5.3 Transcription in prokaryotes and eukaryotes
4 min read•august 16, 2024
Transcription, the process of making RNA from DNA, differs between prokaryotes and eukaryotes. Prokaryotes do it all in one place, while eukaryotes separate the steps. This impacts how genes are organized and expressed in each type of organism.
The machinery for transcription also varies. Prokaryotes use one main enzyme with helper proteins called sigma factors. Eukaryotes have multiple enzymes and a complex array of to control gene expression more precisely.
Transcription in Prokaryotes vs Eukaryotes
Fundamental Differences in Transcription Process
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- Transcription synthesizes RNA from DNA template in both prokaryotes and eukaryotes with key differences
- Prokaryotic transcription occurs in while eukaryotic transcription takes place in
- Prokaryotes couple transcription with translation allowing simultaneous processes
- Eukaryotes separate transcription and translation spatially and temporally
- Prokaryotic genes organize in operons for coordinated transcription of multiple genes
- Eukaryotic genes typically transcribe individually
Initiation and Termination Mechanisms
- Prokaryotic transcription involves single and sigma factors
- Eukaryotic transcription initiation uses multiple RNA polymerases and complex array of transcription factors
- Prokaryotic transcription occurs through rho-dependent or rho-independent mechanisms (intrinsic termination)
- Eukaryotic transcription termination involves additional factors and polyadenylation process
- Poly(A) polymerase adds poly(A) tail to 3' end of
- Cleavage and polyadenylation specificity factor (CPSF) recognizes polyadenylation signal
Structure and Function of RNA Polymerases
Composition and Complexity
- Prokaryotes have single RNA polymerase type
- Eukaryotes possess three main RNA polymerase types (RNA Pol I, II, III)
- RNA Pol I transcribes ribosomal RNA () genes
- RNA Pol II transcribes messenger RNA (mRNA) and some small nuclear RNAs (snRNAs)
- RNA Pol III transcribes transfer RNA () and 5S rRNA genes
- Prokaryotic RNA polymerase core enzyme consists of five subunits (α2ββ'ω)
- Eukaryotic RNA polymerases contain 12 or more subunits
- RNA Pol II has 12 subunits (RPB1-RPB12)
- RNA Pol I and III have 14 and 17 subunits respectively
Functional Differences
- Eukaryotic RNA polymerases require general transcription factors for transcription initiation
- Prokaryotic RNA polymerase initiates transcription with only sigma factors
- Eukaryotic RNA Pol II largest subunit contains unique carboxy-terminal domain (CTD)
- CTD essential for transcription regulation and mRNA processing
- Undergoes phosphorylation cycles during transcription
- Prokaryotic RNA polymerase directly recognizes sequences
- Eukaryotic RNA polymerases rely on transcription factors to recognize and bind promoter elements
- Eukaryotic enzymes generally more processive and accurate due to complex structure and associated factors
- Processivity refers to ability to synthesize long RNA transcripts without dissociating from template
- Higher accuracy results from proofreading mechanisms and associated factors
Sigma Factors in Prokaryotic Transcription
Structure and Function of Sigma Factors
- Sigma factors associate with core RNA polymerase to form holoenzyme in prokaryotes
- Essential for promoter recognition and transcription initiation
- Different sigma factors recognize specific promoter sequences
- Primary sigma factor (σ70 in E. coli) transcribes housekeeping genes during normal growth
- Alternative sigma factors direct RNA polymerase to specific gene sets
- σ32 (heat shock response)
- σS (stationary phase genes)
- σF (flagellar synthesis)
Sigma Factor Mechanism and Regulation
- Sigma factors facilitate DNA double helix unwinding at promoter region
- Enable RNA polymerase to access template strand and initiate transcription
- Sigma factor dissociates from RNA polymerase after transcription initiation
- Allows phase to proceed
- Interplay between sigma factors and regulators enables precise gene expression control
- Anti-sigma factors sequester specific sigma factors to prevent their action
- Sigma factor competition for core RNA polymerase regulates gene expression
- Rapid adaptation to changing environmental conditions through sigma factor switching
Transcription Factors and Enhancers in Eukaryotes
Types and Functions of Transcription Factors
- Transcription factors bind specific DNA sequences to regulate gene expression
- General transcription factors required for pre-initiation complex assembly
- TFIIA stabilizes TBP-DNA interaction
- TFIIB bridges between TBP and RNA Pol II
- TFIID (contains TBP) recognizes TATA box
- Specific transcription factors bind regulatory elements in promoter or regions
- Modulate transcription initiation rate in response to cellular signals
- Examples: NF-κB (immune response), CREB (cAMP-responsive genes)
- Eukaryotic transcription factors contain distinct functional domains
- DNA-binding domains (zinc finger, helix-turn-helix)
- Activation domains (acidic, glutamine-rich)
Enhancers and Transcriptional Regulation
- Enhancers increase transcription rate when bound by appropriate transcription factors
- Located far from promoter (up to 1 Mb away)
- Enhancer-promoter interactions facilitated by coactivators and mediator complexes
- Form DNA loops to bring distant regulatory elements close to promoter
- acts as bridge between enhancer-bound factors and basal transcription machinery
- Combinatorial binding of multiple transcription factors allows complex regulation
- Cell type-specific gene expression
- Developmental stage-specific gene expression
- Enhanceosome formation involves cooperative binding of multiple factors
- Example: interferon-β enhanceosome requires coordinated binding of NF-κB, IRFs, and ATF-2/c-Jun
Key Terms to Review (21)
Cytoplasm: Cytoplasm is the gel-like substance within a cell, encompassing all the organelles and cellular components outside of the nucleus. It plays a crucial role in cellular processes, including the transport of materials and the site for biochemical reactions. The cytoplasm is essential for maintaining the cell's shape and consistency while facilitating various cellular functions, such as protein synthesis and cellular signaling.
Elongation: Elongation is the process during protein synthesis where amino acids are added one by one to a growing polypeptide chain. This occurs in both transcription and translation, as RNA is synthesized from DNA and proteins are built from mRNA, respectively. Understanding elongation helps clarify how genetic information is translated into functional proteins and how the process is coordinated in prokaryotic and eukaryotic cells.
Enhancer: An enhancer is a regulatory DNA sequence that increases the likelihood of transcription of specific genes by providing binding sites for transcription factors and other proteins. Enhancers can function over long distances and interact with promoters to enhance gene expression, making them essential for the precise regulation of genes in various contexts, such as development and response to environmental signals.
Gene silencing: Gene silencing is a biological process that reduces or eliminates the expression of a specific gene, often through mechanisms like RNA interference (RNAi) and the action of microRNAs. This phenomenon plays a crucial role in regulating gene activity, ensuring that genes are expressed only when needed, and maintaining cellular homeostasis. By controlling gene expression, gene silencing influences various cellular processes including development, differentiation, and response to environmental signals.
Helicase: Helicase is an essential enzyme responsible for unwinding the DNA double helix during processes like replication and transcription. By separating the two strands of DNA, helicase enables other enzymes to access the genetic information necessary for synthesizing RNA or copying DNA. Its activity is crucial for ensuring that these fundamental biological processes occur smoothly and accurately.
Initiation: Initiation is the first step in the processes of transcription and translation, where specific sequences in DNA or RNA are recognized to start the synthesis of RNA or proteins. This step is crucial as it sets the stage for the entire process, determining how and when genes are expressed, which is essential for cell function and response.
Mediator complex: The mediator complex is a multi-protein complex that plays a crucial role in the regulation of gene transcription by serving as a bridge between transcription factors and RNA polymerase II. It helps to facilitate the assembly of the transcription machinery at the promoter region of genes, allowing for precise control of transcription initiation in eukaryotic cells. By interacting with various enhancers, silencers, and insulators, the mediator complex integrates diverse signals to regulate gene expression effectively.
MRNA: mRNA, or messenger RNA, is a type of RNA that serves as the intermediary between the DNA in the cell's nucleus and the ribosomes in the cytoplasm, where proteins are synthesized. It carries genetic information copied from DNA in a sequence of nucleotides, dictating the order of amino acids during protein synthesis, which is crucial for cellular function and regulation.
Nucleus: The nucleus is a membrane-bound organelle found in eukaryotic cells that contains the cell's genetic material, organized as DNA molecules. It acts as the control center for cellular activities, including gene expression and replication, thereby playing a vital role in cellular function and inheritance.
Operon: An operon is a cluster of genes under the control of a single promoter and regulated together, allowing for coordinated expression in response to environmental changes. This system is crucial for gene regulation, particularly in prokaryotes, where it enables efficient adaptation to varying conditions by controlling the transcription of related genes simultaneously.
Promoter: A promoter is a specific DNA sequence located upstream of a gene that serves as the binding site for RNA polymerase and transcription factors, initiating the process of transcription. It plays a crucial role in determining when and how much a gene is expressed, influencing cellular functions and responses.
Rna polymerase: RNA polymerase is an enzyme responsible for synthesizing RNA from a DNA template during the process of transcription. This enzyme plays a crucial role in gene expression and regulation, serving as a key player in both prokaryotic and eukaryotic cells by facilitating the conversion of genetic information stored in DNA into functional RNA molecules.
Rna processing: RNA processing is the series of modifications that pre-mRNA undergoes after transcription and before it becomes mature mRNA. This process is essential for eukaryotic cells, where the initial RNA transcript must be altered through capping, polyadenylation, and splicing to produce a functional mRNA that can be translated into proteins. In prokaryotes, however, RNA processing is minimal, as transcription and translation occur simultaneously in the cytoplasm.
RRNA: Ribosomal RNA (rRNA) is a type of non-coding RNA that plays a crucial role in the synthesis of proteins by forming the core of ribosome structure and catalyzing peptide bond formation. As a key component of ribosomes, rRNA facilitates the translation of messenger RNA (mRNA) into proteins, linking the genetic code to functional polypeptides.
Silencer: A silencer is a DNA sequence that binds repressor proteins to inhibit the transcription of a gene, effectively reducing or shutting down gene expression. This mechanism is essential for controlling when and where specific genes are active, helping maintain cellular function and identity. Silencers play a crucial role in gene regulation, as they ensure that certain genes are turned off in specific cell types or developmental stages.
Splicing: Splicing is a crucial process in molecular biology where introns, non-coding regions of pre-mRNA, are removed and exons, the coding sequences, are joined together to form mature mRNA. This modification is essential for the proper expression of genes, allowing eukaryotic cells to produce functional proteins. The splicing process also contributes to mRNA diversity through alternative splicing, which can result in different protein products from a single gene.
Termination: Termination is the final step in the processes of transcription and translation, where the synthesis of RNA or protein is concluded. This crucial event ensures that the molecular machinery knows when to stop adding nucleotides during transcription or amino acids during translation, allowing for the proper completion of genes and the correct folding of proteins.
The central dogma: The central dogma of molecular biology is a framework that describes the flow of genetic information within a biological system. It outlines the processes of transcription and translation, where DNA is first transcribed into RNA and then translated into proteins, which are essential for various cellular functions. This concept underscores the relationship between genes and the proteins they encode, highlighting how genetic instructions are utilized to produce functional biomolecules.
Transcription factors: Transcription factors are proteins that bind to specific DNA sequences, playing a crucial role in regulating the transcription of genes. They can enhance or suppress gene expression by interacting with other proteins and the transcription machinery, which is essential for cellular functions and responses.
Transcriptional activation: Transcriptional activation is the process by which specific proteins, known as transcription factors, increase the likelihood that a particular gene will be transcribed into RNA. This involves a complex interplay of regulatory elements that can enhance or inhibit gene expression, playing a crucial role in determining how genes are turned on or off in response to various signals.
TRNA: tRNA, or transfer RNA, is a type of RNA molecule that plays a critical role in translating the genetic code from mRNA into proteins. It serves as an adapter, matching amino acids with their corresponding codons on the mRNA strand during protein synthesis, ensuring that the correct amino acids are assembled in the right order to form functional proteins.