TMEM16 and OSCA/TMEM63 proteins share a conserved potential to permeate ions and phospholipids

Abstract

The calcium-activated TMEM16 proteins and the mechanosensitive/osmolarity-activated OSCA/TMEM63 proteins belong to the Transmembrane Channel/Scramblase (TCS) superfamily. Within the superfamily, OSCA/TMEM63 proteins, as well as TMEM16A and TMEM16B, are thought to function solely as ion channels. However, most TMEM16 members, including TMEM16F, maintain an additional function as scramblases, rapidly exchanging phospholipids between leaflets of the membrane. Although recent studies have advanced our understanding of TCS structure-function relationships, the molecular determinants of TCS ion and lipid permeation remain unclear. Here, we show that single mutations along the transmembrane helix (TM) 4/6 interface allow non-scrambling TCS members to permeate phospholipids. In particular, this study highlights the key role of TM 4 in controlling TCS ion and lipid permeation and offers novel insights into the evolution of the TCS superfamily, suggesting that, like TMEM16s, the OSCA/TMEM63 family maintains a conserved potential to permeate ions and phospholipids.

Keywords: OSCA; TMEM16; TMEM63; evolution; human; ion channel; molecular biophysics; scramblase; structural biology.

Figure 1.. Lysine mutations along TM 4 enable TMEM16F channel and scramblase activities in the absence of calcium stimulation.

(a) Top: TMEM16F is a calcium-activated phospholipid scramblase. Bottom: TM 4 mutant locations mapped on TMEM16F CaPLSase structure with side chains shown as yellow sticks (PDB 6QPB). (b) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged TMEM16F wildtype (WT), I521K, M522K, and T526K (center column). CF 594-conjugated Annexin V (AnV, right column) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left column). (c) Quantification of the percentage of cells with AnV labeling for TMEM16F WT (n = 5), I521K (n = 5), M522K (n = 5), and T526K (n = 5) transfected cells (Figure 1—source data 1). Values were derived from images of biological replicates. Statistical comparisons to T526K were done using unpaired t-tests with Welch’s correction (ns: p > 0.05, ****p < 0.0001). (d) Representative current recordings and (e) current–voltage (I–V) relationships (Figure 1—source data 1) of whole-cell patches from TMEM16F KO HEK293T cells expressing eGFP-tagged TMEM16F WT (n = 6), I521K (n = 5), M522K (n = 5), and T526K (n = 7). Currents were elicited by the voltage protocol shown with the pipette solution containing 5 mM EGTA(Ethylene glycol tetraacetic acid). Dotted line denotes zero current. (f) Quantification of current at +160 mV (Figure 1—source data 1). Currents in (e) and (f) were normalized to cell capacitance. Statistical comparisons to T526K were done using unpaired t-tests with Welch’s correction (*p < 0.05, **p <0 .01). (g) Lysine mutations along TM 4 in TMEM16F enable spontaneous phospholipid permeation in the absence of calcium. All error bars represent standard error of the mean (SEM) calculated from replicate images or independent patches.

Figure 1—figure supplement 1.. Conformational changes in transmembrane helices (TMs) 4 and 6 are associated with TMEM16 scramblase activities.

(a) Phylogenetic tree of TMEM16 (calcium-activated chloride channel [CaCC], red; putative and validated CaPLSase, green), OSCA (purple), and TMEM63 (gold) families. Structure alignments of (b) fungal NhTMEM16 in calcium-bound open (PDB 6QM9, pink) and calcium-bound closed (PDB 6QMB, gray), (c) fungal AfTMEM16 in calcium-bound open (PDB 6E0H, cyan) and calcium-free closed (PDB 6DZ7, gray), (d) human TMEM16K in calcium-bound open (PDB 5OC9, orange) and calcium-bound closed (PDB 6R7X, gray), and (e) mouse TMEM16F F518H in calcium-bound open (PDB 8B8J, green) and calcium-free closed (PDB 8B8G, gray) conformations. (f) Sequence alignment of TM 4 region for mouse TMEM16F, mouse TMEM16A, human TMEM16K, fungal AfTMEM16, fungal NhTMEM16, thale cress OSCA1.2, mouse TMEM63A, human TMEM63B, and mouse TMC1. Yellow and cyan highlighting denotes residues identified in this work and hydrophobic gate residues previously identified, respectively.

Figure 1—figure supplement 2.. Alternative side chains at I521 cause differential phosphatidylserine (PS) exposure.

(a) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged TMEM16F wildtype (WT), I521A, and I521E (center column). CF 594-conjugated Annexin V (AnV, right column) labeled PS exposing cells. BF denotes bright field images (left column). (b) Quantification of the percentage of cells with AnV labeling for TMEM16F WT (n = 5), I521A (n = 5), and I521E (n = 5) transfected cells (Figure 1—figure supplement 2—source data 1). Values were derived from images of biological replicates. Statistical comparisons were not conducted due to zero variance within each group.

Figure 2.. I611K on TM 6 enables TMEM16F channel and scramblase activities in the absence of calcium stimulation.

(a) I611 highlighted on the TMEM16F CaPLSase structure with side chains shown as yellow sticks (PDB 6QPB). (b) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged TMEM16F wildtype (WT) and I611K (center column). CF 594-conjugated Annexin V (AnV, right column) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left column). (c) Quantification of the percentage of cells with AnV labeling for TMEM16F WT (n = 5) and I611K (n = 5) transfected cells (Figure 2—source data 1). Values were derived from images of biological replicates. Statistical comparison was done using an unpaired t-test with Welch’s correction (****p < 0.0001). (d) Representative current recordings and (e) current–voltage (I–V) relationships (Figure 2—source data 1) of whole-cell patches from TMEM16F KO HEK293T cells expressing eGFP-tagged TMEM16F WT (n = 6) and I611K (n = 5). Currents were elicited by the voltage protocol shown with the pipette solution containing 5 mM EGTA. Dotted line denotes zero current. (f) Quantification of current at +160 mV (Figure 2—source data 1). Currents in (e) and (f) were normalized to cell capacitance. Statistical comparison was done using an unpaired t-test with Welch’s correction (***p < 0.001). (g) A lysine mutation on TM 6 in TMEM16F enables spontaneous phospholipid permeation in the absence of calcium. All error bars represent standard error of the mean (SEM) calculated from replicate images or independent patches.

Figure 3.. Lysine mutations along TM 4 enable TMEM16A channel and scramblase activities in the absence of calcium stimulation.

(a) Top: TMEM16A is a calcium-activated chloride channel (CaCC). Bottom: TM 4 mutant locations mapped on TMEM16A CaCC structure with side chains shown as yellow sticks (PDB 5OYG). (b) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged TMEM16A wildtype (WT), I546K, I547K, and E551K (center column). CF 594-conjugated Annexin V (AnV, right column) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left column). (c) Quantification of the percentage of cells with AnV labeling for TMEM16A WT (n = 4), I546K (n = 4), I547K (n = 4), and E551K (n = 5) transfected cells (Figure 3—source data 1). Values were derived from images of biological replicates. Statistical comparisons were done using unpaired t-tests with Welch’s correction (*p < 0.05, **p < 0.01). (d) Representative whole-cell current recordings and (e) current–voltage (I–V) relationships (Figure 3—source data 1) of whole-cell patches from TMEM16F KO HEK293T cells expressing eGFP-tagged TMEM16A WT (n = 14), I546K (n = 5), I547K (n = 5), and E551K (n = 6). Currents were elicited by the voltage protocol shown with the pipette containing 5 mM EGTA. Dotted line denotes zero current. (f) Quantification of current at +160 mV (Figure 3—source data 1). Currents in (e) and (f) were normalized to cell capacitance with the mean ± SEM calculated from independent patches. Statistical comparisons were done using unpaired t-tests with Welch’s correction (*p < 0.05, ****p < 0.0001). (g) Lysine mutations along TM 4 in TMEM16A enable spontaneous phospholipid permeation in the absence of calcium. All error bars represent standard error of the mean (SEM) calculated from replicate images or independent patches.

Figure 3—figure supplement 1.. Ani9 attenuates ion channel and phospholipid scramblase activities of TMEM16A I546K.

(a) Representative whole-cell current recordings elicited by the voltage protocol shown (left) for TMEM16A I546K before, during, and after application of 10 µM Ani9. (b) Representative time-course of Ani9 application and wash-off (Figure 3—figure supplement 1—source data 1). (c) Quantification of peak current from (b) before (bath), during (Ani9), and after (wash) Ani9 application (n = 5) (Figure 3—figure supplement 1—source data 1). Statistical comparisons were done using unpaired t-tests with Welch’s correction (*p < 0.05, **p < 0.01). (d) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged TMEM16A wildtype (WT) or I546K (center columns). CF 594-conjugated Annexin V (AnV) (right columns) failed to label any phosphatidylserine (PS) exposing cells (n = 4). BF denotes bright field images (left columns). (e) Ani9 attenuates mutant-induced phospholipid permeability.

Figure 4.. Lysine mutations along TM 4 enable OSCA1.2 channel and scramblase activities.

(a) Top: OSCA1.2 is a cation non-selective ion channel gated by membrane tension. Bottom: TM 4 mutant locations mapped onto the TM 4/6 interface of OSCA1.2 (PDB 6MGV) with key residues shown as yellow sticks. (b) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged OSCA1.2 wildtype (WT), L438K, or A439K mutants (center column). CF 594-conjugated Annexin V (AnV) (right column) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left column). Asterisk highlights a PS-positive cell for the A439K mutant. (c) Quantification of the percentage of cells with AnV labeling for OSCA1.2 WT (n = 4), L438K (n = 7), and A439K-transfected cells (n = 6) (Figure 4—source data 1). Statistical comparisons were conducted with unpaired t-tests with Welch’s correction (*p < 0.05, ****p < 0.0001). (d) Representative current recordings and (e) normalized conductance–voltage (G–V) relationships of inside-out patches from TMEM16F KO HEK293T cells expressing eGFP-tagged OSCA1.2 WT (n = 8), L438K (n = 8), and A439K (n = 6) (Figure 4—source data 1). Currents were elicited by the voltage protocol shown next to the listed pressures. Dotted lines denote zero current. (f) Quantification of half-maximal voltage at −50 mmHg for WT (109 mV), L438K (67 mV), and A439K (63 mV) (Figure 4—source data 1). Statistical comparison was conducted with unpaired t-tests with Welch’s correction (***p < 0.001, ****p < 0.0001). (g) Quantification of activation $\tau$_on at −50 mmHg and 160 mV for WT (41 ms), L438K (13 ms), and A439K (16 ms) (Figure 4—source data 1). Statistical comparison was conducted with unpaired t-tests with Welch’s correction (***p < 0.001, ****p < 0.0001). (h) A lysine mutation along TM 4 converts the OSCA1.2 channel into a phospholipid scramblase with spontaneous phospholipid permeability. All error bars represent standard error of the mean (SEM) calculated from replicate images or independent patches.

Figure 4—figure supplement 1.. Atomistic molecular dynamics (MD) simulations of OSCA1.2 wildtype (WT) and L438K exhibit differential hydration of the pore region.

(a) Representative timepoints (900 ns) for OSCA1.2 WT (left) and L438K (right). (b) Quantification of water occupancy in the pore region for WT (black) and L438K (red) over the duration of the simulation (Figure 4—figure supplement 1—source data 1). The pore region was defined as within 7 Å of I432, which is centrally positioned in the upper pore.

Figure 4—figure supplement 2.. Role of K435 in OSCA1.2 mutant phospholipid permeability.

(a) TM 4 mutant locations mapped onto the TM 4/6 interface of OSCA1.2 (PDB 6MGV) with key residues shown as yellow sticks. (b) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged OSCA1.2 wildtype (WT), K435L, K435L/L438K, or L438K mutants (center column). CF 594-conjugated Annexin V (AnV) (right column) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left column). (c) Quantification of the percentage of cells with AnV labeling for OSCA1.2 WT (n = 4), K435L (n = 6), K435L/L438K (n = 6), and L438K-transfected cells (n = 7) (Figure 4—figure supplement 2—source data 1). Statistical comparisons were conducted with unpaired t-tests with Welch’s correction (ns: p > 0.05, ***p < 0.001, ****p < 0.0001). Error bars represent standard error of the mean (SEM) calculated from replicate images.

Figure 4—figure supplement 3.. Hypotonic stimulation activates the OSCA1.2 ion channel.

(a) Representative current recordings elicited by the voltage protocol shown for mock (GFP) and OSCA1.2 wildtype (WT)-transfected cells before (black) and after (blue) reduction of bath osmolarity from 310 to 120 mOsm/kg. (b) Quantification of peak currents from (a) for mock (n = 5) and WT (n = 4) after reduction of bath osmolarity (Figure 4—figure supplement 2—source data 1). Statistical comparison was conducted with an unpaired t-test with Welch’s correction (**p < 0.01). Error bars represent standard error of the mean (SEM) calculated from independent patches.

Figure 5.. OSCA1.2 A439K is an osmolarity-activated scramblase.

Representative images of hypotonic osmolarity stimulation of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged OSCA1.2 (a) wildtype (WT) or (b) the A439K mutant (center columns). CF 594-conjugated Annexin V (AnV) (right columns) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left columns). Each row of representative images corresponds to the indicated time after hypo-osmotic stimulation. (c) Quantification of AnV intensity for OSCA1.2 WT (n = 5) and A439K (n = 5) after hypo-osmotic stimulation (Figure 5—source data 1). Statistical comparison was conducted with an unpaired t-test with Welch’s correction (**p < 0.01). (d) The A439K mutation converts OSCA1.2 to an osmolarity-activated phospholipid scramblase. Error bars represent standard error of the mean (SEM).

Figure 6.. Lysine mutations along TM 4 enable TMEM63A channel and scramblase activities.

(a) Top: TMEM63A is an ion channel gated by high-threshold membrane tension. Bottom: the TM 4/6 interface of HsTMEM63A (PDB 8GRS) with key residues shown as yellow sticks using amino acid numbering corresponding to the mouse ortholog. (b) Representative images of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged TMEM63A wildtype (WT), W472K, S475K, and A476K (center column). CF 594-conjugated Annexin V (AnV) (right column) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left column). (c) Quantification of the percentage of cells with AnV labeling for TMEM63A WT (n = 4), W472K (n = 4), S475K (n = 4), and A476K-transfected cells (n = 4) (Figure 6—source data 1). Statistical comparisons were conducted with unpaired t-tests with Welch’s correction (**p < 0.01, ****p < 0.0001). (d) Representative current recordings and (e) normalized conductance–voltage (I–V) relationships of cell-attached patches from TMEM16F KO HEK293T cells expressing either eGFP mock-transfected (n = 7) or eGFP-tagged TMEM63A WT (n = 7), W472K (n = 7), S475K (n = 5), or A476K (n = 7) (Figure 6—source data 1). Currents represent the subtraction of voltage alone from currents elicited by the voltage and pressure protocols shown. Dotted line denotes zero current. Note that the mock control was normalized to the mean maximal current elicited from WT-transfected cells. (f) Quantification of half-maximal voltage at −80 mmHg for WT (122 mV), W472K (96 mV), S475K (92 mV), and A476K (97 mV) (Figure 6—source data 1). Statistical comparison was conducted with unpaired t-tests with Welch’s correction (*p < 0.05, **p < 0.01, ***p < 0.001). (g) Lysine mutations along TM 4 in TMEM63A enable spontaneous phospholipid permeability. All error bars represent standard error of the mean (SEM) calculated from replicate images or independent patches.

Figure 6—figure supplement 1.. TMEM63A hypotonic stimulation.

Representative images of hypotonic osmolarity stimulation of TMEM16F knockout (KO) HEK293T cells expressing eGFP-tagged TMEM63A (a) wildtype (WT) or (b) the A476K mutant (middle columns). CF 594-conjugated Annexin V (AnV) (right columns) labeled phosphatidylserine (PS) exposing cells. BF denotes bright field images (left columns). Each row of representative images corresponds to the indicated time after hypo-osmotic stimulation. (c) Quantification of AnV intensity for TMEM63A WT (n = 3) and A476K (n = 5) after hypo-osmotic stimulation (Figure 6—figure supplement 1—source data 1). Statistical comparison was conducted with an unpaired t-test with Welch’s correction. Error bars represent standard error of the mean (SEM).

Author response image 1.. Representative inside-out currents for mock (GFP)- and OSCA1.

2 WT-transfected cells. OSCA1.2 is responsible for nA currents elicited by the pressure and voltage protocols shown.

Author response image 2.. Voltage-dependent rectification of OSCA1.2 current.

a. Representative OSCA1.2 trace (bottom) elicited by a voltage-ramp under -50 mmHg (top). b. The difference in inward and outward current amplitudes.

Author response image 3.. Trans-bilayer lipid flipping rates (kflip) accelerate with increasing side chain hydropathy for a residue placed in the center of a model transmembrane helical peptide.

Author response image 4.. Model of gating (and regulatory) mechanisms in the TMEM16 family.

(B) Overall architecture and proposed modules. (C) Pore-dilation gating model for CaCCs. (D) Clamshell gating model for CaPLSases.

Author response image 5.. 200 µM Gd3+ext fails to inhibit OSCA1.2 currents in cell-attached patches.

Pressure-elicited peak currents (n=6 each). Statistical test is an unpaired Student’s t-test.

Author response image 6.. 200 µM Gd3+int completely inhibits OSCA1.2 currents in inside-out patches.

(a) Representative traces in before (black), during (red), and after (blue) Gd3+ application. (b) Representative application timecourse. (c) Quantification of peak currents (n=8 each). Statistical test is one-way ANOVA.

Author response image 7.. AnV intensities of WT- and A439K-transfected cells after 10 minutes of hypotonic stimulation at the listed osmolarities.