Table 1. Saccharomyces cerevisiae genes implicated in cytoplasmic tRNA processing, turnover, and subcellular trafficking.
| Yeast gene | Function | Null mutant phenotype | References |
|---|---|---|---|
| Pre-tRNA end processing | |||
| POP1, POP3, POP4, POP5, POP6, POP7, POP8, RPP1, RPR2, RPR1 | RNase P – 5′ leader endonuclease | Essential | (Chamberlain et al. 1998) |
| LHP1 | tRNA 3′ trailer processing | Not essential | (Yoo and Wolin 1997) |
| REX1 | 3′ trailer exonuclease | Not essential | (Copela et al. 2008; Ozanick et al. 2009) |
| TRZ1 | RNase Z – 3′ trailer endonuclease | Essential | (Takaku et al. 2003) |
| CCA1 | CCA | Essential | (Aebi et al. 1990) |
| THG1 | G-1 addition to tRNAHis | Essential | (Gu et al. 2003) |
| Pre-tRNA splicing | |||
| SEN2, SEN15, SEN34, SEN54 | Splicing endonuclease | Essential | (Ho et al. 1990; Trotta et al. 1997) |
| TPT1 | 2′-phosphotransferase | Essential | (Culver et al. 1997) |
| TRL1 | tRNA ligase | Essential | (Phizicky et al. 1986) |
| tRNA Modification | |||
| DUS1 | D16, D17 | Not essential | (Bishop et al. 2002; Xing et al. 2002) |
| DUS2 | D20 | Not essential | (Xing et al. 2004) |
| DUS3 | D47 | Not essential | (Xing et al. 2004) |
| DUS4 | D20a, D20b | Not essential | (Xing et al l. 2004) |
| ELP1, ELP2, ELP3, ELP4, ELP5, ELP6, KTI11, KTI12, KTI13, KTI14, SIT4, SAP185, SAP190 | mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34 | Many phenotypes | (Huang et al. 2005; Huang et al. 2008; Jablonowski et al. 2004) |
| NFS1, ISU1, ISU2, CFD1, NBP35, CIA1, URM1, UBA4, NCS2, NCS6, TUM1 | mcm5s2U34 | Not essential | (Bjork et al. 2007; Huang et al. 2008; Nakai et al. 2007; Nakai et al. 2004) |
| MOD5 | i6A37 | Loss of suppression | (Dihanich et al. 1987) |
| PUS1 | Ψ26, Ψ27,Ψ28 Ψ34, Ψ(35), Ψ36, Ψ65, Ψ67 | Not essential | (Motorin et al.. 1998; Simos et al. 1996) |
| PUS3 | Ψ38, Ψ39 | Slow growth | (Lecointe et al.1998) |
| PUS4 | Ψ55 | Not essential | (Becker et al. 1997) |
| PUS6 | Ψ31 | Not essential | (Ansmant et al. 2001) |
| PUS7 | Ψ13, Ψ35 | Not essential | (Behm-Ansmant et al. 2003) |
| PUS8 | Ψ32 | Not essential | (Behm-Ansmant et al. 2004) |
| RIT1 | Ar(p)64 | Not essential | (Astrom and Bystrom 1994) |
| SUA5, KEOPS, TCD1, TCD2 | ct6A37 | Very sick | (El Yacoubi et al. 2009; Miyauchi et al. 2013) |
| TAD1 | I37 | Not essential | (Gerber et al. 1998) |
| TAD2, TAD3 | I34 | Essential | (Gerber and Keller 1999) |
| TAN1 | ac4C12 | Temperature sensitive | (Johansson and Bystrom 2004) |
| TRM1 | m2,2G26 | Not essential | (Ellis et al. 1986) |
| TRM2 | m5U54 | Not essential | (Hopper et al. 1982; Nordlund et al. 2000) |
| TRM3 | Gm18 | Not essential | (Cavaille et al. 1999) |
| TRM4 | m5C34, m5C40, m5C48, m5C49 | Not essential | (Motorin and Grosjean 1999) |
| TRM5 | m1G37, m1I37, yW37 | Very sick | (Bjork et al. 2001) |
| TRM6, TRM61 | m1A58 | Essential | (Anderson et al. 1998) |
| TRM7, TRM732 | Cm32 | Synthetic slow growth with trm734Δ; paromomycin sensitive | (Guy et al. 2012; Pintard et al. 2002) |
| TRM7, TRM734 | Cm34, Gm34, ncm5Um34 | Synthetic slow growth with trm732Δ; paromomycin sensitive | (Guy et al. 2012; Pintard et al. 2002) |
| TRM8, TRM82 | m7G46 | Not essential | (Alexandrov et al. 2002) |
| TRM9, TRM112 | mcm5U34 and mcm5s2U34 | Not essential; paromomycin sensitive | (Kalhor and Clarke 2003; Studte et al. 2008) |
| TRM10 | m1G9 | Not essential | (Jackman et al. 2003) |
| TRM11, TRM112 | m2G10 | Not essential | (Purushothaman et al. 2005) |
| TRM13 | Am4, Gm4, Cm4 | Not essential | (Wilkinson et al. 2007) |
| TRM44 | Um44 | Not essential | (Kotelawala et al. 2008) |
| TRM140 | m3C32 | Not essential | (D’Silva et al. 2011; Noma et al. 2011) |
| TYW1, TYW2, TYW3, TYW4, TRM5 | yW37 | Not essential; reading frame maintenance | (Kalhor et al. 2005; Noma et al. 2006) |
| tRNA turnover/cleavage | |||
| TRF4 | 3′ poly(A) polymerase; TRAMP component | Not essential | (Kadaba et al. 2004, 2006) |
| RRP44 | 3′ to 5′ exonuclease; exosome component | Essential | (Kadaba et al. 2004, 2006) |
| MET22 | Methionine biosynthesis | pAp accumulation; Rat1 and Xrn1 inhibition | (Dichtl et al. 1997; Chernyakov et al. 2008) |
| RAT1 | 5′ to 3′ exonuclease – RTD component | Essential | (Chernyakov et al. 2008) |
| XRN1 | 5′ to 3′ exonuclease – RTD component | Not essential | (Chernyakov et al. 2008) |
| RNY1 | endonuclease generating tRNA ∼halves | Not Essential | (Thompson and Parker 2009b) |
| tRNA subcellular trafficking | |||
| LOS1 | Export, reexport | Not essential | (Hopper et al. 1980; Murthi et al. 2010) |
| MSN5 | Reexport | Not essential | (Murthi et al. 2010) |
| MTR10 | Retrograde import | Sick | (Shaheen and Hopper 2005) |
For complex modifications, underlined portion indicates the part of the modification due to the corresponding gene(s).