15.2 Prokaryotic Transcription
4 min read•june 14, 2024
Prokaryotic transcription is a vital process where DNA is converted into RNA. It involves three key steps: , , and . Each step plays a crucial role in accurately producing RNA molecules that guide protein synthesis in bacterial cells.
Promoters and termination mechanisms are essential for regulating gene expression in prokaryotes. Promoters control when and how often genes are transcribed, while termination signals ensure transcription stops at the right place. These elements allow bacteria to adapt quickly to changing environments.
Prokaryotic Transcription
Steps of prokaryotic transcription
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- Initiation
- binds to the located upstream of the gene to be transcribed ()
- Promoter contains specific -10 and -35 consensus sequences that are recognized by the RNA polymerase (TATAAT and TTGACA)
- , a subunit of RNA polymerase, helps the enzyme recognize and bind to the promoter sequence
- Upon binding, the DNA double helix unwinds and separates, forming a that allows access to the
- Elongation
- RNA polymerase reads the template strand in the 3' to 5' direction, synthesizing the complementary RNA strand
- Ribonucleotides (ATP, UTP, CTP, GTP) are added to the growing RNA chain in the 5' to 3' direction, following the base-pairing rules
- RNA polymerase catalyzes the formation of phosphodiester bonds between the ribonucleotides, extending the RNA strand
- Sigma factor is released from the RNA polymerase complex after transcription initiation, allowing the enzyme to proceed with elongation
- RNA polymerase continues to synthesize the RNA molecule until it reaches a specific termination signal on the DNA template
- Termination
- Transcription termination in prokaryotes occurs through two main mechanisms: Rho-dependent and
- involves the , an ATP-dependent RNA helicase that binds to the nascent RNA and causes the RNA polymerase to dissociate from the DNA template ()
- Rho-independent termination, also known as , occurs when the nascent RNA forms a loop structure followed by a string of uracil residues, causing the RNA polymerase to stall and dissociate from the DNA template ()
Promoters in prokaryotic gene regulation
- Promoters are DNA sequences located upstream of the transcription start site that play a crucial role in regulating gene expression in prokaryotes (lac promoter)
- RNA polymerase recognizes and binds to the promoter region to initiate the transcription process
- The strength of a promoter determines the frequency at which transcription initiation occurs
- Strong promoters have consensus sequences that closely match the ideal -10 (TATAAT) and -35 (TTGACA) sequences, leading to higher rates of transcription
- Weak promoters have sequences that deviate from the consensus, resulting in lower transcription rates and reduced gene expression
- Regulatory proteins can bind to specific sites within or near the promoter region and affect the transcription process
- Activator proteins enhance transcription by recruiting RNA polymerase to the promoter or facilitating its binding ()
- proteins inhibit transcription by blocking RNA polymerase from binding to the promoter or preventing its progression along the DNA template ()
- Environmental signals, such as changes in nutrient availability (glucose), temperature, or other factors, can influence the binding of regulatory proteins to the promoter, allowing bacteria to adapt to changing conditions
- , including activators and repressors, play a crucial role in modulating gene expression by interacting with the promoter region
Prokaryotic transcription termination mechanisms
- Rho-dependent termination
- Requires the involvement of the Rho protein, an ATP-dependent RNA helicase
- Rho binds to specific sites on the nascent RNA called Rho utilization sites (rut) and moves along the RNA in the 5' to 3' direction
- Rho uses energy from to translocate along the RNA and catch up to the RNA polymerase
- When Rho reaches the RNA polymerase, it causes the enzyme to dissociate from the DNA template, effectively terminating transcription
- Rho-independent termination
- Also known as intrinsic termination, this mechanism relies on the formation of a specific secondary structure in the nascent RNA
- The termination signal consists of a stable structure followed by a string of uracil residues
- RNA polymerase stalls at the uracil-rich region due to the weak base-pairing between the RNA and DNA strands
- The stalling of RNA polymerase leads to its dissociation from the DNA template, terminating the transcription process
- Rho-independent termination does not require any additional proteins or factors, as the termination signal is encoded within the DNA sequence itself
- Comparison of the two mechanisms
- Both Rho-dependent and Rho-independent termination result in the dissociation of RNA polymerase from the DNA template and the release of the newly synthesized RNA molecule
- Rho-dependent termination requires the participation of the Rho protein and the hydrolysis of ATP, while Rho-independent termination relies solely on the formation of a specific RNA secondary structure
- Rho-dependent termination can occur at various locations downstream of the gene being transcribed, whereas Rho-independent termination occurs at specific sites encoded by the DNA sequence
RNA Polymerase and DNA Strands in Transcription
- RNA polymerase is composed of two main components:
- : Contains the catalytic subunits responsible for RNA synthesis
- : The complete RNA polymerase complex, including the core enzyme and sigma factor
- During transcription, RNA polymerase interacts with two important DNA strands:
- Template strand: The DNA strand that is read by RNA polymerase to synthesize the complementary RNA molecule
- : The non-template DNA strand that has the same sequence as the RNA transcript (except for thymine being replaced by uracil)
- are the building blocks of RNA, added one by one to the growing RNA chain during elongation
Key Terms to Review (46)
-35 sequence: The -35 sequence is a conserved DNA sequence found in prokaryotic promoters, located approximately 35 base pairs upstream from the transcription start site. It plays a crucial role in the initiation of transcription by providing a binding site for the sigma factor of RNA polymerase, facilitating the proper assembly of the transcription machinery at the promoter region. The presence and specific sequence of the -35 region are essential for effective gene expression in prokaryotes.
Aminoacyl tRNA synthetases: Aminoacyl tRNA synthetases are enzymes that attach the correct amino acid to its corresponding tRNA molecule during protein synthesis. They play a crucial role in translating genetic information into functional proteins.
Antitermination: Antitermination is a regulatory mechanism in prokaryotic transcription that prevents the premature termination of RNA synthesis by RNA polymerase. This process allows for the continuous transcription of specific genes under certain conditions, ensuring that essential genes can be expressed fully when needed. Antitermination plays a crucial role in controlling gene expression, particularly in response to environmental signals or during specific developmental stages.
ATP hydrolysis: ATP hydrolysis is a biochemical reaction in which adenosine triphosphate (ATP) is broken down into adenosine diphosphate (ADP) and an inorganic phosphate (Pi), releasing energy that is used to fuel various cellular processes. This reaction is crucial for driving endergonic reactions, enabling vital functions like muscle contraction, active transport, and biosynthesis, while adhering to the laws of thermodynamics.
Attenuation: Attenuation is a regulatory mechanism in prokaryotic organisms that controls gene expression by influencing the transcription of specific genes. This process often involves the formation of a transcription terminator that stops RNA synthesis prematurely, allowing the cell to respond to changes in environmental conditions or nutrient availability. By modulating gene expression, attenuation serves as a means for prokaryotes to conserve energy and resources while adapting to their surroundings.
CAP protein: CAP protein, or Catabolite Activator Protein, is a transcriptional regulator in prokaryotes that enhances the expression of certain genes in the presence of low glucose levels. It plays a critical role in ensuring that bacteria can efficiently utilize available energy sources by activating the transcription of operons involved in the metabolism of alternative sugars when glucose is scarce. CAP works closely with cAMP, a signaling molecule that binds to CAP and enables it to interact with RNA polymerase, facilitating the transcription process.
Coding strand: The coding strand is the DNA strand that has the same sequence as the mRNA produced during transcription, except for the substitution of thymine (T) with uracil (U). This strand serves as a template for RNA polymerase during prokaryotic transcription, guiding the synthesis of messenger RNA (mRNA) that will be translated into proteins.
Core enzyme: The core enzyme is a fundamental component of RNA polymerase in prokaryotes, responsible for the synthesis of RNA during transcription. This enzyme consists of multiple subunits that work together to catalyze the polymerization of ribonucleotides into an RNA strand. The core enzyme is essential for transcription initiation, elongation, and termination, making it a critical player in gene expression regulation in prokaryotic organisms.
Dideoxynucleotides: Dideoxynucleotides are modified nucleotides lacking a 3' hydroxyl group, which prevents the addition of further nucleotides during DNA synthesis. They are essential components in Sanger sequencing for terminating DNA strand elongation at specific bases.
Elongation: Elongation refers to the stage in transcription and translation where nucleotides or amino acids are sequentially added to a growing RNA or polypeptide chain, respectively. During this process, RNA polymerase or ribosomes catalyze the addition of these building blocks, allowing for the synthesis of RNA in transcription and proteins in translation. Elongation is crucial for gene expression and is characterized by specific mechanisms that ensure accuracy and efficiency.
Eukaryotic initiation factor-2 (eIF-2): Eukaryotic initiation factor-2 (eIF-2) is a protein complex essential for the initiation of mRNA translation in eukaryotic cells. It plays a critical role in the formation of the pre-initiation complex by binding GTP and the initiator tRNA, facilitating its attachment to the small ribosomal subunit.
Hairpin loop: A hairpin loop is a secondary structure formed in nucleic acids, particularly RNA, where a sequence of nucleotides folds back on itself to create a double-stranded region, followed by a loop. This structure plays an important role in various biological processes, including prokaryotic transcription, where it can influence the termination of transcription by destabilizing the RNA polymerase complex and promoting the release of newly synthesized RNA.
His operon: The his operon is a group of genes in prokaryotes that are involved in the biosynthesis of the amino acid histidine. It is a classic example of a regulated operon, where the expression of these genes is controlled based on the availability of histidine in the environment. This allows bacteria to efficiently manage their resources, turning on or off the operon as needed to either synthesize histidine or utilize it from external sources.
Holoenzyme: A holoenzyme is a fully functional enzyme complex that includes both the protein component, known as the apoenzyme, and any necessary non-protein molecules called cofactors or coenzymes. This combination is crucial for the enzyme to exhibit its catalytic activity, allowing it to carry out biochemical reactions effectively. In prokaryotic transcription, the holoenzyme is particularly important as it is responsible for synthesizing RNA from a DNA template.
Initiation: Initiation is the first step in the processes of transcription and translation, where the necessary components come together to begin the synthesis of RNA or proteins. In transcription, it involves the binding of RNA polymerase to the promoter region of DNA, while in translation, it marks the assembly of the ribosome and the first tRNA carrying the amino acid to start protein synthesis. This step is crucial as it sets the stage for accurate and efficient gene expression.
Initiation site: The initiation site is the specific location on DNA where transcription begins. It is typically marked by the +1 nucleotide, where RNA polymerase starts synthesizing RNA.
Intrinsic termination: Intrinsic termination is a mechanism that causes the end of transcription in prokaryotes, relying on specific sequences in the DNA template. This process occurs when the RNA polymerase transcribes a region of DNA that forms a hairpin loop structure in the RNA, followed by a series of uracil nucleotides. The formation of this hairpin disrupts the interaction between RNA polymerase and the RNA transcript, leading to the release of the newly synthesized RNA molecule.
Lac operon: The lac operon is a well-studied model of gene regulation in prokaryotes, specifically in E. coli, that controls the metabolism of lactose. It consists of structural genes that encode proteins necessary for lactose uptake and breakdown, alongside regulatory elements that govern their expression in response to the presence or absence of lactose and glucose. This system exemplifies how prokaryotic cells efficiently manage gene expression to adapt to changing environmental conditions.
Lac repressor: The lac repressor is a protein that regulates the transcription of the lactose operon in E. coli by binding to the operator region and preventing RNA polymerase from transcribing the genes needed for lactose metabolism. This protein plays a crucial role in the gene regulation process, responding to the presence or absence of lactose to control whether the operon is active or inactive, thus maintaining metabolic efficiency.
Messenger RNA (mRNA): Messenger RNA (mRNA) is a single-stranded molecule that carries genetic information from DNA to the ribosome, where proteins are synthesized. It serves as a template for translating genetic code into amino acids, forming proteins.
MRNA: mRNA, or messenger RNA, is a single-stranded molecule that carries genetic information from DNA to the ribosome, where proteins are synthesized. This process is essential for translating the genetic code into functional proteins, connecting it to various cellular processes and regulation mechanisms.
Nontemplate strand: The nontemplate strand, also known as the coding strand, is the DNA strand whose sequence matches the RNA transcript produced during transcription. It is complementary to the template strand used by RNA polymerase for synthesis of mRNA.
Nucleotides: Nucleotides are the building blocks of nucleic acids, consisting of a nitrogenous base, a five-carbon sugar, and one or more phosphate groups. They play a crucial role in various biological processes, such as energy transfer, cellular signaling, and the synthesis of DNA and RNA.
Operator: An operator is a DNA sequence that acts as a regulatory element, controlling the transcription of adjacent genes. It is the binding site for repressor proteins which can inhibit gene expression by blocking RNA polymerase.
Operator: An operator is a regulatory DNA sequence that plays a crucial role in the control of gene expression in prokaryotic cells. It serves as the binding site for repressor proteins, which can inhibit the transcription of adjacent genes. The presence or absence of these proteins at the operator can determine whether genes are turned on or off, directly influencing the cell's ability to respond to environmental changes.
Pribnow box: The Pribnow box is a conserved sequence found in bacterial promoters, crucial for the initiation of transcription in prokaryotic cells. Typically located about 10 base pairs upstream from the transcription start site, this sequence helps RNA polymerase recognize and bind to the promoter region. Its presence is essential for the proper functioning of the transcription machinery in bacteria, impacting gene expression and regulation.
Promoter region: The promoter region is a specific sequence of DNA located upstream of a gene that serves as a binding site for RNA polymerase and transcription factors, initiating the process of transcription. This region plays a crucial role in determining the efficiency and regulation of gene expression, as it contains essential elements that facilitate the assembly of the transcription machinery.
Repressor: A repressor is a type of protein that binds to specific DNA sequences to prevent the transcription of certain genes, effectively regulating gene expression. By inhibiting the binding of RNA polymerase to the promoter region, repressors play a crucial role in controlling which genes are expressed at any given time, helping organisms adapt to environmental changes and conserve energy by not producing unnecessary proteins.
Rho protein: Rho protein is a key termination factor in prokaryotic transcription, functioning to stop the synthesis of RNA by recognizing specific sequences and promoting the dissociation of RNA polymerase from the DNA template. This protein is essential for ensuring that transcription occurs accurately and efficiently, contributing to the regulation of gene expression in bacteria.
Rho-dependent termination: Rho-dependent termination is a mechanism in prokaryotic transcription that involves the Rho protein recognizing specific sequences on the RNA strand, facilitating the dissociation of the RNA polymerase from the DNA template. This process is critical for ensuring that transcription stops at the appropriate locations and is necessary for the accurate expression of genes. The Rho factor plays a crucial role in regulating gene expression by ensuring that mRNA synthesis is completed correctly and efficiently.
Rho-independent termination: Rho-independent termination is a mechanism in prokaryotic transcription that leads to the cessation of RNA synthesis without the involvement of the Rho protein. This process typically occurs when a newly synthesized RNA transcript forms a stable hairpin structure followed by a series of uracil residues, leading to the destabilization of the RNA-DNA hybrid and eventual dissociation of the RNA polymerase from the DNA template.
Ribosomal RNA (rRNA): Ribosomal RNA (rRNA) is a type of RNA that combines with proteins to form ribosomes. These ribosomes are the cellular structures where protein synthesis occurs.
RNA polymerase: RNA polymerase is an enzyme that synthesizes RNA from a DNA template during the process of transcription. It plays a crucial role in converting genetic information stored in DNA into RNA, which is necessary for protein synthesis and gene expression regulation. This enzyme interacts with various transcription factors and is essential for the transcription process in both prokaryotic and eukaryotic organisms.
RRNA: Ribosomal RNA (rRNA) is a type of non-coding RNA that is a fundamental component of ribosomes, which are the cellular structures responsible for protein synthesis. rRNA molecules provide structural support and catalyze the chemical reactions involved in translating messenger RNA (mRNA) into proteins. This makes rRNA crucial for cellular function and gene expression, linking it closely to the processes of transcription and translation.
Rut sites: Rut sites refer to specific locations in the environment where male animals, particularly in species such as deer, engage in mating behaviors during the breeding season. These sites are often characterized by signs of territorial marking, such as scrapes, rubs, and vocalizations, which signal the presence of dominant males and attract females.
Sigma factor: A sigma factor is a protein that binds to RNA polymerase in prokaryotic cells, guiding it to specific promoter regions of DNA to initiate transcription. By recognizing and attaching to specific sequences in the promoter, sigma factors play a crucial role in the regulation of gene expression, allowing the organism to respond to various environmental conditions by turning genes on or off as needed.
Stable hairpin: A stable hairpin is a secondary structure formed when a single-stranded RNA molecule folds back on itself, creating a double-stranded stem with a loop at the end. It often plays a crucial role in the termination of transcription in prokaryotes.
TATA box: The TATA box is a DNA sequence found in the promoter region of many genes in eukaryotes, essential for the initiation of transcription. It serves as a binding site for transcription factors and RNA polymerase II, playing a critical role in the regulation of gene expression by facilitating the formation of the transcription initiation complex.
Template strand: The template strand is the single strand of DNA that serves as a guide for the synthesis of a complementary strand during processes like DNA replication and transcription. It is crucial because the sequence of nucleotides on the template strand determines the sequence of the newly synthesized strand, ensuring accurate copying of genetic information. The template strand is read in a specific direction to facilitate the addition of complementary nucleotides.
Termination: Termination refers to the final step in the processes of transcription and translation, signaling the end of RNA synthesis in transcription and the completion of polypeptide synthesis in translation. It is a crucial event that ensures the accurate production of RNA and proteins, maintaining cellular functions. This process involves specific sequences and factors that recognize when to halt synthesis, ensuring that only the required genetic information is produced and that proteins are properly folded and functional.
Transcription bubble: A transcription bubble is a localized region of unwound DNA that occurs during the process of transcription, where RNA polymerase synthesizes RNA from a DNA template. This bubble forms as the enzyme separates the two strands of the double helix, allowing access to the coding region of a gene. In this way, the transcription bubble plays a crucial role in enabling the synthesis of RNA in both prokaryotic and eukaryotic organisms.
Transcription bubble.: The transcription bubble is a localized region where the DNA double helix unwinds, allowing RNA polymerase to access the template strand for RNA synthesis. It typically encompasses about 17 base pairs and moves along the DNA as transcription proceeds.
Transcription factors: Transcription factors are proteins that help regulate the transcription of genes by binding to specific DNA sequences. They play a critical role in turning genes on or off in response to various cellular signals.
Transcription factors: Transcription factors are proteins that bind to specific DNA sequences, playing a crucial role in regulating the transcription of genes from DNA to mRNA. They act as essential mediators in cellular responses to signaling molecules, orchestrating gene expression patterns that determine cell function and identity. By interacting with other proteins and RNA polymerase, transcription factors help facilitate or inhibit the process of transcription, influencing how cells respond to various signals and environmental changes.
TRNA: tRNA, or transfer RNA, is a type of RNA molecule that plays a crucial role in protein synthesis by transporting specific amino acids to the ribosome during translation. It acts as an adapter, matching its anticodon with the corresponding codon on the mRNA strand, ensuring that the correct amino acid is added to the growing polypeptide chain. This process is essential for translating the genetic information encoded in DNA into functional proteins.
Trp operon: The trp operon is a group of genes in prokaryotes that are involved in the biosynthesis of the amino acid tryptophan. This operon is a classic example of gene regulation, where its expression is tightly controlled based on the availability of tryptophan in the environment, showcasing mechanisms of feedback inhibition and transcriptional control.