Title: Family-specific scaling laws in bacterial genomes,
Abstract: 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.