Comments for Current Comments http://www.elsevierblogs.com/currentcomments Wed, 30 Jan 2013 13:32:03 +0000 hourly 1 http://wordpress.org/?v=3.2.1 Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by Suparna Sanyal http://www.elsevierblogs.com/currentcomments/?p=686#comment-761 Suparna Sanyal Wed, 30 Jan 2013 13:32:03 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-761 This is an excellent proposal for universal nomenclature of the ribosomal proteins and should be used. I wish that this article was available earlier. Recently, patent reviewers have turned down one of our works on chromosomal engineering of a bacterial r-protein for they mixed it up with a different protein from the eukaryotic ribosome having the same number. Now we can write a solid rebuttal with reference to this work. This will be extremely helpful for non-experts as well. This is an excellent proposal for universal nomenclature of the ribosomal proteins and should be used. I wish that this article was available earlier. Recently, patent reviewers have turned down one of our works on chromosomal engineering of a bacterial r-protein for they mixed it up with a different protein from the eukaryotic ribosome having the same number. Now we can write a solid rebuttal with reference to this work. This will be extremely helpful for non-experts as well.

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by warner http://www.elsevierblogs.com/currentcomments/?p=686#comment-760 warner Mon, 14 Jan 2013 17:13:07 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-760 This is the third time I’ve been through this: previously with McConkey et al , MGG 169, 1, ’79 for mammalian RPs & Mager et al NAR 25, 4872, ’97 for yeast RPs. In each case some of my favorite proteins were renamed, and some of my papers faded even further into obscurity, perhaps justifiably. I note, however, that most of the positive comments so far have come from the bacterial community, whose members have nothing to lose! In any case, I agree that further progress on the ribosome will be aided by some uniform nomenclature, and admit to having torn out more than one hair trying to sort between coli, yeast, and mammals!! Nevertheless, some problems have not been faced. I would guess that there have been more papers published on S6 kinases than on all the E. coli ribosomal proteins put together. Why not call the bacterial protein S6b and leave the eukaryotic nomenclature alone? Do you really want THX to remain, rather than making it S22? Should RACK1 remain or should it be given an ‘empty’ name, such as S23? Whatever is done, I am in strong agreement with Dinman that there must be widespread and readily available information on the cross referencing, both for the students/researchers involved, and particularly for the information services. Has there been any communication with the latter? How have they dealt with the proteasomal nomenclature/literature? As for Remme’s comment, the current S4X, S4Y1, S4Y2 seem more useful, as they give further information. It is critical that you hear from people in the plant world, where there are far more instances of multiple genes for individual RPs. Are they comfortable with the proposed system? Will they participate? This is the third time I’ve been through this: previously with McConkey et al , MGG 169, 1, ’79 for mammalian RPs & Mager et al NAR 25, 4872, ’97 for yeast RPs. In each case some of my favorite proteins were renamed, and some of my papers faded even further into obscurity, perhaps justifiably. I note, however, that most of the positive comments so far have come from the bacterial community, whose members have nothing to lose! In any case, I agree that further progress on the ribosome will be aided by some uniform nomenclature, and admit to having torn out more than one hair trying to sort between coli, yeast, and mammals!! Nevertheless, some problems have not been faced. I would guess that there have been more papers published on S6 kinases than on all the E. coli ribosomal proteins put together. Why not call the bacterial protein S6b and leave the eukaryotic nomenclature alone? Do you really want THX to remain, rather than making it S22? Should RACK1 remain or should it be given an ‘empty’ name, such as S23?
Whatever is done, I am in strong agreement with Dinman that there must be widespread and readily available information on the cross referencing, both for the students/researchers involved, and particularly for the information services. Has there been any communication with the latter? How have they dealt with the proteasomal nomenclature/literature?
As for Remme’s comment, the current S4X, S4Y1, S4Y2 seem more useful, as they give further information. It is critical that you hear from people in the plant world, where there are far more instances of multiple genes for individual RPs. Are they comfortable with the proposed system? Will they participate?

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by jremme http://www.elsevierblogs.com/currentcomments/?p=686#comment-758 jremme Thu, 03 Jan 2013 19:00:50 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-758 This is very good nomenclature for ribosomal proteins. There are several r-potein paralogs that complicate the nomenclature e.g. S4 has three paralogs in human genome. Could it be reasonable to label them with capital letters (S4A, S4B, S4C)? This is very good nomenclature for ribosomal proteins. There are several r-potein paralogs that complicate the nomenclature e.g. S4 has three paralogs in human genome. Could it be reasonable to label them with capital letters (S4A, S4B, S4C)?

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by Dinman http://www.elsevierblogs.com/currentcomments/?p=686#comment-757 Dinman Fri, 21 Dec 2012 19:03:21 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-757 I too agree with Marat & Company's suggestion. My one concern is that future researchers be able to cross reference the new protein names with prior literature. Otherwise, much of what has previously been reported will be unusable for future generations of scientists. This happened in the yeast ribosome field when its nomenclature was unified in 1997. Only the "old guys" knew which protein was which, and a lot of the older literature was rendered useless. For example, the protein currently known as yeast L5 was also called L1 or L11 by different groups, and unless you know whose nomenclature was being applied, the old nomenclature was useless. And now, yeast L5 will be called L18. So, there really is a need to properly annotate the old names and cross reference them with the old literature. I will be an NCBI annotation workshop that will address this very issue in the spring of 2013. I will support this proposal at the meeting. However, what I would like to ask of the ribosome community is information pertaining to "old RP" names, with information concerning what labs used them and publications in which they appeared. That information will enable the people at NCBI to properly cross-reference the new names with the old literature. I too agree with Marat & Company’s suggestion. My one concern is that future researchers be able to cross reference the new protein names with prior literature. Otherwise, much of what has previously been reported will be unusable for future generations of scientists. This happened in the yeast ribosome field when its nomenclature was unified in 1997. Only the “old guys” knew which protein was which, and a lot of the older literature was rendered useless. For example, the protein currently known as yeast L5 was also called L1 or L11 by different groups, and unless you know whose nomenclature was being applied, the old nomenclature was useless. And now, yeast L5 will be called L18. So, there really is a need to properly annotate the old names and cross reference them with the old literature. I will be an NCBI annotation workshop that will address this very issue in the spring of 2013. I will support this proposal at the meeting. However, what I would like to ask of the ribosome community is information pertaining to “old RP” names, with information concerning what labs used them and publications in which they appeared. That information will enable the people at NCBI to properly cross-reference the new names with the old literature.

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by Bhanu Jena http://www.elsevierblogs.com/currentcomments/?p=686#comment-756 Bhanu Jena Thu, 20 Dec 2012 17:35:55 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-756 The article on “ribosomal protein nomenclature” is a timely and important issue not only for investigators already invested in ribosomal research but also for fellows and students whose current or future research interests intersect with the ribosome. Imagine a student attempting to navigate through the complexity of multiple identities for any ribosomal protein that lacks a commonly agreed upon nomenclature; where and how do they productively initiate a search. Unifying the nomenclature for ribosomal proteins will serve as the organizational foundation for the general nomenclature approach of proteins in other subcellular organelles or supramolecular structures within cells such as the nuclear pore (Annu. Rev. Biochem. 2011, 80:613-643) or the porosome complex (Exp. Biol. Med. 2012, 237:748-757; J. Proteomics 2012, 75:3952-3962), irrespective of the organism or cell where it was first identified. The article on “ribosomal protein nomenclature” is a timely and important issue not only for investigators already invested in ribosomal research but also for fellows and students whose current or future research interests intersect with the ribosome. Imagine a student attempting to navigate through the complexity of multiple identities for any ribosomal protein that lacks a commonly agreed upon nomenclature; where and how do they productively initiate a search. Unifying the nomenclature for ribosomal proteins will serve as the organizational foundation for the general nomenclature approach of proteins in other subcellular organelles or supramolecular structures within cells such as the nuclear pore (Annu. Rev. Biochem. 2011, 80:613-643) or the porosome complex (Exp. Biol. Med. 2012, 237:748-757; J. Proteomics 2012, 75:3952-3962), irrespective of the organism or cell where it was first identified.

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by Akira Wada http://www.elsevierblogs.com/currentcomments/?p=686#comment-754 Akira Wada Wed, 19 Dec 2012 15:17:27 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-754 In 1987 I discovered E.coli ribosomal proteins A (L35) and B (L36) by RFHR 2D PAGE, and named the genes for L35 and L36 rpmI and rpmJ, respectively ("Primary structures of and genes for new ribosomal proteins A and B in Escherichia coli" Akira Wada and Tomoyuki Sako (1987) J.Biochem. 101, 817-820). I agree with the proposal for nomenclature for ribosomal proteins AKIRA WADA, Ph.D. In 1987 I discovered E.coli ribosomal proteins A (L35) and B (L36) by RFHR 2D PAGE, and named the genes for L35 and L36 rpmI and rpmJ, respectively (“Primary structures of and genes for new ribosomal proteins A and B in Escherichia coli” Akira Wada and Tomoyuki Sako (1987) J.Biochem. 101, 817-820).

I agree with the proposal for nomenclature for ribosomal proteins

AKIRA WADA, Ph.D.

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by HarryNoller http://www.elsevierblogs.com/currentcomments/?p=686#comment-753 HarryNoller Mon, 17 Dec 2012 21:30:38 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-753 OK - I misunderstood the Tables. Having been straightened out by Anders, I heartily agree with the proposal. Please disregard my previous rant. -Harry OK – I misunderstood the Tables. Having been straightened out by Anders,
I heartily agree with the proposal. Please disregard my previous rant.

-Harry

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by HarryNoller http://www.elsevierblogs.com/currentcomments/?p=686#comment-752 HarryNoller Mon, 17 Dec 2012 18:57:49 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-752 I am disappointed that the proposed system uses "historical" names for the euk and archaeal proteins, instead of the functional/structural ones. Why use different names for proteins S4, S7, S9, S10 etc just because they come from different organisms? We now know for the first time which proteins are actually equivalent between bacteria, archaea and eukaryotes. But this rare opportunity to standardize things is about to be wasted. Just imagine: when someone says "S5", everyone could know what they were talking about! But in this proposed system (see Table I), one person might be thinking "S2" or the other could be thinking "S7". There are three names for S5 instead of one, even though we know which protein is which. To avoid this confusion, you will first have to ask "Which organism are you talking about?" You will then have to pull out Table 1 or Table 2 and look up the bacterial, archaeal or euk equivalent. Few researchers, if any, will have memorized these tables. It is easy to see that this will create an artificial barrier between people working on bacterial and eukaryotic ribosomes (and between their respective literatures.) The only purpose for nomenclature systems is to clarify and standardize. Otherwise, we will just continue calling things by our pet names, and having no idea what each other is talking about. The sticking point, I am guessing, is not to offend euk people who are used to calling their proteins by different names (although Susan Liebman was calling the yeast equivalents of S4 and S5 by their coli names over 20 years ago already - see for example MCB 1990, 10:6544). By far the most work has been done on the bacterial (mainly E.coli) system. An enormous structure-function-genetic literature exists for this system, and we have all struggled to keep the nomenclature as simple as possible. Why not ask the euk people to just bite the bullet and accept the fact that the protein called S5 was first characterized in E. coli (as were all the other bacterial proteins)? Just because its euk equivalent has been named something different (S2), because no one noticed its homology to bacterial S5 at the time it was sequenced, is a crazy reason to rename it. I have already had numerous discussions in which two of us were talking about completely different proteins without realizing it. Naming things for historical or political reasons is counterproductive. Why not name all the equivalent proteins by the coli names, and give new names to the proteins that are actually different in euks and archaes? I am disappointed that the proposed system uses “historical” names for the euk and archaeal proteins, instead of the functional/structural ones. Why use different names for proteins S4, S7, S9, S10 etc just because they come from different organisms? We now know for the first time which proteins are actually equivalent between bacteria, archaea and eukaryotes. But this rare opportunity to standardize things is about to be wasted.
Just imagine: when someone says “S5″, everyone could know what they were talking about! But in this proposed system (see Table I), one person might be thinking “S2″ or the other could be thinking “S7″. There are three names for S5 instead of one, even though we know which protein is which. To avoid this confusion, you will first have to ask “Which organism are you talking about?” You will then have to pull out Table 1 or Table 2 and look up the bacterial, archaeal or euk equivalent. Few researchers, if any, will have memorized these tables. It is easy to see that this will create an artificial barrier between people working on bacterial and eukaryotic ribosomes (and between their respective literatures.) The only purpose for nomenclature systems is to clarify and standardize. Otherwise, we will just continue calling things by our pet names, and having no idea what each other is talking about.
The sticking point, I am guessing, is not to offend euk people who are used to calling their proteins by different names (although Susan Liebman was calling the yeast equivalents of S4 and S5 by their coli names over 20 years ago already – see for example MCB 1990, 10:6544). By far the most work has been done on the bacterial (mainly E.coli) system. An enormous structure-function-genetic literature exists for this system, and we have all struggled to keep the nomenclature as simple as possible. Why not ask the euk people to just bite the bullet and accept the fact that the protein called S5 was first characterized in E. coli (as were all the other bacterial proteins)? Just because its euk equivalent has been named something different (S2), because no one noticed its homology to bacterial S5 at the time it was sequenced, is a crazy reason to rename it. I have already had numerous discussions in which two of us were talking about completely different proteins without realizing it. Naming things for historical or political reasons is counterproductive.
Why not name all the equivalent proteins by the coli names, and give new names to the proteins that are actually different in euks and archaes?

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by HarryNoller http://www.elsevierblogs.com/currentcomments/?p=686#comment-751 HarryNoller Mon, 17 Dec 2012 18:10:03 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-751 This is an excellent proposal that should be implemented immediately and enforced by all journals. The ribosome is far too complicated to have multiple names for the same thing. This is an excellent proposal that should be implemented immediately and enforced by all journals. The ribosome is far too complicated to have multiple names for the same thing.

]]> Comment on A suggestion for a uniform set of names for ribosomal proteins from eukaryotic species by Knud http://www.elsevierblogs.com/currentcomments/?p=686#comment-750 Knud Mon, 17 Dec 2012 17:35:08 +0000 http://www.elsevierblogs.com/currentcomments/?p=686#comment-750 Dear colleagues, We all should accept and use the new nomenclature for ribosomal proteins, which will finish the current Babylonic chaos concerning the names of the ribosomal proteins. It will be important and extremely helpful to understand easier and better the results published for ribosomal proteins derived from different species and domains. KHN Dear colleagues,

We all should accept and use the new nomenclature for ribosomal proteins, which will finish the current Babylonic chaos concerning the names of the ribosomal proteins. It will be important and extremely helpful to understand easier and better the results published for ribosomal proteins derived from different species and domains.
KHN

]]>