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MindMap Gallery Biology-Prokaryotes Transcriptional Regulation

Biology-Prokaryotes Transcriptional Regulation

This is a mind map about prokaryotic transcription regulation, regulatory proteins and transcription initiation, examples of prokaryotic transcription initiation regulation, etc.

Edited at 2023-11-24 18:17:15

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Biology-Prokaryotes Transcriptional Regulation

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Outline

Prokaryotic transcriptional regulation

Regulatory proteins and transcription initiation

regulatory protein

Positive regulatory protein/activator/activator: DNA-binding protein, one surface binds to a certain DNA site near the promoter, and the other surface interacts with RNA polymerase to recruit - the protein cooperatively binds DNA

Negative regulatory protein\suppressor/repressor: DNA-binding protein, assembled at a site that overlaps with the polymerase binding region. The site on DNA where the repressor binds is called an operator.

Transcription initiation regulation

Closed → open complex: constitutive expression (local level expression)

Allosteric regulation: activators induce conformational changes through cooperative binding and allosteric effects

Remote activation: the proximity of distant DNA sites causes DNA strands to circularize

Examples of regulation of transcription initiation in prokaryotes

operon

Unit of prokaryotic gene expression and regulation

structure

Structural genes: encode enzymes related to a certain metabolic process

Control elements: such as operator elements

Regulator gene: encodes a protein that binds to a regulatory element and may be encoded by other operons

lactose lac operon

structural genes

LacZ: encodes a lactose-hydrolyzing beta-galactosidase

LacY: encoding lactose permease, a cell membrane protein that can transfer lactose into cells

LacA: Encodes thiogalactopyranoside transacetylase, which eliminates the toxicity of thiogalactopyranoside transferred into cells by LacY at the same time.

The LacZYA transcription unit contains an operator site O[lac], which overlaps with the P[lac] promoter and can bind to the repressor.

control mechanism

activators and repressors

Activator: metabolite activated protein CAP (cAMP receptor protein, CRP), the activator responds to glucose concentration

Repressor: encoded by the lacⅠ gene, responds to lactose concentration, and binds to the operator to prevent RNA polymerase from binding to the promoter.

lac repressor and regulation of CAP activity

lac repressor

In the presence of lactose, the background level of transferase transfers lactose into cells and is converted into lactose by β-galactosidase. Lactose acts as an inducer and binds to the lac repressor to inactivate it, allowing the operon to be expressed.

In the absence of lactose, the lac repressor prevents LacZYA transcription, and only very low background transcription activity exists: the lac repressor binds to DNA, and RNA polymerase cannot bind to the promoter site.

CAP

When the glucose concentration is low, cAMP binds to the activator CAP, and CAP allosterically binds to DNA, recruiting RNA polymerase to the promoter and activating operon expression.

When the glucose concentration is high, the cAMP concentration is reduced, thereby indirectly shutting down CAP and initiating the expression of the operon.

positive regulatory mechanism

Summary: CAP activator is activated by binding to cAMP, binds to the CAP binding site upstream of the promoter, and recruits RNA polymerase to the promoter to activate transcription by interacting with the CTD of the RNA polymerase α subunit.

CAP activity regulation: Since the lac promoter lacks an upstream element (UP), in the absence of CAP, the binding ability of RNA polymerase to the promoter is also low, and it can only transcribe at a low efficiency. After adding CAP, the transcription proceeds at a high efficiency. conduct. Glucose is the allosteric factor of CAP: the CAP protein is in the DNA-binding conformation only when CAP forms a complex with cAMP.

Negative regulatory mechanism-lactose regulation

araBAD operon

The promoter of the araBAD operon of E. coli is activated in the presence of arabinose but in the absence of glucose, directing the expression of genes encoding related enzymes required for arabinose metabolism. Activating factors: AraC, CAP

Control method

In the presence of arabinose, AraC combines with arabinose to form a conformation that can bind DNA and binds to the two half-sites. The upstream of the site is the CAP site. In the absence of glucose, CAP binds here and assists in activating transcription.

In the absence of arabinose, the araBAD gene is not expressed. When AraC does not bind arabinose, it adopts a different conformation to bind to DNA. The DNA forms a loop between the two half-sites, which affects CAP binding and therefore does not activate the promoter.

Expression vector function

Arabinose is very powerful in inducing activation of the araBAD promoter, so the araBAD promoter is often used as an expression vector.

Tryptophan Trp operon

Structural genes: trpE, trpD, trpC, trpB, trpA. Among them, trpE is close to the regulatory site. When the concentration of tryptophan in the cell is very low, the structural genes can be expressed efficiently under regulation.

Regulatory sites: promoter site trpP, overlapping operator gene site trp0, leader region trpC - encoding a leader peptide and an RNA attenuator

Control method

The tryptophan operon is a blocking operon

Repression system (coarse adjustment)

The Trp repressor must form a complex with tryptophan before it can bind to the operator, so tryptophan is called a corepressor. The corepressor protein (trpP gene mutation product) combines with tryptophan to form an active repressor. Tryptophan inhibits its own expression through negative feedback regulation

When the tryptophan content in the culture medium is high, it binds to the free co-repressor protein and tightly binds it to the DNA of the operator region to inhibit gene transcription; when the culture medium is insufficient in tryptophan, the co-repressor loses tryptophan and ceases to function. The operator region is dissociated, the trp operon is derepressed, and transcription begins.

Weakening the system (fine tuning)

Because the tryptophan concentration decreases, the repressor cannot be assisted by the co-repressor, and Trp transcription is initiated. As the tryptophan concentration increases, the Trp operon inhibits transcription by terminating transcription prematurely. This control method is attenuation.

When the concentration of tryptophan in the culture medium is low, there are few tRNAtrp loaded with tryptophan, and the translation speed through two adjacent trp codons is very slow. When the transcription of the leader peptide region 4 is completed, the ribosome has just moved to region 1, resulting in 2 :3 region pairing, the 3:4 pairing of the terminator cannot be formed, and transcription continues, eventually forming a full-length mRNA.

When the concentration of tryptophan in the culture medium is high, the ribosomes pass through two adjacent tryptophan codons smoothly, and the ribosomes reach region 2 before region 4 is transcribed, eventually leading to the smooth pairing of region 3:4 to form a terminator, and transcription stops early. The operon is transcribed into leader RNA.

Selective delta factor

Different delta factors determine the specificity of RNA polymerase binding to promoters

Heat shock response: When the temperature of E. coli is above 77°C, the content of heat shock delta factor increases.

The phage encodes its own delta factor and uses the host's RNA polymerase to selectively express genes

allosteric transcriptional activator

nnJC

Has ATPase activity and uses allosteric effects to promote the formation of open initiation complexes

Regulates the expression of genes related to nitrogen metabolism (such as glnA)

Has DNA binding and activation domains

Only when the nitrogen concentration is very low, the kinase NtrB phosphorylates NtrC, changes its conformation, exposes its DNA binding domain and binds to a specific promoter pre-sequence, and then uses ATPase activity to hydrolyze ATP to obtain energy to convert the closed complex into an open one. Complex

Activates gene transcription by twisting promoter DNA

Controls transcription of the mercury-resistant enzyme gene merT

When there is no mercury in the environment, MerR binds to a section of DNA between -10~-35 of the merT promoter, and the polymerase can bind to the promoter but cannot initiate transcription.

When mercury binds to MerR, the conformation of MerR changes, twisting the bound DNA. The distortion causes merT promoter-10~-35 to form a structure similar to a strong promoter, and the polymerase initiates promoter expression.

NtrC and MerR function through allosteric activation: NtrC activator's own conformational change exposes the DNA binding domain; MerR activator causes DNA conformational changes

ribonucleic acid switch

RNA elements directly serve as sensors for small molecule metabolites, and the RNA elements regulate the transcription or translation of genes. This is a mechanism that does not require protein regulation and only regulates expression through changes in RNA structure.

Mode of action

Ribonucleic acid switches exert regulatory effects at the level of transcription termination through attenuation mechanisms

Ribonucleic acid switches regulate RNA structure and shield ribosome binding sites, thereby regulating protein translation at the level

Lambda phage growth mode selection

regulatory genes

The cⅠ gene encodes a lambda repressor, which can both activate and inhibit transcription.

Cro only inhibits transcription

Cro and lambda repressors can bind to any of the six operators, each with a different affinity; lambda repressors bind cooperatively to the operator site

Promoter: P[R], P[L] are strong constitutive promoters and do not require the assistance of activating factors; P[R] is weak

control mechanism

Lytic growth: A single Cro dimer binds OR3. This site overlaps with P[RM], so Cro represses this promoter. Neither the repressor nor cro bind to OR1 and OR2, so P[R]/P[ L] binds RNA polymerase and directs cleavage gene transcription

Lysogenic growth: P[RM] is open, P[R], P[L] are closed. The repressor cooperatively binds to OR1 and OR2 to prevent RNA polymerase from binding to P[R] and inhibits transcription from this promoter, but the binding of the repressor activates transcription from P[RM].

Transition from lysogeny to cleavage: the lambda repressor cleaves itself under the action of RecA to remove the C-terminal domain of the repressor. Dimerization and cooperativity no longer exist, and the loss of inhibition promotes the removal of P[R] and P [L] Start transcription

CⅡ

An activator that controls lysogenic or lytic growth or infection of a new host, binds to the upstream microstore of promoter P[RE], and stimulates the transcription of the cⅠ gene from this site

Mode of action: Once infected, transcription from the two promoters P[R] and P[L] will start immediately. P[R] directs the synthesis of cro and cⅡ. The expression of cro causes the phage to lyse and grow, and the expression of cⅡ is guided by Transcription of the repressor gene enables the phage to enter lysogenic growth. In order to successfully enter lysogenic growth, the repressor must bind OR1, OR2 and activate P[RM] before cro represses the promoter. cⅡ determines the cⅠ gene transcription efficiency, that is, the inhibitory factor production efficiency, which is a key step in determining how to develop.

activity regulation

Degraded by a specific protease FtsH, which is encoded by the hf1 gene

When the growth is good, FtsH activity is high, cII is effectively destroyed, the inhibitor cannot be synthesized, and the phage tends to lyse and grow; under harsh conditions, the opposite is true, and cII degradation slows down.

In the absence of N protein and Q protein, transcription controlled by these two regulatory proteins can also be started well, but unless the regulatory protein modifies RNA polymerase, transcription will still be terminated, so N protein and Q protein are called anti- terminator protein