. 2010 Mar 31;76:123–177. doi: 10.1016/S0065-3527(10)76004-8

Table I.

Functional grouping and roles of the identified host genes affecting TBSV RNA replication and recombination^a

Gene	Cellular function	Viral replication^b	Viral recombination	Interaction
1. Translation/protein biosynthesis
BFR1	mRNP complexes/polyribosomes			p33/RNA
DED1	DEAD-box RNA helicase, translation	Required
EFB1	Translation elongation factor 1β			p33
ERB1	Maturation of ribosomal RNAs	Stimulatory^c		p33, p92
GCD2	δ-subunit of eIF2B	Stimulatory^c		RNA
HBS1	GTP binding, similarity to EF-1α	Stimulatory^c		p33
IPI3	Rix1 complex, pre-rRNA processing			p33
MRPL32	Protein biosynthesis	Inhibitory
NOG1	Putative GTPase, ribosome biogenesis	Inhibitory
NOG2	Putative GTPase, ribosome biogenesis	Inhibitory
NOP53	Processing of 27S pre-rRNA	Inhibitory^c		RNA
RPL1B	Protein biosynthesis	Inhibitory
RPL4A	Component of the large ribosomal subunit			RNA
RPL7A	Protein biosynthesis	Inhibitory
RPL8A	Ribosomal protein L4			p33/p92/RNA
RPL17A	Structural constituent of ribosome	Inhibitory
RPL26B	Component of the large ribosomal subunit			RNA
RPS21B	Protein biosynthesis	Required
SAS10	Ribosomal processome			p33/p92/RNA
SSF2	rRNA binding			RNA
STM1	Required for optimal translation	Stimulatory^c		p33/p92/RNA
TEF1^d	Translational elongation factor eEF1A	Required		p33/p92/RNA/replicase
TEF2^d	Translational elongation factor eEF1A	Required		p33/p92/RNA/replicase
TEF4	Translation elongation factor	Required
TIF1	Translation initiation factor eIF4A			p33
TIF11	Translation initiation factor eIF1A			p33/p92
TSR2	pre-rRNA processing			p33
YCR016W	Ribosome biogenesis (predicted)			p33/p92/RNA
2. Protein metabolism, posttranslation modification
ARO1	Aromatic amino acid synthesis	Required
BRE1	Ubiquitin-protein ligase	Required
CDC34^d	Ubiquitin-conjugating enzyme or E2	Required, stimulatory^c		p33/replicase
CKA1	α-subunit of protein kinase CK2			RNA
DOA4^d	Protein deubiquitination	Required
EPL1	Histone acetyltransferase activity	Required
LGE1	Protein monoubiquitination	Required
MAK3	Protein amino acid acetylation	Required
MAP1	Methionine aminopeptidase			p92/RNA
MET1	Uroporphyrin methyltransferase	Required
MOB1	Protein amino acid phosphorylation	Required
MPS1	Protein threonine/tyrosine kinase		Accelerator
NOB1	Protein involved in proteasome maturation			p92/RNA
OTU2	Predicted cysteine proteases	Inhibitory^c		p33/p92/RNA
RAD6	Ubiquitin-conjugating enzyme	Required
RPT4	Endopeptidase		Accelerator
RSP5^d	Ubiquitin-protein ligase	Inhibitory		p33/p92
SLN1	Protein histidine kinase activity	Required
SIW14	Protein tyrosine phosphatase	Required
UBA1	Ubiquitin-activating enzyme			p33
UBP3	Ubiquitin-specific protease		Suppressor
UBP10	Ubiquitin-specific protease			p33/p92/RNA
UBP15	Ubiquitin-specific protease			p33
YDR161W	ER-associated protein degradation			p33
3. RNA-binding proteins/RNA metabolism
BUD21	snoRNA binding	Inhibitory, inhibitory^c		p33/RNA
CCR4	3′–5′ exoribonuclease	Required
CTL1	Polynucleotide 5′-phosphatase		Suppressor
CWC25	pre-mRNA splicing			RNA
DBP2	RNA helicase of the DEAD-box protein family	Stimulatory^c		RNA
DBP3	Putative RNA helicase/DEAD-box family			p92
DIM1	Essential 18S rRNA dimethylase			RNA
DEG1	Nonessential tRNA: pseudouridine synthase	Inhibitory^c		RNA
GLO3	GTPase activation, ER-Golgi transport			RNA
GRC3	Possibly involved in rRNA processing	Inhibitory
HAS1	Putative ATP-dependent RNA helicase	Inhibitory^c		RNA
IRC5	DEAD-box helicase			RNA
LHP1	RNA-binding protein/maturation of tRNA			RNA
LRP1	Nuclear cofactor for exosome activity			RNA
MET22/HAL2	3′(2′),5′-bisphosphate nucleotidase		Suppressor
MEX67	Poly(A)RNA-binding protein	Required
MSE1	Glutamate-tRNA ligase activity			RNA
NAB2	Polyadenylated RNA binding; hnRNPs	Required
NOP4	RNA binding, ribosomal RNA processing	Inhibitory
NOP10	RNA binding, pseudouridylation, 18S rRNA		Modifier
NPL3	mRNA binding	Required, inhibitory^c		p92/RNA
NSR1^d	RNA binding/rRNA processing	Required
PRP5	RNA helicase in the DEAD-box family	Inhibitory
PRP39	RNA binding, nuclear mRNA splicing	Required
PUS4	Pseudouridine synthase	Inhibitory^c		RNA
RIB2	Cytoplasmic tRNA pseudouridine synthase			p33
RNA14	RNA binding/mRNA cleavage	Required
RNY1	RNAse; endoribonucleases	Inhibitory^c		RNA
RPL15A	Binds to 5.8S rRNA	Inhibitory
RPM2	Ribonuclease P activity		Modifier
RRP9	RNA binding, pre-rRNA processing	Required	Accelerator
RRP42	3′–5′ exoribonuclease activity	Required
SEN1	RNA helicase, processing of tRNA, rRNA	Required	Accelerator
TRM1	tRNA methyltransferase			p33/p92/RNA
TRZ1	tRNase Z, involved in RNA processing	Stimulatory^c		p33
URN1	Pre-mRNA splicing factor			p33/p92
UTP7	Small subunit (SSU) processome	Inhibitory^c		p92/RNA
UTP9	snoRNA binding, interacts with UTP15	Required
UTP15	snoRNA binding, interacts with UTP9	Required
XRN1/KEM1^d	5′–3′ exoribonuclease	Required	Suppressor
YBL055C	3′–5′ exoribonuclease, endoribonuclease			RNA
YKL023W	mRNA degradation			p92/RNA
4. Lipid metabolism
ERG4^d	δ24(24-1)-sterol reductase	Required/sterol level
ERG25^d	Ergosterol biosynthesis	Required/sterol level
FAS2	α-subunit of fatty acid synthetase		Modifier
FOX2	Peroxisomal fatty acid β-oxidation pathway			p33/RNA
INO2	Phospholipid biosynthesis	Required
MCT1	S-malonyltransferase/fatty acid metabolism	Required
POX1	Acyl-CoA oxidase/fatty acid β-oxidation	Required
TGL2	Triacylglycerol lipase/lipid metabolism	Required
5. Protein and vesicle-mediated transport
APM2	Vesicle-mediated transport	Inhibitory^c		RNA
ARL3	Small monomeric GTPase	Required
BRE5	Vesicle-mediated transport	Required
COP1	Protein transporter, COPI vesicle	Required	Suppressor
DID2^d	ESCRT/protein–vacuolar targeting	Required
GOS1	v-SNARE activity/intra-Golgi transport	Required
MCH5	Transporter/membrane associated	Required
MON1	Protein–vacuolar targeting	Required
NUP53	Subunit of the nuclear pore complex			RNA
PEP3	Transporter/vacuolar membrane	Required
PEP7/VPS19	Unknown/Golgi to vacuole transport		Accelerator
PEX19^d	Chaperone/import to peroxisome			p33
PTH1/VAM3	Golgi to vacuole transport		Accelerator
RIC1	Guanyl-nucleotide exchange factor	Required
SEC62	SRP-dependent/protein-membrane targeting			RNA
SNF7^d	ESCRT/late endosome	Required
SNL1	Nuclear pore organization and biogenesis			RNA
SRP40	Nucleocytoplasmic transport/chaperone			RNA
TLG2	t-SNARE, v-SNARE/vesicle fusion	Required
TOM71	Component of the TOM translocase			p33/p92/RNA
VPS4^d	ESCRT/ATPase/late endosome	Required
VPS23/STP22^d	ESCRT/protein–vacuolar targeting	Required
VPS24^d	ESCRT/late endosome	Required
VPS28^d	Protein–vacuolar targeting	Required
VPS29	Retrograde/endosome to Golgi/transport	Required	Accelerator
VPS35	Endosome to Golgi transport		Accelerator
VPS41	Rab guanyl-nucleotide exchange factor	Required
VPS43/VAM7	Golgi to vacuole transport		Accelerator
VPS51	Protein–vacuolar targeting	Required
VPS61	Protein–vacuolar targeting	Required
VPS66	Cytoplasmic protein/vacuolar protein sorting			p92/RNA
VPS69	Protein–vacuolar targeting	Required
YOS9	Protein transporter/ER to Golgi transport	Required
6. Membrane associated
KEG1	Integral membrane protein of the ER	Inhibitory^c		RNA
MSP1	ATPase/mitochondrial translocation	Required
OPT1	Oligopeptide transporter	Required
PMR1(HUR1)^d	Ca²⁺/Mn²⁺ ion pump		Suppressor
SAC1	Inositol/phosphatidylinositol phosphatase	Required
SNF4	Protein kinase activator	Required
STE14	Isoprenylcysteine methyltransferase	Required
STV1	Hydrogen-transporting ATPase	Required
TOK1	Potassium channel	Required
7. Stress-related/chaperone
DDR48	DNA damage-response, heat-shock stress	Inhibitory^c		p33
JJJ1	Cochaperone of Ssa1p	Stimulatory^c		p33/p92/RNA
JJJ3	Contains J-domain			p33
GIM3	Heterohexameric cochaperone prefoldin complex			p33
GRE3	Aldehyde reductase	Required
GTT1	Glutathione transferase	Required
IRA2	Ras GTPase activator	Required
SSA1^d	HSP70 chaperone	Required		p33/p92/replicase
SSA2^d	HSP70 chaperone	Required		p33/p92/replicase
UGA2	Glutamate catabolism	Required
WHI2	Phosphatase activator	Required
8. General metabolism
ALA1	Cytoplasmic alanyl-tRNA synthetase			p33
BEM4	Rho protein signal transduction	Required
COX12	Cytochrome c oxidase	Required
CHO2/PEM1	Phosphatidylethanolamine N-methyltransferase		Accelerator
DCI1	Dodecenoyl-CoA δ-isomerase		Accelerator
DSE1	Cell wall organization and biogenesis	Required
ERR2	Phosphopyruvate hydratase			p33
GLO2	Hydroxyacylglutathione hydrolase	Required
GPH1	Glycogen phosphorylase	Required		p33
GSY2	Glycogen synthase			p33/p92
HAP3	Regulation of carbohydrate metabolism	Required
HOR2	dl-glycerol-3-phosphatase			p33
IPK1	Inositol/phosphatidylinositol kinase		Accelerator
ISN1	Inosine 5′-monophosphate 5′-nucleotidase			p33
LPD1	Pyruvate dehydrogenase	Required
MAM33	Mitochondrial matrix/oxidative phosphorylation			p33
MDH3	Cytoplasmic malate dehydrogenase			RNA
MDM38	Mitochondrial inner membrane protein	Stimulatory^c		RNA
MSB1	Establishment of cell polarity	Required
NAP1	Regulation of microtubule dynamics			p33
PCS60	Peroxisomal AMP-binding protein			RNA
PDC1	Pyruvate decarboxylase			Replicase
PDI1	Protein disulfide isomerase, ER lumen			p33
PHD1	Pseudohyphal growth	Required
PLP2	Actin binding/similarity to phosducins			p33
PYC1	Pyruvate carboxylase isoform			p33
QCR6	Ubiquinol–cytochrome c reductase complex			p33/p92
RIB7	Deaminase, riboflavin biosynthesis		Modifier
RMD7	Cell wall organization and biogenesis	Required
SHO1	Transmembrane osmosensor			p33
SPE3	Spermidine synthase		Modifier
TDH2^d	Glyceraldehyde-3-phosphate dehydrogenase	Required		RNA/replicase
TDH3^d	Glyceraldehyde-3-phosphate dehydrogenase	Required		RNA/replicase
THI3	Carboxy-lyase/thiamin biosynthesis	Required
TUM1	Mitochondrial, similar to rhodanase			p33
YJL218W	Acetyltransferase activity			RNA
YIL064W	S-adenosylmethionine methyltransferase	Required
9. RNA transcription
ARP9	RNA polymerase, actin-related protein	Inhibitory	Accelerator
CDC50	Transcription regulator	Required
HAA1	Transcriptional activator	Inhibitory^c		RNA
MED6	RNA polymerase II transcription mediator	Required
ELF1	A zinc finger transcription elongation factor			p33
IWR1	Affects transcription by pol II			p33/p92
NGG1	Transcription cofactor		Accelerator
POL1	α-DNA polymerase, synthesis of RNA primer		Suppressor
RDS2	Zinc cluster transcription activator			p92
RGR1	Transcription mediator		Suppressor
RPB11^d	RNA polymerase II subunit B12.5	Required	Accelerator
RPO21	RNA polymerase	Required
ROX3	RNA polymerase II transcription mediator	Required
SUB1	Transcriptional coactivator	Inhibitory^c		RNA
SPT3	Transcription cofactor		Modifier
SPT16	Pol II transcription elongation factor			p33/p92
SRB8	RNA polymerase II transcription mediator	Required
SWI3	General RNA polymerase II transcription factor	Required
TEA1	Transcription regulator	Required
TFA2	General RNA polymerase II transcription factor	Required
UME6	Transcription regulator	Required
10. DNA remodeling, metabolism
ADA2^d	Chromatin modification, histone acetylation	Required
ARP8	Nuclear actin-related, chromatin remodeling	Stimulatory^c		p33
DOT1	Nucleosomal histone methylase			p92
DPB4	ε-DNA polymerase	Required
HEX3	DNA recombination	Required
NGG1	Chromatin modification, histone acetylation	Required
ORC6	DNA replication		Modifier
POL30	Proliferating cell nuclear antigen (PCNA)	Stimulatory^c		p33
RSC8	Chromatin remodeling	Required
RTT106	Histone chaperone/Ty transposition			p33
SAS3	Acetyltransferase/chromatin silencing	Required
SIN3	Histone deacetylase	Required
SLX8	DNA metabolism	Required
SLX9	DNA metabolism	Inhibitory
SNF6	Chromatin modeling/SWI/SNF complex	Required
11. Function unknown
BSC2	Unknown	Required
EMI2	Protein of unknown function			p33
FMP40	Protein of unknown function			p33
LDB7	Unknown	Required
YBR007C	Unknown	Required
YBR032W	Unknown	Required
YCR099C	Unknown	Required
YDR327W	Unknown	Inhibitory	Modifier
YFL043C	Unknown	Required
YGL140C	Unknown	Required
YGL242C	Unknown			p33/p92
YGR017W	Unknown			p33/p92
YGR026W	Unknown	Inhibitory^c		RNA
YGR027W	Retrotransposon TYA gag gene			p33
YGR064W	Unknown	Required
YHR009C	Unknown			p33
YHR029C	Unknown	Required
YIL090W	Unknown	Required
YJL175W	Unknown	Required
YKL033W	Cytoplasmic protein with unknown function		Modifier
YLR125W	Unknown/Ty3 transposition			p33
YLR358C	Unknown	Required
YNL196C	Unknown/leucine zipper protein			RNA
YNL321W	Unknown	Required
YOR309C	Hypothetical protein			p92/RNA
YPR050C	Unknown	Required
YPR174C	Unknown			RNA

The shown data are from Jiang et al., 2006, Li et al., 2008, Li et al., 2009, Panavas et al., 2005b, Serva & Nagy, 2006, Serviene et al., 2005, Serviene et al., 2006.

“Required” is based on more than twofold drop in TBSV replication when the host gene is deleted or its expression is downregulated.

Based on protein overexpression in yeast.

Host genes, whose roles/functions have been characterized in details in TBSV replication.