P-bodies


Processing 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 microRNA induced mRNA silencing. 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. 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.
The following activities have been demonstrated to occur in or to be associated with P-bodies:
In neurons, P-bodies move by motor proteins in response to stimulation. This is likely tied to local translation in dendrites.
P-bodies were first described in the scientific literature by Bashkirov et al. 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. 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. Recently evidence has been presented suggesting that GW-bodies and P-bodies may in fact be different cellular components. 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. 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.

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.. These proteins include, but are not limited to, the scaffold protein GW182, Argonaute, 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 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. Hubstenberger et al. used fluorescence-activated particle 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.
In 2018, Youn et al. took a proximity labeling approach called BioID to identify and predict the processing body proteome. 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.
Gene IDProteinReferencesAlso found in stress granules?
MOV10MOV10yes
EDC3EDC3yes
EDC4EDC4yes
ZCCHC11TUT4no
DHX9DHX9no
RPS27ARS27Ano
UPF1RENT1yes
ZCCHC3ZCHC3no
SMARCA5SMCA5no
TOP2ATOP2Ano
HSPA2HSP72no
SPTAN1SPTN1no
SMC1ASMC1Ano
ACTBL2ACTBLyes
SPTBN1SPTB2no
DHX15DHX15no
ARG1ARGI1no
TOP2BTOP2Bno
APOBEC3FABC3Fno
NOP58NOP58yes
RPF2RPF2no
S100A9S10A9yes
DDX41DDX41no
KIF23KIF23yes
AZGP1ZA2Gno
DDX50DDX50yes
SERPINB3SPB3no
SBSNSBSNno
BAZ1BBAZ1Bno
MYO1CMYO1Cno
EIF4A3IF4A3no
SERPINB12SPB12no
EFTUD2U5S1no
RBM15BRB15Bno
AGO2AGO2yes
MYH10MYH10no
DDX10DDX10no
FABP5FABP5no
SLC25A5ADT2no
DMKNDMKNno
DCP2DCP2no
S100A8S10A8no
NCBP1NCBP1no
YTHDC2YTDC2no
NOL6NOL6no
XAB2SYF1no
PUF60PUF60no
RBM19RBM19no
WDR33WDR33no
PNRC1PNRC1no
SLC25A6ADT3no
MCM7MCM7yes
GSDMAGSDMAno
HSPB1HSPB1yes
LYZLYSCno
DHX30DHX30yes
BRIX1BRX1no
MEX3AMEX3Ayes
MSI1MSI1Hyes
RBM25RBM25no
UTP11LUTP11no
UTP15UTP15no
SMG7SMG7yes
AGO1AGO1yes
LGALS7LEG7no
MYO1DMYO1Dno
XRCC5XRCC5no
DDX6DDX6/p54/RCKyes
ZC3HAV1ZCCHVyes
DDX27DDX27no
NUMA1NUMA1no
DSG1DSG1no
NOP56NOP56no
LSM14BLS14Byes
EIF4E2EIF4E2yes
EIF4ENIF14ETyes
LSM14ALS14Ayes
IGF2BP2IF2B2yes
DDX21DDX21yes
DSC1DSC1no
NKRFNKRFno
DCP1BDCP1Bno
SMC3SMC3no
RPS3RS3yes
PUM1PUM1yes
PIPPIPno
RPL26RL26no
GTPBP4NOG1no
PES1PESCno
DCP1ADCP1Ayes
ELAVL2ELAV2yes
IGLC2LAC2no
IGF2BP1IF2B1yes
RPS16RS16no
HNRNPUHNRPUno
IGF2BP3IF2B3yes
SF3B1SF3B1no
STAU2STAU2yes
ZFRZFRno
HNRNPMHNRPMno
ELAVL1ELAV1yes
FAM120AF120Ayes
STRBPSTRBPno
RBM15RBM15no
LMNB2LMNB2no
NIFKMK67Ino
TFTRFEno
HNRNPRHNRPRno
LMNB1LMNB1no
ILF2ILF2no
H2AFYH2AYno
RBM28RBM28no
MATR3MATR3no
SYNCRIPHNRPQyes
HNRNPCL1HNRCLno
APOA1APOA1no
XRCC6XRCC6no
RPS4XRS4Xno
DDX18DDX18no
ILF3ILF3yes
SAFB2SAFB2yes
RBMXRBMXno
ATAD3AATD3Ayes
HNRNPCHNRPCno
RBMXL1RMXL1no
IMMTIMMTno
ALBALBUno
CSNK1DCK1?no
XRN1XRN1yes
TNRC6AGW182yes
TNRC6BTNRC6Byes
TNRC6CTNRC6Cyes
LSM4LSM4no
LSM1LSM1no
LSM2LSM2no
LSM3LSM3yes
LSM5LSM5no
LSM6LSM6no
LSM7LSM7no
CNOT1CCR4/CNOT1yes
CNOT10CNOT10yes
CNOT11CNOT11yes
CNOT2CNOT2yes
CNOT3CNOT3yes
CNOT4CNOT4yes
CNOT6CNOT6yes
CNOT6LCNOT6Lyes
CNOT7CNOT7yes
CNOT8CNOT8yes
CNOT9CNOT9no
RBFOX1RBFOX1yes
ANKHD1ANKHD1yes
ANKRD17ANKRD17yes
BTG3BTG3yes
CEP192CEP192no
CPEB4CPEB4yes
CPVLCPVLyes
DIS3LDIS3Lno
DVL3DVL3no
FAM193AFAM193Ano
GIGYF2GIGYF2yes
HELZHELZyes
KIAA0232KIAA0232yes
KIAA0355KIAA0355no
MARF1MARF1yes
N4BP2N4BP2no
PATL1PATL1yes
RNF219RNF219yes
ST7ST7yes
TMEM131TMEM131yes
TNKS1BP1TNKS1BP1yes
TTC17TTC17yes