ORIGINAL PAPER Comparative Evolutionary Analysis of Cell Cycle Proteins Networks in Fission and Budding Yeast Praveen K. Singh • Madhvi Shakya Ó Springer Science+Business Media New York 2014 Abstract Fission yeast and budding yeast are the two distantly related species with common ancestors. Various studies have shown significant differences in metabolic networks and regulatory networks. Cell cycle regulatory proteins in both species have differences in structural as well as in functional organization. Orthologous proteins in cell cycle regulatory protein networks seem to play con- temporary role in both species during the evolution but little is known about non-orthologous proteins. Here, we used system biology approach to compare topological parameters of orthologous and non-orthologous proteins to find their contributions during the evolution to make an efficient cell cycle regulation. Observed results have shown a significant role of non-orthologous proteins in fission yeast in maintaining the efficiency of cell cycle regulation with less number of proteins as compared to budding yeast. Keywords Protein networks  Cell cycle  Topology  Evolution Introduction Proteins perform their functions by their cooperative interactions of stable protein complexes or by transient interactions. These interactions create a network-like structure which underlies the important features of bio- logical systems such as structural modularity, error toler- ance, and stability [1–4]. Still no more research has been done to understand what deriving forces underlie the net- work structures. Network analyses of these protein inter- actions create an opportunity to understand the evolutionary pattern of protein interactions [5–8]. Archi- tectural exploration of protein interaction network organi- zation has concluded in recent years that these networks follow the scale-free topology which is the actuality of power-law distribution [9, 10]. Topology plays an impor- tant role in local interaction behavior and also affects the dynamic behavior of biological systems [11]. Uncovering the growth patterns and the evolutionary path of the protein interaction network is a serious challenge [6, 12, 13]. Topology can be an important factor to modulate or evolve functions in these networks [14]. This feature inspired us to explore evolutionary process in the sense of topological properties. Here, an approach has been used to explore organizational principles that affect the relationship between topology and network modifications during the evolution. Here, cell cycle networks of evolutionary distant spe- cies, budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, were used to under- stand the evolution of protein interaction networks. Topo- logical properties were compared to predict the structural variations of protein interaction network in these species. Both of these yeasts show the morphological differences in their cell shapes as well in their cell cycle processes. Their divergence is reflected by the life style and cell cycle regulations. Budding yeast mainly regulates its cell cycle at G1/S phase while fission yeast at G2/M phase [15–17]. In budding yeast, G1 and M phases overlap due to the creation of mitotic spindle in early phase, while in fission yeast, P. K. Singh (&) Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal, India e-mail: praveenbt2004@gmail.com M. Shakya Department of Mathematics, Maulana Azad National Institute of Technology, Bhopal, India 123 Cell Biochem Biophys DOI 10.1007/s12013-014-0037-y