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Table 2 rhfΔ mutants with > 2-fold reduction in Ty1 cDNA

From: Host co-factors of the retrovirus-like transposon Ty1

Retrotransposition host factor

Systematic ORF name

Cellular function

Relative Ty1 cDNA level (rhfΔ/RHF)

Genomic DNA samples analyzed (n)

Afr1

YDR085C

Protein required for pheromone-induced projection (shmoo) formation; regulates septin architecture during mating; has an RVXF motif that mediates targeting of Glc7 to mating projections; interacts with Cdc12

0.42

2

Atp17

YDR377W

Subunit f of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis

0.34

2

Bud21

YOR078W

Also known as UTP16; component of small ribosomal subunit (SSU) processosome that contains U3 snoRNA

0.29

2

Cdc50

YCR094W

Endosomal protein that interacts with phospholipid flippase Drs2; interaction with Cdc50p is essential for Drs2 catalytic activity; mutations affect cell polarity and polarized growth

0.38

2

Cth1

YDR151C

Member of the CCCH zinc finger family; has similarity to mammalian Tis11 protein, which activates transcription and also has a role in mRNA degradation; may function with Tis11 in iron homeostasis

0.30

2

Dbf20

YPR111W

Ser/Thr kinase involved in late nuclear division, one of the mitotic exit network (MEN) proteins; necessary for the execution of cytokinesis; ortholog of human NDR2 kinase

0.45

3

Dbp7

YKR024C

Putative ATP-dependent RNA helicase of the DEAD-box family involved in ribosomal biogenesis

<0.01

2

Dfg10

YIL049W

Probable polyprenol reductase that catalyzes conversion of polyprenol to dolichol, the precursor for N-glycosylation; mutations in human ortholog SRD5A3 confer CDG1Q (Congenital Disorders of Glycosylation type 1Q)

0.27

2

Dgr2

YKL121W

Protein of unknown function; null mutant is resistant to 2-deoxy-D-glucose

0.32

3

Dhh1

YDL160C

Cytoplasmic DExD/H-box helicase, stimulates mRNA decapping, coordinates distinct steps in mRNA function and decay, interacts with both the decapping and deadenylase complexes; ortholog of the human oncogene DDX6/p54/RCK

0.23

5

Elp2

YGR200C

Subunit of elongator complex, which is a component of the RNA polymerase holoenzyme and required for modification of wobble uridines in tRNA; ortholog of human ELP2/STATIP1 gene

0.21

2

Hcr1

YLR192C

Dual function protein involved in translation initiation as a substoichiometric component (eIF3j) of translation initiation factor 3 (eIF3) and required for processing of 20 S pre-rRNA; ortholog of human EIF3J gene

0.29

3

Hit1

YJR055W

Unknown function, required for growth at high temperature

0.24

2

Hmo1

YDR174W

Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5′-3′ DNA helicase and Fpr1, a prolyl isomerase

0.19

3

Kgd1

YIL125W

Component of the mitochondrial alpha-ketoglutarate dehydrogenase complex, which catalyzes a key step in the tricarboxylic acid (TCA) cycle, the oxidative decarboxylation of alpha-ketoglutarate to form succinyl-CoA; ortholog of human OGDHL gene

0.27

2

Loc1

YFR001W

Nuclear protein involved in asymmetric localization of ASH1 mRNA; binds double-stranded RNA in vitro; co-localizes with large subunit precursor of ribosome

0.14

3

Los1

YKL205W

Nuclear pore protein involved in nuclear export of pre-tRNA and in re-export of mature tRNAs after retrograde import from the cytoplasm; ortholog of human exportin-T gene, XPOT

0.44

3

Lst7

YGR057C

Protein possibly involved in a post-Golgi secretory pathway; required for the transport of nitrogen-regulated amino acid permease Gap1 from the Golgi to the cell surface

0.44

4

Mrt4

YKL009W

Protein involved in mRNA turnover and large ribosome assembly, co-localizes with large subunit precursor of ribosome; ortholog of human MRTO4 gene

0.17

2

Ncl1

YBL024W

S-adenosyl-L-methionine-dependent tRNA: m5C-methyltransferase, methylates cytosine to m5C at several positions in tRNAs and intron-containing pre-tRNAs; similar to Nop2 and human proliferation associated nucleolar protein p120

0.49

4

Oca4

YCR095C

Cytoplasmic protein required for replication of Brome mosaic virus in S. cerevisiae, which is a model system for studying replication of positive-strand RNA viruses

0.43

2

Ref2

YDR195W

RNA-binding protein involved in the cleavage step of mRNA 3′-end formation prior to polyadenylation, and in snoRNA maturation; part of holo-CPF subcomplex APT, which associates with 3′-ends of snoRNA- and mRNA-encoding genes

0.17

2

Rkm4

YDR257C

Ribosomal lysine methyltransferase specific for monomethylation of Rpl42a and Rpl42b (lysine 55); nuclear SET-domain containing protein

0.41

2

Rpl7a

YGL076C

Protein component of the large (60 S) ribosomal subunit, nearly identical to Rpl7b; ortholog of human L7 ribosomal protein gene

0.15

4

Rpl19a

YBR084C-A

Protein component of the large (60 S) ribosomal subunit, nearly identical to Rpl19b; ortholog of human L19 ribosomal protein gene

0.24

2

Rpl27a

YGL076C

Protein component of the large (60 S) ribosomal subunit; nearly identical to Rpl27b; ortholog of human L27 ribosomal protein gene

0.19

2

Rpl31a

YDL075W

Protein component of the large (60 S) ribosomal subunit, nearly identical to Rpl31b; ortholog of human L31 ribosomal protein gene

0.10

2

Rpl43a

YPR043W

Protein component of the large (60 S) ribosomal subunit, identical to Rpl43b; ortholog of human ribosomal protein L37 gene

0.15

3

Rps19b

YNL302C

Protein component of the small (40 S) ribosomal subunit, required for assembly and maturation of pre-40 S particles; mutations in human RPS19 are associated with Diamond Blackfan anemia; nearly identical to Rps19a

0.28

4

Rps25a

YGR027C

Protein component of the small (40 S) ribosomal subunit; nearly identical to Rps25b; ortholog of human S25 ribosomal protein gene

0.19

2

Rps30a

YLR287C-A

Protein component of the small (40 S) ribosomal subunit; nearly identical to Rps30B; ortholog of human S30 ribosomal protein

0.20

2

Snf5

YBR289W

Subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; functions interdependently in transcriptional activation with Snf2 and Snf6

0.09

2

Snf6

YHL025W

Subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; functions interdependently in transcriptional activation with Snf2 and Snf5

0.27

2

Snt1

YCR033W

Subunit of the Set3C deacetylase complex that interacts directly with the Set3C subunit, Sif2p; putative DNA-binding protein

0.21

2

Spf1

YEL031W

P-type ATPase, ion transporter of the ER membrane involved in ER function and Ca2+ homeostasis; required for regulating Hmg2 degradation

0.42

2

Spt3

YDR392W

Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15 to activate transcription of some RNA polymerase II-dependent genes; also inhibits transcription at some promoters

0.09

3

Spt8

YLR055C

Subunit of the SAGA transcriptional regulatory complex but not present in SAGA-like complex SLIK/SALSA, required for SAGA-mediated inhibition at some promoters

0.10

2

Sse1

YPL106C

ATPase that is a component of the heat shock protein Hsp90 chaperone complex; binds unfolded proteins; member of the HSP70 family

0.25

2

Swi3

YJL176C

Subunit of the SWI/SNF chromatin remodeling complex

0.44

3

Ump1

YBR173C

Short-lived chaperone required for correct maturation of the 20 S proteasome; may inhibit premature dimerization of proteasome half-mers; degraded by proteasome upon completion of its assembly

0.36

3

Upf1

YMR080C

Also known as Nam7; ATP-dependent RNA helicase of the SFI superfamily involved in nonsense mediated mRNA decay; required for efficient translation termination at nonsense codons and targeting of NMD substrates to P-bodies; involved in telomere maintenance

0.25

4

Upf3

YGR072W

Component of the nonsense-mediated mRNA decay (NMD) pathway, along with Upf1 and Upf2; involved in decay of mRNA containing nonsense codons and telomere maintenance; ortholog of human UPF3A and UPF3B genes

0.29

4

YDL124W

YDL124W

NADPH-dependent alpha-keto amide reductase

0.36

2