Talk:Archaea/Archive 1

Confusing
This is very confusing In the section "Comparison of Archaean, Bacterial and Eukaryotic cells". The last paragraph, second sentence reads "For instance, the in most archaea they are formed by surface-layer proteins or an S-layer". Comparing it with earlier revisions it is referring to cell walls, however, I am not qualified to make such a change to the text. Please check revisions "02:56, 12 July 2007 Zharradan.angelfire" and "17:29, 15 July 2007 Bendzh". (85.197.195.138 10:19, 21 August 2007 (UTC))

Extreme environments
Some of Archea also live in less extreme environments. Could somebody check it.


 * http://www.ucmp.berkeley.edu/archaea/archaea.html
 * http://www.icm.uu.se/mikrobio/research/archaea/archaea.html

indicate that, although they can be extremophiles, they aren't necessarily always extremophiles. I've made what I hope is an appropriate change to the wording.

Also what is meant by "are very old"? Compared to what? Is the intended sense of this that their phylogenetic divergence is ancient?

--dja

There's nothing that would suggest that they are any older than Bacteria. They're of course much older than Eucaryota, but Bacterias are also. (Unless I missed some recent findings about Archea) ::All organisms are equally "old". You mean the time of divergence between the groups. DGG 04:41, 17 September 2006 (UTC)

ARNr link
Is the link to ARNr just some remnant rubbish, or does such a thing exist? charlieF 19:18 Mar 18, 2003 (UTC)


 * ARNr is a valid term (try a Google search). It means "ARN ribosome"; however, I have no idea, what it is, but somebody who knows may add this article one day. -- Cordyph 19:23 Mar 18, 2003 (UTC)


 * ARNr is the french version of rRNA or ribosomal RNA. WormRunner 07:37, 8 Dec 2003 (UTC)

Changed paragraph
Someone changed a paragraph to read:

''Althoughnlkn the identity of the Archaea is generally accepted, other biologists have questioned Woese's hypotheses about them. Subsequent studies have confirmed that while they are similar in numerous structural and metabolic features to Bacteria, the Archaeal versions of the two most central processes of molecular biology, transcription and translation, are extremely similar to the eukaryotic versions. While trees of some genes suggest that the Archaea are either closely related or ancestral to the eukaryotes, others do not. The discovery of apparently Archaeal-derived genes in bacteria such as Thermotoga also makes the relationship between eukaryotes and Archaea difficult to determine. The key question that all cell evolution theories must address is why Eukaryotes and Archaea share a similar information processing system to the exclusion of the Bacteria even though most eukaryotic genes are not particularly close to their Archaeal versions.''

Perhaps some of the material from this should be kept, but as it stands I don't think it makes sense. Most notably, differences between archaeans and eukaryotes have always been well-known, but by themselves don't imply that they didn't diverge from a common ancestor. As such, this isn't a "key question," just something that strongly supports the notion that they are close relatives, which most biologists seem to accept.

In light of this, I wonder if saying that their transcription and translation are extremely similar really means that, or just means that they share common traits, making them extremely similar compared to what you would expect assuming they aren't related. I suspect the latter, since I know archaean ribosomes are still essentially prokaryotic in form. However, I don't really know, and it would be nice if someone more familiar with these things could confirm. For in-depth material like this, providing references would be very helpful.

This version removed the possibility that archaeans and eukaryotes arose from within eubacteria. This isn't that common an idea among molecular biologists, since it contradicts rRNA trees, but these are now known to misplace highly divergent groups and there are some other genes that support the notion. At the very least it's important to mention, since it's at the basis of most criticisms of the three-domain system.

Does anyone else have any more information about these things, or suggestions of how to rework the article, keeping it balanced between the different evolutionary hypotheses? Josh 00:46, 14 Oct 2004 (UTC)

This has nothing to do with balance -- the entire *reason* Archaea are interesting is that their information processing systems are Eukaryotic like. Everybody agrees on this, even arch-rivals like Carl Woese and Jim Lake, who disagree on nearly everything. There are basically two ways to explain this -- either Archaea and Eukaryotes are specifically related (depending on rooting, Archaea may be ancestral), as suggested by rRNA and other (mostly other information-system related genes) or that the nucleus of Eukaryotes was derived from a member of the Archaea, and the cytoplasm came from somewhere else (see Jim Lake's recent "Ring of Life" paper for a recent version of this theory).

Carl's "progenote theory", dealing with events near the origin of life, while an interesting theory, is not particularly relevant or supported or refuted by any of this, making your comments relating to it rather confusing -- certainly the progenote, if indeed one existed, wasn't around when eukaryotes arose (quite a recent development).

In terms of transcription, rather than using the "sigma-factor" system discovered in E.coli and once assumed to be the model of "prokaryotic" transcription, Archaea have TATA-binding proteins and TFIIB just like Eukaryotes. Similarly, Archaea have have a translation system using the eukaryotic method initiation and elongation factors -- and is even poisoned by diptheria toxin, which otherwise only affects eukaryotic translation.

The reason why I edited the article -- while the debate rages on about the relation between Archaea and other organisms, unless you stress these key differences betwen Archaea and Bacteria, it isn't at all clear why people study them -- you make it sound as if they are just ordinary bacteria with odd cell walls -- it would be like writing an article about Orlando, Florida and not mentioning Disneyworld!

As for references, while there are literally hundreds on papers on Archaeal transcription and translation, here a a couple of recent ones (note that the first even shows that Archaea have nucleosomes, a further similarity with Eukaryotes, the second, on eukaryotic translation, also has good overviews of Archaeal and Bacterial translation as well):

Xie Y, Reeve JN. Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome. J. Bacteriol. 186:3492-8 (2004)

Kapp LD and Lorsch JR. The molecular mechanics of eukaryotic translation. Annu Rev Biochem. 73:657-704 (2004)

--- Dr. Jonathan H Badger, The Institute for Genomic Research (TIGR), Rockville, MD


 * The biggest problem I have with either version of the paragraph is the opening sentence. It can be taken to imply that the existence of this distinct group of prokaryotes is still being debated.  Taken with the orignial version of the paragraph, the effect is even stronger.  I also think it caused Badger's rewrite to sound more defensive than necessary.


 * I would propose something like, Although the identity of the Archaea has been well established, the exact configuration of their evolutionary tree is still undetermined. or  Subsequent studies have confirmed the status of Archaea as a findamental division of cellular life, yet at the same time raised intriguing questions about their relationship to the other groups, bacteria and eukaryotes.


 * In general, I like Dr. Badger's version of the paragraph a little better, but there is something about his last sentence that doesn't sound quite right to me. I agree with the sentiment, but it seems like too much of a challenge to be in an encyclopedia.  I would suggest The question remains, why ... or Evolutionary theorist are (currently) trying to determine why ....
 * Jmeppley 17:11, 14 Oct 2004 (UTC)

The implication is meant to be there. The idea that the bacteria, archaeans, and eukaryotes are fundamental divisions of life is based mainly on Woese's tree and although widely accepted, several notable biologists have disputed it since. I think we need to make it plain the idea isn't universal because most people tend to assume the matter is settled.

Anyways, Jonathan, thank you for the references and sorry for the wholesale revert. I've reworked the article as well as I can to try and get both points across. Please feel free to change it if there's still any problems. Josh 04:31, 15 Oct 2004 (UTC)

Methanogens
There seems to be a tendency on these pages to consider methanogens as extremophilic. Is this really how they're usually described? There's nothing extreme about digestive tracts, they're home to countless typical bacteria like E. coli and protozoa, which are never described in this way. Josh 21:25, 15 Oct 2004 (UTC)

Hi, Josh, I like the new rewrite. As for methanogens being extremophilic, it depends on the species -- while the most famous methanogen, Methanococcus jannaschii, is an extremophile living down in the thermal vents at the bottom of the ocean at 85C and extreme pressure, other species, such as Methanococcus maripaludis live at normal temperatures like 30C and at atmospheric pressure. Archaea are more common that people originally realized, and the discovery of extremely thermophilic bacteria like Thermotoga has shown that not only Archaea can live at high temperatures.Jonathan Badger

Photosynthesis
In the sentence "For instance the halobacteria can use light to produce ATP, although none conduct photosynthesis in the usual sense.", does the word "none" refer to halobacteria alone or all archaea? It seeems wrong to give the impression that archaea didn't/don't do photosynthesis (I have seen many references to photosynthetic archaea, for example ). JDG 13:37, 26 Nov 2004 (UTC)

It refers to all Archaea. The references will be about halobacteria (including Natronobacterium), which do collect energy from light, but don't have an electron transport chain. I'll try and make the distinction a little clearer in the article. Josh