P-bodies

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In cellular biology, P-bodies, or processing bodies, are distinct foci formed by phase separation within the cytoplasm of a eukaryotic cell consisting of many enzymes involved in mRNA turnover. [1] 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 microRNA (miRNA) induced mRNA silencing. [2] 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. [3] [4] 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. [5]

Contents

P-bodies were originally proposed to be the sites of mRNA degradation in the cell and involved in decapping and digestion of mRNAs earmarked for destruction. [6] [7] Later work called this into question suggesting P bodies store mRNA until needed for translation. [8] [5] [9]

In neurons, P-bodies are moved by motor proteins in response to stimulation. This is likely tied to local translation in dendrites. [10]

History

P-bodies were first described in the scientific literature by Bashkirov et al. [11] 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. [12] [13] [14] , when researchers demonstrated that multiple proteins involved with mRNA degradation localize to the foci. Their importance was recognized after experimental evidence was obtained pointing to P-bodies as the sites of mRNA degradation in the cell. [7] The researchers named these structures processing bodies or "P bodies". During this time, many descriptive names were used also 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. [7] Recently evidence has been presented suggesting that GW-bodies and P-bodies may in fact be different cellular components. [15] 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. [5] 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. [16]

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). [2] [17] [18] [19] [20] 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

In 2017, a new method to purify processing bodies was published. [5] 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. [5] Notably this work provided the most compelling evidence up to this date that P-bodies might not be the sites of degradation in the cell and instead used for storage of translationally repressed mRNA. This observation was further supported by single molecule imaging of mRNA by the Chao group in 2017. [21]

In 2018, Youn et al. took a proximity labeling approach called BioID to identify and predict the processing body proteome. [22] 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. [22]

Gene IDProteinReferencesAlso found in stress granules?
MOV10MOV10 [5] [22] Yes
EDC3EDC3 [22] Yes
EDC4EDC4 [5] Yes
ZCCHC11TUT4 [5] No
DHX9DHX9 [5] No
RPS27ARS27A [5] No
UPF1RENT1 [5] Yes
ZCCHC3ZCHC3 [5] No
SMARCA5SMCA5 [5] No
TOP2ATOP2A [5] No
HSPA2HSP72 [5] No
SPTAN1SPTN1 [5] No
SMC1ASMC1A [5] No
ACTBL2ACTBL [5] Yes
SPTBN1SPTB2 [5] No
DHX15DHX15 [5] No
ARG1ARGI1 [5] No
TOP2BTOP2B [5] No
APOBEC3FABC3F [5] No
NOP58NOP58 [5] Yes
RPF2RPF2 [5] No
S100A9S100A9 [5] Yes
DDX41DDX41 [5] No
KIF23KIF23 [5] Yes
AZGP1ZA2G [5] No
DDX50DDX50 [5] Yes
SERPINB3SPB3 [5] No
SBSNSBSN [5] No
BAZ1BBAZ1B [5] No
MYO1CMYO1C [5] No
EIF4A3IF4A3 [5] No
SERPINB12SPB12 [5] No
EFTUD2U5S1 [5] No
RBM15BRB15B [5] No
AGO2AGO2 [5] Yes
MYH10MYH10 [5] No
DDX10DDX10 [5] No
FABP5FABP5 [5] No
SLC25A5ADT2 [5] No
DMKNDMKN [5] No
DCP2DCP2 [5] [13] [14] [23] No
S100A8S10A8 [5] No
NCBP1NCBP1 [5] No
YTHDC2YTDC2 [5] No
NOL6NOL6 [5] No
XAB2SYF1 [5] No
PUF60PUF60 [5] No
RBM19RBM19 [5] No
WDR33WDR33 [5] No
PNRC1PNRC1 [5] No
SLC25A6ADT3 [5] No
MCM7MCM7 [5] Yes
GSDMAGSDMA [5] No
HSPB1HSPB1 [5] Yes
LYZLYSC [5] No
DHX30DHX30 [5] Yes
BRIX1BRX1 [5] No
MEX3AMEX3A [5] Yes
MSI1MSI1H [5] Yes
RBM25RBM25 [5] No
UTP11LUTP11 [5] No
UTP15UTP15 [5] No
SMG7SMG7 [5] [22] Yes
AGO1AGO1 [5] Yes
LGALS7LEG7 [5] No
MYO1DMYO1D [5] No
XRCC5XRCC5 [5] No
DDX6DDX6/p54/RCK [5] [22] [24] [25] Yes
ZC3HAV1ZCCHV [5] Yes
DDX27DDX27 [5] No
NUMA1NUMA1 [5] No
DSG1DSG1 [5] No
NOP56NOP56 [5] No
LSM14BLS14B [5] Yes
EIF4E2EIF4E2 [22] Yes
EIF4ENIF14ET [5] [22] Yes
LSM14ALS14A [5] [22] Yes
IGF2BP2IF2B2 [5] Yes
DDX21DDX21 [5] Yes
DSC1DSC1 [5] No
NKRFNKRF [5] No
DCP1BDCP1B [5] [25] No
SMC3SMC3 [5] No
RPS3RS3 [5] Yes
PUM1PUM1 [5] Yes
PIPPIP [5] No
RPL26RL26 [5] No
GTPBP4NOG1 [5] No
PES1PESC [5] No
DCP1ADCP1A [5] [13] [14] [23] [26] No
ELAVL2ELAV2 [5] Yes
IGLC2LAC2 [5] No
IGF2BP1IF2B1 [5] Yes
RPS16RS16 [5] No
HNRNPUHNRPU [5] No
IGF2BP3IF2B3 [5] Yes
SF3B1SF3B1 [5] No
STAU2STAU2 [5] Yes
ZFRZFR [5] No
HNRNPMHNRPM [5] No
ELAVL1ELAV1 [5] Yes
FAM120AF120A [5] Yes
STRBPSTRBP [5] No
RBM15RBM15 [5] No
LMNB2LMNB2 [5] No
NIFKMK67I [5] No
TFTRFE [5] No
HNRNPRHNRPR [5] No
LMNB1LMNB1 [5] No
ILF2ILF2 [5] No
H2AFYH2AY [5] No
RBM28RBM28 [5] No
MATR3MATR3 [5] No
SYNCRIPHNRPQ [5] Yes
HNRNPCL1HNRCL [5] No
APOA1APOA1 [5] No
XRCC6XRCC6 [5] No
RPS4XRS4X [5] No
DDX18DDX18 [5] No
ILF3ILF3 [5] Yes
SAFB2SAFB2 [5] Yes
RBMXRBMX [5] No
ATAD3AATD3A [5] Yes
HNRNPCHNRPC [5] No
RBMXL1RMXL1 [5] No
IMMTIMMT [5] No
ALBALBU [5] No
CSNK1DCK1𝛿 [24] No
XRN1XRN1 [11] [13] [22] [23] Yes
TNRC6AGW182 [22] [23] [27] [26] [28] Yes
TNRC6BTNRC6B [22] Yes
TNRC6CTNRC6C [22] Yes
LSM4LSM4 [26] [13] No
LSM1LSM1 [13] No
LSM2LSM2 [13] No
LSM3LSM3 [13] [25] Yes
LSM5LSM5 [13] No
LSM6LSM6 [13] No
LSM7LSM7 [13] No
CNOT1CCR4/CNOT1 [25] [22] Yes
CNOT10CNOT10 [22] Yes
CNOT11CNOT11 [22] Yes
CNOT2CNOT2 [22] Yes
CNOT3CNOT3 [22] Yes
CNOT4CNOT4 [22] Yes
CNOT6CNOT6 [22] Yes
CNOT6LCNOT6L [22] Yes
CNOT7CNOT7 [22] Yes
CNOT8CNOT8 [22] Yes
CNOT9CNOT9 [22] No
RBFOX1RBFOX1 [29] Yes
ANKHD1ANKHD1 [22] Yes
ANKRD17ANKRD17 [22] Yes
BTG3BTG3 [22] Yes
CEP192CEP192 [22] No
CPEB4CPEB4 [22] Yes
CPVLCPVL [22] Yes
DIS3LDIS3L [22] No
DVL3DVL3 [22] No
FAM193AFAM193A [22] No
GIGYF2GIGYF2 [22] Yes
HELZHELZ [22] Yes
KIAA0232 KIAA0232 [22] Yes
KIAA0355KIAA0355 [22] No
MARF1MARF1 [22] Yes
N4BP2N4BP2 [22] No
PATL1PATL1 [22] Yes
RNF219RNF219 [22] Yes
ST7ST7 [22] Yes
TMEM131TMEM131 [22] Yes
TNKS1BP1TNKS1BP1 [22] Yes
TTC17TTC17 [22] Yes

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References

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  9. ↑ Horvathova, Ivana; Voigt, Franka; Kotrys, Anna V.; Zhan, Yinxiu; Artus-Revel, Caroline G.; Eglinger, Jan; Stadler, Michael B.; Giorgetti, Luca; Chao, Jeffrey A. (2017-11-02). "The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells". Molecular Cell. 68 (3): 615–625.e9. doi: 10.1016/j.molcel.2017.09.030 . ISSN   1097-2765. PMID   29056324.
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  13. 1 2 3 4 5 6 7 8 9 10 11 Ingelfinger D, Arndt-Jovin DJ, Lührmann R, Achsel T (December 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. PMC   1370355 . PMID   12515382.
  14. 1 2 3 van Dijk E, Cougot N, Meyer S, Babajko S, Wahle E, Séraphin B (December 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.
  15. ↑ Gibbings DJ, Ciaudo C, Erhardt M, Voinnet O (September 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.
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  24. 1 2 Zhang B, Shi Q, Varia SN, Xing S, Klett BM, Cook LA, Herman PK (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. PMC   4937477 . PMID   27182950.
  25. 1 2 3 4 Cougot N, Babajko S, Séraphin B (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. PMC   2172085 . PMID   15067023.
  26. 1 2 3 Eystathioy T, Jakymiw A, Chan EK, Séraphin B, Cougot N, Fritzler MJ (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. PMC   1370480 . PMID   13130130.
  27. ↑ Eystathioy T, Chan EK, Tenenbaum SA, Keene JD, Griffith K, Fritzler MJ (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. PMC   102273 . PMID   11950943.
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  29. ↑ Kucherenko MM, Shcherbata HR (January 2018). "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. PMC   5778076 . PMID   29358748.

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