Regulation of Histidine and Hut Operons

Salmonella typhimurium causes food poisoning.  When nitrogen and carbohydrates are deprived of their sources, its hut operon gets activated.  The activated system produces enzymes, which uses freely available Histidine as a source of nitrogen.  It is a unique mechanism. Hut means Histidine utilizing and Histidine operon means all the genes responsible for the synthesis of Histidine from a precursor.


Histidine--H-->Uroconate---U--->Imadozole propionate---I--->


--->Form-immino glutamate--G->Glutamate


Gene: H, enzyme= histidinase,

Gene: U, enzyme= Urokinase,

Gene: I, enzyme= Imadozole propionate hydrolase,

Gene: G, enzyme= Form-immino glutamate hydrolase.


Glutamate, Formate and Ammonia are used as metabolites.  The whole organization of the operon including the regulator which is unusual.  The genes for G and I are under the control of one Promoter cum operator, and U and H are under another promoter cum operator.  Located in between these operons, Hut repressor gene is present with its own promoter.

When carbohydrate and nitrogen sources are available, the Hut repressor is constitutively expressed.  The hut repressor binds to both operators of I and G and U and H and blocks the transcription.


In the absence of glucose, adenine cyclase becomes active and by its action it generate adequate amounts of cAMP, which in turn binds to CRP; this complex binds to the activator region in the upstream of the promoter. 

Though RNAP complex is bound to their respective promoters, for its activation it requires an unusual component, non-adenylated Gln-synthase. 


In the absence of (CH2O) n and N2 sources and in the presence of Histidine, the amino acid Histidine binds to the repressor; the binding induces conformational change in the repressor and repressor falls off the operator of each of the operons. 

·       By quirk of the nature’s design the hut repressor complex binds to its own promoter and blocks the production of hut repressor.

Once the repressors are removed from the operator, both genes are expressed to produce the respective enzymes, which metabolize the Histidine and use the products. 

·       This is an excellent example, where an enzyme is involved in activating an operon.  The non-adenylated form of Gln-synthase acts as an activator, but not the adenylated form of Gln-synthase.  But the activated form of Gln-synthase called Gln-synthase-A. It is responsible for the synthesis of glutamine from Glutamate. 

Active glutamate is adenylated or simply called Gln-A and non-adenylated as Gln.  And it is the non-adenylated form of Gln synthase is responsible for activation of Hut-operon.



    Crp  P   O    I        G        Hu-R       O    P   crp  P   O    U       H


        Gln                                                                     Gln






Regulation of Histidine Operon:


Histidine is an important and an essential amino acid.  It is synthesized in cells using an elaborate biochemical steps; starting from Phospho ribosyl pyrophosphate (PrPP) to L Histidine.  It requires ten steps and ten enzymes, and it means ten genes. Interestingly most of the enzymes are monomers.   All the genes are clustered into one operon under the control of one promoter-operator.  This type of organization is found, in both E.coli and S.typhimurium.



  P-O  genes--->

P1-o-> G(1)-D(10)-C(8)-p2-B(7)-H(5)-A(4)-F(6)-p3-I(3)-E(2)


 (-)35---(-10)>pppAUC----leader-----20ATG----uuuTer-160-170--> next ATG-at+1—for the first Gene in the histidine operon----


Numerical 1 to 10 indicates the steps in biochermical pathway in the synthesis of histidine.  But the order of genes in the operon are in the same way as the genes involved in synthesis.

Transcription starts at +1 at and ATG in the  leader starts at 20 and the leader terminates at +160-170—(leader sequence),and at 228 another ATG for histidine operon starts. This region acts as attenuator sequence.





Translated Leader: M.T.R.V.Q.F.K.H.H.H.H.H.H.H.P.D---ter—M





E.coli K12: Histidine operon cistrons sequence


I-P-O>--E-I-F-A-H-F-B-C-D-G t/t


The 5’ leader sequence also contain similar attenuator sequences as found in Solmonells typhimurium operon.





 1. pRpp + ATPà phosphoribosyl ATP

ATP phosporibosyltransferase- his (G)



2. Phosphoribosyl ATP + H2Oà Phosporibosyl-AMP

PR-pyrophotase-his (I)



3. Phosporibosyl-AMP +H2O  -> PhosphoribosylformiminoAICAR-P.

Phosphoribosyl AMP cyclohydrolase His (I)




Phosphoribosylformimino-5-amino-1-phosphoribosyl-4amidozole carboximide isomerase-his-A


5.Phosphoribulosylformimino-AICAR+glutamate->D-erythroimidozole glycerol-P

Imidazole glycerol phosphate synthase His F and  His H


6. D-erythroimidozole glycerol-P -> Imidazole acetol -P

Imidazoleglycerol phosphate dehydrtase –his(B)


7. Imidazole acetol –P-> L histidinol-P

Histidinol phosphate aminotransferase-his (C)


8. L histidinol-P-> Histidinol

Histidinol phosphotases-his (B)


9. Histidinol-> Histidine

Histidinol dehydrogenase –his (D)


Size of Genes:




Size (bp)

Mol.wt (KD)


Size(bp) Mol.wt



735 (~27)



B1 and B2

1068  39,105(~)

1065 (B1,B2)



1008 (~43)








1302 (~75)




774 (~41)




897 (~36.8)




588 (~44)




612 (~75)










The leader sequence has 4 blocks with intra strand complementarity, thus they can form 4 stem loop structure, such as 1,2,3 and 4.

When His is low or absent translation stops at H codons, and 2 and 3 block base pair, thus allow transcription to continue.  If His is present translation proceeds beyond his codons and terminates in the second loop, this provides the formation of 3 and 4 form base pairing, which generates transcription terminator stem loop with uuuuu 3’ends


Some of Operons leader length used for attenuation :


Trp                        -14-   MKAIFVLKGWWRTS

Phe-A         -16-    MKHIPFFFAFFFTFP

His              -16-    MTRVQFKHHHHHHHPD

Thr              -21-    MKRISTTITTTITITTQNGAG





S. typhimurium Histidine Synthetic Pathway:


1. PRRP +ATP-----> Phospho Ribosyl-ATP

2. Phospho Ribosyl-ATP-----> Phospho Ribosyl-AMP

3.Phospho Ribosyl-AMP-> PR- formimino AIC-R-phosphate

4.PR-formimino AIC-R-phosphate---->Phospho ribulosyl formimino AIC R-phosphate

5. and 6. Phospho ribulosyl formimino AIC R-phosphate

          -P ----> Imidozole glycerol 3-P

7. Imidozole glycerol 3-P -------> Imadazole acetol phosphate

          8.Imadazole acetol phosphate----->L Histidinol phosphate

9.  L Histidinol phosphate---> L Histidinol

10. L Histidinol----> L Histidine.

Note: Gene in the pathway are not the same as found in the operon.




Organizaniztion of the E.coli Histidine operon:





The pathway shown is of E.col K12 

Enzymes in sequence:

G. PRPP –ATP pyrophosphorylase,

E.  PR-AMP pyrophospho hydrolase,

I.  Hydrolase,

A. Isomerase,

H. Amido transferse

F. Cyclase,

B. IGP dehydrase,

C. IAP transaminase,

B. HP phophotase,

D. Histidinol dehydrogenase




These are the sequence of reactions.  In structural organization of individual gene in the operon, the first gene in the operon is  gene-2 and the last is gene-1.




Name of the enzyme


Enzyme -1

PrPP pyro phosphorylase



Pr-AMP pyro phospho hydrolase









Amido transferase



ribotide cyclase



IGP dehydrase



IAP transaminase



Hp phosphotase



Histidinol dehydrogenase



The Histidine operon is regulated in the fashion of Tryptophan operon by attenuator mechanism.  Before the start of the first cistron the transcript has a long leader sequence, which can generate two stem loop structure, one of which contains stem loop with UUUU sequences.  This develops when Histidine present and the ribosome progresses through Histidine codons and stops at a terminator codon, this generates terminator stem loop.  But when Histidine is absent the translating ribosome stops at his codons for the lack of his carrying tRNA, this generates hair-pin loop between the 2nd and the 3rd part of the leader sequence, thus transcription is not terminated.  The attenuator mechanism is more or less similar to that of Tryptophan operon.


Arginine Operon:




Gene products operate the pathway from enzyme 1-to 8