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Table 3 Examples of yeast buffering two-gene families (SSL double-KO phenotype)

From: Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation

Name

Function

Name

Function

E-value

Sequence identity (%)

YIL159W BNR1

Formin, nucleates the formation of linear actin filaments, involved in cell processes such as budding and mitotic spindle orientation which require the formation of polarized actin cables, functionally redundant with BNI1

YNL271C BNI1

Formin, nucleates the formation of linear actin filaments, involved in cell processes such as budding and mitotic spindle orientation which require the formation of polarized actin cables, functionally redundant with BNR1

1E-82

32

YML075C HMG1

One of two isozymes of HMG-CoA reductase that catalyzes the conversion of HMG-CoA to mevalonate, which is a rate-limiting step in sterol biosynthesis; localizes to the nuclear envelope; overproduction induces the formation of karmellae

YLR450W HMG2

One of two isozymes of HMG-CoA reductase that convert HMG-CoA to mevalonate, a rate-limiting step in sterol biosynthesis; overproduction induces assembly of peripheral ER membrane arrays and short nuclear-associated membrane stacks

0

62

YKR067W GPT2

Glycerol-3-phosphate acyltransferase located in both lipid particles and the ER; involved in the stepwise acylation of glycerol-3-phosphate and dihydroxyacetone, which are intermediate steps in lipid biosynthesis

YBL011W SCT1

Glycerol 3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase of the glycerolipid biosynthesis pathway, prefers 16-carbon fatty acids, similar to Gpt2p, gene is constitutively transcribed

2E-118

36

YEL042W GDA1

Guanosine diphosphatase located in the Golgi, involved in the transport of GDP-mannose into the Golgi lumen by converting GDP to GMP after mannose is transferred its substrate

YER005W YND1

Apyrase with wide substrate specificity, involved in preventing the inhibition of glycosylation by hydrolyzing nucleoside tri- and diphosphates which are inhibitors of glycotransferases; partially redundant with Gda1p

5E-28

27

YKL020C SPT23

ER membrane protein involved in regulation of OLE1 transcription, acts with homolog Mga2p; inactive ER form dimerizes and one subunit is then activated by ubiquitin/proteasome-dependent processing followed by nuclear targeting

YIR033W MGA2

ER membrane protein involved in regulation of OLE1 transcription, acts with homolog Spt23p; inactive ER form dimerizes and one subunit is then activated by ubiquitin/proteasome-dependent processing followed by nuclear targeting

1E-163

37

YGR038W ORM1

Evolutionarily conserved protein with similarity to Orm2p, required for resistance to agents that induce the unfolded protein response; human ortholog is located in the endoplasmic reticulum

YLR350W ORM2

Evolutionarily conserved protein with similarity to Orm1p, required for resistance to agents that induce the unfolded protein response; human ortholog is located in the endoplasmic reticulum

3E-68

72

YER087C-B SBH1

Beta subunit of the Sec61p ER translocation complex (Sec61p-Sss1p-Sbh1p); involved in protein translocation into the endoplasmic reticulum; interacts with the exocyst complex

YER019C-A SBH2

Ssh1p-Sss1p-Sbh2p complex component, involved in protein translocation into the endoplasmic reticulum

8E-19

55

YHL003C LAG1

Ceramide synthase component, involved in synthesis of ceramide from C26(acyl)-coenzyme A and dihydrosphingosine or phytosphingosine, functionally equivalent to Lac1p

YKL008C LAC1

Ceramide synthase component, involved in synthesis of ceramide from C26(acyl)-coenzyme A and dihydrosphingosine or phytosphingosine, functionally equivalent to Lag1p

6E-169

73

YHR066W SSF1

Constituent of 66S pre-ribosomal particles, required for ribosomal large subunit maturation; functionally redundant with Ssf2p

YDR312W SSF2

Protein required for ribosomal large subunit maturation, functionally redundant with Ssf1p

0

94

YPR159W KRE6

Protein required for beta-1,6 glucan biosynthesis; putative beta-glucan synthase; appears functionally redundant with Skn1p

YGR143W SKN1

Protein involved in sphingolipid biosynthesis; type II membrane protein with similarity to Kre6p

0

68

  1. Two-gene families and their phenotypes in double-KOs are a good model for buffering by gene duplicates. We distinguish between 'buffering genes' (50), i. e. gene pairs resulting in a synthetic sick or lethal (SSL) phenotype upon double-KO; and 'non-buffering genes' (eight), i. e. gene pairs that result in a viable phenotype upon double gene-KO, and which are thus unlikely to buffer for each other in single gene-KO.
  2. Tables 3 and 4 list the functions of a subset of buffering and all eight non-buffering gene pairs, respectively, with one pair per row. The ten buffering gene pairs in this table originate from the same large-scale screens as the eight non-buffering pairs in table 4. The remaining 40 buffering gene pairs originate from small-scale screens, and are listed in the Additional file 2. The descriptions of functions are taken from SGD [66]. Buffering genes (this table) are more often described as having identical functions than non-buffering genes (Table 4).