P-bodies
Processing bodies (P-bodies) are distinct foci formed by phase separation within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover. P-bodies are highly conserved structures and have been observed in somatic cells originating from vertebrates and invertebrates, plants and yeast. To date, P-bodies have been demonstrated to play fundamental roles in general mRNA decay, nonsense-mediated mRNA decay, adenylate-uridylate-rich element mediated mRNA decay, and miRNA induced mRNA silencing.[1] Not all mRNAs which enter P-bodies are degraded, as it has been demonstrated that some mRNAs can exit P-bodies and re-initiate translation.[2][3] Purification and sequencing of the mRNA from purified processing bodies showed that these mRNAs are largely translationally repressed upstream of translation initiation and are protected from 5' mRNA decay.[4]
The following activities have been demonstrated to occur in or to be associated with P-bodies:
- decapping and degradation of unwanted mRNAs[5]
- storing mRNA until needed for translation[4]
- aiding in translational repression by miRNAs (related to siRNAs)
In neurons, P-bodies are moved by motor proteins in response to stimulation. This is likely tied to local translation in dendrites.[6]
P-bodies were first described in the scientific literature by Bashkirov et al.[7] in 1997, in which they describe "small granules… discrete, prominent foci" as the cytoplasmic location of the mouse exoribonuclease mXrn1p. It wasn’t until 2002 that a glimpse into the nature and importance of these cytoplasmic foci was published.[8][9][10] In 2002, researchers demonstrated that multiple proteins involved with mRNA degradation localize to the foci. During this time, many descriptive names were used to identify the processing bodies, including "GW-bodies" and "decapping-bodies"; however "P-bodies" was the term chosen and is now widely used and accepted in the scientific literature.[5] Recently evidence has been presented suggesting that GW-bodies and P-bodies may in fact be different cellular components.[11] The evidence being that GW182 and Ago2, both associated with miRNA gene silencing, are found exclusively in multivesicular bodies or GW-bodies and are not localized to P-bodies. Also of note, P-bodies are not equivalent to stress granules and they contain largely non-overlapping proteins.[4] The two structures support overlapping cellular functions but generally occur under different stimuli. Hoyle et al. suggests a novel site termed EGP bodies, or stress granules, may be responsible for mRNA storage as these sites lack the decapping enzyme.[12]
Associations with microRNA
microRNA mediated repression occurs in two ways, either by translational repression or stimulating mRNA decay. miRNA recruit the RISC complex to the mRNA to which they are bound. The link to P-bodies comes by the fact that many, if not most, of the proteins necessary for miRNA gene silencing are localized to P-bodies, as reviewed by Kulkarni et al. (2010).[1][13][14][15][16] These proteins include, but are not limited to, the scaffold protein GW182, Argonaute (Ago), decapping enzymes and RNA helicases. The current evidence points toward P-bodies as being scaffolding centers of miRNA function, especially due to the evidence that a knock down of GW182 disrupts P-body formation. However, there remain many unanswered questions about P-bodies and their relationship to miRNA activity. Specifically, it is unknown whether there is a context dependent (stress state versus normal) specificity to the P-body's mechanism of action. Based on the evidence that P-bodies sometimes are the site of mRNA decay and sometimes the mRNA can exit the P-bodies and re-initiate translation, the question remains of what controls this switch. Another ambiguous point to be addressed is whether the proteins that localize to P-bodies are actively functioning in the miRNA gene silencing process or whether they are merely on standby.
Protein composition of processing bodies
In 2017, a new method to purify processing bodies was published.[4] Hubstenberger et al. used fluorescence-activated particle sorting (a method based on the ideas of fluorescence-activated cell sorting) to purify processing bodies from human epithelial cells. From these purified processing bodies they were able to use mass spectrometry and RNA sequencing to determine which proteins and RNAs are found in processing bodies, respectively. This study identified 125 proteins that are significantly associated with processing bodies.[4]
In 2018, Youn et al. took a proximity labeling approach called BioID to identify and predict the processing body proteome.[17] They engineered cells to express several processing body-localized proteins as fusion proteins with the BirA* enzyme. When the cells are incubated with biotin, BirA* will biotinylate proteins that are nearby, thus tagging the proteins within processing bodies with a biotin tag. Streptavidin was then used to isolate the tagged proteins and mass spectrometry to identify them. Using this approach, Youn et al. identified 42 proteins that localize to processing bodies.[17]
Gene ID | Protein | References | Also found in stress granules? |
---|---|---|---|
MOV10 | MOV10 | [4][17] | yes |
EDC3 | EDC3 | [17] | yes |
EDC4 | EDC4 | [4] | yes |
ZCCHC11 | TUT4 | [4] | no |
DHX9 | DHX9 | [4] | no |
RPS27A | RS27A | [4] | no |
UPF1 | RENT1 | [4] | yes |
ZCCHC3 | ZCHC3 | [4] | no |
SMARCA5 | SMCA5 | [4] | no |
TOP2A | TOP2A | [4] | no |
HSPA2 | HSP72 | [4] | no |
SPTAN1 | SPTN1 | [4] | no |
SMC1A | SMC1A | [4] | no |
ACTBL2 | ACTBL | [4] | yes |
SPTBN1 | SPTB2 | [4] | no |
DHX15 | DHX15 | [4] | no |
ARG1 | ARGI1 | [4] | no |
TOP2B | TOP2B | [4] | no |
APOBEC3F | ABC3F | [4] | no |
NOP58 | NOP58 | [4] | yes |
RPF2 | RPF2 | [4] | no |
S100A9 | S10A9 | [4] | yes |
DDX41 | DDX41 | [4] | no |
KIF23 | KIF23 | [4] | yes |
AZGP1 | ZA2G | [4] | no |
DDX50 | DDX50 | [4] | yes |
SERPINB3 | SPB3 | [4] | no |
SBSN | SBSN | [4] | no |
BAZ1B | BAZ1B | [4] | no |
MYO1C | MYO1C | [4] | no |
EIF4A3 | IF4A3 | [4] | no |
SERPINB12 | SPB12 | [4] | no |
EFTUD2 | U5S1 | [4] | no |
RBM15B | RB15B | [4] | no |
AGO2 | AGO2 | [4] | yes |
MYH10 | MYH10 | [4] | no |
DDX10 | DDX10 | [4] | no |
FABP5 | FABP5 | [4] | no |
SLC25A5 | ADT2 | [4] | no |
DMKN | DMKN | [4] | no |
DCP2 | DCP2 | [4][9][10][18] | no |
S100A8 | S10A8 | [4] | no |
NCBP1 | NCBP1 | [4] | no |
YTHDC2 | YTDC2 | [4] | no |
NOL6 | NOL6 | [4] | no |
XAB2 | SYF1 | [4] | no |
PUF60 | PUF60 | [4] | no |
RBM19 | RBM19 | [4] | no |
WDR33 | WDR33 | [4] | no |
PNRC1 | PNRC1 | [4] | no |
SLC25A6 | ADT3 | [4] | no |
MCM7 | MCM7 | [4] | yes |
GSDMA | GSDMA | [4] | no |
HSPB1 | HSPB1 | [4] | yes |
LYZ | LYSC | [4] | no |
DHX30 | DHX30 | [4] | yes |
BRIX1 | BRX1 | [4] | no |
MEX3A | MEX3A | [4] | yes |
MSI1 | MSI1H | [4] | yes |
RBM25 | RBM25 | [4] | no |
UTP11L | UTP11 | [4] | no |
UTP15 | UTP15 | [4] | no |
SMG7 | SMG7 | [4][17] | yes |
AGO1 | AGO1 | [4] | yes |
LGALS7 | LEG7 | [4] | no |
MYO1D | MYO1D | [4] | no |
XRCC5 | XRCC5 | [4] | no |
DDX6 | DDX6/p54/RCK | [4][17][19][20] | yes |
ZC3HAV1 | ZCCHV | [4] | yes |
DDX27 | DDX27 | [4] | no |
NUMA1 | NUMA1 | [4] | no |
DSG1 | DSG1 | [4] | no |
NOP56 | NOP56 | [4] | no |
LSM14B | LS14B | [4] | yes |
EIF4E2 | EIF4E2 | [17] | yes |
EIF4ENIF1 | 4ET | [4][17] | yes |
LSM14A | LS14A | [4][17] | yes |
IGF2BP2 | IF2B2 | [4] | yes |
DDX21 | DDX21 | [4] | yes |
DSC1 | DSC1 | [4] | no |
NKRF | NKRF | [4] | no |
DCP1B | DCP1B | [4][20] | no |
SMC3 | SMC3 | [4] | no |
RPS3 | RS3 | [4] | yes |
PUM1 | PUM1 | [4] | yes |
PIP | PIP | [4] | no |
RPL26 | RL26 | [4] | no |
GTPBP4 | NOG1 | [4] | no |
PES1 | PESC | [4] | no |
DCP1A | DCP1A | [4][9][10][18][21] | yes |
ELAVL2 | ELAV2 | [4] | yes |
IGLC2 | LAC2 | [4] | no |
IGF2BP1 | IF2B1 | [4] | yes |
RPS16 | RS16 | [4] | no |
HNRNPU | HNRPU | [4] | no |
IGF2BP3 | IF2B3 | [4] | yes |
SF3B1 | SF3B1 | [4] | no |
STAU2 | STAU2 | [4] | yes |
ZFR | ZFR | [4] | no |
HNRNPM | HNRPM | [4] | no |
ELAVL1 | ELAV1 | [4] | yes |
FAM120A | F120A | [4] | yes |
STRBP | STRBP | [4] | no |
RBM15 | RBM15 | [4] | no |
LMNB2 | LMNB2 | [4] | no |
NIFK | MK67I | [4] | no |
TF | TRFE | [4] | no |
HNRNPR | HNRPR | [4] | no |
LMNB1 | LMNB1 | [4] | no |
ILF2 | ILF2 | [4] | no |
H2AFY | H2AY | [4] | no |
RBM28 | RBM28 | [4] | no |
MATR3 | MATR3 | [4] | no |
SYNCRIP | HNRPQ | [4] | yes |
HNRNPCL1 | HNRCL | [4] | no |
APOA1 | APOA1 | [4] | no |
XRCC6 | XRCC6 | [4] | no |
RPS4X | RS4X | [4] | no |
DDX18 | DDX18 | [4] | no |
ILF3 | ILF3 | [4] | yes |
SAFB2 | SAFB2 | [4] | yes |
RBMX | RBMX | [4] | no |
ATAD3A | ATD3A | [4] | yes |
HNRNPC | HNRPC | [4] | no |
RBMXL1 | RMXL1 | [4] | no |
IMMT | IMMT | [4] | no |
ALB | ALBU | [4] | no |
CSNK1D | CK1𝛿 | [19] | no |
XRN1 | XRN1 | [7][9][17][18] | yes |
TNRC6A | GW182 | [17][18][22][21][23] | yes |
TNRC6B | TNRC6B | [17] | yes |
TNRC6C | TNRC6C | [17] | yes |
LSM4 | LSM4 | [21][9] | no |
LSM1 | LSM1 | [9] | no |
LSM2 | LSM2 | [9] | no |
LSM3 | LSM3 | [9][20] | yes |
LSM5 | LSM5 | [9] | no |
LSM6 | LSM6 | [9] | no |
LSM7 | LSM7 | [9] | no |
CNOT1 | CCR4/CNOT1 | [20][17] | yes |
CNOT10 | CNOT10 | [17] | yes |
CNOT11 | CNOT11 | [17] | yes |
CNOT2 | CNOT2 | [17] | yes |
CNOT3 | CNOT3 | [17] | yes |
CNOT4 | CNOT4 | [17] | yes |
CNOT6 | CNOT6 | [17] | yes |
CNOT6L | CNOT6L | [17] | yes |
CNOT7 | CNOT7 | [17] | yes |
CNOT8 | CNOT8 | [17] | yes |
CNOT9 | CNOT9 | [17] | no |
RBFOX1 | RBFOX1 | [24] | yes |
ANKHD1 | ANKHD1 | [17] | yes |
ANKRD17 | ANKRD17 | [17] | yes |
BTG3 | BTG3 | [17] | yes |
CEP192 | CEP192 | [17] | no |
CPEB4 | CPEB4 | [17] | yes |
CPVL | CPVL | [17] | yes |
DIS3L | DIS3L | [17] | no |
DVL3 | DVL3 | [17] | no |
FAM193A | FAM193A | [17] | no |
GIGYF2 | GIGYF2 | [17] | yes |
HELZ | HELZ | [17] | yes |
KIAA0232 | KIAA0232 | [17] | yes |
KIAA0355 | KIAA0355 | [17] | no |
MARF1 | MARF1 | [17] | yes |
N4BP2 | N4BP2 | [17] | no |
PATL1 | PATL1 | [17] | yes |
RNF219 | RNF219 | [17] | yes |
ST7 | ST7 | [17] | yes |
TMEM131 | TMEM131 | [17] | yes |
TNKS1BP1 | TNKS1BP1 | [17] | yes |
TTC17 | TTC17 | [17] | yes |
References
- Kulkarni, M.; Ozgur, S.; Stoecklin, G. (2010). "On track with P-bodies". Biochemical Society Transactions. 38 (Pt 1): 242–251. doi:10.1042/BST0380242. PMID 20074068.
- Brengues, M.; Teixeira, D.; Parker, R. (2005). "Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies". Science. 310 (5747): 486–489. Bibcode:2005Sci...310..486B. doi:10.1126/science.1115791. PMC 1863069. PMID 16141371.
- Bhattacharyya, S.; Habermacher, R.; Martine, U.; Closs, E.; Filipowicz, W. (2006). "Relief of microRNA-mediated translational repression in human cells subjected to stress". Cell. 125 (6): 1111–1124. doi:10.1016/j.cell.2006.04.031. PMID 16777601. S2CID 18353167.
- Hubstenberger, Arnaud; Courel, Maïté; Bénard, Marianne; Souquere, Sylvie; Ernoult-Lange, Michèle; Chouaib, Racha; Yi, Zhou; Morlot, Jean-Baptiste; Munier, Annie (2017-09-27). "P-Body Purification Reveals the Condensation of Repressed mRNA Regulons". Molecular Cell. 68 (1): 144–157.e5. doi:10.1016/j.molcel.2017.09.003. ISSN 1097-4164. PMID 28965817.
- Sheth, Ujwal; Parker, Roy (2003-05-02). "Decapping and decay of messenger RNA occur in cytoplasmic processing bodies". Science. 300 (5620): 805–808. Bibcode:2003Sci...300..805S. doi:10.1126/science.1082320. ISSN 1095-9203. PMC 1876714. PMID 12730603.
- Cougot, Nicolas; Bhattacharyya, Suvendra N.; Tapia-arancibia, Lucie; Bordonne, Remy; Filipowicz, Witold; Bertrand, Edouard; Rage, Florence (2008). "Dendrites of Mammalian Neurons Contain Specialized P-Body-Like Structures That Respond to Neuronal Activation". Journal of Neuroscience. 28 (51): 13793–804. doi:10.1523/JNEUROSCI.4155-08.2008. PMC 6671906. PMID 19091970.
- Bashkirov, V. I.; Scherthan, H.; Solinger, J. A.; Buerstedde, J. -M.; Heyer, W. -D. (1997). "A Mouse Cytoplasmic Exoribonuclease (mXRN1p) with Preference for G4 Tetraplex Substrates". Journal of Cell Biology. 136 (4): 761–73. doi:10.1083/jcb.136.4.761. PMC 2132493. PMID 9049243.
- Eystathioy, T.; Chan, E.; Tenenbaum, S.; Keene, J.; Griffith, K.; Fritzler, M. (2002). "A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles". Molecular Biology of the Cell. 13 (4): 1338–1351. doi:10.1091/mbc.01-11-0544. PMC 102273. PMID 11950943.
- Ingelfinger, D.; Arndt-Jovin, D. J.; Lührmann, R.; Achsel, T. (2002). "The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci". RNA. 8 (12): 1489–1501. doi:10.1017/S1355838202021726 (inactive 2021-01-14). PMC 1370355. PMID 12515382.CS1 maint: DOI inactive as of January 2021 (link)
- Van Dijk, E.; Cougot, N.; Meyer, S.; Babajko, S.; Wahle, E.; Séraphin, B. (2002). "Human Dcp2: A catalytically active mRNA decapping enzyme located in specific cytoplasmic structures". The EMBO Journal. 21 (24): 6915–6924. doi:10.1093/emboj/cdf678. PMC 139098. PMID 12486012.
- Gibbings, D.; Ciaudo, C.; Erhardt, M.; Voinnet, O. (2009). "Multivesicular bodies associate with components of miRNA effector complexes and modulate miRNA activity". Nature Cell Biology. 11 (9): 1143–1149. doi:10.1038/ncb1929. PMID 19684575. S2CID 205286867.
- Hoyle, N.; Castelli, L.; Campbell, S.; Holmes, L.; Ashe, M. (2007). "Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies". Journal of Cell Biology. 179 (1): 65–74. doi:10.1083/jcb.200707010. PMC 2064737. PMID 17908917.
- Liu, J.; Valencia-Sanchez, M.; Hannon, G.; Parker, R. (2005). "MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies". Nature Cell Biology. 7 (7): 719–723. doi:10.1038/ncb1274. PMC 1855297. PMID 15937477.
- Liu, J.; Rivas, F.; Wohlschlegel, J.; Yates Jr, 3.; Parker, R.; Hannon, G. (2005). "A role for the P-body component GW182 in microRNA function". Nature Cell Biology. 7 (12): 1261–1266. doi:10.1038/ncb1333. PMC 1804202. PMID 16284623.CS1 maint: numeric names: authors list (link)
- Sen, G.; Blau, H. (2005). "Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies". Nature Cell Biology. 7 (6): 633–636. doi:10.1038/ncb1265. PMID 15908945. S2CID 6085169.
- Eystathioy, T.; Jakymiw, A.; Chan, E. K.; Séraphin, B.; Cougot, N.; Fritzler, M. J. (2003). "The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies". RNA. 9 (10): 1171–1173. doi:10.1261/rna.5810203. PMC 1370480. PMID 13130130.
- Youn, Ji-Young; Dunham, Wade H.; Hong, Seo Jung; Knight, James D.R.; Bashkurov, Mikhail; Chen, Ginny I.; Bagci, Halil; Rathod, Bhavisha; MacLeod, Graham (2018). "High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies". Molecular Cell. 0 (3): 517–532.e11. doi:10.1016/j.molcel.2017.12.020. ISSN 1097-2765. PMID 29395067.
- Kedersha, Nancy; Stoecklin, Georg; Ayodele, Maranatha; Yacono, Patrick; Lykke-Andersen, Jens; Fritzler, Marvin J.; Scheuner, Donalyn; Kaufman, Randal J.; Golan, David E. (2005-06-20). "Stress granules and processing bodies are dynamically linked sites of mRNP remodeling". The Journal of Cell Biology. 169 (6): 871–884. doi:10.1083/jcb.200502088. ISSN 0021-9525. PMC 2171635. PMID 15967811.
- Zhang, Bo; Shi, Qian; Varia, Sapna N.; Xing, Siyuan; Klett, Bethany M.; Cook, Laura A.; Herman, Paul K. (July 2016). "The Activity-Dependent Regulation of Protein Kinase Stability by the Localization to P-Bodies". Genetics. 203 (3): 1191–1202. doi:10.1534/genetics.116.187419. ISSN 1943-2631. PMC 4937477. PMID 27182950.
- Cougot, Nicolas; Babajko, Sylvie; Séraphin, Bertrand (April 2004). "Cytoplasmic foci are sites of mRNA decay in human cells". The Journal of Cell Biology. 165 (1): 31–40. doi:10.1083/jcb.200309008. ISSN 0021-9525. PMC 2172085. PMID 15067023.
- Eystathioy, Theophany; Jakymiw, Andrew; Chan, Edward K. L.; Séraphin, Bertrand; Cougot, Nicolas; Fritzler, Marvin J. (October 2003). "The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies". RNA. 9 (10): 1171–1173. doi:10.1261/rna.5810203. ISSN 1355-8382. PMC 1370480. PMID 13130130.
- Eystathioy, Theophany; Chan, Edward K. L.; Tenenbaum, Scott A.; Keene, Jack D.; Griffith, Kevin; Fritzler, Marvin J. (April 2002). "A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles". Molecular Biology of the Cell. 13 (4): 1338–1351. doi:10.1091/mbc.01-11-0544. ISSN 1059-1524. PMC 102273. PMID 11950943.
- Yang, Zheng; Jakymiw, Andrew; Wood, Malcolm R.; Eystathioy, Theophany; Rubin, Robert L.; Fritzler, Marvin J.; Chan, Edward K. L. (2004-11-01). "GW182 is critical for the stability of GW bodies expressed during the cell cycle and cell proliferation". Journal of Cell Science. 117 (Pt 23): 5567–5578. doi:10.1242/jcs.01477. ISSN 0021-9533. PMID 15494374.
- Kucherenko, Mariya M.; Shcherbata, Halyna R. (2018-01-22). "Stress-dependent miR-980 regulation of Rbfox1/A2bp1 promotes ribonucleoprotein granule formation and cell survival". Nature Communications. 9 (1): 312. Bibcode:2018NatCo...9..312K. doi:10.1038/s41467-017-02757-w. ISSN 2041-1723. PMC 5778076. PMID 29358748.
Further reading
- Kulkarni et al. provide a review of P-bodies and a table of all proteins detected in the P-bodies as of 2010. Kulkarni, M.; Ozgur, S.; Stoecklin, G. (2010). "On track with P-bodies". Biochemical Society Transactions. 38 (Pt 1): 242–251. doi:10.1042/BST0380242. PMID 20074068.
- Eulalio, Ana; Behm-Ansmant, Isabelle; Izaurralde, Elisa (January 2007). "P bodies: at the crossroads of post-transcriptional pathways". Nat Rev Mol Cell Biol. 8 (1): 9–22. doi:10.1038/nrm2080. PMID 17183357. S2CID 41419388.
- Marx, J. (2005). "MOLECULAR BIOLOGY: P-Bodies Mark the Spot for Controlling Protein Production". Science. 310 (5749): 764–765. doi:10.1126/science.310.5749.764. PMID 16272094. S2CID 11106208.
- Anderson, P.; Kedersha, N. (2009). "RNA granules: post-transcriptional and epigenetic modulators of gene expression". Nature Reviews Molecular Cell Biology. 10 (6): 430–436. doi:10.1038/nrm2694. PMID 19461665. S2CID 26578027.