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Messenger RNA (mRNA)
1184
Mesoderm
and more, if possible. The investigator then does a critical experiment designed to make all the outcomes (O1, O2, O3, . . . ) possible. There can only be one outcome, e.g., O2 in this case. Then the investigator can reason: O1 is not observed, so H1 is not true. O3 is not observed, so H3 is not true. O2 is observed, so H2 is probably correct. Again, the experiment does not prove H2 is true; but H2 has withstood a powerful test, especially if the hypothesis and experiment are quantitative and the results agree closely with the prediction. This reasoning is exactly what Meselson and Stahl used in testing the replication prediction of the Watson±Crick model. See also: DNA Structure; Semiconservative Replication
Mesoderm See: Developmental Genetics
Messenger RNA (mRNA) A Liljas Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0821
Messenger RNA (mRNA) is an intermediate in the translation of genetic sequences into protein. Genomic DNA is transcribed into mRNA, which, when bound to the ribosome, can be translated.
Genetic Code The genetic code is the universal dictionary by which genetic information is translated into the functional machinery of living organisms, the proteins. The words (codons) of the genetic message are three nucleotides long. Since there are four different nucleotides used in mRNA, this results in a dictionary of 64 words. There are 20 amino acids that are normally used in proteins and which are translated. In addition the translation needs a definition of `start' and `stop.' The start codon also defines the reading frame (the sequence of nucleotide triplets) that is to be translated. The start or initiator codon is identical to the methionine codon. Special mechanisms are used to identify the correct initiation site; in addition there are three stop codons: UAA, UAG, and UGA. Thus 61 codons are available for 20 amino acids, and hence the
genetic code is degenerate. In the case of leucine, serine, and arginine, there are as many as six codons, whereas methionine and tryptophan have only one codon.
Transcription Genomic DNA cannot be translated but has to be copied or transcribed into RNA by different RNA polymerases. Here the classic mechanism discovered by Watson and Crick applies. One strand of the double-stranded DNA (the negative strand) is copied with Watson±Crick base-pairing into a positive strand of RNA. This occurs in the 50 to 30 direction. The double-stranded DNA is opened up in a `bubble' that travels along the duplex during transcription. Here, a DNA±RNA hybrid is formed transiently. The process of transcription is in all cases strongly regulated. Some genes are transcribed frequently, whereas others are transcribed only rarely. Again some genes are transcribed in a brief period in the life of the cell, whereas others are copied more or less continuously. In eukarya, transcription is performed in the nucleus and the transcript is transported into the cytoplasm to be translated. Transcription and translation in mitochondria and chloroplasts is performed in these cellular organelles. In the case of eubacteria and archaea, the whole process is performed in the cytoplasm. The eubacterial transcripts frequently contain several genes controlled by one operator, i.e., mRNA is polycistronic.
Processing of Transcribed RNA Some transcribed RNAs are never translated but have their same cellular functions as RNA. These are primarily the ribosomal RNA (rRNA) and transfer RNA (tRNA) molecules. The transcribed RNA, called the `primary transcript,' frequently has to be processed to become mRNA. Several different processes are involved. The processes in eukarya differ from those in eubacteria. The primary transcripts normally contain longer or shorter regions, which are not translated. They form so-called introns, while the translated regions form exons. The splicing machinery removes the introns by cutting and ligation. Eukaryotic mRNAs are also modified by the addition of a poly(A) tail beyond the 30 end of the message. In eukarya the primary transcripts are also frequently edited to become mRNAs. This is sometimes done by changes of U to C or vice versa. More extensive editing occurs in mitochondria from trypanosomes, where the mRNAs are extensively modified
MET 1185 by large enzymatic particles that use templates called `guide RNAs.'
Translation on Ribosomes The process of translation occurs on the ribosome, in the cytoplasm or in the cellular organelles, mitochondria and chloroplasts. The ribosome is a complex of a few large rRNA molecules and between 50 and 90 different proteins. The ribosome is made up of two subunits (large and small) with different functions that dissociate from each other at the end of the process. Translation is traditionally divided into three steps: initiation, elongation, and termination. A fourth step, ribosome recycling, also belongs to the process. Soluble protein factors catalyze the process by binding to the ribosome transiently. More than 10 factors participate in eubacterial translation, whereas a considerably larger number participate in eukaryal translation. The mRNA is bound to the small ribosomal subunit. Since the messenger is bound between the subunits, they have to dissociate to be able to bind a tRNA. The decoding site for interactions between the mRNA and the anticodon is part of the A-site for aminoacyltRNA and located on the small subunit. The neighboring P-site is the location of the tRNA with the nascent peptide. The initiation codon is recognized in different ways in eukarya and bacteria. In eubacteria a nucleotide sequence of the mRNA rich in As and Gs is usually found 3±10 nucleotides upstream of the initiator codon. These sequences are complementary to a region of the 30 end of the 16S ribosomal RNAs. Binding of this region of the mRNA to the 30 end of the 16S rRNA is called the Shine±Dalgarno interaction. The initiator tRNA (fMet-tRNA) complexed with initiation factor 2 recognizes the initation codon AUG and binds to the P-site of the small subunit of the ribosome. In eukaryal systems, the binding site on the mRNA for the ribosome is recognized quite differently. The eukaryal mRNAs are usually capped at the terminal 50 position. This means that they have an N7methylated GTP linked by a 50 ±50 pyrophosphate bond to the terminal nucleotide. The cap is situated at a varying distance from the initiation codon, the first AUG. Some of the eukaryal initiation factors interact with the small subunit, while others interact with the capped mRNA. The initiator tRNA binds to the small subunit in complex with the eukaryal initiation factor 2. The small subunit then scans the mRNA for the initiator AUG codon, which will be recognized by the bound initiator tRNA. In both eukarya and bacteria, the large subunit subsequently associates with this complex to initiate protein synthesis.
Reading Frame and Usage of Genetic Code The initiator AUG codon not only defines the start but also the reading frame of a mRNA. Translation proceeds from this starting point in steps of three nucleotides (one codon) by binding a cognate tRNA through base-pairing. The frequent occurrence of termination codons out of frame prevents translation in the wrong frame for more than short stretches. However, there are mRNAs for which the correct translation needs a change of reading frame. This is the case for Escherichia coli termination or release factor-2 (RF2). The readthrough of a stop codon requires a tRNA that would decode a stop (nonsense) codon as a sense codon and incorporate a specific amino acid. Such tRNAs are called suppressor tRNAs. In a few proteins in eubacteria and eukarya, selenocystein (Se-Cys) is required. This is not incorporated by a posttranslational modification as in other cases of nonstandard amino acids. Se-Cys is rather incorporated during translation in response to one of the stop codons. The mechanism for this involves a special tRNA (tRNASec) which reads the stop codon and a specialized version of elongation factor T4.
Further Reading
Spirin AS (1999) Ribosomes. New York: Kluwer. Garrett RA, Douthwaite SR, Liljas A, Matheson AT, Moore PB and Noller HF (eds) (2000) The Ribosome: Structure, Function, Antibiotics and Cellular Interactions. Washington, DC: ASM Press.
See also: Anticodons; Genetic Code; Introns and Exons; Ribosomes; Transcription; Transfer RNA (tRNA)
MET E Gherardi Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.1595
MET is the product of the c-met proto-oncogene and the membrane receptor for the polypeptide growth factor hepatocyte growth factor/scatter factor (HGF/ SF). The MET locus maps to 7q21±q31 and is tightly linked to the cystic fibrosis (CF) locus. MET was discovered as an activated oncogene in a human osteogenic sarcoma cell line treated with N-methyl-N0 nitro-nitroso-guanidine in which activation resulted from a genomic rearrangement involving sequences
Mesoderm
and more, if possible. The investigator then does a critical experiment designed to make all the outcomes (O1, O2, O3, . . . ) possible. There can only be one outcome, e.g., O2 in this case. Then the investigator can reason: O1 is not observed, so H1 is not true. O3 is not observed, so H3 is not true. O2 is observed, so H2 is probably correct. Again, the experiment does not prove H2 is true; but H2 has withstood a powerful test, especially if the hypothesis and experiment are quantitative and the results agree closely with the prediction. This reasoning is exactly what Meselson and Stahl used in testing the replication prediction of the Watson±Crick model. See also: DNA Structure; Semiconservative Replication
Mesoderm See: Developmental Genetics
Messenger RNA (mRNA) A Liljas Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0821
Messenger RNA (mRNA) is an intermediate in the translation of genetic sequences into protein. Genomic DNA is transcribed into mRNA, which, when bound to the ribosome, can be translated.
Genetic Code The genetic code is the universal dictionary by which genetic information is translated into the functional machinery of living organisms, the proteins. The words (codons) of the genetic message are three nucleotides long. Since there are four different nucleotides used in mRNA, this results in a dictionary of 64 words. There are 20 amino acids that are normally used in proteins and which are translated. In addition the translation needs a definition of `start' and `stop.' The start codon also defines the reading frame (the sequence of nucleotide triplets) that is to be translated. The start or initiator codon is identical to the methionine codon. Special mechanisms are used to identify the correct initiation site; in addition there are three stop codons: UAA, UAG, and UGA. Thus 61 codons are available for 20 amino acids, and hence the
genetic code is degenerate. In the case of leucine, serine, and arginine, there are as many as six codons, whereas methionine and tryptophan have only one codon.
Transcription Genomic DNA cannot be translated but has to be copied or transcribed into RNA by different RNA polymerases. Here the classic mechanism discovered by Watson and Crick applies. One strand of the double-stranded DNA (the negative strand) is copied with Watson±Crick base-pairing into a positive strand of RNA. This occurs in the 50 to 30 direction. The double-stranded DNA is opened up in a `bubble' that travels along the duplex during transcription. Here, a DNA±RNA hybrid is formed transiently. The process of transcription is in all cases strongly regulated. Some genes are transcribed frequently, whereas others are transcribed only rarely. Again some genes are transcribed in a brief period in the life of the cell, whereas others are copied more or less continuously. In eukarya, transcription is performed in the nucleus and the transcript is transported into the cytoplasm to be translated. Transcription and translation in mitochondria and chloroplasts is performed in these cellular organelles. In the case of eubacteria and archaea, the whole process is performed in the cytoplasm. The eubacterial transcripts frequently contain several genes controlled by one operator, i.e., mRNA is polycistronic.
Processing of Transcribed RNA Some transcribed RNAs are never translated but have their same cellular functions as RNA. These are primarily the ribosomal RNA (rRNA) and transfer RNA (tRNA) molecules. The transcribed RNA, called the `primary transcript,' frequently has to be processed to become mRNA. Several different processes are involved. The processes in eukarya differ from those in eubacteria. The primary transcripts normally contain longer or shorter regions, which are not translated. They form so-called introns, while the translated regions form exons. The splicing machinery removes the introns by cutting and ligation. Eukaryotic mRNAs are also modified by the addition of a poly(A) tail beyond the 30 end of the message. In eukarya the primary transcripts are also frequently edited to become mRNAs. This is sometimes done by changes of U to C or vice versa. More extensive editing occurs in mitochondria from trypanosomes, where the mRNAs are extensively modified
MET 1185 by large enzymatic particles that use templates called `guide RNAs.'
Translation on Ribosomes The process of translation occurs on the ribosome, in the cytoplasm or in the cellular organelles, mitochondria and chloroplasts. The ribosome is a complex of a few large rRNA molecules and between 50 and 90 different proteins. The ribosome is made up of two subunits (large and small) with different functions that dissociate from each other at the end of the process. Translation is traditionally divided into three steps: initiation, elongation, and termination. A fourth step, ribosome recycling, also belongs to the process. Soluble protein factors catalyze the process by binding to the ribosome transiently. More than 10 factors participate in eubacterial translation, whereas a considerably larger number participate in eukaryal translation. The mRNA is bound to the small ribosomal subunit. Since the messenger is bound between the subunits, they have to dissociate to be able to bind a tRNA. The decoding site for interactions between the mRNA and the anticodon is part of the A-site for aminoacyltRNA and located on the small subunit. The neighboring P-site is the location of the tRNA with the nascent peptide. The initiation codon is recognized in different ways in eukarya and bacteria. In eubacteria a nucleotide sequence of the mRNA rich in As and Gs is usually found 3±10 nucleotides upstream of the initiator codon. These sequences are complementary to a region of the 30 end of the 16S ribosomal RNAs. Binding of this region of the mRNA to the 30 end of the 16S rRNA is called the Shine±Dalgarno interaction. The initiator tRNA (fMet-tRNA) complexed with initiation factor 2 recognizes the initation codon AUG and binds to the P-site of the small subunit of the ribosome. In eukaryal systems, the binding site on the mRNA for the ribosome is recognized quite differently. The eukaryal mRNAs are usually capped at the terminal 50 position. This means that they have an N7methylated GTP linked by a 50 ±50 pyrophosphate bond to the terminal nucleotide. The cap is situated at a varying distance from the initiation codon, the first AUG. Some of the eukaryal initiation factors interact with the small subunit, while others interact with the capped mRNA. The initiator tRNA binds to the small subunit in complex with the eukaryal initiation factor 2. The small subunit then scans the mRNA for the initiator AUG codon, which will be recognized by the bound initiator tRNA. In both eukarya and bacteria, the large subunit subsequently associates with this complex to initiate protein synthesis.
Reading Frame and Usage of Genetic Code The initiator AUG codon not only defines the start but also the reading frame of a mRNA. Translation proceeds from this starting point in steps of three nucleotides (one codon) by binding a cognate tRNA through base-pairing. The frequent occurrence of termination codons out of frame prevents translation in the wrong frame for more than short stretches. However, there are mRNAs for which the correct translation needs a change of reading frame. This is the case for Escherichia coli termination or release factor-2 (RF2). The readthrough of a stop codon requires a tRNA that would decode a stop (nonsense) codon as a sense codon and incorporate a specific amino acid. Such tRNAs are called suppressor tRNAs. In a few proteins in eubacteria and eukarya, selenocystein (Se-Cys) is required. This is not incorporated by a posttranslational modification as in other cases of nonstandard amino acids. Se-Cys is rather incorporated during translation in response to one of the stop codons. The mechanism for this involves a special tRNA (tRNASec) which reads the stop codon and a specialized version of elongation factor T4.
Further Reading
Spirin AS (1999) Ribosomes. New York: Kluwer. Garrett RA, Douthwaite SR, Liljas A, Matheson AT, Moore PB and Noller HF (eds) (2000) The Ribosome: Structure, Function, Antibiotics and Cellular Interactions. Washington, DC: ASM Press.
See also: Anticodons; Genetic Code; Introns and Exons; Ribosomes; Transcription; Transfer RNA (tRNA)
MET E Gherardi Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.1595
MET is the product of the c-met proto-oncogene and the membrane receptor for the polypeptide growth factor hepatocyte growth factor/scatter factor (HGF/ SF). The MET locus maps to 7q21±q31 and is tightly linked to the cystic fibrosis (CF) locus. MET was discovered as an activated oncogene in a human osteogenic sarcoma cell line treated with N-methyl-N0 nitro-nitroso-guanidine in which activation resulted from a genomic rearrangement involving sequences