Biology subjects

Cimini, G.

Publications and source records attributed to Cimini, G..

3 recordsLinked to original sources

bioRxiv2020

Bacterial protein interaction networks: connectivityis ruled by gene conservation, essentiality andfunction

Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we relate conservation, essentiality and functional repertoire of a gene to the connectivity k of the corresponding protein in the PPI networks. Focusing on a set of 42 bacterial species with reasonably separated evolutionary trajectories, we investigate three issues: i) whether the distribution of connectivity values changes between PPI subnetworks of essential and nonessential genes; ii) how gene conservation, measured both by the evolutionary retention index (ERI) and by evolutionary pressures (evaluated through the ratio Ka/Ks and ENC plots) is related to the the connectivity of the corresponding protein; iii) how PPI connectivities are modulated by evolutionary and functional relationships, as represented by the Clusters of Orthologous Proteins (COGs). We show that conservation, essentiality and functional specialization of genes control in a quite universal way the topology of the emerging bacterial PPI networks. Noteworthy, a structural transition in the network is observed such that, for connectivities k [≥] 40, bacterial PPI networks are mostly populated by genes that are conserved, essential and which, in most cases, belong to the COG cluster J, related to ribosomal functions and to the processing of genetic information.

genomics↗

bioRxiv2020

Co-evolution between codon usage and Protein-Protein Interaction Networks in Bacterial genomes

In this work, we study the correlation between codon usage and the network features of the PPI in bacteria genomes. We want to extend the information by Dilucca et al. (2015) about E.Colis genome for a set of other 34 bacteria. We use PCA techniques in the space of codon bias indices (compAI, compAI_w, tAI, NC) and GC content to show that genes with similar patterns of codon usage feature have a significantly higher probability that their encoded proteins interact within the PPI. And vice-versa, we show that interacting in the PPI have a coherent codon usage. This work could allow for future investigations into the possible effects that codon bias signal can have on the topology of protein interaction network and, as such, to improve existing bioinformatics methods for predicting protein interactions.

genomics↗

bioRxiv2019

Bacterial protein interaction networks: connectivity is ruled by gene conservation, essentiality and function

Protein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work we study how conservation, essentiality and functional repertoire of a gene relate to the connectivity k of the corresponding protein in the PPI networks. Focusing on a set of 42 mostly distantly related bacterial species, we investigate three issues: i) whether the distribution of connectivity values changes between PPI subnetworks of essential and nonessential genes; ii) how gene conservation, measured both by the evolutionary retention index (ERI) and by evolutionary pressure (as represented by the ratio Ka/Ks) is related to the the connectivity of the corresponding protein; iii) how PPI connectivities are modulated by evolutionary and functionaly relationships, as represented by the Clusters of Orthologous Proteins (COGs). We show that conservation, essentiality and functional specialization of genes control in a universal way the topology of the emerging bacterial PPI networks. Noteworthy, a structural transition in the network is observed such that, for connectivities k [≥] 40, bacterial PPI networks are mostly populated by genes that are conserved, essential and which, in most cases, belong to the COG cluster J, related to ribosomal functions and to the processing of genetic information.

systems biology↗