Forgac, M. Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology. Nature Rev. Mol. Cell Biol. 8, 917–929 (2007)
Article
Pallen, M. J. & Matzke, N. J. From the origin of species to the origin of bacterial flagella. Nature Rev. Microbiol. 4, 784–790 (2006)
ChemPortISIArticle
Liu, R. & Ochman, H. Stepwise formation of the bacterial flagellar system. Proc. Natl Acad. Sci. USA 104, 7116–7121 (2007)
ChemPortPubMedArticle
Mulkidjanian, A. Y., Makarova, K. S., Galperin, M. Y. & Koonin, E. V. Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nature Rev. Microbiol. 5, 892–899 (2007)
ChemPortISIArticle
Dolezal, P., Likic, V., Tachezy, J. & Lithgow, T. Evolution of the molecular machines for protein import into mitochondria. Science 313, 314–318 (2006)
ChemPortISIPubMedArticle
Clements, A. et al. The reducible complexity of a mitochondrial molecular machine. Proc. Natl Acad. Sci. USA 106, 15791–15795 (2009)
PubMedArticle
Archibald, J. M., Logsdon, J. M., Jr & Doolittle, W. F. Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes. Mol. Biol. Evol. 17, 1456–1466 (2000)
ChemPortISIPubMed
Gabaldón, T., Rainey, D. & Huynen, M. A. Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (complex I). J. Mol. Biol. 348, 857–870 (2005)
ChemPortISIPubMedArticle
Thornton, J. W. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Rev. Genet. 5, 366–375 (2004)
Article
Liberles, D., ed. Ancestral Sequence Reconstruction (Oxford Univ. Press, 2007)
Harms, M. J. & Thornton, J. W. Analyzing protein structure and function using ancestral gene reconstruction. Curr. Opin. Struct. Biol. 20, 360–366 (2010)
ChemPortISIPubMedArticle
Frattini, A. et al. Defects in TCIRG1 subunit of the vacuolar proton pump are responsible for a subset of human autosomal recessive osteopetrosis. Nature Genet. 25, 343–346 (2000)
Pérez-Sayáns, M., Somoza-Martìn, J. M., Barros-Angueira, F., Rey, J. M. & Garcìa-Garcìa, A. V-ATPase inhibitors and implication in cancer treatment. Cancer Treat. Rev. 35, 707–713 (2009)
ChemPortISIPubMedArticle
Xu, L. et al. Inhibition of host vacuolar H+-ATPase activity by a Legionella pneumophila effector. PLoS Pathog. 6, e1000822 (2010)
ChemPortPubMedArticle
Hirata, T. et al. Subunit rotation of vacuolar-type proton pumping ATPase: relative rotation of the g and c subunits. J. Biol. Chem. 278, 23714–23719 (2003)
ChemPortISIPubMedArticle
Imamura, H. et al. Rotation scheme of V1-motor is different from that of F1-motor. Proc. Natl Acad. Sci. USA 102, 17929–17933 (2005)
ChemPortPubMedArticle
Powell, B., Graham, L. A. & Stevens, T. H. Molecular characterization of the yeast vacuolar H+-ATPase proton pore. J. Biol. Chem. 275, 23654–23660 (2000)
ChemPortISIPubMedArticle
Umemoto, N., Yoshihisa, T., Hirata, R. & Anraku, Y. Roles of the VMA3 gene product, subunit c of the vacuolar membrane H+-ATPase on vacuolar acidification and protein transport. A study with VMA3-disrupted mutants of Saccharomyces cerevisiae. J. Biol. Chem. 265, 18447–18453 (1990)
ChemPortISIPubMed
Umemoto, N., Ohya, Y. & Anraku, Y. VMA11, a novel gene that encodes a putative proteolipid, is indispensable for expression of yeast vacuolar membrane H+-ATPase activity. J. Biol. Chem. 266, 24526–24532 (1991)
ChemPortISIPubMed
Taylor, J. W. & Berbee, M. L. Dating divergences in the fungal tree of life: review and new analyses. Mycologia 98, 838–849 (2006)
ISIPubMedArticle
Yang, Z., Kumar, S. & Nei, M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641–1650 (1995)
ChemPortISIPubMed
Kane, P. M. The where, when, and how of organelle acidification by the yeast vacuolar H+-ATPase. Microbiol. Mol. Biol. Rev. 70, 177–191 (2006)
ChemPortISIPubMedArticle
Hirata, R., Graham, L. A., Takatsuki, A., Stevens, T. H. & Anraku, Y. Vma11 and vma16 encode second and third proteolipid subunits of the Saccharomyces cerevisiae vacuolar membrane H+-ATPase. J. Biol. Chem. 272, 4795–4803 (1997)
ChemPortISIPubMedArticle
Wang, Y., Cipriano, D. J. & Forgac, M. Arrangement of subunits in the proteolipid ring of the V-ATPase. J. Biol. Chem. 282, 34058–34065 (2007)
ChemPortISIPubMedArticle
Ohno, S. Evolution by Gene Duplication (Springer, 1970)
Jacob, F. Evolution and tinkering. Science 196, 1161–1166 (1977)
ChemPortISIPubMedArticle
Lynch, M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl Acad. Sci. USA 104, 8597–8604 (2007)
ChemPortPubMedArticle
Hietpas, R. T., Jensen, J. D. & Bolon, D. N. Experimental illumination of a fitness landscape. Proc. Natl Acad. Sci. USA 108, 7896–7901 (2011)
ChemPortPubMedArticle
Tong, A. H. Y. et al. Global mapping of the yeast genetic interaction network. Science 303, 808–813 (2004)
ChemPortISIPubMedArticle
Pereira-Leal, J. B., Levy, E. D., Kamp, C. & Teichmann, S. A. Evolution of protein complexes by duplication of homomeric interactions. Genome Biol. 8, R51 (2007)
ChemPortPubMedArticle
Ryan, M., Graham, L. A. & Stevens, T. H. Voa1p functions in V-ATPase assembly in the yeast endoplasmic reticulum. Mol. Biol. Cell 19, 5131–5142 (2008)
ChemPortISIPubMedArticle
Löytynoja, A. & Goldman, N. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl Acad. Sci. USA 102, 10557–10562 (2005)
ChemPortPubMedArticle
Löytynoja, A. & Goldman, N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320, 1632–1635 (2008)
ChemPortISIPubMedArticle
Whelan, S. & Goldman, N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18, 691–699 (2001)
ChemPortISIPubMed
Abascal, F., Zardoya, R. & Posada, D. Prottest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104–2105 (2005)
ChemPortISIPubMedArticle
Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003)
ISIPubMedArticle
Anisimova, M. & Gascuel, O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 55, 539–552 (2006)
ISIPubMedArticle
Aguinaldo, A. M. A. et al. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387, 489–493 (1997)
ChemPortISIPubMedArticle
Yang, Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007)
ChemPortISIPubMedArticle
Fitch, W. M. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416 (1971)
ISIArticle
Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994)
ChemPortISIPubMedArticle
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004)
ChemPortISIPubMedArticle
Do, C. B., Mahabhashyam, M. S., Brudno, M. & Batzoglou, S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 15, 330–340 (2005)
ChemPortISIPubMedArticle
Fletcher, W. & Yang, Z. Indelible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26, 1879–1888 (2009)
ChemPortISIPubMedArticle
Sambrook, J. & Russel, D. W. Molecular Cloning: A Laboratory Manual 3rd edn (Cold Spring Harbor Laboratory Press, 2001)
Goldstein, A. L. & McCuster, J. H. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15, 1541–1553 (1999)
ChemPortISIPubMedArticle
Zheng, L., Baumann, U. & Reymond, J. L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32, e115 (2004)
PubMed