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A Conserved Amphipathic Helix Is Required for Membrane Tubule Formation by Yop1p

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A Conserved Amphipathic Helix Is Required for Membrane Tubule Formation by Yop1p A conserved amphipathic helix is required for PNAS PLUS membrane tubule formation by Yop1p Jacob P. Brady, Jolyon K. Claridge, Peter G. Smith, and Jason R. Schnell1 Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom Edited by William F. DeGrado, School of Pharmacy, University of California, San Francisco, CA, and approved December 31, 2014 (received for review August 18, 2014) The integral membrane proteins of the DP1 (deleted in polyposis) C-terminal tubulin binding domains providing a link between ER and reticulon families are responsible for maintaining the high morphology and the cytoskeleton (19). membrane curvature required for both smooth endoplasmic retic- The RHDs are proposed to form hydrophobic hairpins too ulum (ER) tubules and the edges of ER sheets, and mutations in short to traverse the membrane fully, leading to greater dis- these proteins lead to motor neuron diseases, such as hereditary placement of lipids from the outer leaflet than from the in- spastic paraplegia. Reticulon/DP1 proteins contain reticulon ho- ner leaflet. By this mechanism, a combination of hydrophobic mology domains (RHDs) that have unusually long hydrophobic wedging and oligomeric scaffolding could lead to the stabiliza- segments and are proposed to adopt intramembrane helical hair- tion of the tubular ER membrane. However, there is currently pins that stabilize membrane curvature. We have characterized no structural information available for these intramembrane the secondary structure and dynamics of the DP1 family protein domains, and the exact mechanism of curvature generation and produced from the YOP1 gene (Yop1p) and identified a C-termi- stabilization remains unknown. The mechanism for exclusive nal conserved amphipathic helix (APH) that, on its own, interacts localization of RHD proteins to highly curved membranes also strongly with negatively charged membranes and is necessary remains unclear; however, the transmembrane domains have for membrane tubule formation. Analyses of DP1 and reticulon been implicated in both membrane localization and curvature family members indicate that most, if not all, contain C-terminal stabilization (4, 20, 21). sequences capable of forming APHs. Together, these results in- Yop1p is one of the best characterized of the RHD-containing dicate that APHs play a previously unrecognized role in RHD proteins (4, 5). It is a member of the DP1 family and has the membrane curvature stabilization. highest functional and sequence conservation with human REEP5 (19). Yop1p can be purified from yeast membranes and Yop1p | DP1 | reticulon | tubular ER | amphipathic helix reconstituted into lipids to generate tubules of ≈17 nm in di- ameter (5). To investigate possible mechanisms of membrane he endoplasmic reticulum (ER) is the largest membrane- deformation by RHDs, we determined the secondary structure Tbound organelle in the eukaryotic cell and adopts diverse and dynamics of Yop1p in lipid- and detergent-containing morphologies, including tubules that extend outward to the cell micelles. Our results indicate that the transmembrane domains BIOCHEMISTRY periphery and sheet-like structures closer to the nucleus (1, 2). contain enough helical residues to traverse the hydrophobic bi- The regions of high membrane curvature that are found in the layer of the ER fully. In addition, an amphipathic helix (APH) ER tubules and sheets are stabilized by the DP1 (deleted in was discovered that is C-terminal to the transmembrane domains polyposis) and reticulon classes of integral membrane proteins in a region previously shown to be important for function (5). We (3–5). Consistent with their role in ER morphology, similar show here that the APH on its own interacts with membranes proteins have not been found in prokaryotes (6). and that deletion of the APH abolishes membrane tubule for- There are six human DP1 proteins originally identified as mation in vitro. The amphipathic nature of the helix, as well as accessory proteins facilitating the expression of odorant recep- tors, and thus termed receptor expression-enhancing proteins Significance (REEPs) (7). The ability of REEPs to facilitate receptor traf- ficking has recently been related back to their ER shaping ac- The first structural studies, to our knowledge, of a reticulon tivities (8). The importance of REEPs in ER morphology is also homology domain (RHD), which is essential for maintaining highlighted by their implication in human diseases that are as- smooth endoplasmic reticulum (ER) tubules and the edges of sociated with neurons having long axons and requiring an ex- ER sheets, are described. We show here that the RHD of the pro- tended tubular ER (9, 10). For example, mutations in the tein Yop1p from the YOP1 gene has hydrophobic helices long transmembrane domain of REEP1, which is primarily expressed enough to cross the membrane fully but contains a previously in neurons (11), lead to pure forms of hereditary spastic para- uncharacterized amphipathic helix (APH) that is necessary for plegia (HSP) (12, 13). membrane tubule formation. The APH is highly conserved in its The reticulon family in humans comprises four members, amino acid properties and its location relative to the RHD both Rtn1–Rtn4 (6). Rtn4 is of particular interest because it is pri- in the DP1 (deleted in polyposis) and reticulon families. These marily responsible for generating or stabilizing the tubular ER in results place the DP1/reticulon proteins into the large and mammalian cells. Rtn4 is critical in neuronal cell processes be- growing class of membrane-remodeling proteins that use APHs to influence membrane curvature. cause it inhibits spontaneous neurite outgrowth (14) and restricts neuronal plasticity (15), and it has been implicated in several Author contributions: J.P.B. and J.R.S. designed research; J.P.B., J.K.C., and P.G.S. per- neural diseases, including schizophrenia and motor neuron dis- formed research; J.P.B. analyzed data; and J.P.B. and J.R.S. wrote the paper. ease (16–18). The authors declare no conflict of interest. The DP1 and reticulon proteins have in common a region This article is a PNAS Direct Submission. ≈ containing two, unusually long hydrophobic segments ( 35 aa in Freely available online through the PNAS open access option. length each) known as a reticulon homology domain (RHD) (6). 1To whom correspondence should be addressed. Email: [email protected]. – In humans, REEPs 1 6 are similar overall; however, the RHD This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. of REEPs 1–4 is truncated (Fig. S1). REEPs 1–4 also possess 1073/pnas.1415882112/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1415882112 PNAS | Published online February 2, 2015 | E639–E648 Downloaded by guest on September 29, 2021 its position C-terminal to the last transmembrane domain, is Solubilization of Yop1p into Mixed Micelles for Solution NMR. For highly conserved across the DP1 and reticulon families, and thus solution NMR studies, Yop1p was reconstituted into either may play a role in membrane curvature stabilization by all LMPG alone or mixed micelles containing 20 mM lipid 1,2- family members. dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and 40 mM LMPG (Q = 0.5). DPPC has an acyl chain length commonly Results found in yeast membranes (23), and thus was expected to provide Bacterially Expressed Yop1p Oligomerizes and Forms Membrane a more native-like environment than the lysolipid LMPG by Tubules in Vitro. Based on previous work (5), a Yop1p construct itself. Fig. S2 shows NOE cross-peaks from the amide protons of lacking 23 N-terminal and 15 C-terminal residues (residues 24–165; Yop1p to the DPPC methyl and methylene groups in mixed hereafter referred to as Yop1p) was chosen for structural studies. micelles in which the acyl chains of LMPG were deuterated, This construct was expressed in Escherichia coli using the single- demonstrating that the protein is in direct contact with the lipid acyl chains. Estimations of the rotational correlation times, τ ,of protein production (SPP) system (22), and subsequently purified c Yop1p derived from 15N-1H cross-correlated relaxation (24) in- and refolded into 2% (wt/vol) (42 mM) 1-myristoyl-2-hydroxy-sn- ′ rac creased from 7.9 ns in LMPG alone to 11.9 ns in DPPC, consistent glycero-3-phospho-(1 - -glycerol) (LMPG) micelles. The similar- with Yop1 being associated with the larger mixed micelles. ity of the bacterially expressed Yop1p protein to the protein ex- Nearly complete assignment of backbone 1H, 15N, 13Cα,and13C′ pressed in yeast was initially assessed by oligomerization, which is resonances and side-chain 13Cβ resonances (>95%) was achieved correlated with Yop1p function (3, 5). Oligomerization of Yop1p for Yop1p in both LMPG micelles and LMPG/DPPC (Q = 0.5) has been demonstrated previously by cross-linking (3), sucrose mixed micelles (Fig. 2 and Fig. S3A). Comparison of the TALOS- gradient ultracentrifugation (5), and fluorescence recovery after N secondary structure predictions between Yop1p in LMPG and photobleaching (3), all of which suggest that Yop1p forms oligomers mixed micelles revealed the appearance of an N-terminal helix containing four to seven copies. Glutaraldehyde cross-linking was and slight increases in helical propensities for those helices also used to assess the oligomeric state of E. coli-expressed Yop1p and identified in LMPG. The increases in helicity were most apparent indicated that Yop1p was primarily monomeric in 2% (wt/vol) at the edges of the transmembrane domains and the regions LMPG. By contrast, cross-linking at a lower LMPG concentra- around helical Pro (P35, P71, P115, and P146) (Fig. S3 B and C). tion of 0.01% resulted in a distribution of oligomeric species up In addition, several heteronuclear single quantum coherence to at least trimers being observed with no apparent aggregation (HSQC) peaks, including the HSQC peak for G44, which was (Fig. 1A). strongly exchange-broadened in LMPG, gave more homogeneous To confirm that the bacterially expressed and refolded Yop1p signals in mixed micelles.
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