TY - JOUR
T1 - CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism
AU - Rammohan, Jayan
AU - Manzano, Ana Ruiz
AU - Garner, Ashley L.
AU - Stallings, Christina L.
AU - Galburt, Eric A.
N1 - Publisher Copyright:
© 2015 The Author(s).
PY - 2015/3/31
Y1 - 2015/3/31
N2 - CarD is an essential and global transcriptional regulator in mycobacteria. While its biological role is unclear, CarD functions by interacting directly with RNA polymerase (RNAP) holoenzyme promoter complexes. Here, using a fluorescent reporter of open complex, we quantitate RPo formation in real time and show that Mycobacterium tuberculosis CarD has a dramatic effect on the energetics of RNAP bound complexes on the M. tuberculosis rrnAP3 ribosomal RNA promoter. The data reveal that Mycobacterium bovis RNAP exhibits an unstable RPo that is stabilized by CarD and suggest that CarD uses a twotiered, concentration-dependent mechanism by associating with open and closed complexes with different affinities. Specifically, the kinetics of opencomplex formation can be explained by a model where, at saturating concentrations of CarD, the rate of bubble collapse is slowed and the rate of opening is accelerated. The kinetics and open-complex stabilities of CarD mutants further clarify the roles played by the key residues W85, K90 and R25 previously shown to affect CarD-dependent gene regulation in vivo. In contrast to M. bovis RNAP, Escherichia coli RNAP efficiently forms RPo onrrnAP3, suggesting an important difference between the polymerases themselves and highlighting how transcriptional machinery can vary across bacterial genera.
AB - CarD is an essential and global transcriptional regulator in mycobacteria. While its biological role is unclear, CarD functions by interacting directly with RNA polymerase (RNAP) holoenzyme promoter complexes. Here, using a fluorescent reporter of open complex, we quantitate RPo formation in real time and show that Mycobacterium tuberculosis CarD has a dramatic effect on the energetics of RNAP bound complexes on the M. tuberculosis rrnAP3 ribosomal RNA promoter. The data reveal that Mycobacterium bovis RNAP exhibits an unstable RPo that is stabilized by CarD and suggest that CarD uses a twotiered, concentration-dependent mechanism by associating with open and closed complexes with different affinities. Specifically, the kinetics of opencomplex formation can be explained by a model where, at saturating concentrations of CarD, the rate of bubble collapse is slowed and the rate of opening is accelerated. The kinetics and open-complex stabilities of CarD mutants further clarify the roles played by the key residues W85, K90 and R25 previously shown to affect CarD-dependent gene regulation in vivo. In contrast to M. bovis RNAP, Escherichia coli RNAP efficiently forms RPo onrrnAP3, suggesting an important difference between the polymerases themselves and highlighting how transcriptional machinery can vary across bacterial genera.
UR - http://www.scopus.com/inward/record.url?scp=84942288248&partnerID=8YFLogxK
U2 - 10.1093/nar/gkv078
DO - 10.1093/nar/gkv078
M3 - Article
C2 - 25697505
AN - SCOPUS:84942288248
SN - 0305-1048
VL - 43
SP - 3272
EP - 3285
JO - Nucleic acids research
JF - Nucleic acids research
IS - 6
ER -