Institute of Molecular Biology

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Tom H. Stevens

Tom H. Stevens

Professor, Chemistry and Biochemistry
Member, IMB

Ph.D., California Institute of Technology
M.S., San Francisco State University
B.A., San Francisco State University

Office: Streisinger Hall Room 255C
Office Phone: 541-346-5884
Lab: Streisinger Hall Room 255
Lab Phone: 541-346-4608

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Research Interests

Research in the Stevens lab is concerned with the process of protein sorting and membrane assembly in yeast cells. Using yeast molecular genetics, we have identified a large number of genes required for the correct targeting and transport of proteins to the membrane-bounded organelle called the vacuole. These vacuolar protein sorting (VPS) genes have been found to encode proteins such as a dynamin-like GTPase, a protein-sorting receptor, a protein kinase, a lipid kinase, a RAS inhibitor-like protein, and an increasingly large number of proteins involved in transport vesicle targeting/fusion such as Rab-like GTPases and SNARE proteins. To characterize the function of some of these proteins we use biochemical, cell biological and molecular genetic approaches. Biochemical approaches are being used to isolate a number of the VPS proteins and to study the membrane-associated protein complexes in which they are found.

Schematic drawing of the yeast endomembrane pathways
Schematic drawing of the yeast endomembrane pathways. Proteins exiting the Golgi complex can be transported by either the CPY pathway (arrow 1) through the prevacuole to the vacuole, or by the ALP pathway (arrow 2). Proteins can also reach the prevacuole by endocytosis (arrow 3), and proteins in the prevacuole transit a common pathway to the vacuole (arrow 5). Golgi membrane proteins such as DPAP A are retrieved from the prevacuole back to the Golgi (arrow 4).

The group also has a long-standing interest in the assembly, targeting, structure and function of the vacuolar H+-translocating ATPase (V-ATPase; see figure). The V-ATPase complex consists of fourteen subunits, and all but one of these are encoded by a single yeast gene. The large hydrophobic V-ATPase “a” subunit has two isoforms, Vph1 and Stv1, with the Vph1-associated V-ATPase complex localizing to the vacuole membrane and the Stv1-associated V-ATPase restricted to Golgi and endosomal membranes. The mechanism of differential localization of these two forms of the yeast V-ATPase is under active investigation in the lab. We are investigating the proteins responsible for maintaining this differential localization, as well as the protein-based signals that specify the distinct localizations.

We have also identified five genes that encode proteins required for V-ATPase complex assembly but are not themselves part of the final V-ATPase enzyme complex. These five proteins reside in the yeast cell endoplasmic reticulum and constitute the dedicated assembly machinery for the V-ATPase. A number of molecular genetic and biochemical approaches are being taken to characterize the assembly complex and to study the interaction of this assembly complex with V-ATPase subunits along the assembly pathway within the endoplasmic reticulum.

Targeting of V-ATPase complexes
Targeting of V-ATPase complexes:
The membrane sector of the V-ATPase complex (V 0 sector) is assembled in the ER, and the assembled V-ATPase complex is then transported to the Golgi complex. The Stv1-containing V-ATPase complex cycles between the endosome and the Golgi complex, and the Vph1-containing V-ATPase complex is transported to the limiting vacuole membrane.

The lab has also employed ancestral gene reconstruction to investigate the V-ATPase enzyme complex in more detail. Ancestral reconstruction of the two V-ATPase subunit a isoforms has generated the most likely predecessor gene prior to gene duplication. This Anc.a protein functions with the remaining 13 V-ATPase subunits and has characteristics of both the Stv1- and Vph1-containing V-ATPase complexes. Ancestral reconstruction of the most likely predecessor of the Vma3 and Vma11 proteolipid V-ATPase subunits has led to the synthesis of an Anc.3-11 the functions with the remaining 12 V-ATPase subunits to form a functional enzyme complex. The Anc.3-11 protein allows the assembly of a proteolipid ring with two different polypeptides (Anc.3-11 and Vma16) rather than the modern-day ring with three different polypeptides (Vma3, Vma11 & Vma16). These investigations have revealed important insights into the modern-day V-ATPase complex as well as the evolution of this V-ATPase molecular machine.

Assembly of the VO sector in the ER Assembly of the V 0 sector in the ER: Vma21p interacts with the proteolipid ring V-ATPase subunits of Vma3p (c), Vma11p (c’), and Vma16p (c’’). Vma12p and Vma22p form a complex on the ER membrane and interact with newly synthesized “a” subunit (Vph1p and Stv1p), and then Vma21p “escorts” this V 0 sector into vesicles budding from the ER membrane. Vma21p accompanies the V-ATPase to the Golgi complex, where its C-terminal KKXX ER retention signal is recognized by the COPI machinery and this assembly/escort factor is recycled to the ER. The assembled V-ATPase is then transported on to the endosome and/or vacuole.

Recent publications

(pulled from pubmed)

Recent publications

(pulled from pubmed)

Homotypic vacuole fusion in yeast requires organelle acidification and not the V-ATPase membrane domain.
Coonrod EM, Graham LA, Carpp LN, Carr TM, Stirrat L, Bowers K, Bryant NJ, Stevens TH
Dev Cell 2013 Nov 25;27(4):462-8
Evolution of increased complexity in a molecular machine.
Finnigan GC, Hanson-Smith V, Stevens TH, Thornton JW
Nature 2012 Jan 9;481(7381):360-4
The reconstructed ancestral subunit a functions as both V-ATPase isoforms Vph1p and Stv1p in Saccharomyces cerevisiae.
Finnigan GC, Hanson-Smith V, Houser BD, Park HJ, Stevens TH
Mol Biol Cell 2011 Sep;22(17):3176-91
Voa1p functions in V-ATPase assembly in the yeast endoplasmic reticulum.
Ryan M, Graham LA, Stevens TH
Mol Biol Cell 2008 Dec;19(12):5131-42
Vma9p (subunit e) is an integral membrane V0 subunit of the yeast V-ATPase.
Compton MA, Graham LA, Stevens TH
J Biol Chem 2006 Jun 2;281(22):15312-9
Vta1p and Vps46p regulate the membrane association and ATPase activity of Vps4p at the yeast multivesicular body.
Lottridge JM, Flannery AR, Vincelli JL, Stevens TH
Proc Natl Acad Sci U S A 2006 Apr 18;103(16):6202-7
Vps51p mediates the association of the GARP (Vps52/53/54) complex with the late Golgi t-SNARE Tlg1p.
Conibear E, Cleck JN, Stevens TH
Mol Biol Cell 2003 Apr;14(4):1610-23
Ykt6p is a multifunctional yeast R-SNARE that is required for multiple membrane transport pathways to the vacuole.
Kweon Y, Rothe A, Conibear E, Stevens TH
Mol Biol Cell 2003 May;14(5):1868-81
Structure and assembly of the yeast V-ATPase.
Graham LA, Flannery AR, Stevens TH
J Bioenerg Biomembr 2003 Aug;35(4):301-12
Studying yeast vacuoles.
Conibear E, Stevens TH
Methods Enzymol 2002;351:408-32
Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae.
Sagermann M, Stevens TH, Matthews BW
Proc Natl Acad Sci U S A 2001 Jun 19;98(13):7134-9
Composition and assembly of the yeast vacuolar H(+)-ATPase complex.
Graham LA, Powell B, Stevens TH
J Exp Biol 2000 Jan;203(Pt 1):61-70
VPS21 controls entry of endocytosed and biosynthetic proteins into the yeast prevacuolar compartment.
Gerrard SR, Bryant NJ, Stevens TH
Mol Biol Cell 2000 Feb;11(2):613-26
Molecular characterization of the yeast vacuolar H+-ATPase proton pore.
Powell B, Graham LA, Stevens TH
J Biol Chem 2000 Aug 4;275(31):23654-60
The yeast endosomal t-SNARE, Pep12p, functions in the absence of its transmembrane domain.
Gerrard SR, Mecklem AB, Stevens TH
Traffic 2000 Jan;1(1):45-55
Assembly of the yeast vacuolar proton-translocating ATPase.
Graham LA, Stevens TH
J Bioenerg Biomembr 1999 Feb;31(1):39-47
Vacuole biogenesis in Saccharomyces cerevisiae: protein transport pathways to the yeast vacuole.
Bryant NJ, Stevens TH
Microbiol Mol Biol Rev 1998 Mar;62(1):230-47
Retrograde traffic out of the yeast vacuole to the TGN occurs via the prevacuolar/endosomal compartment.
Bryant NJ, Piper RC, Weisman LS, Stevens TH
J Cell Biol 1998 Aug 10;142(3):651-63
Multiple sorting pathways between the late Golgi and the vacuole in yeast.
Conibear E, Stevens TH
Biochim Biophys Acta 1998 Aug 14;1404(1-2):211-30