Anticancer gene

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Anticancer_gene 

Anticancer genes have a special ability to target and kill cancer cells without harming healthy ones. They do this through processes like programmed cell death, known as apoptosis, and other mechanisms like necrosis and autophagy. In the late 1990s, researchers discovered these genes while studying cancer cells. Sometimes, mutations or changes in these genes can occur, which might lead to cancer. These changes can include small alterations in the DNA sequence or larger rearrangements that affect the gene's function. When these anticancer genes are lost or altered, it can disrupt their ability to control cell growth, potentially leading to the development of cancer.

Anticancer genes as therapeutics

Main article: Gene therapy for cancer

Cancer is a group of diseases where cells multiply uncontrollably. Normally, cells have a built-in process called apoptosis that triggers cell death to prevent excessive growth. However, when these processes are disrupted, cancer can develop. Studies show that cancer is one of the leading causes of death worldwide. Despite this, recent advancements in treatment have significantly increased survival rates for many patients.

The treatment for cancer varies depending on its type and how advanced it is. Chemotherapy is a common treatment that uses drugs to kill cancer cells. It works by damaging the DNA of cancer cells or stopping them from dividing. This process can also impact genes that control cell growth, affecting both cancer-causing and anticancer genes.

Summary of anticancer genes

Anti-cancer gene	Functional p53 required	Blocked by Bcl-2	Caspases involved	Activated by phosphorylation	Engaging cell death pathway	Subcellular localization in cancer cells	Type of cell death
Apoptin	No	No	Yes	Yes	Intrinsic	Nucleus	Apoptosis
Brevinin-2R	Undetermined	Yes	No	Undetermined	Intrinsic	Cytoplasm	Autophagy
E4orf4	No	No	No	Yes	Intrinsic	Nucleus, cytoplasm	Mitotic catastrophe
HAMLET	No	No	Yes	No	Intrinsic	Nucleus, ER, mitochondria	Apoptosis, autophagy
MDA-7	No	Yes	Yes	No	Intrinsic	Receptor-binding, ER	Apoptosis
Noxa	No	Yes	Yes	Undetermined	Intrinsic	Mitochondria	Apoptosis
NS1	No	No	No	Yes	Intrinsic	Cytoplasm	Apoptosis
ORCTL3	Undetermined	Undetermined	Yes	Undetermined	Intrinsic	Plasma membrane, ER, golgi	Apoptosis
PAR-4	No	No	Yes	Yes	Extrinsic, Intrinsic	Nucleus, ER, plasma membrane	Apoptosis
TRAIL	No	Yes	Yes	No	Extrinsic	Receptor-binding	Apoptosis

Common anticancer gene examples

APOPTIN

History

Apoptin was the first anticancer gene to be identified. It originates from the Chicken Anemia Virus (CAV), which has circular DNA. This virus belongs to the Gyrovirus family and is being researched for its potential in cancer treatment and diagnosis. The apoptin protein, also known as viral protein 3 (VP3), was first isolated from chickens and has been found to cause programmed cell death in human cancer cells.

Apoptin induces apoptosis, or cell death, in deformed or cancerous cells independently of a protein called p53, meaning it is active in cells deficient of p53, as well as those with mutated or wild-type p53 expression. In cancer cells, apoptin is mostly found in the nucleus and is activated, while in normal cells, it remains inactive in the cytoplasm. This difference allows apoptin to selectively target cancer cells.

Research has shown that apoptin can detect early changes that lead to cancer and can convert survival signals in cancer cells into signals for cell death. It interacts with various proteins, such as DEDAF, Nur77, Nmi, Hippi, and APC1. Studies using animal models and genetically modified mice have demonstrated that apoptin is a safe and effective anticancer agent, capable of significantly reducing tumor size. It holds promise for future cancer therapies as a treatment target and an early indicator of tumor-specific processes.

Action

Apoptin is unique in its ability to attack deformed and cancerous cells while sparing healthy ones. It induces apoptosis through a pathway that involves mitochondria but does not rely on the p53 protein or death receptors typically involved in cell death. In healthy cells, apoptin stays in the cytoplasm, but in cancer cells, it moves to the nucleus after being activated by a process called phosphorylation. This movement is triggered by the enzyme CDK2 at a specific site on the protein.

For apoptin to function fully, it requires interactions with other molecules such as DNA, cyclinA-CDK2, and FADD. Current therapeutic agents using apoptin have shown effectiveness in treating types of cancer like Lewis lung carcinomas and osteosarcomas, with potential applications in liver cancer treatment.

Brevinin-2R

Depiction of Rana ridibunda.

Brevinin 2R:

Skin from the frog Rana brevipoda porsa (now known as Pelophylax porosus) was used to isolate the unique non-hemolytic defensin known as brevinin-2R. Malignant cells such as T-cell leukemia Jurkat, B-cell lymphoma BJAB, colon cancers HT29/219, SW742, fibrosarcoma L929, breast cancer MCF-7, and A549 (lung carcinoma) exhibit preferential cytotoxicity towards it in comparison to primary cells such T cells, human lung fibroblasts, and peripheral blood mononuclear cells (PBMC). Jurkat, MCF-7, and L929 overexpressing cells as well as MCF-7 cells overexpressing a dominant-negative mutant of a pro-apoptotic BNIP3 (TM-BNIP3) were largely resistant to Brevinin-2R treatment.

Action

These 25 amino acid peptides, in contrast to the majority of peptides within the Brevinine family, have low hemolytic action. Not only does the peptide have a reduced hemolytic action, it also is semi-selective towards cancer cells and leaves non-cancerous cells largely unharmed. This peptide works to prevent the progression of cancer by arresting the cell cycle at the G2/M phase, resulting in an induction of apoptosis.

This defensin traditionally works as a part of the innate immune system, working as an antimicrobial defense. However, this peptide is currently being studied as an anticancer peptide. Brevinin-2R works to trigger cell death by reducing the mitochondrial membrane potential resulting in lower cellular ATP levels while simultaneously increasing the concentration of reactive oxygen species. Currently and somewhat unrelated, Brevinin-2R is being considered for diabetic treatments. In treating type II diabetes, or diabetes mellitus, Brevinins have been shown to promote insulin release. Finally, these peptides even have the capability to increase the rate of tissue regeneration, as seen with the frog in which Brevinin-2R was isolated from.

E4orf4

History

Early region 4 open-reading-frame 4 (E4orf4) is an adenovirus protein of 14kDa which regulates growth in all stages of the adenovirus (Ad) infection. E4orf4 partners mainly with protein phosphatase 2A (PP2A) and Src kinases to induce cell death. Modeling of this protein reveals that it is likely made up of 3 α-helices with N- and C-terminal loops. It has a small stretch of amino acids in positions 66–75, which are highly basic, and likely are a place of nuclear and nucleolar targeting, as well as a place for Src kinases to bind.

Action

E4orf4 is an important regulator of adenoviruses. Additionally, outside of the context of the virus, it causes programmed cell death both in the context of a healthy cellular environment, and cancer. E4orf4 is a key regulator of Ad by down-regulating both viral and cellular genes, which plays an important role in regulating the proliferation of the virus. In turn, the down-regulation also impacts the alternative splicing of the viral RNA and protein translation. In the absence of a viral infection, E4orf4 induces apoptosis in a p53 and caspase-independent manner; however, there is still communication between this pathway and the caspase-dependent apoptosis pathway. In the context of cancer, E4orf4 is even more efficient at inducing cell death than in healthy cells, which could be an important finding for potential cancer therapies. It has been discovered that the mechanisms behind the function of E4orf4 are closely associated with several other proteins including the B55 subunit of PP2A. E4orf4 binds to PP2A to reduce the phosphorylation of the DNA damage response (DDR) proteins. Consequently, this reduces the function of DDR and limits DNA repair. Many cancer cells have defects in the DDR pathways and targeting these cells with E4orf4 can potentially destroy the remaining DDR pathways, resulting in cancer cell death.

The main mechanism behind the specificity of cancer cell targeting by E4orf4 is unknown but there are multiple hypotheses that scientists are considering: 1) The activation of the oncogenic state causes dormant apoptotic signals to be initiated and cause cell death to be more easily achieved by different signals. 2) There has been some indication that cancer cells become addicted to oncogenic pathways. E4orf4 may inhibit these pathways, causing cell death in cancer cells, but not normal cells. 3) E4orf4 may use oncogenes that have been activated in cancer cells, including Src, to cause cell death. 4) Cancer cells have disrupted cell cycle checkpoints and E4orf4 can take advantage of this by disrupting checkpoints in mitosis. 5) A Drosophila model demonstrated that E4orf4 can inhibit classical apoptosis in healthy tissues. It has been considered that this function of E4orf4 is lost in cancer cells causing a more effective killing of cells. 6) E4orf4 has been shown to cause structural changes in mitochondria, which could impact metabolic reprogramming and may affect cancer and healthy cells differently.

HAMLET

Crystal Structure of Calcium-bound α-lactalbumin.

History

HAMLET is known as an anticancer protein complex found in breast milk. One of the two molecules of this complex is multimeric alpha lactalbumin (MAL), which was first discovered during a study in 1995 that investigated how breast milk affects bacteria transformed with lung cancer. This study found that transformed cells were selected for apoptosis at a much higher rate than the untransformed, healthy cells. A later study in 2000, ascertained that oleic acid, a C18:1 fatty acid, is a cofactor that binds to MAL forming HAMLET. This complex, in a partially unfolded state, then displays apoptotic activity in cancer cells.

Action

Apoptosis, or programmed cell death, can occur through activation of three different pathways, intrinsic, extrinsic, or tumor necrosis factor. HAMLET proceeds by both a multifaceted intrinsic pathway and the caspase cascade, a subsection of the TNF pathway, through targeting many different cell components. First, after uptake by the cell, HAMLET proceeds to the mitochondria and depolarize the membranes at cytochrome c. Consequently, mitochondria-dependent apoptosis factors are released as well as the caspase cascade is activated. Second, proteasomes are targeted by HAMLET through a mechanism that is less understood. Research does suggest that HAMLET directly binds to the proteasome leading to its inhibition. Third, HAMLET has been found to target the nucleus, specifically histones. HAMLET irreversibly binds to histones leading to the inactivation of transcription and chromatin condensation, which inevitably causes apoptosis. Lastly, studies show that cells treated by HAMLET exhibit behaviors common to macroautophagy. This includes the presence of cytoplasmic vacuoles, double-membrane vesicles, and a dose-dependent decrease in ATP levels.

MDA-7

History

Melanoma differentiation associated gene-7 (mda-7), and also known as IL-24, was discovered in the mid-1900s using subtraction hybridization. mda-7 is classified in the interleukin IL-10 family because of similar structure and amino acid sequence to other interleukins in that class, the chromosomal location (human chromosome 1q32-33), and the shared properties it has with cytokines. Protein structural studies reveal that it is a dimer and glycosylated. It has been found that its expression is either not present or present at very low levels in tumor cells, including advanced stage melanoma and metastatic disease, compared to normal non-transformed cells. Multiple studies within the past 15 years have demonstrated that increasing mda-7 expression in tumor cells results in growth arrest and cell death in many different cell lines. When mda-7 is over-expressed in normal cells, no change in growth or cell viability is detected. mda-7 is also considered a radio-sensitizing cytokine because it generates a reactive oxygen species and causes stress in endoplasmic reticulum. mda-7 has been used in several clinical trials because of its ability to induce apoptosis, prevent tumor angiogenesis, cause immune-regulation, and increase radiation lethality. It was seen in one Phase I clinical trial that injecting mda-7 via an adenovirus directly into a tumor resulted in safe tumor regulation and immune activation.

Action

mda-7 interacts with two of the type II cytokine hetero-dymeric receptor complexes IL-20R1/IL-20R2 and IL-22R1/IL-20R2. It has been seen that in some contexts, mda-7 activates STAT transcription factors. However, the STAT pathway is not always activated and is not required for mda-7 cell growth arrest and cell death. mda-7 can be placed into tumor cell lines via transfection or adenovirus-transduction; it has been seen that following this, apoptosis is induced only in the tumor cells and results in no toxicity in the healthy cells. Its function as a tumor suppressor is not fully understood, but it has been observed that in the context of melanoma, mda-7 expression is drastically decreased. While there are no official studies published backing this claim, it is thought that mda-7 could potentially act as a paracrine factor, be involved in signaling short-range, and immune function in skin. mda-7 is also thought to have a pro-inflammatory purpose. It is also possible that mda-7 induces cytokine secretion, which causes antigen-presenting cells to present tumor antigens, resulting in an immune response against tumors. It has also been discovered that mda-7, and its translated protein MDA-7, interacts with kinases including serine/threonine protein kinase (PKR). Further studies will need to be performed to better understand the mechanisms of mda-7 action.

NOXA

History

Noxa, isolated from mice, is a member of the Bcl-2 family and is able to regulate cell death through a variety of intracellular stress signals. Having been discovered nearly three decades ago in 1990 by Hijikata et al., this gene product was isolated this protein from an adult T-cell leukemia (ATL) library This gene, and its protein in which it encodes for, has been studied as a potential therapeutic in chronic lymphocytic leukemia (CLL), the most common leukemia found in adults in the Western world. In humans, the Noxa homologue is known as APR/PMAIP1.

Action

Upon receiving intrinsic death signals, the gene NOXA encodes for the protein Noxa through a three-exon transcript. This protein binds to anti-apoptotic proteins resulting in these proteins' inhibition. As a p53 inducible gene, NOXA is transcribed and translated to Noxa in response to DNA damage and hypoxia induced apoptosis. A constitutive gene found in the brain, thymus, spleen, and several other organs, it initiates apoptosis through Bax-mediated mitochondrial-dysfunction through the inhibition of the Bcl2 family's antiapoptotic members. Through gene knockout studies, it was shown that double deficient Noxa there was no spontaneous tumor development as commonly observed with knockout of p53. Noxa has been shown to be involved in the maintenance of memory CD4+ T Th1/Th2 cell homeostasis where in the absence of Noxa, Th2 memory T-cell death results.

NS1

History

In the 1960s rodent parvovirus was discovered by Dr. Helene Toolan to have an oncosuppressive activity. However, the specific gene found in the parvovirus genome, which is called NS1, that causes the oncosuppressive activity was not characterized until later. NS1 is a small protein (only 672 amino acids) with 5 distinct domains that exert different functions that inevitably lead to apoptosis and cell death. NS1 activates cell death through two different pathways, apoptosis/lysosomal-like programmed cell death and necrosis/cytolysis.

Action

NS1 is considered a regulatory protein due to its activity in transcription, translation, and protein-protein interactions, which allows the parvovirus to replicate unhindered. However, scientists are primarily interested in utilizing its cytolytic activity since this has been proven to be active in cancerous cells. The first way NS1 propagates cell death through cytolysis is by interrupting the cell cycle at the S/G2 junction, causing a stress response in the cell. Specifically, NS1 interacts with many molecules and compounds important in the transition and inhibits their activity. When NS1 expression reaches a certain threshold, the triggered stress response finally causes caspase 3/9-mediated programmed cell death. Another way that NS1 causes cytolysis is through degradation of the cytoskeleton of the cell. NS1 specifically targets and degrades the microfilament tropomyosin using casein kinase II, actin filaments through activation of actin-severing protein gelsolin, and vimentin through an unknown mechanism. The last NS1-mediated mechanism of cytolysis involves the depolarization of the mitochondria. This results in the release of many reactive oxygen species, causing DNA damage. When DNA is damaged, a DNA damage response occurs, which in this case results in cell death.

ORCTL3

History

Organic Cation Transporter Like-3 (ORCTL3) was first discovered as a result of a large-scale DNA sequencing project in search of genes with a tumor-specific apoptosis activity.^[34] The name ORCTL3 was decided upon because of its structural homology to proteins belonging to the family of organic cation transporters. However, the name is a misnomer as after examining the properties of ORCTL3, it was revealed that ORCTL3 is a transporter for urate. The ORCTL3 gene spans around 12 kb of genomic DNA and consists of ten exons. It was shown that the 2.4 kb transcript of this gene is universally expressed in all human tissues. Additionally, ORCTL3 transfection into numerous tumorigenic cells induced apoptosis, while normal and primary cells remained healthy.

Action

ORCTL3 is a 90 kDa protein composed of 351 amino acids. It is suggested that the protein spans the cell membrane several times, based on computational methods. Overexpressed ORCTL3 is localized to the endoplasmic reticulum (ER), Golgi and the plasma membrane but not to mitochondria. ORCTL3 was identified as the first high-affinity nicotinate exchanger in kidneys and intestine. Nicotinate is an essential vitamin (Vitamin B3) that is involved in NAD+ synthesis, which in turn is important for energetic processes, signal transduction pathways, and the activation of the NAD+ -dependent histone deacetylase SIRT1. ORCTL3 has been shown to be activated for apoptosis induction in renal cells in vitro, in vivo and ex vivo. For its apoptosis effect ORCTL3 targets stearoyl-CoA desaturase (SCD), an enzyme that introduces a double bond in the fatty acid stearic acid. The fact that SCD is commonly overexpressed in cancer and oncogene transformed cells might explain the tumor-specificity of ORCTL3 to some extent, however, the existence of other additional targets of ORCTL3 cannot formally be ruled out.

Par-4

History

Prostate apoptosis response-4 (Par-4) is a tumor suppressor protein with a pro-apoptotic function. Par-4 was first discovered in rat prostate cancer cells as part of an effort determined in discovering genes that were induced in response to increased Ca²⁺ in cells, although it is now known to be ubiquitously expressed in a wide variety of tissues across many different species. The Par-4 gene is located on the minus strand of chromosome 12q21.2, spanning 99.06 kb of DNA and containing seven exons and six introns. Par-4 is known to be downregulated in certain terminally differentiated cells such as neurons, specific retinal cells, and smooth muscle cells as well as in certain cancer cells such as renal cancers, neuroblastoma, and leukemia. Par-4 has also been shown to be generally higher in dying cells, consistent with its pro-apoptotic functions.

Action

Par-4 is a 38 kDa multi-domain protein composed of about 340 amino acids. Conserved domains among human, mouse, and rat homologs include the leucine zipper (LZ) domain at the C-terminal region, two nuclear localization sequences, NLS1 and NLS2, in the N-terminal region, and a nuclear export sequence within the LZ domain. Although Par-4 mutations are rare, it was identified that an A to T point mutation affecting residue 189 localized in exon 3 causes premature termination of Par-4 in human endometrial carcinoma. Knockout of Par-4 in mice leads to the development of spontaneous tumors in various tissues revealed by increased proliferative response of peripheral T cells, inhibition of apoptosis, increased NF-κB activity, and decreased JNK activity. Par-4 overexpression is sufficient to induce apoptosis in most cancer cells in the absence of a second apoptotic signal, but does not induce apoptosis in normal or immortalized cells.

The anticancer function of Par-4 is achieved by two distinct means: activating the molecular components of the cell-death machinery and inhibiting pro-survival factors. One essential apoptotic function of Par-4 is inhibiting the NF-κB pathway, which is a key contributing factor in many tumors and prevents cell death by activating the expression of pro-survival genes. Par-4 also assists in PCD by enabling the trafficking of specific ligands such and cell surface death receptors, such as FasL and Fas, respectively, to the plasma membrane thus activating the extrinsic death pathway. Overexpression of Par-4 selectively induces apoptosis in cancer cells, attributed to the selective activation via phosphorylation of the T155 residue by protein kinase A (PKA). It has been shown that two events are required for Par-4 activation: nuclear entry and phosphorylation by PKA.

TRAIL

Crystal Structure of Human TRAIL.

History

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a member of the tumor necrosis factor (TNF) family that also includes Fas ligands, TNFα, and TL1A. It was discovered in 1995 by Wiley et al. and then further characterized in 1996 by Pitti et al. The former study discovered that TRAIL is localized to surfaces of cells in most human tissues, excluding the brain, liver, and testes, while the latter study was able to elicit that the protein is a type II membrane protein that can also be cleaved into a soluble form.

Action

The intrigue surrounding TRAIL is all due to this protein's ability both in vivo and in vitro to specifically target tumor cells for apoptosis while leaving healthy cells intact. This activity proceeds by both the intrinsic and extrinsic pathway. First, the homotrimer of TRAIL binds three molecules of either TRAIL-receptor 1 or 2, which are transmembrane proteins that contain a cytoplasmic death domain. Once TRAIL is bound, Fas, caspase-8, and caspase-10 associate with the death domain forming death-inducing signaling complex (DISC) that proceeds through two different mechanisms depending on the cell type. In one cell type, DISC can directly activate the effector caspase leading to apoptosis, while in the other the complex activates a bcl-2-mediated pathway in a similar fashion as HAMLET that results in the release of cytochrome c from the mitochondria, which then causes the activation of effector caspase. The latter mechanism is the focus of many oncogenic therapies because p53, the tumor suppressor gene, activates the same pathway. Since cancer is commonly caused by the inactivation of p53, TRAIL could mediate this effect by still activating the apoptotic pathway.

TP53

Structure of TP53 bound to DNA.

History

TP-53 is a gene that encodes for the protein p53; this protein is a tumor suppressor. p53 was discovered in 1979 stemming from a study involving cancer immunology and the role of viruses in some cancers. The protein was so named because it was measured to have a weight of 53 kDa. This study was conducted by David Philip Lane and technician Alan K. Roberts, in Lionel V. Crawford's lab in London. It was seen in this study that p53 could bind to viral tumor antigens. This information was corroborated during the same year when a separate study found that p53 had immunoreactivity with serum from tumors containing antibodies. This later study was run by Daniel I. H. Linzer and Arnold J. Levine out of Princeton University. Further papers came out around the same time all mentioning the discovery of a tumor-suppressing protein. While p53 was first officially identified in 1979, many labs in previous years had come across the same protein, without knowing what it was. In the mid-1970s, a scientist by the name of Peter Tegtmeyer happened upon a protein with an approximate size of 50 kDa. However, because he was focusing his studies on SV40, a tumor-causing virus affecting monkeys and humans, he did not pay much attention to this protein.

Action

The p53 protein is a tumor-suppressing transcription factor (TF), which can recognize when there is an alteration in a cell's DNA caused by factors including chemical toxins, radiation, ultraviolet (UV) rays, and other damaging agents. Crucially, p53 plays a role in determining whether the damaged genetic material in the cell can be repaired, or if the cell should be destroyed through apoptosis. The individual topologically associating domains (TADs) target different genes and unique effector pathways. It has been observed that inactivating both of the TADs detrimentally affects the ability of p53 to suppress tumor growth and interact with target genes. When only one TAD is inactivated, p53 can still suppress specific tumors; however, it can no longer successfully engage in transactivation. The C-terminal domain (CTD) is an intrinsically disordered domain (IDD), which can take on different conformations depending on what it is binding with and is a location of many post-translational modifications, resulting in its ability to regulate p53 function depending on what it is bound to and what modifications are linked with the CTD. This domain also aids in the binding of the central DNA-binding domain (DBD) to specific DNA sequences; the CTD is a positive regulator of DNA binding and stabilizes the interaction of the DNA with the DBD. p53 is unique as a transcription factor in that it can recognize and bind response elements (RE) in many different environments and doesn't need other transcription factors to cooperatively bind with it like many other TFs.

Mutations in the p53 pathway have been observed in almost all cancer types including breast cancer, bladder cancer, lung cancer, ovarian cancer, cholangiocarcinoma, head and neck squamous cell carcinoma, melanoma, wilms tumor, and other cancers often due to a single point mutation in p53. Li-Fraumeni Syndrome is a condition linked to inherited mutations, at least 140 mutations, in the TP-53 gene. This condition largely increases the risk of developing cancers like breast cancer, bone cancer, and soft tissue sarcomas. Specifically, this impacts children and young adults. A majority of these mutations in the TP-53 gene are single amino acid changes, but other mutations cause a small portion of the DNA to be absent. This leads to a faulty p53 protein that fails to recognize DNA damage in cells, control cell growth, and initiate apoptosis in cells with damaged DNA. Consequently, cells containing erroneous DNA can uncontrollably divide.

BRCA gene mutations:

The tumor suppressing BRCA genes frequently help in cancer prevention. They control how cells divide and develop and help repair DNA damage BRCA gene abnormalities, however, can the likelihood of having specific cancers is raised. Cancers BRCA1 and BRCA2 are the two BRCA recognized cancer-causing gene alterations. The likelihood that a woman may develop ovarian and breast cancer is increased by certain gene abnormalities. Male breast cancer and prostate cancer risk are both increased by BRCA2 gene mutations Men and women with BRCA2 gene mutations have a marginally increased chance of acquiring pancreatic cancer.

Common misconceptions

Often, genes are confused with the proteins they code for. Genes are composed of nucleotides, while proteins are composed of amino acids. The genes serve as codes and blueprints to create either proteins of interest, or various non-coding ribonucleic acids (ncRNAs), which exhibit various effects, such as working to prevent cancer within cells.

Central Dogma schematic depicting the protein product via the transcription and translation of a gene.

Ribosomal RNA

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Ribosomal_RNA

Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins, though this ratio differs between prokaryotes and eukaryotes.

Structure

Although the primary structure of rRNA sequences can vary across organisms, base-pairing within these sequences commonly forms stem-loop configurations. The length and position of these rRNA stem-loops allow them to create three-dimensional rRNA structures that are similar across species. Because of these configurations, rRNA can form tight and specific interactions with ribosomal proteins to form ribosomal subunits. These ribosomal proteins contain basic residues (as opposed to acidic residues) and aromatic residues (i.e. phenylalanine, tyrosine and tryptophan) allowing them to form chemical interactions with their associated RNA regions, such as stacking interactions. Ribosomal proteins can also cross-link to the sugar-phosphate backbone of rRNA with binding sites that consist of basic residues (i.e. lysine and arginine). All ribosomal proteins (including the specific sequences that bind to rRNA) have been identified. These interactions along with the association of the small and large ribosomal subunits result in a functioning ribosome capable of synthesizing proteins.

An example of a fully-assembled small subunit of ribosomal RNA in prokaryotes, specifically Thermus thermophilus. The actual ribosomal RNA (16S) is shown coiled in orange with ribosomal proteins attaching in blue.

Ribosomal RNA organizes into two types of major ribosomal subunit: the large subunit (LSU) and the small subunit (SSU). One of each type come together to form a functioning ribosome. The subunits are at times referred to by their size-sedimentation measurements (a number with an "S" suffix). In prokaryotes, the LSU and SSU are called the 50S and 30S subunits, respectively. In eukaryotes, they are a little larger; the LSU and SSU of eukaryotes are termed the 60S and 40S subunits, respectively.

In the ribosomes of prokaryotes such as bacteria, the SSU contains a single small rRNA molecule (~1500 nucleotides) while the LSU contains one single small rRNA and a single large rRNA molecule (~3000 nucleotides). These are combined with ~50 ribosomal proteins to form ribosomal subunits. There are three types of rRNA found in prokaryotic ribosomes: 23S and 5S rRNA in the LSU and 16S rRNA in the SSU.

In the ribosomes of eukaryotes such as humans, the SSU contains a single small rRNA (~1800 nucleotides) while the LSU contains two small rRNAs and one molecule of large rRNA (~5000 nucleotides). Eukaryotic rRNA has over 70 ribosomal proteins which interact to form larger and more polymorphic ribosomal units in comparison to prokaryotes. There are four types of rRNA in eukaryotes: 3 species in the LSU and 1 in the SSU. Yeast has been the traditional model for observation of eukaryotic rRNA behavior and processes, leading to a deficit in diversification of research. It has only been within the last decade that technical advances (specifically in the field of Cryo-EM) have allowed for preliminary investigation into ribosomal behavior in other eukaryotes. In yeast, the LSU contains the 5S, 5.8S and 28S rRNAs. The combined 5.8S and 28S are roughly equivalent in size and function to the prokaryotic 23S rRNA subtype, minus expansion segments (ESs) that are localized to the surface of the ribosome which were thought to occur only in eukaryotes. However recently, the Asgard phyla, namely, Lokiarchaeota and Heimdallarchaeota, considered the closest archaeal relatives to Eukarya, were reported to possess two supersized ESs in their 23S rRNAs. Likewise, the 5S rRNA contains a 108‐nucleotide insertion in the ribosomes of the halophilic archaeon Halococcus morrhuae.

A eukaryotic SSU contains the 18S rRNA subunit, which also contains ESs. SSU ESs are generally smaller than LSU ESs.

SSU and LSU rRNA sequences are widely used for study of evolutionary relationships among organisms, since they are of ancient origin, are found in all known forms of life and are resistant to horizontal gene transfer. rRNA sequences are conserved (unchanged) over time due to their crucial role in the function of the ribosome. Phylogenic information derived from the 16s rRNA is currently used as the main method of delineation between similar prokaryotic species by calculating nucleotide similarity. The canonical tree of life is the lineage of the translation system.

LSU rRNA subtypes have been called ribozymes because ribosomal proteins cannot bind to the catalytic site of the ribosome in this area (specifically the peptidyl transferase center, or PTC).

The SSU rRNA subtypes decode mRNA in its decoding center (DC). Ribosomal proteins cannot enter the DC.

The structure of rRNA is able to drastically change to affect tRNA binding to the ribosome during translation of other mRNAs. In 16S rRNA, this is thought to occur when certain nucleotides in the rRNA appear to alternate base pairing between one nucleotide or another, forming a "switch" that alters the rRNA's conformation. This process is able to affect the structure of the LSU and SSU, suggesting that this conformational switch in the rRNA structure affects the entire ribosome in its ability to match a codon with its anticodon in tRNA selection as well as decode mRNA.

Assembly

Ribosomal RNA's integration and assembly into ribosomes begins with their folding, modification, processing and assembly with ribosomal proteins to form the two ribosomal subunits, the LSU and the SSU. In Prokaryotes, rRNA incorporation occurs in the cytoplasm due to the lack of membrane-bound organelles. In Eukaryotes, however, this process primarily takes place in the nucleolus and is initiated by the synthesis of pre-RNA. This requires the presence of all three RNA polymerases. In fact, the transcription of pre-RNA by RNA polymerase I accounts for about 60% of cell's total cellular RNA transcription. This is followed by the folding of the pre-RNA so that it can be assembled with ribosomal proteins. This folding is catalyzed by endo- and exonucleases, RNA helicases, GTPases and ATPases. The rRNA subsequently undergoes endo- and exonucleolytic processing to remove external and internal transcribed spacers. The pre-RNA then undergoes modifications such as methylation or pseudouridinylation before ribosome assembly factors and ribosomal proteins assemble with the pre-RNA to form pre-ribosomal particles. Upon going under more maturation steps and subsequent exit from the nucleolus into the cytoplasm, these particles combine to form the ribosomes. The basic and aromatic residues found within the primary structure of rRNA allow for favorable stacking interactions and attraction to ribosomal proteins, creating a cross-linking effect between the backbone of rRNA and other components of the ribosomal unit.

Function

A simplified depiction of a ribosome (with SSU and LSU artificially detached here for visualization purposes) depicting the A and P sites and both the small and large ribosomal subunits operating in conjunction.

Universally conserved secondary structural elements in rRNA among different species show that these sequences are some of the oldest discovered. They serve critical roles in forming the catalytic sites of translation of mRNA. During translation of mRNA, rRNA functions to bind both mRNA and tRNA to facilitate the process of translating mRNA's codon sequence into amino acids. rRNA initiates the catalysis of protein synthesis when tRNA is sandwiched between the SSU and LSU. In the SSU, the mRNA interacts with the anticodons of the tRNA. In the LSU, the amino acid acceptor stem of the tRNA interacts with the LSU rRNA. The ribosome catalyzes ester-amide exchange, transferring the C-terminus of a nascent peptide from a tRNA to the amine of an amino acid. These processes are able to occur due to sites within the ribosome in which these molecules can bind, formed by the rRNA stem-loops. A ribosome has three of these binding sites called the A, P and E sites:

• In general, the A (aminoacyl) site contains an aminoacyl-tRNA (a tRNA esterified to an amino acid on the 3' end).
• The P (peptidyl) site contains a tRNA esterified to the nascent peptide. The free amino (NH₂) group of the A site tRNA attacks the ester linkage of P site tRNA, causing transfer of the nascent peptide to the amino acid in the A site. This reaction is takes place in the peptidyl transferase center
• The E (exit) site contains a tRNA that has been discharged, with a free 3' end (with no amino acid or nascent peptide).

A single mRNA can be translated simultaneously by multiple ribosomes. This is called a polysome.

In prokaryotes, much work has been done to further identify the importance of rRNA in translation of mRNA. For example, it has been found that the A site consists primarily of 16S rRNA. Apart from various protein elements that interact with tRNA at this site, it is hypothesized that if these proteins were removed without altering ribosomal structure, the site would continue to function normally. In the P site, through the observation of crystal structures it has been shown the 3' end of 16s rRNA can fold into the site as if a molecule of mRNA. This results in intermolecular interactions that stabilize the subunits. Similarly, like the A site, the P site primarily contains rRNA with few proteins. The peptidyl transferase center, for example, is formed by nucleotides from the 23S rRNA subunit. In fact, studies have shown that the peptidyl transferase center contains no proteins, and is entirely initiated by the presence of rRNA. Unlike the A and P sites, the E site contains more proteins. Because proteins are not essential for the functioning of the A and P sites, the E site molecular composition shows that it is perhaps evolved later. In primitive ribosomes, it is likely that tRNAs exited from the P site. Additionally, it has been shown that E-site tRNA bind with both the 16S and 23S rRNA subunits.

Subunits and associated ribosomal RNA

Diagram of ribosomal RNA types and how they combine to create the ribosomal subunits.

Both prokaryotic and eukaryotic ribosomes can be broken down into two subunits, one large and one small. The exemplary species used in the table below for their respective rRNAs are the bacterium Escherichia coli (prokaryote) and human (eukaryote). Note that "nt" represents the length of the rRNA type in nucleotides and the "S" (such as in "16S) represents Svedberg units.

Type	Size	Large subunit (LSU rRNA)	Small subunit (SSU rRNA)
prokaryotic	70S	50S (5S : 120 nt, 23S  : 2906 nt)	30S (16S : 1542 nt)
eukaryotic (nuclear)	80S	60S (5S : 121 nt, 5.8S : 156 nt, 28S : 5070 nt)	40S (18S : 1869 nt)
eukaryotic (mitochondrial)	55S	39S 16S (Mitochondrially encoded 16S rRNA : approx. 1,571 nt)	28S 12S (Mitochondrially encoded 12S rRNA : approx. 955 nt)

S units of the subunits (or the rRNAs) cannot simply be added because they represent measures of sedimentation rate rather than of mass. The sedimentation rate of each subunit is affected by its shape, as well as by its mass. The nt units can be added as these represent the integer number of units in the linear rRNA polymers (for example, the total length of the human rRNA = 7216 nt).

Gene clusters coding for rRNA are commonly called "ribosomal DNA" or rDNA (note that the term seems to imply that ribosomes contain DNA, which is not the case).

In prokaryotes

In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal RNAs). Therefore it can be deduced that in both bacteria and archaea there is one rRNA gene that codes for all three rRNA types :16S, 23S and 5S.

Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon. As shown by the image in this section, there is an internal transcribed spacer between 16S and 23S rRNA genes. There may be one or more copies of the operon dispersed in the genome (for example, Escherichia coli has seven). Typically in bacteria there are between one and fifteen copies.

Archaea contains either a single rRNA gene operon or up to four copies of the same operon.

The 3' end of the 16S ribosomal RNA (in a ribosome) recognizes a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence.

In eukaryotes

Small subunit ribosomal RNA, 5' domain taken from the Rfam database. This example is RF00177, a fragment from an uncultured bacterium.

In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats. In humans, approximately 300–400 repeats are present in five clusters, located on chromosomes 13 (RNR1), 14 (RNR2), 15 (RNR3), 21 (RNR4) and 22 (RNR5). Diploid humans have 10 clusters of genomic rDNA which in total make up less than 0.5% of the human genome.

It was previously accepted that repeat rDNA sequences were identical and served as redundancies or failsafes to account for natural replication errors and point mutations. However, sequence variation in rDNA (and subsequently rRNA) in humans across multiple chromosomes has been observed, both within and between human individuals. Many of these variations are palindromic sequences and potential errors due to replication. Certain variants are also expressed in a tissue-specific manner in mice.

Mammalian cells have 2 mitochondrial (12S and 16S) rRNA molecules and 4 types of cytoplasmic rRNA (the 28S, 5.8S, 18S, and 5S subunits). The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 internally transcribed spacers. The first spacer corresponds to the one found in bacteria and archaea, and the other spacer is an insertion into what was the 23S rRNA in prokaryotes. The 45S rDNA is organized into 5 clusters (each has 30–40 repeats) on chromosomes 13, 14, 15, 21, and 22. These are transcribed by RNA polymerase I. The DNA for the 5S subunit occurs in tandem arrays (~200–300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is transcribed by RNA polymerase III. The 18S rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5S, 5.8S and 28S in mammals, 25S in plants, rRNAs).

In flies, the large subunit contains four rRNA species instead of three with a split in the 5.8S rRNA that presents a shorter 5.8S subunit (123 nt) and a 30 nucleotide subunit named the 2S rRNA. Both fragments are separated by an internally transcribed spacer of 28 nucleotides. Since the 2S rRNA is small and highly abundant, its presence can interfere with construction of sRNA libraries and compromise the quantification of other sRNAs. The 2S subunit is retrieved in fruit fly and dark-winged fungus gnat species but absent from mosquitoes.

The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography. The secondary structure of SSU rRNA contains 4 distinct domains—the 5', central, 3' major and 3' minor domains. A model of the secondary structure for the 5' domain (500-800 nucleotides) is shown.

Biosynthesis

Main article: Ribosome biogenesis

In eukaryotes

As the building-blocks for the organelle, production of rRNA is ultimately the rate-limiting step in the synthesis of a ribosome. In the nucleolus, rRNA is synthesized by RNA polymerase I using the specialty genes (rDNA) that encode for it, which are found repeatedly throughout the genome. The genes coding for 18S, 28S and 5.8S rRNA are located in the nucleolus organizer region and are transcribed into large precursor rRNA (pre-rRNA) molecules by RNA polymerase I. These pre-rRNA molecules are separated by external and internal spacer sequences and then methylated, which is key for later assembly and folding. After separation and release as individual molecules, assembly proteins bind to each naked rRNA strand and fold it into its functional form using cooperative assembly and progressive addition of more folding proteins as needed. The exact details of how the folding proteins bind to the rRNA and how correct folding is achieved remains unknown. The rRNA complexes are then further processed by reactions involving exo- and endo-nucleolytic cleavages guided by snoRNA (small nucleolar RNAs) in complex with proteins. As these complexes are compacted together to form a cohesive unit, interactions between rRNA and surrounding ribosomal proteins are constantly remodeled throughout assembly in order to provide stability and protect binding sites. This process is referred to as the "maturation" phase of the rRNA lifecycle. The modifications that occur during maturation of rRNA have been found to contribute directly to control of gene expression by providing physical regulation of translational access of tRNA and mRNA. Some studies have found that extensive methylation of various rRNA types is also necessary during this time to maintain ribosome stability.

The genes for 5S rRNA are located inside the nucleolus and are transcribed into pre-5S rRNA by RNA polymerase III. The pre-5S rRNA enters the nucleolus for processing and assembly with 28S and 5.8S rRNA to form the LSU. 18S rRNA forms the SSUs by combining with numerous ribosomal proteins. Once both subunits are assembled, they are individually exported into the cytoplasm to form the 80S unit and begin initiation of translation of mRNA.

Ribosomal RNA is non-coding and is never translated into proteins of any kind: rRNA is only transcribed from rDNA and then matured for use as a structural building block for ribosomes. Transcribed rRNA is bound to ribosomal proteins to form the subunits of ribosomes and acts as the physical structure that pushes mRNA and tRNA through the ribosome to process and translate them.

Eukaryotic regulation

Synthesis of rRNA is up-regulated and down-regulated to maintain homeostasis by a variety of processes and interactions:

• The kinase AKT indirectly promotes synthesis of rRNA as RNA polymerase I is AKT-dependent.
• Certain angiogenic ribonucleases, such as angiogenin (ANG), can translocate and accumulate in the nucleolus. When the concentration of ANG becomes too high, some studies have found that ANG can bind to the promoter region of rDNA and unnecessarily increase rRNA transcription. This can be damaging to the nucleolus and can even lead to unchecked transcription and cancer.
• During times of cellular glucose restriction, AMP-activated protein kinase (AMPK) discourages metabolic processes that consume energy but are non-essential. As a result, it is capable of phosphorylating RNA polymerase I (at the Ser-635 site) in order to down-regulate rRNA synthesis by disrupting transcription initiation.
• Impairment or removal of more than one pseudouridine or 29-O-methylation regions from the ribosome decoding center significantly reduces rate of rRNA transcription by reducing the rate of incorporation of new amino acids.
• Formation of heterochromatin is essential to silencing rRNA transcription, without which ribosomal RNA is synthesized unchecked and greatly decreases the lifespan of the organism.

In prokaryotes

Similar to eukaryotes, the production of rRNA is the rate-limiting step in the prokaryotic synthesis of a ribosome. In E. coli, it has been found that rRNA is transcribed from the two promoters P1 and P2 found within seven different rrn operons. The P1 promoter is specifically responsible for regulating rRNA synthesis during moderate to high bacterial growth rates. Because the transcriptional activity of this promoter is directly proportional to the growth rate, it is primarily responsible for rRNA regulation. An increased rRNA concentration serves as a negative feedback mechanism to ribosome synthesis. High NTP concentration has been found to be required for efficient transcription of the rrn P1 promoters. They are thought to form stabilizing complexes with RNA polymerase and the promoters. In bacteria specifically, this association of high NTP concentration with increased rRNA synthesis provides a molecular explanation as to why ribosomal and thus protein synthesis is dependent on growth-rate. A low growth-rate yields lower rRNA / ribosomal synthesis rates while a higher growth rate yields a higher rRNA / ribosomal synthesis rate. This allows a cell to save energy or increase its metabolic activity dependent on its needs and available resources.

In prokaryotic cells, each rRNA gene or operon is transcribed into a single RNA precursor that includes 16S, 23S, 5S rRNA and tRNA sequences along with transcribed spacers. The RNA processing then begins before the transcription is complete. During processing reactions, the rRNAs and tRNAs are released as separate molecules.

Prokaryotic regulation

Because of the vital role rRNA plays in the cell physiology of prokaryotes, there is much overlap in rRNA regulation mechanisms. At the transcriptional level, there are both positive and negative effectors of rRNA transcription that facilitate a cell's maintenance of homeostasis:

• An UP element upstream of the rrn P1 promoter can bind a subunit of RNA polymerase, thus promoting transcription of rRNA.
• Transcription factors such as FIS bind upstream of the promoter and interact with RNA polymerase which facilitates transcription.
• Anti-termination factors bind downstream of the rrn P2 promoter, preventing premature transcription termination.
• Due to the stringent response, when the availability of amino acids is low, ppGpp (a negative effector) can inhibit transcription from both the P1 and P2 promoters.

Degradation

Ribosomal RNA is quite stable in comparison to other common types of RNA and persists for longer periods of time in a healthy cellular environment. Once assembled into functional units, ribosomal RNA within ribosomes are stable in the stationary phase of the cell life cycle for many hours. Degradation can be triggered via "stalling" of a ribosome, a state that occurs when the ribosome recognizes faulty mRNA or encounters other processing difficulties that causes translation by the ribosome to cease. Once a ribosome stalls, a specialized pathway on the ribosome is initiated to target the entire complex for disassembly.

In eukaryotes

As with any protein or RNA, rRNA production is prone to errors resulting in the production of non-functional rRNA. To correct this, the cell allows for degradation of rRNA through the non-functional rRNA decay (NRD) pathway. Much of the research in this topic was conducted on eukaryotic cells, specifically Saccharomyces cerevisiae yeast. Currently, only a basic understanding of how cells are able to target functionally defective ribosomes for ubiquination and degradation in eukaryotes is available.

• The NRD pathway for the 40S subunit may be independent or separate from the NRD pathway for the 60S subunit. It has been observed that certain genes were able to affect degradation of certain pre-RNAs, but not others.
• Numerous proteins are involved in the NRD pathway, such as Mms1p and Rtt101p, which are believed to complex together to target ribosomes for degradation. Mms1p and Rtt101p are found to bind together and Rtt101p is believed to recruit a ubiquitin E3 ligase complex, allowing for the non-functional ribosomes to be ubiquinated before being degraded.
  • Prokaryotes lack a homolog for Mms1, so it is unclear how prokaryotes are able to degrade non-functional rRNAs.
• The growth rate of eukaryotic cells did not seem to be significantly affected by the accumulation of non-functional rRNAs.

In prokaryotes

Although there is far less research available on ribosomal RNA degradation in prokaryotes in comparison to eukaryotes, there has still been interest on whether bacteria follow a similar degradation scheme in comparison to the NRD in eukaryotes. Much of the research done for prokaryotes has been conducted on Escherichia coli. Many differences were found between eukaryotic and prokaryotic rRNA degradation, leading researchers to believe that the two degrade using different pathways.

• Certain mutations in rRNA that were able to trigger rRNA degradation in eukaryotes were unable to do so in prokaryotes.
• Point mutations in a 23S rRNA would cause both 23S and 16S rRNAs to be degraded, in comparison to eukaryotes, in which mutations in one subunit would only cause that subunit to be degraded.
• Researchers found that removal of a whole helix structure (H69) from the 23S rRNA did not trigger its degradation. This led them to believe that H69 was critical for endonucleases to recognize and degrade the mutated rRNA.

Sequence conservation and stability

Due to the prevalent and unwavering nature of rRNA across all organisms, the study of its resistance to gene transfer, mutation, and alteration without destruction of the organism has become a popular field of interest. Ribosomal RNA genes have been found to be tolerant to modification and incursion. When rRNA sequencing is altered, cells have been found to become compromised and quickly cease normal function. These key traits of rRNA have become especially important for gene database projects (comprehensive online resources such as SILVA or SINA) where alignment of ribosomal RNA sequences from across the different biologic domains greatly eases "taxonomic assignment, phylogenetic analysis and the investigation of microbial diversity."

Examples of resilience:

• Addition of large, nonsensical RNA fragments into many parts of the 16S rRNA unit does not observably alter the function of the ribosomal unit as a whole.
• Non-coding RNA_RD7 has the capability to alter processing of rRNA to make the molecules resistant to degradation by carboxylic acid. This is a crucial mechanism in maintaining rRNA concentrations during active growth when acid build-up (due to the substrate phosphorylation required to produce ATP) can become toxic to intracellular functions.
• Insertion of hammerhead ribozymes that are capable of cis-cleavages along 16S rRNA greatly inhibit function and diminish stability.
• While most cellular functions degrade heavily after only short period of exposure to hypoxic environments, rRNA remains un-degraded and resolved after six days of prolonged hypoxia. Only after such an extended period of time do rRNA intermediates (indicative of degradation finally occurring) begin to present themselves.

Significance

This diagram depicts how rRNA sequencing in prokaryotes can ultimately be used to produce pharmaceuticals to combat disease caused by the very microbes the rRNA was originally obtained from.

Ribosomal RNA characteristics are important in evolution, thus taxonomy and medicine.

• rRNA is one of only a few gene products present in all cells. For this reason, genes that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic group, calculate related groups, and estimate rates of species divergence. As a result, many thousands of rRNA sequences are known and stored in specialized databases such as RDP-II and SILVA.
• Alterations to rRNA are what allow certain disease-causing bacteria, such as Mycobacterium tuberculosis (the bacterium that causes tuberculosis) to develop extreme drug resistance. Due to similar issues, this has become a prevalent problem in veterinary medicine where the main method for handling bacterial infection in pets is administration of drugs that attack the peptidyl-transferase centre (PTC) of the bacterial ribosome. Mutations in 23S rRNA have created perfect resistance to these drugs as they operate together in an unknown fashion to bypass the PTC entirely.
• rRNA is the target of numerous clinically relevant antibiotics: chloramphenicol, erythromycin, kasugamycin, micrococcin, paromomycin, linezolid, alpha-sarcin, spectinomycin, streptomycin, and thiostrepton.
• rRNA have been shown to be the origin of species-specific microRNAs, like miR-663 in humans and miR-712 in mice. These particular miRNAs originate from the internal transcribed spacers of the rRNA.