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Very Short Dispersed Repeats Very Short Dispersed Repeats

Very Short Dispersed Repeats - PowerPoint Presentation

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Very Short Dispersed Repeats - PPT Presentation

Also palindromes What are they Short sequences between 4 and 13ish nucleotides one might even say theyre 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 ID: 552500

coli escherichia mycobacterium phage escherichia coli phage mycobacterium dna sequences haemophilus genome influenzae palindromes sequence uptake occurrences mycobacteriophages hip1 dus mycobacteriophage short

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Slide1

Very Short Dispersed Repeats

Also, palindromesSlide2

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”Slide3

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.Slide4

Occurrence of Highly Iterated Palindromes (HIP1) in CyanobacteriaSlide5

Palindromic Sequence in Cyanobacteria

5’-GCGATCGC-3’

3’-CGCTAGCG-5’

But not all cyanobacteria

have this sequenceSlide6
Slide7

Blast Search

What is the purpose of HIP1?

ATGCATGATACGTA

GCGATCGC

CACCCGGGATT

GCGATCGC

Match: GCGATCGC

What genes are nearby?

Prior research shows DAM methylase recognition and DNA profiling Slide8

Thermosynechococcus

elongatus

BP1 &

Synechococcus

Elongatus

PCC 6301Slide9

Prochlorococcus marinus mit9301 &

Trichodesmium Erythraeum IMS101Slide10

Results?

Hypothetical Proteins-highest peak in Themosynechococcus and Trichodesmium

Many metabolic proteins such as Ferredoxin, peptidase

Program to overlap nearby genes in different organismsSlide11

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 in

Escherichia 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 Slide12

O

ccurrences

of DNA uptake sequence from

Haemophilus influenzae in other Pasteurellaceae bacteria

By: Noha MudhaffarSlide13

AAGTGCGGT

1516 (479 – 1001)

1913428

0.3815231Slide14

Highly Repeated Sequences Slide15

Family: PasteurellaceaeSlide16

Organism

Length

GC-FRACTION

Occurrences of DNA USS

Actinobacillus-succinogenes-130Z

2319663

0.44918594

1690

Haemophilus-influenzae-86-028NP

1913428

0.3815231

1516

Actinobacillus-actinomycetemcomitans-HK1651

1995520

0.44412282

1507

Mannheimia-succiniciproducens-MBEL55E

2314078

0.42537978

1485

Haemophilus-influenzae-R2846

1824242

0.37971717

1461

Haemophilus-somnus-2336

2263857

0.37378067

1355

Haemophilus-somnus-129PT

2012878

0.37191722

1245

Haemophilus-influenzae-R2866

1933340

0.38079283

952

Pasteurella-multocida-subsp-multocida-str-Pm70

2257487

0.40404883

927

Haemophilus-influenzae-86028NP

1738864

0.38510486

888

Haemophilus-influenzae-Rd-KW20

1830138

 

0.38147888

737

Actinobacillus-pleuropneumoniae-L20

2274482

0.41299513

73

Actinobacillus-pleuropneumoniae-serovar-1-str-4074

2292348

0.41376877

63

Mannheimia-haemolytica

2498406

0.40754706

59

Haemophilus-ducreyi-35000HP

1698955

0.38220495

41Slide17

Organism

Length

GC-FRACTION

Occurrences of DNA USS

Escherichia-coli-DH10B

5004529

0.5103499

19

Escherichia-coli-53638

5289471

0.5095685

22

Escherichia-coli-HS

4643538

0.5081961

5

Escherichia-coli-E24377A

4980187

0.50621593

19

Escherichia-coli-E2348-69

5059346

0.5050742

18

Escherichia-coli-F11

5206906

0.5049682

19

Escherichia-coli-042

5379979

0.50532633

24

Escherichia-coli-E110019

5384084

0.5077157

17

Escherichia-coli-K12

4639221

0.50788873

23

Escherichia-coli-O157-H7

5594477

0.5048416

27

Escherichia-coli-B7A

5202558

0.5084804

15

Escherichia-coli-APEC-O1

5497653

0.5033812

14

Escherichia-coli-B171

5299753

0.50713533

19

Escherichia-coli-CFT073

5231428

0.50474805

7

Escherichia-coli-W3110

4646332

0.5079958

22

Escherichia-coli-E22

5516160

0.506397

22

Escherichia-coli-O157-H7-EDL933

5528445

0.5038297

10

Escherichia-coli-ATCC-8739

4746218

0.5086652

23 Slide18

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.Slide19

The E

volutionary

C

hange of DNA Uptake Sequences in Neisseria meningitides.Slide20

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:

NeisseriaceaeGenus: NeisseriaSpecies:Neisseria

meningitidis Slide21

DNA Uptake Sequence

AT-DUS

AG-DUSSlide22

A Closer Look

Strain

# of DUS

DUS

Sequence

G+C (%)

Length of Genome (

bp

)

N.

meningitidis

MC58

1477

5’

ATGCCGTCTGAA’3

51.52272351 N. Meningitidis

Z249114495’AG

GCCGTCTGAA’3

51.8

2184406

N.

Gonorrhoeae

FA10901522

5’A

T

GCCGTCTGAA’3

52.7

2153922Slide23

DUS InversionSlide24

Phylogeny

16s

rRNA

DUSSlide25

References

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. 2013Slide26

Six nucleotide palindromic sequences in Mycobacteriophage

genomes

What about them? That’s a great question. I’m glad you asked.Slide27

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

?

?Slide28

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 A2Slide29

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.Slide30

Occurrences of all 6 nucleotide palindromes over the actual genomes of

Mycobacteriophages

(or at least the 186 that

BioBIKE knows) Slide31

Which phages are outliers to the right? (>2000 occurrences) - these 15

((

Mycobacterium-phage-Cali

2485) – C, C1

(

Mycobacterium-phage-

Catera

2466) – C, C1

(

Mycobacterium-phage-Alice

2437) – C, C1

(

Mycobacterium-phage-

LRRHood

2445) – C, C1

(

Mycobacterium-phage-Rizal

2465) – C, C1

(

Mycobacterium-phage-Nappy

2528) – C,

C1

(

Mycobacterium-phage-Ghost

2524) – C, C1

(

Mycobacterium-phage-

Drazdys

2506) – C,

C1

(

Mycobacterium-phage-

ScottMcG

2480) – C, C1

(

Mycobacterium-phage-Spud

2485) – C, C1

(

Mycobacterium-phage-

Sebata

2519) –

C, C1

(

Mycobacterium-phage-

Pio

2505) - C, C1

(

Mycobacterium-phage-Bxz1

2501) – C, C1

(

Mycobacterium-phage-

LinStu

2478) – C,

C1

(

Mycobacterium-phage-ET08

2466))

– C, C1

All of the cluster C1 phages in

BioBIKE

!Slide32

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

!Slide33

Which sequences are occurring so frequently?

GGCGCC GACGTC CGCGCG ACCGGT

GTCGAC GCGCGC CCCGGG

TGGCCA CAGCTG AGGCCT

CGATCG CTGCAG TGCGCA

Many of these are recognition sites for restriction enzymes. Significant? There’s a chance.

Warrants more investigation? It seems likely.Slide34

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.0016329 cyanobacteria picture: http://www.um.edu.mt/__

data/assets/image/0005/166604/oculatella2.jpgmycobacteriophage picture: 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