Unbiased proteomic and forward genetic screens reveal that mechanosensitive ion channel MSL10 functions at ER-plasma membrane contact sites in Arabidopsis thaliana

Abstract

Mechanosensitive (MS) ion channels are an evolutionarily conserved way for cells to sense mechanical forces and transduce them into ionic signals. The channel properties of Arabidopsis thaliana MscS-Like (MSL)10 have been well studied, but how MSL10 signals remains largely unknown. To uncover signaling partners of MSL10, we employed a proteomic screen and a forward genetic screen; both unexpectedly implicated endoplasmic reticulum-plasma membrane contact sites (EPCSs) in MSL10 function. The proteomic screen revealed that MSL10 associates with multiple proteins associated with EPCSs. Of these, only VAMP-associated proteins (VAP)27-1 and VAP27-3 interacted directly with MSL10. The forward genetic screen, for suppressors of a gain-of-function MSL10 allele (msl10-3G, MSL10^S640L), identified mutations in the synaptotagmin (SYT)5 and SYT7 genes. We also found that EPCSs were expanded in leaves of msl10-3G plants compared to the wild type. Taken together, these results indicate that MSL10 associates and functions with EPCS proteins, providing a new cell-level framework for understanding MSL10 signaling. In addition, placing a mechanosensory protein at EPCSs provides new insight into the function and regulation of this type of subcellular compartment.

Keywords: A. thaliana; VAMP-associated proteins; mechanosensitive ion channel; mechanotransduction; membrane contact sites; plant biology; synaptotagmins.

Figure 1.. Co-immunoprecipitation–liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies the MSL10-GFP interactome, which shares similarities to previous endoplasmic reticulum–plasma membrane contact site (EPCS) interactomes.

(A) Volcano plot showing the abundance of proteins detected in immunoprecipitations of MSL10-GFP in 35S:MSL10-GFP seedlings (right) compared to those identified in mock immunoprecipitations using WT Col-0 seedlings (left). Proteins were identified by LC-MS/MS, and the average abundance of each was quantified from the MS1 precursor ion intensities. Only those proteins with at least eight peptide spectral matches are shown. Each protein is plotted based on its -log₁₀(p-value) of significance based on four biological replicates relative to its log₂(fold change) of abundance (35S:MSL10-GFP/ WT). Proteins also detected in immunoprecipitations with the EPCS proteins SYT1 (Ishikawa et al., 2020), VST1 (dataset filtered for proteins with >8 peptide-spectral matches [PSMs]; Ho et al., 2016), and VAP27-1/3 (Stefano et al., 2018) or plasmodesmata-associated RTNLB3/6 (Kriechbaumer et al., 2015) are represented as red circles; proteins unique to the MSL10 interactome are represented as black squares. The 11 most significantly enriched proteins are labeled (p-value<0.002). (B) The overlap of the indicated interactomes with that of MSL10. The VAP27-1/3 interactome (Stefano et al., 2018) was not included here because only eight selected interactors were reported.

Figure 1—figure supplement 1.. Similar proteins were identified in MSL10-GFP and MSL10^7D-GFP immunoprecipitations.

(A) Volcano plots showing the preferential abundance of proteins detected in immunoprecipitations of 35S:MSL10-GFP (left, reproduced from Figure 1A) or 35S:MSL10^7D-GFP (right) compared to those of mock immunoprecipitations of WT Col-0 seedlings. (B) displays the relative abundance of proteins in 35S:MSL10-GFP (right) vs. 35S:MSL10^7D-GFP (left) immunoprecipitations. Proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the average abundance of each was quantified from the MS1 precursor ion intensities, and only those proteins with at least eight peptide spectral matches are shown. Each protein is plotted based on its -log₁₀(p-value) of significance based on four biological replicates relative to its log₂(fold change) of abundance. Data points indicated as red circles have previously detected in interactomes of SYT1 (Ishikawa et al., 2020), VAP27-1/3 (Stefano et al., 2018), RTNLB3/6 (Kriechbaumer et al., 2015), and VST1 (Ho et al., 2016). Labeled are proteins that were selected for further testing in Figure 2A, selected because in either the MSL10-GFP and/or MSL10^7D-GFP co-immunoprecipitations they were above the cutoffs indicated as dashed gray lines: fold change > 4 and p-values<0.05. Those with red labels have been found previously in endoplasmic reticulum–plasma membrane contact site (EPCS) or plasmodesmatal interactomes, and those in blue have not.

Figure 2.. MSL10 interacts with VAP27-1 and VAP27-3.

(A) Mating-based split-ubiquitin (mbSUS) assay. VAMP-associated protein 27-1 (VAP27-1), VAP27-3, synaptotagmin 1 (SYT1), actin 8 (ACT8), dynamin-like (DL1), RAB GTPase homolog 1c (RAB1c), coatomer α1 subunit (αCOP1), LOW EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (LOS1), METHIONINE OVERACCULATOR 3 (MTO3), AT3G44330, regulatory particle triple-A 1A (RPT1a), catalase 2 (CAT2), AT3G62360, and Ras-related nuclear protein 1 (RAN1) were fused to NubG and tested for interaction with Cub-tagged MSL10. Proteins labeled in red were previously detected at endoplasmic reticulum–plasma membrane contact sites (EPCSs). The results in (A) are consistent with a second independent mbSUS assay using independent transformants. (B, C) In vivo Förster resonance energy transfer–fluorescence lifetime imaging microscopy (FRET-FLIM) on UBQ:MSL10-GFP and UBQ:mRFP-VAP27-1 or UBQ:mRFP-VAP27-3 transiently expressed in tobacco. (B) Representative heat maps of the fluorescence lifetime (τ) of GFP measured in tobacco abaxial epidermal cells 5 days post-infiltration. Scale = 50 µm. (C) Average GFP fluorescence lifetime. Each data point represents the value from one field of view (three fields of view per plant from four infiltrated plants for a total of n = 12 for each combination). Error bars, SD. Groups indicated by the same letter are not statistically different according to ANOVA with Tukey’s post-hoc test.

Figure 2—figure supplement 1.. MSL10 signaling mutants interact with VAP27-1 and VAP27-3, and the VAP27 MSP domain is dispensable for interaction.

Mating-based split-ubiquitin assays testing (A) the interaction of full-length VAP27-1 and VAP27-3 with mutant versions of full-length MSL10 and (B) the interaction of full-length MSL10 with variants of VAP27-1 and VAP27-3 that lacked their major sperm protein (MSP) domain (VAP27-1∆6-125 and VAP27-3∆23-142). MSL10^7A is a phosphodead variant in which the seven phosphoserines in the N-terminus of MSL10 are mutated to alanine (Veley et al., 2014; Basu et al., 2020b). The MSL10^S640L substitution (msl10-3G allele) occurs in the cytosolic C-terminal domain of MSL10 (Zou et al., 2016). Both variants trigger constitutive overactivation of MSL10 cell death signaling. At right in (B): measurements of β-galactosidase activity in a liquid-based assay testing the same combinations at left using CPRG as substrate.

Figure 3.. A subpopulation of MSL10 co-localizes with a subpopulation of VAP27-1 and VAP27-3.

(A) Equatorial deconvolved confocal laser scanning micrographs of leaf abaxial epidermal cells from stable Arabidopsis T1 lines co-expressing MSL10-GFP and mRFP-VAP27-3 driven by their endogenous promoters. Scale = 5 µm. (B) Mander’s overlap coefficients M1 and M2 calculated from images taken from four independent T1 lines. (C, D) Deconvolved confocal micrographs showing a Z-slice at the top (cortical, C) and the middle (equatorial, D) of tobacco epidermal cells transiently expressing UBQ:MSL10-GFP and UBQ:mRFP-VAP27-1 or UBQ:mRFP-VAP27-3. Images were taken 5 days after infiltration. Scale = 5 µm.

Figure 4.. Some endoplasmic reticulum–plasma membrane contact sites (EPCSs) are expanded in msl10-3G plants.

Confocal Z-projections (maximum intensity projection of Z-slices from the top to the middle of cells) of GFP-tagged proteins in the indicated MSL10 backgrounds. MAPPER-GFP (A), VAP27-1-GFP (D), and SYT1-GFP (E) in 4-week-old abaxial leaf epidermal cells. Plants shown here are cousins (A, E) or siblings (D). Green, GFP; magenta, chlorophyll autofluorescence. Scale = 10 µm. Quantification of the percentage of the leaf epidermal cell volume taken up by MAPPER-GFP (B, C) or SYT1-GFP (F, G) puncta in plants in the msl10-1 or msl10-3G background compared to WT cousins. Each data point represents a biological replicate: the mean value of 20–50 epidermal cells from one plant, n = 10–25 plants per genotype from two or three separately grown flats. Error bars, SD. Means were compared by Student’s t-tests when data was normally distributed (B, F) or Mann–Whitney U-tests when it was not (C, G).

Figure 4—figure supplement 1.. MSL10 does not influence rearrangements in endoplasmic reticulum–plasma membrane contact sites (EPCS) morphology in response to osmotic stress in seedlings.

Confocal maximum intensity Z-projections of cotyledon epidermal cells. Green, GFP; magenta, chlorophyll autofluorescence. Scale = 10 µm. The seedlings being compared in (A, B) are F3 cousins. (A) Five-day-old seedlings were transferred from plates and incubated for 16 hr in liquid 1/10× MS or 1/10× MS + 100 mM NaCl. (B) Seedlings were grown on 1× MS or 1× MS +140 mM mannitol plates for 5 days. Seedlings were transferred to liquid media of the same concentration supplemented with 600 nM isoxaben and allowed to equilibrate for 4 hr before imaging (as described in Basu and Haswell, 2020a). MAPPER-GFP puncta size is larger in the presence of mannitol, in contrast to observations by Lee et al., 2019, and the difference might be attributable to the presence of mannitol in the plates for the entire life of the seedlings, used here. A subset of seedlings incubating in 1× MS + 140 mM mannitol + 600 nM isoxaben were transferred to liquid 1× MS + 600 nM isoxaben to trigger cell swelling, and these were imaged 24 hr later. (C) Five-day-old seedlings stably expressing UBQ:SYT1-GFP were mounted in water. Cotyledons were imaged before and after a 300 g weight was applied to a 22 × 22 mm coverslip for 20 s.

Figure 5.. A forward genetic screen identified sdm26 and sdm34, dominant suppressors of msl10-3G height and ectopic cell death phenotypes.

(A) Schematic of the screen. (B) Images of the indicated plants after 4–5 weeks of growth. (C) Segregation of height phenotypes in the BC₁F2 generation compared to the expected segregation ratio assuming the sdm alleles are dominant. (D) Siblings of backcrossed sdm26 and sdm34 mutants that were fixed for the sdm (suppressed dwarfing) or msl10-3G (dwarf) phenotypes. Top: 5-week-old BC₁F₂ plants of the indicated genotypes. Middle: 4-week-old BC₁F₃ progeny of plants at the top, as indicated with dashed lines. Bottom: leaves of 4-week-old BC₁F3 plants stained with Trypan blue to assess cell death. These results are representative of at least five other plants for each genotype, in two separate experiments. Scale = 300 µm.

Figure 5—figure supplement 1.. Intragenic sdm mutants and tests confirming that sdm26 and sdm34 causal mutations are extragenic.

(A) Intragenic sdm mutations mapped onto the predicted MSL10 topology. In pink is the cytosolic N-terminal domain, in teal is the cytoplasmic C-terminal domain, and in orange is the pore-lining MscS domain. The asterisk marks the location of one sdm mutation predicted to retain the intron between the first and second exons. (B) Pictures of 5-week-old F2 plants. From the sdm26 × msl10-1 cross, 1 out of 21 F2 plants screened had a dwarf msl10-3G phenotype, indicated with the asterisk. From the sdm34 × msl10-1 cross, there were 2 out of 23 F2 plants that had the dwarfed phenotype. Other F2 plants from both crosses had either a WT or intermediate height. That the msl10-3G (dwarf) phenotype could be recovered after crossing to the null msl10-1 line indicated that the sdm26 and sdm34 alleles were not linked to MSL10, confirming that they were extragenic suppressors.

Figure 6.. SYT5 S66F and SYT7 G427R are the causal mutations in sdm26 and sdm34, respectively.

(A) Overview of backcrossing and mapping-by-sequencing of sdm mutants. (B) Location of sdm26 and sdm34 missense mutations in the SYT5 and SYT7 proteins, respectively. UniProt was used to predict protein domains and their location. TM, transmembrane; SMP, synaptogamin-like mitochondrial-lipid-binding protein domain; CC, coiled coil; C2, Ca²⁺ binding. (C) Conservation of Ser66 and Gly427 residues in SYT5 and SYT7 homologs, respectively, in the predicted proteomes of selected angiosperms. (D, E) Phenotypes of msl10-3G plants expressing WT or sdm mutant SYT5 and SYT7 transgenes. (D) Top: images of representative T1 lines. Bottom: Trypan blue staining of a leaf from the same plants. Scale = 300 µm. (E) Mean and standard deviation of plant height of n = 9–32 T1 lines per construct, pooled from two similar experiments. Groups indicated with the same letters are not significantly different as assessed by ANOVA with Scheffe’s post-hoc test.

Figure 6—figure supplement 1.. Mapping-by-sequencing reveals the chromosomal regions containing the causal mutations of sdm26.

sdm26 was backcrossed to msl10-3G plants, and the segregating BC₁F2 population was pooled by phenotype and sent for whole-genome sequencing (WGS). Segregating BC₁F2 populations were pooled by phenotype and sent for WGS. (A) For each SNP identified, the frequency at which this mutant nucleotide was detected compared to the reference nucleotide was calculated and plotted against its chromosomal position. Regions where SNPs are represented with orange triangles were predicted to contain the causal mutation as mutant alleles were absent in the msl10-3G phenotypic pool (dwarfed) and present in the sdm phenotypic pool (suppressed dwarfing) near the expected frequency of 0.66. (B) Details of the SNPs in the chromosomal intervals identified in (A). Gene names and functional descriptions were obtained from TAIR.

Figure 6—figure supplement 2.. Mapping-by-sequencing reveals the chromosomal regions containing the causal mutations of sdm34.

sdm34 was backcrossed to msl10-3G plants, and the segregating BC₁F2 population was pooled by phenotype and sent for whole-genome sequencing (WGS). Segregating BC₁F2 populations were pooled by phenotype and sent for WGS. For each SNP identified, the frequency at which this mutant nucleotide was detected compared to the reference nucleotide was calculated and plotted against its chromosomal position. Regions where SNPs are represented with orange triangles were predicted to contain the causal mutation as mutant alleles were absent in the msl10-3G phenotypic pool (dwarfed) and present in the sdm phenotypic pool (suppressed dwarfing) near the expected frequency of 0.66. (B) Details of the SNPs in the chromosomal intervals identified in (A). Gene names and functional descriptions were obtained from TAIR.

Figure 7.. sdm26 and sdm34 alleles do not suppress expanded endoplasmic reticulum–plasma membrane contact sites (EPCSs) in msl10-3G leaves.

(A, C) Confocal Z-projections (maximum intensity projection of Z-slices from the top to the middle of cells) of MAPPER-GFP fluorescence in 4-week-old abaxial leaf epidermal cells of the indicated genotypes. Scale = 10 µm. (B, D) Quantification of the percentage of the leaf epidermal cell volume taken up by MAPPER-GFP puncta in plants of the indicated genotypes. Each data point represents a biological replicate (the mean value of 20–50 epidermal cells from one plant), n = 6–23 plants per genotype from three separately grown flats. Error bars, SD. Groups indicated with the same letters are not significantly different as assessed by Kruskal–Wallis with Dunn’s post-hoc test when measurements were not normally distributed (B) or ANOVA with Scheffe’s post-hoc test when they were (D).

Figure 7—figure supplement 1.. Null syt1, syt5, and syt7 alleles do not suppress msl10-3G phenotypes, and sdm26 and sdm34 mutations do not alter SYT5 or SYT7 localization, transcript levels, or MSL10 protein levels.

(A) Plants with the null syt5, syt7, or syt1-2 alleles were crossed to msl10-3G plants. Top row: shown are 4-week-old F3 cousins that are homozygous for the msl10-3G allele and homozygous for either the WT or null alleles. Bottom row: Trypan blue staining of 4-week-old leaves from the same plants. Scale = 300 µm. (B) Height of 6-week-old plants homozygous for both the msl10-3G allele and either WT or null SYT5 or SYT7 alleles. (C) Cortical confocal slices of tobacco abaxial epidermal cells transiently co-expressing mRFP-tagged SYT5 and SYT7 constructs under the control of the UBQ10 promoter and an endoplasmic reticulum (ER) marker (ER-CFP; Nelson et al., 2007). Scale = 5 µm. (D) qPCR showing relative SYT5 and SYT7 transcript levels in sdm26 and sdm34 mutants, normalized to EF1α abundance using the 2^-∆∆Ct method. RNA was extracted from 4-week-old rosette leaves of backcrossed sdm26 and sdm34 mutants. Error bars = SD. Groups indicated with the same letters are not significantly different as assessed by ANOVA with Tukey’s post-hoc test. (E, F) MSL10pMSL10-GFP transgenes were introduced into plants heterozygous for the sdm26 (SYT5 S66F) or sdm34 (SYT7 G427R) alleles (the msl10-3G allele had previously been crossed away). Heterozygous T1 plants were identified, and MSL10-GFP stability was compared in T2 siblings that were homozygous for either SYT allele. (E) Deconvolved images of MSL10-GFP signal in leaf epidermal cells of 4-week-old T2 plants. Scale = 10 µm. (F) Immunoblot of MSL10-GFP protein extracted from leaves of 4-week-old T2 siblings. Blots were re-probed with anti-α-tubulin as a loading control. Uncropped images are included as Figure 7—figure supplement 1—source data 1.

Figure 8.. MSL10 does not interact with SYT5 or SYT7 nor reliably alter their localization.

(A, D) Confocal Z-projections (maximum intensity projection of Z-slices from the top to the middle of cells) of abaxial leaf epidermal cells from 4-week-old plants with the indicated MSL10 alleles. Scale = 15 µm. Quantification of the percentage of the leaf epidermal cell volume taken up by SYT7-GFP (B, C) or SYT5-GFP (E, F) puncta in plants in the msl10-1 or msl10-3G backgrounds compared to WT siblings (A–C) or cousins (D–F). Each data point represents a biological replicate (the mean value of 20–50 epidermal cells from one plant), n = 6–19 plants per genotype from 2 to 4 separately grown flats. Error bars, SD. Means were compared by Student’s t-tests. (G) Mating-based split-ubiquitin assay testing the interaction of MSL10 with SYT5 and SYT7, performed as in Figure 2A. (H) Fluorescence lifetime (τ) of GFP measured using Förster resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM) when UBQ:MSL10-GFP was transiently expressed in tobacco leaves for 5 days, with or without UBQ:SYT-mRFP . Each data point represents the value from one field of view (three fields of view per plant from three infiltrated plants for a total of n = 9 for each combination). Error bars, SD. Groups indicated by the same letter are not statistically different according to ANOVA with Tukey’s post-hoc test.

Figure 8—figure supplement 1.. SYT7-GFP localization in leaf epidermal cells varies between experiments.

(A–D) each represent single experiments of separately grown UBQ:SYT7-GFP x msl10-3G F2 siblings. Left: representative deconvolved confocal Z-projections (maximum intensity projection of Z-slices from the top to the middle of cells) of SYT7-GFP fluorescence in 4-week-old abaxial epidermal cells with the indicated genotypes. Right: quantification of the percentage of the leaf epidermal cell volume taken up by SYT7-GFP puncta in plants of each genotype. Each data point represents a biological replicate: the mean value of 10–30 epidermal cells from one plant, 4–6 plants per genotype per experiment. Error bars, SD. Means were compared by Student’s t-tests.

Figure 9.. Conceptual model of interactions between MSL10 and EPCS proteins.

Author response image 1.. SYT1, SYT5, and SYT7 dynamics are not appreciably altered by MSL10.

Fluorescence recovery after photobleaching (FRAP) curves for SYT1-GFP, SYT5-GFP, and SYT7-GFP in leaf epidermal cells of 4–5-week-old plants with the indicated MSL10 genotypes. The number of individual plants examined is indicated above. The fluorescence intensity of the photobleached ROI was normalized to that of an unbleached, control ROI and by setting the initial fluorescence intensity to 100%. Error bars = SD.