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Chapter 5 Mind Map of Prokaryotic Gene Expression Regulation
Molecular biology Prokaryotic gene expression regulation, including gene expression characteristics, gene expression regulation characteristics, transcriptional level regulation, etc.
Edited at 2023-11-08 17:37:49- bacteria
This is a mind map about bacteria, and its main contents include: overview, morphology, types, structure, reproduction, distribution, application, and expansion. The summary is comprehensive and meticulous, suitable as review materials.
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Chapter 5 Mind Map of Prokaryotic Gene Expression Regulation
- bacteria
This is a mind map about bacteria, and its main contents include: overview, morphology, types, structure, reproduction, distribution, application, and expansion. The summary is comprehensive and meticulous, suitable as review materials.
- Plant asexual reproduction
This is a mind map about plant asexual reproduction, and its main contents include: concept, spore reproduction, vegetative reproduction, tissue culture, and buds. The summary is comprehensive and meticulous, suitable as review materials.
- Reproductive development of animals
This is a mind map about the reproductive development of animals, and its main contents include: insects, frogs, birds, sexual reproduction, and asexual reproduction. The summary is comprehensive and meticulous, suitable as review materials.
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- Outline
Prokaryotic gene expression regulation
Gene expression characteristics
Gene expression is condition-specific
The expression levels of many genes (inducible and repressible genes) are affected by nutritional status and environmental factors
Gene transcription is mostly in operon units
It consists of a promoter, an operator gene and a group of functionally related structural genes controlled by it.
The specificity of gene transcription is determined by the σ factor
Transcription and translation coupling
Gene expression regulation characteristics
Gene expression is regulated at multiple links
Transcription (especially transcription initiation and elongation) is the most important link in gene expression regulation
Transcription factors are DNA-binding proteins
The effects of transcription factors include negative regulation and positive regulation
Negative regulation: repressor protein
Positive regulation: activator protein
Prokaryotes mainly rely on negative regulation
There is a coordinated regulatory mechanism
There is an attenuation control mechanism
There is an emergency response control mechanism
Regulation at the transcriptional level
Regulation of RNA synthesis
regulatory elements
Cis-acting element - DNA
promoter, terminator
Promoter: A DNA sequence that can be recognized, combined and initiated by RNA polymerase to initiate gene transcription.
Terminator: A DNA sequence that gives RNA polymerase a signal to terminate transcription.
operator gene
Often adjacent to the promoter or overlapping with the promoter sequence
is the binding site for repressor proteins
The repressor protein binds to the operator gene, preventing the binding of RNA polymerase to the promoter, thus inhibiting the transcription of structural genes.
activin binding site
Often located upstream of the promoter
is the binding site for activator proteins
When activating proteins bind to this site, they enhance the transcription initiation activity of RNA polymerase.
trans-acting element - regulatory protein
repressor protein
repressor, negative regulator
Combined with the operator gene, the RNA polymerase cannot bind to the promoter, or cannot initiate transcription after binding.
Mediates negative regulation
activator protein
activator, positive regulator
Binds to the activator protein binding site to enhance the transcription initiation activity of RNA polymerase
Mediates positive regulation
effector
inducer
effector that causes operon expression
Passivated repressor protein→negative regulatory induction
activating protein → positive regulation induction
corepressor
effector that turns the operon off
Activated repressor protein → negative regulatory repression
Passivated activator → positive regulatory repression
Initiation control (promoter control)
Regulation of transcription initiation at the operon level
repressor negative regulatory system
Inducible operon (lactose operon, catabolism)
With lactose, the repressor protein encoded by the regulatory gene is active, binds to the operator gene, and the gene is turned off.
Without lactose, the repressor protein encoded by the regulatory gene loses activity and cannot bind to the manipulated gene, causing gene expression
Repressor operon (tryptophan operon, anabolism)
Without trp, the repressor protein is inactive, cannot bind to the operator gene, and the gene is turned on.
A large number of trp, trp binds to the repressor protein, and then binds to the operator gene, turning the gene off
cAMP-CAP positive regulatory system
key concepts
CAP: Catabolic gene activating protein, also known as CRP (CAMP receptor protein), is a positive regulator necessary for some promoters to initiate transcription.
CAP site: CAP binding site
cAMP: cyclic AMP, intracellular second messenger, inducer
Glucose effect: Bacteria preferentially use glucose as a carbon source
CAP-cAMP complex promotes transcription
cAMP levels are inversely related to glucose levels
control
Reduce cAMP activity and CAP is inactive
Only when cAMP-CAP binds to the CAP site on DNA can the lactose operon be opened and genes can be expressed.
Glucose inhibits adenylyl cyclase activity through metabolites, thereby reducing cAMP content, making CAP unable to bind to DNA, the lactose operon is closed, genes are not expressed, β-galactosidase content is low, and lactose is not utilized.
Dual regulation of the lactose operon: it is regulated by both positive and negative systems at the same time. Only when cAMP-CAP binds to the CAP binding site and the repressor protein breaks away from the operator can the expression of structural genes begin.
Termination regulation (attenuator regulation)
Coupling of transcription and translation is the basis of attenuation regulation
concept
Attenuation: A negative regulatory mechanism achieved by an attenuator in the leader region of an operon that stops ongoing transcription. Only exists in prokaryotes
Attenuator: A nucleotide sequence in DNA that can cause premature termination of transcription (region 123-150)
Leader peptide: It is a polypeptide composed of 14 amino acids, which contains two tryptophan trp
control
Low Tryptophan Concentrations → Read More
High tryptophan concentration → attenuation
Shortage of other/all amino acids → attenuation
Dual negative regulation of the tryptophan operon: repressive regulation and attenuation regulation complement each other
Link: The former acts on the transcription initiation link, and the latter acts on the transcription elongation link.
Signal: The former is tryptophan level; the latter is tryptophanyl tRNA level
Features: The former is effective and economical; the latter is subtle and rapid
arabian operon
structural genes
araBAD
regulatory elements
two promoters
araBAD promoter araPBAD
araC promoter araPC
Four other regulatory elements araO2, araO1, araI1, araI2
control mechanism
No arabinose: The regulatory protein binds to I1 and O2, blocking the transcription of the arabinose gene and producing a negative regulatory effect.
With arabinose: the regulatory protein is converted into an activator that binds to I1 and I2, activating arabinose gene transcription. Initiation of transcription also requires the joint participation of CAMP-CRP. produce positive regulatory effects
Features
AraC has dual functions, it is both a repressor protein and an activator protein
Can play both negative and positive regulatory roles
AraC itself is also subject to autologous regulation
Strict control
bacterial emergency response
triggering condition
Bacteria sometimes encounter emergencies such as amino acid starvation—a total lack of amino acids.
emergency response
Stops nearly all biochemical reactions that produce various RNAs, sugars, fats, and proteins
control mechanism
Inducer: empty tRNA
Emergency Signal: Magic Spot Nucleotide
Mechanism: Empty tRNA regulates the synthesis rate of protein and RNA
Translation level control
Effects of mRNA stability on translation
The bacterial reproduction cycle is 20-30 minutes and requires rapid synthesis or degradation of mRNA to adapt to environmental changes.
Most bacterial mRNAs are short-lived
mRNA lifetime is regulated by RNA-binding proteins
5‘The impact of UTR on translation
SD sequence: a purine nucleotide-rich sequence (9-12bp) before the start codon of the mRNA
Riboswitch: an RNA structural element on mRNA that can bind to free metabolites or other small molecule ligands to cause conformational changes in the mRNA, thereby regulating gene expression.
Homeopathic regulation: self-shape changes caused by the combination of aptamer domain and small molecules
Trans-regulation: the change in its own shape caused by connecting to an antisense RNA or DNA fragment
Regulatory effects of antisense RNA
Genes that are transcribed to produce antisense RNA are called antisense genes
This type of complementary RNA that interferes with the function of mRNA is called micRNA, or antisense RNA.
Negative regulation through binding of complementary RNA sequences to specific target mRNAs
Effects of rare codons on translation
Proteins that use rare codons with a higher frequency have lower expression rates
Proteins that use rare codons more frequently in cells are mostly regulatory proteins, while structural genes use rare codons less frequently.
Impact of overlapping genes on translation
Overlapping codes ensure that two consecutive genes are translated by the same ribosome
Coupled translation is an important means to ensure that two gene products are equal in quantity
Other ways to control translation levels
Ribosomal frameshift
Ribosome code hopping
ribosome rescue
Common knowledge about gene expression regulation
gene expression concept
Typical gene expression is the process in which genes produce biologically active proteins through transcription and translation.
Some genes are only transcribed but not translated. The process of transcribing and synthesizing RNA from rRNA and tRNA encoding genes also belongs to gene expression.
gene expression pattern
constitutive expression
Definition: It is rarely affected by internal and external environmental factors. It is only affected by the promoter and RNA polymerase and can be continuously expressed in all cells at any stage of individual development. It is necessary in the entire life process.
Gene: Housekeeping Gene
type
Some gene products, such as tRNA, rRNA, RNA pol
Enzymes involved in basic metabolism
Almost all basic components of cells
tissue-specific expression
Definition: Refers to a type of gene expression that is prone to changes in expression levels due to environmental changes.
inducible expression
The phenomenon of increased gene expression levels in response to changes in environmental conditions is called induction
inducible genes
inhibitory expression
The phenomenon of reduced gene expression levels as environmental conditions change is called repression
repressible genes
collaborative expression
Definition: Under the control of a certain mechanism, a group of functionally related genes need to be coordinated and expressed together, which is called coordinated expression.
The expression of prokaryotic operons and regulators is coordinated expression
gene expression patterns
time specificity
Definition: According to functional requirements, the expression of a specific gene occurs strictly in a specific time sequence, which is called the time specificity of gene expression.
Time specificity of gene expression in multicellular organisms is also called stage specificity
spatial specificity
Definition: During the entire process of individual growth, a certain gene product appears sequentially in different tissue spaces in the individual, which is called spatial specificity of gene expression, also known as cell or tissue specificity.
gene expression regulation
Definition: The same genetic information (same structural genes) contained in various cells of the body selectively and programmatically expresses a specific number of specific genes according to different developmental stages, different tissue cells and different functional states of the body. .
regulatory factors
DNA sequence
protein
small RNA
Regulatory mechanism
interactions between nucleic acid molecules
Interactions between nucleic acids and protein molecules
interactions between protein molecules
regulatory elements
cis-acting element
It does not encode any protein itself, but only provides an action site to interact with trans-acting factors.
Sequences that exist in gene flanking sequences that can affect gene expression include promoters, enhancer regulatory sequences, and inducible elements. Their role is to participate in the regulation of gene expression.
trans-acting element
Proteins that can directly or indirectly recognize or bind to the core sequences of various cis-acting elements, thereby participating in regulating the transcription efficiency of target genes.
control level
basic control point
structural activation of genes
Transcription initiation
most important stage
Post-transcriptional processing and transport
Translation and post-translation processing
biological significance
Adapt to the environment, maintain growth and proliferation (prokaryotic, eukaryotic)
Maintain ontogeny and differentiation (eukaryotic)