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1:

The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers.

Koonin EV, Makarova KS, Rogozin IB, Davidovic L, Letellier MC, Pellegrini L.

Genome Biol. 2003;4(3):R19. Epub 2003 Feb 28.

PMID: 12620104 [PubMed - indexed for MEDLINE]

3:

Conservation of intramembrane proteolytic activity and substrate specificity in prokaryotic and eukaryotic rhomboids.

Urban S, Schlieper D, Freeman M.

Curr Biol. 2002 Sep 3;12(17):1507-12.

PMID: 12225666 [PubMed - indexed for MEDLINE]

4:

Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases.

Lemberg MK, Freeman M.

Genome Res. 2007 Nov;17(11):1634-46. Epub 2007 Oct 15.

PMID: 17938163 [PubMed - indexed for MEDLINE]

5:

Cross genome comparisons of serine proteases in Arabidopsis and rice.

Tripathi LP, Sowdhamini R.

BMC Genomics. 2006 Aug 9;7:200.

PMID: 16895613 [PubMed - indexed for MEDLINE]

6:

A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain.

Aravind L, Iyer LM, Leipe DD, Koonin EV.

Genome Biol. 2004;5(5):R30. Epub 2004 Apr 16.

PMID: 15128444 [PubMed - indexed for MEDLINE]

7:

Molecular evolution before the origin of species.

Davis BK.

Prog Biophys Mol Biol. 2002 May-Jul;79(1-3):77-133. Review.

PMID: 12225777 [PubMed - indexed for MEDLINE]

8:

Rhomboid-like proteins in Apicomplexa: phylogeny and nomenclature.

Dowse TJ, Soldati D.

Trends Parasitol. 2005 Jun;21(6):254-8. Review.

PMID: 15922242 [PubMed - indexed for MEDLINE]

9:

A conserved mechanism for extracellular signaling in eukaryotes and prokaryotes.

Gallio M, Sturgill G, Rather P, Kylsten P.

Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12208-13. Epub 2002 Sep 9.

PMID: 12221285 [PubMed - indexed for MEDLINE]

10:

Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.

PMID: 11734060 [PubMed - indexed for MEDLINE]

11:

The origins of modern proteomes.

Kurland CG, Canbäck B, Berg OG.

Biochimie. 2007 Dec;89(12):1454-63. Epub 2007 Sep 15.

PMID: 17949885 [PubMed - indexed for MEDLINE]

12:

Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins.

Aravind L, Koonin EV.

Proteins. 2002 Mar 1;46(4):355-67.

PMID: 11835511 [PubMed - indexed for MEDLINE]

13:

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

Chen B, Zhong D, Monteiro A.

BMC Genomics. 2006 Jun 17;7:156.

PMID: 16780600 [PubMed - indexed for MEDLINE]

14:

Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.

Iyer LM, Makarova KS, Koonin EV, Aravind L.

Nucleic Acids Res. 2004 Oct 5;32(17):5260-79. Print 2004.

PMID: 15466593 [PubMed - indexed for MEDLINE]

15:

Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.

Wolf YI, Aravind L, Grishin NV, Koonin EV.

Genome Res. 1999 Aug;9(8):689-710.

PMID: 10447505 [PubMed - indexed for MEDLINE]

16:

Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea.

Koonin EV, Mushegian AR, Galperin MY, Walker DR.

Mol Microbiol. 1997 Aug;25(4):619-37.

PMID: 9379893 [PubMed - indexed for MEDLINE]

17:

Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade.

Kinch LN, Ginalski K, Grishin NV.

Protein Sci. 2006 Jan;15(1):84-93. Epub 2005 Dec 1.

PMID: 16322567 [PubMed - indexed for MEDLINE]

18:

Substrate specificity of rhomboid intramembrane proteases is governed by helix-breaking residues in the substrate transmembrane domain.

Urban S, Freeman M.

Mol Cell. 2003 Jun;11(6):1425-34.

PMID: 12820957 [PubMed - indexed for MEDLINE]

19:

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.

Aravind L, Makarova KS, Koonin EV.

Nucleic Acids Res. 2000 Sep 15;28(18):3417-32.

PMID: 10982859 [PubMed - indexed for MEDLINE]

20:

Stress genes and proteins in the archaea.

Macario AJ, Lange M, Ahring BK, De Macario EC.

Microbiol Mol Biol Rev. 1999 Dec;63(4):923-67, table of contents. Review.

PMID: 10585970 [PubMed - indexed for MEDLINE]

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