Mural at NASA Ames Research Center

1. Mural at NASA Ames Research Center Homing Endonucleases

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

4. Homing Self Splicing Domain Homing Endonuclaease Domain

6. Ribonucleotide Reductase Intein Group I Introns Group II Introns

7. Inteins

8. Group I Introns

9. Group II Introns

10. The Homing Cycle

11. 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].

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

13. XAlleles with empty Target Site (I) X-alleles are converted to Z-alleles through the function of the homing endonuclease, leading to super Mendelian inheritance of Z X < Z (III) Carriers of the Y-allele are less fit than carriers of the X allele. Y < X YAlleles harboring a dysfunctional Homing Endonuclease ZAlleles invaded by a functional Homing Endonuclease 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

14. 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 Biology11:324(2011)

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

16. Distribution of 24 intein alleles in 118 Halobacterial genomes Tree from 55 ribosomal proteins(phyml, WAG, Gamma+I)Inteins identified with PSSMs

17. 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

18. 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.

19. ML-Phylogeny of Intein in DNA polymerase II insertion site a (pol-II-a) other Euryarchaeota Methanomicrobia Nanohaloarchaea Halobacteria Halorubrum branches with aLRT support < .85

20. 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) - Methanoregulaformicica (0-1% salt, Methanomicrobia)