A proteomic study of the arabidopsis nuclear matrix

Abstract

The eukaryotic nucleus has been proposed to be organized by two interdependent nucleoprotein structures, the DNA-based chromatin and the RNA-dependent nuclear matrix. The functional composition and molecular organization of the second component have not yet been resolved. Here, we describe the isolation of the nuclear matrix from the model plant Arabidopsis, its initial characterization by confocal and electron microscopy, and the identification of 36 proteins by mass spectrometry. Electron microscopy of resinless samples confirmed a structure very similar to that described for the animal nuclear matrix. Two-dimensional gel electrophoresis resolved approximately 300 protein spots. Proteins were identified in batches by ESI tandem mass spectrometry after resolution by 1D SDS-PAGE. Among the identified proteins were a number of demonstrated or predicted Arabidopsis homologs of nucleolar proteins such as IMP4, Nop56, Nop58, fibrillarins, nucleolin, as well as ribosomal components and a putative histone deacetylase. Others included homologs of eEF-1, HSP/HSC70, and DnaJ, which have also been identified in the nucleolus or nuclear matrix of human cells, as well as a number of novel proteins with unknown function. This study is the first proteomic approach towards the characterization of a higher plant nuclear matrix. It demonstrates the striking similarities both in structure and protein composition of the operationally defined nuclear matrix across kingdoms whose unicellular ancestors have separated more than one billion years ago.

Subnuclear domain proteins in cancer cells support transcription factor RUNX2 functions in DNA damage response

“…lamin A/C and B, Numa, matrin-3) and many proteins involved in RNA metabolism. These observations are entirely consistent with results from a number of recent proteomic studies that characterize nuclear matrix proteins from embryonic stem cells, tumor cell types and plant cells (Oehr, 2003;Calikowski et al, 2003;Barboro et al, 2009;Albrethsen et al, 2010;Nasrabadi et al, 2010;Warters et al, 2010).…”

Nuclear Matrix Proteome Analysis of Drosophila melanogaster

“…A proteomics study of the Arabidopsis nuclear matrix shows the presence of nucleolar proteins such as IMP4, Nop56, Nop58, fibrillarins, and nucleolin; ribosomal proteins L7, L5, and L18; a number of ␣-tubulins and ␤-tubulins; homologues of translation elongation factor eEF-1; and the heat shock protein At-hsc70-3 (15). These proteins have also been identified in the nucleolus and nuclear matrix fractions of human cells.…”

“…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)(16)(17)(18). Major advancements in the field of proteomics now provide further scope for extensive analysis of NuMat in this context.…”

A Case of Selfish Nucleolar Segregation

“…The nucleolus is a prominent and sophisticated nuclear compartment [1][2][3][4] that maintains protein synthesis machinery by actively transcribing genes for ribosomal RNAs, modifying and processing of these RNAs, assembling ribosomal subunits, transporting and modifying ribosomal and other RNPs. [5][6][7] In addition, the nucleolus plays an important role as a pool of "dormant" proteins 8 some of which are key regulators of the cell cycle.…”

“…As a result, the nucleolus possesses an unparalleled degree of functional and structural autonomy among other nuclear compartments, while maintaining extensive transport exchange with other parts of the nucleus. 7 The nucleolus uses scores of highly specialized proteins, [1][2][3][4] from RNA polymerases to replication factors and structural proteins, exemplifying its unique identity both in chromatin and in the nucleus. Nucleolar autonomy is also evident during assembly and disassembly of nucleoli in Metazoa, via highly organized, structurally integrated and localized pathways.…”