Presentation on theme: "Very Short Dispersed Repeats Also, palindromes. What are they? Short sequences (between 4 and 13-ish nucleotides) – one might even say they’re very."— Presentation transcript:
Very Short Dispersed Repeats Also, palindromes
What are they? Short sequences (between 4 and 13-ish nucleotides) – one might even say they’re very short Occur multiple times in the genome, at dispersed intervals (not repeated right next to each other) – “distributed or spread over a wide interval”
It turns out that many of these very short dispersed sequences are palindromic – what does that mean? The sequence is read the same in the 5’ 3’ direction as it is in the 3’ 5’ direction.
Occurrence of Highly Iterated Palindromes (HIP1) in Cyanobacteria
Palindromic Sequence in Cyanobacteria 5’-GCGATCGC-3’ 3’-CGCTAGCG-5’ But not all cyanobacteria have this sequence
Blast Search What is the purpose of HIP1? ATGCATGATACGTAGCGATCGCCACCCGGGATTGCGATCGC Match: GCGATCGC What genes are nearby? Prior research shows DAM methylase recognition and DNA profiling
Results? Hypothetical Proteins-highest peak in Themosynechococcus and Trichodesmium Many metabolic proteins such as Ferredoxin, peptidase Program to overlap nearby genes in different organisms
References Robinson, P. J., Cranenburgh, R. M., Head, I. M. and Robinson, N. J. (1997), HIP1 propagates in cyanobacterial DNA via nucleotide substitutions but promotes excision at similar frequencies inEscherichia coli and Synechococcus PCC 7942. Molecular Microbiology, 24: 181–189. Robinson, P. J., Gupta, A., Bleasby, A., Whitton, B., Morby, AP. Singular over- representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria Moya, A. Delaye, L. Abundance and distribution of the highly iterated palindrome 1(HIP1) among prokaryotes Mob Genet Elements. 2011 Sep-Oct; 1(3) 159-168
O ccurrences of DNA uptake sequence from Haemophilus influenzae in other Pasteurellaceae bacteria By: Noha Mudhaffar
Reference Frequency and Distribution of DNA Uptake Signal Sequences in the Haemophilus influenzae Rd Genome. Genomic Sequence of an Otitis Media Isolate of Nontypeable Haemophilus influenzae: Comparative Study with H. influenzae Serotype d, Strain KW20. Xu Z, Yue M, Zhou R, Jin Q, Fan Y, et al. (2011) Genomic Characterization of Haemophilus parasuis SH0165, a Highly Virulent Strain of Serovar 5 Prevalent in China. PLoS ONE 6(5): e19631. doi:10.1371/journal.pone.0019631. DNA uptake signal sequences in naturally transformable bacteria.
The Evolutionary Change of DNA Uptake Sequences in Neisseria meningitides.
What are DNA Uptake Sequences (DUS)? Neisseria sp. Constitute ~1% of genome. Homology 5’GCCGTCTGAA’3 Kingdom: Bacteria Phylum: Proteobacteria Class: Betaproteobacteria Order: Neisseriales Family: Neisseriaceae Genus: Neisseria Species:Neisseria meningitidis
DNA Uptake Sequence AT-DUS AG-DUS
A Closer Look Strain# of DUS DUS SequenceG+C (%)Length of Genome (bp) N. meningitidis MC58 14775’ATGCCGTCTGAA’351.52272351 N. Meningitidis Z2491 14495’AGGCCGTCTGAA’351.82184406 N. Gonorrhoeae FA1090 15225’ATGCCGTCTGAA’352.72153922
Phylogeny 16s rRNA DUS
References http://phil.cdc.gov/phil/details.asp?pid=2678 http://phil.cdc.gov/phil/details.asp?pid=2678 Frye SA, Nilsen M, Tønjum T, Ambur OH. Dialects of the DNA uptake sequence in Neisseriaceae. PLoS Genet. 2013
Six nucleotide palindromic sequences in Mycobacteriophage genomes What about them? That’s a great question. I’m glad you asked.
How did we get here from Very Short Dispersed Repeats? A very short story. Point A: “Singular over-representation of an octameric palindrome, HIP1, in DNA from many cyanobacteria.” From there: what about palindromes in mycobacteriophages? ?
Avoidance of 6 nt palindromes in Mycobacteriophages Mycobacterial genomes generally do not avoid 6 palindrome sequence. Generally, this means that the viruses that infect them will not either. When two of the mycobacteriophage genomes were examined, they were found to avoid palindromes of size 6. “The sole exception is provided by the two M. tuberculosis phages D29 and L5, which strongly avoid palindromes of size 6.” (Rocha, et. al) 2001 L5 and D29 – Mycobacteriophage cluster A2
Generated 186 random sequences of the same length of the average Mycobacteriophage genome (70627 nucleotides long) and same GC content (64%) and counted the number of occurrences of all 6 nucleotide palindromes in these randomly generated sequences.
Occurrences of all 6 nucleotide palindromes over the actual genomes of Mycobacteriophages (or at least the 186 that BioBIKE knows)
What’re C1 cluster phages? “Only two of these (Subclusters C1 and C2) correspond to phages with myoviral morphologies (with contractile tails)” Okay, so they’re of the family Myoviridae. This means they are: generally lytic, and lack the necessary genes to become lysogenic. They have a contractile tail, and contracting the tail requires ATP. C cluster phage isolated by Michael Kiflezghi!
Which sequences are occurring so frequently? GGCGCCGACGTCCGCGCGACCGGT GTCGACGCGCGCCCCGGG TGGCCACAGCTGAGGCCT CGATCGCTGCAGTGCGCA Many of these are recognition sites for restriction enzymes. Significant? There’s a chance. Warrants more investigation? It seems likely.
References and credit for pictures phagesdb.org Rocha, E., Danchin, A., & Viari, A. (2001). Evolutionary role of Restriction/Modification systems as revealed by comparative genome analysis. Genome Research, (11), 946-958. doi:10.1101/gr.153101 Discussion of avoidance of palindromic sequences of length 4 and 6 and possible reasons for this avoidance in bacteria and bacteriophages. Mentions 2 mycobacteriophages that exhibit an avoidance for 6nt palindromes, L5 and D29. Article Source: Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution. Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, et al. (2011) Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution. PLoS ONE 6(1): e16329. doi: 10.1371/journal.pone.0016329Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution cyanobacteria picture: http://www.um.edu.mt/__data/assets/image/0005/166604/oculatella2.jpg http://www.um.edu.mt/__data/assets/image/0005/166604/oculatella2.jpg mycobacteriophage picture: http://openi.nlm.nih.gov/imgs/512/165/2884959/2884959_2711fig1.png http://openi.nlm.nih.gov/imgs/512/165/2884959/2884959_2711fig1.png coral snake: http://upload.wikimedia.org/wikipedia/commons/8/8a/Coral_snake.jpg