Gene Expression by Owen Borville September 10, 2024
Gene expression is the process of turning on a gene to produce RNA and proteins, where the information encoded in a gene is turned into a function to control the assembly of protein molecules and RNA.
Gene Expression among Prokaryotic organisms vs Eukaryotic organisms
Since prokaryotic organisms don't have a membrane bound cell nucleus and the DNA floats freely in the cytoplasm of the cell, and RNA transcription, translation, protein formation occur very quickly, almost simultaneously. Gene expression is regulated primarily at the transcriptional level.
Eukaryotic cells, however, have intracellular organelles that add to their complexity. Eukaryotic cells contain a nucleus and DNA is confined to the nuclear compartment. RNA transcription occurs prior to protein formation, and it takes place in the nucleus. Translation of RNA to protein occurs in the cytoplasm. Gene expression is regulated at many levels including epigenetic (heritable changes that do not involve changes in the DNA sequence and when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors), transcriptional (the process by which a cell makes an RNA copy of a piece of DNA), nuclear shuttling (the process by which proteins and ribonucleoprotein particles move across the nuclear envelope to and from the nucleus), post-transcriptional (control of gene expression after the RNA molecule has been created but before it is translated into protein), translational (when RNA is translated to a protein), and post-translational (control of gene expression after a protein has been created)
Prokaryotic Gene Regulation
The DNA of prokaryotes is organized into a circular chromosome, supercoiled within the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called operons.
In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers.
Repressors and activators are proteins produced in the cell that regulate gene expression by binding to specific DNA sites adjacent to the genes they control.
In general, activators bind to the promoter site, while repressors bind to operator regions. Repressors prevent transcription of a gene in response to an external stimulus, whereas activators increase the transcription of a gene in response to an external stimulus. Inducers are small molecules that may be produced by the cell or that are in the cell’s environment. Inducers either activate or repress transcription depending on the needs of the cell and the availability of substrate.
Tryptophan is an amino acid that can be (ingested when available in the environment) or synthesized by prokaryotic cells when necessary to survive by using enzymes encoded by five genes located next to each other and called the tryptophan (trp) operon. This trp are transcribed onto a single mRNA and translated to produce all five enzymes.
The trp operon includes three important regions: the coding region, the trp operator, and the trp promoter. The coding region includes the genes for the five tryptophan biosynthesis enzymes. Just before the coding region is the transcriptional start site. The promoter sequence, to which RNA polymerase binds to initiate transcription, is before or “upstream” of the transcriptional start site. Between the promoter and the transcriptional start site is the operator region.
The trp operator contains the DNA code to which the trp repressor protein can bind. Two tryptophan molecules bind to the trp repressor to allow for bonding to the trp operator. Negative regulators are proteins that prevent transcription.
Positive regulators can turn genes on and activate them, such as CAP (catabolite activator protein) which is a protein that complexes with cAMP to bind to the promoter sequences of operons which control sugar processing when glucose is not available. Cyclic amp (cAMP) is an alternative sugar when glucose is not available. CAP binding stabilizes the binding of RNA polymerase to the promoter region and increases transcription of the associated protein-coding genes.
The third type of gene regulation in prokaryotic cells occurs through inducible operons, which have proteins that bind to activate or repress transcription depending on the local environment and the needs of the cell. The lac operon is is a common inducible operon. When glucose is low, an alternative sugar source is lactose, in which the lac operon can acquire, process, encode, and break down into glucose and galactose. For the lac operon to be activated, glucose level must be very low, and lactose must be present.
Eukaryotic Epigenetic Gene Regulation
Eukaryotic gene regulation is more complex than prokaryotic gene regulation because transcription and translation processes are separated. The human genome encodes over 20,000 genes.
Epigenetic Gene Control
The first level of organization, or packing, is the winding of DNA strands around histone proteins, which package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions. The proteins can move along the DNA strands and perform transcription at any chromosomal region. Signals located on both the proteins and DNA determine whether a chromosomal region should be opened or closed.
The DNA molecule itself can be modified by methylation, an epigenetic modification that leads to gene silencing and is a process involving adding a methyl group to the DNA molecule. The DNA methylation occurs at specific regions called CpG islands (cytosine and guanine dinucleotide DNA pairs) found in the promoter regions of genes.
Transcription factors (RNA polymerase and other proteins) are proteins that bind to the DNA at the promoter or enhancer region and that influences or initiates transcription of a gene.
Eukaryotic Transcription Gene Regulation
In addition to RNA polymerase, two types of transcription factors regulate eukaryotic transcription: General (or basal) transcription factors bind to the core promoter region to assist with the binding of RNA polymerase. Specific transcription factors bind to various regions outside of the core promoter region and interact with the proteins at the core promoter to enhance or repress the activity of the polymerase.
The promoter region of the genes are immediately upstream of the coding sequence. Longer promoters allow for more space for proteins to bind and adds more control to the transcription process. The length of the promoter can vary widely among genes, and therefore the level of control of gene expression can widely vary. The purpose of the promoter is to bind transcription factors that control the initiation of transcription. Cis-acting elements are transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it, and therefore these adjacent genes and DNA interact with each other in order to control and regulate gene expression.
Enhancers are segments of DNA that are upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence, increase, or enhance the transcription of a specific gene. Enhancer regions are binding sequences, or sites, for specific transcription factors. Because the enhancer region may be distant from the promoter, DNA can and must physically bend in order to allow the proteins at the two sites to come into contact.
Eukaryotic cells have mechanisms to prevent transcription (like prokaryotes) called transcriptional repressors that can bind to a promoter or enhancer region to block transcription by responding to external stimuli.
Eukaryotic post-transcriptional gene regulation
Processing of RNA that takes place after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification.
RNA Splicing is the first stage of post-transcriptional control. In eukaryotic cells, the RNA transcript often contains regions called introns that are removed prior to translation. The regions of RNA that code for proteins are called exons. After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing. The splicing is performed by ribonucleoproteins called spliceosomes that recognize the intron ends, cut at these ends, and bring or join the exons together by ligation.
Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the ends of the strand from degrading during its journey. The 5' cap and the pony-A tail (3') cap protect the ends of the mRNA as it travels out of the nucleus into the cytoplasm.
RNA-binding proteins (RBP) are proteins that binds to the 3' or 5' UTR to increase or decrease the RNA stability. Untranslated regions (UTR) are segments of the RNA molecule that are not translated into proteins. These untranslated regions lie before (upstream or 5' UTR) and after (downstream or 3' UTR) the protein-coding region. These untranslated regions regulate mRNA localization, stability, and protein translation.
RNA stability is also controlled by microRNAs (miRNAs) are short RNA molecules that are chopped or cut by a protein called a Dicer. These miRNAs bind to a specific sequence of the RNA. In addition, miRNAs associate with a ribonucleoprotein complex called (RISC) RNA-induced silencing complex to impede translation of the message or lead to the degradation of the mRNA.
Eukaryotic Translation
Similar to transcription, translation is controlled by proteins that bind and initiate the process. The complex that assembles to start the process is the translation initiation complex. In eukaryotes, translation is initiated by binding the met-tRNAi to the 40S ribosome by way of the eukaryotic initiation factor-2 (eIF-2). The eIF-2 protein binds to the high energy molecule guanosine triphosphate (GTP). The tRNA-eIF2-GTP complex then binds to the 40S ribosome. Next a second complex forms on the mRNA with a larger 60S ribosomal subunit.
When eIF2 is phosphorylated, translation is blocked, however, when eIF2 is not phosphorylated, translation occurs.
Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups, which regulate the activity and how long they stay in the cell. Chemical modification can result from external environmental stimuli like stress, lack of nutrients, heat or ultraviolet light exposure. The addition of a ubiquitin group to a protein marks that protein to be degraded, and are sent to the proteasome organelle that removes proteins.
Cancer is associated with many different diseases and occurs when mutations modify cell-cycle control that allows cells to grow uncontrollably and abnormally. Proteins control cell cycle checkpoints and a faulty protein can allow mutated cells to pass through checkpoints without being stopped, leading to cancer diseases.
Cancer can be described as a disease of altered gene expression. Cell mutations can turn a gene on the should not be on or turn off a gene that should be on. Histone acetylation is
epigenetic modification that leads to gene expression and is a process involving adding or removing an acetyl functional group.
Changes in epigenetic regulation, including histone acetylation, transcription factors by phosphorylation, RNA stability, protein translation control and modification, and post-translational control can be detected in cancer.
Some genes in normal cells work to prevent excess and inappropriate cell growth, also known as tumor-suppressor genes. Proto-oncogenes are positive cell-cycle regulators, but when mutated, these oncogenes cause cancer through uncontrolled cell growth and division. Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes.
Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Researchers have been investigating how to control the transcriptional activation of gene expression in cancer. Changes in the post-transcriptional control of a gene can also result in cancer. There are many examples of how translational or post-translational modifications of proteins arise in cancer. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumors.
Gene expression is the process of turning on a gene to produce RNA and proteins, where the information encoded in a gene is turned into a function to control the assembly of protein molecules and RNA.
Gene Expression among Prokaryotic organisms vs Eukaryotic organisms
Since prokaryotic organisms don't have a membrane bound cell nucleus and the DNA floats freely in the cytoplasm of the cell, and RNA transcription, translation, protein formation occur very quickly, almost simultaneously. Gene expression is regulated primarily at the transcriptional level.
Eukaryotic cells, however, have intracellular organelles that add to their complexity. Eukaryotic cells contain a nucleus and DNA is confined to the nuclear compartment. RNA transcription occurs prior to protein formation, and it takes place in the nucleus. Translation of RNA to protein occurs in the cytoplasm. Gene expression is regulated at many levels including epigenetic (heritable changes that do not involve changes in the DNA sequence and when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors), transcriptional (the process by which a cell makes an RNA copy of a piece of DNA), nuclear shuttling (the process by which proteins and ribonucleoprotein particles move across the nuclear envelope to and from the nucleus), post-transcriptional (control of gene expression after the RNA molecule has been created but before it is translated into protein), translational (when RNA is translated to a protein), and post-translational (control of gene expression after a protein has been created)
Prokaryotic Gene Regulation
The DNA of prokaryotes is organized into a circular chromosome, supercoiled within the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called operons.
In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers.
Repressors and activators are proteins produced in the cell that regulate gene expression by binding to specific DNA sites adjacent to the genes they control.
In general, activators bind to the promoter site, while repressors bind to operator regions. Repressors prevent transcription of a gene in response to an external stimulus, whereas activators increase the transcription of a gene in response to an external stimulus. Inducers are small molecules that may be produced by the cell or that are in the cell’s environment. Inducers either activate or repress transcription depending on the needs of the cell and the availability of substrate.
Tryptophan is an amino acid that can be (ingested when available in the environment) or synthesized by prokaryotic cells when necessary to survive by using enzymes encoded by five genes located next to each other and called the tryptophan (trp) operon. This trp are transcribed onto a single mRNA and translated to produce all five enzymes.
The trp operon includes three important regions: the coding region, the trp operator, and the trp promoter. The coding region includes the genes for the five tryptophan biosynthesis enzymes. Just before the coding region is the transcriptional start site. The promoter sequence, to which RNA polymerase binds to initiate transcription, is before or “upstream” of the transcriptional start site. Between the promoter and the transcriptional start site is the operator region.
The trp operator contains the DNA code to which the trp repressor protein can bind. Two tryptophan molecules bind to the trp repressor to allow for bonding to the trp operator. Negative regulators are proteins that prevent transcription.
Positive regulators can turn genes on and activate them, such as CAP (catabolite activator protein) which is a protein that complexes with cAMP to bind to the promoter sequences of operons which control sugar processing when glucose is not available. Cyclic amp (cAMP) is an alternative sugar when glucose is not available. CAP binding stabilizes the binding of RNA polymerase to the promoter region and increases transcription of the associated protein-coding genes.
The third type of gene regulation in prokaryotic cells occurs through inducible operons, which have proteins that bind to activate or repress transcription depending on the local environment and the needs of the cell. The lac operon is is a common inducible operon. When glucose is low, an alternative sugar source is lactose, in which the lac operon can acquire, process, encode, and break down into glucose and galactose. For the lac operon to be activated, glucose level must be very low, and lactose must be present.
Eukaryotic Epigenetic Gene Regulation
Eukaryotic gene regulation is more complex than prokaryotic gene regulation because transcription and translation processes are separated. The human genome encodes over 20,000 genes.
Epigenetic Gene Control
The first level of organization, or packing, is the winding of DNA strands around histone proteins, which package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions. The proteins can move along the DNA strands and perform transcription at any chromosomal region. Signals located on both the proteins and DNA determine whether a chromosomal region should be opened or closed.
The DNA molecule itself can be modified by methylation, an epigenetic modification that leads to gene silencing and is a process involving adding a methyl group to the DNA molecule. The DNA methylation occurs at specific regions called CpG islands (cytosine and guanine dinucleotide DNA pairs) found in the promoter regions of genes.
Transcription factors (RNA polymerase and other proteins) are proteins that bind to the DNA at the promoter or enhancer region and that influences or initiates transcription of a gene.
Eukaryotic Transcription Gene Regulation
In addition to RNA polymerase, two types of transcription factors regulate eukaryotic transcription: General (or basal) transcription factors bind to the core promoter region to assist with the binding of RNA polymerase. Specific transcription factors bind to various regions outside of the core promoter region and interact with the proteins at the core promoter to enhance or repress the activity of the polymerase.
The promoter region of the genes are immediately upstream of the coding sequence. Longer promoters allow for more space for proteins to bind and adds more control to the transcription process. The length of the promoter can vary widely among genes, and therefore the level of control of gene expression can widely vary. The purpose of the promoter is to bind transcription factors that control the initiation of transcription. Cis-acting elements are transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it, and therefore these adjacent genes and DNA interact with each other in order to control and regulate gene expression.
Enhancers are segments of DNA that are upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence, increase, or enhance the transcription of a specific gene. Enhancer regions are binding sequences, or sites, for specific transcription factors. Because the enhancer region may be distant from the promoter, DNA can and must physically bend in order to allow the proteins at the two sites to come into contact.
Eukaryotic cells have mechanisms to prevent transcription (like prokaryotes) called transcriptional repressors that can bind to a promoter or enhancer region to block transcription by responding to external stimuli.
Eukaryotic post-transcriptional gene regulation
Processing of RNA that takes place after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification.
RNA Splicing is the first stage of post-transcriptional control. In eukaryotic cells, the RNA transcript often contains regions called introns that are removed prior to translation. The regions of RNA that code for proteins are called exons. After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing. The splicing is performed by ribonucleoproteins called spliceosomes that recognize the intron ends, cut at these ends, and bring or join the exons together by ligation.
Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the ends of the strand from degrading during its journey. The 5' cap and the pony-A tail (3') cap protect the ends of the mRNA as it travels out of the nucleus into the cytoplasm.
RNA-binding proteins (RBP) are proteins that binds to the 3' or 5' UTR to increase or decrease the RNA stability. Untranslated regions (UTR) are segments of the RNA molecule that are not translated into proteins. These untranslated regions lie before (upstream or 5' UTR) and after (downstream or 3' UTR) the protein-coding region. These untranslated regions regulate mRNA localization, stability, and protein translation.
RNA stability is also controlled by microRNAs (miRNAs) are short RNA molecules that are chopped or cut by a protein called a Dicer. These miRNAs bind to a specific sequence of the RNA. In addition, miRNAs associate with a ribonucleoprotein complex called (RISC) RNA-induced silencing complex to impede translation of the message or lead to the degradation of the mRNA.
Eukaryotic Translation
Similar to transcription, translation is controlled by proteins that bind and initiate the process. The complex that assembles to start the process is the translation initiation complex. In eukaryotes, translation is initiated by binding the met-tRNAi to the 40S ribosome by way of the eukaryotic initiation factor-2 (eIF-2). The eIF-2 protein binds to the high energy molecule guanosine triphosphate (GTP). The tRNA-eIF2-GTP complex then binds to the 40S ribosome. Next a second complex forms on the mRNA with a larger 60S ribosomal subunit.
When eIF2 is phosphorylated, translation is blocked, however, when eIF2 is not phosphorylated, translation occurs.
Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups, which regulate the activity and how long they stay in the cell. Chemical modification can result from external environmental stimuli like stress, lack of nutrients, heat or ultraviolet light exposure. The addition of a ubiquitin group to a protein marks that protein to be degraded, and are sent to the proteasome organelle that removes proteins.
Cancer is associated with many different diseases and occurs when mutations modify cell-cycle control that allows cells to grow uncontrollably and abnormally. Proteins control cell cycle checkpoints and a faulty protein can allow mutated cells to pass through checkpoints without being stopped, leading to cancer diseases.
Cancer can be described as a disease of altered gene expression. Cell mutations can turn a gene on the should not be on or turn off a gene that should be on. Histone acetylation is
epigenetic modification that leads to gene expression and is a process involving adding or removing an acetyl functional group.
Changes in epigenetic regulation, including histone acetylation, transcription factors by phosphorylation, RNA stability, protein translation control and modification, and post-translational control can be detected in cancer.
Some genes in normal cells work to prevent excess and inappropriate cell growth, also known as tumor-suppressor genes. Proto-oncogenes are positive cell-cycle regulators, but when mutated, these oncogenes cause cancer through uncontrolled cell growth and division. Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes.
Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Researchers have been investigating how to control the transcriptional activation of gene expression in cancer. Changes in the post-transcriptional control of a gene can also result in cancer. There are many examples of how translational or post-translational modifications of proteins arise in cancer. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumors.