To be or not to be a nucleoid protein: A comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins

In the last decade it has become increasingly clear that mitochondrial DNA (mtDNA) is not naked but associated with proteins in poorly defined structures called nucleoids that are essential for mtDNA maintenance. The function of nucleoids is not simply to package mtDNA but also to provide a stable environment for its replication, transcription and repair. Even though their properties and dynamics have begun to be revealed in recent years, their structural and molecular organization remains largely unknown in mammals. Although, there are a number of proteins identified to be nucleoid associated by using several biochemical isolation methods combined with mass spectrometric analysis, the main difficulties in the identification of these proteins are their low abundance and the assumed dynamic composition of nucleoids. Considering various purification methods, there is a thin line between the stringency and specificity in the identification of potential nucleoid associated proteins. In this review, the main focus is to provide a comprehensive comparison of the so far published purification and analysis methods to generate a list of potentially nucleoid associated proteins, but also, to discuss the disadvantages and possible improvements in proteomic analyses.