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McrA Expression Gene
McrA Expression Gene
GENE 08535
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.
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
A C GT PE TABLE I
Plasmid pPA2 encodes a functional McrA protein
BL21 (DE3)[-pT7-7] 1
BL21(DE3)[pPA2] 4 x 10 -z +
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 ~ ~
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
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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