Nuclear Matrix Proteome Analysis of Drosophila melanogaster

Abstract

The nucleus is a highly structured organelle and contains many functional compartments. Although the structural basis for this complex spatial organization of compartments is unknown, a major component of this organization is likely to be the non-chromatin scaffolding called nuclear matrix (NuMat). Experimental evidence over the past decades indicates that most of the nuclear functions are at least transiently associated with the NuMat, although the components of NuMat itself are poorly known. Here, we report NuMat proteome analysis from Drosophila melanogaster embryos and discuss its links with nuclear architecture and functions. In the NuMat proteome, we found structural proteins, chaperones, DNA/RNAbinding proteins, chromatin remodeling and transcription factors. This complexity of NuMat proteome is an indicator of its structural and functional significance. The eukaryotic cell nucleus contains a number of structural features like heterochromatin, nucleolus, nuclear lamina, and nuclear territories and functional features like transcription foci, replication foci, Cajal bodies, stress-induced foci, etc.(1-7). Packaging of the genome on the other hand also results in non-random distribution of a variety of structural features like chromatin domains that help to regulate expression of genes (8). How these complex structural and functional domains are established and maintained is not known. It is likely that the non-chromatin scaffolding called nuclear matrix (9) plays an important role in this process. Nuclear matrix (NuMat) 1 mainly consists of the nuclear lamina, the nucleolar remnants, and an internal nuclear meshwork of fibers of unknown constitution that can be seen by electron microscopy (10). These fibers have ultrastructural features reminiscent of intermediate filaments of the cytosol (11). The protein component of nucleoplasmic filaments, however, is largely unknown. Earlier studies on a few proteins isolated from nuclear matrix from different organisms have shown them to be DNA-and RNA-binding and structural components of the nuclear pore complex (12), enzymes (13), and nuclear membrane proteins (14). This diversity among the small number of identified NuMat constituents reflects the link of nuclear architecture with the variety of nuclear functions. The importance of NuMat constituents in nuclear processes has been apparent for a long time, and several studies have been carried out to identify the proteins of this complex structure in different organisms (15-18). Major advancements in the field of proteomics now provide further scope for extensive analysis of NuMat in this context.Here, we present a comprehensive analysis of the NuMat proteome of Drosophila melanogaster. NuMat preparations from D. melanogaster embryos were separated by one-dimensional gel electrophoresis, and the proteins were identified by LC-MS/MS. We also report a remarkable variation in the NuMat proteome depending on developmental stages, indicating a link between embryonic development and nuclear architecture. Finally, immunos...

Dynamics of nuclear matrix proteome during embryonic development in Drosophila melanogaster

“…NuMat preparations from these embryos were identified by LC-MS/MS. While our earlier report shed light on the changing pattern of the NuMat proteome during development (Kallappagoudar et al 2010), this study shows that NuMat proteome is indeed dynamic with remarkable variation between the two developmental stages. Thus, this analysis establishes a link between the dynamics of both embryonic development as well as nuclear architecture.…”

“…In fact, in a recent study, an extensive analysis of NuMat proteome composition has reflected the rich variety of functional categories of proteins associated with NuMat, providing further implications of its role in the diverse nuclear processes. These proteins included structural proteins, heat shock proteins, chaperones, DNA binding and mitotic scaffolding proteins, chromatin remodeling proteins, transcription-and translation-associated proteins and also ribosomal proteins (Kallappagoudar et al 2010). Taken together, these studies have further strengthened the concept of NuMat being associated with processes such as embryonic development and differentiation and hence the interplay between the dynamics of nuclear architecture and regulation of gene expression during these key molecular events.…”

Drosophila Small Heat Shock Proteins: An Update on Their Features and Functions

“…Recently, Hsp26 has been found in the nuclear matrix of Drosophila Schneider 2 (S2) cells and embryos together with Hsp27 (Kallappagoudar et al 2010 ). To our knowledge, this is the fi rst report showing a nuclear localization for this cytoplasmic sHsp.…”

Brca2/Pds5 complexes mobilize persistent meiotic recombination sites to the nuclear envelope

“…4E). Proteomic analyses have shown that other cohesin subunits also associate with the nuclear envelope (Kallappagoudar et al, 2010), and it is possible that such interactions might stabilize interactions between the homologous chromatids. Considering that exchange between the chromatids requires their precise alignment over extensive regions around homologous recombination intermediates, it is tempting to speculate that the Brca2-mediated Pds5-Pds5 interactions might serve the simultaneous clamping of two cohesin rings around the homologs.…”