Transfer RNA
TRNA is short for transfer RNA. Transfer RNAs are small ribonucleic acid (RNA). The length mature tRNAs is typically 73 to 95 nucleotides. They give the correct amino acid in the translation to give the corresponding codon on the mRNA.
- 3.1 tRNA genes
- 3.2 Transcription of tRNA
- 3.3 Maturation of tRNA precursors
Structure
TRNA molecules are typically from 73 to 95 nucleotides of a single RNA strand. In addition to the four basic building blocks of RNA ( adenosine, uridine, cytidine and guanosine ) tRNA contains a lot of different, modified standard bases. So you have identified, for example, the nucleosides dihydrouridine (D), inosine (I), thiouridine, pseudouridine ( Ψ ) and 5- methyluridine ( ribothymidine, T). Often, the bases are also different degrees of methylation.
Each tRNA molecule pairs occur on conjugating bases to form double-stranded regions of. In a two-dimensional representation of tRNA has a cloverleaf -like secondary structure. This structure forms a stem and three loops: a dihydrouracil, a TΨC and anticodon loop (see picture right).
The so-called dihydrouracil loop owes its name to Dihydrouracilresten often contained in it. In pictures it is usually shown on the left. However, always Dihydrouracilreste are not present in any dihydrouracil loop. The dihydrouracil loop serves mainly the recognition of tRNA by aminoacyl -tRNA synthetase. On the anticodon loop is a specific base triplet called the anticodon. The loop always consists of five conjugating pairs and seven unpaired bases, three of which form the anticodon. This interacts with the complementary codon of the mRNA -read (see section function).
The pictures shown in the right TΨC loop contains seven unpaired bases, three of which form the eponymous sequence TΨC. Here Ψ stands for pseudouridine. This loop / this arm binds to the 5S rRNA of the large ribosomal subunit. Between this loop and the anticodon loop is called a loop variable. Depending on this tRNA has a different length.
The acceptor is phosphorylated at its 5 'end. Its 3 ' end of the sequence always shows CCA -3'. The 3 'end, an adenosine, presents its ribose, which has an important physiological role. To this end, the 3'- OH group of the ribose, the carboxy group of a corresponding amino acid is esterified and thus bound to the tRNA ( cf. section function).
Most often be found, the modified bases are chosen from non-conjugated bases of the trefoil. The actual three dimensional tertiary structure resembles a (shown inverted ), "L ", the two arms form the amino acid acceptor stem and the anticodon loop. The functionally important sections are therefore as far apart as possible. The three-dimensional structure of tRNA from yeast was elucidated at a resolution of 300 pm (3 Å) independently by two groups in 1974 by Rich and Klug. 2000, a structure with an improved resolution of 1.93 Å has been published.
A tRNAPhe from S. cerevisiae
A tRNAMet not the initiator tRNA ( see below) from S. cerevisiae
Function
During translation in the protein has the appropriate amino acid can be attached to the peptide chain at the mRNA in ribosome according to the genetic code for each base triplet. This task is mediated by the tRNA. There are for each amino acid, at least one, but often several different tRNAs.
Loading of the tRNA with an amino acid
TRNAs are loaded depending on their sequence with ATP consumption of the respective aminoacyl -tRNA synthetase at the 3'- end specifically with the corresponding amino acid. To the carboxyl group of the amino acid in the ester bond is to the 3'- hydroxy group of the ribose of the adenosine and an amino acyl group attached is formed. Frequently, the aminoacyl -tRNA synthetase recognizes to the anticodon of the tRNA. But there may be other structural elements in the recognition play a role, mainly acceptor.
A special case are the tRNAs that are charged with alanine ( tRNAAla ). Independent of the organism, the tRNAAla on a G -U base pair at positions 3 and 70 in the acceptor. If one of these two bases exchanged with another through (goal -directed) mutagenesis, the resulting tRNA can not be loaded by the alanyl- tRNAAla synthetase with alanine.
Initially it was assumed that in all organisms for each amino acid, there is exactly one aminoacyl- tRNA synthetase that can load all belonging to the corresponding amino acid tRNAs. Later, however, discovered that some organisms, one or more aminoacyl -tRNA synthetases are missing, but this can install the corresponding amino acids in their proteins and possess the necessary tRNAs. Thus, they must have some other mechanism for loading these tRNAs. So lacking in many bacteria, archaea, chloroplasts and mitochondria an aminoacyl -tRNA synthetase for glutamine. Instead, the aminoacyl- tRNA synthetase binds glutamate for this. Both tRNA for glutamate as well as to tRNA for glutamine The "error " to the tRNA -bound glutamate for glutamine is then converted by a transamidase in glutamine.
Incorporation of amino acids into the nascent chain
The aminoacylated tRNAs can be used by the ribosomes, the protein biosynthesis. Fits tie the anticodon of the corresponding base codon of messenger RNA (mRNA ), then the tRNA can be deposited there, and arriving here amino acid to the nascent protein.
According to the genetic code would have for each base triplet coding for an amino acid and not for a stop codon, a tRNA exist - which is generally 61 However, it was found that the number of tRNA which deviates significantly down. The exact number differs in the organisms, but there are no more than 41 Nevertheless, be used in all organisms all base triplets coding for protein. This difference is explained by the wobble theory.
This goes back to Francis Crick theory is that the first two bases of the codon and the last two bases of the anticodon form for " classical " Watson -Crick base pairing hydrogen bonds; G pairs with C and A so always with U. According to Crick's studies, the possibility of base pairing between the third base of the codon and the first base of the anticodon can be extended and does not follow this strict rule. It also speaks of the " wobble position ".
For example, if the first base of the anti-codons is a U, it can recognize an A or G of the codon. Sometimes this is also a first base inosine, it is able to interact with both U, C and A of the codon. The results are summarized in the right table.
Frequently, the first base of the anti-codons is modified. This has an effect on the recognition of the corresponding third base of the codon. For example, if the first base of the anticodon a lysidine ( K2C ), it will be detected in bacteria only from an A. In mitochondria of some eukaryotes base paired 5 - Formylcytidin ( F5C ) with A or G. In echinoderms and the mitochondria of squid has been discovered that 7- methylguanosine ( m7G ) can interact with all four standard bases.
Accordingly, by the fact that the genetic code is a degenerate code in which can encode several base triplets for the same amino acid, often only two bases for the detection necessary because often different base triplets for the same amino acid only in a base.
Initiator tRNAs
The first codon of an mRNA, usually AUG coding for a L-methionine, for which a particular tRNA is used. This also called initiator tRNA tRNAi differs from another methioninspezifischen tRNAMet that is necessary for the recognition of the AUG codon in a reading frame. Although both tRNAs are loaded by the same methionyl -tRNA synthetase with methionine tRNAMet can not be used for the start codon.
In bacteria, for example E. coli initiator tRNA is expressed as tRNAifMet. The "f " in the name indicates that the loaded methionine tRNA is modified with a formyl group. This reaction is catalyzed a methionyl -tRNA formyltransferase ( EC 2.1.2.9 ), while N10 - formyltetrahydrofolate ( 10-CHO-THF ) to tetrahydrofolate ( THF). The tRNAifMet differs in important respects from the tRNAMet, so that the latter is not recognized by the formyltransferase and therefore only tRNAifMet used for initiation. So does not base pairing between the first cytosine and adenine in the acceptor stem instead (see photo). In the anticodon stem has three consecutive G-C base pairs. Finally, the initiator tRNA has a CCU sequence in the D- loop. Together, these differences provide a slightly different conformation.
The initiator tRNA in eukaryotes, as well as in archaea is not formylated. Therefore, one refers to them as tRNAiMet.
A tRNAiMet from S. cerevisiae
A tRNAiMet of man
Biosynthesis of tRNA
TRNA genes
Organisms vary in their number of tRNA genes in their genome. The nematode Caenorhabditis elegans, a typical model organism for genetic studies, has 29 647 genes in its nuclear genome, which encode 620 of them for tRNA. The baker's yeast has 275 tRNA genes in their genome.
In prokaryotes, several genes in the operon are usually grouped together. The genes may encode for protein sequences or different RNA products, including tRNA. In general, as several tRNA will be combined on a single operon, and these may also contain protein-coding genes.
In eukaryotes must be distinguished between the tRNA genes on the DNA in the nucleus and tRNA genes on the DNA from the mitochondria or plastids, such as chloroplasts. In the plastid genes are organized in operons similar to prokaryotes. The provision of tRNA genes ( for example, 30 tRNA genes in Marchantia polymorpha ) contains all tRNA groups which are necessary for the protein synthesis in plastids.
However, is not always in front of a complete set of tRNA genes in mitochondria, so that - must be imported tRNAs from the cytosol into the organelle - depending on the species. While in almost all Opisthokonta (eg in man or in yeast ) all mitochondrial tRNA genes encoded by the mitochondrial DNA, most of tRNAs have, for example, to be imported into cnidarians or Apicomplexa.
Transcription of the tRNA
Prokaryotes have only one RNA polymerase. This transcribed the reading frame of an operon, such that generally a polycistronic mRNA is produced. From this possibly the tRNAs must be removed by endonucleolytic cuts in the intercistronic regions.
In eukaryotes the tRNA is transcribed in the nucleus by RNA polymerase III. Protein-coding genes are transcribed on the other hand there by RNA polymerase II. TRNA is transcribed by a plastid RNA polymerase is similar to the prokaryotes (see Endosymbiontentheorie ). This RNA polymerase is also encoded in the plastid, while another has to be imported from the cytoplasm. In the mitochondria there are two RNA polymerases, both of which must be imported. They are related to the nuclear encoded plastid enzyme.
In archaea exists for transcription in prokaryotes such as only an RNA polymerase. Compared to prokaryotes, but this is more complex. The size, number of the subunits and their amino acid sequences are rather similar to the eukaryotic RNA polymerases.
Maturation of the precursor tRNA
The costs incurred by the transcription pre - tRNAs may include introns. In bacteria, the splicing of this intron occurs autocatalytically, whereas the introns are removed in eukaryotes and archaea by tRNA splicing endonuclease.
In eukaryotes, both the tRNA synthesis and the first post-transcriptional processings such as the trimming of the 5'-and 3' - ends, and the base modifications posttransskriptionale attaching the 3' - CCA sequence in the cell nucleus takes place. The export to the cytosol is mediated by proteins such as LOS1. Occurs in the cytosol on the outer membrane of mitochondria splicing, if introns are present, and also further modifications before the mature tRNA.
Variations of tRNA forms in the animal kingdom
The illustrated above "classical " form of tRNA with three-armed " cloverleaf " structure has been confirmed in previous studies in most tRNAs. In some tribes, but highly modified mitochondrial tRNAs ( mt- tRNAs ) were found, in which different parts of the normal structure were heavily modified, or completely lost. It seems unlikely that this is caused by mutations become functionless pseudogenes. In a tRNA sequence of the D- arm in the entire animal kingdom, suggesting that was already modified this sequence on the ancestor of all modern animals missing. Especially highly modified mitochondrial tRNA structures have been identified in nematodes and arachnids. Some mt- tRNAs having lost a large part of the usual structures without losing their ability to function. In most cases, instead of the lost structure, a replacement structure, eg an additional loop (TV - replacement loop ) formed. Why, here but the loss of an otherwise highly conserved structure whose mutation would have to be all assumptions upon which almost always lethal in exceptional cases, has not been elucidated so far.