Family-specific scaling laws in bacterial genomes

• Published in: Nucleic acids research 2017-07, Vol.45 (13), p.7615-7622
• Main Authors: De Lazzari, Eleonora, Grilli, Jacopo, Maslov, Sergei, Cosentino Lagomarsino, Marco
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - classification; Bacterial Proteins - genetics; Biological Physics; Computational Biology; Evolution, Molecular; Genome Size; Genome, Bacterial; Physics; Protein Domains - genetics; Proteome - chemistry; Proteome - classification; Proteome - genetics; Transcription Factors - chemistry; Transcription Factors - classification; Transcription Factors - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkx510

Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, sharing a specific functional annotation across genomes of given size. The size of these functional categories change, on average, as power-laws in the total number of protein-coding genes. Here, we show that such regularities are not restricted to the overall behavior of high-level functional categories, but also exist systematically at the level of single evolutionary families of protein domains. Specifically, the number of proteins within each family follows family-specific scaling laws with genome size. Functionally similar sets of families tend to follow similar scaling laws, but this is not always the case. To understand this systematically, we provide a comprehensive classification of families based on their scaling properties. Additionally, we develop a quantitative score for the heterogeneity of the scaling of families belonging to a given category or predefined group. Under the common reasonable assumption that selection is driven solely or mainly by biological function, these findings point to fine-tuned and interdependent functional roles of specific protein domains, beyond our current functional annotations. This analysis provides a deeper view on the links between evolutionary expansion of protein families and the functional constraints shaping the gene repertoire of bacterial genomes.