Name: riboswitch control of bacterial genes
Uploaded: 2025-06-13T06:18:47.000Z
Duration: 1 min 23 s
Channel: JoVE

The post-transcriptional riboswitches are regulatory mechanisms that prematurely terminate mRNA synthesis.Riboswitches located in mRNA leader regions toggle between alternative three-dimensional structures based on the presence of an effector molecule.For example, in Bacillus subtilis, the rfn operon encodes enzymes that catalyze riboflavin biosynthesis.After transcription begins, the leader region of the operon mRNA folds into a structure called the rfn box.Under low intracellular riboflavin levels, the folding pattern of the rfn box allows the transcription of the enzymes for riboflavin biosynthesis.The operon expression increases intracellular riboflavin. Some of the synthesized riboflavin is converted to flavin mononucleotide, or FMN, which acts as an effector molecule for the riboswitch of the rfn box.When intracellular FMN concentration increases, FMN binds to the rfn box, triggering a change in its folding pattern.As a result, the mRNA forms a terminator loop, disrupting RNA polymerase binding and halting transcription.

transcriptional regulation: riboswitches

Transcriptional Regulation: Riboswitches

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus subtilis.Structure and Function of Riboswitches Riboswitches form specific three-dimensional structures in response to the presence or absence of small molecule effectors. In the transcriptional regulation model, the riboswitch can influence the formation of terminator or anti-terminator structures in the mRNA, thereby controlling the continuation or termination of transcription.The rfn Box and Riboflavin Biosynthesis The rfn operon in Bacillus subtilis encodes enzymes necessary for riboflavin biosynthesis. Its leader region contains a riboswitch, known as the rfn box, which governs the transcription of the operon. Under low intracellular riboflavin levels, the rfn box adopts a folding pattern that permits RNA polymerase to transcribe the operon, allowing the synthesis of enzymes required for riboflavin production.Effector Binding and Transcription Termination As transcription proceeds and riboflavin is synthesized, some riboflavin is converted into flavin mononucleotide (FMN), a coenzyme derivative. FMN acts as an effector molecule for the rfn box riboswitch. When FMN levels reach a threshold, it binds to the rfn box, inducing a conformational change in the riboswitch structure. This shift promotes the formation of a terminator loop in the mRNA, which disrupts RNA polymerase activity and halts transcription prematurely.Biological Significance Riboswitches, such as the rfn box, allow precise feedback regulation of metabolic pathways, ensuring enzyme synthesis occurs only when substrate levels are low. By halting gene expression in response to sufficient effector concentrations, riboswitches conserve cellular resources and maintain metabolic balance. This mechanism highlights the efficiency and adaptability of RNA-based regulatory systems in prokaryotes.

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These ...

Education

JoVE Core

Microbiology

Unit

Bacterial Genetics and Gene Regulation

KEY TERMS AND CONCEPTS

riboswitch control of bacterial genes

Riboswitches are RNA control elements that can turn bacterial genes on or off. They sit in the leader region of some mRNAs. When a small molecule binds, the RNA changes shape and affects whether transcription continues.

These RNA switches work by forming alternative secondary structures. A riboswitch can promote either a terminator or an anti-terminator structure in the mRNA. The terminator structure stops RNA polymerase, while the anti-terminator allows transcription to keep going.

A clear example is the rfn operon in Bacillus subtilis. This operon carries genes needed for riboflavin biosynthesis. Its leader region contains a riboswitch called the rfn box, which controls expression of the operon.

When intracellular riboflavin levels are low, the rfn box folds in a way that lets RNA polymerase transcribe the operon. The cell then makes the enzymes needed to produce riboflavin. As riboflavin is made, some of it is converted into flavin mononucleotide, or FMN, a coenzyme derivative.

FMN acts as the effector molecule for the rfn box riboswitch. When FMN reaches a high enough level, it binds to the riboswitch and changes its shape. This change helps form a terminator loop in the mRNA, which stops transcription early.

This feedback system helps the cell save resources and keep metabolism balanced. Riboswitches like the rfn box make sure enzyme production happens when substrate levels are low and slows down when enough product is present. They show how RNA-based regulation can precisely control bacterial gene expression.

Riboswitch Control of Bacterial Genes

translation in prokaryotes

Bacterial Protein Synthesis Steps

Bacterial protein synthesis turns mRNA instructions into a working protein through three main stages: initiation, elongation, and termination. In prokaryotes, this process is tightly coordinated by the ribosome, tRNA, and several helper factors. Each stage helps move the growing protein forward in an ordered way. Initiation starts when the ribosomal subunits and initiation factors assemble on the mRNA. In bacteria, the 30S subunit recognizes the Shine-Dalgarno sequence, a conserved region just...

prokaryotic dna replication

DNA Copying in Prokaryotes

Prokaryotic DNA replication is the process that copies DNA in bacteria and other prokaryotes. It allows the cell to pass genetic information to new cells during division. Replication begins at a specific start site on the DNA called the origin of replication. The process then moves in both directions, so two replication forks form and the DNA is copied from each side. Several key enzymes help carry out this process. Helicase unwinds the DNA strands, primase lays down a short RNA primer, and...

prokaryotic gene structure and organization

prokaryotic-gene-structure-and-organization

How Prokaryotic Genes Start and Stop

Prokaryotic genes are organized so transcription and translation can begin, run, and stop with precision. Their genomes contain coding regions and non-coding regions that work together to control gene expression and protein synthesis. Coding regions carry the instructions for proteins or functional RNA molecules. Structural genes are transcribed into messenger RNA (mRNA) and then translated into polypeptides. These sequences usually begin with a start codon, often AUG, and end with one of the...

transcription in prokaryotes

RNA Polymerase Steps in Prokaryotes

Transcription in prokaryotes follows a set of RNA polymerase steps that turn genetic information into RNA. The process has three main stages: initiation, elongation, and termination. Each stage uses specific molecular interactions to control when and how RNA is made. During initiation in bacteria, the RNA polymerase core enzyme joins with a sigma factor to form a holoenzyme. In E. coli, the sigma factor σ70 helps the holoenzyme recognize the -10 region, also called the Pribnow box, and the -35...

coordination of gene expression processes in bacteria

coordination-of-gene-expression-processes-in-bacteria

Bacterial Gene Expression and Collision Control

Bacterial gene expression links DNA replication, transcription, and translation in a tightly timed way. This coupling helps bacteria make proteins quickly and respond fast to changes in their environment. It also creates conflicts that bacteria must control with specific repair and rescue steps. As the replisome unwinds DNA during replication, RNA polymerase reads the template strand and makes mRNA at the same time. Ribosomes can attach to the new mRNA right away, and several ribosomes may...

bacterial protein maturation

Bacterial Protein Folding and Quality Control

Bacterial protein folding and quality control help new proteins reach their correct shape and function. As a polypeptide leaves the ribosome, it begins to mature through early chemical changes and folding steps. These steps are tightly regulated and often rely on chaperone proteins. The process starts with N-terminal modifications. In bacteria, the first amino acid is usually N-formylmethionine, or fMet, and this N-terminal group is often changed as the protein emerges from the ribosome. The...

bacterial translocation and protein secretion

bacterial-translocation-and-protein-secretion

How Bacteria Export Proteins Across Membranes

Bacteria export proteins across membranes using specialized translocation systems. These pathways move proteins to the plasma membrane, periplasm, outer membrane, or the outside of the cell. They are important for membrane assembly, enzyme activity in the periplasm, and interactions with the environment. The Sec and Tat pathways divide the work between proteins that are still unfolded and proteins that must stay folded. Most export proteins begin with an N-terminal signal sequence. This short...

gram-negative bacterial protein secretion systems

gram-negative-bacterial-protein-secretion-systems

How Gram-Negative Bacteria Export Proteins

Gram-negative bacteria use protein secretion systems to move proteins across their double-membrane envelope. These systems send proteins either into the extracellular environment or into host cells. They are grouped into one-step and two-step pathways based on how they move the proteins. One-step secretion systems move proteins across both membranes in a single route. Type I secretion system (T1SS) exports substrates such as toxins and proteases directly from the cytoplasm outside the cell. It...

constitutive and regulated gene expression

constitutive-and-regulated-gene-expression

Prokaryotic Gene Expression Control

Prokaryotic gene expression includes both constant and controlled patterns of protein production. These systems help cells make essential proteins while also responding to changes in the environment. Constitutive genes, also called housekeeping genes, are expressed continuously. They code for proteins needed for basic cell functions, including glycolysis enzymes, ribosomal parts for protein synthesis, and proteins used in DNA replication. This steady expression keeps the cell’s core machinery...

operon model

Gene Control in Bacterial Operons

Gene control in bacterial operons lets prokaryotes turn related genes on or off together. An operon is a cluster of structural genes that are transcribed under the control of one promoter. The promoter helps RNA polymerase bind and start transcription. An operator lies downstream and serves as a DNA binding site for regulatory proteins. These regulatory proteins determine whether the structural genes are transcribed. Repressors can block transcription, and activators can support it. Small...

inducible operons: lac operon

Lactose Switch in the lac Operon

The lac operon in Escherichia coli controls lactose metabolism with inducible gene regulation and metabolic flexibility. It helps the bacterium use glucose first when it is available, then switch to lactose when glucose becomes scarce. This system is a classic example of how bacteria match gene expression to changing food sources. The lac operon includes three structural genes: lacZ, lacY, and lacA. These genes make beta-galactosidase, lactose permease, and thiogalactoside transacetylase,...

repressible operon: trp operon

Tryptophan Feedback Control in the trp Operon

The trp operon in Escherichia coli controls tryptophan production with feedback regulation. It is a repressible operon, so it turns off when enough tryptophan is already present. This saves the cell from making more of an amino acid it does not need. The operon includes five structural genes, trpE, trpD, trpC, trpB, and trpA. These genes code for enzymes used in tryptophan biosynthesis. They are transcribed together as one mRNA and are controlled by a promoter, an operator, and a leader...

Riboswitches are RNA control elements that can turn bacterial genes on or off. They sit in the leader region of some mRNAs. When a small molecule binds, the RNA changes shape and affects whether transcription continues. These RNA switches work by forming alternative secondary structures. A riboswitch can promote either a terminator or an anti-terminator structure in the mRNA. The terminator structure stops RNA polymerase, while the anti-terminator allows transcription to keep going. A clear...

translational regulation

How Bacteria Control Translation

Bacteria control translation by changing how easily ribosomes can reach mRNA. This regulation depends on RNA structures and signals inside the cell or in the environment. It helps prokaryotes make proteins only when they are needed. Translational riboswitches are one way bacteria manage this process. These RNA elements sit in the leader region of an mRNA and control the Shine-Dalgarno sequence, or SD sequence, which is the ribosome-binding site. When an effector molecule binds, the RNA changes...

global regulatory systems

Bacterial Gene Regulation in Changing Environments

Bacterial gene regulation helps cells respond quickly to changing environments. Global regulatory systems connect outside signals to gene expression, so bacteria can adapt efficiently when conditions shift. These systems include regulons, two-component systems, sigma factors, and secondary messengers. A regulon is a group of genes and operons controlled by the same global regulator. This lets bacteria focus on the resources that are most useful in a given condition. A common example is the...

chemotaxis in e. coli

How E. coli Uses Chemical Cues to Move

Chemotaxis helps Escherichia coli move by sensing chemical cues in its environment. The bacterium travels toward helpful conditions and away from harmful ones. This movement depends on a signal pathway that connects chemical detection to flagellar motion. E. coli detects these chemical gradients with methyl-accepting chemotaxis proteins, or MCPs. These membrane chemoreceptors sense attractants such as sugars and amino acids, as well as repellents such as toxic compounds. They do not measure a...

gene regulation in microbial communities: quorum sensing

gene-regulation-in-microbial-communities-quorum-sensing

Bacterial Quorum Sensing and Autoinducers

Bacterial quorum sensing is a communication system that helps cells change gene expression as their population grows. Bacteria release small signaling molecules called autoinducers. When enough autoinducers build up, the cells respond together and turn on genes linked to survival, resource use, and environmental adaptation. Gram-positive and Gram-negative bacteria use different kinds of autoinducers. Gram-positive bacteria use peptide-based signals. These peptides are made inside the cell,...

gene regulation during sporulation

How Bacteria Switch On Spore Formation

Bacteria can switch on spore formation when conditions become unfavorable. In some Gram-positive bacteria, including Bacillus subtilis and Clostridium species, this process helps the cell survive extreme environmental stress. Sporulation leads to a highly resistant endospore, which is a dormant survival form. Sporulation begins when nutrients are depleted. A phosphorelay system controls the response. In this pathway, a sensor kinase such as KinA detects stress and autophosphorylates, which...

stringent response in e. coli

How E. coli Slows Growth Under Stress

E. coli can slow its growth when nutrients become limited. This change is controlled by the stringent response, a stress pathway that helps bacteria adjust their gene expression and metabolism during starvation. When resources are abundant, cells grow quickly. When nutrients drop, they move toward stationary phase. Nutrient scarcity lowers the level of amino acids inside the cell. This leads to a buildup of uncharged tRNAs, which are tRNAs not carrying amino acids. When these tRNAs enter the...

other stress responses in bacteria

Bacterial Stress Signaling for Low Nutrients

Bacterial stress signaling helps cells survive low nutrients and protein damage. Two key systems are the Pho regulon and the heat shock response. Together, they show how bacteria adapt to changing environmental conditions. The Pho regulon helps bacteria respond to phosphorus scarcity. Bacteria need phosphorus for nucleic acid synthesis, energy metabolism, and membrane integrity. This system uses two proteins, the sensor kinase PhoR and the response regulator PhoB. When phosphorus is low, PhoR...

mutations in microorganisms

Microbial Mutations and Antibiotic Resistance

Mutations are heritable changes in DNA or RNA that can alter how microorganisms grow and function. A mutation may change the base sequence of a gene and turn a wild type cell into a mutant form. These forward mutations add genetic diversity and can change a visible trait, or phenotype. Mutation rates vary among organisms. RNA viruses have the highest mutation rates because they lack strong proofreading during genome copying. Eukaryotes, which have larger and more complex genomes, usually...

spontaneous and induced mutations

DNA Damage from Replication Errors and Mutagens

DNA damage can begin with replication errors or with exposure to mutagens that change DNA. Spontaneous mutations happen infrequently during DNA replication. One cause is tautomeric shifts in nitrogenous bases, when a base shifts between keto and enol forms or amino and imino forms. This change can disrupt normal base pairing and lead to mutations. Reactive oxygen species, or ROS, also damage DNA during aerobic metabolism. ROS can cause depurination, which is the loss of a purine base, or...

point and frameshift mutations

DNA Changes That Alter Proteins

DNA changes can alter proteins in several ways. A point mutation is a change in a single nucleotide base pair. Depending on how that change affects protein synthesis, the result can be silent, missense, or nonsense. A silent mutation changes a nucleotide but does not change the amino acid sequence. This happens because the genetic code is redundant, which means more than one codon can code for the same amino acid. For example, ACC and ACA both code for threonine, so the protein may keep the...

plasmids

Plasmids and Bacterial DNA Transfer

Plasmids are small DNA molecules found outside the main chromosome in bacteria, archaea, and some eukaryotic microbes such as yeast. They are usually circular and often carry fewer than 30 genes, although some plasmids are linear. Their copy number can vary. Single-copy plasmids are present once per cell, while multi-copy plasmids can reach more than 100 copies. Most plasmids replicate on their own by using the host cell’s DNA replication machinery. Some plasmids are episomes, which means they...

transposons

Transposons and Antibiotic Resistance

Transposons are mobile DNA elements that can move within a chromosome or shift to a different chromosome. They are also called jumping genes. These small genetic elements range from about 700 to 40,000 base pairs and are found in all organisms. In some cases, they can even move between DNA molecules such as plasmids or viruses, which adds to genetic variation. Barbara McClintock first discovered transposons in the 1940s while studying maize genetics. Her work later earned the Nobel Prize in...

horizontal gene transfer

How Bacteria Share Genes Quickly

Horizontal gene transfer lets bacteria and other microbes share genetic material within the same generation. This is different from vertical gene transfer, which passes DNA from parent to offspring. It helps microbes evolve, adapt, and survive in shared places like the human gut. Several mobile genetic elements help move DNA from one cell to another. These include plasmids, prophages, integrons, insertion sequences, and transposons. The three main routes are transformation, conjugation, and...

transformation

DNA Uptake in Competent Cells

DNA uptake in competent cells is a key process in microbial genetics. Microbes can release free DNA into their surroundings when cells lyse. Other cells can then take up this extracellular DNA through transformation. If the foreign DNA becomes part of the genome and changes the cell's genetics, the cell has been transformed. Cells that can do this are called competent. Competence can happen naturally in some bacteria and archaea. It can also be induced artificially in the lab. Natural...

conjugation

Bacterial DNA Transfer by Conjugation

Bacterial DNA transfer by conjugation is a form of horizontal gene transfer in bacteria and some archaea. It helps cells gain new traits and adapt to changing conditions. One important example is the spread of antibiotic resistance genes through conjugative plasmids, which can help bacteria survive treatments that would otherwise be lethal. Conjugation requires direct contact between cells. A donor cell, called F+, carries the conjugative plasmid. A recipient cell, called F−, does not have it.

mechanism of conjugation

Bacterial Plasmid Transfer by Conjugation

Bacterial conjugation is a form of horizontal gene transfer that moves DNA between bacterial cells through direct contact. A donor cell carries a conjugative plasmid, which contains the genes needed for pilus formation, DNA replication, and DNA transfer. This plasmid starts the process and drives the transfer from one cell to another. The tra region on the conjugative plasmid codes for proteins that build the pilus, a hair-like structure that extends from the donor cell. The pilus helps the...

transduction

Phage-Mediated Gene Transfer

Phage-mediated gene transfer is called transduction, and it is one of the three main forms of horizontal gene transfer along with transformation and conjugation. It is unique because bacteriophages, which are bacterial viruses, move DNA from one bacterium to another. Generalized transduction happens during the lytic cycle of a bacteriophage. The phage infects a bacterial cell, makes new virions, and then causes the cell to lyse, or burst. During this process, a random piece of bacterial DNA...

development of antibiotic resistance

How Bacteria Resist Antibiotics

Antibiotic resistance happens when bacteria gain ways to survive antibiotic treatment. It can be built into the cell, gained through mutation, or passed between bacteria through horizontal gene transfer. This makes bacterial infections harder to treat and increases the need for new treatment strategies. Some bacteria resist antibiotics through their natural structure. Gram-negative bacteria have an outer wall that blocks certain drugs from entering. Enterococcus faecium can also change its...

key terms and concepts

Learn how riboswitches use RNA folding to control bacterial transcription, using the Bacillus subtilis rfn operon and FMN as an example.

Riboswitch Control of Bacterial Genes | JoVE K12

JoVE Core Microbiology provides an engaging introduction to the microbial world and its influence on health, industry, and the environment. This comprehensive collection covers key concepts such as microbial structure, metabolism, genetics, and ecology. It introduces essential laboratory techniques and microscopy methods through visually engaging animations. Corresponding scientist-in-action videos bridge classroom concepts with real-world research and applications.

microbiology

Riboswitch Control of Bacterial Genes

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