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Gene, 157 (1995) 201-207

© 1995 Elsevier Science B.V. All rights reserved. 0378-1119/95/$09.50 201

GENE 08535

Expression of the mcrA gene of Escherichia coli is regulated post-


transcriptionally, possibly by sequestration of the Shine-Dalgarno region*
(S1 analysis; primer extension; overexpression; regulation)

R. Shivapriya, Ranjan Prasad, Iyer Lakshmi Narayanan, S. Krishnaswamy and K. Dharmalingam

School of Biotechnology, Madurai Kamaraj University, Madurai-625 021, India

Received by R.M. Blumenthal: 28 May 1994; Accepted: 20 September 1994; Received at publishers: 20 October 1994

SUMMARY

The polypeptides encoded by the mcrA gene were analysed using a T7 expression system. Cloned fragments of 1.6
and 1.0 kb displayed an McrA +/RglA + phenotype and directed synthesis of a 31-kDa polypeptide. A derivative of these
clones altered at an internal HindIII site displayed an McrA +/RglA- phenotype and directed production of a 23-kDa
polypeptide. Smaller inserts displayed McrA-/RglA phenotypes, though a 0.7-kb insert did direct production of a
24-kDa polypeptide. A construct carrying the 1.0-kb mcrA insert yielded a single 1.3-kb transcript. The mcrA transcript
was found to start from C, G, T and G, namely the fourth, fifth, sixth and seventh nucleotides (nt), respectively,
downstream from the last nt of the putative - 10 region. Two mcrA transcriptional/transational fusions were made in
the pT7-7 expression vector and the protein encoded by these constructs were analysed. Regulation of mcrA expression
was studied by quantitative Northern analysis of RNA from various mcrA clones. Together with a computer analysis
of the translation initiation region in these mRNAs, the result~ suggest that the expression of mcrA may be regulated
at the translational level.

INTRODUCTION and Wilson, 1986; Noyer-Weidner et al., 1986) in specific


sequence contexts. The Mcr restriction systems are gov-
The Mcr restriction systems of E. coli restrict DNA erned by two loci, mcrA and mcrBC [ Raleigh and Wilson,
containing hydroxymethyl cytosine (hmC; Revel, 1967) 1986). The McrA system restricts DNA methylated by
and methyl cytosine (mC; Blumenthal et al., 1985; Raleigh M.HpaII (CmCGG; Raleigh and Wilson, 1986) and
M.SssI (mCG) (Kelleher and Raleigh, 1991). It also
Correspondence to: Dr. K. Dharmalingam, School of Biotechnology, restricts the hmC DNA of all T-even phages (Revel,
Madurai Kamaraj University, Madurai-625 021, India. Tel. (91-452)
1967), though wild-type phages are refractory to restric-
85-215~ Fax (91-452) 85-205; Telex: 445-337 MKU IN;
e-mail: dharm % bic-mku@dbt.ernet.in tion as the hmC residues are glucosylated: this restriction
*Presented at the Third New England BioLahs Workshop on Biological of glucose-less phage is known as RglA phenotype. The
DNA Modification, Vilnius, Lithuania, 22 28 May 1994. mcrA gene which has been mapped to 25.24 min on the
E. coli chromosome (Ravi et al., 1985; Raleigh et al., 1989)
Abbreviations: A, absorbance (lcm); aa, amino acid(s); Ap,
ampicillin; bp, base pair(s); DMSO, dimethylsulfoxide; GCG, Genetics has been sequenced and comprises a 831-bp ORF
Computer Group (Madison, WI, USA); hmC, hydroxymethylcytosine; (Ramalingam, 1990; Hiom and Sedgwick, 1991;
IPTG, isopropyl-13-D-thiogalactopyranoside; kb, kilobase(s) or 1000 bp; Ramalingam et al., 1992). This ORF could encode a poly-
Kin, kanamycin; nt, nucleotide(s); ORF, open reading frame; RBS, peptide of 277 aa (31.39 kDa).
ribosome-binding site(s); SDS-PAGE, sodium dodecylsulfate-
polyacrylamide-gel electrophoresis; ss, single strand(ed); Tc, tetracy-
In this communication the polypeptides from various
cline; TE, 10 mM Tris.C1/1 mM EDTA pH 7.6; tsp, transcription start mcrA constructs were analysed using the T7 expression
point(s); [], denotes plasmid-carrier state. system. The transcript analysis by primer extension

SSDI 0378-1119194)00746-2
202

located the tsp. Comparison of quantitative Northern codon introduced by frame shift (Fig. 2, lanes 7 and 8).
blots and translation products implied that protein syn- A slightly larger (24 kDa) polypeptide synthesized by
thesis is possibly regulated during translation. This possi- pDRR551.4 could be due to the absence of the stop codon
bility is supported by theoretical analysis of the in the insert while the nearest stop codon in the vector
secondary structure of mRNA in the translation initia- is not known, leading to an alternate C terminus.
tion region.
(b) Low-resolution SI analysis
Total RNA isolated from H R l l 2 carrying pBR322
RESULTS AND DISCUSSION with various mcrA segments were used for analysing the
number and size of the transcripts encoded by mcrA.
(a) Polypeptides encoded by mcrA Total RNA including the chromosomal mcrA transcript
Earlier results using mini cells (Ramalingam, 1990) isolated from W3110 and HR112 were used as controls.
showed that three polypeptides of 29, 18 and 17 kDa were In the construct carrying the 1.0-kb mcrA (McrA--,
encoded by a 1.6-kb PstI fragment carrying the mcrA RglA ÷ ) a single transcript of 1.3 kb was detected by the
gene. In order to confirm this, the T7 promoter expression mcrA probe (Fig. 3, lane 1). The size of the hybridising
system was used. Fig. 1 shows the constructs and their transcript is larger than anticipated, which could be due
McrA/RglA phenotypes. The polypeptides encoded by to the reduced mobility of RNA-DNA hybrid compared
these constructs are shown in Fig. 2. Plasmids to the DNA molecular mass markers. The constructs car-
pDRR551.3 and pDRR551.1 produced a single 31-kDa rying the 0,7-kb and the 0.9-kb fragments failed to make
polypeptide (Fig. 2, lanes 2 and 4) as predicted, while any detectable rectA-specific transcript (Fig. 3, lanes 3
pDRR551.2 failed to produce any protein, (Fig. 2, lane and 4). It is surprising that the 0.7-kb region did not
3). These results indicate that the direction of transcrip- make any transcript despite having all the promoter
tion is from left to right as shown in Fig. 1. Plasmid sequences intact. Possibly, sequences downstream from
pDRR551.4 yielded a 24-kDa polypeptide (Fig. 2, lane the H i n d l I I site have a stabilizing role on the mRNA. It
5), while pDRR551.5 failed to synthesize any polypeptide has been suggested by Wong and Chang (1986) and Mott
(Fig. 2, lane 6). Plasmids pDRR551.6 and 551.7 have 4-nt et al. (1985) that specific mRNA structures located down-
insertional mutation in the H i n d l I l site (cut, filled and stream from some genes have a stabilizing effect, possibly
ligated) and produce a 23-kDa protein due to the stop by acting as barriers to 3' exonuclease activity. The

TTP Phenotype
P H Hp P McrA RglA
I I I pDRR551.1 + +

l ORF I

ORF II ~H
P Hp P
I I .1 pDRR551,2 ÷ +
P H ~tp/Pv
I pDRR551.3 + +

I pDRR551,4 _ _

I I pDRR551.5 _ _
H
m_t I I pDRR551.6 + _
~I Hp/Pv
~.~_L I L pDRR551,7 + _

Fig. 1. Restriction map of pDRR551.1 and pDRR551.2, which carry the 1.6-kb PstI fragment in two differentorientations, with respect to the T7
promoter, weremade by ligating the 1.6-kb PstI fragment to pT7-1.3digested with PstI. Plasmid pDRR551.3, carryingthe 1.0-kb PstI-HpaI fragment
was constructed by digesting pDRR551.1 with HpaI+ PvulI followed by self ligation. The plasmid pDRR551.4, carrying the 0.7-kb PstI-HindlII
region, was constructed by digesting pDRR551.1 with HindlII followed by self ligation. The plasmid pDRR551.5, carrying the 0.9-kb HindlII-Pstl
region of rectA, was constructed by ligating the 0.9-kb HindlII fragmentobtained on restrictiondigestion of pDRR451.1 (pBR322 carrying the 1.6-kb
mcrA) with HindlII to pT7-1.3 resricted with HindllI and dephosphorylatedusing calf intestinal phosphatase. The plasmid pDRR551.6, carrying the
1.6-kb PstI fragment with a mutation in the HindlII site, was constructed by subjecting pDRR551.1 to partial digestion with HindlII followed by
electrophoresisand elution of the full-lengthlinear molecule.The ends were then filledwith dNTPs using Klenow fragment of E. coli DNA polymerase
I and ligated. The plasmid pDRR551.7, carrying the 1.0-kb PstI-HpaI region with the HindlII site mutated, was constructed by digesting pDRR551.6
with HpaI+PvulI followedby self ligation. P, Pstl; H, HindlII; H*, Filled-in HindlII site; Hp, HpaI; Pv, PvulI.
203

1 2 3 4 5 6 7 8 4 6
kDa kDa

66.2 - - kD

45-

31
29-

24
23
21.5 - - - 2.0

14.4 - - - 1.5

- 1.3

Fig. 2. Polypeptides encoded by mcrA constructs. The various mcrA


recombinants in the expression vector pT7-1.3 were used to transform - 0.9
iiii
E. coli HRll2[pGP1-2], which in turn carries the gene for T7 RNA - 0.8
polymerase under the control of the temperature-sensitive ci857 repres-
sor. The transformants were grown in 20 ml LB containing 50 ~tg Ap/ml
and 30 Ixg K m ml at 30°C until A55o was 0.6. Cells from 1.0 ml of culture - 0.5
were harvested, washed thrice in 1 x M9 solution, and resuspended in
1 ml of 1 x M9 solution. The culture was induced by shifting the temper-
ature to 42°C for 30 min. Rifampmm was added to a final concentration
of 500 ~tg/ml. and the culture was incubated for additional 15 min before
shifting to 30°C. The culture was incubated at 30°C for 30 min. The
proteins were labeled with [35S]methionine (20 l~Ci/ml) for 5 min
harvested, resuspended in 1 x sample buffer (62.5 mM Tris pH 8/2%
SDS/10% glycerol/0.5% 13-mercaptoethanol/0.025% bromophenol
blue). The samples were denatured in a boiling water bath for 5 min Fig. 3. Total RNA was isolated from HRI12 carrying pBR322 with
and analysed by 0.1% SDS-12% PAGE by loading equal counts in various mcrA fragments. Low-resolution S1 analysis was carried out as
each lane. Eventhough there is no chase period in this experiment, the described by Berk and Sharp (1977), with slight modification. Total
lower molecular mass band could not be due to translational pausing, RNA (25 ~g from recombinants and 100 fag from HRII2 and W3110)
since we could see only one band in each track. The gel was processed was precipitated with 100~tg of ssDNA from 19HL5 (19HL5 is an
for fluorography using 20%PPO in DMSO. Lanes: 1, pT7-1.3 (control); Ml3mpl9 recombinant carrying the 1.6-kb PstI fragment and the
2, pDRR551.1 (l.6-kb PstI); 3, pDRR551.2 (l.6-kb PstI); 4, pDRR551.3 ssDNA from this is complementary to mcrA mRNA). The pellet was
(1.0-kb PstI-HpaI); 5, pDRR551.4 (0.7-kb PstI-HindlIl); 6, pDRR551.5 air dried and resuspended in 20 lal of hybridisation buffer containing
(0.9-kb HindllI-PstI); 7, pDRR551.6 (1.6-kb PstI with the HindlII site 80% formamide. The sample was incubated at 80°C for 3 min to dena-
mutated); 8, pDRR551.7 (l.0-kb PstI-HpaI with the HindlII site ture secondary structure and shifted to 47°C for 3 h. The samples were
mutated). treated with 300 units of nuclease S1 at 37°C for 1 h. The reaction was
stopped by the addition of S1 stop solution. The RNA-DNA hybrid
was precipitated using cold absolute ethanol, after the addition of
absence of transcript m this case is consistent with the carrier tRNA. The pellet was resuspended in 20 p_l of TE and electro-
lack of McrA + phenotype. The HindIII site mutated con- phoresed on a 1.2% agarose gel along with DNA digested with HindIIl
and EcoRI. The electrophoresis was stopped when the dye reached 3/4
struct made two transcripts of sizes 1.3-kb and 0.75-kb of the length of the gel and transferred to nylon membrane using alkali
(Fig. 3, lanes 2 and 5). The relative abundance of the transfer buffer. The membrane was probed with radiolabeled 1.6-kb
smaller 0.75-kb transcript could be due to premature ter- PstI fragment of mcrA with high stringency. Lanes: l, pDRR451.3
mination of transcription. In W3110, the chromosomally (1.0-kb PstI-HpaI); 2 and 5, pDRR451.6 (1.6-kb PstI with HindlII site
mutated); 3, pDRR451.4 (0.7-kb HindIII-PstI); 4, pDRR451.5 (0.9-kb
located mcrA did not make a detectable level of tran-
HindIII-PstI); 6, W3110.
scripts, even when a tenfold excess of total RNA was
analysed (Fig. 3, lane 6). This could be attributed to
either a low transcription rate or to instability of the transcription terminators in either direction). A 15-nt
transcript, or both. primer, homologous to nt 17 to 32 downstream from the
ATG start codon, was used to prime synthesis of radiola-
(c) High-resolution transcript mapping beled complementary DNA strands with M-MuLV
Total RNA was isolated from HR112 carrying pRSD1 reverse transcriptase from the RNA template. The strands
(1.6-kb mcrA fragment cloned between rrnC and trpA were separated and loaded onto a sequencing gel along
204

A C GT PE TABLE I
Plasmid pPA2 encodes a functional McrA protein

Strain a Efficiency of plating b Inferred McrA


of LHpalI phenotype

BL21 (DE3)[-pT7-7] 1
BL21(DE3)[pPA2] 4 x 10 -z +

a The bacterial cultures were grown in LB medium containing 0.2%


maltose and I0 m M MgSO 4 at 37°C, without IPTG. Phage )~HpaII
was serially diluted, and 0.1 ml of each dilution was mixed with 0.2 ml
of cells and incubated at 37°C for 20 min. Soft agar (4 ml) was added
to each tube and the mixture was overlaid on bottom agar plates. Phage
)~HpaII is obtained by propagating phage L in a strain carrying
M.HpaII methylase clone.
b Efficiency of plating was calculated as the ratio of the titer of phage
on the test strain to that on the permissive strain HR112.

-35 -10 ~,~ . . . . RBS


1TG'rrGcAAITrTATCAATAAAAGTAGTA1"rGTCGTGAAAAA1-rGAITAAAGAIlAATAT is a new one created at the junction. The Plasmid pPN2
slan c,,don Alul (Fig. 5b) carries a 1.3-kb NdeI-PstI fragment of the mcrA
TATGCATG i i i i i GATAATAATGGAA'n'GAACTGAAAGCT
gene cloned between the NdeI and PstI sites of pT7-7.
ACCTTAACrrGACTr - 5" This fusion deletes 71 N-terminal aa of McrA and the
Fig. 4. High-resolution 5' tsp mapping of mcrA was done as described ORF now starts at the second ATG in the mcrA gene.
by Ausubel et al. (1987). Primer extension was done by M-MuLV
The polypeptides encoded by these two constructs were
reverse transcriptase with total RNA preparation from E. coil H R l l 2
carrying pRSD1 as the template source. Plasmid pRSD1 was con- labelled with [35S]methionine and analysed on SDS-
structed by cloning the 1.6-kb mcrA BamHI fragment into pFD666 PAGE. Plasmid pPA2 encoded a 29-kDa polypeptide as
(Denis and Brzezinski, 1992) which possesses rrnC and trpA trans- expected (Fig. 6, lane 2). This 29-kDa McrA polypeptide
cription terminators flanking the multiple cloning site. Primer
was found to form inclusion bodies and was visible by
5'-TTCAGTTCAATTCCA anneals to a sequence spanning 17 32 nt
downstream of the ATG start codon. The newly synthesized strand was Coomassie staining (data not shown). The overexpressed
labelled by 1-32P]dATP in the reaction. The strands were separated on 29-kDa McrA accounted for 4-6% of the total protein
a 9 M urea-8% polyacrylamide sequencing gel. A sequencing reaction based on a densitometer scan of the gel.
done with the same primer and a mRNA equivalent ss DNA template The McrA phenotype caused by the gene fusion in
was loaded alongside. The tsp have been marked with asterisks. Putative
- 3 5 , - 1 0 and RBS sequences have been shown. Arrows indicate the
pPA2 was determined and is shown in Table I. Under
two other probable tsp. ATG start codon and primer annealing region uninduced condition due to leaky expression the 29-kDa
are also shown. PE, primer extension. protein displayed McrA activity but no RglA activity.

with a sequence ladder made with the same primer and (e) Regulation of mcrA expression
single stranded DNA template corresponding to mcrA Quantitative Northern analysis was carried out using
mRNA. Asterisks in Fig. 4 show transcripts originating total RNA isolated from induced or uninduced cultures
from C, G, T and G, namely the fourth, fifth, sixth and of BL21(DE3) carrying pDRR551.1, pPA2 or pPN2.
seventh nt respectively downstream from last nt in a puta- Total RNA from HR112 carrying pBR322 with the 1.6-kb
tive - 1 0 sequence. Two other probable tsp have also PstI fragment served as control. The results are shown
been shown with arrows. Sequences in the - 10 and - 35 in Fig. 7. Equal amounts of mcrA specific mRNA was
regions are in accordence with the conserved pattern of made by all the three constructs. This suggested the possi-
normal E. coli promoters (Oliphant and Struhl, 1988; bility of regulation at the level of translation, since pPN2
Hawley and McClure, 1983). did not make any protein and the 31-kDa McrA from
pDRR551.1 is not made in enough quantities to be
(d) Overexpression and regulation of mcrA expression detected on Coomassie staining (data not shown).
Two mcrA translational fusions were made in the Low translational efficiency could be due to either of
expression vector pT7-7, which carries the strong T7 RBS the following reasons. (i) The native RBS is not strong
in addition to the T7 promoter. Plasmid pPA2 (Fig. 5a) enough. The proposed RBS sequence for mcrA is
carries the 1.5-kb AluI-PstI fragment of mcrA gene, 5'-AAGA whereas the consensus sequence found in most
cloned between the Sinai and PstI sites of pT7-7. The of the efficiently expressed proteins is 5'-UAAGGAGG.
resulting fusion replaces 13 N-terminal aa from McrA Gold (1988) reported a threefold higher translational
with 6 aa from the pT7.7 vector. The seventh codon (Pro) rate in vivo for mRNA containing the sequence
205

Hincll Hlnoll

/_ ~:~,,,

/
/
/"
//
/// ~T7

__
b Z/ [
/ I 1
C GA'i-r C GAAC'i-rC T C G ATT CG A A C "FI'CT GATAG A C'I'TC(~AAATTA,t, TAC GACT CA C T.8.TAGGG ~ ~

Met AJa Arg tie

XDal R~IS Ndel EcORI


AtIIA AII Pm Qlu ~ ~ l t I~J

271 Xbal RB$ NdoI

Fig. 5. The plasmid map of pPA2 (a) and pPN2 (b), with the nt and aa sequence around the fusion region is shown. (a) Plasmid pPA2 was constructed
by subjecting the 1.6-kb PstI fragment to partial digestion with AluI and ligating it to pT7-7 (Tabor and Richardson, 1985) cut with Sinai + PstI.
Fusion of the first AluI site in the mcrA gene with the SmaI site in pT7-7 maintains the reading frame. This results in deletion of 13 codons from the
N terminus of merA and addition of six codons from the vector. In addition, the seventh codon at the junction region codes for a new aa Pro
(underlined). The in-frame fusion was verified by sequencing the fusion region. The number denotes aa in fusion products. (b) Plasmid pPN2 was
constructed by ligating the 1.3-kb Ndel-PstI fragment of the mcrA gene with pT7-7 cut with NdeI+PstI. This resulted in the fusion of ATG in the
ORFII of mcrA gene with that of the vector thus maintaining the reading frame. The numbers denote aa in fusion products.

1 2 3 INDUCED UNINDUCED
I ! I I I I pDRR
51,
I
t ~i~i~ t t Control
t ~ pPA2

l w ,o
Control

Fig. 7. Quantitative Northern blot. Total RNA isolated from


HR112[pDRR451.1] 11.6 kb, pBR322 construct) and from uninduced
and induced culture of BL21(DE3) carrying pDRR551.1, pPA2 or
pPN2, was serially diluted (0.325-5.0 lag) in 2 x sample buffer containig
80% formamide. The samples were denatured by keeping at 65°C for
15 min and were then immediately plunged into ice. Two volumes of
--29kDa 20 x SSC were added and the samples were applied to a nitrocellulose
membrane, using Hoefer's slot blot apparatus. The membrane was then
probed with radiolabelled 1.6-kb mcrA DNA. Arrows show slot blots
of 1.6-kb probe DNA control. SSC=0.5 M NaCI/0.015 M Na3.citrate
pH 7.6.
i
!

i
! 5'-UAAGGAGG compared to t h e m R N A containing
!
5 ' - A A G G A as the R B S s e q u e n c e . R i n g q u i s t et al. (1992)
h a v e also r e p o r t e d s i m i l a r results for l a c Z e x p r e s s i o n . (ii)
T h e R B S is n o t freely accessible for b i n d i n g to t h e r R N A
! b e c a u s e p o s s i b l e s e c o n d a r y s t r u c t u r e s f o r m in the t r a n s l a -
Fig. 6. Polypeptides encoded by pPA2 and pPN2 (sse Fig, 5) were ana- t i o n a l s t a r t region. It is k n o w n that, a p a r t f r o m the R B S ,
lysed using E. coil BL21(DE3), which carries the gene for T7 RNA poly- the nt s e q u e n c e s p r e s e n t u p s t r e a m a n d d o w n s t r e a m f r o m
merase under the control of the lacUV5 promoter in an int- prophage. t h e R B S p l a y a r o l e in t r a n s l a t i o n (Steitz, 1975; S c h n e i d e r
The cultures were grown at 37°C in 1 x M9 medium until A55owas 0.6. A et al., 1986; Bingham and Busby, 1987; Olins and
1-ml culture was induced with IPTG (0.4 raM) for 30 min. Rifampicin
R a n g w a l a , 1989).
was added (500 lag/ml) and incubated for an additional 30 min. after which
the proteins were labeled with 20 laCi [ a5S]methionine and analysed by Possible secondary structure around the translation
0.1% SDS-12% PAGE. Lanes: 1, pT7-7; 2, pPA2; 3, pPN2. i n i t i a t i o n r e g i o n in m c r A m R N A was assessed u s i n g the
206

p r o g r a m F O L D of the G C G package (Devereux et al., pressed using the pPA2 construct. The t r u n c a t i o n of the
1984). The results are s h o w n in Fig. 8. It is evident that N - t e r m i n a l 13 aa a n d s u b s e q u e n t fusion with 6 aa from
the RBS in p P N 2 m a y be sequestered in the secondary pT7.7 abolishes RglA activity a n d so does the H i n d I I I
structure, whereas it appears to be freely accessible in frame-shift m u t a t i o n that occurs at the C - t e r m i n a l end.
pPA2 a n d partially free in pDRR551.1, consistent with However, the M c r A p h e n o t y p e is retained in both
the levels of expression obtained. situations.
(5) The expression of m c r A is regulated at the level of
(f) Conclusions translation.
(I) The m c r A gene encodes a 31-kDa protein.
(2) Frame-shift m u t a t i o n at the H i n d l I I site within
m c r A leads to the p r o d u c t i o n of a t r u n c a t e d polypeptide
ACKNOWLEDGEMENTS
of 23 kDa, a n d the strains carrying these m u t a t i o n s are
R g l A - b u t M c r A ÷.
This work was s u p p o r t e d by D e p a r t m e n t of Science
(3) T r a n s c r i p t i o n of the m c r A gene starts from C,G,T
and Technology, Government of India grant,
a n d G, n a m e l y the fourth, fifth, sixth a n d seventh nt, SP/SO/D-50/91. We wish to t h a n k Dr. E,A. Raleigh for
respectively, d o w n s t r e a m from the last n t of the putative
the i m p r o v e m e n t of the m a n u s c r i p t a n d Dr. M.G.
- 10 sequence.
M a r i n u s for his suggestions.
(4) A t r u n c a t e d (29 kDa) M c r A p r o t e i n can be overex-

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