Molec. gen. Genet. 133,299--316 (1974) © by Springer-Verlag 1974

Physiology and Genetics of Carbamoylphosphate Synthesis in Escherichia coli K12 Max Mergeay, Daniel Gigot, Jacques Beckmann, Nicolas Glansdorff, and Andr6 Pi6rard Laboratoire de Microbiologie de l'Universit~ Libre de Bruxelles, Erfelijkheidsleer en Mikrobiologie, Vrije Universiteit Brussel and Institut de Recherches du C.E.R.I.A., Brnxelles Received July 9, 1974 Summary. 76 mutants have been isolated in which the function of the single carbamoylphosphate synthetase of Escherichia coli K 12 is affected. A wide variety of phenotypes have been observed among these mutants, the most typical ones being: requirement for arginine and uracil, arginineless behaviour, sensitivity towards arginine and sensitivity towards uracil. The mutations have been localized by reciprocal transduction and deletion mapping; all are clustered in the same locus, car. The study of carbamoylphosphate synthesizing activities of these mutants and the combination of car mutations in various in vivo as well as in vitro complementation tests lead to the conclusion that car contains two genes: carA, covering the left part of the locus and coding for the" glutamine subunit" of the enzyme; carB, to the right, governing the synthesis of the heavy subunit of the enzyme.

Introduction Carbamoylphosphate (CP) is involved directly in the biosynthetic pathways of arginine and the pyrimidines of which it is a common precursor. In some euearyotes and particularly in fungi, CP is synthesized by two distinct enzymatic systems which are integrated into autonomous regulatory circuits corresponding to the arginine and pyrimidine regulons. This situation does not prevail among procaryotcs: single mutations which result in a simultaneous requirement for pyrimidines and arginine have been described in Escherichia coli and other enteric bacteria (Roepke, 1947 ; Beckwith et al., 1962; Prozesky and Coetzec, 1966; Yan and Demerec, 1965), in Pseudomonas aeruginosa (Loutit, 1952), in Streptomyces coelicolor (Hopwood, 1967) and probably in Bacillus subtilis (Issaly et al., 1970). The existence of such mutations suggests that a unique enzymatic system catalyzes the synthesis of CP required for both biosynthetic pathways. I n E . coli, these biauxotrophic mutations have been shown to affect a single carbamoylphosphate synthetase whose synthesis is subject to cumulative repression by arginine and pyrimidines. This enzyme uses glutamine as the amino group donor for CP formation (Pi6rard and Wiame, 1964). Ammonia can replace glutamine i n vitro but probably has to be ruled out as a physiological substrate of the enzyme in view of the low affinity exhibited by the enzyme towards this amino group donor (Anderson and Meister, 1965; Kalman, Duffield and Brzozowski, 1966). Khedouri et al. (1966) have shown that the binding of glutamine to the enzyme is followed by the transfer of the amide group to another site of the

300

M. Mergeay et al.

enzyme which is also able to bind ammonia. More recently, Trotta et al. (1971) characterized the enzyme from E. coli B as an aggregate of two kinds of subunits. A heavy subunit (molecular weight 130000) is able to catalyze the synthesis of CP from ammonia, HCO~ and ATP; it also bears the binding sites for the effectors of the enzyme. A light subunit (molecular weight 42000) is responsible for the capacity of using glntamine and bears the binding site for this substrate (Pinkus et al., 1972). During the study of the regulation of carbamoylphoshpate synthetase, several mutants, or revertants of biauxotrophie mutants exhibiting sensitivity to pyrimidines were obtained (Novick and Maas, 1961; Gorini and Kalman, 1963; Pi6rard et al., 1965). The study of that sensitivity led to the demonstration that uridine 5'-monophosphate (UMP) is a feedback inhibitor of the wild type enzyme (Pi6rard et al., 1965). Further in vitro studies have shown that the inhibition can be antagonized by ornithine (Pi6rardi 1966) or inosine 5'-monophosphate (Anderson and Meister, 1966). Since the cellular pool of ornithine is under the control of arginine through feedback inhibition of acetylglutamate synthetase (E.C. 2.3.1.1), the first enzyme of the arginine pathway (Vyas and Maas, 1963), the antagonistic effects of UMP and ornithine on the activity of carbamoylphosphate synthetase provide an efficient way of controlling the supply of CP according to the needs of both the arginine and pyrimidine pathways. Such a balanced distribution is typical of the "single enzyme" solution to the control problem of branching metabolic pathways. The control of carbamoylphosphate synthetase in Salmonella t y p h i m u r i u m is very similar to that of E. coli (Abd-E1-A1 and Ingraham, 1969a). In E. coli, the mutations affecting carbamoylphosphate synthetase (Pi6rard et al., 1965) lie in the locus car I presumably synonymous with the p y r A locus of S. typhiraurium (Yan and Demerec, 1965). Various non-auxotrophic phenotypes have been obtained in addition to mutant forms of car which exhibit a double requirement for arginine and pyrimidines. Such mutations of the car locus do not completely abolish CP synthesis but lead to perturbations in growth following the addition of arginine or pyrimidines to the growth medium. In all cases, the optimal growth rate is restored by the simultaneous addition of arginine and a pyrimidine base or ribonucleoside. Previously described phenotypes include, in addition to sensitivity to uracil: the partial release of the double auxotrophy due to higher concentrations of a substrate, HCO~ (Charles and Roberts, 1968; Mergeay, 1969). sensitivity to arginine (Pi6rard et al., 1965; Eisenstark, 1967; Abd-E1-A1 and Ingraham, 1969b; Mergeay, 1969). Suboptimal growth rate in the presence of arginine alone (Abd-E1-A1 et al., 1969; Mergeay, 1969). 1 The symbol cap, used for this locus in previous communications (Pi6raxd et at., 1965; Pi~rard st at., 1973), has been discarded in order to avoid confusion with other loci. The symbol pyrA which has been proposed for the Salmonella locus (Yan and Demerec, 1965) and was also used for the E. coli locus (Taylor and Trotter, 1972) is misleading for another reason: indeed, the biosynthesis of CP has to be considered as separate from the arginine and pyrimidine pathways. Therefore, we propose the new symbol car and, as the locus comprises two adjacent genes, carA and carB.

Physiology and Genetics of Carbamoylphosphate Synthesis in E. coli

301

I n this p a p e r we p r e s e n t a f u n c t i o n a l a n d fine s t r u c t u r e analysis of t h e car locus, p a y i n g p a r t i c u l a r a t t e n t i o n to t h e t o p o g r a p h y of those m u t a t i o n s which do n o t m a k e E. coli c o m p l e t e l y d e p e n d e n t on a s i m u l t a n e o u s s u p p l y of arginine a n d uracil. W e shall describe t h e isolation of car m u t a n t s b y t h e use of various m u t a gcns, t h e physiological analysis of t h e m u t a n t s o b t a i n e d , t h e d e t e r m i n a t i o n of t h e m u t a t i o n classes b y responses to m u t a g e n s a n d to nonsense suppressors, t h e physiological analysis of t h e r e v e r t a n t s o b t a i n e d a n d t h e t r a n s d n c t i o n a l genetic m a p p i n g a n d t h e f u n c t i o n a l analysis of t h e locus. Our results i n d i c a t e t h a t t h e car region contains t w o genes: carA coding for t h e " g l u t a m i n e " s u b u n i t , a n d carB for t h e " a m m o n i a " s u b u n i t of c a r b a m o y l p h o s p h a t e s y n t h e t a s e . These conclusions were r e a c h e d t h r o u g h t h e s t u d y of CP s y n t h e s i z i n g activities of t h e v a r i o u s car m u t a n t s a n d following t h e sucessful p e r f o r m a n c e of in vitro as well as in vivo c o m p l e m e n t a t i o n t e s t s b e t w e e n car m u t a t i o n s l o c a t e d in t h e left (nearer to thr) a n d r i g h t (nearer to lea) regions of t h e locus. Materials and Methods Media The minimal medium (132), the liquid broth (869) and the medium for phage experiments (857) have been described previously (Glansdorff, 1965). The final concentration of carbon source (glucose, lactose, for example) in the minimal medium was 0.5 %. Metabolite requirements were satisfied as follows (final concentrations): L-arginine, L-ornithine, L-citrulline, 100 ~g/ml; DL-leucine, 80 ~g/ml; L-histidine, L-methionine, adenine, 50 ~g/ml; OL-threonine, 200 ~g/ml; thiamine, 1 ~g/ml; uracil, 50 or i00 tzg/ml. Strains Most of the mutants described in this work were obtained from strains P4X (Hfr metB or Hfr metB thrA) and CA244.1 (F+ carrying a trp and a lac amber, UAG, nonsense mutation). For the genetic analysis, car mutations were introduced by tranduetion into strain P678. Thr- Car- Leu+ recombinants were selected and purified. We are grateful to Drs. D e Haan, Lavall6 and Grainger-Roberts for gifts of mutants. Mutagenesis and M u t a n t Selection by the Penicillin Method a) Selection of mutants by penicillin treatment was performed according to the procedure of Gorini and Kaufman (1960). The non-selective medium was minimal medium supplemented with arginine (100 tzg/ml) and uracil (50 ~g/ml). The selective medium was either minimal medium or minimal medium supplemented with arginine or uracil, according to the required mutant class. b) Mutagenesis with N-methyl-N'-nitro-l~-nitrosoguanidine (NG) was performed according to the procedure of Adelberg et al. (1965) with a NG concentration of 300 ~g/ml. Genetic A n a l y s i s Genetic analysis was performed by transduction with the E. coli phage 363 (Jacob, 1955) following the method previously described (Pi~rard et al., 1965; Glansdorff, 1965). The cotransducible marker used as topological reference was the thrA mutation of the P678 strain of Lederberg (see Bachmann, 1972). In these transductions the recipients were all of the Thr- Car- type and the donors were Thr + Car-. Two mapping characteristics were examined: tentative distance estimates between two markers (ratio of Car + to Thr + recombinants)

302

M. Mergeay et al.

location of car mutations, carried out with respect to deletion carB8 and from the results of pairs of transductions in different coupling phases as described earlier (Pi6rard et at., 1965), a n d recalled in the text.

Response to Mutagens Responses to the following mutagens were investigated (Whitfield et at., 1966) : N-methylN'-nitro-N-nitrosoguanidine, 2-aminopurine (2AP), diethyl sulfate (DES), ethyl methane sulfonate (EMS) and ICR-191A (a substituted acridine able to induce frameshift mutations).

Nonsense Mutations Nonsense mutations in strain CA244.1 (car, trp(UAG), /ac(UAG)) were detected b y transduction of nonsense suppressors into the strain. One step Trp + Lac + transductants were selected and suppression or phenotypic modification of car mutations was assayed. The tested suppressors were supD, supE, supF (amber), supB and supC (ochre). Nonsense car mutations of Hfr P 4 X were detected b y infecting Car+ revertants with MS2 phage harbouring nonsense mutations (Van Montagu et at., 1967). We t h a n k Dr. R. Thomas for providing suppressor strains and Dr. Van Montagu for the MS2 phage mutants.

Functional A n a l y s i s a) Abortive Transduction. Microeolonies of abortive t r a n s d u c t a n t s ( H a r t m a n et at., 1960) resulting from complementation between car mutations were looked for under a binocular microscope at a magnification of 40. The cells were poured onto the agar surface of s t a n d a r d Petri dishes containing 40 ml of glucose minimal agar supplemented with uracil. I n the presence of uracil absolutely no growth of any car m u t a n t is observed a n d in particular, no microcolonies appear when a few hundred donor type cells are added to the recipient lawn. I n C a r - × Car + transductions, the microcolonies become visible after 40 hours and are 3 to 5 times as numerous as ordinary transductants. I n Car- × Car- transductions, the microcolonies, when present, o u t n u m b e r the ordinary transduct~nts by a factor of 20 to 50. b) Formation o] Stable Merodiptoids. A recA strain harbouring a F ' carrying the carB8 marker was constructed according to the method of Low (1968). The strain KA158 (recA thr.leu.pro-his-thi.Str-r lac-gal) used to trap the episome was a gift from Dr. I. Mattern. The car male strain crossed with this recA strain was a Thr+ curB8 Leu+ Pro + t t f r of the P 4 X type, which transfers markers in the order pro-leu-ara-car-thrA. A Thr + Car+ Leu + recombinant was obtained which transfers a n episome carrying the whole thr-pro region. Mating with thrA car recipients was performed in broth with exponentially growing cultures at a cell density of 4.10S/ml with a F - / F ' ratio of 1011, for 40 rain at 37 ° C. Cells were then poured on plates selecting for Thr+ Car+ or Thr+ recombinants and recombinants were counted after 30 h r incubation at 37 ° C. Preparation o / B a c t e r i a l Extracts and E n z y m e A s s a y The car m u t a n t s which exhibit complete auxotrophy for arginine a n d uracil were grown on minimal medium supplemented with an excess of arginine (100 ~zg/ml) and a limiting a m o u n t of uracil (5 tzg/ml). Cells were harvested at least two hr after growth h a d stopped, to allow for derepression. Leaky car m u t a n t s were grown on minimal medium or minimal medium supplemented with arginine a n d harvested at mid exponential phase. Ceils were suspended in 0.05 M potassium phosphate buffer, p t I 7.5 and sonically disrupted for 3 rain in a M.S.E. Mullard disintegrator. Cell-extracts were centrifuged for 10 rain a t 10000 × g a n d dialyzed b y filtration through Sephadex G25. Carbamoylphosphate synthetase activity was estimated b y coupling it with ornithine earbamoyltransferase (E.C. 2.1.3.3) in the presence of 0.006 M ornithine. This method, which provides the most sensitive assay of earbamoylphosphate synthetase in crude extracts has been previously described (Pi~rard et at., 1972). The activity was measured with either 0.01 M glutamine or 0.1 M NI-I4C1 as the nitrogen donor.

Physiology and Genetics of Carbamoylphosphate Synthesis in E. coli

303

I n vitro Complementation Tests Equal volumes of extracts of mutants to be tested (each containing similar protein concentrations, 3 to 4 mg per ml) were mixed and incubated at 370 C. After 10 rain incubation, carbamoylphosphate synthetase activities with glutamine and ammonia were determined as previously described (Pi~rard et al., 1972). Cell-extracts used in the early in vitro complementation tests were dialyzed on Sephadex G25. However, this treatment was found unnecessary and wa~ dropped for the routine complementation tests. Purified subunits of E. coli K12 carbamoylphosphate synthetase used in a few complementation tests were prepared according to Trotta et al. (1971).

Results Mutant Selection and Phenotype Analysis 76 mutants deficient in CP synthesis are described in this study. Table 1 gives some of the more diversified responses of these mutants. A high percentage of them exhibits phenotypes which differ from the double auxotrophy for arginine and uracil. These non-auxotrophic mutants, three of which have been described previously (Pi@rard et al., 1965 ; Charles and Roberts, 1968) may for convenience be classified into four main groups:bradytrophic, auxotrophic for arginine, arginine sensitive and uracil sensitive. I n addition, the growth of several mutants is stimulated by the supplementation of carbon dioxide to the gas phase. In particular, carbon dioxide reverses the sensitivity to uracil of a large proportion of the uracil sensitive mutants (see Table 1). The response of the car mutants to an increased concentration of ammonium ion in the growth medium was also studied. The growth of eight of the mutants is significantly improved under such conditions (Table 1). Some revertants of frameshift mutants or suppressed clones of nonsense mutants exhibit phenotypes similar to those of non-auxotrophic mutants. For example, m u t a n t car-591 is reverted to wild type with supF (which incorporates tyrosine), car-591 containing a supE mutation requires arginine alone, car-602 responds to three amber suppressors, supD, supE and supF but in the three cases, the response obtained differs from the wild type. All three organisms are highly sensitive to uracil. The combination car-602 snpE (glutamine insertion) does not allow growth on minimal medium, unless arginine is provided, car-602 supD (serine insertion) grows slowly on minimal medium, grows well on minimal medium plus arginine; car-602 supF (tyrosine insertion) grows well on both arginine and minimal medium. Thus there appears to be a phenotype gradation from supE to

supF. Among revertants from presumed frameshift mutants (spontaneous or ICR induced, ICR and/or DES revertible, auxotrophic for arginine and uracil), some are wild type and some others have a m u t a n t phenotype, car-66 gives only wild type revertants. Among the spor~taneous or ICR induced revert~nts from car-121, the majority have a wild type phenotype, but a few are sensitive to both arginine and uracil, rare ones are only sensitive to uracil. All ICR induced revertants of car-175 are sensitive to arginine.

Genetic Map o/the Locus The map of the car locus presented here (Fig. 1) is an extension of the previously published one (Pi@rard et al., 1965).

304

l~I. Mergeay et al.

oo VV

ddddddddddddddd V VV

V

ddddddd VVV VVV

~.~ VV

V

VVV

V

VVV

VVV

+ + ÷ ÷ + + ÷ + + + ÷ + ÷ + + ÷ + ÷ + + + + + + ÷ ÷ + ÷ + ÷ ÷ + + ÷ ÷ ÷ + ÷ + ÷ ÷ ÷ + + ÷ + + + + + + + + +

00

~.~

IIIII

I I I I I I I [ I I~1~1

~ I I +

i I~l

+~

+~lf

0

i

o

4

I I [ ++

I

++ I ~÷÷~

[ I t I I I I

J I [ I I I I I I

~++*l-~lllllll

Physiology and Genetics of Carbamoylphosphate Synthesis in E. coli

V

VVVV

V

VVV

÷++÷÷ ÷++÷÷

+÷+++÷+ ÷+÷÷÷÷÷

®

-~I ] I÷+

21

Molec. gen Oenet. 133

V

V

VVVVVVVV

VVVV

÷÷÷÷÷++÷÷+++ ÷÷÷+++÷÷÷+÷÷

I I I I I J~l

÷ ÷ i i I-F-÷ I -~I i L L+-F-÷

VVV

•

I r I I I r+

I q n÷ n

V

+÷÷÷÷÷÷÷÷ +÷÷+÷÷÷÷÷

o ~

I I I I+

V

I

I I

i [ I r [ i I I n

i [

•

• J J n J J -J--~

J ~-

j J

lille

+

ll++I

305

M. M e r g e a y et a~.

306

o VVVVVVV

b "r.

dddddd V

VVVVVVV

¢+

~

V

+

o "~

'~

~

~

o

~'~

•~

~

o

_

~

~ ~.~ =~ o.-

~

~°

+++++++++++++++ +++++++++++++++

0

,-~

"~

0

0

0

IIIIII

II

IIII

II[III

I-H

÷ ++÷+I

IIIIII

I+

÷ ++++I

°~

!

~ =7

,-¢1

,-~ o

~,.o

i

~,~,~

~ ~.~.~ ~

Physiology and Genetics of Carbamoylphosphate Synthesis in E. coli car A

car B

I

[]

115

so

[]

I

I

594

1~7 '

19o I

51 I

I

A,

[]

~

[~7 I

J'

6s I ~

[] []

21 62 32 63

4 101 12 602 40 504

11

[ffTl

307

I

B-~

117

[]

libel

~2~/

~

A

182

1003

34

42

i75

I

I

i

i

i

car B8

deletion

Fig. 1. Fine structure map of the car locus. The data given in Table 2 have been used for ordering the car mutations. In addition, transductions have been performed between the carB8 mutation and 29 of the car mutations mentioned on the map. Wild type recombinants were obtained with car 177, 45, 70,190, 221, 522 and 1002; no wild type recombinants were obtained with car 51, 594, 1001, 4, 40, 66, 1003, 101, 604, 801, 803, 34, 42 and 55 (no Car+recombinants for a total of 104 Thr+) nor with car 61, 223, 602, 21,13,117, 222 and 121 (no Car+ recombinants for a total of 2.10s Thr+). Squares indicate mutations which do not confer auxotrophy for arginine and uracil. This map has not been drawn to scale. Some distance estimates are given in Fig. 2

Pairs of new mutations have been mapped, as was done before, by determining their relative order with respect to the thrA locus. Transductions were performed between thrA car recipients and Thr + car donors. Cotransduction of thrA and car is about 50 %. Therefore, in the absence of negative interference, the proportion of Car+ recombinants being Thr+ will approach 50 % if the order is : t h r A - r e c i p i e n t car m u t a t i o n - - d o n o r car mutation. I n the reciprocal configuration, when the donor car mutation is switched to the recipient strain and vice-versa, a lower % is expected. The first configuration usually gives a value of 35 to 55% and the reciprocal arrangement 15 to 30% (Pi6rard et al., 1965). Table 2 gathers the results of the crosses. The presentation follows the pattern used by Syvanen and Both (1973) in a recent paper on the genes coding for aspartate earbamoyltransferase. The donor and recipients markers are listed in order of increasing distance from the thrA locus. The diagonal line divides the table into "large" a n d " small" %. The donor marker of a given row is to the right of all recipient markers corresponding to data listed on the left side of the line. The recipient marker of a given column is to the right of all donor markers corresponding to data listed above the line. Fig. 1 presents the order that seems to be denoted by the data reported in Table 2. I t also indicates the extent of deletion car-8, which the functional analysis (see below) shows to be confined to carB. The order presented in Fig. 1 is supported by the distance estimates reported in Fig. 2. The following two major points can be made: Over the whole length of the locus, mutations which are expressed by non-auxotrophic phenotypes are interspersed with mutations leading to complete auxotrophy for arginine and uracil.

308

M. M e r g e a y et al. T a b l e 2. P e r c e n t a g e T h r +

Donor

car m u t a t i o n s of

cA~r

mutation

177

178

44

FR

50

190

1

115

2

12

22

16

17

177 50

522

1002

51

223

11 a

15 a

6 20

1 45

46

7O

50

34

50

45

26

FR

31

I 16

44

221 522

221

16 12

16 50 a

45 41

38 a

51

14 23 c

I

47 a

33

1002

[ 25°

l0 s 16

36

5O

31 a

9c 36c

35

35

33 c

45

14 c

21 a

37 • 25 c

25c

20 a

61 124

51 39 a

223

39 a

594 1001

39

42 a

801

52

36 b

35 a

37a

33

40

32

38

28

66

43

28

101

27

27 b

4O 604

48

8O3

40

43

4

28

8O 671 34 13

59 30

40 a

44

34 b

41 s

36b

41 a

40 33 b

222

30 b

117 32

1003 62

44 s

44 36 a

32

49

63 42

49 a

37 29 a

T h r e e 3oints t r a n s d u c t i o n s . N u m b e r s give t h e % of T h r + r e c o m b i n a n t s a m o n g t h e Car + r e c o m h i n a n t s for e a c h t r a n s d u c t i o n . S u p e r s c r i p t s a, b, c refer to crosses w h i c h h a v e b e e n m a d e in reciprocal c o u p l i n g p h a s e s . S u p e r s c r i p t a i n d i c a t e s t h a t t h e differences o b s e r v e d b e t w e e n t h e % o b t a i n e d in a p a i r of reciprocal t e s t s is h i g h l y significant ( p ~ 0 . 0 5 ) . S u p e r s c r i p t b indicates a lower significance ( 0 . 0 5 < ~ 0 . 1 0 ) , a n d s u p e r s c r i p t c indicates a m b i g u i t y . R e s u l t s of s u c h a m b i g u o u s crosses are

Physiology ~nd Genetics of C a r b a m o y l p h o s p h a t e Synthesis in E. coli

309

a m o n g Car + r e c o m b i n a n t s t h e thrArecipient 11

1001

12

182

9a

34

222

117

32

21

42

18

121

175

14 a

10

12 a

7a

15

13

16

27 b 25

25 a

22

27

21 b

14

24 b

27 b

11 a

23

22

17 a FR

18

5

FR

17 a

23 ~

17 a 7 13

17 b

I FR

27

19 19

FR 28 40 FR

17

26

22 b

12

16

12 21

23 a

25 a

18 a

16 a

15

26

13

5

6

10

16

11

12

10

10

FR

12

FR

7 19

24

8

11 14

23

14

10

32

FR

13 34

36 a

FR

18

20

16

30 47

43

42 a

18

23

20

14 a

8

FR

, 7a

FR

16 a

19

31 38

8

33

8

7

11

18

20

21 22 b 30 c

10

I

6O

23 c

24 b

40 a

34

31 a

40

FR [

13 b

18

I

39 a

30 c

I 15

1

10 b

16

clustered o n or n e a r t h e diagonal line. F R refers to crosses giving v e r y few r e c o m b i n a n t s , t h u s n o t allowing meaningful statistical evaluation. I n m o s t cases t h e results corresponding to b o t h kinds of ambiguities are enclosed in boxes along t h e diagonal line. F o r t h e p a r t i c u l a r pair car522---car51, t h e localization deduced f r o m three-points t r a n s d u e t i o n s conflicts w i t h the conclusions of deletion m a p p i n g ; t h e l a t t e r m e t h o d , u s i n g deletion carB8 gives t h e order thrA---car522----car51.

M. Mergeay et at.

310 50 ~

177 .':0.2 50

2.8

(

522

1.3 ~ 11 '~ O.S

177":

0.8

70

2.8 1.7

34 ~

1.2

522 ¢

63

70

°6~,-I ~

3.s

J" 175

/-*2 0"~? 55

°5"12 ,~

1.45

34

3.o

~'- h2 --1'2=121

"K5

1001 1.1

2.o

;182'°s

~ 175

13 Q-~~117

66

~ 12 -

72

32. ) 4 2

4.0

8.1

50 <

2.7

1.3 • 12

221 --°8=-1001

~522 (

0_9

z,.7

1001 ~

SO

1.5

) 1001 ,c

2.9

221 o.,~_~51 50 '{

66

:,, 121

:, 4.2 1.z.

117

~'- 63

Fig. 2. Distance estimations between car markers (ratio of Car+ to Thr+ recombinants) based on a selection of additive recombinational frequency data. A correlation between the absence of ambiguity in three-points crosses and additivity relationships among recombination frequencies seems to exist. Exceptions to additivity were noted for other markers. Recipient strains used in the crosses are designated by the head of the arrows

The eight car mutations (car-45, 70, 174, 177, 178, 190, 522 and 1002) corresponding to phenotypes that are improved by high concentrations of ammonium ion in the growth medium (Table 1) are located in the left part of the car locus (to the left of deletion car-8).

Carbamoylphosphate Synthetaze Activity o/ the car Mutants The car mutants described in this study have been tested for CP synthesizing activities from glutamine and ammonia. A large proportion of these mutants are characterized by requirement of arginine and pyrimidines: they show considerably reduced activity with both nitrogen donors (Table 1). The car mutants which do not behave as simultaneous auxotrophs for arginine and uracil, in a majority of cases, exhibit a decrease of carbamoylphosphate synthet&se activity with both glutamine and ammonia. However, it was noticed that: Six of these non-auxotrophic mutants are characterized by a considerable loss of glutamine activity, while significant activity with NH~ is preserved (car-70, 174, 177, 178, 190 and 522). Three others display a modification in the ratio of activities with the two nitrogen donors (car-12, d5 and 221). Eight of the latter nine mutants, namely car-45, 70, 174. 177, 178, 190, 522 and 1002, bear mutations which are located in the left part of the car locus (to the

Physiology and Genetics of Carbamoylphosphate Synthesis in E. coli

311

left of deletion car-8) and have already been distinguished during the phenotypic analysis by their positive growth response to high ammonium ion concentrations. Such observations could be interpreted as meaning that the left part of the locus is mainly concerned with the glutamine activity of the enzyme. Confirmation of this suggestion was looked for through the functional analysis of the locus. One mutations, car-12, is located within the car-8 deletion and will be discussed separately in the next section. Functional A n a l y s i s o/the car Locus

Three types of complcmentation tests have been used in order to determine the number of functional units in the car locus. 1. I n vitro complementation. 2. Abortive transduction. 3. Functional analysis of stable merodiploids. Significant restoration of the glutamine-dependent carbamoylphosphate synthetase is observed after mixing extracts of mutants harbouring car mutations previously shown to reside in the left part of the locus with mutants harbouring mutations shown to reside in the right part. Some representatives of these complementation tests are shown in Table 3. As shown also, many in vitro complementation tests have been performed between two car mutants of the left region or between two car mutants of the right region and were found uniformly negative. The ammonia-dependent carbamoylphosphate synthesizing activity is not affected in such eomplementation tests (not shown). I n addition, comparable restoration of activity can be obtained by combining an extract of car-178 with the purified light subunit of the wild type enzyme or an extract of m u t a n t car-8 with the purified heavy subunit. The ratios of glutamine and ammonia activities, the affinities for the substrates, the response to the allosterie effectors and the susceptibility to thermal denaturaTable 3. In vitro complementation tests between carA and carB mutants carA mutant

Glutamine-dependent carbamoylphosphate synthetase activity in 0.1 ml extract of the carA mutant in the presence of 0.1 ml extract of various carB mutants a b none

none carA70 carA174 carA177 carA178 carA190

-0.003 < 0.001 0.011 0.023 <: 0.001

carB4

<0.001 0.078 0.060 __c 0.384 0.060

carB8

<:0.001 0.089 0.063 0.429 0.633 0.063

carB12

carB55

0.029 0.113 0.067 __c 0.471 0.067

0.011 0.072 0.050 __c 0.242 0.050

carB66

<0.001 0.086 0.056 0.396 0.524 0.060

a Experimental conditions as described under "Materials and Methods". b The following activities were measured after combining, under the same conditions, extracts of pairs of carA or pairs of carB mutants: carATO+carA178, 0.023; carA70-~carA190, 0.004; carA174-~carA177, 0.013; carA174-~carA178, 0.023; carA174~-carA190, 0.002; carA177 ~-carA178, 0.031; carA177~-carA190, 0.012; carA178-~carA190, 0.022; carB4JrcarB8, < 0.001 ; carB4-~carB12, 0.024; carBd~-carB55, 0.013; carB8+carB12, 0.026; carB8+carB55, 0.013; carB8~-carB66, 0.002; carB12-FcarB55, 0.039. c Tests not performed.

312

M. Mergeay etal. Table 4. I n vivo eomplementation tests between carA and carB mutants A. Abortive transduction a Recipient

Donor

Presence of microcolonies

car B8 curB8 carA177 carA178 carA177 carA178 curB8 carB8 car B8 car B8 carB8 carA17 8 carA177

car B8 + carA177 carA178 + + car B34 carA177 carA178 carA190 carA522 car B8 curB8

-+ --+ + -+ + + + + +

B. Merodiploidsa Recipient

Episome

Thr+Car+/Thr + recombinants

thrA carA177 thrA carB34

Thr+ carB8 Thr+ carB8

0.81 __<0.002

a Conditions as in "Materials and Methods ". tion of the reconstructed activities are very similar to those of the wild type earbamoylphosphate synthetase. The presence of two functional units within the car locus, as suggested by i n vitro complementation, is supported by the results of i n vivo complementation tests (see Table 4). On the basis of the complementation tests, the car locus can be divided in two functional units: 1° the c a r d gene (from car-177 to car-522) codes for the smaller subunit of the enzyme (concerned with the glutamine activity) and apparently is also the shorter one (Fig. 2). 2 ° the c a r B gene, which codes for the subunit active towards ammonia. The lettering of the car mutants listed in Tables 1, 3 and 4 expresses the conclusions drawn from the three types of complementation tests, from the pattern of residual catalytic activities analyzed in the previous sections (Table 1)and from the map (Fig. 1). Three mutants (car-51,221 and 1002), have not yet been assigned a letter, because sufficient correlation has not been obtained between their topology and their functional analysis. Mutation car-12, located within the c u r B 8 deletion but conferring a phenotype which is similar to that of some of the c a r A mutants, is clearly identified as a c a r B mutation following the functional analysis (see Table 3). Discussion E . coli carbamoylphosphate synthetase catalyzes an elaborate reaction involving three substrates. The activity of this single enzyme which supplies CP for two

Physiology and Genetics of Carbamoylphosphate Synthesis in E. coli

313

important biosynthetic pathways is controlled by several classes of allosteric effectors; they aifect the distribution o* the enzyme between at least three different conformational states (Anderson and Marvin, 1970). Mutational alterations in the gene encoding such an enzyme are likely to result not only in direct modifications of substrates or effectors binding sites but also in subtle perturbations of the balance between the various conformational states of the enzyme. Indeed, in view of the regulatory properties of the enzyme and of its double function in the arginine and pyrimidines pathways, it is quite likely t h a t mutations in the car locus lead to a wide variety of phenotypes. This is illustrated by the extreme sensitivity of the regulation of the enzyme to base pair substitution as can be seen in directed suppression and reversion data. For example, the three combinations carB602 supD, E or F lead to sensitivity towards uracil but show different growth rates on minimal medium. Observations of this kind are considered to be fruitful in two respects. First, they offer the possibility of deducing the wild type codon of a particular site on the map. Indeed, in the present case, assuming carA602 to be a single point mutation, we know t h a t the wild type codon does not code for serine, inserted by supD, glutamine, inserted by supE, nor tyrosine, inserted by supF. The mutation is not reverted by 2-aminopurine and is probably not an ( A T ~ G C ) transition; this leads one to discard also the codon for tryptophan. Among the three remaining possibilities, lysine, leucine and glutamic acid, the latter (glutamic acid) is the most probable, since the basic or neutral amino acids inserted by the three suppressors used give a m u t a n t phenotype. Second, once the amino acid sequence of the enzyme is determined by chemical means, the use of suppressors and numerous nonsense mutants will make it possible to observe the effect of changing amino acids at defined sites along the sequence. All mutations affecting the synthesis of CP obtained in this work lie in the car locus. Over the whole length of this locus, mutations expressed by partially auxotrophic phenotypes are distributed at random among mutations leading to a strict requirement for arginine plus uracil. Yet, the important observation was made t h a t a number of car mutations, all located in the left part of the locus, cause a significant loss of glutamine dependent carbamoylphosphate synthetase activity but affect the ammonia activity to a much lesser degree. These mutations are reminiscent of those obtained in Neurospora crassa (Davis, 1967) and in Saccharomyces cerevisiae (Pi6rard at al., 1973) where they were shown to affect a distinct subunit responsible for the glutamine dependent activity of the arginine pathway carbamoylphosphate synthetase. The selection of such mutations in E. coli has prompted us, despite earlier failures (Pi6rard et al., 1965 ; Pi6rard et al., 1973), to reinvestigate the functional organization of the car locus. Complementation tests involving pairs of mutations t h a t were not investigated previously have given positive results. On the basis of these results, the left region of the locus appears to code for t h e " glutaminase" subunit of the enzyme which was recently characterized b y Trotta et al. (1971). The right part of the locus, probably entirely deleted in m u t a n t carBS, governs the synthesis of the heavy subunit which bears all the catalytic and regulatory binding sites of the enzyme, except t h a t of glutamine. The efficiency of complementation is however not constant for all mutants. Besides, some mutations in the carA gene, like some in carB, are expressed by a

314

M. Mergeay et al.

strict a u x o t r o p h y for arginine a n d uracil a n d lead to a n a b s o l u t e lack of measurable c a r b a m o y l p h o s p h a t e s y n t h e t a s e a c t i v i t y w i t h either g l u t a m i n e or a m m o n i a . Moreover, in a d d i t i o n to t h e positive c o m p l e m e n t a t i o n tests r e p o r t e d , a n u m b e r of n e g a t i v e tests h a v e been obtained. These findings are q u i t e likely t h e reason for t h e failures e n c o u n t e r e d dm'ing previous i n v e s t i g a t i o n s of t h e f u n c t i o n a l organiza t i o n of t h e locus (Pi6rard et al., 1965; P i 6 r a r d et al., 1973). The simplest inter. p r e t a t i o n of these findings would be t h a t t h e a d j a c e n t genes carA a n d carB form a single operon a n d t h a t m u t a t i o n s in carA m a y e x e r t p o l a r effects on t h e expression of carB. H o w e v e r , such a n a s s u m p t i o n would l e a d to difficulties in t h e i n t e r p r e t a t i o n of t h e responses of some car m u t a t i o n s to mutagens. F o r e x a m p l e , if one applies t h e criteria successively defined b y W h i t h f i e l d et al. (1966), M a r t i n (1967) a n d Oeschger a n d H a r t m a n (1970), t h e m u t a t i o n carATO could be a frameshift. Y e t it e x h i b i t s m e a s u r a b l e residual a c t i v i t y of t h e carB f u n c t i o n ( a m m o n i a as s u b s t r a t e ) a n d of b o t h carA a n d carB functions a s s a y e d t o g e t h e r (glutamine as substrate). T h e b e h a v i o u r of this m u t a n t could suggest a counterclockwise p o l a r i t y , in c o n t r a s t to t h e suggestion m a d e above. A n u n e q u i v o c a l i n t e r p r e t a t i o n of such d a t a will n o t be possible as long as t h e direction of t h e t r a n s c r i p t i o n of t h e car locus is n o t known. :For this reason, a s y s t e m a t i c i n v e s t i g a t i o n of t h e effects of t h e various carA m u t a n t s on t h e expression of t h e carB gene a n d of t h e carB m u t a t i o n s on t h e expression of carA has been u n d e r t a k e n . So far no clear a n s w e r has been o b t a i n e d . Acknowledgements. This work has been supported by grants from the Fonds de la Recherche Fondamentale Collective and the Nationaal Fonds voor Wetenschappelijk Onderzoek. M. Mergeay was a boursier of the Institut pour l'Encouragement de la Recherche Scientifique dans l'Indnstrie et l'Agrieulturc. We are grateful to Dr. H. J. Creech for a gift of ICR-191.

References Abd-EI-A1, A., Ingraham, J . L . : Control of carbamylphosphate synthesis in Salmonella typhimurium. J. biol. Chem. 244, 40334038 (1969a) Abd-E1-A1, A., Ingraham, J. L. : Cold sensitivity and other phenotypcs resulting from mutation in pyrA gene. J. biol. Chem. 244, 4039-4045 (1969b) Abd-E1-Al, A., Kessler, D. P., Ingraham, J . L . : Arginine-auxotrophic phenotype resulting from a mutation in the pyrA gene of Escherichia coli b/r. J. Bact. 97, 466-468 (1969) Adelberg, E. A., Mandel, M., Chein Ching Chen, G. : Optimal conditions for mutagenesis by N-methyl-N'-nitro-N-nitrosoguanidine in Escherichia coli K12. Biochem. biophys. Res. Commun. 18, 788-795 (1965) Anderson, P. IV[.,~¢Ieister, A.: Evidence for an activated form of carbon dioxide in the reaction catalyzed by Escherichia coli carbamylphosphate synthetase. Biochemistry 4, 2803-2809 (1965) Anderson, P. M., Meister, A.: Control of carbamylphosphate synthetasc by purine and pyrimidinc nucleotides. Biochemistry 5, 3164-3169 (1966) Anderson, P. M., Marvin, S. V. : Effect of allosteric effectors and adenosine triphosphate on the aggregation and rate of inhibition by N-ethylmaleimide of carbamylphosphate synthetase of Escherichia coli. Biochemistry 9, 171-178 (1970) Bachman, B. J. : Pedigrees of some mutant strains of Escherichla coli K12. Bact. Rev. 36, 525-557 (1972) Beckwith, J. R., Pardee, A. B., Austrian, R., Jacob, F. : Coordination of the synthesis of the enzymes in the pyrimidine pathway of E. coli, J. molec. Biol. 5, 618-634 (1962) Charles, H. P., Roberts, G. A. : Carbon dioxide as a growth factor for mutants of Escherichia coll. J. gen. Microbiol. 51, 211-224 (1968)

Physiology and Genetics of Carbamoylphosphate Synthesis in E. coli

315

Davis, R . H . : Channeling in Neurospora metabolism. In: Organizational biosynthesis (ed. J. H. Vogel, J. O. Lampen and V. Bryzon), p. 303-322. New York: Academic Press 1967 Eisenstark, A.: Linkage of arginine sensitive (ars) and uracil-arginine requiring (pyrA) loci of Salmonella typhimurium. Nature (Lond.) 213, 1263-1264 (1967) Glansdorff, N.: Topography of cotransducible arginine mutations in Escheriehia coli K12. Genetics 51, 167-179 (1965) Gorini, L., Kalman, S. M.: Control by uracil of carbamylphosphate synthesis in Escherichia coli. Biochim. biophys. Acta (Amst.) 69, 355-360 (1963) Gorini, L. Kanfman, H. : Selecting bacterial mutants by the penicillin method. Science 131, 604-605 (1960) Hartman, P.E., Hartman, Z., Serman, D.: Complementation mapping by abortive transduction of histidine requiring mutants. J. gen. Microbiol. 22, 354-368 (1960) Hopwood, D. A. : Genetic analysis and genome structure in Streptomyces eoelieolor. Baet. Rev. 31, 373403 (1969) Issaly, I. M., Issaly, A. S., Reissig, J. L. : Carbamylphosphate biosynthesis in Bacillus subtilis. Biochim. biophys. Acta (Amst.) 198, 482-494 (1970) Jacob, F. : Transduction of lysogeny in Escherichia coli. Virology 1, 207-220 (1955) Kalman, S.M., Duffield, P. tI., Brozozowski, I.: Purification and properties of a bacterial carbamylphosphate synthetase. J. biol. Chem. 241, 1871-1877 (1966) Khedouri, E., Anderson, P. M., Meister, A.: Selective inactivation of the glutamine binding site of Escherichia coli carbamylphosphate syathetase by 2-amino-4-oxo-5-chloropentanoic acid. Biochemistry 5, 3552-3556 (1966) Loutit, J. S. : Studies on nutritionally deficient strains of Pseudomonas aeruginosa. 1. The production by X-rays and the isolation of nutritionally deficient strains. Aust. J. exp. Biol. reed. Sci. 86, 287-294 (1952) Low, B. : Formation of merodiploids in mating with a class of rec- recipient strain of Escherichia coli K12. Proe. nat. Acad. Sci. (Wash.) 66, 160-167 (1968) Martin, R. G. : Frameshift mutants in the histidine operon of Salmonella typhimurium. J. molec. Biol. 26, 311-328 (1967) Mergeay, IV[.: Physiologic et g~n~tique d'un branchement m~tabolique: la biosynth~se du carbamylphosphate chez Escheriehia coli. Th~se de doetorat, Universit~ Libre de Bruxelles (•969) Novick, P. R., Maas, W. K. : Control by endogenously synthesized arginine of the formation of ornithine transcarbamylase in Escherichia coli. J. Bact. 81, 236-240 (1961) Oeschger, N. S., I-Iartman, P. E. : ICR-indnced frameshift mutations in the histidine operon of Salmonella. J. Bact. 191, 490-504 (1970) Pi6rard, A.: Control of the activity o[ Escherichia coli earbamoylphosphate synthetase by antagonistic allosteric effectors. Science 154, 1572-1573 (1966) Pi6rard, A., Glansdorff, N., Mergeay, M., Wiame, J.-M. : Control of the biosynthesis of carbamoylphosphate in Escherichia coll. J. molec. Biol. 14, 23-26 (1965) Pi6rard, A., Glansdorff, N., Yashphe, J. : Mutations affecting uridine monophosphate pyrophosphorylase or the argR gene in Escheriehia coll. Effects on carbamoylphosphate and pyrimidine biosynthesis and on uracil uptake. Molec. gen. Genet. 118, 235-245 (1972) Pi6rard, A., Grenson, M., Glansdorff, N., Wiame, J.-M. : A comparison of the organization of carbamoylphosphate synthesis in Saccharomyces cerevisiae and Escherichia eoli, based on genetical and biochemical evidences. In: The enzymes of glutamine metabolism (ed. S. Prusiner and E. R. Stadtman), p. 483-503. New York: Academic Press 1973 Pi~rard, A., Wiame, J.-M. : Regulation and mutation affecting a glutamine dependent formation of carbamylphosphate in Escherichia coli. Biochem. biophys. Res. Commun. 15, 76-81 (1964) Pinkns, M. L., Meister, A. : Identification of a reactive cystein residue at the glutamine binding site of carbamylphosphate synthetase. J. biol. Chem. 247, 6119-6127 (1972) Prozesky, O. M., Coetzee, J. N. : Linked transduction in Proteus mirabilis. Nature (Lond.) 209, 1262 (1966) Roepke, R. R., Mercer, F. E. : Lethal and sublethal effects of X rays on Escherichia coli as related to the yield of biochemical mutant. J. Bact. 54, 731-743 (1947)

316

M. Mergeay et al.

Syvanen, J. M., Roth, J. R. : Structural genes for catalytic and regulatory subunits of aspartate transcarbamylase. J. molec. Biol. 76, 363-368 (1973) Taylor, A. L., Trotter, C. D. : Linkage map of Escherichia coli strain K-12. Bact. Rev. 86, 504-524 (1972) Trotta, P.P., Burr, M.E., Haschenmeyer, R.H., Meister, A.: Reversible dissociation of carbamylphosphate synthetase into a regulated synthesis subunit and a subunit required for glutamine utilization. Proc. nat. Acad. Sci. (Wash.) 68, 2599-2603 (1971) Van Montagu, M., Leurs, C., Brachet, P., Thomas, R.: A set of amber mutants of bacteriophages lambda and MS2 suitable for the identification of suppressors. Mutation Res. 4, 698-700 (1967) Vyas, S., Maas, W . K . : Feedback inhibition of a.cetylglutamate synthetase by arginine in Escherichia coli. Arch. Biochem. Biophys. 100, 542-546 (1963) Whitfield, H. J., Martin, R. G., Ames, B. N. : Classification of aminotransferase (C genes) mutants in the histidine operon. J. molec. Biol. 21, 335-355 (1966) ¥an, Y., Demerec, M.: Genetic analysis of pyrimidine mutants of Salmonella typhimurium. Genetics 52, 643-651 (1965) C o m m u n i c a t e d b y W. Maas Max Mergeay Department of Radiobiology S.C.K./C.E.N. B-2400 Mol Belgium Jacques Beckmann Department of Molecular Biology Weizmann Institute Rehovoth, Israel

Daniel Gigot Nicolas Glansdorff Andr~ Pi6rard Institut de Recherehes du C.E.R.I.A. Avenue E. Gryzon 1 B-1070 Bruxelles Belgium