTTAATTCCTTTACCCCTCACGGGGA
  TGGAAAC" 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

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28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16
GTTTTAATTCCTTTACCCCTCACGGGGATGGAAAC13
GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9
GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4
GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4
GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
Sequences Found In Cyanobacteria
Copy
Nostoc PCC 7120
1 2 3 4 5 6
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28 GTTACTTACCATCACTTCCCCGCAAGGGGATGGAAAC16
GTTTTAATTCCTTTACCCCTCACGGGGATGGAAAC13
GTTTCTATTAACACAAATCCCTATCAGGGATTGAAAC 9
GTTGCAACACCATATAATCCCTATTAGGGATTGAAAC 4
GTTAAAACCCTCTAAAATCCCTATCAGGGATTGAAAC 4
GTTGCAACCCTCCTTCCAGTAATGGGAGGGTTGAAAG
Sequences Found In Cyanobacteria
Copy
0 2 147 35 146 0
0 0 0 0 0 0
Nostoc PCC 7120
1 2 3 4 5 6
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What conclusions can be drawn?

• Anabaena 7120 has at least four unique CRISPRs
  that were found in Anabaena variabilis

common ancestor of cyanobacteria
retained all six CRISPRs
lost two CRISPRs
Anabaena variabilis
Anabaena 7120
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What conclusions can be drawn?

• Anabaena 7120 has at least four unique CRISPRs
  that were found in Anabaena variabilis

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The End
The End

• Special thanks to Dr. James Godde
• Assistant Professor at Monmouth, Illinois
• Contact number 309-457-2350
• Email jgodde_at_monm.edu