Family-specific scaling laws in bacterial genomes
  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.
