| Comments |
"The bacterial chromosome is densely covered with TFs that bind DNA both specifically and nonspecifically (Li et al., 2009). The crowded space on DNA imposes constraints on the abundance of TFs because overcrowding by nonspecifically associated DNA-binding proteins could drastically reduce the overall binding kinetics (Hammar et al., 2012 and Li et al., 2009). Thus, although higher concentrations of any given TF would allow it to find its cognate DNA sites more rapidly (von Hippel, 2007), too many TFs in total would mask binding sites. Based on [researchers'] protein-abundance estimates, [they] found that the average distance between DNA-binding proteins is only ~36 bp on the E. coli chromosome (assuming that most DNA-binding proteins are associated with DNA nonspecifically and are randomly distributed throughout the genome see Extended Experimental Procedures), which is close to the theoretically optimal density for rapid binding ( Li et al., 2009)." |