Microbiology (2008), 154, 1837–1844 DOI 10.1099/mic.0.

2008/018549-0

Mini-Review Transcription factor dynamics

P. J. Lewis, G. P. Doherty and J. Clarke3
Correspondence School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308,
P. J. Lewis Australia
Peter.Lewis@newcastle.edu.au

Gene expression is a fundamental process that is highly conserved from humans to bacteria. The
first step in gene expression, transcription, is performed by structurally conserved DNA-
dependent RNA polymerases (RNAPs), which results in the synthesis of an RNA molecule from a
DNA template. In bacteria, a single species of RNAP is responsible for transcribing both stable
RNA (i.e. t- and rRNA) and protein-encoding genes (i.e. mRNA), unlike eukaryotic systems, which
use three distinct RNAP species to transcribe the different gene classes (RNAP I transcribes
most rRNA, RNAP II transcribes mRNA, and RNAP III transcribes tRNA and 5S rRNA). The
versatility of bacterial RNAP is dependent on both dynamic interactions with co-factors and the
coding sequence of the template DNA, which allows RNAP to respond appropriately to the
transcriptional needs of the cell. Although the majority of the research on gene expression has
focused on the initiation stage, regulation of the elongation phase is essential for cell viability and
represents an important topic for study. The elongation factors that associate with RNAP are
unique and highly conserved among prokaryotes, making disruption of their interactions a
potentially important target for antibiotic development. One of the most significant advances in
molecular biology over the last decade has been the use of green fluorescent protein (GFP) and
its spectral variants to observe the subcellular localization of proteins in live intact cells. This
review discusses transcription dynamics with respect to RNAP and its associated transcription
elongation factors in the two best-studied prokaryotes, Escherichia coli and Bacillus subtilis.

RNAP and the transcription machinery downstream double-stranded DNA separates into a single-
stranded DNA template, which enters the primary channel
Prokaryotic RNA polymerase (RNAP) is a large
and contacts the active site to allow polymerization of RNA
(~400 kDa) multi-subunit enzyme comprising a2bb9v
(Borukhov & Nudler, 2008). Due to the crowding of the
subunits which form a crab-claw-like structure. Although
primary channel by the DNA : RNA hybrid, nucleotide
little sequence homology exists between eubacterial RNAP,
triphosphates (NTPs) must access the active site through
archaeal RNAP and eukaryotic RNAPII, the crab-claw
an alternative route. They do this through a pore on RNAP
structure is remarkably conserved (Zhang et al., 1999;
called the secondary channel (sometimes referred to as the
Cramer et al., 2001; Hirata et al., 2008). The two a subunits
nucleotide entry channel), which allows unobscured access
act as a scaffold to hold the catalytic b and b9 subunits
to the active site not only for NTPs but also for other
together, forming the crab-claw-like structure (Zhang et
regulatory proteins and molecules. The elongating RNA
al., 1999). The exact role of the v subunit is unclear but it
molecule is separated from the DNA template by a wedge-
is related in both structure and sequence to the eukaryotic
like domain on RNAP to redirect the nascent RNA
polymerase subunit Rpb6 (Minakhin et al., 2001). It
molecule through a third channel called the RNA exit
appears to be responsible for controlling transcription in
channel, which then allows upstream DNA to reanneal as it
response to nutrient shifts, correct folding of the b9 subunit
exits RNAP (for a review see Borukhov & Nudler, 2008).
and its assembly into the core multi-subunit enzyme
Many of the regulatory roles of transcription factors are
(Mukherjee et al., 1999; Vrentas et al., 2005; Chatterji et al.,
exerted through interaction with these structural elements
2007). The channel formed by b and b9 is referred to as the
(Borukhov et al., 2005).
primary channel, which contains a deep positively charged
cleft housing the enzyme’s active site. During transcription, For initiation of transcription to occur, RNAP must first
associate with a s factor to form what is termed the
Abbreviations: EC, elongation complex; RNAP, RNA polymerase; TF, holoenzyme (a2bb9vs), which allows RNAP to recognize
transcription foci. and bind promoter DNA sequences. The housekeeping s
3Present address: Flinders Microscopy and Image Analysis Facility, factor is s70 in Escherichia coli and sA in Bacillus subtilis
Department of Anatomy and Histology School of Medicine, Flinders and is responsible for initiating transcription from most
University, GPO Box 2100, Adelaide 5001, Australia. promoters. Other s factors also exist and are usually stress

2008/018549 G 2008 SGM Printed in Great Britain 1837

P. J. Lewis, G. P. Doherty and J. Clarke
induced to allow the organism to become virulent or adapt
to any number of environmental cues such as hyperosmo-
larity, heat shock, oxidative stress, nutrient deprivation and
variations in pH (Gruber & Gross, 2003; Kazmierczak et al.,
2005).
Following s factor dissociation and promoter escape,
RNAP enters the elongation phase of transcription, where
a raft of other co-factors combine to influence the
sensitivity of RNAP to regulatory pause and termination
signals. There are two basic classes of elongation complexes
(ECs): the antitermination ECs involved in rRNA synthesis,
and mRNA ECs, which respond in dramatically different
ways to intrinsic and extrinsic pause and termination
signals (Condon et al., 1995; Landick et al., 1996; Torres
et al., 2004). As the name suggests, mRNA ECs are
responsible for transcribing protein-encoding genes. These
complexes are highly sensitive to both intrinsic and
extrinsic pause and termination signals to ensure efficient
regulation of gene expression, particularly in response to
cellular metabolic needs, while maintaining the fidelity of
the transcript. Antitermination ECs are highly processive,
capable of synthesizing transcripts several kilobases in
length, and are usually associated with the transcription of
rRNA operons (Condon et al., 1995). They are largely
resistant to pause and termination signals and have an
overall elongation rate double that of mRNA ECs (Vogel &
Jensen, 1994), and this helps satisfy the cellular thirst for
rRNA at high growth rates. Although representing only
about 1 % of chromosomally encoded genes, rRNA
accounts for up to 80 % of cellular RNA at high growth
rates to ensure the demand for ribosome production is
met, making the formation of antitermination complexes
vitally important.
Factors regulating ECs
Some of the better-studied transcription factors involved in
regulating ECs are the Nus and Gre factors. NusA and
NusG are global transcription elongation factors that
regulate both classes of ECs. During mRNA transcription
NusA acts to decrease the rate of transcription elongation,
which has been shown to be important for ensuring the
efficient coupling of transcription and translation (Landick
et al., 1996; Burns et al., 1998; Ingham et al., 1999; Gusarov
& Nudler, 2001). NusA has a somewhat contradictory role
when it comes to regulating elongation of antitermination
ECs. Instead of increasing the half-life of paused complexes
as it does during mRNA transcription, NusA increases the
elongation rate of antitermination complexes (Richardson
& Greenblatt, 1996; Burns et al., 1998). The mechanism by
which NusA achieves such opposing roles in transcription
remains unclear, but it may have to do with the
stoichiometry of NusA to RNAP. It has been found that
during mRNA transcription there is one NusA molecule
involved, while antitermination complexes have two, the
second of which probably binds a conserved box element in
the nascent rRNA transcript (Davies et al., 2005). NusG
1838
acts to increase elongation rates of both mRNA and
antitermination ECs by decreasing pausing (Burns et al.,
1998). NusG has been found to be essential in Gram-
negative bacteria, most likely due to interactions with the
termination factor Rho during mRNA transcription, whilst
a drastically reduced growth rate is observed when NusG is
knocked out in Gram-positives (Li et al., 1993; Ingham
et al., 1999; Zellars & Squires, 1999; Pasman & von Hippel,
2000). This may be due in part to the much lower levels of
Rho present in Gram-positive organisms such as B. subtilis,
compared to the Gram-negative E. coli (Ingham et al.,
1999). NusB and NusE (also known as ribosomal protein
S10) are only known to play roles in regulating anti-
termination ECs. NusB is the first transcription factor to be
recruited to antitermination ECs and binds the nascent
rRNA transcript during the initial stages of elongation.
NusE then forms a heterodimer with NusB to stabilize this
complex, which allows the other factors such as NusA and
NusG to bind (Greive et al., 2005). Each of the Nus factors
are essential for antitermination, and (at the very least)
cause increased doubling times in organisms when their
genes are mutated or deleted.
Potential obstacles to transcription elongation that ECs
encounter in vivo include DNA lesions and DNA-binding
proteins, which can act as road blocks. In some instances
these cause the EC to stall, which can lead to a further build
up of trailing ECs. These stalled arrays of transcription
complexes are not only highly detrimental to transcription,
but can also block DNA replication forks (Borukhov et al.,
2005). The Gre factors are involved in restarting these
paused complexes to relieve the genome of these obstacles
(Borukhov et al., 1993; Erie et al., 1993; Orlova et al.,
1995). Although the Gre factors have only been thought to
regulate mRNA ECs, there is some evidence that they may
also be involved in regulating initiation from both mRNA
and rRNA promoters (Hsu et al., 1995; Potrykus et al.,
2006; Stepanova et al., 2007).
Organization of the chromosome and gene
dosage effects
Bacterial DNA often consists of a single circular chro-
mosome containing genes that are often grouped into
operons. These operons are usually transcribed from a
single promoter and contain genes of related function,
allowing the cell to streamline the control of transcription.
The order and orientation of genes and operons around the
chromosome is highly strategic and driven by biophysical
forces to ensure the cell can rapidly adapt to environmental
cues by regulating gene expression. This is thought to be
the reason why genes encoding transcription factors such
as lacI are often in close proximity to the operons they
regulate, in this case the lac operon (Kolesov et al., 2007).
These forces have also driven the duplication of rRNA
operons to maximize rRNA expression, which is directly
linked to growth rate. Rapidly growing organisms such as
Vibrio natriegens contain up to 13 rRNA operons and have
Microbiology 154
 Transcription factor dynamics

a doubling time of 10 min, whilst a slower-growing

organism such as Mycobacterium tuberculosis contains a
single rRNA operon and has a doubling time of over 24 h.
B. subtilis and E. coli contain 10 and 7 rRNA operons,
respectively, and both have a doubling time under 20 min
in rich media (see Lewis, 2007, for references on rRNA
operon levels in bacterial genomes).
Chromosome replication occurs bi-directionally from the
origin until the replication forks meet at the termination
site. Therefore, during the replication cycle, there is more
origin-proximal template DNA available for transcription
than sequences closer to the termination site. Due to the
ability of rapidly growing bacteria to undergo multi-fork
DNA replication, up to three rounds of replication can be
ongoing in a cell, exponentially increasing the transcription
potential of sequences located close to the origin of
replication (Couturier & Rocha, 2006). Rapidly growing
organisms have taken advantage of this gene dosage effect
by localizing highly transcribed genes around the origin. It
is, therefore, no coincidence that rRNA operons are
clustered in groups in the origin-proximal half of the
chromosome in both B. subtilis and E. coli (Fig. 1A).

Do bacteria have a nucleolus?

Nucleoli are nuclear organelles dedicated to the transcrip-
tion of rRNA and have generally been assumed to be
unique to eukaryotes. The lack of a nuclear membrane, let
alone subnucleoid organelles, would strongly suggest that
prokaryotes do not contain structures akin to the
eukaryotic nucleolus. Furthermore, rRNA operons are
generally separated by other highly expressed mRNA genes
such as those encoding the transcriptional and ribosomal
machinery. It would, therefore, seem reasonable to assume
on the face of this that no nucleoli-like structures exist in
prokaryotes. However, examination of GFP-labelled RNAP
from E. coli and B. subtilis indicated that such a subcellular
structure could exist (Lewis et al., 2000; Cabrera & Jin,
2003). During periods of rapid growth, RNAP-GFP
localizes in a region coincident with the nucleoid, in a
manner expected of a DNA-binding protein. Closer
examination has revealed that RNAP-GFP localizes in
discrete subnucleoid regions of higher intensity, called
transcription foci (TF; arrows in Fig. 1B). Several lines of
evidence have shown that these foci predominantly
represent sites of rRNA synthesis (Lewis et al., 2000;
Lewis, 2007). One of these lines of evidence showed that by
synthetically inducing the stringent response, which directs
transcription away from rRNA operons towards biosyn-
thetic operons, these TF were found to disappear in GFP-
labelled RNAP strains of both B. subtilis and E. coli (Lewis
et al., 2000; Cabrera & Jin, 2003; Davies et al., 2005).
Furthermore, relA mutant strains in E. coli that are unable
to synthesize the small molecule alarmone ppGpp, and do
not undergo the stringent response, retain TF under these
conditions (arrows in Fig. 2; Cabrera & Jin, 2003). High
transcriptional activity is known to cause nucleoid
Fig. 1. Subcellular organization of RNAP in B. subtilis and E. coli.
The circular maps of the 4.2 Mb B. subtilis (left) and 4.6 Mb E. coli
(right) chromosomes are shown in (A), with the position of rRNA
(rrn) operons shown relative to the origin of chromosome
replication (oriC) and the terminus (terC). The images in (B)
present the subcellular localization of RNAP through GFP-tagging
of the C terminus of the b9 subunit in B. subtilis (left) and E. coli
(right), showing the accumulation of RNAP into transcription foci
(TF; red arrows) in both species. Cartoons are shown below the
cells to illustrate cell dimensions. There are two B. subtilis cells
each containing two nucleoids and one E. coli cell containing two
nucleoids. In both images cells are growing rapidly and contain two
nucleoids on which RNAP is assembling, as is depicted in the
cartoon in (C). RNAP localized to TF represents enzyme heavily
loaded onto rRNA operons as well as mRNA encoding structural
genes, whereas less intensely fluorescent regions represent
loading principally onto structural genes (C). The cartoon cell
depicted has two nucleoids (ovals) each with two TF and is a
representation of the cells shown on the left in (B). Thus, the two
nucleoids in this cartoon cell represent chromosomes that are
undergoing replication that contain two segregated origin regions
which also correspond to the TF (see text for details). The E. coli
cells shown in (B) were taken from Fig. 1 of Cabrera & Jin (2006)
with permission from Elsevier.

http://mic.sgmjournals.org 1839
P. J. Lewis, G. P. Doherty and J. Clarke

Fig. 2. TF disappear on induction of the stringent response in E. coli. The figure shows a time-course of cells of the wild-type
(wt, top) and a relA mutant (bottom) following exposure to the amino acid analogue serine hydroxamate, used to induce the
stringent response. Representative TF are indicated with arrows. The bright TF in the wild-type cells rapidly disappear on
exposure to serine hydroxamate so that within 10 min, no TF are visible and fluorescence is due to GFP-labelled RNAP.
Conversely, in the relA mutant, which is unable to synthesis ppGpp, the stringent response is not induced by serine
hydroxamate and TF remain clearly visible throughout the time-course. Figure adapted from Fig. 5 of Cabrera & Jin (2003) with
permission.

compaction due to overwinding of downstream DNA, and
this can also be observed in Fig. 2, where the nucleoids in
wild-type cells become more diffuse on induction of the
stringent response, whereas those of the relA mutant
remain highly compacted (Cabrera & Jin, 2006). These data
strongly suggest that TF represent the sites of rRNA
synthesis. However, with rRNA operons scattered around
half of the chromosome in both B. subtilis and E. coli (Fig.
1A) an important question to address was whether these
nucleoli-like structures contained only rRNA operons, and
if so, how could these structures form if the rRNA operons
were widely distributed around the chromosome? One
model of how this may occur is through complex folding of
the nucleoid. The more origin-distal operons could be
brought to a nucleolus-like structure by reorganizing the
nucleoid to co-localize all of the rRNA operons. However,
the nucleoid is not static and this model fails to take into
account the cell cycle of rapidly growing bacteria, in which
multi-fork replication and simultaneous chromosome
segregation is under way, and in B. subtilis TF have been
shown to duplicate and segregate in a manner very similar
to that of origin regions (Lewis, 2007). It is difficult to
resolve how the newly replicated sequences could be
brought to a nucleolus-like structure and at what stage in
the replication/segregation cycle this would occur. Indeed,
work in B. subtilis suggests that the formation of nucleoli
does not occur, and that TF represent the heavy loading of
RNAP onto the seven rRNA operons clustered close to the
origin of replication (Davies & Lewis, 2003). In this work
several of the rRNA operons were labelled through
insertion of lacO repeats to which fluorescently labelled
LacI could bind, and the origin regions were fluorescently
co-labelled (using the origin-organizer Spo0J); the results
indicated little co-localization of the more origin-distal
rRNA operons with oriC regions. Although there is little
doubt that the signal from TF is predominantly attributed
to the transcription of rRNA operons, a small proportion
must also be attributed to highly transcribed mRNA genes
that are located around the origin of replication. Although
still highly transcribed, we propose that the signals from
the more origin-distal rRNA operons are probably
drowned out by the ‘noise’ from highly transcribed
mRNA genes adjacent to them. Thus, TF represent the
heavy loading of RNAP onto origin-proximal rRNA genes,
plus RNAP involved in mRNA synthesis in that region,
whereas less intensely fluorescent regions represent RNAP
loading onto origin-distal structural genes (Fig. 1C).
Transcription factor localization
Since we now know the sites of different classes of
transcription, a great deal of information can be gained
from determining the subcellular location of transcription
factors. The transcription factors NusA, NusB, NusG and
GreA are highly conserved throughout prokaryotes and are
even present in the minimal genome of Mycoplasma
genitalium. Using the same system as that used for tagging
B. subtilis RNAP in vivo (Lewis & Marston, 1999; Lewis et
al., 2000), functional GFP fusions were made to NusA,
NusB, NusG and GreA and their subcellular localization
patterns observed (Davies et al., 2005; Doherty et al., 2006).
The localization of these fusions is shown in Fig. 3, and all

1840 Microbiology 154

 Transcription factor dynamics

Fig. 3. Localization of GFP-labelled transcription elongation factors in B. subtilis. The distribution pattern of NusA is shown in
(A); it is very similar to that of RNAP. Panel (B) shows the distribution of NusA following induction of the stringent response. TF
have disappeared and fluorescence is homogeneously distributed throughout the nucleoids, showing that NusA foci also
correspond to sites of rRNA transcription. The distribution of NusB is shown in (C) and is largely restricted to sites of rRNA
synthesis. The cell marked with an arrow is magnified in the inset box; the foci marked with the white asterisk represent NusB
thought to be loaded onto rRNA transcription elongation complexes on origin-proximal rrn genes, and the yellow asterisk
possibly represents NusB loaded onto complexes transcribing an origin-distal rrn (see text for further details). The localization of
NusG is shown in (D), and is very similar to that of RNAP and NusA. Panel (E) shows GreA localization. Fluorescence is
homogeneously distributed throughout the nucleoids, suggesting little or no role for GreA in transcription of rRNA genes. Panel
(F) shows GreA distribution following treatment of the culture with high concentrations of chloramphenicol to collapse the
nucleoids. GreA signal remains coincident with nucleoids, showing that despite the molar excess of GreA over RNAP, it is
specifically bound to RNAP, suggesting that there is more than one binding site for Gre factors. Cells in all panels are shown at
the same magnification. Scale bar, 5 mm.

have been shown to be nucleoid associated (Davies et al.,
2005; Doherty et al., 2006). However, they display vastly
different patterns which reflect the biochemical roles they
have been assigned. NusA and NusG, as mentioned earlier,
are global transcription factors in E. coli and are known to
participate in both mRNA and antitermination EC
formation (Richardson & Greenblatt, 1996; Ingham et al.,
1999). Similar to RNAP, both of these are localized
throughout the nucleoid as well as being recruited to TF
(Fig. 3A, D). In the case of NusA, these foci have been
shown to co-localize with TF from RNAP in a dual-labelled
strain (Davies et al., 2005) and disappear (as do NusG and
B foci) on induction of the stringent response (Fig. 3B). As
for RNAP, this strongly suggests that the foci formed by
Nus factors predominantly represent sites of rRNA
synthesis. NusB shows a striking pattern of highly defined
TF, with very little signal dispersed throughout the rest of
the nucleoid (Fig. 3C), consistent with biochemical studies
from E. coli and Mycobacterium tuberculosis suggesting that
it is restricted to antitermination complex formation
(Torres et al., 2004; Greive et al., 2005). Furthermore, a
dual-labelled strain showed that these foci co-localize with
RNAP (Doherty et al., 2006), and are rapidly reduced upon
induction of the stringent response. One striking difference
between NusB (and NusA to a lesser extent) and RNAP
localization to TF is observed in slow-growing cells when
NusB (and NusA) TF are still clearly visible, but they are
almost totally absent with the RNAP-GFP fusion (Lewis et
al., 2000; Davies et al., 2005; Doherty et al., 2006). This is
due to the relatively low level of recruitment of RNAP to
rRNA operons at low growth rates, when the demand for
ribosomes is much less than at higher growth rates (Lewis
et al., 2000). However, NusB is still required for
antitermination complex formation at low growth rates,

http://mic.sgmjournals.org 1841
P. J. Lewis, G. P. Doherty and J. Clarke
Table 1. Summary of the localization and quantification data for
B. subtilis RNA polymerase and transcription elongation factors
and so TF can still be observed under these conditions,
making this a useful fusion for monitoring sites of rRNA
synthesis at all growth rates (Doherty et al., 2006).
Interestingly, we think the well-defined foci observed with
the NusB-GFP fusion represent antitermination complexes
loaded on individual rRNA operons or clusters. In the
boxed cell in Fig. 3C, the white asterisk indicates several
overlapping foci, likely to represent ECs loaded onto
origin-proximal rRNA operons, whereas the yellow asterisk
most likely represents loading onto an origin-distal operon,
such as rrnB (see Fig. 1A). GreA localizes homogeneously
throughout the nucleoid and shows no evidence of being
recruited to TF, which is consistent with its biochemical
role of predominately regulating mRNA ECs (Fig. 3E).
As these fusions were created by single crossover into the
locus of the respective wild-type gene, they are all driven by
the wild-type promoter. For this reason, all expression
levels should be equal to that of the wild-type protein,
allowing quantitative analysis to be performed. Using a
combination of native PAGE, quantitative Western blots
and image analysis, the cellular levels, along with the
percentage of each respective protein that was recruited to
TF was determined for RNAP, NusA, NusB, NusG and
GreA (Davies et al., 2005; Doherty et al., 2006). This
allowed a model for the composition of mRNA and rRNA
antitermination complexes to be determined; it is sum-
marized in Table 1. For each RNAP there are two NusA
molecules (confirmed by quantitative pull-down assays;
Davies et al., 2005) and one molecule each of NusB and
NusG in rRNA antitermination complexes, whilst during
mRNA transcription there is just one NusA, one NusG and
possibly as many as three GreA molecules needed to form
mRNA transcription complexes. The high levels of GreA
1842
are real and similarly large amounts of GreA and GreB have
been reported in E. coli (Koulich et al., 1998). However,
structural models suggest that only a single Gre factor is
required to bind RNAP (via the secondary channel) to
exert its biochemical role (Opalka et al., 2003).
Nevertheless, the high amounts of GreA are most likely
RNAP-associated. Gre proteins bind RNAP, not nucleic
acids, and on compaction of nucleoids with high levels of
chloramphenicol, GreA remains coincident with them
(Doherty et al., 2006; Fig. 3E, F). Also, on overexpression
of untagged GreA in the GreA-GFP labelled strain,
fluorescence becomes delocalized, indicating that the high
natural levels of Gre factors represent binding to specific
sites on RNAP that are usually saturated (Doherty et al.,
2006). The reason why there are such high levels of Gre
factors in the cell, and where they bind on RNAP, remains
to be determined.
Conclusions
Although not as defined as in eukaryotes, it is clear that
significant partitioning of transcription exists in prokar-
yotes. Through selective tagging of the transcription
machinery we can identify global events as well as specific
classes of transcription, such as rRNA synthesis using
NusB. Using standardized growth media and imaging
approaches we can determine the relative levels of
different components of the transcription apparatus at
an individual cell level, and combined with quantitative in
vitro approaches, determine the composition of complexes
involved in different classes of transcription (Davies et al.,
2005; Doherty et al., 2006). As imaging techniques
continue to improve it will also be possible to monitor
the dynamics of transcription complexes in more detail
using approaches similar to those that have been adopted
for analysis of signal transduction in Rhodobacter
spheroides and DNA replication in E. coli (Leake et al.,
2006; Reyes-Lamothe et al., 2008). We can also monitor
dynamic responses to stimuli, such as induction of the
stringent response (Figs 2 and 3; Cabrera & Jin, 2003),
showing that live cell monitoring could represent a rapid,
cheap and sensitive approach to assessing the effects of
novel antimicrobial compounds. It is interesting to note
that the levels of transcription factors are very high within
the cell (close to equimolar with RNAP), suggesting that
the bulk of RNAP within the cell is present in the form of
ECs. Genomic CHIP-ChiP experiments that are under
way in several laboratories will provide information on
global RNAP and transcription factor distribution and
enable a more detailed analysis of ECs involved in
transcription of individual genes/operons. Finally,
through investigation of the subcellular localization
pattern it will be possible to assign (at least partially)
function to unknown proteins identified through isolation
of protein complexes by various affinity approaches
currently being used to investigate transcription complex
composition.
Microbiology 154

Acknowledgements
Work in the Lewis laboratory is supported by funding from the ARC,
NHMRC, DEST and the University of Newcastle. The authors wish to
thank Din Jin for permission to use data in this review. Due to the
limitations of minireviews, it has not been possible to use primary
references for all sources of information, and the authors wish to
acknowledge the work of those whom we have not been able to
directly include in this article.
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