Table 3 Comparison of SCI1-BioID candidates with previous studies investigating SmSTRIPAK interactors.

From: Establishment of in vivo proximity labeling with biotin using TurboID in the filamentous fungus Sordaria macrospora

Candidates identified in SCI1-BioID

Phosphoproteome studies

Pulldown experiments

TAP/MS experiments

Märker et al. (2020)23

Stein et al. (2020)24

Reschka (2018)25

Bloemendal et al. (2012)21

Nordzieke et al. (2015)22

Protein ID

Name of (homolog) protein

Regulation

Regulation

PRO11

SmMOB3

SCI1

PRO22

PRO45

SMAC_05559

SCI1 [Sm]

–

–

×

–

×

–

×

SMAC_08794

PRO11 [Sm]

–

–

×

×

×

×

×

SMAC_00877

SmMOB3 [Sm]

–

×

×

×

–

–

×

SMAC_02580

PRO22 [Sm]

–

–

×

–

–

×

–

SMAC_00725

Biotin apo-protein ligase [Nc]

Not identified

Not identified

–

–

–

–

–

SMAC_04678

SmPP2Ac1 [Sm]

Not identified

not identified

–

–

–

×

–

SMAC_05070

signal recognition particle 54 kDa protein [Sm]

Not identified

not identified

–

–

–

–

–

SMAC_01219

NAD-dependent protein deacetylase [Sm]

–

–

–

–

–

–

–

SMAC_03234

pre-mRNA-splicing factor SPF27 [Mm]

Not identified

not identified

–

–

–

–

–

  1. Significantly enriched proteins of the SCI1-BioID experiment (enrichment factor ≥ 4) were compared to the results of phosphoproteome studies23,24, pulldown25 and TAP/MS experiments21,22 with SmSTRIPAK subunits in S. macrospora. For phosphoproteome analysis, the SmSTRIPAK single and double subunit deletion strains ΔSmpp2Ac1, Δpro11, Δpro2223 and Δpro11, Δpro11Δpro22, ΔSmpp2Ac1Δpro2224 were used. Peptides were labeled using the iTRAQ approach for relative quantification and phosphopeptides were enriched using TiO2. Phosphopeptides with a Log2 ratio two times higher than the standard deviation of the total dataset of the given protein were considered regulated. Proteins with regulated phosphopeptides in at least one knockout strain are marked with an “×” in the “regulation” column. Downregulations of phosphopeptides in the associated deletion strain were ignored (e.g., downregulation of SmPP2Ac1 phosphopeptides in ΔSmPP2Ac1). Pulldown experiments were carried out using HA-PRO11, HA-PRO11-eGFP, FLAG-SmMOB3, SmMOB3-eGFP and SCI1-eGFP as bait. Criteria for enrichment were: at least two peptides per protein, peptide mass confidence high, not enriched in negative control and at least seven spectral counts in two out of three biological replicates25. TAP/MS experiments were performed with PRO2221 and PRO45 as bait22. For TAP/MS experiments, only proteins identified in all biological replicates were marked with “×”. Protein names were identified through the UniProtKB BLAST (for identity % and e-values see Supplementary Table S5). [Sm], Sordaria macrospora; [Nc], Neurospora crassa; [Nt], Neurospora tetrasperma; [Mm], Madurella mycetomatis.
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