Table I. Proteins involved in the regulation of bulk cytoplasmic mRNA degradation in plants.
AtRRP44A, AtRRP6L1, and AtRRP6L2 are components of the exosome complex, but they are not included here because subcellular localization data suggest that they are nuclear proteins and, hence, components of the nuclear exosome (Lange et al., 2008; Zhang et al., 2010). At, Arabidopsis thaliana; Ca, Capsicum annuum; Nb, Nicotiana benthamiana; Os, Oryza sativa; Ta, Triticum aestivum.
| Protein | Molecular Function | Gene Symbol | Gene Identifier | Biological Functions | References |
|---|---|---|---|---|---|
| Deadenylation | |||||
| CCR4-NOT complex | |||||
| Carbon catabolite repressor4 | 3′-5′ exoribonuclease, EEP superfamily | AtCCR4a | AT3G58560 | Suc and starch metabolism | Suzuki et al. (2015) |
| AtCCR4b | AT3G58580 | ||||
| OsCCR4a | Os10g27230 | Unknown | Chou et al. (2017) | ||
| OsCCR4b | Os03g07080 | ||||
| CCR4-associated factor1 | 3′-5′ exoribonuclease, DEDD superfamily | AtCAF1a | AT3G44260 | Defense response to bacterial pathogens; abiotic stress response | Liang et al. (2009); Walley et al. (2010) |
| AtCAF1b | AT5G22250 | ||||
| OsCAF1A | Os08g34170 | Unknown | Chou et al. (2014, 2017) | ||
| OsCAF1B | Os04g58810 | ||||
| OsCAF1G | Os09g24990 | ||||
| OsCAF1H | Os02g55300 | ||||
| CaCAF1 | Development and defense response | Sarowar et al. (2007) | |||
| Negative on TATA1 | CCR4-NOT complex scaffold | OsNOT1 | Os10g40780 | Unknown | Chou et al. (2017) |
| Nocturnin | Poly(A)-specific 3′-5′ exoribonuclease, EEP superfamily | AtHESP | AT1G31500 | Circadian clock regulation | Delis et al. (2016) |
| Poly(A) RNase | Poly(A)-specific 3′-5′ exoribonuclease, DEDD superfamily | AtPARN/AHG2 | AT1G55870 | Embryogenesis; ABA sensitivity; abiotic stress response | Reverdatto et al. (2004); Nishimura et al. (2005) |
| 5′-3′ mRNA decay | |||||
| Decapping complex | |||||
| Decapping1 | Decapping cofactor | AtDCP1 | AT1G08370 | Postembryonic development; dehydration and heat stress response | Xu et al. (2006); Xu and Chua (2012); Motomura et al. (2015) |
| Decapping2 | Decapping enzyme | AtDCP2/TDT | AT5G13570 | Postembryonic development; heat stress response | Xu et al. (2006); Motomura et al. (2015) |
| Decapping5 | Decapping enhancer | AtDCP5 | AT1G26110 | Postembryonic development; osmotic stress response | Xu and Chua (2009, 2012) |
| Enhancer of mRNA decapping4 | Core decapping complex scaffold | AtEDC4/VCS | AT3G13300 | Postembryonic development; osmotic stress response; seed dormancy and germination | Xu et al. (2006); Goeres et al. (2007); Soma et al. (2017) |
| TaEDC4 | Traes_6DL_3FBA5B70E | Plant-fungal pathogen interaction | Petre et al. (2016) | ||
| LSM1-7 complex | Decapping enhancer | AtLSM1a | AT1G19120 | Postembryonic development; heat stress tolerance; ABA-mediated response to cold, drought, and salt tolerance | Perea-Resa et al. (2012, 2016); Golisz et al. (2013); Okamoto et al. (2016) |
| AtLSM1b | AT3G14080 | ||||
| AtLSM2 | AT1G03330 | ||||
| AtLSM3a | AT1G21190 | ||||
| AtLSM3b | AT1G76860 | ||||
| AtLSM4 | AT5G27720 | ||||
| AtLSM5 | AT5G48870 | ||||
| AtLSM6a | AT2G43810 | ||||
| AtLSM6b | AT3G59810 | ||||
| AtLSM7 | AT2G03870 | ||||
| Protein-associated with topoisomerase1 | Decapping enhancer, translation repressor? | AtPAT1 | AT1G79090 | Immune response | Roux et al. (2015) |
| DEAD-box RNA helicase | AtDHH1 | AT3G61240 | Unknown | Xu et al. (2006); Bhullar et al. (2017) | |
| Asymmetric leaf2 | Decapping activator | AtAS2 | AT1G65620 | Plant-virus interaction | Ye et al. (2015) |
| 5′-3′ mRNA decay | |||||
| Exoribonuclease4 | 5′-3′ exoribonuclease | AtXRN4/EIN5 | AT1G54490 | Ethylene response/signaling; heat stress response | Potuschak et al. (2006); Merret et al. (2013) |
| NbXRN4 | gi|242037819 | Defense response to viral pathogen | Peng et al. (2011); Lee et al. (2016) | ||
| LA-related protein1A | Heat-specific cofactor of AtXRN4 | AtLARP1A | AT5G21160 | Heat stress response | Merret et al. (2013) |
| 3′-5′ mRNA decay | |||||
| Cytoplasmic exosome | |||||
| rRNA processing proteins | RNase PH domain-containing proteins; hexameric core ring subunits of exosome | AtRRP41 | AT3G61620 | Female gametogenesis | Chekanova et al. (2007) |
| AtRRP42 | AT3G07750 | Unknown | Chekanova et al. (2007) | ||
| AtRRP43 | AT1G60080 | Unknown | Chekanova et al. (2007) | ||
| AtRRP45A | AT3G12990 | Essential for viability; cuticular wax biosynthesis | Hooker et al. (2007) | ||
| AtRRP45B/CER7 | AT3G60500 | ||||
| AtRRP46 | AT3G46210 | Unknown | Chekanova et al. (2007) | ||
| AtRRP41L/MTR3 | AT4G27490 | Germination and seedling development | Yang et al. (2013) | ||
| S1/KH domain-containing proteins; cap structure subunits of core exosome | AtRRP4 | AT1G03360 | Postzygotic development | Chekanova et al. (2007) | |
| AtRRP40A | AT2G25355 | Unknown | Chekanova et al. (2007) | ||
| AtRRP40B | AT4G32175 | Unknown | Chekanova et al. (2007) | ||
| AtCSL4 | AT5G38885 | Unknown | Chekanova et al. (2007) | ||
| RNase II-type 3′-5′ exoribonuclease | AtRRP44B/SOV | AT1G77680 | Compensation of VCS function in postembryonic development | Zhang et al. (2010); Kumakura et al. (2013) | |
| RNase D-type 3′-5′ exoribonuclease, DEDD superfamily | AtRRP6L3 | AT2G32415 | Unknown | Lange et al. (2008) | |
| Superkiller (SKI) complex | |||||
| Superkiller proteins | Auxiliary factors of the exosome | AtSKI2 | AT3G46960 | Cuticular wax biosynthesis | Zhao and Kunst (2016) |
| AtSKI3 | AT1G76630 | ||||
| AtSKI8/VIP3 | AT4G29830 | ||||