Regulation of Alternative Sigma Factors

MI65CH03-Shingler ARI 10 August 2011 9:34
Regulation of Alternative
Sigma Factor Use
Soa

Osterberg, Teresa del Peso-Santos,
and Victoria Shingler
Department of Molecular Biology, Umea University, 901 87 Umea , Sweden;
email: victoria.shingler@molbiol.umu.se
Annu. Rev. Microbiol. 2011. 65:3755
First published online as a Review in Advance on
May 31, 2011
The Annual Review of Microbiology is online at
micro.annualreviews.org
This articles doi:
10.1146/annurev.micro.112408.134219
Copyright c 2011 by Annual Reviews.
All rights reserved
0066-4227/11/1013-0037$20.00
Keywords
transcription, antisigma factors, ppGpp, DksA, Crl
Abstract
Alternative bacterial sigma factors bind the catalytic core RNA poly-
merase to confer promoter selectivity on the holoenzyme. The different
holoenzymes are thus programmed to recognize the distinct promoter
classes in the genome to allow coordinated activation of discrete sets
of genes needed for adaptive responses. To form the holoenzymes, the
different sigma factors must be available to compete for their common
substrate (core RNA polymerase). This review highlights (a) the roles
of antisigma factors in controlling the availability of alternative sigma
factors and (b) the involvement of diverse regulatory molecules that
promote the use of alternative sigma factors through subversion of the
domineering housekeeping
70
. The latter include the nucleotide alar-
mone ppGpp and small proteins (DksA, Rsd, and Crl), which directly
target the transcriptional machinery to mediate their effects.
37
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Click here for quick links to
Annual Reviews content online,
including:
Other articles in this volume
Top cited articles
Top downloaded articles
Our comprehensive search
Further
ANNUAL
REVIEWS
Core RNA
polymerase
(core-RNAP): the
multisubunit catalytic
machinery of bacterial
RNA synthesis
Sigma factor (): a
dissociable subunit of
bacterial RNAP that
binds with 1:1
stoichiometry to core-
RNAPs and is essential
for initiation of
transcription from
promoters by the
resulting RNAP
holoenzyme
Contents
INTRODUCTION . . . . . . . . . . . . . . . . . . 38
THE TRANSCRIPTION CYCLE
AND DEPLOYMENT OF SIGMA
FACTOR DOMAINS . . . . . . . . . . . . . 39
The Sigma Cycle . . . . . . . . . . . . . . . . . . 39
The
70
Family . . . . . . . . . . . . . . . . . . . . 39
The
54
Family . . . . . . . . . . . . . . . . . . . . 41
ANTISIGMA FACTORS AND
THEIR ANTAGONISTS . . . . . . . . . 41
Counteracting Physicochemical
Assaults . . . . . . . . . . . . . . . . . . . . . . . . 42
Responses to Iron Limitation . . . . . . . 42
Partner Switching and Sigma Factor
Mimicry Mechanisms . . . . . . . . . . . 44
Checkpoint Coupling to Organelle
Biogenesis . . . . . . . . . . . . . . . . . . . . . . 45
PROMOTION OF ALTERNATIVE
SIGMA FACTOR ACTIVITY
THROUGH SUBVERSION
OF
70
. . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Alternative Sigma Factors Are Not
Created Equal . . . . . . . . . . . . . . . . . . 46
The Bacterial Alarmone ppGpp and
Its Cohort DksA . . . . . . . . . . . . . . . . 46
ppGpp and Sigma Factor
Competition. . . . . . . . . . . . . . . . . . . . 47
Modulation of Sigma Factor Usage
Through Diversion of
70
. . . . . . . 48
CONCLUSIONS . . . . . . . . . . . . . . . . . . . . 49
INTRODUCTION
The temporal and conditional control of tran-
scription initiation is a primary access point
for regulating gene expression in all domains
of life. In eubacteria, the evolutionarily con-
served 380-kDa catalytic core RNA poly-
merase (core-RNAP; subunit composition con-
sists of
2
) canaccurately synthesize RNA

and terminate transcription at appropriate sites.
However, promoter DNA recognition and ini-
tiation of transcription is dependent on a dis-
sociable sixth subunit, namely a sigma factor
(). Association of a given sigma factor with
core-RNAP dictates the DNA-binding speci-
city of the resulting holoenzyme (-RNAP)
by providing the majority of determinants for
recognition of promoter DNA motifs. All bac-
terial species have a housekeeping sigma factor
responsible for transcription from the major-
ity of promoters, and most encode additional
alternative sigmas used to redirect RNAP to
sets of genes required for adaptive responses
(30, 37). Thus, the trademark ability of most
bacteria to adapt to changing ecological con-
ditions is underpinned by highly regulated dy-
namic changes in the functional pools of the
different -RNAPs that dictate when, and to
what extent, the different promoter classes in
the genome can be occupied.
Because promoter-binding by a given -
RNAP holoenzyme is a prerequisite for cor-
rect transcriptional initiation, the composition
of the holoenzyme pool provides the back-
ground against which other promoter-output
modulating factors must act. These include
classical DNA-binding transcriptional regula-
tors (repressors and activators) and regulatory
molecules such as the nucleotide guanosine
tetraphosphate (ppGpp) and proteins such as
DksA that directly target the active site of -
RNAP to modulate its performance at promot-
ers (reviewed in Reference 33).
The repertoire of alternative sigma factors
used to globally alter and coordinate transcrip-
tional responses to changing cellular demands
varies widely between different species and gen-
erally reects the lifestyle of the bacterium. For
example, dedicated intracellular pathogens that
thrive in a relatively constant environment fre-
quently possess only a single sigma factor (e.g.,
Mycoplasma genitalium). The gut commensal
Escherichia coli has 7 sigmas, whereas soil and
water bacteria, which are exposed to a plethora
of uctuating physicochemical and nutritional
stresses in their natural environments, possess
many morereaching an excess of a remark-
able 60 alternative sigma factors in Streptomyces
coelicolor (30). The roles of alternative sigma
factors in counteracting stress, during biogene-
sis of extracellular appendages, and in develop-
mental programs such as spore formation are
38

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
-RNAP:
holoenzyme RNA
polymerase
RNAP: RNA
polymerase
Guanosine
tetraphosphate
(ppGpp): the effector
molecule of the
stringent response;
used here to also
encompass pppGpp
most familiar from studies of the model or-
ganisms E. coli and Bacillus subtilis. However,
these represent just a limited subset of the myr-
iad physiological processes controlled by alter-
native sigma factors, which extend to pivotal
roles in other development programs, e.g., pro-
duction of aerial hyphae by S. coelicolor, regula-
tion of photosynthesis and circadian rhythms
in cyanobacteria, and control of transcrip-
tion by bacteria-like RNAP in plant plastids
(30, 37).
The ability of sigma factors to capture core-
RNAP to form a holoenzyme is determined by
their free concentrations and afnity for core-
RNAP. To accommodate the intermittent and
environment-specic requirement for alterna-
tive sigma factors, bacteria have evolved so-
phisticated regulatory systems to control their
production, activity, and availability. In this
review we rst provide a brief overview of the
interactions of sigma factors with core-RNAP
and promoters as a preface to highlighting how
these critical interfaces are exploited by anti-
sigma factors. Second, we focus on mechanisms
by which targeting of the housekeeping sigma
and/or its holoenzyme by regulatory molecules
can provide a more general strategy to promote
the use of many alternative sigma factors.
THE TRANSCRIPTION CYCLE
AND DEPLOYMENT OF SIGMA
FACTOR DOMAINS
The Sigma Cycle
Withinthe holoenzyme, the sigma factor makes
multiple and extensive contacts with core-
RNAP and plays an active role in initial pro-
moter engagement to form a closed promoter
complex and in subsequent steps of DNA melt-
ing to form the open promoter complex re-
quired for transcriptional initiation (Figure 1).
Tight -core-RNAP association is sequentially
broken prior to promoter escape of RNAP into
the elongation mode (66). However, complete
detachment of the sigma is not a prerequi-
site for transcriptional elongation per se, and
a partially attached sigma can cause elongation
Initiation Elongation
a
Stochastic release
Core-RNAP
RNA
Promoter
engagement
Sigma binding
Termination
Competition
b
R+P RP
c
RP
i
RP
o
NTPs
RP
init
NTPs
RP
E
Figure 1
The sigma cycle allows reprogramming of core RNA polymerase
(core-RNAP). (a) Schematic illustration of the transcription cycle in which
sigma factors compete for association with core-RNAP to direct the
holoenzyme to engage promoters. (b) Simplied schematic of the multiple
reversible steps of transcriptional initiation: -RNAP (R) binds promoter DNA
(P) to form the initial closed complex (RP
c
), which, through sigma-assisted
formation of a number of unstable intermediate complexes (RP
i
), eventually
leads to the open complex (RP
o
), which is competent to initiate transcription.
Note that reversible steps of initiation end as the elongation complex (RP
E
)
escapes the promoter.
stalling by binding promoter-element mim-
ics within DNA. Nevertheless, the majority of
sigma factors are rapidly, albeit stochastically,
released during elongation (65, 74) to join the
pool of free sigma for competitive association
with core-RNAP. The release of sigma during
each round of transcription provides the cen-
tral mechanism for reprogramming the levels
of the alternative -RNAP holoenzyme pools
and thus cognate promoter occupancy.
The
70
Family
With the exception of homologs of E. coli
54
(see below), all alternative sigmas belong
to the extensive
70
family, named after the
www.annualreviews.org Control of Sigma Factor Use 39
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
54
70
a
b
4

3

2

1.1
3.2
DNA
melting
Core
binding
DNA-binding
inhibition
3.2 loop
Core binding bEBP
interactions
DNA interactions
24 12
NCR
UP element 35 Ext. 10 10 Discriminator
RpoN box
TTGACA TGn TATAAT GGGnnn
4
.
2
4
.
1
3
.
1
3
.
0
2
.
4
2
.
3
2
.
2
2
.
1
1
.
2
C N
C N
1.1
I II Region III
TTGGCACG TTGC
Figure 2
Sigma factor domains and their functions. (a) For
70
proteins, roles of the
conserved subregions within the
2
,
3
, and
4
globular domains as described
in the text are highlighted. NCR indicates the location of a nonconserved
region. Consensus for the 35 hexamer (35 to 30), the extended 10
element (Ext.; 15 to 13), the 10 hexamer (12 to 7), and discriminator
DNA (6 to 1, with an optimal GGG 6 to 4), relative to the
transcriptional +1 start, are taken from References 33 and 56. (b) For
54
proteins, consensus for the 24 (27 to 20) and 12 (15 to 12) elements,
which encompass almost invariant GG and GC recognition motifs
(underlined), are taken from Reference 78. Abbreviation: bEBP, bacterial
enhancer-binding protein.
Antisigma factor:
any agonist that
through binding to a
sigma factor inhibits
its ability to associate
with core-RNAP
ECF:
extracytoplasmic
function
housekeeping
70
of E. coli (also known as
D
;
A
in B. subtilis and many other species). A dual
(or sometimes triple) naming system for E. coli
sigmas is prevalent in the current literature;
therefore, after their rst introduction we use
only numerical or gene name superscripting for
E. coli sigmas.
Extensive biochemical, genetic, and struc-
tural analysis has underscored the roles of
different domains of housekeeping sigmas
in providing four of the ve known inter-
actions that occur with the promoter DNA
(Figure 2a). At some promoters, a fth
interaction is provided by the -subunits
of core-RNAP at an AT-rich UP-element
DNA (reviewed in Reference 33). The most
conspicuous
70
-promoter recognition ele-
ments are the 35 and 10 hexamers that are
contacted by the
4
and
2
domains of
70
,
respectively (17, 66). Subregion 1.2 within the
2
domain can also provide promoter contacts
through the discriminator DNA downstream
of the 10 element (34). At extended 10
promoters, which frequently lack a discernable
35 element, additional promoter contacts are
provided by interaction between the
3
domain
and DNA just upstream of the 10 element. A
nonconserved region of highly variable length
intersperses the
2
domain of some house-
keeping sigmas. For E. coli
70
, this region has
been implicated in assisting dissociation of the
sigma factor to alleviate pausing during the
early stages of elongation (54).
The
70
family of proteins is divided into
subgroups based on phylogenic relations and
differential possession of the four conserved do-
mains (
2
,
3
,
4
, and region 1.1) (Figure 2a)
(reviewed in References 30 and 68). Group 1
comprises housekeeping sigmas that possess all
four domains, including the group-specic re-
gion 1.1, which is involved in autoinhibition of
DNA binding by free sigmas. Group 2 sigmas,
represented by the E. coli stationary/stress fac-
tor
38/S
, are related most closely to Group 1
but are dispensable for growth. Group 3 sig-
mas, which are more distantly related to Group
1 (e.g., E. coli
28/F/FliA
and
32/H
; B. subtilis
F
), also possess all three globular domains and
usually control regulons in response to devel-
opmental checkpoints or heat shock. The
3
domains of E. coli
28
and
32
interact with
composite extended 10/10 elements that ac-
count for the unusually long consensus recog-
nition elements of their cognate promoters (50,
51). The nal and most divergent group of sig-
mas is Group 4the extracytoplasmic function
(ECF) subfamily, so named because most re-
spond to signals arising from the extracytoplas-
mic environment (e.g., E. coli
24/E
and
FecI
).
Group 4 represents the most stripped-down
version of sigmas, possessing the only two key
sigma domains (
2
and
4
) that are structurally
conserved even among the most divergent fam-
ily members.
40

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
The
54
Family
This second class of sigma factors is uniquely
represented by orthologs of E. coli
54/N
, which
directs recognition of distinct promoter motifs
located at positions 24 and 12 relative to
the transcriptional start (Figure 2b). Although
initially identied for their role in nitrogen
assimilation,
54
proteins are widely distributed
in bacteria and are utilized in coordinating
many different physiological processes ranging
from utilization of alternative carbon sources,
through assembly of motility organs, to pro-
duction of extracellular alginate. Although
54
proteins need to perform many of the same
functions as other sigmas, they bear no primary
sequence similarity to
70
proteins and regulate
transcription by a different mechanism. A key
feature of
54
-RNAP that contrasts other
holoenzymes is its complete inability to spon-
taneously isomerize (melt) DNA to form open
promoter complexes. This step strictly re-
quires assistance from mechanotranscriptional
activators (also known as bacterial enhancer
binding proteins, or bEBPs) that utilize ATP
hydrolysis to drive conformational changes for
this transition (reviewed in Reference 78).
Genetic and biochemical data on the roles
of the three main subregions of
54
(regions
I to III, Figure 2b) have recently been aug-
mented by structural analysis and cryoelectron
microscopy reconstructions (12, 42). Region I
mediates weak contact with the 12 promoter
element and with core-RNAP such that it
occludes loading of promoter DNA into the
active site. The varying region II links regions I
and III, which makes the main contacts with the
24and12promoter elements andwithcore-
RNAP(Figure 2b). Activation by an obligatory
activator serves two functions. First, relocating
region I from an inhibitory conformation al-
lows entrance of the DNA. Second, facilitating
correct promoter DNA-
54
alignment allows
for open complex formation (12). Because of
the unique properties imparted by
54
(e.g., un-
usual promoter recognition, the ability to bind
DNAinthe absence of core-RNAP, and the ne-
cessity for ATP-utilizing mechanoactivators),
54
-dependent transcription is considered a
second paradigm of bacterial transcription.
Although the
54
and the
70
family members
lack sequence identity, they do bind overlap-
ping surfaces of core-RNAP, and performance
of
54
-RNAP is affected by the same mobile
modules of the core-RNAP - and
-subunits
that inuence
70
-dependent transcription,
albeit with different regulatory outcomes (21,
88). Hence,
54
is not exempt from funda-
mental regulatory mechanisms that involve
competitive association with core-RNAP.
ANTISIGMA FACTORS AND
THEIR ANTAGONISTS
Modulating the levels and/or activities of differ-
ent sigma factors, and consequently the levels
of cognate RNAPholoenzymes, provides a sim-
ple yet versatile means to control the basal-line
occupancy of distinct promoter classes. Mech-
anisms known to modulate the activities of sig-
mas are diverse and include phosphorylation-
activated binding to a partner protein that
tags the sigma for destruction (e.g., interac-
tion between the E. coli response regulator
RssB and
38
) (89), proteolytic cleavage of
inactive prosigmas to remove inhibitory N-
terminal extensions (e.g., B. subtilis pro
E
and
pro
K
) (41), and signal-cued use of alterna-
tive start codons to generate high-molecular-
weight variants that are vulnerable to rapid
proteolytic turnover (e.g., S. coelicolor
R
and
its Mycobacterium ortholog) (49). For some sig-
mas, protein levels are controlled at all steps of
gene expressionfromtranscription initiation,
through mRNAstability and control of transla-
tional efciency by small noncoding RNAs, to
signal-responsive proteolytic degradation (e.g.,
E. coli
38
and
32
) (31, 38). In many other cases,
however, the primary level of control involves
sequestering by antisigma factors to prevent
their association with core-RNAP. The follow-
ing sections provide an overviewof selected sig-
mas that illustrate different systems that control
the release of sigma factor activities when they
are needed.
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Coantisigma factor:
a factor that acts in
concert with a partner
to bind and sequester a
sigma factor and
thereby prevent
association with
core-RNAP
Counteracting Physicochemical
Assaults
The Group 4 ECF sigmas encompass 60% of
all sigma factors in bacteria (15) and are chiey
associatedwithcounteractingphysical or chem-
ical stresses or communicating the availability
of iron. A common feature of most ECFs is
that their activity is regulated by stoichiomet-
ric association with an antisigma factor, which
is usually coexpressed through transcriptional
coupling of the genes within an operon. This is
the case for E. coli ECF
24
, which controls re-
sponses to membrane stress and represents one
of the rare exceptions to the dispensable nature
of alternative sigma factors (23).
The
24
gene (rpoE) is cotranscribed
with those of its antisigma factor RseA and
its coantisigma factor RseB, which tightly
tether
24
to the membrane in an inactive state
(Figure 3a). The molecular details of the three-
compartment proteolytic cascade that governs
24
availability have previously been extensively
reviewed (4, 14, 36), so only anoverviewis given
here. The DegS serine protease is both the
molecular sensor of stress-induced misfolded
proteins within the periplasm and the initiator
of the RIP (regulated intramembrane proteol-
ysis) cascade that releases
24
. Activation of the
proteolytic activity of DegS results in cleavage
of the antisigma RseA within its periplasmic
region (site 1 cleavage), rendering it as a
substrate for the metalloprotease RseP, which
in turn processes RseA within its inner mem-
brane spanning region (site 2 cleavage). The
released cytoplamsic RseA/
24
subcomplex still
sequesters
24
but has an exposed tag for recog-
nition by the adaptor protein SspB that directs
the complex to ClpXP for nal processing to
free
24
for association with core-RNAP.
Similar RIPcascades likely control the avail-
ability of gram-negative
24
orthologs and
other ECFs such as
AlgU
, which is involved
in the production of alginate by Pseudomonas
aeruginosa with devastating consequences for
cystic brosis patients (reviewed in Reference
36). Likewise, although gram-positive bacte-
ria lack a periplasm and the mechanistic details
differ, a conceptually similar RIP cascade con-
trols the stress responses mediated by B. sub-
tilis
W
that is cotranscribed with its antisigma
RsiW(36). Sequestering of a sigma to the mem-
brane is an efcient means to couple availabil-
ity to extracellular signals or those that result
in alterations within the periplasmic compart-
ment. A few ECFs, however, govern responses
to intracellular stress and are consequently con-
trolled by cytoplasmic antisigma factors. This
is the case for the S. coelicolor
R
/RsrA (48) and
the Rhodobacter sphaeroides
E
/ChrR (6) systems
that control responses to damaging oxygen
species.
Irrespective of the cellular location, efcient
sequestering requires the sigma/antisigma in-
teractions to be tight and mask portions of
key interfaces usually involved in interacting
with core-RNAP (19). The cytoplasmic por-
tion of E. coli RseA has been estimated to bind
E
with 300-fold-higher afnity than core-
RNAP. Structural analysis has shown that se-
questering involves the N-terminal domain of
RseA, which sterically occludes the critical
2
and
4
domains of this ECF (18). Despite little
primary sequence homology, an analogous do-
main with a common fold within ChrRlikewise
exploits the same interfaces in its interactions
with
E
of R. sphaeroides (15). Bioinformatic
searches indicate that the common domain of
RseA and ChrR (ASD, antisigma domain) is
fused to diverse signaling domains in >30% of
all ECFs (i.e., 20%of all annotated sigma fac-
tor genes). Thus, manipulation of the geometry
of the critical
2
and
4
domains likely underlies
sequestering and release by cognate antisigma
factors in many systems.
Responses to Iron Limitation
In addition to stress responses, ECFs are also
frequently involved in processes that ensure
a sufciency of iron, which is often in lim-
ited environmental supply. For example, in
Pseudomonas putida, 13 of its 19 ECFs ap-
pear to be dedicated to this essential element
(61). This subgroup of ECFs is usually co-
transcribed with a cognate antisigma factor to
42

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Sequestered
P
P
P
a
b c
Cytoplasm
Inner
membrane
Inner
membrane
Periplasm
Outer
membrane
Outer
membrane
Stress
DegS
OmpC
RseB RseB
RseA
24/E
RseP
OmpC*
SspB
ClpXP
Available
PhyR
NepR
EcfG1
Sequestered
Stress
Available
Basal body
FlgM
Sequestered
28/FliA
Available
Hook
mimic
domain
1
2
3
Figure 3
Control of sigma factor availability by antisigma factors. (a) Schematic illustration of DegS/RseP RIP
(regulated intramembrane proteolysis) protease cascade (all blue elements) that releases
24/E
from
sequestration at the membrane by its antisigma factor RseA and coantisigma factor RseB. Activity of the RIP
cascade is triggered by stress that elicits misfolded proteins in the periplasm (such as OmpC
) to eventually
release a RseA/
24
subcomplex that is guided to the cytosolic ClpXP protease by SspB for nal trimming to
release
24
to compete for core RNA polymerase (core-RNAP). The sequential cleavage sites (1 to 3) within
RseA are indicated. (b) The antisigma factor NepR sequesters
ECfG1
within the cytoplasm until stress
signals result in the phosphorylation of the receiver domain of the anti-antisigma factor PhyR.
Phosphorylation of PhyR exposes a sigma mimic domain of PhyR that recruits and sequesters the antisigma
(NepR), thus leaving
ECfG1
free to associate with core-RNAP. (c) The antisigma factor FlgM likewise
sequesters
FliA
within the cytosol. However, in this instance, completion of the agella basal body allows
export of partially unstructured FlgM, resulting in a pool of available
28
ready for holoenzyme formation.
control expression of genes involved in the
uptake of iron-scavenging siderophoresrst
through an outer membrane siderophore trans-
porter and then from the periplasm to the cy-
tosol via an ABC-type transporter. The most
extensively studied siderophore signaling path-
way is that of the Fec system for ferric citrate
uptake in E. coli, which represents a paradigm
system for responses to a signal that can only
enter the cell through transport.
Signaling involves communication from
the cell surface siderophore transporter (FecA)
to the inner-membrane-anchored antisigma
factor (FecR), which sequesters
FecI
to the
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Anti-antisigma
factor: a factor that
antagonizes or
counteracts the activity
of an antisigma factor
cytoplasmic side of the inner membrane. Cell
surface binding of ferric citrate to the FecA
transporter triggers structural changes that
facilitate interaction between the N-proximal
portion of FecA and the C-terminal portion
of the antisigma FecR within the periplasm.
FecR then transmits the signal across the inner
membrane to its N-terminal portion to relieve
inhibition of
FecI
activity in the cytoplasm
compartment. The regions of FecA that are
involved in transducing signals arising from
siderophore transport are comparatively well
understood; however, the details of the mecha-
nisms that underlie the propagationof the ferric
citrate-bindingsignal tothe C-terminal portion
of FecR, and from there through FecR to affect
FecI
activity, remain an open question (14).
In some Fec-like systems the antisigma fac-
tor only has a negative effect on sigma activ-
ity and, upon receiving the activating signal,
may well simply release the sigma for asso-
ciation with core-RNAP, as is typical of an-
tisigma factors. However, for
FecI
/FecR and
some other related systems, activation through
the FecA transporter converts the antisigma
factor from a negative to a positive regulator
that stimulates the activity of the cognate sigma
factor (63 and references therein). In these
cases, the antisigma likely remains bound to the
sigma to achieve this outcome. Genetic analysis
with truncates and point mutations of
FecI
has
demonstrated that FecR sequesters
FecI
only
via interaction with its
4
domain, and that this
interaction is required for
FecI
to function as
a sigma factor (60). Sequestering solely via the
4
domain may be a reection of the relative
unimportance of the 35 element (that is usu-
ally bound by a
4
domain) for
FecI
-dependent
transcription (5). Rather than
FecI
release, sig-
naling to the cytoplasmic N terminus of FecR
stimulates
FecI
association with the
-subunit
of RNAP (59). Because portions of FecR,
FecI
,
and
stably interact simultaneously (59), and

activation via FecR also promotes novel pro-
moter interactions with DNA at +13 from
the transcriptional start site (5), the activation
model that emerges is one in which FecR re-
mains a functional part of the transcriptional
initiation complex. Tethering to the inner
membrane via FecR would not necessarily im-
pose a hindrance to transcriptional elongation
because the sigma factor is released during (or
shortly after) transcriptional initiation. How-
ever, it does pose the interesting conundrum
of how the
FecI
-RNAP holoenzyme locates a
target promoter from its restricted location.
Partner Switching and Sigma Factor
Mimicry Mechanisms
Bacillus species provide prime examples of
cascade production and compartmentalization
of sigma factors, as well as other paradigms
of how the activities of alternative sigmas
can be controlled. Both the
F
forespore
developmental program and the expression of
the
B
stress regulon of B. subtilis are governed
by analogous phosphorylation-dependent
partner switch mechanisms (reviewed in
References 35 and 41). In these systems,
switching between alternative binding partners
of the antisigma factorfrom the sigma factor
to an anti-antisigma factoris the critical
step that releases the sigma to perform its
function. The activity of
F
is regulated by
the serine kinase antisigma factor SpoIIAB and
the anti-antisigma factor SpoIIAA, which are
cotranscribed with the
F
gene (sigF) in the
spoIIA operon. Structural determinations have
highlighted the importance of the
3
domain of
F
for sequestration by its antisigma (SpoIIAB)
(16). Dimeric SpoIIAB binds asymmetrically
to a single molecule of
F
and occludes its
3
domain from interaction with core-RNAP.
As a result of the asymmetric binding, one of
the SpoIIAB protomers is more accessible for
binding to the anti-antisigma factor (SpoIIAA)
that, upon docking to SpoIIAB, displaces
F
to leave it free to associate with core-RNAP.
SpoIIAB then phosphorylates its new partner
SpoIIAA in a reaction that dissociates the
ADP-bound form of SpoIIAB, which in turn
associates with any unphosphorylated SpoIIAA
to form a complex that inhibits both the kinase
and antisigma activity of SpoIIAB (41, 62, and
references therein).
44

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Binding partner switching is also an in-
tegral component of the general stress re-
sponse in Alphaproteobacteria that lack an
E. coli
38
or B. subtilis
B
ortholog. However, in
these organisms, control involves the unusual
anti-antisigma PhyR, which has a C-terminal
response-regulator (RR) domain coupled to
an ECF-like domain. Upon phosphorylation,
Methylobacterium extorquens PhyR binds NepR,
an antisigma factor that normally sequesters
the ECF
EcfG1
(Figure 3b) (26). Although the
ECF-like domain of PhyR shares high homol-
ogy with
EcfG1
, it lacks critical residues that
would be involved in DNA binding (82) and
thus appears to serve as a pure mimic to en-
tice NepR away to free
EcfG1
to serve its du-
ties. A recent structure of Caulobacter crescen-
tus PhyR in its unphosphorylated state shows
predictable structures for its component parts.
However, extensive interactions between the
RR domain and the ECF domain (
2
linked to
4
) force the
2
and
4
modules into a compact
conformation that presumably prevents recog-
nition by NepR until PhyR is phosphorylated
(40). Based on the distinct structural compo-
nents, and the fact that the ECF domain alone
can act as an anti-antisigma, the authors pro-
pose that the RR domain can be considered as
an antianti-antisigma factor. The counterpart
sensor kinase(s) (or anti-antianti-antisigma fac-
tor) that would serve to phosphorylate PhyR,
and thus initiate the whole cascade, remains to
be identied. However, a variety of candidate
periplasmic or cytoplasmic sensor kinases are
encoded in the vicinity of phyR genes in differ-
ent organisms (81).
Checkpoint Coupling
to Organelle Biogenesis
Flagella are characteristically assembled in
a stepwise manner through temporally con-
trolled expression of their component parts.
The hierarchical expression of agella genes
can be achieved by diverse mechanisms but usu-
ally involves a master regulator that initiates the
cascade and coupling of late agella gene ex-
pression to completion of the hook basal body
structure to form a developmental checkpoint
(79). In most agellated bacteria, the key play-
ers in this developmental checkpoint are an an-
tisigma factor (FlgM) and a specic sigma fac-
tor (E. coli
FliA
, B. subtilis
D
) that is required
for transcription of genes encoding the agella
lament subunits and proteins involved in bac-
terial taxis. Upon completion of the hook basal
body structure, FlgM can be secreted through
the type III system housed within the basal
body, thus releasing
FliA
for association with
core-RNAP (Figure 3c). Hence, this mecha-
nism uses secretion as a signal that cues com-
pletion of a functional active structure to ensure
that lament and taxis proteins are expressed
only when appropriate (43).
NMR studies have established that FlgM
is intrinsically partially disordered, with only
the C-terminal half structured when in associ-
ation with
FliA
and under molecular crowding
conditions that would prevail in vivo (22, 24).
The naturally unfolded state of FlgM (com-
plete or partial) has been suggested to facili-
tate secretionof FlgMthroughthe narrowhook
basal body structure (22). Biochemical and ge-
netic evidence that implicates multiple regions
of
FliA
in its sequestration by the C-terminal
of FlgMhas beenreinforcedby crystallographic
data from the Aquifex aeolicus
FliA
/FlgM com-
plex, which shows a highly compact conforma-
tionof the
2
,
3
, and
4
domains of
FliA
, which
masks its DNA-binding and core-RNAP asso-
ciation determinants (80).
The FlgM and
FliA
genes are not encoded
within an operon, rather the levels of FlgM
are frequently under complex regulation that
includes (a) dual promoter control of the gM
gene, in which one promoter is
FliA
dependent
and thus provides an autorepressing feedback
circuitry; and (b) translational modulation of
FlgM protein levels, which adjusts the relative
FlgM:
FliA
ratios within the cell (reviewed in
Reference 79). Recently, mathematic modeling
and experimental rewiring of the gM and
iA gene promoters have provided strong
support for a previously proposed model
in which FlgM secretion, in addition to
enforcing the developmental checkpoint,
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
functions as a proxy-measuring system that
continually ne-tunes FlgM and
FliA
levels
to provide a sensing mechanism that may also
control agella numbers (77).
PROMOTION OF ALTERNATIVE
SIGMA FACTOR ACTIVITY
THROUGH SUBVERSION OF
70
Alternative Sigma Factors Are Not
Created Equal
As highlighted in Figure 1, active transcrip-
tion and the sigma cycle provide the means
for reconstituting alternative -RNAP holoen-
zymes. However, as exemplied by the nd-
ings in E. coli, alternative sigmas generally have
lower afnity for core-RNAP than the house-
keeping
70
, with the poorest (
38
) estimated
to be approximately 10-fold lower (57). More-
over, even when presented with conditions that
maximize the levels of active alternative sig-
mas, the cellular concentrations of alternative
sigmas are greatly exceeded by those of
70
(29, 72, 75). The levels of E. coli
70
and core-
RNAP are relatively constant over the growth
curve and under different growth conditions.
Although absolute values differ somewhat, the
number of
70
molecules is consistently esti-
mated to exceed that of core-RNAP by approx-
imately threefold (29, 72, 75). Because much of
the core-RNAP is employed in catalyzing RNA
synthesis, competition between sigma factors to
form a holoenzyme with the limited free core-
RNAP will be erce.
Many approaches, including articial ma-
nipulations of sigma factor levels and the use
of sigma factor mutants that are altered in
their afnity, and thus their competitiveness,
for core-RNAP, have clearly established that
sigma factor competition for core-RNAP lim-
its output from promoters dependent on al-
ternative sigmas such as
38
,
32
, and
54
(46,
53). This is likely the case for all alternative
sigmas, which raises the question of how low-
level and/or weak-afnity alternative sigma fac-
tors gain sufcient access to core-RNAP to
drive transcription from promoters under their
control. The following sections present evi-
dence that global regulatory subversion of the
household
70
to concomitantly enhance for-
mationof alternative -RNAPs provides at least
a partial solution to the problem.
The Bacterial Alarmone ppGpp
and Its Cohort DksA
The nucleotide ppGpp (also known as magic
spot) is the primary mediator of the stringent
response to amino acid starvation, where
translational capacity is balanced to reduced
demand through downregulation of transcrip-
tion from tRNA and rRNA operon promoters
(stringent
70
promoters). In addition to amino
acid starvation, iron, carbon, and nitrogen
limitations, as well as many environmental
physicochemical stresses that reduce growth
rate, cause induction of the intracellular levels
of ppGpp (73). The rapid elevation of ppGpp
levels during the hungry phase (just prior to the
transition between exponential and stationary
growth in rich media), or through articial
manipulation of ppGpp levels under normally
nonpermissive conditions, markedly enhances
output from many promoters dependent on
alternative sigmas (e.g., E. coli
38
,
32
,
24
, and
54
) (20, 28, 46, 53, 84). It is now evident that
ppGpp is the mediator of a far greater network
that holistically redirects the global transcrip-
tional capacity of the cell fromgenes for growth
toward those for adaptive survival responses
(32, 73).
Targeting of the -RNAP by ppGpp specif-
ically alters its performance at susceptible pro-
moters to either decrease (e.g., stringent
70
promoters) or increase (e.g., some
70
pro-
moters involved in amino acid transport or in
virulence, and some specic
24
- and
FliA
-
dependent promoters) their activities (2, 20,
47, 67, 70, 71). The exact location and lig-
anding residues for ppGpp within the ac-
tive site cleft of core-RNAP remain elusive
(86). Nevertheless, it appears clear that ppGpp
binding to RNAP lowers the energy required
for transition between intermediates in the
pathway leading to open-complex formation.
46

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Depending on the rate-limiting step and rel-
ative stabilities of consecutive intermediates,
lowering the energy required for conversion
from one intermediate to the next would fa-
vor either the reverse or forward reactions in
Figure 1b, leading to promoter-specic nega-
tive or positive outcomes (reviewed in Refer-
ence 33).
The in vivo and in vitro effects of ppGpp at
promoters are frequently amplied by DksA
a member of a family of regulators that binds
RNAP and accesses the active site through the
secondary channel. DksA mediates long-range
structural changes within RNAP that alter in-
teraction with the 6 to +6 region at
70
pro-
moters (11, 55, 76). Although it remains to be
experimentally tested in most cases, there is no
reason why DksA could not also affect the per-
formance of any -RNAP, although the con-
sequences might differ. DksA and ppGpp can
have mutually independent and sometimes op-
posing effects (1, 3, 75, and references therein);
however, DksA sensitizes RNAP to the cellular
levels of ppGpp to account for their common
coaction (70). In E. coli and P. putida, DksA lev-
els are relatively constant (9, 75); therefore, it
is the changing levels of ppGppthe herald
of stressthat instigate proactive promoter-
specic and global transcriptional responses
that allow the cell to prepare for tough times
ahead.
ppGpp and Sigma Factor Competition
As a global regulator, ppGpp by denition has
pleiotropic effects in vivo, and thus many dif-
ferent mechanisms frequently converge to ulti-
mately account for the total effect of ppGpp on
output from a given promoter. These include
promoter-specic effects onthe performance of
holoenzymes at kinetically susceptible promot-
ers (see above), which in turn can initiate ad-
ditional regulatory cascades through the gene
products they encode. However, these regula-
tory consequences cannot account for the full
effect of ppGpp in vivo. For example, ppGpp
aids stability of
S
through production of anti-
adaptors to result in higher cellular levels of
S
under stress conditions (reviewed in Reference
8). Nevertheless, a
S
promoter that is not de-
pendent directly onppGpp still requires ppGpp
for activity in vivo even when reduced
S
lev-
els are compensated for by ectopic expression
(46, 52). Likewise, although the levels of
54
are constant irrespective of the presence or ab-
sence of ppGpp and/or DksA, the activities of
54
promoters that are not enhanced directly by
either factor in vitro are still greatly stimulated
by the presence of these molecules invivo(9, 10,
53, 84). These ndings demand an alternative
explanation for the action of ppGpp.
In E. coli, elevated intracellular levels of
ppGpp result in decreased association of
70
and core-RNAP (but not decreased
70
lev-
els per se), so that less
70
-RNAP is avail-
able to occupy cognate
70
promoters (32, 39).
In addition, a proteomic approach has shown
that underproduction of
70
-RNAP essentially
mimics the stringent response (58). Separa-
tion and immunological detection of free and
core-RNAP-associated sigma has been used to
demonstrate that elevated ppGpp, which de-
creases
70
-RNAPlevels, concomitantly results
inincreased
38
-RNAPand
32
-RNAPholoen-
zyme levels (46). Although not experimentally
tested, this would be anticipated to also be
the case for other -RNAPs. These data, to-
gether with the nding that the requirement
for ppGpp to achieve efcient
38
- and
54
-
dependent transcriptioncanbe simply bypassed
using
70
mutants that are defective in their
ability to compete for binding to core-RNAP
(10, 46, 53, 84), make a convincing case for
the idea that ppGpp plays a determining role
in the outcome of sigma factor competition to
favor holoenzyme formation with alternative
sigmas.
Whereas the importance of ppGpp in vivo
is clear, it remains to be resolved if ppGpp
and/or DksA can actively alter sigma factor
competition, or if their effects occur indirectly
(passively) through
70
-dependent transcrip-
tion. An active role has been suggested based
on the observation that ppGpp enhanced tran-
scription from a
32
-dependent promoter only
under conditions of competition with
70
in
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
vitro (46). However, such stimulation was not
found in similar experiments with
54
in com-
petition with
70
, neither in the presence nor
in the absence of ppGpp and/or DksA (10, 53,
83). In addition to altering sigma factor compe-
tition,
70
- and core-RNAP - and
-bypass
mutants also functionally mimic the action of
ppGpp and DksA by further destabilizing the
notoriously unstable open complexes of rRNA
operon promoters (7, 83). The latter property
suggests a passive mechanism by which these
regulatory molecules could alter sigma factor
competition.
A unifying model has been proposed that
would explain the properties of bypass mutants
and enhanced performance by any alternative
sigma in the presence of ppGpp (10, 83). This
model, like many before it, invokes passive
regulation through the consequences of the
negative action of ppGpp and DksA at the
seven powerful stringent
70
-rRNA operon
promoters. In E. coli, the activities of these
70
promoters sequester approximately 60%70%
of the transcriptional machinery during rapid
growth in rich media (13). Under these con-
ditions, where ppGpp levels are low, much of
the core-RNAP is occupied in catalysis of the
transcripts from these powerful promoters,
leaving little available for association with any
sigma factor. This would lead to low levels
of alternative holoenzymes and consequent
low occupancy and output from promoters
under their control. Under slow growth and/or
stress conditions that elicit high levels of
ppGpp, however, the potent downregulation
of transcription from the
70
-rRNA operon
promoters would lead to increased levels of
core-RNAP available for holoenzyme forma-
tion. As a consequence, alternative -RNAP
levels would increase even in the absence of
a change in sigma levels, leading to enhanced
promoter output from cognate promoters.
Within this model, decreased
70
availability
and
70
-RNAP mutants would mimic high lev-
els of ppGppby reducing transcriptionfromthe
powerful stringent
70
-rRNA operon promot-
ers and by altering core-RNAP to sigma factor
association to favor alternative holoenzyme
formation. A prediction from this model is that
low-afnity promoters that have holoenzyme
binding as a rate-limiting step would be more
susceptible to loss of these regulatory molecules
than high-afnity counterpartsa prediction
that has been experimentally veried to be the
case for
54
-dependent transcription (9, 10).
Modulation of Sigma Factor Usage
Through Diversion of
70
The model outlined above does not exclude,
nor is it incompatible with, the possible exis-
tence of unknown factor(s) that may addition-
ally contribute to the in vivo requirement for
ppGpp and DksA. Analogous to the discovery
of the role of DksA in ppGpp-mediated reg-
ulation, it cannot be ruled out that some other
protein(s) may facilitate ppGpp-mediated regu-
lation of alternative -RNAPs or aid their for-
mation in vivo. On the contrary, the ppGpp-
triggered reduction of
70
-RNAP levels (but
not those of
70
itself ) demands that
70
is
diverted to prevent its association with core-
RNAP. The answer to how this is achieved is
not currently fully understood. However, as de-
scribed below, the Rsd (regulator of sigma D)
protein is likely a major contributor, and fac-
tors such as the Crl protein are also potentially
involved.
Rsd was initially identied through a search
for factors that might allow alternative sigma
factors to compete for limiting core-RNAP in
E. coli (45). By forming 1:1 complexes with
70
,
Rsd specically sequesters free
70
and can also
actively remove
70
from
70
-RNAP in vitro
(44, 87). Biochemical and genetic studies of Rsd
and its AlgQ homolog have shown that these
proteins sequester
70
primarily through in-
teractions with the
4
domain (which contacts
35 elements), although other contact points
with
70
-RNAP are also involved (25, 44).
Structural studies of Rsd in complex with
4
of
70
have revealed that Rsd binding occludes
residues critical for
4
/core-RNA interactions
(69). By binding
70
and occluding association
with core-RNAP, Rsd falls under the denition
of an antisigma factor. However, this denition
48

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
seems inappropriate because Rsd can be vastly
overexpressed without compromising growth.
Transcription of the Rsd gene is directed
by the activities of two promoters, and is par-
tially under ppGpp control, leading to ele-
vated levels of Rsd when competition for core-
RNAPwould be at its highest (45, 72). The idea
that Rsd might facilitate formation of alterna-
tive holoenzymes via reducing the availability
of
70
has been spurred by the ndings that
overexpression of Rsd results in increased out-
put from some
54
-,
38
-, and
32
-dependent
promoters (46, 53, 64), and because addition
of Rsd can facilitate sigma factor exchange in
vitro (L. Holmfeld & V. Shingler, unpublished
data). Consistent with the idea that Rsd could
facilitate access of alternative sigmas to core-
RNAP, the naturally elevated levels of Rsd in
stationary-phase E. coli sequester a signicant
portion (25%) of
70
(72). However, it should
be emphasized that Rsd null mutants have min-
imal effects on
38
- and
54
-dependent pro-
moter outputs that are enhanced by overexpres-
sion of Rsd (9, 64), suggesting that Rsd does
not act alone to bring about these regulatory
events. An intriguing nding from structural
studies of the Rsd/
4
complex is that a network
of interactions connects the binding interface
with other potential binding cavities located on
the surface of Rsd. Although some of these in-
teractions may be involved in recognition of
70
-RNAP, this observation raises the possibil-
ity of functional coupling of Rsd/
70
binding
with binding of some as yet unknown protein
and/or small regulatory molecule (69). If this is
indeed the case, identication of such an entity
would surely further our understanding of the
physiological role of Rsd.
The E. coli Crl protein binds
38
and pref-
erentially favors
38
in competition with
70
for core-RNAP, presumably by facilitating
38
-
RNAPholoenzyme formation(27, 85). The Crl
protein is restricted in its genome distribution
and the global regulatory effect of Crl is lim-
ited to promoters of the
38
regulon (85). This
makes it unlikely that Crl has any signicant
effects on the levels of other -RNAP holoen-
zymes. Nevertheless, it does pose an alternative
scenario to specic
70
sequestration to at least
partially account for reciprocal alterations in
70
-RNAP versus alternative -RNAP holoen-
zyme levels. Given the large number of genes of
unknown function in E. coli and other bacteria,
it is certainly plausible that analogous facilita-
tors of other alternative holoenzymes exist but
have eluded detection.
CONCLUSIONS
Regulation of alternative sigma factor activity is
usually complex, with multiple tiers of control
toregulate boththeir expressionlevels andtheir
activities. One major mechanism is sequester-
ing by an antisigma factor, which provides sys-
tems for signal-specic control of sigma fac-
tor availability and thus the activity of promot-
ers they regulate. Where known in any depth,
these systems are exquisitely attunedtoboththe
type of signal (i.e., the compartment fromwhich
the signal arises) and the constraints imposed by
the nature of the signal (e.g., the need for iron
transport into the cell). However, for many al-
ternative sigmas, particularly those of the ex-
tensive ECF Group 4 family, only a few have
beenstudied inany detail. Inmany cases neither
the signal nor the factor(s) that controls their
activity is known, which severely curtails un-
derstanding their role in microbial physiology.
Given the novel mechanisms that have recently
been identied by studying new members of
this familysuch as the use of alternative start
codons to generate proteolytically vulnerable
variants of S. coelicolor
R
(49) and molecu-
lar mimicry of
EcfG1
in Alphaproteobacteria
(26)it is not unreasonable to expect the reper-
toire of mechanisms that can control sigma fac-
tor availability to continue to expand.
Sequestering by an antisigma factor both
protects the sigma factor from proteolytic at-
tack and provides immediate availability upon
demand. Genetic and structural studies of
sigma/antisigma interactions have identied
repeated themes within sequestering mecha-
nisms, namely manipulation of the geometry
of the key globular sigma domains (
2
,
3
,
and/or
4
) to mask critical regions involved in
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
interaction with core-RNAP and promoter
DNA. Likewise, similar studies have also
started to unravel and test models of how
antisigma/anti-antisigma interactions break
these interactions to free sigmas to perform
their function.
In addition to dedicated signaling pathways,
the activities of many E. coli alternative sigma
factors can be coordinately stimulated by the
global regulator ppGpp, and this is likely to also
be the case in other organisms. The adoption
of ppGpp to stimulate the activities of alterna-
tive sigmas is perhaps not surprising because
stresses that elicit ppGpp synthesis overlap
greatly with those that cue the need for alter-
native sigmas. Much evidence has accumulated
that this stimulatory effect occurs througha role
of ppGpp in determining the outcome of sigma
factor competition for limiting core-RNAP
to holistically favor association of alternative
sigmas over
70
. However, much remains to be
learned about how this is brought about.
SUMMARY POINTS
1. The transcription cycle provides the means to rapidly strip off the sigma factor to gen-
erate naked core-RNAP ready for reprogramming by any available sigma. However, the
activities and availability of most sigma factors are intricately controlled.
2. Antisigma factors manipulate the geometry of key regions of sigma factors to prevent
their interaction with core-RNAP. Cognate dedicated signal transduction pathways that
release the activities of sigma factors present a dazzling array of mechanismsfrom
sophisticated protease cascades, through sigma factor mimicry and partner switching, to
the conceptually simple but elegant solution of secretion of an antisigma factor to link
activity to organelle biogenesis.
3. When free to interact with core-RNAP, all alternative sigma factors must compete
ercely with
70
(and each other) for a limited amount of core-RNAP in order to direct
transcription from the promoters they control.
4. Alternative sigma factors are aided in their battle against
70
by the alarmone ppGpp
through mechanisms that divert
70
or otherwise counteract its association with
core-RNAP.
FUTURE ISSUES
1. Has the repertoire of mechanisms that can control the availability of alternative sigma
factors reached its limit, or are there future surprises ahead?
2. Do ppGpp and DksA affect transcription mediated by all -RNAP holoenzymes?
3. Does the effect of ppGpp and DksAon sigma factor competition operate purely passively,
or is there an active component involved?
4. How is the dominating
70
subdued to allow alternative sigma factors sufcient access to
limitedcore-RNAP? Is Rsdthe only answer, or doother
70
sequesters exist? Does Rsdact
in concert with a coregulator and/or with Crl-like facilitators of alternative holoenzyme
formation?
50

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
DISCLOSURE STATEMENT
The authors are not aware of any afliations, memberships, funding, or nancial holdings that
might be perceived as affecting the objectivity of this review.
ACKNOWLEDGMENTS
Apologies are due to all researchers whose original contributions could not be cited due to space
limitations. Our work is supported by the Swedish Research Council (grant number 621-2008-
3557 to V.S.) and the European Molecular Biology Organization through a Long Term Research
Fellowship (grant number 540-2009 to T. del P.-S.).
LITERATURE CITED
1.

Aberg A, Fernandez-Vazquez J, Cabrer-Panes JD, Sanchez A, Balsalobre C. 2009. Similar and divergent
effects of ppGpp and DksA deciencies on transcription in Escherichia coli. J. Bacteriol. 191:322636
2.

Aberg A, Shingler V, Balsalobre C. 2006. (p)ppGpp regulates type 1 mbriation of Escherichia coli by
modulating the expression of the site-specic recombinase FimB. Mol. Microbiol. 60:152033
3.

Aberg A, Shingler V, Balsalobre C. 2008. Regulation of the mB promoter: a case of differential regulation
by ppGpp and DksA in vivo. Mol. Microbiol. 67:122341
4. Ades SE. 2008. Regulation by destruction: design of the
E
envelope stress response. Curr. Opin. Microbiol.
11:53540
5. Angerer A, Enz S, Ochs M, Braun V. 1995. Transcriptional regulation of ferric citrate transport in
Escherichia coli K-12. Fecl belongs to a new subfamily of sigma 70-type factors that respond to extracyto-
plasmic stimuli. Mol. Microbiol. 18:16374
6. Anthony JR, Newman JD, Donohue TJ. 2004. Interactions between the Rhodobacter sphaeroides ECF sigma
factor,
E
, and its anti-sigma factor, ChrR. J. Mol. Biol. 341:34560
7. Barker MM, Gaal T, Gourse RL. 2001. Mechanism of regulation of transcription initiation by ppGpp.
II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J. Mol.
Biol. 305:689702
8. Battesti A, Majdalani N, Gottesman S. 2011. The RpoS-mediated general stress response in Escherichia
coli. Annu. Rev. Microbiol. 65:189213
9. Bernardo LM, Johansson LU, Sk arfstad E, Shingler V. 2009.
54
-Promoter discrimination and regulation
by ppGpp and DksA. J. Biol. Chem. 284:82838
10. Bernardo LM, Johansson LU, Solera D, Sk arfstad E, Shingler V. 2006. The guanosine tetraphosphate
(ppGpp) alarmone, DksA and promoter afnity for RNA polymerase in regulation of
54
-dependent
transcription. Mol. Microbiol. 60:74964
11. Blankschien MD, Lee JH, Grace ED, Lennon CW, Halliday JA, et al. 2009. Super DksAs: substitutions
in DksA enhancing its effects on transcription initiation. EMBO J. 28:172031
12. Bose D, Pape T, Burrows PC, Rappas M, Wigneshweraraj SR, et al. 2008. Organization of an activator-
bound RNA polymerase holoenzyme. Mol. Cell 32:33746
13. Bremer H, Dennis PP. 1996. Modulation of chemical composition and other parameters of the cell by
growth rate. In Escherichia coli and Salmonella: Cellular and Molecular Biology, ed. FC Neidhardt, RI
Curtis, JL Ingraham, ECC Lin, KB Low, et al., 2:155369. Washington, DC: ASM Press
14. Brooks BE, Buchanan SK. 2008. Signaling mechanisms for activation of extracytoplasmic function (ECF)
sigma factors. Biochim. Biophys. Acta 1778:193045
15. Campbell EA, Greenwell R, Anthony JR, Wang S, Lim L, et al. 2007. A conserved structural module
regulates transcriptional responses to diverse stress signals in bacteria. Mol. Cell 27:793805
16. Campbell EA, Masuda S, Sun JL, Muzzin O, Olson CA, et al. 2002. Crystal structure of the Bacillus
stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor
F
. Cell 108:795807
17. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, et al. 2002. Structure of the bacterial RNA
polymerase promoter specicity subunit. Mol. Cell 9:52739
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
18. Campbell EA, Tupy JL, Gruber TM, Wang S, Sharp MM, et al. 2003. Crystal structure of Escherichia coli
E
with the cytoplasmic domain of its anti-sigma RseA. Mol. Cell 11:106778
19. Brings together and
highlights the structural
means by which
antisigmas operate to
mask key determinants
of sigmas.
19. Campbell EA, Westblade LF, Darst SA. 2008. Regulation of bacterial RNA polymerase factor
activity: a structural perspective. Curr. Opin. Microbiol. 11:12127
20. Costanzo A, Nicoloff H, Barchinger SE, Banta AB, Gourse RL, Ades SE. 2008. ppGpp and DksA likely
regulate the activity of the extracytoplasmic stress factor
E
in Escherichia coli by both direct and indirect
mechanisms. Mol. Microbiol. 67:61932
21. Datwyler SA, Meares CF. 2000. Protein-protein interactions mapped by articial proteases: where sigma
factors bind to RNA polymerase. Trends Biochem. Sci. 25:40814
22. Daughdrill GW, Chadsey MS, Karlinsey JE, Hughes KT, Dahlquist FW. 1997. The C-terminal half of
the anti-sigma factor, FlgM, becomes structured when bound to its target,
28
. Nat. Struct. Biol. 4:28591
23. De Las Penas A, Connolly L, Gross CA. 1997.
E
is an essential sigma factor in Escherichia coli. J. Bacteriol.
179:686264
24. Dedmon MM, Patel CN, Young GB, Pielak GJ. 2002. FlgM gains structure in living cells. Proc. Natl.
Acad. Sci. USA 99:1268184
25. Dove SL, Hochschild A. 2001. Bacterial two-hybrid analysis of interactions between region 4 of the
70
subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from
Pseudomonas aeruginosa. J. Bacteriol. 183:641321
26. A conceptually new
way to entice an
antisigma from its
target sigma.
26. Francez-Charlot A, Frunzke J, Reichen C, Ebneter JZ, Gourion B, Vorholt JA. 2009. Sigma factor
mimicry involved in regulation of general stress response. Proc. Natl. Acad. Sci. USA 106:346772
27. Gaal T, Mandel MJ, Silhavy TJ, Gourse RL. 2006. Crl facilitates RNApolymerase holoenzyme formation.
J. Bacteriol. 188:796670
28. Gentry DR, Hernandez VJ, Nguyen LH, Jensen DB, Cashel M. 1993. Synthesis of the stationary-phase
sigma factor
S
is positively regulated by ppGpp. J. Bacteriol. 175:798289
29. Grigorova IL, Phleger NJ, Mutalik VK, Gross CA. 2006. Insights into transcriptional regulation and
sigma competition from an equilibrium model of RNA polymerase binding to DNA. Proc. Natl. Acad. Sci.
USA 103:533237
30. Gruber TM, Gross CA. 2003. Multiple sigma subunits and the partitioning of bacterial transcription
space. Annu. Rev. Microbiol. 57:44166
31. Guisbert E, Yura T, Rhodius VA, Gross CA. 2008. Convergence of molecular, modeling, and systems
approaches for an understanding of the Escherichia coli heat shock response. Microbiol. Mol. Biol. Rev.
72:54554
32. An elegant approach
to address the difcult
problem of determining
the relative proportions
of free versus
DNA-bound -RNAP.
32. Gummesson B, Magnusson LU, Lovmar M, Kvint K, Persson O, et al. 2009. Increased RNA
polymerase availability directs resources towards growth at the expense of maintenance. EMBO
J. 28:220919
33. Haugen SP, Ross W, Gourse RL. 2008. Advances in bacterial promoter recognition and its control by
factors that do not bind DNA. Nat. Rev. Microbiol. 6:50719
34. Claries the identity
of a previously
unappreciated promoter
recognition element
that can be exploited to
regulate promoter
output.
34. Haugen SP, Ross W, Manrique M, Gourse RL. 2008. Fine structure of the promoter- region
1.2 interaction. Proc. Natl. Acad. Sci. USA 105:329297
35. Hecker M, Pane-Farre J, Volker U. 2007. SigB-dependent general stress response in Bacillus subtilis and
related Gram-positive bacteria. Annu. Rev. Microbiol. 61:21536
36. Heinrich J, Wiegert T. 2009. Regulated intramembrane proteolysis in the control of extracytoplasmic
function sigma factors. Res. Microbiol. 160:696703
37. Helmann JD. 2002. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46:47110
38. Hengge R. 2009. Proteolysis of
S
(RpoS) and the general stress response in Escherichia coli. Res. Microbiol.
160:66776
39. Hernandez VJ, Cashel M. 1995. Changes in conserved region 3 of Escherichia coli
70
mediate ppGpp-
dependent functions in vivo. J. Mol. Biol. 252:53649
40. Herrou J, Foreman R, Fiebig A, Crosson S. 2010. A structural model of anti-anti-sigma inhibition by a
two-component receiver domain: the PhyR stress response regulator. Mol. Microbiol. 78:290304
41. Hilbert DW, Piggot PJ. 2004. Compartmentalization of gene expression during Bacillus subtilis spore
formation. Microbiol. Mol. Biol. Rev. 68:23462
52

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
42. Hong E, Doucleff M, Wemmer DE. 2009. Structure of the RNA polymerase core-binding domain of
54
reveals a likely conformational fracture point. J. Mol. Biol. 390:7082
43. Hughes KT, Gillen KL, Semon MJ, Karlinsey JE. 1993. Sensing structural intermediates in bacterial
agellar assembly by export of a negative regulator. Science 262:127780
44. Ilag LL, Westblade LF, Deshayes C, Kolb A, Busby SJ, Robinson CV. 2004. Mass spectrometry of
Escherichia coli RNA polymerase: interactions of the core enzyme with
70
and Rsd protein. Structure
12:26975
45. Jishage M, Ishihama A. 1998. A stationary phase protein in Escherichia coli with binding activity to the
major sigma subunit of RNA polymerase. Proc. Natl. Acad. Sci. USA 95:495358
46. First extensive
compilation of evidence
that ppGpp plays a
determining role to
favor holoenzyme
formation with
alternative s (see also
Reference 53).
46. Jishage M, Kvint K, Shingler V, Nystr om T. 2002. Regulation of sigma factor competition by the
alarmone ppGpp. Genes Dev. 16:126070
47. Johansson LUM, Solera D, Bernardo LB, Moscoso JA, Shingler V. 2008.
54
-RNA polymerase controls
70
-dependent transcription from a non-overlapping divergent promoter. Mol. Microbiol. 70:70923
48. Kang JG, Paget MS, Seok YJ, Hahn MY, Bae JB, et al. 1999. RsrA, an anti-sigma factor regulated by
redox change. EMBO J. 18:429298
49. A conceptually new
way to control sigma
factor activity, with new
insights into regulator
system dynamics.
49. Kim MS, Hahn MY, Cho Y, Cho SN, Roe JH. 2009. Positive and negative feedback regulatory
loops of thiol-oxidative stress response mediated by an unstable isoform of
R
in actinomycetes.
Mol. Microbiol. 73:81525
50. Koo BM, Rhodius VA, Campbell EA, Gross CA. 2009. Dissection of recognition determinants of Es-
cherichia coli
32
suggests a composite 10 region with an extended 10 motif and a core 10 element.
Mol. Microbiol. 72:81529
51. Koo BM, Rhodius VA, Campbell EA, Gross CA. 2009. Mutational analysis of Escherichia coli
28
and its
target promoters reveals recognition of a composite 10 region, comprised of an extended 10 motif
and a core 10 element. Mol. Microbiol. 72:83043
52. Kvint K, Farewell A, Nystr om T. 2000. RpoS-dependent promoters require guanosine tetraphosphate
for induction even in the presence of high levels of
S
. J. Biol. Chem. 275:1479598
53. First extensive
compilation of evidence
that ppGpp plays a
determining role to
favor holoenzyme
formation with
alternative sigmas (see
also Reference 46).
53. Laurie AD, Bernardo LM, Sze CC, Sk arfstad E, Szalewska-Palasz A, et al. 2003. The role of the
alarmone (p)ppGpp in
54
competition for core RNA polymerase. J. Biol. Chem. 278:1494503
54. Leibman M, Hochschild A. 2007. A-core interaction of the RNApolymerase holoenzyme that enhances
promoter escape. EMBO J. 26:157990
55. Lennon CW, Gaal T, Ross W, Gourse RL. 2009. Escherichia coli DksA binds to free RNA polymerase
with higher afnity than to RNA polymerase in an open complex. J. Bacteriol. 191:585458
56. Lisser S, Margalit H. 1993. Compilation of E. coli mRNA promoter sequences. Nucleic Acids Res. 21:1507
16
57. Maeda H, Fujita N, Ishihama A. 2000. Competition among seven Escherichia coli sigma subunits: relative
binding afnities to the core RNA polymerase. Nucleic Acids Res. 28:3497503
58. Magnusson LU, Nystr om T, Farewell A. 2003. Underproduction of
70
mimics a stringent response. A
proteome approach. J. Biol. Chem. 278:96873
59. Mahren S, Braun V. 2003. The FecI extracytoplasmic-function sigma factor of Escherichia coli interacts
with the
subunit of RNA polymerase. J. Bacteriol. 185:1796802

60. Mahren S, Enz S, Braun V. 2002. Functional interaction of region 4 of the extracytoplasmic function
sigma factor FecI with the cytoplasmic portion of the FecR transmembrane protein of the Escherichia coli
ferric citrate transport system. J. Bacteriol. 184:370411
61. Martinez-Bueno MA, Tobes R, Rey M, Ramos JL. 2002. Detection of multiple extracytoplasmic function
(ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas
aeruginosa PA01. Environ. Microbiol. 4:84255
62. Masuda S, Murakami KS, Wang S, Anders Olson C, Donigian J, et al. 2004. Crystal structures of the ADP
and ATP bound forms of the Bacillus anti- factor SpoIIAB in complex with the anti-anti- SpoIIAA.
J. Mol. Biol. 340:94156
63. Mettrick KA, Lamont IL. 2009. Different roles for anti-sigma factors in siderophore signalling pathways
of Pseudomonas aeruginosa. Mol. Microbiol. 74:125771
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
64. Mitchell JE, Oshima T, Piper SE, Webster CL, Westblade LF, et al. 2007. The Escherichia coli regulator
of sigma 70 protein, Rsd, can up-regulate some stress-dependent promoters by sequestering sigma 70.
J. Bacteriol. 189:348995
65. Mooney RA, Darst SA, Landick R. 2005. Sigma and RNApolymerase: an on-again, off-again relationship?
Mol. Cell 20:33545
66. Murakami KS, Darst SA. 2003. Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol.
13:3139
67.

Osterberg S, Sk arfstad E, Shingler V. 2010. The sigma-factor FliA, ppGpp and DksA coordinate tran-
scriptional control of the aer2 gene of Pseudomonas putida. Environ. Microbiol. 12:143951
68. Paget MS, Helmann JD. 2003. The sigma70 family of sigma factors. Genome Biol. 4:203
69. Patikoglou GA, Westblade LF, Campbell EA, Lamour V, Lane WJ, Darst SA. 2007. Crystal structure of
the Escherichia coli regulator of
70
, Rsd, in complex with
70
domain 4. J. Mol. Biol. 372:64959
70. The advent of
understanding the role
of DksA, especially its
role in ppGpp-mediated
regulation.
70. Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, et al. 2004. DksA: a critical component
of the transcription initiation machinery that potentiates the regulation of rRNA promoters by
ppGpp and the initiating NTP. Cell 118:31122
71. Paul BJ, Berkmen MB, Gourse RL. 2005. DksA potentiates direct activation of amino acid promoters by
ppGpp. Proc. Natl. Acad. Sci. USA 102:782328
72. Piper SE, Mitchell JE, Lee DJ, Busby SJ. 2009. A global view of Escherichia coli Rsd protein and its
interactions. Mol. Biosyst. 5:194347
73. Potrykus K, Cashel M. 2008. (p)ppGpp: still magical? Annu. Rev. Microbiol. 62:3551
74. Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ. 2005. Holoenzyme switching and stochastic release
of sigma factors from RNA polymerase in vivo. Mol. Cell 20:35766
75. Rutherford ST, Lemke JJ, Vrentas CE, Gaal T, Ross W, Gourse RL. 2007. Effects of DksA, GreA,
and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary
channel of RNA polymerase. J. Mol. Biol. 366:124357
76. Rutherford ST, Villers CL, Lee JH, Ross W, Gourse RL. 2009. Allosteric control of Escherichia coli rRNA
promoter complexes by DksA. Genes Dev. 23:23648
77. Saini S, Floess E, Aldridge C, Brown J, Aldridge PD, Rao CV. 2011. Continuous control of agellar gene
expression by the
28
-FlgM regulatory circuit in Salmonella enterica. Mol. Microbiol. 79:26478
78. Shingler V. 2010. Signal sensory systems that impact
54
-dependent transcription. FEMS Microbiol. Rev.
35:42540
79. Smith TG, Hoover TR. 2009. Deciphering bacterial agellar gene regulatory networks in the genomic
era. Adv. Appl. Microbiol. 67:25795
80. Sorenson MK, Ray SS, Darst SA. 2004. Crystal structure of the agellar /anti- complex
28
/FlgM
reveals an intact factor in an inactive conformation. Mol. Cell 14:12738
81. Staron A, Mascher T. 2010. General stress response in -proteobacteria: PhyRand beyond. Mol. Microbiol.
78:27177
82. Staron A, Soa HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T. 2009. The third pillar of bacterial
signal transduction: classication of the extracytoplasmic function (ECF) sigma factor protein family. Mol.
Microbiol. 74:55781
83. Szalewska-Palasz A, Johansson LU, Bernardo LM, Sk arfstad E, Stec E, et al. 2007. Properties of RNA
polymerase bypass mutants: implications for the role of ppGpp and its co-factor DksA in controlling
transcription dependent on
54
. J. Biol. Chem. 282:1804656
84. Sze CC, Shingler V. 1999. The alarmone (p)ppGpp mediates physiological-responsive control at the
54
-dependent Po promoter. Mol. Microbiol. 31:121728
85. Typas A, Barembruch C, Possling A, Hengge R. 2007. Stationary phase reorganisation of the Escherichia
coli transcription machinery by Crl protein, a ne-tuner of
S
activity and levels. EMBO J. 26:156978
86. Vrentas CE, Gaal T, BerkmenMB, RutherfordST, HaugenSP, et al. 2008. Still looking for the magic spot:
the crystallographically dened binding site for ppGpp on RNA polymerase is unlikely to be responsible
for rRNA transcription regulation. J. Mol. Biol. 377:55164
87. Westblade LF, Ilag LL, Powell AK, Kolb A, Robinson CV, Busby SJ. 2004. Studies of the Escherichia coli
Rsd-sigma70 complex. J. Mol. Biol. 335:68592
54

Osterberg
del Peso-Santos
Shingler
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
88. Wigneshweraraj SR, Fujita N, Ishihama A, Buck M. 2000. Conservation of sigma-core RNA polymerase
proximity relationships betweenthe enhancer-independent andenhancer-dependent sigma classes. EMBO
J. 19:303848
89. Zhou Y, Gottesman S, Hoskins JR, Maurizi MR, Wickner S. 2001. The RssB response regulator directly
targets
S
for degradation by ClpXP. Genes Dev. 15:62737
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
MI65-Frontmatter ARI 11 August 2011 7:34
Annual Review of
Microbiology
Volume 65, 2011 Contents
To the Happy Few
Hiroshi Nikaido p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 1
Regulation of DnaA Assembly and Activity: Taking Directions from
the Genome
Alan C. Leonard and Julia E. Grimwade p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 19
Regulation of Alternative Sigma Factor Use
Soa

Osterberg, Teresa del Peso-Santos, and Victoria Shingler p p p p p p p p p p p p p p p p p p p p p p p p p p p p 37
Fungal Protein Production: Design and Production
of Chimeric Proteins
Peter J. Punt, Anthony Levasseur, Hans Visser, Jan Wery, and Eric Record p p p p p p p p p p p p p 57
Structure and Function of MARTX Toxins and Other Large
Repetitive RTX Proteins
Karla J.F. Satchell p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 71
Eukaryotic Picoplankton in Surface Oceans
Ramon Massana p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 91
Life on the Outside: The Rescue of Coxiella burnetii from Its Host Cell
Anders Omsland and Robert A. Heinzen p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 111
Molecular Mechanisms of Staphylococcus aureus Iron Acquisition
Neal D. Hammer and Eric P. Skaar p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 129
Protein Quality Control in the Bacterial Periplasm
Melisa Merdanovic, Tim Clausen, Markus Kaiser, Robert Huber,
and Michael Ehrmann p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 149
Prospects for the Future Using Genomics and Proteomics
in Clinical Microbiology
Pierre-Edouard Fournier and Didier Raoult p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 169
The RpoS-Mediated General Stress Response in Escherichia coli
Aurelia Battesti, Nadim Majdalani, and Susan Gottesman p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 189
Bacterial Osmoregulation: A Paradigm for the Study
of Cellular Homeostasis
Janet M. Wood p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 215
vi
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Lipoprotein Sorting in Bacteria
Suguru Okuda and Hajime Tokuda p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 239
Ligand-Binding PAS Domains in a Genomic, Cellular,
and Structural Context
Jonathan T. Henry and Sean Crosson p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 261
How Viruses and Toxins Disassemble to Enter Host Cells
Takamasa Inoue, Paul Moore, and Billy Tsai p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 287
Turning Hepatitis C into a Real Virus
Catherine L. Murray and Charles M. Rice p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 307
Recombination and DNA Repair in Helicobacter pylori
Marion S. Dorer, Tate H. Sessler, and Nina R. Salama p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 329
Kin Discrimination and Cooperation in Microbes
Joan E. Strassmann, Owen M. Gilbert, and David C. Queller p p p p p p p p p p p p p p p p p p p p p p p p p p 349
Dinoagellate Genome Evolution
Jennifer H. Wisecaver and Jeremiah D. Hackett p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 369
Motility and Chemotaxis in Campylobacter and Helicobacter
Paphavee Lertsethtakarn, Karen M. Ottemann, and David R. Hendrixson p p p p p p p p p p p p 389
The Human Gut Microbiome: Ecology and Recent
Evolutionary Changes
Jens Walter and Ruth Ley p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 411
Approaches to Capturing and Designing Biologically Active Small
Molecules Produced by Uncultured Microbes
J orn Piel p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 431
Epidemiological Expansion, Structural Studies, and Clinical
Challenges of New -Lactamases from Gram-Negative Bacteria
Karen Bush and Jed F. Fisher p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 455
Gene Regulation in Borrelia burgdorferi
D. Scott Samuels p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 479
Biology of Clostridium difcile: Implications for Epidemiology
and Diagnosis
Karen C. Carroll and John G. Bartlett p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 501
Interactions of the Human Pathogenic Brucella Species
with Their Hosts
Vidya L. Atluri, Mariana N. Xavier, Maarten F. de Jong,
Andreas B. den Hartigh, and Ren ee M. Tsolis p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 523
Contents vii
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
Metabolic Pathways Required for the Intracellular Survival
of Leishmania
Malcolm J. McConville and Thomas Naderer p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 543
Capsules of Streptococcus pneumoniae and Other Bacteria: Paradigms for
Polysaccharide Biosynthesis and Regulation
Janet Yother p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 563
Synthetic Poliovirus and Other Designer Viruses: What Have We
Learned from Them?
Eckard Wimmer and Aniko V. Paul p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 583
Regulation of Antigenic Variation in Giardia lamblia
C esar G. Prucca, Fernando D. Rivero, and Hugo D. Luj an p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 611
Alternative Pathways of Carbon Dioxide Fixation: Insights into the
Early Evolution of Life?
Georg Fuchs p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 631
Index
Cumulative Index of Contributing Authors, Volumes 6165 p p p p p p p p p p p p p p p p p p p p p p p p p p p 659
Errata
An online log of corrections to Annual Review of Microbiology articles may be found at
http://micro.annualreviews.org/
viii Contents
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.
ANNUAL REVIEWS
Its about time. Your time. Its time well spent.
ANNUAL REVIEWS | Connect With Our Experts
Tel: 800.523.8635 (US/CAN) | Tel: 650.493.4400 | Fax: 650.424.0910 | Email: service@annualreviews.org
New From Annual Reviews:
Annual Review of Statistics and Its Application
Volume 1 Online January 2014 http://statistics.annualreviews.org
Editor: Stephen E. Fienberg, Carnegie Mellon University
Associate Editors: Nancy Reid, University of Toronto
Stephen M. Stigler, University of Chicago
The Annual Review of Statistics and Its Application aims to inform statisticians and quantitative methodologists, as
well as all scientists and users of statistics about major methodological advances and the computational tools that
allow for their implementation. It will include developments in the feld of statistics, including theoretical statistical
underpinnings of new methodology, as well as developments in specifc application domains such as biostatistics
and bioinformatics, economics, machine learning, psychology, sociology, and aspects of the physical sciences.
Complimentary online access to the frst volume will be available until January 2015.
TABLE OF CONTENTS:
What Is Statistics? Stephen E. Fienberg
A Systematic Statistical Approach to Evaluating Evidence
from Observational Studies, David Madigan, Paul E. Stang,
Jesse A. Berlin, Martijn Schuemie, J. Marc Overhage,
Marc A. Suchard, Bill Dumouchel, Abraham G. Hartzema,
Patrick B. Ryan
The Role of Statistics in the Discovery of a Higgs Boson,
David A. van Dyk
Brain Imaging Analysis, F. DuBois Bowman
Statistics and Climate, Peter Guttorp
Climate Simulators and Climate Projections,
Jonathan Rougier, Michael Goldstein
Probabilistic Forecasting, Tilmann Gneiting,
Matthias Katzfuss
Bayesian Computational Tools, Christian P. Robert
Bayesian Computation Via Markov Chain Monte Carlo,
Radu V. Craiu, Jefrey S. Rosenthal
Build, Compute, Critique, Repeat: Data Analysis with Latent
Variable Models, David M. Blei
Structured Regularizers for High-Dimensional Problems:
Statistical and Computational Issues, Martin J. Wainwright
High-Dimensional Statistics with a View Toward Applications
in Biology, Peter Bhlmann, Markus Kalisch, Lukas Meier
Next-Generation Statistical Genetics: Modeling, Penalization,
and Optimization in High-Dimensional Data, Kenneth Lange,
Jeanette C. Papp, Janet S. Sinsheimer, Eric M. Sobel
Breaking Bad: Two Decades of Life-Course Data Analysis
in Criminology, Developmental Psychology, and Beyond,
Elena A. Erosheva, Ross L. Matsueda, Donatello Telesca
Event History Analysis, Niels Keiding
Statistical Evaluation of Forensic DNA Profle Evidence,
Christopher D. Steele, David J. Balding
Using League Table Rankings in Public Policy Formation:
Statistical Issues, Harvey Goldstein
Statistical Ecology, Ruth King
Estimating the Number of Species in Microbial Diversity
Studies, John Bunge, Amy Willis, Fiona Walsh
Dynamic Treatment Regimes, Bibhas Chakraborty,
Susan A. Murphy
Statistics and Related Topics in Single-Molecule Biophysics,
Hong Qian, S.C. Kou
Statistics and Quantitative Risk Management for Banking
and Insurance, Paul Embrechts, Marius Hofert
Access this and all other Annual Reviews journals via your institution at www.annualreviews.org.
A
n
n
u
.

R
e
v
.

M
i
c
r
o
b
i
o
l
.

2
0
1
1
.
6
5
:
3
7
-
5
5
.

D
o
w
n
l
o
a
d
e
d

f
r
o
m

w
w
w
.
a
n
n
u
a
l
r
e
v
i
e
w
s
.
o
r
g
b
y

U
n
i
v
e
r
s
i
d
a
d
e

F
e
d
e
r
a
l

d
e

V
i
c
o
s
a

o
n

0
3
/
1
0
/
1
4
.

F
o
r

p
e
r
s
o
n
a
l

u
s
e

o
n
l
y
.

Regulation of Alternative Sigma Factors

Загружено:

Сведения о документе

Исходное описание:

Авторское право

Доступные форматы

Поделиться этим документом

Поделиться или встроить документ

Параметры публикации

Этот документ был вам полезен?

Это неприемлемый материал?

Авторское право:

Доступные форматы

Regulation of Alternative Sigma Factors

Загружено:

Авторское право:

Доступные форматы

MI65CH03-Shingler ARI 10 August 2011 9:34

) canaccurately synthesize RNA

stably interact simultaneously (59), and

subunit of RNA polymerase. J. Bacteriol. 185:1796802

Вам также может понравиться