Mural at NASA Ames Research Center

Mural at N

AS

A A

mes R

esearch Center

Homing Endonucleases

Sequence nearly identical to the carrot vma1 gene – except for central region of about 1200 nucleotides.

Homing

Self Splicing Domain

Homing Endonuclaease Domain

Ribonucleotide Reductase

InteinGroup I IntronsGroup II Introns

Inteins

Group I Introns

Group II Introns

The Homing Cycle

Homing cycle of a parasitic genetic element (modified from [3, 13]). Recent findings suggest that due to complex population structure the cycle might not operate in synchrony in different subpopulations. The red arrows indicate the trajectory of the functioning HE and the black arrows the fate of the host gene. The precise loss can occur through recombination with an intein or intron free allele, or, in case of introns, through recombination with a reverse transcript of the spliced mRNA [39, 40].

From: Gogarten et al., Annu. Rev. Microbiol. 2002. 56:263–87

XXAlleles with empty

Target Site

ZZAlleles invaded by a functional Homing

Endonuclease

YYAlleles harboring a

dysfunctional Homing

Endonuclease

(I) X-alleles are converted to Z-

alleles through the function of

the homing endonuclease,

leading to super Mendelian

inheritance of Z

X < Z

Y > Z(II) Carriers of the Y-allele are more fit than carriers of the Z

allele. The presence of a dysfunctional homing endonuclease provides

immunity to invasion by Z

(III)

Carri

ers o

f the

Y-all

ele ar

e

less fi

t tha

n ca

rrier

s of t

he X

allele

. Y <

X

Long term persistence of the HE containing allele is possible within a single well mixed population. Different trajectories result depending on the size of the selective disadvantage caused by the functioning HE and the frequency of efficient homing.

Collaboration with Adi Barzel, Uri Obolski, Martin Kupiec, Lilach Hadany from Tel Aviv University Barzel et al BMC Evolutionary Biology 11:324(2011)

Intein Allele

Extein Annotationcdc21-a

cell division control protein 21cdc21-b

cdc21-c

polB-d

DNA polymerase BpolB-a

polB-b

polB-c

pol-IIaDNA polymerase II large subunit

pol-IIb*

dtd** deoxycytadine triphosphate deaminasegyrB DNA gyrase subunit B

helicase-b* ATP-dependent helicaseligase** ATP-dependent DNA ligase I

rfc-aReplication factor C small subunit

rfc-d*

rir1-l*

Ribonucleoside-diphosphate reductaserir1-k

rir1-b

rir1-g

rir1-m*

rpolA DNA-directed RNA polymerase subunit Audp UDP-glucose 6-dehydrogenasetopA DNA topoisomerase I

top6B DNA topoisomerase VI subunit B

* intein alleles discovered in this work ** denotes extein sequences not previously reported to be invaded by an intein

Distribution of 24 intein alleles in 118 Halobacterial genomes

Tree from 55 ribosomal proteins(phyml, WAG, Gamma+I)

Inteins identified with PSSMs

Clustering / phylogenetic tree (mrBayes) based on intein presence and absence and concatenated intein sequences.

clusters with >.95 post. prob.

clusters not in the ribosomal reference tree

Intein Allele Tree TopologyHalo-

bacteriaBacteri

aOther

Euryarchaeotacdc21-a Monophyletic 55 4 16cdc21-c Monophyletic 1 0 0dtd** Monophyletic 6 0 0gyrB Monophyletic 6 17 1

helicase-b* Monophyletic 1 2 1ligase** Monophyletic 1 0 0pol-IIb* Monophyletic 9 0 1polB-c Monophyletic 20 2 3polB-d Monophyletic 6 0 1rfc-a Monophyletic 16 0 13

rfc-d* Monophyletic 5 0 0rir1-b Monophyletic 15 51 5rir1-g Monophyletic 4 15 0rir1-k Monophyletic 5 1 0rir1-l* Monophyletic 3 3 0

rir1-m* Monophyletic 1 4 0rpolA Monophyletic 10 0 0top6B Monophyletic 8 0 0topA Monophyletic 4 0 1Udp Monophyletic 7 2 6

polB-a Salinibacter inside Haloarchaea 16 2 1

polB-bHalanaerobium/Salinibacter with

Haloarchaea38 3 0

pol-IIa Methanoregula inside Haloarchaea 75 1 15cdc21-b Thermococcus inside Haloarchaea 51 1 4

Haloarchaeal inteins and their homologs in other groups

* intein alleles discovered in this work ** denotes extein sequences not previously reported to be invaded by an intein.

branches with aLRT support < .85

Halobacteria

Methanomicrobia

other Euryarchaeota

Nanohaloarchaea

ML-Phylogeny of Intein in DNA polymerase II insertion site a (pol-II-a)

Halorubrum

Conclusion• The distribution of intein alleles suggests frequent intein gain and

loss inside the haloarchaea.

• Clustering of genomes based on intein sequences suggests that most of the intein transfers are between closely related organisms.

• Only few transfers occurred between haloarchaea and other archaea and bacteria. These include - Salinibacter ruber (halophile, 20-30% salt, Bacteroidetes), - Halanaerobium saccharolyticum (halophile, 9-15% salt, Firmicutes), - Thermococcus barophilus (thermophile, 2-3% salt, Thermococci) - Methanoregula formicica (0-1% salt, Methanomicrobia)