Sequence of ribosomal RNA

Sequence of ribosomal RNA

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Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, Complete nucleotide sequence of a 16s rRNA gene from E. coli, suggests that it uses DNA to find the sequence. Would it be possible to isolate the rRNA and derive the sequence from that?

As far as I know it'spossible to reverse transcribe a rRNA gene, you may not get the best yields though. The secondary / tertiary structures will be a problem, however, there are reverse transcriptase's commercially available that can handle secondary structure: Thermo-X™ Reverse Transcriptase from Invitrogen or Sensiscript™ from Qiagen.

Unequivocally, YES.

Before DNA sequencing was used to deduce the sequence of cloned or reverse-transcribed RNA molecules, slower and more cumbersome direct sequencing of RNA was performed using the method of Sanger et al. (Sanger, F., Brownlee, G. G. and Barrel B. G. (1965) J. Mol. Biol. 13, pp. 373-398). This used ribonucleases in a manner somewhat similar to pre-Edmann protein sequencing.

Because of its abundance and ease of purification ribosomal RNA was a suitable species for this approach, and Carbon et al reported the complete sequence of E. coli 16S rRNA in 1978 (Carbon P., Ehresmann C., Ehresmann, B. and Ebel J.P. (1978) FEBS Letters 94, pp. 152-156).

Sigh! How little do modern molecular biologists know about the history of their subject.

Nucleotide sequence of the Physarum polycephalum small subunit ribosomal RNA as inferred from the gene sequence: secondary structure and evolutionary implications

The nucleotide sequence of the Physarum polycephalum small subunit ribosomal RNA (SSU rRNA) gene has been determined. Sequence data indicate that the mature 19S SSU rRNA is 1,964 nucleotides long. A complete secondary structure model for P. polycephalum SSU rRNA has been constructed on the basis of the Escherichia coli 16S rRNA model and data from comparative analyses of 28 different eukaryotic sequences. A "four-helix" model is presented for the central domain variable region. This model can be applied both to vertebrate and most lower eukaryotic SSU rRNAs. The increased size of P. polycephalum SSU rRNA relative to the smaller SSU rRNAs from such other lower eukaryotes, as Dictyostelium, Tetrahymena or Saccharomyces is due mainly to three G+C-rich insertions found in two regions known to be of variable length in eukaryotes. In a phylogenetic tree constructed from pairwise comparisons of eukaryotic SSU rRNA sequences, the acellular myxomycete P. polycephalum is seen to diverge before the appearance of the cellular myxomycete Dictyostelium discoideum.

Fact Sheet: Ribosomal RNA (rRNA), the details

The ribosome is a cellular machine found in all organisms. It serves to convert the instructions found in messenger RNA (mRNA, which itself is made from instructions in DNA) into the chains of amino-acids that make up proteins. That is, the ribosome is responsible for the synthesis of proteins.

Structure and shape of the E.coli 70S ribosome. The large 50S ribosomal subunit (red) and small 30S ribosomal subunit (blue) are shown with a 200 Ã…ngstrom (20 nm) scale bar. For the 50S subunit, the 23S (dark red) and 5S (orange red) rRNAs and the ribosomal proteins (pink) are shown. For the 30S subunit, the 16S rRNA (dark blue) and the ribosomal proteins (light blue) are shown.

The ribosome itself is highly complex. It is made up of dozens of distinct proteins (the exact number varies a little bit between species) as well as a few specialized RNA molecules known as ribosomal RNA (rRNA). Note – these rRNAs do not carry instructions to make specific proteins like mRNAs. The ribosomal proteins are rRNAs are arranged into two distinct ribosomal pieces of different size, known generally as the large and small subunit of the ribosome.

The RNA World

The key catalytic activity of the ribosome – the creation of a chemical bond between two amino acids (known as a peptide bond) – comes from the RNA component of the ribosome. This, and other catalytic roles for RNA, were discovered relatively recently and were a bit of a surprise, since for many years it had been thought that all catalytic activities in cells were from proteins. The catalytic role of rRNA is a key piece of support for the “RNA world” hypothesis, which postulates that the first evolving chemical entities on Earth were RNA molecules. These RNAs served simultaneously as both genotype (i.e., genetic material) and phenotype (i.e., they had catalytic activities that allowed for some function). At some point in the evolution of life, some of these RNAs “discovered” DNA as a more stable storage medium for information, and proteins as a more versatile way to mediate enzymatic reactions. However, some catalytic functions of RNA (e.g., synthesis of proteins) are still present in modern organisms as a relic of earlier times.

Homology of the ribosome across life

Most of the individual components of the ribosome have equivalent counterparts across all forms of life. The matching components in different species (e.g., ribosomal proteins, or femur bones) are considered to be homologous – which means they are thought to have evolved from a common ancestor that also had that component (i.e. the ancestor also had a version of the same ribosomal protein).This is true for many of the proteins found in the ribosome and also for the ribosomal RNAs (for more detail see section below on Homology of ribosomal components . We can compare ribosomal components of different species, much as we can compare bones between different mammals, in essence “lining up” the sequences of the equivalent component to see where they differ.

Homology of ribosomal components

Homology refers to similarity of traits due to shared ancestry. The human hand is homologous to the cat paw and whale flipper. The three structures have evolved characteristics to different purposes, but share an underlying bone structure passed down from an ancestor common to all mammals.

Underlying the shared bone structures are shared genetic structures. Homologous genes encode homologous traits, from skeletons and organs down to the invisible components of cells. The ribosome is one of the oldest and most essential cellular players, and is homologous in all organisms. We infer homology of ribosomes across all life because they not only look and act alike, but also have remarkably similar gene sequences.

For example, the ribosome of the bacterium Escherichia coli includes a protein known as ribosomal protein L4 (“L” here stands for the fact that this protein is a component of the large subunit of the ribosome). In the genome of E. coli there is a region that includes the instructions for making this protein, known as the rpl4 gene. This gene is transcribed into mRNA, and the mRNA translated into the rpl4 protein. All organisms on the planet have a protein in their ribosomes comparable to L4 from E. coli. And, of course, all these organisms also have a gene in their genome that is equivalent to the rpl4 gene from E. coli (they could not have a L4 protein if they did not have a gene encoding it in their genome). In fact, it is not just that all organisms have a protein that is “like” the E. coli L4. All the L4-like proteins in all species are so similar to each other in their amino acid sequence, that it has been inferred that a common ancestor of all modern day organisms also possessed an L4-like protein.

The same pattern generally holds true for dozens of other ribosomal proteins, as well as for multiple ribosomal RNAs. We can line up the components of one species’ ribosome with the components of other species ribosomes much as we can compare bones between different mammals. From these comparisons it has been inferred that a common ancestor of all modern day organisms had a ribosome that was very similar to the ribosomes found across all forms of life today. The equivalent ribosomal components in different organisms (e.g., L4 in E. coli and humans) are considered to have evolved from a common ancestral component (i.e., L4 in a common ancestor of humans and E. coli). (Of course, at some point, long in the past, the ancestors of E. coli and humans split into different lineages – more on this “Tree of Life” in a bit).

The L4 proteins of different species are considered to be homologous.

Distinct rRNAs in different organisms

Bacteria and Archaea possess three distinct rRNAs, sometimes referred to as the 5S, 16S, and 23S forms. The “S” in this nomenclature refers to Svelberg units, a measure of an experimental technique called sedimentation (see next paragraph for more detail on this). The 16S rRNA is the sole rRNA in the small subunit of the ribosome and thus is sometimes referred to as the small subunit rRNA or ss-rRNA. The 5S and 23S are both components of the large subunit of the ribosome.

Sedimentation in the lab is in essence an accelerated form of the settling of particles that occurs in formation of sediment in lake and ocean floors. In the lab one can accelerate the process by very rapidly (10s of thousands of RPM) spinning samples in a centrifuge. To study the components of a cell such as the different parts of the ribosome, researchers break open cells and then spin the components in a tube inside a centrifuge. Different components of the cell settle in different regions of the “sedimentation gradient” in the tube (with the specific region given a numerical value – the higher the number the less easily something moves through the gradient). The exact region in which something settles is based on a combination of its size, shape and density. For most bacteria and archaea, the main forms of ribosomal RNA settle at the 5S, 16S, and 23S regions of a sedimentation gradient. For most eukaryotes, the main forms of ribosomal RNA settle at slightly different regions and thus have different numerical values (e.g., humans have 5S, 5.8S, 18S, and 28S and 40S. The 5.8S and 5S are homologous to the 5S of bacteria and archaea, the 18S is homologous to the 16S, and the 28S is homologous to the 23S.

3D structure of the 5S rRNA

Key features of rRNAs for phylogenetics

The function of rRNAs is very similar across all species. The core function of the ribosome is basically the same across different groups of organisms. However, this does not mean the rRNAs are identical between species. The actual sequence of the nucleotides in rRNAs (and in the rDNA genes) does vary between species. For our purposes there are three key features of the variation in rRNA sequence between species.

First, the rRNA molecules in the ribosome fold over into complex three dimensional shapes. The specific shape that they take is highly conserved between species. However, the linear sequence of nucleotides in each rRNA (also known as the primary sequence) can vary without affecting the function since different primary sequences can fold into in essence the same shape.

Second, when a single species splits into two distinct evolutionary lineages, differences can accumulate in the sequence of the rRNAs between the two lineages. Biologists call the process “sequence divergence.” The divergence of rRNA sequences generally occurs very slowly (they are among the most slowly evolving of genes, but changes still happen). In addition, the structure and function of the rRNAs generally stay the same between species (and changes in the actual structure are usually lethal).

Third, some regions of rRNAs evolve (i.e., diverge) slowly and others diverge rapidly. Some regions are basically the same across most or all taxa. This shared sequence has allowed researchers to use a specialized laboratory method known as polymerase chain reaction (PCR) to help read the sequences of rRNAs from different (and even unknown) species.

For background on protein synthesis and the ribosome, go here.

For information on the use of rRNA sequences in microbial ecology go here.

This document was produced by microBEnet. It was written by Jonathan Eisen and David Coil, and edited by Elizabeth Lester with feedback from Hal Levin.

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1. Howard Hughes Medical Institute: Interactive Click and Learn Presentations

a. RNA Diversity (, Multimedia Document) – The RNA Diversity Click and Learn presentation includes 13 slides of information that you can click on the view to learn about the different types, structures, and sizes of RNA and many types of ribozymes.

b. RNA Interference (, Multimedia Document) – The RNA Interference Click and Learn presentation includes 16 slides of information that you can click on the view to learn about how double-stranded RNA mediates the effect of gene silencing, known as RNA Interference.

2. University of Utah’s Genetic Science Learning Center: DNA to Proteins

a. Build a DNA Molecule (, Multimedia Page)

Part c

Types of Ribonucleic Acid (RNA): mRNA, tRNA and rRNA

It carries the genetic message from the chromosomes (DNA) to the ribosome (site of protein synthesis). This RNA is formed in the nucleus (or nuclear zone in prokaryotes) containing complementary base sequence to a part of one strand of DNA (gene).

The base sequence in the mRNA specifies the amino acid sequence in the polypeptide chains. In prokaryotes a single mRNA molecule codes either for one polypeptide chain, hence called monocistronic, or it may code for more than one polypeptide, thus called polycistronic. In eukaryotes, most of the mRNAs are monocistronic.

RNA Type # 2. Transfer RNA (tRNA):

It is an adapter molecule that reads the information encoded in the mRNA and accordingly transfers the appropriate amino acid to the growing polypeptide chain during protein synthesis. There is at least one kind of tRNA for each amino acid. Some amino acids have two or more specific tRNAs. At least 32 tRNA’s are required to recognize all the amino acid codons (64 — 3 = 61).

Most cells have to about 40-50 distinct tRNAs. Some tRNA’s can recognize more than one codon (due to wobbling). tRNAs have between 73 and 93 nu­cleotides in their structures. Eight or more nucleotides are unusual modified bases which are methylated derivatives of the principal bases. Most tRNA’s have guanylate (pG) at 5′ end and have the base sequence CCA at 3′ end.

These are single stranded and there is maximum intra- chain base pairing which gives it a clover leaf shape structure, with four arms.

The four arms of tRNA are:

(iii) Dihydrouridine arm (DHU arm) and

(iv) Ribothymidine – pseudouridine arm (TΨC Arm).

The amino acyl arm carries a specific amino acid esterified to its carboxyl group at the 2′ or 3′ hydroxyl group of the adenosine present at the 3′ end of the tRNA. The anticodon arm contains the anticodon, i.e., a sequence of three nucleotide bases complementary to the genetic code in mRNA for that particular amino acid. The two RNAs are paired anti-parallel, i.e., the first base of the codon (5′ → 3′) pairs with the third base of the anticodon (3′ → 5′) creating codon-anticodon interaction as shown.

There are totally 64 codons formed by multiple combinations of any three nucleotide bases out of the four nucleotides forming the nucleic acids. At least one codon specifies one amino acid and some amino acid have more than one codon, but the number of different tRNA’s for each amino acid is not the .fame as the number of its codons.

This is because some tRNAs contain the first anticodon nucleotide inosinate (I), which can base pair by hydrogen bonds with three nucleotides, viz., U, C and A. Therefore, all those amino acid codons which differ at the third nucleotide will have the same tRNA. This is known as wobbling, e.g., there are six codons for arginine, but only four different types of tRNA Ar g are available in the cell. One of these tRNA contains the anticodon (3′) GCI (5′) and will pair with three codons for arginine.

The other three codons for arginine, viz., CGG, AGA and AGG have different tRNAs. The DHU arm contains the unusual nucleotide dihydrouracil and the TΨC arm contains ribothymidine (T) and pseudouridine (Ψ) which has an unusual carbon-carbon bond between the base and pentose sugar. The functions of DHU arm is recognition of its proper aminoacyl-tRNA synthetase and TΨC arm is involved in binding of the aminoacyl-tRNA to the ribosomal surface.

RNA Type # 3. Ribosomal RNA (rRNA):

Ribosomal RNA molecules in association with proteins forms the seat of protein synthesis or the protein synthesis machinery called the ribosome. The RNAs are designated depending upon their sedimentation coefficients. The rRNAs found in prokaryotes are 5S, 23S and 16S. Those found in eukaryotes are 5S, 18S 28S, and 5.8S. rRNA is single stranded with intra-chain hydrogen bonding.

The fate of an intervening sequence RNA: Excision and cyclization of the Tetrahymena ribosomal RNA intervening sequence in vivo

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The Central Dogma of Biology

There are several different kinds of RNA made by the cell. mRNA - messenger RNA is a copy of a gene. It acts as a photocpoy of a gene by having a sequence complementary to one strand of the DNA and identical to the other strand. The mRNA acts as a busboy to carry the information stored in the DNA in the nucleus to the cytoplasm where the ribosomes can make it into protein.

tRNA - transfer RNA is a small RNA that has a very specific secondary and tertiary structure such that it can bind an amino acid at one end, and mRNA at the other end. It acts as an adaptor to carry the amino acid elements of a protein to the appropriate place as coded for by the mRNA.

rRNA - ribosomal RNA is one of the structural components of the ribosome. It has sequence complementarity to regions of the mRNA so that the ribosome knows where to bind to an mRNA it needs to make protein from.

snRNA - small nuclear RNA is involved in the machinery that processes RNA's as they travel between the nucleus and the cytoplasm. We will discuss these later in the context of eukaryotic gene structure.

The Genetic Code

Note the degeneracy of the genetic code. Each amino acid might have up to six codons that specify it. It is also interesting to note that different organisms have different frequencies of codon usage. A giraffe might use CGC for arginine much more often than CGA, and the reverse might be true for a sperm whale. Another interesting point is that some species vary from the codon association described above, and use different codons fo different amino acids. In general, however, the code depicted can be relied upon.

How do tRNAs recognize to which codon to bring an amino acid? The tRNA has an anticodon on its mRNA-binding end that is complementary to the codon on the mRNA. Each tRNA only binds the appropriate amino acid for its anticodon.

Watch the video: 16s rRNA (August 2022).