Ribosomal RNA
The ribosomal RNA ( rRNA ) is the ribonucleic acid , from which, together with proteins , the ribosomes are constructed.
properties
Ribosomal RNA is generated in the nucleolus by transcription using a DNA template (the rDNA ). It is changed in the nucleolus, some parts ( ITS sequences ) are removed, and over 200 nucleobases are enzymatically modified. The rRNA then binds to ribosomal proteins (approx. 50 proteins in prokaryotes , approx. 80 in eukaryotes ), creating ribosomes. As RNA-binding proteins, these proteins belong to the ribonucleoproteins .
The ribosome is the place of protein synthesis . Three or four different rRNA molecules are involved in the construction of a ribosome. The ribosomal ribonucleic acid has enzymatic , structural and recognition functions in this network . So z. B. the peptide bond of consecutive amino acids is catalyzed by the rRNA, while enzymatic activity in living organisms is usually exerted by proteins. In order to be able to meet the high demand of the cell for rRNA - the rRNA can make up up to 90% of the total RNA of a cell - the rDNA template can be found several to many times on the chromosomes.
Ribosomes from prokaryotes contain three rRNA molecules of different sizes, those from eukaryotes four. The size of the rRNAs is usually given in Svedberg (S) according to their sedimentation behavior . The number of nucleobases or nucleotides of the rRNA molecules in question varies depending on the species. The ribosomal RNA is the RNA polymerase I generated. The information in the table is therefore examples:
| Ribosome | Subunit | rRNA | Nucleotides |
|---|---|---|---|
| 70S | 50S | 23S | 2900 nt |
| 5S | 120 nt | ||
| 30S | 16S | 1500 nt |
| Ribosome | Subunit | rRNA | Nucleotides |
|---|---|---|---|
| 80S | 60S | 28S | 4718 nt |
| 5.8S | 160 nt | ||
| 5S | 120 nt | ||
| 40S | 18S | 1874 nt |
Prokaryotic rRNA
The 16S rRNA, together with various proteins, makes up about 2/3 of the mass of the smaller 30S subunit of the prokaryotic ribosomes and has an important function in the translation initiation phase : The 3 'end of the 16S rRNA binds to the shine through base pairing . Dalgarno sequence of the mRNA . This brings the start codon of the mRNA into the correct position in the ribosome. This position is called the P position.
Eukaryotic rRNA
When one speaks of eukaryotic rRNA, that of the mitochondria and plastids is always excluded. These have their own ribosomes (like the mitochondrial ribosomes ), which, however, correspond more to a prokaryotic pattern. There are, however, many variations. So contain z. For example, the mitochondrial ribosomes of many species, including those of humans, only have two rRNA molecules.
The regions of the chromosomes that harbor the rDNA assemble in the cell nucleus during the interphase of the cell cycle to form one or more nucleoli , also called nuclear bodies. The rRNA is transcribed there by RNA polymerase I, while mRNA is transcribed by RNA polymerase II. First, a 45S pre-rRNA is generated, the processing of which provides the 18S, 5.8S and 28S rRNAs in equal numbers. Only the 5S rRNA is independently transcribed elsewhere, specifically by RNA polymerase III. These and the ribosomal proteins (which were synthesized in the cytosol ) are brought to the nucleus, where the large and small subunits of the ribosome are formed from them, and are then released from the nucleus. Naked, d. H. RNA not covered by proteins would be damaged too quickly. A special regulation mechanism ensures that the 5S rRNA is formed in the right amount.
Applications
The sequence of the rRNA is determined in the course of phylogenomic investigations to determine the degree of relationship (rRNA and ITS). This allows a phylogenetic tree to be created. Other markers are the elongation factor Tu (EfTu), the gene of subunit I of cytochrome c oxidase , the gene of cytochrome b of cytochrome c reductase , the genes for ATP synthetase and the genes for heat shock proteins .
The antibiotic classes of tetracyclines and aminoglycosides bind to rRNA.
Phylogenetics
Ribosomal RNA gained enormous importance in the last decades as a tool for the elucidation of the tribal history , the evolution of life and the investigation of family relationships among the organisms. The analysis of rRNA is now a recognized method for classifying a species in the universal family tree of life and for determining the most closely related species. The mentioned similarity of the RNA from mitochondria and plastids is a strong support of the endosymbiont hypothesis for these organelles.
Ribosomal RNA was probably part of the first living units on earth and thus the ancestor of all organisms living today ( endosymbiont theory ). It is part of the basic equipment of every cell living today. At the same time, it has the same function in all organisms and the genes of the rRNA are probably only rarely subject to horizontal gene transfer . It is therefore assumed that the rRNA molecules evolve in all organisms at a comparable rate and not only reflect the development history of the respective rRNA gene, but that of an entire organism. They are considered to be the ideal “ molecular chronometer ” with the help of which family relationships among organisms can be reconstructed.
RNA is a more unstable molecule than DNA and its analysis is therefore technically more complex. Therefore, in practice, one almost always works with the genes of the rRNA, i.e. the rDNA, and derives the sequence of the rRNA from this.
findings
The family trees developed on the basis of the ribosomal RNA are now considered reliable and most of the relationships calculated with them have also been confirmed with other methods. However, the application of the rRNA method cannot be used solely for the correct classification of an organism . The calculated position in the family tree must always be confirmed using other methods. This still includes morphological and physiological characteristics. For example, it is not possible to define a new species on the basis of an rRNA analysis alone.
The rRNA-based phylogenetics is of great importance for microorganisms, because unicellular organisms are difficult to classify based on morphological and physiological characteristics alone. The analysis of ribosomal RNA is a quick and reliable addition. On the basis of empirical data it is now assumed that bacteria whose 16S rRNA sequences match 97–98% can be assigned to a species.
DNA has been isolated from various environmental samples (e.g. water, soil or sewage sludge) and rRNA sequences have been determined from this. In one gram of forest soil, for example, rRNA genes from around 13,000 (!) Different "species" were found. If one compares these sequences with those of cultivable and therefore known microorganisms, one can estimate that today we only know 1–5% of all microorganisms. The existence of the vast majority of bacteria and archaea is only known from their rRNA sequences, without having any idea of what they live on and what role they play in nature.
All bacteria that have been validly described (i.e. cultivable ) so far are - depending on the author - currently classified into 26 phyla or strains . However, the vast majority of all bacteria are distributed over only a few strains, for example the Proteobacteria , Firmicutes and Actinobacteria . Most phyla, on the other hand, are only represented by one or a few cultivable representatives (for example Acidobacteria ), although it is known that these groups must include many more representatives.
26 further phyla are postulated only with the help of rRNA sequences isolated from environmental samples, without having previously cultivated and characterized a representative.
The most important consequence of the application of rRNA-based phylogenetics has so far been the division of all organisms into the three domains of bacteria, archaea and eukaryotes. But the current division of the primordial mouths ( protostomia ), the most species-rich group of animals, into molting animals ( ecdysozoa , including insects , roundworms ) and lophotrochozoa (lophotrochozoa, including molluscs , annelids ) has been developed primarily on the basis of studies of the 18S rRNA of the ribosomes.
Web links
Individual evidence
- ↑ Entry RF00177 in the Rfam database, accessed on May 31, 2017.
- ↑ M. Penzo, A. Galbiati, D. Treré, L. Montanaro: The importance of being (slightly) modified: The role of rRNA editing on gene expression control and its connections with cancer. In: Biochimica et Biophysica Acta . Volume 1866, Number 2, December 2016, pp. 330–338, doi: 10.1016 / j.bbcan.2016.10.007 , PMID 27815156 .
- ^ Mary Campbell: Biochemistry. Cengage Learning, 2007, ISBN 978-0-495-39041-1 , p. 254.
- ↑ WS Yip, NG Vincent, SJ Baserga: Ribonucleoproteins in archaeal pre-rRNA processing and modification. In: Archaea. Volume 2013, 2013, p. 614735, doi: 10.1155 / 2013/614735 , PMID 23554567 , PMC 3608112 (free full text).
- ^ Klaus Urich: Comparative Animal Biochemistry. Springer Science & Business Media, 1994, ISBN 978-3-540-57420-0 , pp. 45-46.
- ↑ SJ Goodfellow, JC Zomerdijk: Basic mechanisms in RNA polymerase I transcription of the ribosomal RNA genes. In: Sub-cellular biochemistry. Volume 61, 2013, pp. 211-236, doi : 10.1007 / 978-94-007-4525-4_10 , PMID 23150253 , PMC 3855190 (free full text).
- ^ AW Coleman: Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure. In: Trends in genetics: TIG. Volume 31, number 3, March 2015, pp. 157-163, doi: 10.1016 / j.tig.2015.01.002 , PMID 25648500 .
- ↑ K. Fukuda, M. Ogawa, H. Taniguchi, M. Saito: Molecular Approaches to Studying Microbial Communities: Targeting the 16S Ribosomal RNA Gene. In: Journal of UOEH. Volume 38, Number 3, September 2016, pp. 223-232, doi: 10.7888 / juoeh.38.223 , PMID 27627970 .
- ↑ AL Torres-Machorro, R. Hernández, AM Cevallos, I. López-Villaseñor: Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? In: FEMS microbiology reviews. Volume 34, number 1, January 2010, pp. 59-86, doi: 10.1111 / j.1574-6976.2009.00196.x , PMID 19930463 .
- ↑ CU Chukwudi: rRNA Binding Sites and the Molecular Mechanism of Action of the Tetracyclines. In: Antimicrobial agents and chemotherapy. Volume 60, number 8, August 2016, pp. 4433-4441, doi: 10.1128 / AAC.00594-16 , PMID 27246781 , PMC 4958212 (free full text).
- ↑ J. Trylska, M. Kulik: Interactions of aminoglycoside antibiotics with rRNA. In: Biochemical Society transactions. Volume 44, number 4, August 2016, pp. 987-993, doi: 10.1042 / BST20160087 , PMID 27528743 .