Microbiology (2014), 160, 1291–1297
DOI 10.1099/mic.0.077594-0
Regulation of gene expression at low temperature:
role of cold-inducible promoters
Review
Ashish Kumar Singh,1 Kirti Sad,1 Shailendra Kumar Singh1
and Sisinthy Shivaji2
Correspondence
1
Ashish Kumar Singh
2
Centre of Biotechnology (University of Allahabad), Allahabad, India
L. V. Prasad Eye Institute, Hyderabad, India
[email protected]
Psychrophilic micro-organisms are the most dominant flora in cold habitats. Their unique ability to
survive and multiply at low temperatures (,5 6C) is based on their ability to modulate the rigidity
of the membrane, to transcribe, to translate and to catalyse biochemical reactions at low
temperature. A number of genes are known to be upregulated during growth at low temperature
and cold-inducible promoters are known to regulate the expression of genes at low temperature.
In this review, we attempted to compile promoter sequences of genes that are cold-inducible so
as to identify similarities and to compare the distinct features of each type of promoter when
microbes are grown in the cold.
Received 24 January 2014
Accepted 17 April 2014
Introduction
A large proportion of the Earth’s biosphere (.75 %) is
either transiently or permanently cold, as in the polar ice
caps, glaciers and deep sea where the temperature is usually
low (,5 uC) (Cavicchioli & Torsten, 2000; Russell, 1998).
In these cold habitats, psychrophilic micro-organisms that
generally grow at an optimum temperature of 20–30 uC
and also have the ability to divide at low temperatures
(,5 uC) are among the most dominant flora (Baross &
Morita, 1978). Studies have established that psychrophilic
micro-organisms adapt to low temperature due to their
ability to modulate the fluidity of the membranes, to
transcribe, to translate and to catalyse biochemical reactions
at low temperature (Barria et al., 2013; Singh & Shivaji,
2010; Sundareswaran et al., 2010; Uma et al., 1999). It was
also demonstrated that a RNA polymerase isolated from
Pseudomonas syringae (Lz4W) (Shivaji et al., 1989) had the
ability to transcribe at low temperature (Uma et al., 1999)
unlike the RNA polymerase of mesophilic Escherichia coli. A
number of genes, including AAT in Pseudomonas syringae
(Lz4W) (Sundareswaran et al., 2010), trmE in Pseudomonas
syringae (Lz4W) (Singh et al., 2009), hutU in Pseudomonas
syringae (Lz4W) (Janiyani & Ray, 2002), rpoS in Pseudomonas putida (Jovcic et al., 2008), deaD in Methanococcoides
burtonii (Lim et al., 2000), crhC in Anabaena sp. (Chamot
et al., 1999), cspI in E. coli (Wang et al., 1999), cspG in E. coli
(Nakashima et al., 1996), cspB in E. coli (Lee et al., 1994),
csdA in E. coli (Toone et al., 1991), cspA and cspB in
Caulobacter crescentus (Mazzon et al., 2012), cspA in E. coli,
and RecBCD (Goldstein et al., 1990; Pavankumar et al.,
2010; Sinha et al., 2013), are known to be upregulated during
Abbreviation: UTR, untranslated region.
077594 G 2014 The Authors
cold shock by a cold-inducible promoter. In psychrophilic
Pseudomonas syringae (Lz4W) it was observed that hutU is
upregulated upon cold shock by a cold-inducible promoter
that regulates the hutU operon. Two promoters have been
recognized for hutU, with one of the promoters active at
normal temperature as well as at low temperature (22 and
4 uC), whereas the another is active only at low temperature
(4 uC) (Janiyani & Ray, 2002). Recently, two other coldinducible promoters that regulate the expression of tRNA
modification have been identified: GTPase (trmE) and
the aspartate aminotransferase gene (AAT) in psychrophilic Pseudomonas syringae (Lz4W) (Singh et al., 2009;
Sundareswaran et al., 2010). In the cold-adapted Gramnegative bacterium Pseudoalteromonas haloplanktis (TAC125),
several cold-inducible promoters were isolated by cloning the
TAC125 genomic DNA fragments in a shuttle vector and the
promoters containing recombinant clones were selected based
on their ability to express a promoterless lacZ gene (Duilio
et al., 2004). Using this approach, the nucleotide sequences of
several selected inserts and the transcription start sites of the
transcribed mRNA were determined. A promoter consensus
sequence for Pseudoalteromonas haloplanktis (TAC125) was
proposed on the basis of a sequence comparison between the
various active promoters (Duilio et al., 2004).
The nature of the promoter, its regulatory elements and the
mechanisms of transcription at low temperature are poorly
understood. Therefore, in this review, we have attempted
to compile promoter sequences of genes that are coldinducible so as to identify similarities and to compare the
distinct features of each type of promoter when microbes
are grown in the cold (Lisser & Margalit, 1993; Duilio et al.,
2004; Singh et al., 2009).
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A. K. Singh and others
Promoter characteristics of psychrophilic bacteria
59 Untranslated region (UTR)
The 59 UTR refers to the nucleotide sequence present
between the transcription and translation start sites in the
mRNA. Previous studies indicated that in E. coli, Anabaena
sp. and Methanococcoides burtonii, the DEAD-box RNA
helicase gene (deaD) and the four csp genes, which are
cold-regulated, contain a 59 UTR .100 bp in length (Fang
et al., 1998; Lim et al., 2000; Janiyani & Ray, 2002; Singh
et al., 2009) (Table 1). Further, in E. coli, overexpression
of the 59 UTR of cspA, cspB and csdA mRNA following
cold shock induced prolonged synthesis of CspA, CspB and
CsdA or simultaneous derepression of cspA, cspB and csdA
(Fang et al., 1998; Jiang et al., 1996). Overexpression of the
E. coli cspI 59 UTR also caused derepression of the coldshock response of cspI, but the derepression was weaker
compared with the cspA 59 UTR (Wang et al., 1999). The
authors concluded that the optimal temperature ranges for
induction of the four E. coli cold-shock-induced csp genes
(cspA, B, G and I) were not the same, thereby indicating
that whilst the 59 UTR and cold-box elements may be
involved in regulation of gene expression, specific sequence
differences in the 59 UTR and cold-box elements may play
important roles in regulation. Thus, it is apparent that
the 59 UTR plays an important role with respect to regulation of cold-inducible genes, but studies using cspA : : lacZ
fusions, which contained a variety of deletions of the 59 UTR
(Mitta et al., 1997; Yamanaka, 1999), indicated that deleting
the cold-box had little effect on cold-shock induction
of b-galactosidase activity and, instead, a region 11 bp
upstream of the ribosome-binding site was important
for translational efficiency of gene expression. These data
indicate that the precise mechanism by which regulation
occurs is unclear. These observations are not in accordance
with the trmE gene of psychrophilic Pseudomonas syringae
(Lz4W), which has one of the longest 59 UTRs of 343 bp
compared with the 59 UTR in cold-inducible genes in other
bacteria (Singh et al., 2009) (Table 1) and which has been
demonstrated to be essential for regulation of cold-inducible
trmE (Singh et al., 2009) based on promoter deletion
experiments.
actA coding for ActA, the major virulence factor in Listeria
monocytogenes, also has a long 59 UTR of 150 bp which
when deleted dramatically influenced actA expression levels
(Wong et al., 2004), thus implying that secondary structural
motifs within the actA mRNA 59 UTR determine overall
levels of actA expression. The 59 UTR has also been reported
to be important for mRNA stabilization following cold
shock (Mitta et al., 1997). The conservation of the long 59
UTR in low-temperature-regulated genes suggests strongly
that their occurrence is more than a coincidence and supports
their role in gene regulation. In most vertebrates, the 59 UTRs
are ,100 bp, but in genes that are tightly controlled, the 59
UTR is longer (Uhlmann-Schiffler et al., 2002), and such
structures can modulate translation by the formation of
secondary structures and by RNA–protein interaction (Gray
& Wickens, 1998; Mazzon et al., 2012; Uhlmann-Schiffler
et al., 2002).
Several conserved promoter elements, such as the 210 and
235 regions, cold-box, UP element, DEAD-box and Shine–
Dalgarno sequence, have been reported in the 59 UTR region
(Singh et al., 2009) (Fig. 1).
Conserved regions (”10 and ”35 region). In bacterial
promoters, two conserved regions at nucleotide positions
25 to 210 and 233 to 238 are referred to as 210 and 235
regions, respectively. The consensus sequences for the 210
and 235 regions for E. coli based on 300 genes were
TATAAT and TTGACA, respectively (Lisser & Margalit,
1993). These 210 and 235 consensus sequences differed
from the consensus sequences TGGATT and GGAAAT in
the trmE promoter from different species of Pseudomonas,
Brevibacterium linens, Arthrobacter sulfureus and Marinomonas primoryensis (Fig. 2). It was also observed that the
consensus sequences for the 210 and 235 regions in the
same organism varied with the gene, as was the case in trmE
(Singh et al., 2009), hutU (Janiyani & Ray, 2002) and cti
(Kiran et al., 2005) in Pseudomonas syringae (Lz4W). The
consensus sequences for the 210 and 235 regions for
Pseudoalteromonas haloplanktis were reported as TRGRTW
and TATRAY, respectively (where R, A/G; Y, T/C; W, A/T;
X, T/G; S, G/C) (Duilio et al., 2004). Thus, it would appear
Table 1. Length of the 59 UTR in cold-inducible genes of bacteria
Micro-organism
Gene
5§ UTR length (bp)
Reference
Pseudomonas syringae (Lz4W)
Pseudomonas putida
Pseudomonas syringae (Lz4W)
Methanococcoides burtonii
Anabaena sp.
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
trmE
rpoS
hutU
deaD
crhC
cspI
cspG
cspB
csdA
cspA
343
368
170
113
116
145
161
161
226
159
Singh et al. (2009)
Jovcic et al. (2008)
Janiyani & Ray (2002)
Lim et al. (2000)
Chamot et al. (1999)
Wang et al. (1999)
Nakashima et al. (1996)
Lee et al. (1994)
Toone et al. (1991)
Goldstein et al. (1990)
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Microbiology 160
Cold-inducible promoters and gene expression
Ash 57
AGCTACAAGTCGATGGCCCGCATGCGCGCTGTGGCACCAAAACTGGCCGCTCTGAAAGAGCAGTTCGGT
GATGATCGCCAGAAAATGTCGCAAGCGATGATGGAGCTGTACAAGAAAGAGAAGATCAATCCGCTGGGC
GGCTGCTTGCCGATTCTGGTGCAGATGCCGGTCTTCCTGTCCTTGTACTGGGTACTTCTGGAAAGTGT
UP element
TGAAATGCGCCAGGCGCCGTTCATGCTCTGGATTACCGACCTGTCGATCAAGGACCCGTTCTTCATTCT
–35
–10
+1
GCCGATCATCATGGGCGCAACCATGTTCATCCAGCAGCGTCTGAACCCGACTCCTCCGGATCCGATGCA
GGCCAAGGTGATGAAGCTGATGCCAATCATCTTCACCTTCTTCTTCCTGTGGTTCCCGGCTGGTCTGGT
GCTGTACTGGGTTGTGAACAACTGCCTGTCCATCGCCCAACAGTGGTACATCACACGTAAGGTCGAAGC
Cold-box
DEAD-box
TGCTACCAAAAAAGCAGCCGAGTAACTTACTCTGGTGAGCACCACTCAAAACGCCCCCTAGTGGGGCGT
Conserved region
TTTGCTTTCCATCACTTTTGTTTTGAGGCCTGTTTTATG-----Ash 59
SDS
Fig. 1. Nucleotide sequence of the trmE promoter of Pseudomonas syringae (Lz4W) and its regulatory elements. The
transcription start site +1 (A), ”10 region (TGGATT), ”35 region (TGAAAT), UP element (TACTTCTGGAAAGT), cold-box
(TGAACAACTGC), DEAD-box (AACAGTGGTA), conserved region (CAAAAA), Shine–Dalgarno sequence (SDS; GAGG)
and translation start site (ATG) are highlighted (Singh et al., 2009). The arrows indicate the direction of the primers, the
transcription start site and the translation start site. The primer sequences are Ash 57, 59-GCTGCAGCAAGCTACAAGTCGATGGCCC), and Ash 59, 59-GGGGTACCCCACACCACCTCGGCCTTG.
that these regions vary from organism to organism and may
also depend on the gene analysed; it would be interesting
to analyse further more promoters from psychrophilic
organisms to support the existing results. Based on the sitespecific deletion study for the trmE promoter of Pseudomonas syringae (Lz4W), it has been reported that both 210
and –35 regions are essential for transcription, and probably
the 210 region is more important as deletion of this region
resulted in almost total loss of promoter activity (Singh
et al., 2009). It has been observed that in mesophilic bacteria
such as E. coli, these two regions (210 and 235) have a
spacing of 16–18 nt (Lisser & Margalit, 1993). In contrast
to the mesophilic bacteria, the psychrophilic bacteria
Pseudomonas syringae (Lz4W) and Pseudoalteromonas
haloplanktis have a spacing of 22 nt between these two
regions (210 and 235) (Duilio et al., 2004; Singh et al.,
2009) (Fig. 2).
Cold-box. Several cold-inducible genes in bacteria are
known to contain a cold-box element within the 59 UTR
(Graumann et al., 1997; Graumann & Marahiel, 1998;
Panoff et al., 1998; Phadtare et al., 1999; Singh et al., 2009;
Thieringer et al., 1998; Yamanaka et al., 1998) and the
cold-box sequences are conserved (Fig. 3). Furthermore,
alignment of the cold-box sequences from cold-inducible
genes of various bacteria such as E. coli, Anabaena sp.,
Methanococcoides burtonii, Bacillus subtilis, Brevibacterium
linens, Arthrobacter sulfureus, Marinomonas primoryensis,
Pseudomonas syringae (Lz4W) and other different species of
Pseudomonas led to the identification of a consensus
sequence for the cold-box as TGA(A/C)NAAC(T/A)G(C/
A) (where N represents any nucleotide) (Fig. 3). 59 UTR
sequences with conserved elements (different to the cold-box
http://mic.sgmjournals.org
sequence) have also been identified in cold-induced genes in
Bacillus (Graumann et al., 1997).
The genes that contain the cold-box element within the
59 UTR are regulated by cold shock, and appear to be
controlled by a range of transcriptional and translational
control mechanisms (reviewed by Graumann & Marahiel,
1998; Panoff et al., 1998; Phadtare et al., 1999; Thieringer
et al., 1998; Yamanaka et al., 1998; Mitta et al., 1997). As
noted above, the 59 UTRs in most vertebrates are ,100 bp,
but are longer in genes that are tightly controlled (UhlmannSchiffler et al., 2002), and such structures can modulate
translation by the formation of secondary structures and by
RNA–protein interaction (Gray & Wickens, 1998; UhlmannSchiffler et al., 2002). In E. coli, deletion of the cold-box
region abolished the derepression caused by overexpression
of the 59 UTR of cspA mRNA (Fang et al., 1998) indicating
that derepression occurs at the level of transcription and it
is probably brought about by the binding of a putative
repressor to the cold-box of the mRNA of cold-inducible
genes. Deletion of the cold-box region from cspA on the
chromosome also caused derepression of cspA, confirming
that the cold-box functions as a binding site for the putative
repressor (Fang et al., 1998). Wang et al. (1999) indicated
that the optimal temperature ranges for induction of the
four E. coli cold-shock-induced csp genes (cspA, B, G and I)
were different, thereby indicating that specific sequence
differences in the 59 UTR and cold-box elements may play
important roles in regulation. Interestingly, it has also been
suggested that CspE (a non-cold-shock-induced protein
in the E. coli Csp family) binds to the cold-box of cspA and
functions as a negative regulator of expression at 37 uC (Bae
et al., 1997). These observations are not in accordance with
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A. K. Singh and others
–35 region
–10 region
TGAAATGCGCCAGGCGCCGTTCATGCTCTGGATTACCGA
CGAGATGCGCCAGGCCCCATGGATGCTGTGGATC----GGAAATGCGCCAGGCGCCGTTCATGCTGTGGATT----GGAAATGCGTCAGGCCCCGTGGATGTTCTGGATC----GGAAATGCGCCAGGCGCCGTGGCTCGGCTGGATC----GGAAATGCGCCAGGCCCCATGGATACTGTGGATT----GGAAATGCGTCAGGCTCCCTGGATCCTGTGGATA----TGAAATGCGCCAGGCGCCCTTCCTGCTCTGGATT----TGAAATGCGCCAGGCGCCGTTCATGCTCTGGATT----TGAAATGCGCCCGGCGCCCTTCCTGCTCTGGATT----C
GGAAAT--------(22)-----------TGGATT
1. Pseudomonas syringae (Lz4W)
2. Pseudomonas entomophila
3. Pseudomonas fluorescens
4. Pseudomonas mendocina
5. Pseudomonas aeruginosa
6. Pseudomonas putida
7. Pseudomonas syringae
8. Brevibacterium linens
9. Arthrobacter sulfureus
10. Marinomonas primoryensis
Consensus sequence of
1–10 above
11. Pseudoalteromonas haloplanktis consensus
sequence of 11 promoters
12. Escherichia coli consensus
sequence
TRGRTW --------(22)--------- TATRAY----TTGACA -------(16–18)------- TATAAT-----
Fig. 2. Comparison of the nucleotide sequence of the ”10 and ”35 regions of the trmE promoter of Pseudomonas syringae
(Lz4W) (AM944531) with the ”10 and ”35 regions of the trmE promoter from Pseudomonas entomophila (CT573326),
Pseudomonas fluorescens (CP000094), Pseudomonas mendocina (CP000680), Pseudomonas aeruginosa (CP000348),
Pseudomonas putida (CP000926), Pseudomonas syringae (CP000075), Brevibacterium linens (AM944530), Arthrobacter
sulfureus (AM944532) and Marinomonas primoryensis (AM944533). (GenBank accession numbers of the respective
sequences are given in parentheses.) The consensus sequences of the ”10 and ”35 regions based on promoters of 11 genes
from a cold-adapted bacterium Pseudoalteromonas haloplanktis (Duilio et al., 2004) and 300 different genes of E. coli (Lisser &
Margalit, 1993) are also shown.
the trmE promoter data where it has been observed that
deletion of the cold-box inhibits expression of the gene
(Singh et al., 2009). These data indicate that the precise
mechanism by which the cold-box regulates gene expression
is unclear.
A
A
A
A
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A
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T
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G
originally by the analysis of 31 promoters of E. coli in the
region upstream to the 235 region. It is an AT-rich region
(64–91 %) which is centred around the region 238 to
259 with a consensus sequence nnAAA(A/T)(A/T)T(A/
Pseudomonas syringae (Lz4W)
Pseudomonas syringae
Pseudomonas entomophila
Pseudomonas fluorescens
Pseudomonas mendocina
Pseudomonas aeruginosa
Pseudomonas putida
Brevibacterium linens
Arthrobacter sulfureus
Marinomonas primoryensis
Escherichia coli cspB
Escherichia coli cspA
Escherichia coli csdA
Escherichia coli cspG
Escherichia coli cspI
Methanococcoides burtonii
Bacillus subtilis cspB
Bacillus subtilis cshB
Bacillus subtilis cshA
Anabaena sp. chrC
T
T
T
T
T
T
T
T
T
T
T
T
T
T
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C
Consensus sequence
T G A A N A A C T G C
1294
G
G
G
G
C
C
G
G
G
G
G
G
G
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UP element. The UP element sequence was identified
C
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A
Fig. 3. Comparison of the nucleotide
sequence of the cold-box of the trmE promoter
of Pseudomonas syringae Lz4W (AM944531)
with the cold-box of the trmE promoter
from Pseudomonas syringae (CP000075),
Pseudomonas entomophila (CT573326), Pseudomonas fluorescens (CP000094), Pseudomonas mendocina (CP000680), Pseudomonas aeruginosa (CP000438), Pseudomonas putida (CP000926), Brevibacterium
linens (AM944530), Arthrobacter sulfureus
(AM944532) and Marinomonas primoryensis
(AM944533), and the cold-inducible genes of E.
coli [cspA (AE000433), cspB (AE000252),
csdA (M63288), cspG (AE000201) and cspI
(AE000252)], Methanococcoides burtonii
[deaD (AF199442)], Bacillus subtilis [cspB
(X59715), cshA (NC000964) and cshB
(NC000964)] and Anabaena sp. [crhC
(AF040045)]. (GenBank accession numbers of
the respective sequences are given in parentheses.) The consensus sequence is also
shown.
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Microbiology 160
Cold-inducible promoters and gene expression
Pseudomonas syringae (Lz4W)
Pseudomonas entomophila
Pseudomonas mendocina
Pseudomonas aeruginosa
Pseudomonas putida
Pseudomonas syringae
Brevibacterium linens
Arthrobacter sulfureus
Marinomonas primoryensis
Consensus sequence
T
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A
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T
C
T
C
C
T
T
T
T
C
T A C T N C T G G A A A G T
Fig. 4. Comparison of the nucleotide sequence of the UP element of the trmE promoter of Pseudomonas syringae (Lz4W) with
the UP element of the trmE promoter from Pseudomonas entomophila (CT573326), Pseudomonas mendocina (CP000680),
Pseudomonas aeruginosa (CP000438), Pseudomonas putida (CP000926), Pseudomonas syringae (CP000075),
Brevibacterium linens (AM944530), Arthrobacter sulfureus (AM944532) and Marinomonas primoryensis (AM944533).
(GenBank accession numbers of the respective sequences are given in parentheses.) The consensus sequence based on
these nine trmE sequences is also shown.
T)TTTTnnAAAAnn (Estrem et al., 1998). A similar UP
element sequence (TACTTCTGGAAAGT) was identified in
psychrophilic Pseudomonas syringae (Lz4W), which was
64.3 % AT-rich and centred around the region 241 to 254
in the trmE promoter. This UP element sequence of
psychrophilic organisms is unique and it did not match
with the consensus sequence of E. coli (Estrem et al., 1998).
In fact, the analysis of trmE promoters from different
bacterial species of Pseudomonas, Brevibacterium linens,
Arthrobacter sulfureus and Marinomonas primoryensis
identified the consensus UP element sequence as TACTNCTGGAAAGT (Fig. 4) (Singh et al., 2009). Previous
studies have indicated that the UP element of the bacterial
promoter stimulates transcription by interacting with the
a-subunit of RNA polymerase (Mitta et al., 1997; Ross &
Gourse, 2005). This may indeed be the case also in the case
of psychrophilic Pseudomonas syringae (Lz4W) as sitespecific deletion of the UP element resulted in a drastic loss
of promoter activity (Singh et al., 2009).
Pseudomonas syringae (Lz4W)
Pseudomonas entomophila
Pseudomonas fluorescens
Pseudomonas mendocina
Pseudomonas aeruginosa
Pseudomonas putida
Pseudomonas syringae
Brevibacterium linens
Arthrobacter sulfureus
Marinomonas primoryensis
Consensus sequence
DEAD-box. The DEAD-box, a homologue of BoxA, is a
conserved sequence AACAGTGGTA in the 59 UTR at
positions +208 to +217 in the deaD gene of Methanococcoides burtonii (Lim et al., 2000). The DEAD-box of
psychrophilic Pseudomonas syringae has 70 % sequence
similarity with the putative BoxA of Methanococcoides
burtonii. In Pseudomonas entomophila, Pseudomonas fluorescens, Pseudomonas mendocina, Pseudomonas aeruginosa,
Pseudomonas putida, Pseudomonas syringae, Brevibacterium
linens, Arthrobacter sulfureus and Marinomonas primoryensis,
a consensus sequences for the DEAD-box has been defined
as A(A/G)CAGTGGTA (Fig. 5). Site-specific deletion of
the DEAD-box from the trmE promoter resulted in a drastic
loss of promoter activity (Singh et al., 2009), confirming
that the DEAD-box is essential in the regulation of
the trmE promoter. Most probably, the DEAD-box is a
transcriptional activator binding site that regulates the
transcription activity of cold-inducible promoters at low
temperature.
A
A
A
A
A
A
A
A
A
A
A
G
A
G
G
G
G
A
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A A
C
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C
A
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G
T
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C
G
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G
G
G
G
G
G
G
T
G
G
G
T
T
T
T
T
T
T
T
T
T
A
A
A
A
A
A
A
A
A
A
C A G T G G T A
Fig. 5. Comparison of the nucleotide sequence of the DEAD-box of the trmE promoter of Pseudomonas syringae Lz4W
(AM944531) with the DEAD-box of the trmE promoter from Pseudomonas entomophila (CT573326), Pseudomonas
fluorescens (CP000094), Pseudomonas mendocina (CP000680), Pseudomonas aeruginosa (CP000438), Pseudomonas
putida (CP000926), Pseudomonas syringae (CP000075), Brevibacterium linens (AM944530), Arthrobacter sulfureus
(AM944532) and Marinomonas primoryensis (AM944533). (GenBank accession numbers of the respective sequences are
given in parentheses.) The consensus sequence is also shown.
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A. K. Singh and others
Transcriptional silencer
A transcriptional silencer has also been identified in the
promoter region of psychrophilic Vibrio sp. strain ABE-1,
which plays an important role in the regulation of the coldinducible isocitrate dehydrogenase (icdII) gene. The 35 bp
transcriptional silencer sequence was identified as 59-GTTATACCATACGGAGCTTAATTCTTTACGTAACA-39 in
the icdII promoter and it centred around the region from
2560 to 2526. The results from deletion studies of the
transcriptional silencer indicated a 20-fold increase in
expression level of the gene at low temperature (15 uC) but
not at higher temperature (37 uC) (Sahara et al., 1999).
Thus, the transcription silencer is another way to regulate
the expression of some cold-inducible genes by its promoter.
Duilio, A., Madonna, S., Tutino, M. L., Pirozzi, M., Sannia, G. & Marino,
G. (2004). Promoters from a cold-adapted bacterium: definition of a
consensus motif and molecular characterization of UP regulative
elements. Extremophiles 8, 125–132.
Estrem, S. T., Gaal, T., Ross, W. & Gourse, R. L. (1998). Identification
of an UP element consensus sequence for bacterial promoters. Proc
Natl Acad Sci U S A 95, 9761–9766.
Fang, L., Hou, Y. & Inouye, M. (1998). Role of the cold-box region in the
59 untranslated region of the cspA mRNA in its transient expression at
low temperature in Escherichia coli. J Bacteriol 180, 90–95.
Goldstein, J., Pollitt, N. S. & Inouye, M. (1990). Major cold shock
protein of Escherichia coli. Proc Natl Acad Sci U S A 87, 283–287.
Graumann, P. L. & Marahiel, M. A. (1998). A superfamily of proteins
that contain the cold-shock domain. Trends Biochem Sci 23, 286–290.
Graumann, P., Wendrich, T. M., Weber, M. H., Schröder, K. & Marahiel,
M. A. (1997). A family of cold shock proteins in Bacillus subtilis is
essential for cellular growth and for efficient protein synthesis at
optimal and low temperatures. Mol Microbiol 25, 741–756.
Conclusions
Bacteria sense and transduce the low-temperature signal to
a response regulator, which then induces the upregulation of
genes. It is also known that bacteria preferentially transcribe
cold-inducible genes at low temperature as a survival
strategy. The cold-inducible promoter regulates the expression of such genes at low temperature. However, the nature
of the cold-inducible promoter, its regulatory elements
and the mechanisms of transcription at low temperature
are poorly understood. This review has compiled all the
advances on cold-inducible promoters and regulation of
gene expression at low temperature. Future studies should
be directed to identify a wide variety of cold-inducible
promoters from different psychrophilic organisms, which
would help in the creation of cold-inducible expression
systems and provide a better understanding of the molecular
mechanisms of cold adaptation.
Gray, N. K. & Wickens, M. (1998). Control of translation initiation in
animals. Annu Rev Cell Dev Biol 14, 399–458.
Janiyani, K. L. & Ray, M. K. (2002). Cloning, sequencing, and expression
of the cold-inducible hutU gene from the Antarctic psychrotrophic
bacterium Pseudomonas syringae. Appl Environ Microbiol 68, 1–10.
Jiang, W., Fang, L. & Inouye, M. (1996). The role of the 59-end
untranslated region of the mRNA for CspA, the major cold-shock
protein of Escherichia coli, in cold-shock adaptation. J Bacteriol 178,
4919–4925.
Jovcic, B., Bertani, I., Venturi, V., Topisirovic, L. & Kojic, M. (2008). 59
Untranslated region of the Pseudomonas putida WCS358 stationary
phase sigma factor rpoS mRNA is involved in RpoS translational
regulation. J Microbiol 46, 56–61.
Kiran, M. D., Annapoorni, S., Suzuki, I., Murata, N. & Shivaji, S. (2005).
Cis–trans isomerase gene in psychrophilic Pseudomonas syringae is
constitutively expressed during growth and under conditions of
temperature and solvent stress. Extremophiles 9, 117–125.
Lee, S. J., Xie, A., Jiang, W., Etchegaray, J. P., Jones, P. G. & Inouye,
M. (1994). Family of the major cold-shock protein, CspA (CS7.4), of
Acknowledgements
A. K. S. would like to thank the Council of Scientific and Industrial
Research, New Delhi, Government of India for a Fellowship. A. K. S.
would also like to thank Dr Awadh Bihar Yadav (Centre of
Biotechnology, University of Allahabad, India) for critical review of
the manuscript.
Escherichia coli, whose members show a high sequence similarity with
the eukaryotic Y-box binding proteins. Mol Microbiol 11, 833–839.
Lim, J., Thomas, T. & Cavicchioli, R. (2000). Low temperature
regulated DEAD-box RNA helicase from the Antarctic archaeon,
Methanococcoides burtonii. J Mol Biol 297, 553–567.
Lisser, S. & Margalit, H. (1993). Compilation of E. coli mRNA
promoter sequences. Nucleic Acids Res 21, 1507–1516.
Mazzon, R. R., Lang, E. A., Silva, C. A. & Marques, M. V. (2012). Cold
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Edited by: S. Spiro
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