Reagent/Resource	Reference or Source	Identifier or Catalog Number
Experimental Models
wt (Arabidopsis thaliana)		Col‐0
wt (Chlamydomonas reinhardtii)	Li et al (2016)	CC‐4533
uba5 (Chlamydomonas reinhardtii)	Li et al (2019)	Cre13.g582350
ufl1 (Chlamydomonas reinhardtii)	Li et al (2019)	Cre16.g686650
ire1 (Chlamydomonas reinhardtii)	Li et al (2019)	Cre08.g371052
c53 (Arabidopsis thaliana)	Stephani et al (2020)	At5g06830
pUbi::C53‐mCherry × GFP‐ATG8A/c53 (Arabidopsis thaliana)	This study	N/A
pUbi::C53sAIM(W276A, W287A, Y304A, W335A)‐mCherry × GFP‐ATG8A/c53 (Arabidopsis thaliana)	This study	N/A
pUbi::C53cAIM(IDWD274WDDI, IDWD285WDDI, IDWD333WDDI)‐mCherry × GFP‐ATG8A/c53 (Arabidopsis thaliana)	This study	N/A
Arabidopsis thaliana: pUbi::C53‐GFP × c53 (Arabidopsis thaliana)	Stephani et al (2020)	N/A
pUbi::C53sAIM(W276A, W287A, Y304A, W335A)‐GFP × c53 (Arabidopsis thaliana)	Stephani et al (2020)	N/A
pUbi::C53cAIM(IDWD274WDDI, IDWD285WDDI, IDWD333WDDI)‐GFP × c53 (Arabidopsis thaliana)	This study	N/A
Recombinant DNA
E. coli: Destination (expression) vector	Stephani et al (2020)	N/A
E. coli: GST‐ATG8A	Stephani et al (2020)	N/A
E. coli: GST‐ATG8ALDS(YL50AA)	Stephani et al (2020)	N/A
E. coli: GST‐GABARAP	Stephani et al (2020)	N/A
E. coli: GST‐CrATG8	This study	N/A
E. coli: GST‐CrUFM1	This study	N/A
E. coli: HIS6‐CrC53	This study	N/A
E. coli: MBP‐CrC53	This study	N/A
E. coli: GST‐AtUFM1	Stephani et al (2020)	N/A
E. coli: GST‐HsUFM1	This study	N/A
E. coli: MBP‐AtC53	Stephani et al (2020)	N/A
E. coli: MBP‐AtC53IDR(239‐372)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC53ΔIDR(1‐239,(KGSGSTSGSG)2,373‐549)	Stephani et al (2020)	N/A
E. coli: MBP‐HsC53	Stephani et al (2020)	N/A
E. coli: MBP‐HsC53IDR(263‐316)	Stephani et al (2020)	N/A
E. coli: MBP‐HsC53ΔIDR(1‐262, (KGSGSTSGSG),317‐506)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC531A (W276A)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC532A (W287A)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC533A (W335A)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC5312A (W276A, W287A)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC5313A (W276A, W335A)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC53 23A (W287A, W335A)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC53123A(W276A, W287A, W335A)	Stephani et al (2020)	N/A
E. coli: MBP‐AtC53sAIM(Y304A, W276A, W287A, W335A)	Stephani et al (2020)	N/A
E. coli: MBP‐HsC53sAIM(W269A, W294A, W312A)	Stephani et al (2020)	N/A
E. coli: MBP	Stephani et al (2020)	N/A
E. coli: HIS6‐GABARAP	Stephani et al (2020)	N/A
E. coli: HIS6‐AtC53	Stephani et al (2020)	N/A
E. coli: mCh‐AtC53 sAIM (Y304A, W276A, W287A, W335A)	This study	N/A
E. coli: mCh‐HsC53 sAIM(W269A, W294A, W312A)	This study	N/A
E. coli: mCh‐AtC53	This study	N/A
E. coli: mCh‐HsC53	This study	N/A
E. coli: GST	Stephani et al (2020)	N/A
E. coli: mCherry	This study	N/A
E. coli: MBP‐ E. coli: AtC53cAIM(IDWD274WDDI, IDWD285WDDI, IDWD333WDDI)	This study	N/A
E. coli: MBP‐HsC53cAIM(IDWG267WDGI, IDWG292WDGI, IDWG310WDGI)	This study	N/A
E. coli: mCh‐AtC53cAIM(IDWD274WDDI, IDWD285WDDI, IDWD333WDDI)	This study	N/A
E. coli: mCh‐HsC53cAIM(IDWG267WDGI, IDWG292WDGI, IDWG310WDGI)	This study	N/A
E. coli: HIS6‐HsC53	Stephani et al (2020)	N/A
E. coli: HIS6‐HsUFM1	Stephani et al (2020)	N/A
E. coli: HIS6‐AtUFM1	Stephani et al (2020)	N/A
E. coli: MBP‐PfC53	This study	N/A
E. coli: MBP‐AcC53	This study	N/A
E. coli: HIS6‐MBP‐3C‐AtC53 IDR (264‐341)	This study	N/A
E. coli: HIS6‐MBP‐3C‐AtC53 IDR1A (W276A) (264‐341)	This study	N/A
E. coli: HIS6‐MBP‐3C‐AtC53 IDR2A (W287A) (264‐341)	This study	N/A
E. coli: HIS6‐3C‐GABARAP	This study	N/A
E. coli: HIS6‐3C‐ATG8A	This study	N/A
E. coli: HIS6‐3C‐AtUFM1	This study	N/A
E. coli: HIS6‐3C‐HsUFM1	This study	N/A
E. coli: HIS6‐MBP‐3C‐HsC53 IDR (263‐316)	This study	N/A
pUbi::C53sAIM(W276A, W287A, Y304A, W335A)‐mCherry	This study	N/A
pUbi::C53cAIM(IDWD274WDDI, IDWD285WDDI, IDWD333WDDI)‐mCherry	This study	N/A
pUbi::C53cAIM(IDWD274WDDI, IDWD285WDDI, IDWD333WDDI)‐GFP	This study	N/A
pUbi::C53‐mCherry	Stephani et al (2020)	N/A
pUbi::C53‐GFP	Stephani et al (2020)	N/A
pUbi::C53sAIM(W276A, W287A, Y304A, W335A)‐GFP	Stephani et al (2020)	N/A
Antibodies
Goat anti‐rabbit IgG HRP‐Conjugate (1:10K)	Biorad	1706515
Goat anti‐mouse IgG‐HRP Conjugate (1:10K)	Biorad	1706516
Rabbit anti‐mCherry (1:5K)	Abcam	ab167453
Goat anti‐GST HRP Conjugate (1:1K)	GE Healthcare	RPN1236
Rabbit anti‐GFP (1:3K)	Invitrogen	A11122
Mouse anti‐GFP (1:3K)	Roche	11814460001
Mouse anti‐MBP (1:3K)	Sigma Aldrich	M1321‐200UL
Rabbit anti‐ATG8A (1:1K)	Agrisera	AS14 2811
Rabbit anti‐C53 (1:5K)	Stephani et al (2020)	N/A
Rabbit anti‐AtUFM1 (1:3K)	This study	N/A
Rabbit anti‐HsUFM1 (1:3K)	Abcam	Ab109305
Oligonucleotides and other sequence‐based reagents
Chlamydomonas reinhardtii primer: E3_P1	This study	AGAGCTCCTGCATACCCTGA
Chlamydomonas reinhardtii primer: E3_E1_SR	This study	CCGAGGAGAAACTGGCCTT
Chlamydomonas reinhardtii primer: E3_E1_oMJ	This study	CAGGCCATGTGAGAGTTTGC
Chlamydomonas reinhardtii primer: E3_P2	This study	CTCCTCAATGAGTGTGGCAA
Chlamydomonas reinhardtii primer: E1_P2	This study	CACACGGACATGACTGGAAC
Chlamydomonas reinhardtii primer: E1_P1	This study	AGAGTTACGGCCGCAGATT
Chemicals, enzymes and other reagents
E. coli: DH5α	In‐house facility	N/A
E. coli: Rosetta2 (DE3) pLysS	In‐house facility	N/A
A. tumefaciens: GV3101 (pSoup)	In‐house facility	N/A
cAIM wt peptide	Synthetized in house	EPLDFDWEIVLEEEM
cAIM mutant peptide	Synthetized in house	EPLDFDAEIALEEEM
AtUBA5 LIR peptide	Synthetized in house	GPLHDDNEWNISVVDD
HsUBA5 LIR peptide	Synthetized in house	EIIHEDNEWGIELVSE
Tunicamycin	SCBT	sc‐3506
DTT	Sigma Aldrich	43815
Concanamycin‐A (conA)	Santa Cruz	sc‐202111A
Gamborg B5 vitamin mixture 1000X	Duchefa	G0415.0250
Gamborg B5 medium (microsalt mixture)	Duchefa	M0302.0025
Gamborg B5 medium (including vitamins)	Duchefa	G0210.0010
Gamborg B5 medium (basal salt mixture)	Duchefa	G0209.0050
Murashige & Skoog vitamin mixture 1000X	Duchefa	M0409.0250
Murashige & Skoog micro salt mixture	Duchefa	M0301.0050
Murashige & Skoog macro salt mixture	Duchefa	M0305.0050
Murshige & Skoog Basal salt mixture with MES	Duchefa	M0254.0050
Murashige & Skoog without nitrogen	Caisson labs	MSP07
MES monohydrate	Applichem	A1074
Puromycin	Sigma Aldrich	P8833
L‐Glutamine	Sigma Aldrich	G7513
M9 Minimal media	In‐house facility	N/A
Ammonium‐15N chloride	Sigma Aldrich	39466‐62‐1
D‐Glucose (U‐13C6, 99%)	Cambridge Isotope Laboratories, Inc.	110187‐42‐3
Thamine hydrochloride	Sigma Aldrich	T1270
Biotin	Sigma Aldrich	B4639
Choline chloride	Alfa Aesar	A15828
Folic acid	Acros Organics	21663
Niacinamide	Sigma Aldrich	N3376
D‐Pantothenic acid hemicalcium salt	Sigma Aldrich	P2250
Pyridoxal hydrochloride	Alfa Aesar	A17855
(‐)‐Riboflavin	Sigma Aldrich	R4500
Ethylenedinitrilotetraacetic acid disodium salt dihydrate	Merck	108454
Iron (III) chloride hexahydrate Fe (III)Cl3 ·6H2O	Merck	103943
Zinc chloride ZnCl2	Merck	108816
Copper (II) chloride dihydrate Cu (II)Cl2 ·2H2O	Sigma Aldrich	221783
Cobalt (II) chloride hexahydrate Co (II)Cl2 ·6H2O	Sigma Aldrich	S2644
Boric acid	Sigma Aldrich	B6768
Manganese (II) chloride tetrahydrate Mn (II)Cl2 ·4H2O	Sigma Aldrich	M3634
GFP‐Trap	Chromotek	Gta‐20
Glutathion Sepharose 4 B	Cytiva	17‐5132‐01
Pierce™ Glutathione Magnetic Agarose Beads	Thermo Scientific™	78601
HisTrap FF 5 ml	Cytiva	17525501
HisTrap FF 1 ml	Cytiva	17531901
Resource Q 6 ml	Cytiva	17117901
Resource S 6 ml	Cytiva	17118001
HiPrep 26/10 Desalting	Cytiva	17508701
HiLoad 16/600 Superdex 75 pg	Cytiva	28989333
HiLoad 16/600 Superdex 200 pg	Cytiva	28989335
GFP‐Trap Magnetic Agarose	Chromotek	Gtma‐20
Protein A Agarose	Sigma	P2545
Software
CLC main work bench 7	Qiagen	N/A
Zen Software	Carl Zeiss	N/A
Image J (Fiji)	NIH	N/A
Image Lab	BioRad	N/A
iBright analysis software	Invitrogen	N/A
Adobe Illustrator 2022	Adobe Inc.	N/A
RStudio 2021.09.2+382 "Ghost Orchid" Release; R version 4.1.2	RStudio; The R Foundation for Statistical Computing	N/A
TopSpin3.2	Bruker	N/A
CcpNmr3.0	Continuum Analytics, Inc.	N/A