"Fishing" for the functional proteome

Length-dependent translation initiation benefits the functional proteome of human cells

We previously found that shorter mRNAs are preferably translated in various eukaryotic cells. However, the theoretical basis of this phenomenon is unclear. We hypothesize that shorter mRNA length correlates to the decreased translational error rate to reduce the energy consumption on defective protein degradation. In this study, we established a computational model to explain the length-dependent translation initiation efficiency. We provided mathematical evidence that this translational preference, rather than the protein degradation, is a major factor to shape the genome-wide length-dependent protein abundance. As deducted, we simulated that shorter mRNA length is a determinant of initiation circularization time. Furthermore, our model unveiled that preferentially translating shorter mRNAs benefits the energy efficiency on the proteome functionality. We proposed that cancer cells tend to hijack this evolutionary mechanism by counteracting the higher translational error rate. In conclusion, our model provides insights into the nature of the global length-dependent translational control and its biological significance.

Protein-reactive natural products

Researchers in the post-genome era are confronted with the daunting task of assigning structure and function to tens of thousands of encoded proteins. To realize this goal, new technologies are emerging for the analysis of protein function on a global scale, such as activity-based protein profiling (ABPP), which aims to develop active site-directed chemical probes for enzyme analysis in whole proteomes. For the pursuit of such chemical proteomic technologies, it is helpful to derive inspiration from protein-reactive natural products. Natural products use a remarkably diverse set of mechanisms to covalently modify enzymes from distinct mechanistic classes, thus providing a wellspring of chemical concepts that can be exploited for the design of active-site-directed proteomic probes. Herein, we highlight several examples of protein-reactive natural products and illustrate how their mechanisms of action have influenced and continue to shape the progression of chemical proteomic technologies like ABPP.

Asymmetric cell divisions in flowering plants - one mother, "two-many" daughters

Plant development shows a fascinating range of asymmetric cell divisions. Over the years, however, cellular differentiation has been interpreted mostly in terms of a mother cell dividing mitotically to produce two daughter cells of different fates. This popular view has masked the significance of an entirely different cell fate specification pathway, where the mother cell first becomes a coenocyte and then cellularizes to simultaneously produce more than two specialized daughter cells. The "one mother - two different daughters" pathways rely on spindle-assisted mechanisms, such as translocation of the nucleus/spindle to a specific cellular site and orientation of the spindle, which are coordinated with cell-specific allocation of cell fate determinants and cytokinesis. By contrast, during "coenocyte-cellularization" pathways, the spindle-assisted mechanisms are irrelevant since cell fate specification emerges only after the nuclear divisions are complete, and the number of specialized daughter cells produced depends on the developmental context. The key events, such as the formation of a coenocyte and migration of the nuclei to specific cellular locations, are coordinated with cellularization by unique types of cell wall formation. Both one mother - two different daughters and the coenocyte-cellularization pathways are used by higher plants in precise spatial and time windows during development. In both the pathways, epigenetic regulation of gene expression is crucial not only for cell fate specification but also for its maintenance through cell lineage. In this review, the focus is on the coenocyte-cellularization pathways in the context of our current understanding of the asymmetric cell divisions. Instances where cell differentiation does not involve an asymmetric division are also discussed to provide a comprehensive account of cell differentiation.

Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis

Functional profiling technologies using arrayed collections of genome-scale siRNA and cDNA arrayed libraries enable the comprehensive global analysis of gene function. However, the current repertoire of high-throughput detection methodologies has limited the scope of cellular phenotypes that can be studied. In this report, we describe the systematic identification of mammalian growth-regulatory factors achieved through the integration of automated microscopy, pattern recognition analysis, and cell-based functional genomics. The effects of 7364 human and mouse proteins, encoded by individually arrayed cDNAs, upon proliferation and viability in U2OS osteosarcoma cells were evaluated in a live-cell, kinetic assay using quantitative image analysis. Overexpression of more than 86 cDNAs (1.15%) conferred dramatic increases in the proliferation, as determined cell enumeration. These included several known growth regulators, as well as previously uncharacterized ones (LRRK1, Ankrd25). In addition, novel functional roles for two genes (5033414D02Rik, 2810429O05Rik), now termed Gatp1 and Gatp2, respectively, were identified. Further analysis demonstrated that these encoded proteins promoted cellular proliferation and transformation in primary cells. Conversely, cells depleted for Gatp1 underwent apoptosis upon serum reduction, suggesting that Gatp1 is essential for cell survival under growth-factor-restricted conditions. Taken together, our findings offer new insight into the regulation of cellular growth and proliferation, and demonstrate the value and feasibility of assessing cellular phenotypes through genome-level computational image analysis.

The Human Genome Project: the role of analytical chemists

The Human Genome Project (HGP) is the most ambitious and important effort in the history of biology. It has provided a complete genetic blueprint for human life, and will provide important insights into human health and development. HGP involves a huge amount of data that is stored on computers all over the world. More than just vast amounts of DNA sequences, the project is about developing sets of integrated maps that involve genetic, physical, and sequence data. The data can be sorted, annotated and organized in many different ways using different types of database software, different analysis algorithms and different forms of interfaces. The genomic sequences of the human and the substantial portions of the mouse genome are expected to be finished by 2005. Analytical chemists took the opportunity, addressing the problem of achieving a high throughput with good sensitivity. This paper discusses how analytical chemists saved the Human Genome Project or at least gave it a helping hand.