Comparative analyses of nuclear proteome: extending its function

Abstract

Organeller proteomics is an emerging technology that is critical in determining the cellular signal transduction pathways. Nucleus, the regulatory hub of the eukaryotic cell is a dynamic system and a repository of various macromolecules that serve as modulators of such signaling that dictate cell fate decisions. Nuclear proteins (NPs) are predicted to comprise about 10–20% of the total cellular proteins, suggesting the involvement of the nucleus in a number of diverse functions. Indeed, NPs constitute a highly organized but complex network that plays diverse roles during development and physiological processes. In plants, relatively little is known about the nature of the molecular components and mechanisms involved in coordinating NP synthesis, their action and function. Proteomic study hold promise to understand the molecular basis of nuclear function using an unbiased comparative and differential approach. We identified a few hundred proteins that include classical and non-canonical nuclear components presumably associated with variety of cellular functions impinging on the complexity of nuclear proteome. Here, we review the nuclear proteome based on our own findings, available literature, and databases focusing on detailed comparative analysis of NPs and their functions in order to understand how plant nucleus works. The review also shed light on the current status of plant nuclear proteome and discusses the future prospect.

Proteomic Analysis of Barley Cell Nuclei Purified by Flow Sorting

“…Cushman, 1995;Zhang et al, 1995;Abdalla et al, 2009Abdalla et al, , 2010Sikorskaite et al, 2013], and root meristem [Silva et al, 2010], and in in vitro cultured cells [Willmitzer and Wagner, 1981]. Currently used extraction protocols directed at nuclear proteins use mechanical homogenization, filtration to remove large detritus, pelleting, suspension in a non-ionic detergent, and finally separation by density gradient centrifugation [for review see Narula et al, 2013]. This sort of scheme has provided descriptions of the Arabidopsis thaliana [Bae et al, 2003;Jones et al, 2009], hot pepper [Lee et al, 2006], rice [Tan et al, 2007;Li et al, 2008;Aki and Yanagisawa, 2009;Choudhary et al, 2009], barrel clover [Repetto et al, 2008], maize [Casati et al, 2008], black-stick lily [Abdalla et al, 2010;Abdalla and Rafudeen, 2012], soybean [Cooper et al, 2011], flax [Renouard et al, 2012], and chickpea [Pandey et al, 2006;Varshney et al, 2013] nuclear proteomes.…”

The Nuclear Proteome of White and Gray Matter from Schizophrenia Postmortem Brains

“…1). These processes are related to the main functions of the nucleus, such as gene expression, transcriptional control, splicing, and release of gene products [10]. …”

“…The nucleus is the largest organelle of most cells and occupies approximately 10% of its volume, although this varies according to the cell type [9]. The nucleus is the compartment where the genetic material of eukaryotic organisms is stored, and nuclear proteins constitute 10-20% of the total cellular proteins and exert important functions related to gene expression, transcriptional control, splicing, and generation of the final gene products [10]. Therefore, the importance of investigating the nuclear proteome for the understanding of any physiological or pathological process is clear, and few such studies have been carried out thus far in the field of psychiatric disorders such as SCZ.…”

Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives

“…Organ level proteomics [200][201][202] ). These studies identified 91 proteins from total element of the cell, whereas 388 proteins were identified from the ECM, 479 proteins were identified from the nucleus and 91 proteins were identified from the membrane.…”