Kaleigh mariam Michael and Nicholas Start Associated Sequences in Enterobacteriophage Kaleigh hedges Ribosomal Binding Site Shine Dalgarno http themedicalbiochemistrypageorg ID: 387008
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Slide1
Short Dispersed Repeats
Kaleigh
,
mariam
, Michael and Nicholas Slide2
Start Associated Sequences in
Enterobacteriophage
Kaleigh
hedges Slide3
Ribosomal Binding Site
(Shine-
Dalgarno
)
http://
themedicalbiochemistrypage.org
/
protein-synthesis.php#polyaSlide4Slide5
Is there a conserved sequence in
Enterobacteriophage
that could help support translation initiation?
Where are these repeats located? How far away from Gene start? What is the associated start codon?
Do the sequences contain the Shine-
Dalgarno
sequence or is it nearby?Slide6
Biobike
/ MEMESlide7
Start Associated Sequences found in
EnterobacterioophageSlide8
Full Length ERIC Sequence Occurrence in Bacteriophage
Michael KiflezghiSlide9
Question: Do Bacteriophage contain ERIC sequences?
Some Bacteriophage have potential (and in some cases realized) clinical applications (1)
Bacteriophage sometimes acquire host DNA (2, 3)Slide10
Enterobacterial
Repetitive
Intergenic
Consensus Sequences
Wilson L A , and Sharp P M
Mol
Biol
Evol
2006;23:1156-1168Slide11
PhAnToMe/
BioBIKE
: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide12
PhAnToMe/
BioBIKE
: detecting the
imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide13
PhAnToMe/
BioBIKE
: detecting the
imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide14
PhAnToMe/
BioBIKE
: detecting the
imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide15
PhAnToMe/
BioBIKE
: detecting the
imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide16
PhAnToMe/
BioBIKE
: detecting the
imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide17
PhAnToMe/
BioBIKE
: detecting the
imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide18
PhAnToMe/
BioBIKE
: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
WindowSlide19
PhAnToMe/
BioBIKE
: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
CACTTACTTGTGTA
AGCTCCCGGAGGAT
TAGGAGGCCCTCGA
ReverseSlide20
PhAnToMe/
BioBIKE
: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
CACTTACTTGTGTA
AGCTCCCGGAGGAT
TAGGAGGCCCTCGA
SCORE = 5Slide21
Preliminary Results
Sequence found in
Enterobacteria
Phage LambdaSlide22
Identification of Possible RNA Hairpin Sequences in sub-cluster B3
Mycobacteriophages
Mariam Sankoh Slide23
How did I get here? Slide24
Where did I go from there? Slide25
Sample Input and Output Slide26
Location Identification of Initial Sequences Slide27
Palindromes within genes
Decrease Function Runtime
Decrease Noise and Repeats
Allow User to Expand Window Size
Grab upstream and downstream sequence
Confirm Repeated Sequences
Function determination of Hairpin Sequences
Improvements to Function
What’s Next? Slide28
Identification of Small Regulatory RNA within Miniature Inverse-Repeat Elements of
E. Coli
K-12
Nicholas RodriguezSlide29
Questions?
Can new genes be created by transposable elements?Slide30
Questions?
Can an organism make use of new genes in an advantageous way?Slide31
Small Regulator y RNA
Short ~19-25bp
Palindromes
Regulate gene expression?Slide32
Proposed MechanismSlide33
Identification of microRNA-Size, Small RNAs in Escherichia
coli. Kang et al 2013
Selectively Sequenced
msRNA
Slide34
ERICSSlide35
Methods
Searched for
msRNAs
in ERICs
Located Motifs from ERICSs in
msRNASlide36
msRNA in ERICsSlide37
Finding MotifsSlide38
Motifs Slide39
Where are the msRNA
?
Near highly expressed genes
Hitching a ride?