P-body (source code)
= P-body
{c}
A \b[P-body], or processing body, is a cytoplasmic assembly of <RNA> and <proteins> associated with nontranslating <messenger RNA> and factors involved in <decapping> and <RNA decay>. Its molecular composition and exchange with the surrounding <cytoplasm> distinguish it from a membrane-bounded container or a fixed pile of cellular waste.
The 2003 yeast study localized decay-related factors and RNA degradation intermediates to these foci, and altered RNA-turnover steps to test their functional relationship to processing.<Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies by Ujwal Sheth and Roy Parker>[Abstract and Figures1–2: components, intermediates and pathway perturbations.]{ref} This connects cellular location to a biochemical pathway; it does not establish that every RNA must pass through a visible focus to be degraded.
A 2005 study tested <P-body assembly> more directly. RNA digestion disrupted enriched P-body preparations. In cells, inhibition of translation initiation increased P-bodies, whereas inhibition of elongation trapped messages in <polysomes> and promoted P-body dissociation.<Processing bodies require RNA for assembly and contain nontranslating mRNAs by Daniela Teixeira and others>[Abstract; Figure6 and corresponding Results: RNA dependence and translation-state experiments.]{ref} The opposite outcomes show why saying only that translation was inhibited leaves an important mechanistic distinction unresolved.
An original pool model explains why a larger focus need not mean faster degradation. Let $N$ count RNA molecules in a processing pool, with entry rate $J$ and first-order removal rate $kN$:
$$
\frac{dN}{dt}=J-kN,\qquad N_{\rm ss}=\frac{J}{k}.
$$
With stipulated $J=6$ molecules per minute and $k=0.3\,\mathrm{min^{-1}}$, the <steady state> contains 20 molecules. Lowering $k$ to $0.1\,\mathrm{min^{-1}}$ increases that pool to 60, while the steady removal flux remains $kN=6$ molecules per minute. Even if removal represents degradation, pool size and throughput are different measurements. This is a teaching model, not measured P-body kinetics; actual pools can also exchange RNA through other routes.
<Fluorescence microscopy> measures labeled components under a stated imaging procedure. Interpreting intensity as RNA number needs an additional response model, and counting spots need not measure either molecular number or reaction flux. Localization, composition, assembly and turnover consequently provide complementary tests of what a P-body is doing.
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