The Arabidopsis V-ATPase is localized to the TGN/EE via a seed plant-specific motif

  1. Upendo Lupanga
  2. Rachel Röhrich
  3. Jana Askani
  4. Stefan Hilmer
  5. Christiane Kiefer
  6. Melanie Krebs
  7. Takehiko Kanazawa
  8. Takashi Ueda
  9. Karin Schumacher  Is a corresponding author
  1. Department of Cell Biology, Centre for Organismal Studies, Heidelberg University, Germany
  2. Electron Microscopy Core Facility, Heidelberg University, Germany
  3. Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Germany
  4. Division of Cellular Dynamics, National Institute for Basic Biology, Japan
  5. The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Japan
11 figures, 1 table and 2 additional files

Figures

Figure 1 with 3 supplements
The targeting signal of VHA‐a1 is located between L132 and E179 and the a1-TD is sufficient for targeting of VHA‐a3 to the TGN/EE.

Root tips of 6-day-old Arabidopsis seedlings were analyzed by confocal laser scanning microscopy (CLSM) (A) The chimeric constructs a1NT179a3-GFP and a1NT228a3-GFP show dual localization at the …

Figure 1—figure supplement 1
The tri-peptide motif that is responsible for the targeting of Stv1p is absent in VHA-a1.

Amino acid sequence alignment of the yeast subunit a isoforms Vph1p and Stv1p with the Arabidopsis isoforms VHA-a1 and VHA-a3. Residues similar between all proteins at the same position are shown …

Figure 1—figure supplement 2
The targeting signal of VHA‐a1 is not located in the first 85 amino acids.

(A) Chimeric proteins were made which consisted of increasing lengths of the VHA‐a1 N‐terminus fused to decreasing lengths of the C‐terminal domain of VHA‐a3. All constructs were fused to GFP. (B) …

Figure 1—figure supplement 3
Three-dimensional models of the VHA-a1 and VHA-a3 N-termini.

Homology modeling of the N- termini of VHA-a1 and VHA-a3 was done using cryo-EM models of Stv1p (PDB607U) and Vph1p (PDB607T) respectively as templates. The models are color ramped.

Figure 2 with 1 supplement
Site-directed mutagenesis reveals the importance of conserved amino acids in the targeting of VHA‐a1 to the TGN/EE.

(A) The VHA-a1-clade consensus sequence for the a1-TD region was made on the weblogo platform (Crooks et al., 2004). Sequence numbers are based on Arabidopsis VHA-a1. Conserved amino acids were …

Figure 2—figure supplement 1
The VHA-a1-TD is conserved in Angiosperms.

Amino acid sequence alignment of representative sequences from the VHA-a1 and VHA-a3 clades. The sequence numbers are in reference to the A. thaliana VHA-a1 sequence. Residues highlighted in black, …

Figure 3 with 1 supplement
VHA-a1 is retained at the ER after AtSar1b-GTP-CFP expression.

After 6 hr of induction with 60 µM DEX, AtSar1b-GTP-CFP is expressed in 6-day-old Arabidopsis root tip cells. (A) VHA-a1-GFP is retained in the ER and also agglomerates to produce bright punctae …

Figure 3—figure supplement 1
AtSar1b-GTP-CFP expression blocks the ER exit of secretory pathway proteins.

(A) EM of high-pressure frozen Arabidopsis root tips. After 6 hr of induction with 60 µM DEX, AtSar1b-GTP-CFP expression causes bloating of the ER, aggregation of Golgi stacks and leads to an …

The mutations in the a1-TD affect an ER-exit motif.

The localization and fluorescence intensity of mutated VHA-a1-GFP proteins was analyzed in the presence (+DEX) and absence (DMSO) of AtSar1b-GTP-CFP. Root tips of 6-day-old Arabidopsis seedlings …

Figure 5 with 1 supplement
Tonoplast localization of mutated VHA-a1 increases in the absence of VHA-a2 and VHA-a3.

(A) The localization of mutated VHA-a1 proteins tagged to GFP were analyzed in the vha-a2 vha-a3 double mutant background after 20 min staining with FM4-64. Root tips of 6-day-old Arabidopsis …

Figure 5—figure supplement 1
A competition exists to enter provacuoles in wild type Arabidopsis root tip cells.

VHA-a3-R729N-GFP is retained in the wild type background and localizes to the tonoplast in the vha-a2 vha-a3 double mutant background. Scale bars = 10 µm.

Figure 6 with 1 supplement
Spermatophyte VHA-a isoforms cluster into two distinct clades, the a1-TD is conserved in the VHA-a1 clade and originates in the gymnosperm sequences.

(A) Phylogenetic analysis of the N-terminal sequences of VHA-a proteins was done. A graphical summary of the tree is depicted. VHA-a isoforms from seed plants including the gymnosperm Pinus taeda

Figure 6—figure supplement 1
Phylogenetic analysis of the N-terminal sequences of VHA-a related proteins.

VHA-a related protein sequences for selected species are shown. Branch support is calculated on the basis of 500 bootstraps.

Figure 7 with 2 supplements
The mutated VHA-a1 subunits complement the vha-a2 vha-a3 double mutant to varying degrees.

Plants were grown in short day conditions (22 °C and 10 hr light) for 6 weeks. (A) All mutant variants of VHA-a1-GFP displayed bigger rosette size than the vha-a2 vha-a3 double mutant. E161S which …

Figure 7—figure supplement 1
The mutated VHA-a1-GFP proteins complement the vha-a2 vha-a3 double mutant to varying degrees in long day conditions.

Plants were grown in long day conditions (22 °C and 16 hr of light) for 4 weeks. All mutant variants of VHA-a1-GFP displayed bigger rosette size than the vha-a2 vha-a3 double mutant. VHA-a1 with the …

Figure 7—figure supplement 2
Protein levels of the mutated VHA-a proteins at the tonoplast.

Abundance of the GFP tagged proteins was determined via western blot. Tonoplast membrane proteins were separated by SDS-PAGE and subsequently immunoblotted with an anti-VHA-a1, VHA-a3 and VHA-B …

Figure 8 with 2 supplements
MpVHA-a containing complexes are functional in Arabidopsis and can replace VHA-a3 and VHA-a2 at the tonoplast.

(A) MpVHA-a-mVenus is dual localized at the tonoplast and TGN/EE in the vha-a2 vha-a3 background. The TGN/EE localization was confirmed by treatment of root cells with 50 µm BFA for 3 hr followed by …

Figure 8—figure supplement 1
Subcellular localization of MpVHA-a-mVenus in M. polymorpha.

(A and B) Single confocal images of M. polymorpha dorsal thallus cells co-expressing mRFP-MpSYP6A and MpVHA-a-mVenus driven by the CaMV35S (A) or MpEF1α (B) promoter. Green, magenta, and blue pseudo …

Figure 8—figure supplement 2
MpVHA-a-mVenus is dual localized at the TGN/EE and tonoplast in Arabidopsis wildtype root cells.

UBQ10:MpVHA-a-mVenus was co-expressed with UBQ10:VHA-a3-pmScarlet-I and VHA-a1:VHA-a1-mRFP in Arabidopsis wildtype. Confocal analysis was done on 6-day-old Arabidopsis roots. (A) MpVHA-a-mvenus …

Figure 9 with 2 supplements
VHA-a1 is essential for pollen development but not for vegetative growth.

(A) The exon-intron structure of the first seven exons of VHA-a1 shows the sites which were targeted in independent CRISPR approaches. vha-a1-1, vha-a1-2, vha-a1-3 and vha-a1-4 are examples for vha–a…

Figure 9—figure supplement 1
vha-a1-1 can be distinguished from the wildtype allele without sequencing and mutations in VHA-a1-GFP lead to absence of GFP signal.

(A) Mutations in VHA-a1 were distinguished from mutations in VHA-a1-GFP by use of specific primers. Shown are the exon-intron structures of gene and transgene. Primer one is VHA-a1 specific, while …

Figure 9—figure supplement 2
MpVHA-a-mVenus is dual localized in vha-a1.

(A) vha-a1 (Cas9+) was crossed with UBQ10:MpVHA-a-mVenus in wildtype background and F1 seedlings were analyzed by CLSM. Root tips of 6-day-old seedlings were analyzed. MpVHA-a-mVenus was dual …

Figure 10 with 2 supplements
VHA-a2 and VHA-a3 replace VHA-a1 at the TGN/EE in vha-a1 during vegetative growth.

(A) vha-a1 vha-a1-GFP hypocotyls are hypersensitive to 125 nM ConcA, in contrast to wildtype hypocotyls indicating that a target of ConcA is present at the TGN/EE. vha-a1 hypocotyls expressing UBQ10:…

Figure 10—figure supplement 1
vha-a1 is hypersensitive to Concanamycin-A (ConcA).

Root morphology of 4-day-old etiolated seedlings. vha-a1 roots are hypersensitive to 125 nM ConcA, in contrast to wild type roots and roots of plants expressing vha-a1 VHA-a1-GFP. Scale bars = 75 µm.

Figure 10—figure supplement 2
vha-a1 vha-a2/+ and vha-a1 vha-a3/+ have reduced rosette sizes.

(A) vha-a1 (Cas9+) was crossed with the vha-a2 vha-a3 double mutant. Analysis of F1 plants revealed that vha-a1 vha-a2/+ vha-a3/+ is reduced in growth. Rosette areas of 3.5-week-old plants were …

A competition exists to enter COPII vesicles in Arabidopsis.

Upper panel: COPII-mediated ER-export is the only way to exit the ER in Marchantia. Marchantia VHA-a (MpVHA-a) does not contain a TGN/EE-retention signal. MpVHA-a complexes acidify the TGN/EE en …

Tables

Appendix 1—key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional information
Strain, strain
background
Arabidopsis thaliana
Col-0Nottingham Arabidopsis
Stock center (NASC)
NASC: N37008
Strain, strain
background
(Marchantia polymorpha)
Tak-1Ishizaki et al., 2008
PMID:18535011
Genetic reagent
Arabidopsis thaliana
vha-a2 vha-a3(Krebs et al., 2010)
PMID:20133698
At2g21410,At4g39080SALK_142642
SALK_29786
Genetic reagent
Arabidopsis thaliana
vha-a1-1this studyAt2g28520See Materials and methods,
Construct design and
plant transformation
Genetic reagent
Arabidopsis thaliana
vha-a1-2this studyAt2g28520See Materials and methods,
Construct design and
plant transformation
Genetic reagent
Arabidopsis thaliana
vha-a1-3this studyAt2g28520See Materials and methods,
Construct design and
plant transformation
Genetic reagent
Arabidopsis thaliana
vha-a1-4this studyAt2g28520See Materials and methods,
Construct design and
plant transformation
Genetic reagent
Arabidopsis thaliana
BRI1: BRI-GFP(Geldner et al., 2007)
PMID:17578906
Genetic reagent
(Marchantia polymorpha)
CaMV35S:mRFPMpSyp6A(Kanazawa et al., 2016)
PMID:26019268
Gene
Arabidopsis thaliana
VHA-a1arabidopsis.orgAt2g28520
Gene
Arabidopsis thaliana
VHA-a3arabidopsis.orgAt4g39080
Gene
Arabidopsis thaliana
Sar1Barabidopsis.orgAt1g56330
Gene
(Rattus norvegicus)
Beta-galactoside
alpha-2,6-sialyltransferase 1 (ST)
RGD3676
Gene
Arabidopsis thaliana
Brassinosteroid
insensitive 1 (BRI1)
arabidopsis.orgAt4g39400
Gene
(Marchantia polymorpha)
MpVHA-aMarchantia genome
database
Mp3g15140
Gene
Arabidopsis thaliana
MpSYP6AMarchantia genome
database
Mp3g18380
Gene
(Amborella trichopoda)
Amborella trichopoda VHA-aPhytozomeevm_27.TU.AmTr
_v1.0_scaffold00080.37
Gene
(Selaginella moellendorffii)
Selaginella moellendorffii
VHA-a
Phytozome182335
Gene
(Pinus taeda)
Pinus taeda VHA-aPineRefSeq, Tree genes5A_I15_VO_L_1_
T_29156/41278
Transfected
construct
Arabidopsis thaliana
CRISPR VHA-a1 U6-26p:
gRNA one and U6-29p:gRNA
two in pHEE401E
this studyMaterials and methods,
Construct design and
plant transformation
Transfected
construct
Arabidopsis thaliana
CRISPR VHA-a1 U6-26p:
gRNA three in pHEE401E
this studyMaterials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
CRISPR VHA-a1 U6-26p:
gRNA four in pHEE401E
this studyMaterials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10: VHA-a1 NT
35 aa-VHA-a3
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10: VHA-a1 NT
85 aa-VHA-a3
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10: VHA-a1 NT
131 aa-VHA-a3
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10: VHA-a1 NT
179 aa-VHA-a3
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10: VHA-a1 NT
228 aa-VHA-a3
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10-GFPthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ:VHA-a3-pmScarlet-Ithis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10
E156Q-GFP
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10
E161S-GFP
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10
F134Y-GFP
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10
L159T-GFP
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10
E156Q + L159T-GFP
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10
L159T + E161S -GFP
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-
intron10 ELE-GFP
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a1-intron10 ΔEEI-GFPthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ:VHA-a3R729N-GFPthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:VHA-a3-a1-TD-GFPthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
Dex:Sar1BH74L-CFPthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ10:MpVHA-a-mVenusthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
(Marchantia polymorpha)
CaMV35S:MpVHA-a-mVenusthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
(Marchantia polymorpha)
MpEF1α:MpVHA-a-mVenusthis studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ: A.trichopoda
-VHA-a-NT-VHA-a1-mCherry
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ:P.taeda-VHA-
a-NT-VHA-a1-mVenus
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ:S.moellendorffii
-VHA-a-NT-VHA-a1-mCherry
this studySee Materials and methods,
Construct design and
plant transformation
Transfected construct
Arabidopsis thaliana
UBQ:ST-GFPthis studySee Materials and methods,
Construct design and
plant transformation
Recombinant DNA reagent
(plasmid)
UBQ10 promoterLampropoulos et al., 2013
PMID:24376629
pGGA006
Recombinant DNA reagent
(plasmid)
pOp6Schürholz et al., 2018
PMID:30026289
pGGA016
Recombinant DNA reagent
(plasmid)
B-DummyLampropoulos et al., 2013
PMID:24376629
pGGB003
Recombinant DNA reagent
(plasmid)
entry module CLampropoulos et al., 2013
PMID:24376629
pGGC000
Recombinant DNA reagent
(plasmid)
pGGC-VHA-a3this studypKSC003See Materials and methods,
Construct design and
plant transformation
Recombinant DNA reagent
(plasmid)
pGGC-VHA-a1-intron 10this studypKSC012See Materials and methods,
Construct design and
plant transformation
Recombinant DNA reagent
(plasmid)
pGGC-STthis studypKSC013See Materials and methods,
Construct design and
plant transformation
Recombinant DNA reagent
(plasmid)
GR-LhG4Schürholz et al., 2018
PMID:30026289
pGGC018
Recombinant DNA reagent
(plasmid)
linker GFPLampropoulos et al., 2013
PMID:24376629
pGGD001
Recombinant DNA reagent
(plasmid)
linker-CFPLampropoulos et al., 2013
PMID:24376629
pGGD004
Recombinant DNA reagent
(plasmid)
GFP (A206K) no linkerLampropoulos et al., 2013
PMID:24376629
pGGD011
Recombinant DNA
reagent (plasmid)
GSL-mVenusthis studyp2456See Materials and methods,
Construct design and
plant transformation
Recombinant DNA
reagent(plasmid)
GSL-pmScarlet-Ithis studyp1324See Materials and methods,
Construct design and
plant transformation
Recombinant DNA
reagent (plasmid)
GSL-mCherryWaadt et al., 2017
PMID:28850185
p2897
Recombinant DNA
reagent (plasmid)
rbcS terminatorLampropoulos et al., 2013
PMID:24376629
pGGE001
Recombinant DNA
reagent (plasmid)
HSP18.2M terminatorWaadt et al., 2017
PMID:28850185
p1296
Recombinant DNA
reagent (plasmid)
BastaRLampropoulos et al., 2013
PMID:24376629
pGGF001
Recombinant DNA
reagent (plasmid)
SulfRLampropoulos et al., 2013
PMID:24376629
pGGF012
Recombinant DNA
reagent (plasmid)
KanRLampropoulos et al., 2013
PMID:24376629
pGGF007
Recombinant DNA
reagent (plasmid)
HygR_pNosWaadt et al., 2017
PMID:28850185
p1317
Recombinant DNA
reagent (plasmid)
HygR_pUbq10Lampropoulos et al., 2013
PMID:24376629
pGGF005
Recombinant DNA
reagent (plasmid)
F-H adapterLampropoulos et al., 2013
PMID:24376629
pGGG001
Recombinant DNA
reagent (plasmid)
H-A adapterLampropoulos et al., 2013
PMID:24376629
pGGG002
Recombinant DNA
reagent (plasmid)
intermediate vector MLampropoulos et al., 2013
PMID:24376629
pGGM000
Recombinant DNA
reagent (plasmid)
intermediate vector NLampropoulos et al., 2013
PMID:24376629
pGGN000
Recombinant DNA
reagent (plasmid)
UBQ10:GR-LHG4:trbcSthis studypKSM002See Materials and methods,
Construct design and
plant transformation
Recombinant DNA
reagent (plasmid)
pOP6:Sar1BH74L-CFPthis studypKSN009See Materials and methods,
Construct design and
plant transformation
Recombinant DNA
reagent (plasmid)
pGGZ001Lampropoulos et al., 2013
PMID:24376629
Recombinant DNA
reagent (plasmid)
pGGZ003Lampropoulos et al., 2013
PMID:24376629
Recombinant DNA
reagent (plasmid)
pGGZ004this studySee Materials and methods,
Construct design and
plant transformation
Recombinant DNA
reagent (plasmid)
pHEE401EWang et al., 2015
PMID:26193878
See Materials and methods,
Construct design and
plant transformation
AntibodyVHA-a1
(rabbit polyclonal)
AgriseraAS142822(1:1000)
AntibodyVHA-a3
(rabbit polyclonal)
AgriseraAS204369(1:1000)
AntibodyVHA-B
(mouse polyclonal)
Ward et al., 1992
PMID:16668845
(1:100)
Antibodyanti-GFP
(rabbit polyclonal)
Roth et al., 2018
PMID:30410018
(1:5000)
Chemical
compound, drug
Concanamycin-A
(ConcA)
Santa Cruzsc-202111A
Chemical
compound, drug
Brefeldin ALC LaboratoriesB-8500
Chemical
compound, drug
FM4-64Thermo Fisher ScientificT13320
Chemical
compound, drug
Dexamethasone (DEX)Sigma-AldrichD4902
Chemical
compound, drug
Malachite Green,
Acid Fuchsin,
Orange G
Thermo Fisher
Scientific
AC413490250,
AC400210250,
AC229820250
Alexander stain
Commercial
assay or kit
CloneJET PCR Cloning kitThermo Fisher
Scientific
K1231
Strain, strain
background (E. coli)
NEBαIn-house facilityCOS Heidelberg
Strain, strain
background
(A. tumefaciens)
GV3101In-house facilityCOS Heidelberg
Strain, strain
background
(A. tumefaciens)
ASE1In-house facilityCOS Heidelberg
Software, algorithmAdobe Illustrator 2020Adobe IncFigure assembly
Software, algorithmZen SoftwareCarl ZeissMicroscopy
Software, algorithmLeica LSFLeicaMicroscopy
Software, algorithmOriginpro 2020OriginStatistics and
graph plotting
Software, algorithmIntas ImagerIntasWestern blot
Software, algorithmImage JNIHImage quantification

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