Activation of s28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization

1110 K. Hollands,D. J. Lee,G. S. LloydandS. J. W. Busby ■

Busby, S., and Ebright, R.H. (1999) Transcription activation
by catabolite activator protein (CAP). J Mol Biol 293: 199-
213.

Busby, S., Kotlarz, D., and Buc, H. (1983) Deletion mutagen-
esis of the Escherichia coli galactose operon promoter
region. J Mol Biol 167: 259-274.

Casadaban, M.J., and Cohen, S.N. (1980) Analysis of gene
control signals by DNA fusion and cloning in Escherichia
coli. J Mol Biol 138: 179-207.

Chen, H., Tang, H., and Ebright, R.H. (2003) Functional inter-
action between RNA polymerase alpha subunit C-terminal
domain and sigma70 in UP-element- and activator-
dependent transcription. Mol Cell 11: 1621-1633.

Cherepanov, P.P., and Wackernagel, W. (1995) Gene dis-
ruption in Escherichia coli: Tc^R and Km^R cassettes with the
option of Flp-catalysed excision of the antibiotic-resistance
determinant. Gene 158: 9-14.

Chilcott, G.S., and Hughes, K.T. (2000) Coupling of flagellar
gene expression to flagellar assembly in Salmonella
enterica serovar Typhimurium and Escherichia coli. Micro-
biol Mol Biol Rev 64: 694-708.

Frye, J., Karlinsey, J.E., Felise, H.R., Marzolf, B., Dowidar,
N., McClelland, M., and Hughes, K.T. (2006) Identification
of new flagellar genes of Salmonella enterica serovar
Typhimurium. J Bacteriol 188: 2233-2243.

Gaston, K., Bell, A., Kolb, A., Buc, H., and Busby, S. (1990)
Stringent spacing requirements for transcription activation
by CRP. Cell 62: 733-743.

Germer, J., Becker, G., Metzner, M., and Hengge-Aronis, R.
(2001) Role of activator site position and a distal
UP-element half-site for sigma factor selectivity at a CRP/
H-NS-activated sigma(S)-dependent promoter in Escheri-
chia coli. Mol Microbiol 41: 705-716.

Gosset, G., Zhang, Z., Nayyar, S., Cuevas, W.A., and Saier,
M.H., Jr (2004) Transcriptome analysis of CRP-dependent
catabolite control of gene expression in Escherichia coli.
J Bacteriol 186: 3516-3524.

Gourse, R.L., Ross, W., and Gaal, T. (2000) UPs and downs
in bacterial transcription initiation: the role of the alpha
subunit of RNA polymerase in promoter recognition. Mol
Microbiol 37: 687-695.

Grainger, D.C., Hurd, D., Harrison, M., Holdstock, J., and
Busby, S.J. (2005) Studies of the distribution of Escheri-
chia coli cAMP-receptor protein and RNA polymerase
along the E. coli chromosome. Proc Natl Acad Sci USA
102: 17693-17698.

Grainger, D.C., Goldberg, M.D., Lee, D.J., and Busby, S.J.W.
(2008) Selective repression by Fis and H-NS at the Escheri-
chia coli dps promoter. Mol Microbiol 68: 1366-1377.

Gruber, T.M., and Gross, C.A. (2003) Multiple sigma subunits
and the partitioning of bacterial transcription space. Annu
Rev Micriobiol 57: 441-466.

Hollands, K., Busby, S.J., and Lloyd, G.S. (2007) New targets
for the cyclic AMP receptor protein in the Escherichia coli
K-12 genome. FEMS Microbiol Lett 274: 89-94.

Ishihama, A. (2000) Functional modulation of Escherichia coli
RNA polymerase. Annu Rev Micriobiol 54: 499-518.

Keseler, I.M., Bonavides-Martinez, C., Collado-Vides, J.,
Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., et al.
(2009) EcoCyc: a comprehensive view of Escherichia coli
biology. Nucleic Acids Res 37: 464-470.

Kolb, A., Busby, S., Buc, H., Garges, S., and Adhya, S.
(1993) Transcriptional regulation by cAMP and its receptor
protein. Annu Rev Biochem 62: 749-795.

Kolb, A., Kotlarz, D., Kusano, S., and Ishihama, A. (1995)
Selectivity of the Escherichia coli RNA polymerase E sigma
38 for overlapping promoters and ability to support CRP
activation. Nucleic Acids Res 23: 819-826.

Koo, B.M., Rhodius, V.A., Campbell, E.A., and Gross, C.A.
(2009) Mutational analysis of Escherichia coli sigma28 and
its target promoters reveals recognition of a composite -10
region, comprised of an ‘extended -10’ motif and a core -10
element. Mol Microbiol 72: 830-843.

Lawson, C.L., Swigon, D., Murakami, K.S., Darst, S.A.,
Berman, H.M., and Ebright, R.H. (2004) Catabolite activa-
tor protein: DNA binding and transcription activation. Curr
Opin Struct Biol 14: 10-20.

Lee, D.J., Busby, S.J., and Lloyd, G.S. (2003) Exploitation of
a chemical nuclease to investigate the location and orien-
tation of the Escherichia coli RNA polymerase alpha
subunit C-terminal domains at simple promoters that are
activated by the cyclic AMP receptor protein. J Biol Chem
278: 52944-52952.

Lloyd, G.S., Busby, S.J., and Savery, N.J. (1998) Spacing
requirements for interactions between the C-terminal
domain of the alpha subunit of Escherichia coli RNA poly-
merase and the cAMP receptor protein. Biochem J 330:
413-420.

Lloyd, G.S., Hollands, K., Godfrey, R.E., and Busby, S.J.
(2008) Transcription initiation in the Escherichia coli K-12
malI-malX intergenic region and the role of the cyclic AMP
receptor protein. FEMS Micriobiol Lett 288: 250-257.

Lodge, J., Fear, J., Busby, S., Gunasekaran, P., and Kamini,
N.R. (1992) Broad host range plasmids carrying the
Escherichia coli lactose and galactose operons. FEMS
Microbiol Lett 74: 271-276.

Miller (1972) Experiments in Molecular Genetics. Cold Spring
Harbor: Cold Spring Harbor Laboratory Press.

Murakami, K.S., Masuda, S., Campbell, E.A., Muzzin, O., and
Darst, S.A. (2002) Structural basis of transcription initia-
tion: an RNA polymerase holoenzyme-DNA complex.
Science 296: 1285-1290.

Park, K., Choi, S., Ko, M., and Park, C. (2001) Novel sigmaF-
dependent genes of Escherichia coli found using a
specified promoter consensus. FEMS Microbiol Lett 202:
243-250.

Rebbapragada, A., Johnson, M.S., Harding, G.P., Zuccarelli,
A.J., Fletcher, H.M., Zhulin, I.B., and Taylor, B.L. (1997)
The Aer protein and the serine chemoreceptor Tsr indepen-
dently sense intracellular energy levels and transduce
oxygen, redox, and energy signals for Escherichia coli
behaviour. Proc Natl Acad Sci USA 94: 10541-10546.

Rhodius, V.A., West, D.M., Webster, C.L., Busby, S.J., and
Savery, N.J. (1997) Transcription activation at class II
CRP-dependent promoters: the role of different activating
regions. Nucleic Acids Res 25: 326-332.

Robison, K., McGuire, A.M., and Church, G.M. (1998) A
comprehensive library of DNA-binding site matrices for 55
proteins applied to the complete Escherichia coli K-12
genome. J Mol Biol 284: 241-254.

Savery, N.J., Lloyd, G.S., Kainz, M., Gaal, T., Ross, W.,
Ebright, R.H., et al. (1998) Transcription activation at Class

© 2009 The Authors

Journal compilation © 2009 Blackwell Publishing Ltd, Molecular Microbiology, 75, 1098-1111

<<   10   11   12   13   14   >>

More intriguing information