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Table 4. Candidate endoplasmic reticulum-associated degradation (ERAD) substrate proteins

   

A

B

C

   

A

B

C

Cytoskeleton/ cell wall

Chs2p

0

4

0

Protein glycosylation/ lipid modification

Pmt2p

0

2

0

Rho3p

0

3

0

Wbp1p

0

3

0

Chs1p

0

3

0

Gpi16p

0

2

0

DNA replication/ transcription

Cdc47p

0

2

0

Pmt4p

0

6

2

Rpo21p*

1

5

1

Alg9p

0

3

0

Tra1p

1

3

1

Ecm39p

0

2

0

Imp2p

0

2

0

Ost3p

0

2

0

Mga2p

0

2

0

Ubiquitin/ proteasome pathway

Cdc48p

2

6

2

Spt23p

0

3

0

Ufd2p

0

7

1

Lipid/ergosterol metabolism

Lcb2p

0

2

0

Rpn3p

0

2

0

Sur2p

0

2

0

Ubc6p

0

4

0

Scs2p

0

2

0

Ddi1p*

0

7

0

Scs3p

0

3

1

Ubr1p

0

4

1

Erg1p*

6

19

2

Ssm4p

4

19

8

Ncp1p*

0

11

2

Cue1p

0

2

0

Erg9p

0

7

0

Cue5p

0

2

0

Tor2p

0

5

0

Vesicle transport/ trafficking

YAL048Cp

0

4

0

YLL012Wp

0

3

0

Erp1p

0

2

0

Erg27p

0

3

1

Sec27p

0

2

0

YML125Cp

0

2

0

Emp24p

0

2

0

Membrane transporter/ permease/pump

Snq2p

0

19

4

Gvp36p

2

5

0

Dnf2p

0

2

0

Vps13p

0

2

0

Pmc1p

1

3

0

Gsf2p

0

3

0

Hip1p

1

4

0

Cvt19p

0

4

0

Yor1p

1

10

2

Nce102p

0

2

0

Neo1p

0

5

0

Other

Gdh3p

0

2

0

Gap1p*

0

3

1

Gly1p*

0

8

0

Bpt1p

0

5

1

Nup145p

0

2

0

Ccc1p

1

5

0

Eno2p

0

2

0

YMR166Cp

0

2

0

Asi2p

0

2

0

Pdr12p

0

5

0

Gdh1p

1

4

0

Protein synthesis/ translocation/ folding

Pth2p*

2

6

1

Gln1p*

3

9

4

Ssh1p

0

2

0

Unknown

Cos2p*

1

10

3

Pdi1p

0

2

0

YIL108Wp

0

12

5

Rps20p*

0

2

0

Yet1p*

0

2

0

Sec11p

0

3

0

YKL100Cp

0

3

0

Kar2p

0

4

0

Ssh4p

0

5

1

Ero1p

0

4

0

YNL058Cp

0

3

0

Sis1p

0

4

1

 

Hsp82p

1

3

0

Columns to the right of each candidate protein show the number of identified unique peptides in the WT (A), npl4-1 (B), and npl4-1∆ubc7 (C) data sets; Shades of gray are proportional to the number of peptides identified.

*An identified ubiquitination site.

Encoded by YIL154C.





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