[ccp4bb] Philosophical question
Dear Theresa, a nicely written explanation from Wikipedia : The Central dogma of molecular biologyhttp://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology describes the process of translationhttp://en.wikipedia.org/wiki/Translation_(biology) of a genehttp://en.wikipedia.org/wiki/Gene to a proteinhttp://en.wikipedia.org/wiki/Protein. Specific sequences of DNAhttp://en.wikipedia.org/wiki/DNA act as a template to synthesize mRNA. The start codonhttp://en.wikipedia.org/wiki/Codon is the first codon of a messenger RNAhttp://en.wikipedia.org/wiki/Messenger_RNA (mRNA) transcript translated by a ribosomehttp://en.wikipedia.org/wiki/Ribosome. The start codon always codes for methioninehttp://en.wikipedia.org/wiki/Methionine in eukaryoteshttp://en.wikipedia.org/wiki/Eukaryote and a modified Met (fMet) in prokaryoteshttp://en.wikipedia.org/wiki/Prokaryotes. The most common start codon is AUG. The start codon is almost always preceded by an untranslated region 5' UTRhttp://en.wikipedia.org/wiki/5%27_UTR. In prokaryoteshttp://en.wikipedia.org/wiki/Prokaryotes this includes the ribosome binding site. Alternate start codons (non ATG) are very rare in eukaryotic genomes. Mitochondrial genomes and prokaryotes use alternate start codons more significantly (mainly GUG and UUG). For example E. colihttp://en.wikipedia.org/wiki/E._coli uses 83% ATG (AUG) (3542/4284), 14% (612) GTG (GUG), 3% (103) TTG (UUG) [1]http://en.wikipedia.org/wiki/Start_codon#cite_note-1 and one or two others (e.g., an ATT and possibly a CTG).[2]http://en.wikipedia.org/wiki/Start_codon#cite_note-Sequence_of_a_1.26-kb_DNA_fragment_containing_the_structural_gene_for_E.coli_initiation_factor_IF3:_presence_of_an_AUU_initiator_codon-2[3]http://en.wikipedia.org/wiki/Start_codon#cite_note-The_Escherichia_coli_heat_shock_gene_htpY:_mutational_analysis.2C_cloning.2C_sequencing.2C_and_transcriptional_regulation.-3 Bioinformatics programs usually allow for alternate start codons when searching for protein coding genes. Note that these alternate start codons are still translated as Met when they are at the start of a protein (even if the codon encodes a different amino acid otherwise). This is because a separate transfer RNAhttp://en.wikipedia.org/wiki/Transfer_RNA (tRNA) is used for initiation. Well-known coding regions that do not have ATG initiation codons are those of lacI (GTG)[4]http://en.wikipedia.org/wiki/Start_codon#cite_note-4[5]http://en.wikipedia.org/wiki/Start_codon#cite_note-Sequence_of_the_lacI_gene.-5 and lacA (TTG)[6]http://en.wikipedia.org/wiki/Start_codon#cite_note-6 in the E. colihttp://en.wikipedia.org/wiki/E._coli lac operonhttp://en.wikipedia.org/wiki/Lac_operon. Hope this helps, Anat. = Anat Bashan , Ph.D Tel:972-8-9344289 @The Ribosome Group The Weizmann Institute of Science Fax:972-8-9344154 The Department of Structural BiologyMobile:972-52-3347229 Rehovot76100 e-mail: anat.bas...@weizmann.ac.ilmailto:anat.bas...@weizmann.ac.il Israel = Dear all I have a somewhat philosophical question. Why do all protein sequences start with a methionine (not referring to mature/processed form)? What is so special about methionine and cannot be replaced by other amino acids? Second, how does the ribosome know the first start codon is for methionine when the codon is not AUG? This is about the alternative start codons like GUG. Thank you. Theresa
Re: [ccp4bb] Philosophical question
Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher
Re: [ccp4bb] Philosophical question
Opher Gileadi wrote: Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher Yes, but why methionine? Half the time it has to be removed by N-terminal peptidase to give a small first residue, or by leader sequence processing. Why use a big expensive amino acid instead of choosing one of the glycine codons? Is there an obvious reason, or just it had to be something, and Met happened to get selected? And why sometimes alternate start codons can be used? and why doesn't initiation occur also at methionines in the middle of proteins? I'm guessing it has to do with 5' untranslated region and ribosome binding sites. So could the start codon actually be anything you want, provided there is a strong ribosome binding site there? Just being philosophical, and not afraid to display my ignorance, eab
Re: [ccp4bb] Philosophical question
Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident--or is there some more beautiful reason? One might argue that since basically all organisms share the convention (are there exceptions, even?), that it must be the best of all possible conventions. I have often wondered whether maybe this particular convention allows for the most effective pathways between proteins of significant function, e.g., through the fewest mutations perhaps? One certainly cannot maintain that every possible protein sequence has been made at some time or another in the history of the biological world (go quantitate!) so there must be a way to ensure that mostly the best ones got made. On the other hand, since many organisms share DNA, maybe they had to agree on a system (I think this is the dogma?). Was there a United Organisms convention at some point, reminiscent of Les Immortels of the French language or POSIX or something, to ensure compliance? What was the penalty for non-compliance? Anyway, I like the question about the methionines, Jacob On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry ber...@upstate.edu wrote: Opher Gileadi wrote: Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher Yes, but why methionine? Half the time it has to be removed by N-terminal peptidase to give a small first residue, or by leader sequence processing. Why use a big expensive amino acid instead of choosing one of the glycine codons? Is there an obvious reason, or just it had to be something, and Met happened to get selected? And why sometimes alternate start codons can be used? and why doesn't initiation occur also at methionines in the middle of proteins? I'm guessing it has to do with 5' untranslated region and ribosome binding sites. So could the start codon actually be anything you want, provided there is a strong ribosome binding site there? Just being philosophical, and not afraid to display my ignorance, eab -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Philosophical question
Just search for genetic code evolution in pubmed and you will find tons of literature on it. The main driving force appears to have been to minimize physico-chemical changes in amino acid properties for frequent mutations. In other words, if you take mutation rates at the single-nucleotide level and use it to predict, via a codon table, the rates of amino acid mutations you will find that it correlates strongly with the observed amino acid rates. Bart On Tue, Mar 19, 2013 at 8:34 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident--or is there some more beautiful reason? One might argue that since basically all organisms share the convention (are there exceptions, even?), that it must be the best of all possible conventions. I have often wondered whether maybe this particular convention allows for the most effective pathways between proteins of significant function, e.g., through the fewest mutations perhaps? One certainly cannot maintain that every possible protein sequence has been made at some time or another in the history of the biological world (go quantitate!) so there must be a way to ensure that mostly the best ones got made. On the other hand, since many organisms share DNA, maybe they had to agree on a system (I think this is the dogma?). Was there a United Organisms convention at some point, reminiscent of Les Immortels of the French language or POSIX or something, to ensure compliance? What was the penalty for non-compliance? Anyway, I like the question about the methionines, Jacob On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry ber...@upstate.eduwrote: Opher Gileadi wrote: Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher Yes, but why methionine? Half the time it has to be removed by N-terminal peptidase to give a small first residue, or by leader sequence processing. Why use a big expensive amino acid instead of choosing one of the glycine codons? Is there an obvious reason, or just it had to be something, and Met happened to get selected? And why sometimes alternate start codons can be used? and why doesn't initiation occur also at methionines in the middle of proteins? I'm guessing it has to do with 5' untranslated region and ribosome binding sites. So could the start codon actually be anything you want, provided there is a strong ribosome binding site there? Just being philosophical, and not afraid to display my ignorance, eab -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Bart Hazes Associate Professor Dept. of Medical Microbiology Immunology University of Alberta
Re: [ccp4bb] Philosophical question
On 03/19/13 10:34, Jacob Keller wrote: Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident- QWERTY didn't just happen. It was designed. Don't kids today know how to use Wikipedia or Google? http://en.wikipedia.org/wiki/QWERTY Still used to this day, the QWERTY layout was devised and created in the early 1870s by Christopher Latham Sholes http://en.wikipedia.org/wiki/Christopher_Latham_Sholes, a newspaper http://en.wikipedia.org/wiki/Newspaper editor and printer who lived in Milwaukee http://en.wikipedia.org/wiki/Milwaukee... The solution was to place commonly used letter-pairs (like th or st) so that their typebars were not neighboring, avoiding jams. Contrary to popular belief, the QWERTY layout was not designed to slow the typist down,^[5] http://en.wikipedia.org/wiki/QWERTY#cite_note-5 , but rather to speed up typing by preventing jams.^http://en.wikipedia.org/wiki/QWERTY#cite_note-why-4 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Philosophical question
I never said QWERTY just happened-- I said it was an accident of history, based on the belief that some people nowadays have stopped using manual typewriters, and they nevertheless still use the QWERTY keyboard. I.e., because of the way history unfolded, we are now locked into using a non-ideal keyboard configuration. I am dubious whether this model, however, would apply to the codon conventions. Jacob On Tue, Mar 19, 2013 at 10:44 AM, David Schuller dj...@cornell.edu wrote: On 03/19/13 10:34, Jacob Keller wrote: Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident- QWERTY didn't just happen. It was designed. Don't kids today know how to use Wikipedia or Google? http://en.wikipedia.org/wiki/QWERTY Still used to this day, the QWERTY layout was devised and created in the early 1870s by Christopher Latham Sholeshttp://en.wikipedia.org/wiki/Christopher_Latham_Sholes, a newspaper http://en.wikipedia.org/wiki/Newspaper editor and printer who lived in Milwaukee http://en.wikipedia.org/wiki/Milwaukee... The solution was to place commonly used letter-pairs (like th or st) so that their typebars were not neighboring, avoiding jams. Contrary to popular belief, the QWERTY layout was not designed to slow the typist down, [5] http://en.wikipedia.org/wiki/QWERTY#cite_note-5, but rather to speed up typing by preventing jams.http://en.wikipedia.org/wiki/QWERTY#cite_note-why-4 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Philosophical question
On Tue, Mar 19, 2013 at 9:34 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: One might argue that since basically all organisms share the convention (are there exceptions, even?), that it must be the best of all possible conventions. There are actually lots of exceptions. For example the UGA stop codon in E. coli codes for Trp in Mycoplasma species. A fairly comprehensive list of the codon variations as annotated by the NCBI can be found here http://www.bioinformatics.org/JaMBW/2/3/TranslationTables.html#SG4 Cheers, Katherine
Re: [ccp4bb] Philosophical question
I believe that the reason all organisms share the convention (more or less) is that it dates back to LUCA - the Last Universal Common Ancestor of all extant life. LUCA must have had the basic transcription and translation machinery that we now see somewhat divergently-evolved versions of in all cells. This does not answer why that particular convention was chosen, but it does count against the idea that it is the best possible system, or indeed should continue to be selected for (except that mutations to this machinery tend to be very much deleterious). -- David On 19 March 2013 14:34, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident--or is there some more beautiful reason? One might argue that since basically all organisms share the convention (are there exceptions, even?), that it must be the best of all possible conventions. I have often wondered whether maybe this particular convention allows for the most effective pathways between proteins of significant function, e.g., through the fewest mutations perhaps? One certainly cannot maintain that every possible protein sequence has been made at some time or another in the history of the biological world (go quantitate!) so there must be a way to ensure that mostly the best ones got made. On the other hand, since many organisms share DNA, maybe they had to agree on a system (I think this is the dogma?). Was there a United Organisms convention at some point, reminiscent of Les Immortels of the French language or POSIX or something, to ensure compliance? What was the penalty for non-compliance? Anyway, I like the question about the methionines, Jacob On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry ber...@upstate.eduwrote: Opher Gileadi wrote: Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher Yes, but why methionine? Half the time it has to be removed by N-terminal peptidase to give a small first residue, or by leader sequence processing. Why use a big expensive amino acid instead of choosing one of the glycine codons? Is there an obvious reason, or just it had to be something, and Met happened to get selected? And why sometimes alternate start codons can be used? and why doesn't initiation occur also at methionines in the middle of proteins? I'm guessing it has to do with 5' untranslated region and ribosome binding sites. So could the start codon actually be anything you want, provided there is a strong ribosome binding site there? Just being philosophical, and not afraid to display my ignorance, eab -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Philosophical question
I don't understand this argument, as it would apply equally to all features of the theoretical LUCA (protein and DNA sequences, etc). To make it logically sound, I think you have either to include some kind of super-high boundary to getting to other possible conventions (you probably imply this) or, as I have suggested, it may be a particularly good, if not the best, solution (a global minimum, one might say). The first hypothesis is similar to the QWERTY keyboard, which is cemented in place by many factors, whereas the second is more survival of the fittest. It should perhaps be noted parenthetically that prima facie the accident of history QWERTY hypothesis is at variance with radical Darwinism. JPK On Tue, Mar 19, 2013 at 1:56 PM, David Waterman dgwater...@gmail.comwrote: I believe that the reason all organisms share the convention (more or less) is that it dates back to LUCA - the Last Universal Common Ancestor of all extant life. LUCA must have had the basic transcription and translation machinery that we now see somewhat divergently-evolved versions of in all cells. This does not answer why that particular convention was chosen, but it does count against the idea that it is the best possible system, or indeed should continue to be selected for (except that mutations to this machinery tend to be very much deleterious). -- David On 19 March 2013 14:34, Jacob Keller j-kell...@fsm.northwestern.eduwrote: Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident--or is there some more beautiful reason? One might argue that since basically all organisms share the convention (are there exceptions, even?), that it must be the best of all possible conventions. I have often wondered whether maybe this particular convention allows for the most effective pathways between proteins of significant function, e.g., through the fewest mutations perhaps? One certainly cannot maintain that every possible protein sequence has been made at some time or another in the history of the biological world (go quantitate!) so there must be a way to ensure that mostly the best ones got made. On the other hand, since many organisms share DNA, maybe they had to agree on a system (I think this is the dogma?). Was there a United Organisms convention at some point, reminiscent of Les Immortels of the French language or POSIX or something, to ensure compliance? What was the penalty for non-compliance? Anyway, I like the question about the methionines, Jacob On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry ber...@upstate.eduwrote: Opher Gileadi wrote: Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher Yes, but why methionine? Half the time it has to be removed by N-terminal peptidase to give a small first residue, or by leader sequence processing. Why use a big expensive amino acid instead of choosing one of the glycine codons? Is there an obvious reason, or just it had to be something, and Met happened to get selected? And why sometimes alternate start codons can be used? and why doesn't initiation occur also at methionines in the middle of proteins? I'm guessing it has to do with 5' untranslated region and ribosome binding sites. So could the start codon actually be anything you want, provided there is a strong ribosome binding site there? Just being philosophical, and not afraid to display my ignorance, eab -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Philosophical question
why doesn't initiation occur also at methionines in the middle of proteins? It can and does. I can show you expression gels where I make full-length protein and a fragment from an internal initiation. Why use a big expensive amino acid instead of choosing one of the glycine codons? I can't quickly track anything down in the literature to back this up, but expensive could be part of it. The cell doesn't want to start translation if there isn't ample resources to finish the job. Perhaps Met concentration is a proxy for anabolic potential of the cell? Or at least was primordially and QWERTY'd in? /wild speculation Shane Caldwell McGill University On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry ber...@upstate.edu wrote: Opher Gileadi wrote: Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher Yes, but why methionine? Half the time it has to be removed by N-terminal peptidase to give a small first residue, or by leader sequence processing. Why use a big expensive amino acid instead of choosing one of the glycine codons? Is there an obvious reason, or just it had to be something, and Met happened to get selected? And why sometimes alternate start codons can be used? and why doesn't initiation occur also at methionines in the middle of proteins? I'm guessing it has to do with 5' untranslated region and ribosome binding sites. So could the start codon actually be anything you want, provided there is a strong ribosome binding site there? Just being philosophical, and not afraid to display my ignorance, eab
Re: [ccp4bb] Philosophical question
On 03/19/2013 02:41 PM, Jacob Keller wrote: I don't understand this argument, as it would apply equally to all features of the theoretical LUCA No it won't. Different features would have different tolerance levels to modifications. Philosophically, one is wrong to expect that living organisms will evolve in a fashion that we find optimal. Whenever I feel that a protein behaves in a way I find stupid, I simply say giraffe laryngeal nerve and all comes back to normal.
Re: [ccp4bb] Philosophical question
I don't understand this argument, as it would apply equally to all features of the theoretical LUCA No it won't. Different features would have different tolerance levels to modifications. Yes, this tolerance is the second (hidden or implicit) principle I referred to. So you'd have to explain why the codon convention is so intolerant/invariant relative to the other features--it seems to me that either it is at an optimum or there is some big barrier holding it in place. And you'd have to explain this without invoking interchange of DNA, viruses, etc, as we're talking about a LUCA here, right? And you'll have to make sure that whatever reason you invoke cannot be applied to other features of this LUCA which are indeed seen to be variable. JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***
Re: [ccp4bb] Philosophical question
It is so intolerant to change because reassigning a codon to a different amino acid type or stop codon affects thousands of proteins that use that codon simultaneously. The probably that none of those mutations are deleterious is extremely small. Genetic code changes are more common in the mitochondrial code. First of all the mitochondrial genome is much smaller, ~16kb for vertebrates. Moreover, in cases I have looked at the change in codon use seems to happen when first there is a case of extreme bias against using a codon. When a codon is (almost) not used at all it can be re-purposed without affecting any proteins. Bart On Tue, Mar 19, 2013 at 2:05 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I don't understand this argument, as it would apply equally to all features of the theoretical LUCA No it won't. Different features would have different tolerance levels to modifications. Yes, this tolerance is the second (hidden or implicit) principle I referred to. So you'd have to explain why the codon convention is so intolerant/invariant relative to the other features--it seems to me that either it is at an optimum or there is some big barrier holding it in place. And you'd have to explain this without invoking interchange of DNA, viruses, etc, as we're talking about a LUCA here, right? And you'll have to make sure that whatever reason you invoke cannot be applied to other features of this LUCA which are indeed seen to be variable. JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Bart Hazes Associate Professor Dept. of Medical Microbiology Immunology University of Alberta
Re: [ccp4bb] Philosophical question
Why use a big expensive amino acid instead of choosing one of the glycine codons? I can't quickly track anything down in the literature to back this up, but expensive could be part of it. The cell doesn't want to start translation if there isn't ample resources to finish the job. Perhaps Met concentration is a proxy for anabolic potential of the cell? Or at least was primordially and QWERTY'd in? That makes sense. Also, It occurred to me after posting that the Met is not necessarily wasted if it gets cleaved off by N-peptidase. It can get loaded onto another tRNA and go through the cycle again. presumably the cost in ATP for loading Met-tRNA and gly-tRNA is the same. Maybe Met makes a better handle for some step in initiation. Shane Caldwell wrote: why doesn't initiation occur also at methionines in the middle of proteins? It can and does. I can show you expression gels where I make full-length protein and a fragment from an internal initiation. Why use a big expensive amino acid instead of choosing one of the glycine codons? I can't quickly track anything down in the literature to back this up, but expensive could be part of it. The cell doesn't want to start translation if there isn't ample resources to finish the job. Perhaps Met concentration is a proxy for anabolic potential of the cell? Or at least was primordially and QWERTY'd in? /wild speculation Shane Caldwell McGill University On Tue, Mar 19, 2013 at 9:46 AM, Edward A. Berry ber...@upstate.edu mailto:ber...@upstate.edu wrote: Opher Gileadi wrote: Hi Theresa, To add to Anat's comments: Although the AUG codon for the first methionine and all other methionines in a protein coding sequence look the same, they are read in a very different way by the ribosomal machinery. The first AUG is recognized by the initiation complex, which includes the separate small ribosomal subunit (40s), a special tRNA-methionine, and initiation factors (proteins) including eIF2. This leads to assembly of a complete ribosome and initiation of protein synthesis. Subsequently, in the process of elongation, AUG codons are read by a different tRNA, which is brought to the 80s ribosome bound to a protein called elongation factor 1a. This is an oversimplification, of course, but the point is that the initiation codon (=the first amino acid to be incorporated to the protein) is read by a special tRNA, hence the universal use of methionine. Opher Yes, but why methionine? Half the time it has to be removed by N-terminal peptidase to give a small first residue, or by leader sequence processing. Why use a big expensive amino acid instead of choosing one of the glycine codons? Is there an obvious reason, or just it had to be something, and Met happened to get selected? And why sometimes alternate start codons can be used? and why doesn't initiation occur also at methionines in the middle of proteins? I'm guessing it has to do with 5' untranslated region and ribosome binding sites. So could the start codon actually be anything you want, provided there is a strong ribosome binding site there? Just being philosophical, and not afraid to display my ignorance, eab
Re: [ccp4bb] Philosophical question
You may want to read: Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding Nature structural molecular biology VOLUME 20 NUMBER 2 FEBRUARY 2013 237 Here they suggest that the codon bias is such it allows translation to pause and folding of the polypeptide. Most proteins probably do not have a problem folding so it does not matter which codon is used. Dan It is so intolerant to change because reassigning a codon to a different amino acid type or stop codon affects thousands of proteins that use that codon simultaneously. The probably that none of those mutations are deleterious is extremely small. Genetic code changes are more common in the mitochondrial code. First of all the mitochondrial genome is much smaller, ~16kb for vertebrates. Moreover, in cases I have looked at the change in codon use seems to happen when first there is a case of extreme bias against using a codon. When a codon is (almost) not used at all it can be re-purposed without affecting any proteins. Bart On Tue, Mar 19, 2013 at 2:05 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: I don't understand this argument, as it would apply equally to all features of the theoretical LUCA No it won't. Different features would have different tolerance levels to modifications. Yes, this tolerance is the second (hidden or implicit) principle I referred to. So you'd have to explain why the codon convention is so intolerant/invariant relative to the other features--it seems to me that either it is at an optimum or there is some big barrier holding it in place. And you'd have to explain this without invoking interchange of DNA, viruses, etc, as we're talking about a LUCA here, right? And you'll have to make sure that whatever reason you invoke cannot be applied to other features of this LUCA which are indeed seen to be variable. JPK
Re: [ccp4bb] Philosophical question
Jacob, So you'd have to explain why the codon convention is so intolerant/invariant relative to the other features--it seems to me that either it is at an optimum or there is some big barrier holding it in place. Because altering codon convention will result in massive translation errors. However the original question refers to start codon and its relation to methionine. Notice that AUG is the *only* codon for methionine. If you change amino acid specificity of the methionine tRNA synthetase, you'd replace every methionine in every protein. It is very unlikely that an organism other than one with a very small genome can survive that. Given high fidelity required of tRNA synthetases, changing their specificity is also not easy. Most mutations are likely to incapacitate the enzyme rather than switch its specificity, resulting in organism that is unable to develop (due to stalled translation), let alone survive. As for the optimization part - I am also not sure what significant benefit you expect from replacing starting methionine with a different amino acid. It is mostly removed anyway. Why that is? My (uneducated) guess is that it is rarely structural and there is benefit in recycling it. Cheers, Ed.
Re: [ccp4bb] Philosophical question
On 03/19/13 14:41, Jacob Keller wrote: I don't understand this argument, as it would apply equally to all features of the theoretical LUCA (protein and DNA sequences, etc). To make it logically sound, I think you have either to include some kind of super-high boundary to getting to other possible conventions (you probably imply this) or, as I have suggested, it may be a particularly good, if not the best, solution (a global minimum, one might say). The first hypothesis is similar to the QWERTY keyboard, which is cemented in place by many factors, whereas the second is more survival of the fittest. It would not be a safe idea to assume that LUCA was a single cell with a single chromosome (i.e. like a modern bacterium.) It would also not be safe to assume that viruses and horizontal gene transfer were not around at that time. As I mentioned privately, I think the relevant slogan would be winner take all rather than survival of the fittest. Another possible explanation for having a recognition tag at the beginning of each transcribed gene: to distinguish between host and virus. This does not imply that Met has any specific advantage over any any other tag which might have been chosen. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Philosophical question
Dear all I have a somewhat philosophical question. Why do all protein sequences start with a methionine (not referring to mature/processed form)? What is so special about methionine and cannot be replaced by other amino acids? Second, how does the ribosome know the first start codon is for methionine when the codon is not AUG? This is about the alternative start codons like GUG. Thank you. Theresa
