SummaryDespite many decades of study, mitotic chromosome structure and composition remain poorly characterized. Here, we have integrated quantitative proteomics with bioinformatic analysis to generate a series of independent classifiers that describe the ∼4,000 proteins identified in isolated mitotic chromosomes. Integrating these classifiers by machine learning uncovers functional relationships between protein complexes in the context of intact chromosomes and reveals which of the ∼560 uncharacterized proteins identified here merits further study. Indeed, of 34 GFP-tagged predicted chromosomal proteins, 30 were chromosomal, including 13 with centromere-association. Of 16 GFP-tagged predicted nonchromosomal proteins, 14 were confirmed to be nonchromosomal. An unbiased analysis of the whole chromosome proteome from genetic knockouts of kinetochore protein Ska3/Rama1 revealed that the APC/C and RanBP2/RanGAP1 complexes depend on the Ska complex for stable association with chromosomes. Our integrated analysis predicts that up to 97 new centromere-associated proteins remain to be discovered in our data set.

Mitotic chromosome formation involves a relatively minor condensation of the chromatin volume coupled with a dramatic reorganization into the characteristic “X” shape. Here we report results of a detailed morphological analysis, which revealed that chromokinesin KIF4 cooperated in a parallel pathway with condensin complexes to promote the lateral compaction of chromatid arms. In this analysis, KIF4 and condensin were mutually dependent for their dynamic localization on the chromatid axes. Depletion of either caused sister chromatids to expand and compromised the “intrinsic structure” of the chromosomes (defined in an in vitro assay), with loss of condensin showing stronger effects. Simultaneous depletion of KIF4 and condensin caused complete loss of chromosome morphology. In these experiments, topoisomerase IIα contributed to shaping mitotic chromosomes by promoting the shortening of the chromatid axes and apparently acting in opposition to the actions of KIF4 and condensins. These three proteins are major determinants in shaping the characteristic mitotic chromosome morphology.

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[1] The regional-scale aerosol transport model Chemical Weather Forecasting System (CFORS) is used for analysis of large-scale dust phenomena during the Asian Pacific Regional Characterization Experiment (ACE-Asia) intensive observation. Dust modeling results are examined with the surface weather reports, satellite-derived dust index (Total Ozone Mapping Spectrometer (TOMS) Aerosol Index (AI)), Mie-scattering lidar observation, and surface aerosol observations. The CFORS dust results are shown to accurately reproduce many of the important observed features. Model analysis shows that the simulated dust vertical loading correlates well with TOMS AI and that the dust loading is transported with the meandering of the synoptic-scale temperature field at the 500-hPa level. Quantitative examination of aerosol optical depth shows that model predictions are within 20% difference of the lidar observations for the major dust episodes. The structure of the ACE-Asia Perfect Dust Storm, which occurred in early April, is clarified with the help of the CFORS model analysis. This storm consisted of two boundary layer components and one elevated dust (>6-km height) feature (resulting from the movement of two large low-pressure systems). Time variation of the CFORS dust fields shows the correct onset timing of the elevated dust for each observation site, but the model results tend to overpredict dust concentrations at lower latitude sites. The horizontal transport flux at 130°E longitude is examined, and the overall dust transport flux at 130°E during March-April is evaluated to be 55 Tg.

[1] The regional-scale aerosol transport model (CFORS) is used in the analysis of black carbon (BC) observed at five remote Japanese islands during the ACE-Asia experiment. BC is modeled online in the regional-scale meteorological model, using emissions estimates for 2000. Two model experiments are conducted (1) a control run that includes all the BC emission, and (2) a sensitivity run without open biomass burning emissions to clarify the impact of biomass burning on the BC levels in the western Pacific. The regional aerosol model (CFORS) is shown to accurately reproduce many of the important features observed. Model analysis shows that the spatial and temporal distributions of black carbon between the northern sites (Rishiri and Sado; located in the Japan Sea) and the southern stations (Hachijo, Chichijima, and Amami-Oshima; in the western Pacific Ocean) are under different flow regimes. It is shown that the major synoptic features controlling BC levels are associated with outflow in the warm conveyor belt of traveling cold fronts and the subsequent postfrontal transport. At the northern stations (Rishiri and Sado), elevated BC concentrations are calculated to be mainly below the heights of 2000 m, and the biomass burning fraction is estimated to be below 20%. At the southern sites (e.g., Chichijima) the contribution due to biomass burning reaches 32% at the surface and 52% in the free atmosphere. CFORS results indicate that the major black carbon source and transport height are different between the northern and southern sites.

We engineered mutants into residues of SMC2 to dissect the role of ATPase function in the condensin complex. These residues are predicted to be involved in ATP binding or hydrolysis and in the Q-loop, which is thought to act as a mediator of conformational changes induced by substrate binding. All the engineered ATPase mutations resulted in lethality when introduced into SMC2 null cells. We found that ATP binding, but not hydrolysis, is essential to allow stable condensin association with chromosomes. How SMC proteins bind and interact with DNA is still a major question. Cohesin may form a ring structure that topologically encircles DNA. We examined whether condensin behaves in an analogous way to its cohesin counterpart, and we have generated a cleavable form of biologically active condensin with PreScission protease sites engineered into the SMC2 protein. This has allowed us to demonstrate that topological integrity of the SMC2-SMC4 heterodimer is not necessary for the stability of the condensin complex in vitro or for its stable association with mitotic chromosomes. Thus, despite their similar molecular organization, condensin and cohesin exhibit fundamental differences in their structure and function.

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