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Formation and Characteristics of tRNA, rRNA and mRNA
This is post no. 1 under the main topic.
The Ribonucleic acid (RNA) exists as three forms in a cell. They are transfer RNA or tRNA, Ribosomal RNA or rRNA and Messenger RNA or mRNA. The messenger RNA as the name implies is carrier of information from DNA to the protein factory of the cell called as the ribosome. In ribosome, the information carried by the mRNA is read by rRNA and they participate in the conversion of the received information into proteins through a process called translation with the help of the tRNA.

Transfer RNA (tRNA): tRNAs are tiny in nature and acts as a tool in translation of mRNA into proteins by linking the base pairs of mRNA and amino acid sequence on a polypeptide. Transfer RNAs are amino acid specific and it scans and detects the parts of mRNA coding the type of aminoacid and enables the exact placement of the aminoacid in the polypeptide chain. The physique of the tRNA molecule resembles that of a clover leaf with several extended loops. They are acceptor arm, Dihydrouracil arm, anticodon arm and TⱷC arm each having a special function.

The acceptor arm as the name indicates acts as the site for aminoacid attachment and the anticodon arm detects the codons in mRNA and aids in their binding. RNA polymerase III is the active enzyme in the process of tRNA synthesis which involves transcription of genes corresponding to tRNA. The sequential array of the nucleotides in tRNA is susceptible to modification by chemical groups which contribute to methylation, saturation of double bond, deletion of amino group, replacement by sulfur group and so on.

Ribosomal RNA (rRNA): rRNAs are the native RNAs of the cell organelle Ribosome (protein factory) and hence the name Ribosomal RNA. They signify their presence by deriving the information from mRNA and participating in protein synthesis. The cell relies on ribosomes for all its protein requirement and the amount of protein synthesized in a cell is directly proportional to the number of ribosome molecules present in the cell. S value denotes the size of the ribosome and they exist as 70s in prokaryotes and 80s in eukaryotes. 70s ribosome is the combination of 50s subunit and 30s subunit. The 50s subunit of prokaryotes has 2 rRNAs and the 30s subunit has 1 rRNA. Whereas the 60s subunit in eukaryotes possess 3 rRNAs and 40s subunit has 1 rRNA.

The occurrence of inter RNA molecule base pairing and intra molecular base pairing stabilizes the structure of the rRNA molecule. The functional proteins are found attached to the rRNAs in ribosomes. Few RNAs possess the characteristics of an enzyme and are called as ribozymes.
The process of formation of rRNA is complex involving several steps before the final product of mature rRNA. In prokaryotes, the RNA polymerase mediated transcription of rRNA genes results in the formation of pre-rRNA. The pre-rRNA exists in folded form and base pairing occurs resulting in the formation of stem-loop structure. This is followed by binding of ribosomal proteins to the folded pre-rRNA and modification of bases by methylation and action of RNAse III on specific points on rRNA causing cleavage and finally trimming the 5′and 3′of the rRNA by the M5, M16 and M23 ribonucleases resulting in the formation of mature rRNA. In eukaryotes, the steps involved in the formation of mature rRNA are similar to prokaryotes except for the additional step of ribonuclease activated trimming in prokaryotes.

Messenger RNA (mRNA): The carriers of information from DNA to the ribosome and poses as the template for synthesis of proteins. RNA polymerase II activated transcription of genes addressing proteins in nucleus results in the formation of mRNA. The format of coding regions separated by the non coding region exists in eukaryotes. The coding regions are called as Exons and the non-coding regions are called as Introns. Like the other two RNAs, mRNA formation is also initiated by the formation of pre-mRNA by transcription of both the coding and non-coding regions present as such. This is followed by a process called as splicing which removes the introns allowing the continuity of the Exons, making it an exact template for protein synthesis. Capping and polyadenylation occurs post splicing. Capping process protects the 5′ end of mRNA from the action of exonucleases and polyadenylation protects the 3′ end of the mRNA. All this described processes are skipped by the prokaryotes as the information is translated much earlier even before the completion of the transcription itself.

The transfer RNA and ribosomal RNA are considered stable whereas the life span of the messenger RNA is short.
This is post no. 2 under the main topic.
Other RNA types

SnRNA – small nuclear RNA

These are short RNA molecules (around 150 nucleotides in length) found in the nucleus of eukaryotic cells. They were actually discovered by accident in the 1960s while doing some experiments with gel electrophoresis, and several functions have been connected with them up to now. The most important one is the processing of pre-mRNA, but they also help in the stability of telomeres and regulation of RNA polymerase II and some transcription factors. Subtype of snRNAs are snoRNAs (small nucleolar RNA), found in the nucleolus, and they are responsible for the synthesis and modification of rRNAs, tRNAs and snRNAs themselves.

The main function of the snRNA, processing of the pre-mRNA, is actually performed along with SM proteins (Sec1/Munc18-like proteins). Together, they form the complexes known as snRNPs (small nuclear ribonucleoproteins). More snRNPs join together to form the spliceosome – complex which actually process the primary transcript of RNA into mature messenger RNA. SnRNAs involved in the processing of pre-mRNA are U1, U2, U4, U5 and U6.

Splicing of pre-mRNA

Spliceosome basically removes the introns (non-coding parts of the DNA/RNA) and ligates the exons (coding parts) back together. It performs this by recognizing specific sequences on the transcript. These are 5’ end splice, 3’ end splice, branch point and polypyrimidine tract.

U1 snRNA attaches the first to the GU nucleotide sequence at the 5’ end splice site, following by U2, which attaches to the branch point. After the U4 and U6 attach, U1 gets removed. U5 also attaches a bit more upstream. U4, U5, and U6 together form the lariant (loop) form of the intron, and they cut it out acting as nuclease.

Alternative splicing

During the splicing of pre-mRNA, alternative splicing also occurs, which basically refers to the arranging of DNA exons in different ways (or completely omitting some) in order to get different mRNAs (and different proteins) from the same gene.
This is post no. 3 under the main topic.
Other RNA types

MiRNA – micro RNA

These are small non-coding RNA molecules (usually about 22 nucleotides long), and their main function is transcriptional and post-transcriptional regulation of gene expression. They were discovered during the 1990s, but their function was well defined one decade later, when they were grouped separately from other RNA molecules.

They are not found in prokaryotes – only in eukaryotes and some viruses whose genetic material consists out of DNA (viruses can also have only RNA). There is difference between animal and plant miRNAs, though. Animal miRNAs are complementary with target mRNA in only 6-8 nucleotides at the 5’ end; this region is called the seed region. Plant miRNAs, on the other hand, bind completely or almost completely to the target mRNAs, and they are not region-specific; they can bind to both 5’ and 3’ UTRs (untranslated regions) as well as to the coding region.

Once they are transcribed, they basically prevent the expression of a certain gene by binding to the specific mRNA that is awaiting translation. This complex of mRNA-miRNA is then degraded by cell’s mechanisms. Some 1000 miRNAs in humans are complementary to around 60% of our genes, so more than half of our genes can be regulated with this mechanism.

Even though the mechanism is well conserved among the species, micro RNAs themselves are not 100% specific. One micro RNA can bind to and silence more messenger RNAs. For example, studies have shown that on average, one miRNA targets around 7 mRNAs, but the number can go as high as 200 mRNAs, which means that one miRNA could affect the expression of hundreds of proteins. Also, one mRNA can be regulated by more micro RNAs.

The mechanism of silencing by micro RNA molecules is very interesting and it provides a lot of ground for manipulation, making research about it absolutely necessary, especially since a lot of diseases are connected to miRNAs, like heart and nervous diseases, obesity, etc.
This is post no. 4 under the main topic.
Other RNA types

SiRNA – small interfering RNA

Small interfering RNA molecules are another type of short RNA molecules that can silence some genes by targeting them for degradation. SiRNAs were discovered at the end of the 20th century by the group of scientists in England. These newly discovered molecules were similar in length to micro RNA molecules (around 22 nucleotides), and their last two nucleotides (at 3’ end) were found overhanging. The 5’ end of small interfering RNA molecules is phosphorylated, while the 3’ end is hydroxylated.

Small interfering RNAs are produced in the cell by the enzyme dicer which cleaves long double stranded mRNA molecules and short hairpin RNAs (it also cleaves pre-micro RNA molecules into miRNAs). Another way for siRNA to be present in the cell is by introducing it inside using transfection. This is very important since scientists are able to make synthetic small interfering RNA molecules. Now, it is only necessary to make siRNAs complementary to the gene we want to silence (post-translational silencing), and insert it into the cell. This mechanism opens a lot of room for genetic experiments, especially those concerning drugs and confirmation of gene function.

The main difference between siRNA and miRNA is in their way of action. While micro RNAs don’t necessarily bind to the target mRNA with great precision, siRNA binds completely (every nucleotide establishes connection with the binding site on the target mRNA). This is due to the fact that micro RNAs are “universal”, meaning that they can bind to more mRNA molecules, while small interfering RNAs bind only to one mRNA from which they have been expressed. Moreover, micro RNAs only inhibit the translation of target mRNA (which goes to p-bodies where it is either stored or degraded), while small interfering RNA cleave the target mRNA themselves.

Their ability to degrade mRNA gives them additional possible functions related to the RNA interference pathways, like the antiviral mechanism or shaping of the chromatin structure.
This is post no. 5 under the main topic.
PiRNA – piwi-interacting RNA

PiRNAs form the largest class of small non-coding RNA molecules and they got their name because of the complexes they form with piwi proteins (RNA-protein complexes). They are typically a bit longer (about 26-31 nucleotides) than the regular miRNA or siRNA (about 21 nucleotides). They are found in germ line cells, and are mostly responsible for silencing of the genes both on genomic level (epigenetic silencing) and on transcriptional level (post-transcriptional gene silencing).

It has been hard to establish all of their functions so far, because there is great variation in both piRNA sequences and in piwi proteins. Until now, more than 50,000 unique piRNA sequences have been identified only in mice. However, the theory about gene silencing is pretty strong. Scientists think that piRNA are mostly responsible for the silencing of transposons as most of them are antisense to transposon sequences. They are expressed mostly during the development of the embryo, but they are also necessary for spermatogenesis.

The way they perform silencing of a particular DNA sequence is through RISC (RNA-induced silencing complex). They form complex with piwi proteins and they direct them to the transposons. It has been noticed that the lack of PIWI proteins results in an increased expression of transposons.

While some characteristics are conserved for the class of piRNA molecules (like the fact that they do not have secondary structure motifs), some are found in only specific piRNAs belonging to some organisms. For example, some piRNAs have a 5’ monophosphate and a 3’ modification which blocks 2’ and 3’ oxygen, which increases the stability of the molecules. These modifications have been confirmed in organisms like C. elegans, D. melanogaster, zebrafish, mice and rats.

PiRNAs are usually grouped together in clusters and can be found throughout the genome in numbers ranging from ten to several thousands of them. This results in some large sequences of up to a hundred kb. They are found both in mammals and in invertebrates and both in male and female germlines.

We actually know little about piRNAs considering how many different types of them are there, and we have yet to use the newest technologies in order to find out more about them.
This is post no. 6 under the main topic.
RasiRNA – repeat associated small interfering RNA

As the name itself suggests, rasiRNAs are involved in the RNAi pathway (RNA interference). They are actually a subclass of piRNAs (piwi-interacting RNAs), which means that they too are expressed in the germline cells.

Overall, rasiRNAs differs from other RNAi pathways (from microRNAs and small interfering RNAs) in the proteins they use. MiRNAs and siRNAs are usually produced by Dicer proteins and use the Ago Argonaute protein subfamily, while rasiRNAs do not need Dicer and they use Piwi Argonaute protein subfamily, of course. However, even though they are the subtype of piRNAs, there are still some differences between these two.

The difference is that piRNAs are present in invertebrates and vertebrates, while rasiRNAs have been discovered only in Drosophila, yeast and some other organisms, while they still have not been found in mammals. This does not mean that they are not present there, though, because the proteins with which they form complexes are present in mammals. Moreover, rasiRNA molecules differ in length from piRNAs. Also, another interesting thing is that in some instances, rasiRNA have been found in plants where they were produced by Dicer complex and there were no piwi proteins present.

So far, scientists have identified three major functions that rasiRNAs have. The first one is about heterochromatin, namely establishing and maintaining its structure. The second one is about transcription and control of the transcripts, but only the ones which emerge from repeat sequences. The last function of rasiRNA is about silencing transposons and retrotransposons.

Transposons and Retrotransposons

Transposons are the elements which can change their position in the genome, replicate themselves autonomously, disrupt other genes, etc., while retrotransposons basically fall into different category of “jumping genes”. The main difference between them is in the enzyme they use (transposons use transposase, while retrotransposons use reverse transcriptase and integrase) and the way they “jump” – transposons are cut from one place and moved to the next one while retrotransposons copy themselves while remaining at the old position as well. There are also some other differences between them. For example, the terminal ends in retrotransposons are much longer than in transposons. Also, the moving of retrotransposons requires RNA, while transposons don’t need it.
This is post no. 7 under the main topic.
SnoRNA – Small Nucleolar RNA

Small nucleolar RNAs also fall into the category of small RNA molecules. Their main function is related to the chemical modification of other RNA molecules and based on that, they are divided into two classes: H/ACA box snoRNAs, responsible for pseudoridylation, and C/D box snoRNAs, responsible for methylation. Pseudoridylation is the production of pseudoridine from uridine through post-transcriptional isomerization. Methylation is the addition of the methyl group to the substrate.

Small nucleolar RNA molecules usually affect ribosomal RNAs, transfer RNAs and small nuclear RNAs. They do so while the targets are still in their pre-mRNA forms and they affect only one or two modifications made on a single molecule of RNA with the help of several other proteins forming snoRNP complex (small nucleolar ribonucleoprotein).

The first step is the recognition of the target sequence through the complementary antisense sequence 10-20 nucleotides long. The second step is the methylation or pseudoridylation. These modifications affect the RNA folding and interaction with ribosomal proteins. Moreover, pseudoridylation adds the possibility for another hydrogen bond, while methylation protects RNA from hydrolysis.

Interestingly, research has shown that some small nucleolar RNAs, whose targets are snRNAs (small nuclear RNAs) function in both methylation and pseudoridylation. These molecules contain both H/ACA and C/D boxes and they are also called Cajal body-specific RNAs because they accumulate in the Cajal body (while most of the other snoRNAs are found in the nucleolus).

Additional functions

Some micro RNA molecules actually start off as small nucleolar RNAs only to be processed into miRNAs. Some of these were first identified as miRNAs with functions (targets) different than those of regular miRNAs, but later on, it was shown that they are actually modified snoRNAs.

Some studies have found that small nucleolar RNAs do not always have to target rRNAs. It has been shown that some snoRNAs can actually control the chromatin structure, its condensation and accessibility. Other studies have shown that some snoRNAs are active during the alternative splicing; namely, they regulate the splicing of trans genes.
This is post no. 8 under the main topic.
LncRNA – Long non-coding RNA

As their name suggests, lncRNA molecules are a bit longer transcripts when compared to miRNAs, siRNAs, snoRNAs, etc. (longer than 200 nucleotides) and they do not code for proteins. They are processed in a similar way like mRNA molecules - they have 5’ Guanine cap added, 3’ poly Adenylation site, and some things are spliced out. However, they do not have open reading frames (required for transcription to be actually successful). They are abundant, though. In fact, some research suggests that there are four times more long non-coding RNA molecules than messenger RNAs.

Unlike other small RNA molecules that are usually well conserved, long non-coding RNAs are not. This is mostly due to the fact that they are longer, because the longer the nucleic acid is, the more variation there will be. There are some parts conserved though, like some elements in introns, elements required for splicing, as well as promoters. Another reason why they are not conserved is because they do not code for any protein, which speeds up their evolutionary change comparing to mRNAs.

Although long non-coding RNAs can be present in thousands, only small portion of them are actually functional, which is kind of intuitive considering the fact that they are non-coding. However, there are a lot of processes in which they are involved, like:

- gene-specific transcription – regulation of gene expression along with transcription factors by targeting transcriptional activators, repressors, or some components of RNA polymerase
- regulation of transcriptional machinery – targeting and regulation of initiation complex by forming a stable RNA-DNA triplex along with the promoter
- post-transcriptional regulation – regulation of post-transcriptional mRNA processing by binding to complementary regions and forming duplexes effectively preventing additional molecules to bind there, which can affect pre-mRNA’s processing, transport, translation, etc.
- epigenetic regulation – affecting epigenetic control (DNA methylation, histone methylation and acetylation) by recruiting other proteins

There are a lot of other processes in which long non-coding RNA molecules are involved, like splicing, translation, gene expression regulation by siRNA, genomic imprinting, X-chromosome inactivation, and others…
This is post no. 9 under the main topic.
Discovery of RNA and its effect on gene therapy and related treatments

The development of molecular biology is truly unique and full of twist and turns that normally can be associated with a novel. It started with the discovery of the double helix of DNA way back in 1953. Since then over thousands and thousands of biological molecules have been identified by various biologists at different times that play key roles in the body of a cell. These identifications of structural elements have helped the biologists to develop different drugs for effective treatments against deadly diseases.
Previously DNA and proteins play key role in the development of drugs as DNA provides the genetic information and proteins being the products of the genes. The discovery of proteins paved the way towards immense advancement in medical sciences with the invention of insulin, the next generation drugs against cancer, interferon and so on. Similarly, the gene therapy involving modified DNA can be used successfully in the treatment of hereditary blindness, hempphilia and many such previously diseases that has no previous treatments.

The RNA in treatments of diseases

Recently the focus has been shifted towards the RNA molecules. Micro RNA has been found to cure Hepatitis C by blocking the related strains causing the disease. Hepatitis C is not a very old disease. It has been noted just 25 years ago. Hepatitis C is responsible for majority of cases of liver cancer and liver transplantation. It kills more people than AIDS do and the death toll is US alone is more than 350000 people per year.
Though the infection is curable with standard treatment protocol using ribavirin and interferon for 50-70% cases, but it is time consuming (takes about 11 months) and associated with severe side effects that include fatigue, anemia, headache, depression and fever. A modified protease has been recently used for treatment, similar to something used to treat AIDS patients. This new technique has given better result and significantly lowered the treatment time. But, the problem is that this new drugs only works against hepatitis C infections from Japan, North America and Europe. So for the rest of the world, something else has to be designed.

RNA drugs against Ebola

The people infected with Ebola virus usually have the initial symptoms identical to that of flue i.e. chills, high fever and muscle pains. But, soon bleeding starts and the virus continue to multiply within the body by destroying the cells. Eventually it starts damaging the organs of the body like liver, spleen, lungs and the blood vessels. It takes only a few days to reach organ failure leading the patients into coma. More than 90% of the infected patients in Central and West Africa have been killed.
This scenario may be changed by the introduction of a small interfering RNA molecule or siRNA. Serious research is going on and a highly promising treatment procedure has been identified using siRNA that worked well in 6 Ebola infected monkeys. The treatment also went well against the uninfected human volunteer, the first safety step in drug testing.

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