Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Toolbox model of evolution of prokaryotic metabolic networks and their
  regulation   It has been reported that the number of transcription factors encoded in
prokaryotic genomes scales approximately quadratically with their total number
of genes. We propose a conceptual explanation of this finding and illustrate it
using a simple model in which metabolic and regulatory networks of prokaryotes
are shaped by horizontal gene transfer of coregulated metabolic pathways.
Adapting to a new environmental condition monitored by a new transcription
factor (e.g., learning to use another nutrient) involves both acquiring new
enzymes and reusing some of the enzymes already encoded in the genome. As the
repertoire of enzymes of an organism (its toolbox) grows larger, it can reuse
its enzyme tools more often and thus needs to get fewer new ones to master each
new task. From this observation, it logically follows that the number of
functional tasks and their regulators increases faster than linearly with the
total number of genes encoding enzymes. Genomes can also shrink, e.g., because
of a loss of a nutrient from the environment, followed by deletion of its
regulator and all enzymes that become redundant. We propose several simple
models of network evolution elaborating on this toolbox argument and
reproducing the empirically observed quadratic scaling. The distribution of
lengths of pathway branches in our model agrees with that of the real-life
metabolic network of Escherichia coli. Thus, our model provides a qualitative
explanation for broad distributions of regulon sizes in prokaryotes.

25
The categories of this paper are: patt-sol
5
The categories of this paper are: gr-qc
13
The categories of this paper are: quant-ph
28
The categories of this paper are: alg-geom
34
The categories of this paper are: chem-ph
20
The categories of this paper are: acc-phys
24
The categories of this paper are: dg-ga
22
The categories of this paper are: chao-dyn
30
The categories of this paper are: q-alg
4
The categories of this paper are: cond-mat
27
The categories of this paper are: comp-gas
37
The categories of this paper are: supr-con
33
The categories of this paper are: plasm-ph
0
The categories of this paper are: hep-ph
7
The categories of this paper are: hep-th
36
The categories of this paper are: cmp-lg