The Stringent Response

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1 The Stringent Response When amino acids are limiting a response is triggered to shut down a wide range of biosynthetic processes This process is called the Stringent Response It results in the synthesis of ppgpp and pppgpp by the RelA protein RelA is associated with a small proportion of ribosomes and detects uncharged trna bound to them

2 Activation of RelA by uncharged trna

3 pppgpp and ppgpp synthesis Synthesis of both is by RelA But ppgpp is also a breakdown product of pppgpp catalysed by ribosomal proteins Turnover is required to allow re-initiation of growth

4 Nucleotide levels control initiation of rrna transcription Geneeal regulatory network Inhibits initiation at the promoters of rrn loci The production of ribosomes, and thus of protein synthesis, in turn responds to the levels of ATP, GTP, which is reflect the nutritional condition of the cell

5 Autogenous control may occur at translation Regulatory protein binds to initiation codon Secondary structure can control initiation

6 Regulation of ribosomal protein synthesis Ribosomal proteins are very basic, and if present in excess will precipitate and form toxic inclusions in the cell So the level of synthesis must be tightly linked to the synthesis of rrna and other ribosomal proteins Find many r-proteins linked in operons

7 Ribosomal protein operons Each operon is controlled by feedback inhibition by one of the ribosomal proteins Regions in pink show the genes under feedback control in each operon

8 Feedback regulation is by protein-rna interaction Feedback loop controlled at the level of translation, not transcription Here, S8 binds to site on its own mrna, blocking translation of L5 - L15 Note synthesis of L14, L24, SecY and SecX are not blocked

9 RNA or protein regulates its own production

10 The difference of the binding affinity

11 Autogenous regulation in macromolecule assemblies

12 Tryptophan biosynthesis Biosynthesis pathway is from phosphoenolpyruvate to chorismate, with the enzymes encoded by Aro H And from chorismate to tryptophan, with enzymes encoded by Trp E-A The two operons are regulated in an overlapping but separate fashion The two pathways have different endpoints: Aro H pathway produces substrates required for a number of products Trp E - pathway is required only for tryptophan biosynthesis

13 Chorismate Biosynthesis Pathway

14 Tryptophan biosynthetic pathway

15 α and β subunits catalyse separate reactions Substrates are channelled inside the heterotetramer Results in greatly increased reaction rates Tryptophan Synthase

16 Feedback regulation of tryptophan biosynthesis Tryptophan synthase is an α 2 β 2 heterotetramer It is allosterically regulated by tryptophan which is an inhibitor Thus the biosynthetic pathway is feedback regulated by its product In the presence of excess tryptophan (from biosynthesis or environmental sources) the biosynthetic pathway is shut down Thus the enzymes are present but inactive, in the presence of the substrates

17 Trp E-A operon structure

18 Trp E-A regulatory sequences

19 Role of operator, Trp R and tryptophan Operator acts as a cis-acting binding site for repressor protein Trp R encodes the repressor Trp R requires tryptophan as a co-repressor Operon is product repressed, a negative feedback loop As level of product increases, level of transcription decreases Overall level of repression is approximately 70 fold

20 Trp R is dimeric Trp R.trp.DNA Structure Requires Trp to bind to DNA Binding to Trp Operator is entirely through water molecules, there are no direct H bonds

21 Coordinate control of multiple transcription units by Trp R Trp R regulates three operons, all involved in tryptophan biosynthesis

22 Trp E-A leader/attenuator

23 Leader/Attenuator structure Leader sequence is 140 bases long mrna It contains a short open reading frame containing two adjacent tryptophan codons (UGG) that is translated to give a 14 residue peptide encoded by residues RNA Pol pause site is a residue 90 Attenuator termination sites is at residue 140 Region contains 4 complementary base pairing regions that can form hairpin loops

24 Transcriptional pause in leader RNA polymerase transcribes leader sequence but pauses at residue 90 Progress depends on the level of tryptophan

25 Role of translation in attenuation Transcription and translation are coupled processes Thus leader sequence is translated while RNA Pol is paused at residue 90 Hairpin loop structures can form in RNA Progress of ribosome depends on level of tryptophan, because of two adjacent trp codons If tryptophan levels are low, the ribosome will stall If tryptophan levels are high then the ribosome will complete translation of the leader peptide

26 With low and high tryptophan levels

27 Secondary structures of trp attenuator Attenuator contains 4 regions that can form hairpin loops These can form alternative possible structures Generally only one of the structures will form at one time

28 1:2 base pairing allows 3:4 Pairing of stems 1 and 2 occurs during RNA synthesis If region 2 is paired with 1, it is unable to pair with 3 Region 3 can then pair with region 4 Thus the role of the 1:2 structure is to ensure 3 is free to pair with 4

29 Region 3:4 is a terminator Role of the 3:4 is to act as a rhoindependent terminator sequence This if 3:4 is able to form, the synthesis of RNA will be terminated before trp E-A mrna is synthesised Thus the synthesis of trp E-A is said to be attenuated (reduced)

30 2:3 formation prevents 3:4 Formation of stem 2:3 occurs if stem 1 single stranded Stem 1 is separated from stem 2 by translation, as the ribosome unwinds the double strands This allows 2:3 to form But then 3:4 cannot form a terminator region

31 Features of the open reading frame in the attenuator Tryptophan codon (UGG) Tryptophan codon (UGG) Termination codon (UGA)

32 Effect of translation on attenuator Translation of leader peptide occurs rapidly after transcription Ribosome unwinds double stranded RNA structures as translation proceed Ribosome covers bases on either side of the codons being translated Pause by RNA Polymerase at position 90 allows ribosome to position correctly to allow attenuator mechanism to function

33 In low tryptophan, RNA pol reads through attenuator If tryptophan is low, then trna-trp levels will be low In low trna-trp the ribosome will stall or slow at the double trp codons This allows the formation of 2:3 stem This allows RNA Pol to read through the terminator region

34 In high tryptophan, RNA pol terminates at the attenuator If tryptophan is high, then trna-trp levels will be high In high trna-trp the ribosome will translate the double trp codons and read through to termination codon This disrupts the formation of 2:3 stem The 3:4 stem forms, which is a terminator sequence

35 Attenuator sensitivity Attenuation reduces transcription from 100% to a minimum of 10% It detects low levels of trna-trp, not of tryptophan directly If trna-trp is absent then the leader will not be translated, but nor will any other protein! So, attenuator works by detecting reduced levels of trna-trp and results in increased levels of read-through into the Trp E-A operon

36 Attenuator and repressor work together to control Trp E-A Attenuator can reduce transcription from 100% to 10% (10 fold) Trp R can reduce transcription initiation by 70 fold (100% to 1.4%) Overall range of regulation is 700 fold (compare with Lac operon at 1000 fold) Assume that attenuator and Trp R operate over similar concentration ranges of trp so that regulation is coordinated

37 Transcription and allosteric regulation also work together Regulation of tryptophan biosynthesis by feedback inhibition of tryptophan synthase by trp allows the shutdown of synthesis without the need to destroy the enzymes Thus although substrates are available, the biosynthetic pathway is controlled Parallel control preventing new biosynthesis of Trp E-A in the presence of trp allows high level of biological efficiency of the process

38 Other Attenuators Attenuators are found for a range of amino acid biosynthesis operons Also found for nucleotide biosynthesis operons All work through hairpin loop structures Amino acid operon attenuators require translation Nucleotide operon attenuators do not need translation Number of residues for product of operon in the attenuator reflects normal level of the product

39 Small RNA molecules can regulate translation

40 Antisense construct offers loss of function study

41 (his, ara operon)

42 The his operon The his operon is also controlled by attenuation However there is no repressor protein to control this operon The attenuator is the only mechanism to regulate gene expression The leader sequence encodes 7 His codons The secondary structures are similar to the Trp operon Met Thr Arg Val Gln Phe Lys HIS HIS HIS HIS HIS HIS HIS Pro Asp

43 phe A and leu operons Both operons have attenuators regulated by one codon, with similar mechanisms to trp and his Met Ser His Ile Val Arg Phe Thr Gly LEU LEU LEU LEU Asn Ala Phe Ile Val Arg Gly Arg Pro Vla Gly Gly Ile Gln His Met Lys His Ile Pro PHE PHE PHE Ala PHE PHE PHE Thr PHE Pro

44 ilv and thr operons are regulated by several aa-trnas These biosynthetic pathways are required for several amino acid products Thus they are regulated by a number of possible aa-trnas Note the regulation of more than one operon by some aa-trnas Met Thr Ala LEU LEU Arg VAL ILE Ser LEU VAL VAL ILE Ser VAL VAL VAL ILE ILE ILE Pro Pro Cys Gly Ala Ala LEU Gly Arg Gly Lys Ala Met Lys Ala ILE ser THR THR ILE THR THR THR ILE THR ILE THR THR Gln Asn Gly Ala Gly

45 Met repressor binds through β sheets to major groove of DNA

46 arabad operon controlled by both positive and negative control by AraC arabad encodes enzymes responsible for arabinose breakdown Operon is catabolite repressed, and thus requires CAP.cAMP for activation of transcription However, activation also requires the complex of AraC.arabinose as an activator Thus explaining how arabad is only transcribed in the presence of arabinose

47 arabad operon structure

48 arabad and arac are transcribed at a basal level by default In the absence of regulation both arac and arabad are transcribed arabad expression is at a low level, because of the lack of activator proteins

49 AraC alone is a repressor protein AraC alone binds to arao 1 repressing arc transcription And to arai 1 and arao 2, repressing arabad transcription In the absence of camp, CAP does not bind to the promoter region

50 Ara C.arabinose is an activator AraC complexed with arabinose releases arao 2, and binds to arai 1 and arai 2, forming an activation complex with CAP.cAMP AraC.arabinose remains bound to arao 1, repressing ara C transcription

51 Orientation of ara promoter elements matters If arai 2 mutated to increase the affinity for AraC then arabinose no longer is required for activation This suggests that the affinity for arao 2 is weaken by arabinose binding If arai 2 orientation is altered then AraC does not activate transcription These data suggest that AraC uses specific and orientation dependent contacts to activate RNA Polymerase

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