Remaining Mysteries of the Cytoplasm

Nothing epitomizes the mystery of life more than the spatial organization and dynamics of the cytoplasm. How can a bunch of molecules, no matter how sophisticated, generate spatially complex behavior on a scale that is much larger than the molecules themselves? In my view, we will be done as cell biologists when we can predict the structure and dynamics of cells from DNA sequence. That goal is still some way off; indeed it is not yet clear if it is conceptually feasible. Below I identify three challenges, one general and two specific, that must be overcome if we are to make progress.

COLLECTIVE PROTEIN BEHAVIOR

Understanding how molecules work together to orchestrate cellular processes is the new frontier in basic cell biology. Reductionist approaches generated parts lists for many cellular processes and detailed biochemical information on some parts. Occasionally, studying a single part gave profound insight into large-scale behavior. Myosin-II in muscle contraction is an example, though we are still far from understanding how sarcomeres assemble. However, most cellular processes depend on multiple proteins and lack the quasi-crystalline organization of muscle. Invariably, we lack quantitative, predictive understanding of the collective behavior that generates such cellular processes and makes them robust, yet controllable and evolvable. Increasingly powerful imaging methods, improved genetic/pharmacological perturbations, and (hopefully) biochemical reconstitutions will all help. But we may also need new conceptual approaches to understand how integrated behavior emerges from complex microscopic dynamics.

Timothy J. Mitchison

BUILDING THE CELL: LOCAL CONTROL VERSUS LOCAL SYNTHESIS

Physical organization and motility of cells requires spatially controlled biochemistry. This could be achieved, in principle, by local control of the behavior of preexisting, freely diffusing proteins (e.g., by nucleation or phosphorylation) or by local synthesis of proteins where they are needed, which requires mRNA localization. Local control has been assumed to dominate except for specific proteins in unusually large cells such as oocytes and neurons. The discovery that many mRNAs are localized (up to 70% of all mRNAs in Drosophila embryos; Lécuyer et al., 2007) challenges this view and suggests spatial control by local synthesis is much more prevalent than previously thought. I suspect that mRNA localization is often important for a different reason: to help control translation in response to local cytoplasmic states. If so, translational regulation must be widespread and sophisticated. Elucidating the function of mRNA localization, be it for local synthesis, translational control, or other purposes, is a key challenge in the spatial biology of cells. mRNA localization is probably critical for organization of large, complex cells such as oocytes, neurons, and ciliated protists, but could also be broadly important in more typical tissue cells.

SIZE SCALING AND SIZE SENSING

Eukaryotic cells vary at least three orders of magnitude in linear dimension (Figure 1), yet the proteins they use for spatial organization are broadly conserved. How can conserved mechanisms accommodate such a large range of length scales? Are special mechanisms required in unusually large cells, where cell size and division rates are large compared with the length and time scales of macromolecule diffusion? Addressing these questions will help us understand how the nanometer and millisecond scales of molecular processes can organize the cytoplasm on micrometer and minute scales. Large embryos, where cell size decreases rapidly due to cleavage while biochemistry remains relatively constant, provide one useful system.

Figure 1.

Eukaryotic cell size extremes. (A) Ostreococcus tauri, a “picoplankton”. Reconstruction from EM tomography after cryo-fixation (Hendersen et al., 2007). n, nucleus; c, chloroplast; m, mitochondrion. (B) Xenopus laevis zygote, a representative large embryo cell. Confocal microscopy of an egg fixed 35 min after fertilization stained for α-tubulin (green) and γ-tubulin (red). The sperm nucleus (n) is moving toward the center of the egg using forces generated by an aster of microtubules (mt) nucleated by the recently duplicated centrosome (c). Source: Wühr and Mitchison, unpublished results.

How do cells sense and control their size? In small, rod-shaped bacteria and fission yeast cells, cell ends are thought to negatively regulate cell division using reaction–diffusion systems (Lose et al., 2008, Moseley et al., 2009). Is this true more generally? Are there other size-sensing mechanisms? Cytoplasm volume scales with genome size when one compares the same cell type between species (Gregory, 2001), and large embryos transition from an embryonic to a somatic cell cycle, and initiate transcription, when their DNA to cytoplasm ratio approaches the somatic value (Newport and Kirschner, 1982). Thus this ratio may be a general size-regulator. How it is sensed is a major unsolved problem with broad implications for cell growth and behavior.