|
Author
|
Topic: Marcus Ross: A Review of Life's Solution by Simon Conway Morris
|
Nel
Member
Member # 614
|
posted 31. December 2003 20:04
Pim:
quote:
It may not have been clear to Nelson but this paper shows that Mike's statements about bacteriorhodopsins being limited to Halobacteriales when in fact the evidence suggest that it is found in bacteria and fungi alike. Certainly horizontal gene transfer would be an explanation for this as Mike suggested but the authors seem to disagree.
Thats strange, considering Mike stated:
quote:
even more interesting is that bacteriorhodopsin has popped up among the cyanobacteria.
It's kind of strange to say that Mike said bacteriorhodopsin was limited to Halobacteriales when he also said it was found in cyanobacteria. Again, don't read to contradict, read to weigh and consider. (I smell Bacon)
The papers you reference suggests that there may be homology between archael proteins and fungi proteins, but that has nothing to do with how they may have "crossed the border" into bacteria.
The paper that Pim is bolding in his edits has nothing to do with fungal rhodopsins but with fungal chaperone proteins. It also states:
quote:
Proteins in both families are of the same approximate size, exhibit seven putative transmembrane -helical spanners (TMSs) and show limited sequence similarity.
The new paper Pim added in edit probably mentions "homologs" because of structural similarities with bacteria, and only mentions a pocket that is similar between archael rhodopsin and alga.
After all these papers, not one has been found that shows homology between bacteriorhodopsin and rhodopsin.
[ 31. December 2003, 20:35: Message edited by: Nelson-Alonso ]
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 31. December 2003 20:42
Mike stated: It is also important to remember that the term “archaeal rhodopsin” is misleading, given that such rhodopsins are restricted to Halobacteriales.
To which Nelson suggests: It's kind of strange to say that Mike said bacteriorhodopsin was limited to Halobacteriales when he also said it was found in cyanobacteria.
Perhaps Mike can explain this contradiction?
Nelson:
After all these papers, not one has been found that shows homology between bacteriorhodopsin and rhodopsin.
An interesting non sequitur and sidetracking of the issues.
I am curious as to what Nelson did with the papers I provided.
Another link just for fun
GPCR introduction: Bacteriorhodopsin and Other Seven-Spanning Membrane Proteins
The evolutionary history of the opsins is quite fascinating indeed.
[ 31. December 2003, 20:42: Message edited by: Pim van Meurs ]
IP: Logged
|
|
Rex Kerr
Member
Member # 632
|
posted 01. January 2004 16:03
Cyanobacteria are bacteria, not archaea.
IP: Logged
|
|
Mike Gene
Member
Member # 149
|
posted 01. January 2004 18:40
Pim,
There is no contradiction. Among archaea, such rhodopsins are restricted to Halobacteriales. That’s why I noted that referring to them as “archaeal rhodopsin” is like referring to lactation as “euakaryotic lactation.” That’s why I also noted, “the fact that rhodopsins are so restricted among archaea suggest they appeared long after archaea significantly diverged.” That’s why I also added it was "interesting" to see them recently detected among cyanobacteria (which, of course, are not archaea).
I know that the term archael rhodopsin seems to be quite a common. That’s why it’s worth mentioning it is also misleading. That something is simply present in Archaea doesn’t make it extraordinarily ancient.
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 01. January 2004 19:22
Thanks Mike, this helps. In fact 'Haloarchaeal rhodopsins" seems to be a term used as well, for instance in Papke et al, Environmental Microbiology (2003) 5(11), 1039–1045
Umemura et al in J Mol Biol. 1999 Jan 8;285(1):163-74. found that the 4 clusters of rhodopsins arose through gene duplication before the halophilic archaea speciation. An interesting finding was that
" The evolution rate of pre-sensory rhodopsin was fivefold faster than that of pre-phoborhodopsin, which suggests that the original function of the ancestral sensor was similar to that of phoborhodopsin, and that sensory rhodopsin evolved from pre-sensory rhodopsin by the accumulation of mutations"
It seems that while originally it was believed that bacteriorhodpsins were limited to halophilic archaea, they now have been found in eurkaryotes and prokaryotes as well.
Domain Bacteria:
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea, Beja et al, 15 SEPTEMBER 2000 VOL 289 SCIENCE
quote:
Extremely halophilic archaea contain retinal binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential
in response to light have been demonstrated only in halophilic archaea.
We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton.
They argue for the possibility of lateral transfer "The finding of archaeal-like rhodopsins in organisms as diverse as marine proteobacteria and eukarya (6) suggests a potential role for lateral gene transfer in their dissemination. "
Domain Eukaryotes:
Neurospora crassa
A eukaryotic protein, NOP-1, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment. Bieszke et al, Biochemistry. 1999 Oct 26;38(43):14138-45
quote:
The results demonstrate a photochemically reactive member of the archaeal rhodopsin family in a eukaryotic cell.
I find it fascinating how science works to retrieve evidence for evolutionary pathways so far in the past.
IP: Logged
|
|
Mike Gene
Member
Member # 149
|
posted 01. January 2004 19:35
Here’s Jarell’s tree for the presence and absence of flagella in Archae:
Because flagella are widely distributed, Jarell infers its presence in the last common ancestor of archaea.
Now imagine were talking about rhodopsin and not flagella. What would the tree look like? You’d have a plus sign with Halobacterium and a minus sign everywhere else. The same sporadic patterns holds true for bacteria and eukaryotes.
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 01. January 2004 21:24
Mike, do you know in how many organisms rhodopsin homology was searched for? It seems to me that flagellation is somewhat easier to detect?
The competing ideas, lateral/horizontal gene transfer and/or common ancestry are fascinating especially given the findings in NOP-1
quote:
The high degree of sequence similarity between NOP-1 and the archaeal opsins in the retinal-binding and ion-pumping residues raises the possibility that NOP-1 is the result of a horizontal gene transfer from an archaeote. This is of particular interest in light of recent proposals regarding the prokaryotic origin of eukaryotic genes and the role of horizontal gene transfer in the evolution of fungal genomes (36, 37). However, the presence of an apparent NOP-1 orthologue in E. nidulans is inconsistent with a recent gene transfer. Furthermore, the presence of an opsin-related protein in the basidiomycete C. versicolor (38) suggests that Yro/Hsp30 gene clade was established at least 400 million years ago (see ref. 39). Based on these observations, the high degree of divergence between archaeal rhodopsins and NOP-1, and the apparent monophyletic nature of the archaeal group, we conclude that NOP-1 is unlikely to reflect a horizontal gene transfer from a halophilic archaeote.
So what might have happened?
quote:
The discovery of NOP-1 has important implications for the evolution of opsins and opsin-related proteins. The close relationship between NOP-1 and archaeal opsins indicates the existence of eukaryotic opsins of ancient origin. The deduced relationships among opsins and opsin-related proteins further suggest that the common ancestors of these proteins may have been involved in ion transport, with alternative functions being derived independently in both archaeal and fungal lineages
The final conclusion?
quote:
There has been a long-standing controversy regarding the relationship between archaeal opsins and the visual opsins present in animals. It is not clear whether the two groups represent homologous proteins that have diverged beyond recognizable sequence homology or are analogous proteins with separate evolutionary origins but similar structures (20). Although the discovery of NOP-1 does not resolve this issue directly, the existence of a fungal protein with clear evolutionary affinities to archaeal opsins places the notion of homology between archaeal and visual opsins within the realm of possibility. Although sequence differences suggest that the visual and archaeal proteins belong to different opsin groups, it is possible that the members of the two groups share ancestry in the opsin/opsin-related protein family, perhaps even among retinal-binding members. In fact, the ancient origin of fungal opsin homologues that we have inferred makes it likely that additional opsin homologues, including members of the NOP-1 and Yro/Hsp30 subfamilies, will be identified in other fungi. It is tempting to speculate that opsin homologues will be found in eukaryotic groups related to the fungi (12, 48) and that these opsins may be directly related to the visual opsins of animals
IP: Logged
|
|
Mike Gene
Member
Member # 149
|
posted 01. January 2004 22:47
Mike, do you know in how many organisms rhodopsin homology was searched for? It seems to me that flagellation is somewhat easier to detect?
When you BLAST with Bacteriorhodopsin sequence, the only thing you retrieve from Archaea are the Halobacteria. Among the bacteria, only cyanobacteria provide matches. Remember that there are 17 completely sequenced Archaeal genomes and 131 bacterial genomes. And there are also gobs of sequence from species whose genomes have not been completely sequenced.
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 02. January 2004 00:28
Do you think BLAST is sufficient to detect these homologies? Especially if homologies are structural rather than sequence based?
Link
An example is the yeast homolog
quote:
Results. Previously, sequence analysis of bacteriorhodopsins had not produced statistically significant alignments with any other protein family. Using INCA, we detected a probable yeast homolog, YRO2, that is also predicted to contain seven transmembrane segments. Additional alignment strategies upheld the finding of probable homology.
Conclusions. INCA is able to identify complete neighborhoods. As the sequence database grows, INCA will be particularly useful in identifying emerging evolutionary links to apparently isolated families. Identifying a yeast homolog of the bacteriorhodopsins demonstrates the approach, and at the same time illustrates the immense span of evolution across the seven transmembrane segment proteins.
and
quote:
As TMSs appear to be stable, folding subunits that join together fairly loosely within the membrane to form a tertiary structure (Popot and Engelman 1990), mutations may be more easily received without forfeit of structural stability than for globular proteins. Thus, the rate of divergence for TMSs can be high. A consequence is that many families of polytopic membrane proteins appear to stand alone in evolution, lacking sequence similarity to other families, despite considerable similarity in their secondary structure, membrane topology, and function. As the number of available sequences continues to grow, it is possible that protein sequences will be discovered that provide a link between these isolated families and other families of polytopic membrane proteins.
And as I suspected
quote:
More than 150 seven transmembrane-spanning proteins have been identified, including the opsins (vertebrate light-absorbing protiens) and many cell-surface receptors for hormones and odourous molecules. Although all of these proteins contain seven regions of 22 hydrophobic residues long enough to span the bilayer, it is rare that individual amino acids are found in the same position across more than one family member. Sequence homology between family members, identified by the BLAST algorithm, therefore remains extremely low despite good evidence that members of the 7 transmembrane rhodopsin superfamily adopt remarkably similar conformations in the plasma membrane.
Link
[ 02. January 2004, 00:43: Message edited by: Pim van Meurs ]
IP: Logged
|
|
Mike Gene
Member
Member # 149
|
posted 02. January 2004 15:48
Pim: Do you think BLAST is sufficient to detect these homologies? Especially if homologies are structural rather than sequence based?
That’s a possibility. But BLAST does connect the halorhodopsin with the versions in cyanobacteria and Neurospora. Are you suggesting that rhodopsin is widely distributed in Archaea, but that it has diverged so much, within Archaea, that a rhodopsin from Halobacteria is more similar to that in bread mold? After all, the INCA program you cited (that picked up the yeast version) didn’t pick up any other rhodopsins in other archaea.
IP: Logged
|
|
Jack Foster
Member
Member # 79
|
posted 06. January 2004 10:41
From the review:
quote:
From the ID and creationist communities, Life’s Solution will likely receive a more tepid response. For all of the difficulties, directionality, and “purpose” that evolution entails, ultimately Conway Morris’ views are incongruent with any strong design claim, such as detectability. Evolution, lest we forget, “is the way the world is.” And Conway Morris’ view is (ironically, much like Richard Dawkins’) steeped in adaptation. Nature controls the course of evolution, but convergence, argues Conway Morris, tells us that perhaps a Higher Purpose controls Nature.
I presume that there will be a certain segment of the design community that will receive this work enthusiastically. I confess to having only read the review at this point. (I'll order right away.) But the gist seems to be completely consistent with the views of the three Mikes: Denton, Gene, and Behe.
I agree that detectability is important to ID. But no one says that detectability is easy, and I can't believe Morris focuses on that. Hey, it could be years before there's a breakthrough that convinces the mainstream on detectability. But IDist have as much right to prove point on detectability as SETI seekers have to search the heavens.
IP: Logged
|
|
|
|
Jack Foster
Member
Member # 79
|
posted 06. January 2004 15:01
Hi Micah:
I ordered the book, starting with a link from ISCID, so I presume you'll get credit.
Hope all is well, and happy new year!
IP: Logged
|
|
|
Printer-friendly view of this topic