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Applied and Environmental Microbiology, January 2000, p. 401-405, Vol. 66, No. 1
0099-2240/0/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Identification of Cold Shock Gene Loci in
Sinorhizobium meliloti by Using a luxAB
Reporter Transposon
Kevin P.
O'Connell,1,*
Ann M.
Gustafson,1,2
M. Deane
Lehmann,1,2 and
Michael F.
Thomashow1,2,3
NSF Center for Microbial
Ecology,1 Department of Crop and Soil
Sciences,3 and Department of
Microbiology,2 Michigan State University, East
Lansing, Michigan 48824
Received 22 June 1999/Accepted 15 October 1999
 |
ABSTRACT |
Using a luxAB reporter transposon, seven mutants of
Sinorhizobium meliloti were identified as containing
insertions in four cold shock loci. LuxAB activity was strongly induced
(25- to 160-fold) after a temperature shift from 30 to 15°C. The
transposon and flanking host DNA from each mutant was cloned, and the
nucleic acid sequence of the insertion site was determined.
Unexpectedly, five of the seven luxAB mutants contained
transposon insertions in the 16S and 23S rRNA genes of two of the three
rrn operons of S. meliloti. Directed insertion
of luxAB genes into each of the three rrn
operons revealed that all three operons were similarly affected by cold
shock. Two other insertions were found to be located downstream of a
homolog of the major Escherichia coli cold shock gene,
cspA. Although the cold shock loci were highly induced in
response to a shift to low temperature, none of the insertions resulted
in a statistically significant decrease in growth rate at 15°C.
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TEXT |
In most environments, bacteria
experience fluctuations in temperature that are both regular (diurnal
and seasonal) and random (as a result of physical disturbances of the
environment). Because temperature has wide-ranging effects on growth
and survival, bacteria have developed responses that allow them to
adapt to changes in temperature. The evolution of cold shock genes is
one such response. Many species of bacteria have been shown to alter
gene expression in response to a shift to low temperature (3, 5,
12, 16, 17, 19). The synthesis of many cellular proteins ceases
and several other proteins, called cold shock proteins (Csps),
accumulate. In the cyanobacterium Synechococcus sp. strain
PCC7002 (20), fatty acid desaturases are induced by cold
shock and appear to be involved in maintaining proper membrane
fluidity. In Bacillus subtilis, the levels of at least 37 proteins increase after cold shock, including enzymes in central
metabolism, SpoVG, ribosomal proteins, and several proteins of unknown
function (12). In Escherichia coli, where the
induction of cold shock genes has been most extensively studied
(23), Csps have been classified based on their level of
increased expression after a temperature downshift. Class I Csps, which
are at low levels at 37°C, increase in synthesis more than 10-fold in
response to cold shock, whereas class II Csps are present at 37°C and
increase modestly in synthesis upon cold shock. Some of the class II
Csps, including GyrA and H-NS, interact with DNA and appear to
influence the structure of the nucleoid at low temperature. However,
the majority of the class I and II Csps that have been described are
involved in enabling ribosomes to translate mRNAs at low temperatures
(23). Paramount among these are CspA, the major cold shock
protein of E. coli, and its homologs. These proteins, which
are referred to as RNA chaperones, bind to RNA and are thought to
"open up" mRNA secondary structures that form at low temperatures,
preventing initiation of translation (14). The inhibition of
translation after cold shock is evidently problematic for many species
since most of those studied possess one or more cspA
homologs that are upregulated in response to a shift to low temperature.
A low temperature has been reported to limit the efficiency of the
Rhizobium-legume symbiosis (22). To better
understand the responses of Rhizobium spp. to low
temperatures, Cloutier et al. (7) examined protein synthesis
in temperate and arctic isolates that had been subjected to a cold
shock. It was found that cold shock induced changes in protein
synthesis in all of the species tested, including Sinorhizobium
meliloti. However, the proteins induced by cold shock in S. meliloti were not identified and a protein the size of CspA was
not observed, raising the question of whether S. meliloti
encodes a cspA homolog. Thus, to further understand the cold
shock response in S. meliloti, we used reporter transposon
mutagenesis to tag, clone, and identify genes in S. meliloti
that are induced by a temperature downshift.
Mutagenesis with the luxAB reporter transposon.
S. meliloti RM1021 was grown in tryptone-yeast extract (TY)
broth medium (4) at 30°C on a rotary shaker. Streptomycin
(SM) and kanamycin (KM) were both added to solid medium at 200 µg/ml (50 µg/ml in broth). To mutagenize strain RM1021 with the luciferase reporter transposon, plasmid pRL1062a was transferred to S. meliloti by triparental mating by using pRK2013 as the helper
plasmid (11). Plasmid pRL1062a carries Tn5-1062,
a Tn5-based reporter transposon containing the
luxAB genes of Vibrio harveyii (8).
Transposon recipients were selected by plating undiluted mating mixes
on solid TY medium containing SM and KM, followed by incubation at 30°C.
Identification of mutants with cold shock loci fused to
luxAB.
One hundred transposon recipients per mating
(>10,000 total) were transferred to TY SM KM plates and grown for 2 days at 30°C. Bacteria were exposed to n-decanal (Sigma
Co., St. Louis, Mo.) spread on the inside of a glass petri dish cover
for 2 min and then visualized with the Hamamatsu Photonic system
essentially as described earlier (8). Colonies of transposon
recipients were transferred to a 10 or 15°C growth chamber for 5 h, reexposed to n-decanal, and then observed again under the
photonic camera. Isolates that appeared brighter after temperature
downshift after two or more assays were selected for further study.
Examining the light emission from transposon recipients grown at 30°C
revealed a variety of levels of light emission (Fig. 1A). While the pattern of light emission
from the majority of transposon recipients did not vary greatly after
cold shock (Fig. 1B), we identified seven mutants whose light emission
was substantially increased by cold shock in repeated experiments (Fig.
1B; Fig. 2A). To quantify the light
emission from each mutant strain, bacteria were grown to an optical
density at 600 nm of approximately 0.4 in TY broth at 30°C. Then, 10 µl of each culture was mixed with 100 µl of n-decanal
solution (5 ml of distilled water, 100 mg of bovine serum albumin, 10 µl of n-decanal) and vortexed for 30 s. Light
emission was measured for 60 s by using a Berthold Lumat
luminometer (model LB-9501; Wallac Co., Gaithersburg, Md.). After we
measured the light emission and culture density, the cultures were
transferred to a 15°C shaking water bath. Light emission and culture
density were measured again 5 h after temperature downshift. Light
emission from the seven mutants increased 25- to 160-fold over a 5-h
period post-cold shock (Fig. 2B). Southern analysis indicated that,
with the exception of RM3166, each mutant contained a single transposon
insertion; RM3166 had two inserts (data not shown).

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FIG. 1.
Screen for light emission induced by temperature
downshift. (A) A total of 100 isolates of S. meliloti RM1021
carrying random insertions of Tn5-1062 were grown at 30°C
on solid TY medium. (B) The same isolates 5 h after temperature
downshift to 15°C are shown. White arrows indicate positions of the
mutant eventually designated RM603.
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FIG. 2.
Comparison of seven mutants with cold shock-induced
luxAB reporter insertions. (A) Light emission before
(30°C) and after (15°C) cold shock during growth on solid TY
medium. (B) Quantitation of light emission (in arbitrary light units)
before and after cold shock during growth in liquid TY medium. Each
column represents the mean ± the standard deviation of three
measurements per strain.
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Identification of cold shock loci.
The transposon and flanking
host DNA were cloned from each mutant that displayed cold shock-induced
light emission. Transposon Tn5-1062 contains a p15A origin
of replication, allowing the direct cloning of flanking DNA sequences
from S. meliloti genomic DNA. Total genomic DNA was isolated
from RM1021 and mutant strains essentially as described earlier
(2); the NaCl-CTAB (cetyltrimethylammonium bromide)
extraction step was omitted from some preparations. Genomic DNA that
had been digested with SacI, EcoRI,
HindIII, or ApaI (New England Biolabs) was
circularized by using T4 ligase and transformed into E. coli
DH5
by electroporation. Plasmid-containing transformants were
selected by plating electroporated cells onto solid Luria-Bertani
medium (19) containing KM (50 µg/ml) and incubating them
overnight at 37°C. After cloning the reporter transposon and flanking
DNA from each strain, cloned DNA was prepared for sequencing from cells
of E. coli by using Qiagen (Valencia, Calif.)
Maxi-Columns. Manual double-stranded DNA sequencing reactions were
performed with the Amersham (Arlington Heights, Ill.) Sequenase 2.0 Kit
and [35S]dATP with primers unique to each end of
Tn5-1062. Additional sequencing reactions were performed at
the Michigan State University Sequencing Facility. The DNA sequences
flanking each transposon insertion mutation were compared to existing
known nucleotide and protein sequences by using the BLAST 2.0 program
(National Center for Biotechnology Information, Bethesda, Md.
[1]) and the GCG (10) and DNASTAR (Madison,
Wis.) sequence analysis packages. Potential open reading frames (ORFs)
were identified by using CodonUse 3.1 (window size, 33; logarithmic
range, 3) for the Apple Macintosh, written by Conrad Halling
(University of Chicago).
Based on sequence similarities, putative gene identifications were
assigned to each cold shock locus (Table
1). Unexpectedly, five of the seven
mutants had insertions in rRNA genes; three in 16S genes (RM3166,
RM603, and RM518) and two in 23S genes (RM523 and RM73) (Fig.
3). Three rrn operons exist in
S. meliloti RM1021 (A. G. Gustafson, K. P. O'Connell, and M. F. Thomashow, unpublished data). To determine
whether we had isolated insertion mutations in each of the three
operons, we digested the genomic DNA of the five mutants and RM1021
with SacI, an enzyme that does not cut within
Tn5-1062, and separated the three wild-type rrn
operons on DNA fragments of different sizes (Fig. 3B). Hybridization
with radiolabelled 23S ribosomal DNA (rDNA) from S. meliloti
revealed that the insertions were located in two of the three
rrn operons (Fig. 3A). Probing with 16S rDNA from S. meliloti gave nearly identical results (as alluded to above,
RM3166 was found to contain a second transposon). The positions of each
insertion within the two operons were determined by using the sequence
of the DNA flanking each insertion (Fig. 3B). The results indicated
that cold shock induced expression of at least two of the three
rrn operons of S. meliloti. The characterization
of rrn-luxAB fusions and the effect of cold shock on
their expression will be described elsewhere (Gustafson et al.,
unpublished data).
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TABLE 1.
Putative identification of interrupted genes in mutants
of RM1021 demonstrating cold-inducible light emission
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FIG. 3.
Mapping of Tn5-1062 insertions. (A) Genomic
DNA from mutants containing Tn5-1062 insertions in
rrn operons cut with SacI and probed with
labelled S. meliloti 16S rDNA. Shifted bands indicate the
presence of the transposon in the corresponding SacI
fragment. (B) Maps of two rrn operons in S. meliloti showing the relative positions of Tn5-1062
insertions in five mutants as determined from hybridization analysis
and comparisons with known rRNA gene sequences. (C) Diagram of the
cspA region of RM1021 showing the relative positions of the
Tn5-1062 insertions.
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The transposon inserts in RM11 and RM509 were found to be located
adjacent to each other just downstream from a homolog of the major
E. coli cold shock gene, cspA (Table 1). The
transposon in mutant RM11 was inserted in the 5' end of the novel ORF;
the insert in RM509 was in the intergenic region between the
cspA homolog and the novel ORF. Presumably, cold
shock-induced expression of the reporter genes in these mutants
resulted from upregulation of the cspA homolog in response
to the low temperature.
Insertion of luxAB into all three rrn
operons.
Only two of the three rrn operons were
identified as putative cold shock loci by transposon mutagenesis.
Therefore, directed luxAB insertions in all three operons
were constructed to determine whether luxAB insertions in
the remaining operon could also be affected by cold shock. As described
above, a portion of the 16S gene from mutant RM603 was cloned by
circularization of Tn5-1062 and flanking DNA. A DNA fragment
containing a portion of the 16S gene and the luxAB and
kanamycin resistance gene of the transposon was cloned into the suicide
vector pSUP202, giving plasmid pKO4 (Fig.
4A). Conjugal transfer of pKO4 into
RM1021 and selection for kanamycin resistance yielded mutants in which
single homologous recombination events had occurred between the 16S
rDNA fragment on pKO4 and each of the three chromosomal 16S rDNA genes.
The insertion of pKO4 into each of the three rrn operons
resulted in a fusion of luxAB with each 16S rRNA gene at the
same position. The insertions were verified by restriction of genomic
DNA with SacI, blotting, and probing with 16S rDNA sequences
(Fig. 4B). Mutants X76 and X78 contained luxAB fusions in
the rrn operon not found in the initial mutant screen (Fig.
3). LuxAB activity increased in strains containing luxAB
fusions in each of the three rrn operons after a temperature
downshift from 30 to 15°C (Fig. 4C), suggesting that all three
rrn operons respond similarly to cold shock.

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FIG. 4.
Insertion of Tn5-1062a sequences into each
rrn operon (16S rRNA gene) by single homologous
recombination. (A) Plasmid pRM603 (the Tn5-1062a insertion
in mutant RM603 and flanking 16S rDNA) was cut with StuI and
HindIII. A HindIII linker was added to
the blunt StuI end, and the 16S rDNA
luxAB-oriA-kan fragment was ligated into the
HindIII site of pSUP202, which does not replicate in
S. meliloti, yielding plasmid pKO4. Conjugal transfer of
pKO4 to RM1021 and selection for resistance to kanamycin yielded
strains that had undergone single homologous recombination events
between pKO4 and each of the three chromosomal rrn operons.
(B) Verification of insertion of pKO4 into each rrn operon
by Southern analysis. (C) Induction of LuxAB activity by cold shock in
strain RM518 (positive control) and mutants with single crossover
insertions of pKO4 in each rrn operon.
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Effect of mutations on growth rate at 15°C.
To determine
whether mutations in the novel ORF and rrn operons affected
the growth of S. meliloti at a low temperature, we compared
the generation times of the wild-type and mutant strains in liquid TY
medium at 30 and 15°C. Triplicate cultures were grown in TY broth,
and cell growth was measured spectrophotometrically at 600 nm. Although
the results hint that there might be a small effect of the insertion
mutations on the growth rate at 15°C, the differences between the
wild-type and mutant strains were not statistically significant
(Student's t test). The doubling times of RM1021 were
2.1 h at 30°C and 13.1 h at 15°C. The doubling times of
the mutants ranged from 2.1 to 2.3 h at 30°C and from 14.3 to
15.5 h at 15°C.
Conclusions.
Our results suggest that all three of the
S. meliloti rrn operons are upregulated in response to a
low-temperature downshift. Finding rrn operons in a screen
for cold shock loci was unexpected; indeed, we are unaware of
rrn operons having been described as cold shock loci in any
organism. These results are intriguing given that many of the known
cold shock proteins in other species have functions associated with
translation. However, the results are counterintuitive since the rate
of rRNA transcription is generally tied to the growth rate of the
bacterium during balanced growth (6, 9), and the growth rate
of S. meliloti at 15°C is only about a sixth of the rate
at 30°C. One interesting possibility is that the rrn
operons might be induced in response to a perceived lack of
translational capacity (feedback response) (16) caused in
some manner by cold shock. Clearly, additional study of this phenomenon
will be required to understand its significance and possible role in
low-temperature adaptation. The finding that reporter insertions in all
three rrn operons respond similarly to cold shock is
consistent with the observation that rrn operons are
coordinately regulated in response to other stimuli (9).
S. meliloti also encodes a homolog of the E. coli
cspA cold shock gene. The observation that a 10.6-kDa protein is
encoded by a downstream putative cold shock gene is consistent with the finding of Cloutier et al. (7) that a protein of about 11.1 kDa accumulated after cold shock in all rhizobial strains studied. A
more complete characterization of this cold shock locus is reported elsewhere (18).
The isolation of multiple cold shock mutants with insertions in the
cspA and rrn operons indicates that our
mutagenesis was beginning to reach saturation. Yet the results of
Cloutier et al. (7) indicate that a number of S. meliloti proteins accumulate in response to cold shock. Why
didn't our screen result in the identification of more cold shock
loci? One possible explanation is that the regulation of many of these
cold shock proteins might not occur at the transcriptional level.
Moreover, a likely contributing reason is that our screen was largely
qualitative in nature; only strains that produced low levels of LuxAB
activity at 30°C and high levels at 15°C were identified as cold
shock mutants in the screen. Thus, the screen was biased toward
identifying class I-type (over 10-fold induced) cold shock loci;
indeed, we identified a cspA homolog. The identification of
class II-type loci, genes that are upregulated only a few fold by low
temperature, would likely have been missed in the screen due in part to
the fact that most inserts that resulted in the production of
luminescence were upregulated about two- to fourfold in response to
cold shock (presumably resulting from a general increase in
luxAB transcript and/or LuxAB protein stability at the cold
shock temperature). To identify class II- type genes in such a
background would require the screen to be conducted in a more
quantitative manner. This, however, is possible with digital
charge-coupled device imaging systems and can be incorporated into
future screens.
 |
ACKNOWLEDGMENTS |
We thank C. P. Wolk for providing pRL1062a and for assistance
with the photonic camera system. We also thank J. Jackson and D. Badillo for technical assistance in screening for cold shock mutants.
This work was supported by the National Science Foundation STC grant
DEB 9120006 in the Center for Microbial Ecology and by the Michigan
Agricultural Experiment Station.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Pharmacology and Experimental Therapeutics, University of Maryland
School of Medicine, 655 W. Baltimore St., Baltimore, MD 21201. Phone: (410) 706-4295. Fax: (410) 706-8012. E-mail:
oconnell{at}alum.mit.edu.
 |
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Applied and Environmental Microbiology, January 2000, p. 401-405, Vol. 66, No. 1
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Copyright © 2000, American Society for Microbiology. All rights reserved.
This article has been cited by other articles:
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O'Connell, K. P., Thomashow, M. F.
(2000). Transcriptional Organization and Regulation of a Polycistronic Cold Shock Operon in Sinorhizobium meliloti RM1021 Encoding Homologs of the Escherichia coli Major Cold Shock Gene cspA and Ribosomal Protein Gene rpsU. Appl. Environ. Microbiol.
66: 392-400
[Abstract]
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