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Swift
2012-Jun-12, 08:11 PM
From Laboratory Equipment on-line (http://www.laboratoryequipment.com/news-Fundamental-DNA-Binding-Protein-Absent-in-Volcanic-Bugs-061212.aspx?et_cid=2693843&et_rid=54636800&linkid=http%3a%2f%2fwww.laboratoryequipment.com%2f news-Fundamental-DNA-Binding-Protein-Absent-in-Volcanic-Bugs-061212.aspx)

A gene previously thought to be present in all life on earth has been found missing in life near volcanoes.

The protein, thought to be one of the fundamental building blocks of life, is not present in certain volcanic single cell organisms.

The scientists studied archaea for the research, which are similar to bacteria but have a separate origin. The research, published in the Proceedings of the National Academy of the Sciences, found the expected gene missing and another in its place.

This missing protein, named SSB, performs an essential role by binding DNA and protecting it from damage. “All cells, whether they are microbial or human, have some things in common. These are the fundamental components or building blocks which were present in the first cells and have been passed on over 3.5 billion years," says Prof. Malcolm White of the School of Biology at the Univ. of St Andrews.

"We have discovered that a gene normally thought to be absolutely essential and conserved throughout every form of life is, in fact, lost in one group of volcanic bugs and [is] replaced by a completely novel gene we have christened ThermoDBP," says White.


Many be important clue with regard to origins of life and exobiology.

Selfsim
2012-Jun-12, 10:04 PM
Interesting.

My initial question here is:

i) "Could it be that the real surprise here is that the speculative idea that all organisms should produce this protein, has simply been falsified ?" (Ie: that knowledge about the state of evolutionary biology isn't as complete, when it comes to a 'universal life model', as all those involved, presently think it is ?)

ii) Is it really all that surprising that adaption through evolution may have influenced this archaea's genetic makeup, such that the expression and synthesis of this protein is not needed by this organism ? There are many other evidence-based examples where such 'fundamental functions' have changed and adapted into other functions, throughout the organism's evolutionary history.


iii) Notice that the author of this article has clearly stated the impacts of this discovery on current research ... and it makes no mention of exobiology.

The fact that it has been posted in this forum, does not 'make it so' !

Regards

Ara Pacis
2012-Jun-12, 10:20 PM
Should we operate under the assumption that they lost/replaced that gene, or that they never had it in the first place, and if the latter does that mean they are a separate abiogenesis or that they merely preceded us on the tree of life and the more common gene is the more recent evolutionary step. Parsimony leads me to suspect the latter of the latter.

transreality
2012-Jun-12, 10:44 PM
If the alternative primitive gene type is found only around the deep sea volcanic vent environment, then that strengthens the case that environment is where abiogenesis may have taken place, rather than an organic rich puddle hit by lightening, or a comet etc.

Selfsim
2012-Jun-12, 11:16 PM
If the alternative primitive gene type is found only around the deep sea volcanic vent environment, then that strengthens the case that environment is where abiogenesis may have taken place, rather than an organic rich puddle hit by lightening, or a comet etc.Huh?
Why do you say that ?

As a starter, this article speaks of 'volcanoes' .. it doesn't mention 'deep-sea volcanoes', (although, admittedly I'm having some difficulty in finding the research paper for the specifics).

Why would it strengthen the case you mention ?

Regards

Selfsim
2012-Jun-12, 11:39 PM
Ok, so here is the abstract (http://www.pnas.org/content/109/7/E398) of the article:

It mentions Thermoproteales (http://en.wikipedia.org/wiki/Thermoproteales) lacking in canonical SSB.

From the Wiki reference, (Scientific journals, second dot point form the bottom), it says:
Zillig W, Stetter KO, Schafer W, Janekovic D, Wunderl S, Holz I, Palm P (1981). "Thermoproteales: a novel type of extremely thermoacidophilic anaerobic archaebacteria isolated from Icelandic solfataras".

Icelandic solfataras are fumeroles (http://en.wikipedia.org/wiki/Fumarole) that emit carbon dioxide, sulphur dioxide, hydrogen chloride and hydrogen sulphide. One such 'Icelandic fumerole' is shown in this Wiki reference (http://en.wikipedia.org/wiki/Fumarole) (third picture down).

Certainly doesn't look to be limited to undersea volcanic vents, to me (??)

Regards

Selfsim
2012-Jun-12, 11:58 PM
The OP referenced article actually says:

Thermoproteales, a clade of hyperthermophilic Crenarchaea
Interestingly, a 'clade' (http://en.wikipedia.org/wiki/Clade) is a group consisting of a species and all of its descendants. A clade is a single branch on the 'tree of life'.
Crenarchaeota (http://en.wikipedia.org/wiki/Crenarchaeota)is a classified phylum of the Archaea kingdom (a Kingdom of its own). They have recently been identified as the most abundant archaea in the marine environment. The Sulfolobus (http://en.wikipedia.org/wiki/Crenarchaeota#Sulfolobus) member was originally isolated from geothermally-heated sulphuric springs in Italy. (It seems that they occur in both marine and, soil and freshwater environments, (http://en.wikipedia.org/wiki/Crenarchaeota#Marine_species) however).

A hyperthermophilic Caldarchaeol (http://en.wikipedia.org/wiki/Caldarchaeol) is a membrane-spanning lipid found in hydrothermophilic archaea.

Just trying to get to 'the bottom' of this (pardon deep-sea puns).
:)

Regards

Swift
2012-Jun-13, 01:51 AM
<snip>
iii) Notice that the author of this article has clearly stated the impacts of this discovery on current research ... and it makes no mention of exobiology.

The fact that it has been posted in this forum, does not 'make it so' !

I only mention exobiology because anything that gives us clues about how life developed on Earth may give us clues as to how it may, or may not, develop elsewhere. That's all.

syzygy42
2012-Jun-13, 04:44 AM
I could not read the paper, but the abstract refers says,


ThermoDBP appears to have displaced the canonical SSB during the diversification of the Thermoproteales, a highly unusual example of the loss of a “ubiquitous” protein during evolution.

From some of the other papers I have read they are referring to the observation that within a clade, there are a core group of proteins that have a common evolutionary tree structure. These are sometimes referred to as signature proteins. One of the difficulties in determining phylogenetic relationships in the Bacteria and Archaea is that there has been abundant and ongoing transfer of genes between distantly related organisms (lateral or horizontal gene transfer). This is especially true early in evolutionary history, prior to the emergence of Eukaryotic cells. People certainly worried that searching for the base of the tree of life would end in a phylogenomic fog. However, with the complete sequencing of genomes from all branches of life (~400 Archaea, ~3000 Bacteria, ~800 Eukaryotes) a set of ubiquitous genes could be found in all of the free-living organisms, i.e. excluding parasites. This set is comprised of proteins involved in macromolecular synthesis and metabolism, e.g., DNA synthesis and repair, RNA synthesis and protein synthesis. SSB is one of these proteins.

To better understand what is being done, I have to introduce a critical measure, orthology. From a completed genome, you can accurately predict the sequence of all of the proteins made by an organism. When you compare the sequence of a protein from one organism to all of the proteins in a second organism with a program called BLAST (http://www.ncbi.nlm.nih.gov/guide/sequence-analysis/), you can rank the proteins according to an alignment score (measured in bits) that measures the relatedness between two proteins. You then take the highest scoring protein from the second organism and perform a BLAST search on the first organism. If the original protein ranks the highest in the reciprocal search the genes/proteins are said to be orthologous. These searches are extended to compare all proteins of one organism against each set of proteins for all of the other organisms. Orthologous proteins almost always have nearly identical functions in each organism. From this analysis, you can get a good idea of the metabolism and physiology of an organism.

The set of ubiquitous proteins were identified in these searches and further analysis revealed that individual genes were rarely replaced by a gene from a distantly related organism. This is in contrast to fairly extensive lateral gene transfer for genes involve in metabolism and other processes. The working model is that there is extensive physical interaction among the core proteins that is necessary for their function. Over extended evolutionary time, small changes at the interacting surfaces of these proteins accumulate to a point where a protein from a different organism cannot function as well as the native protein. If a lateral gene transfer does occur, that organism is at a selective disadvantage and will not survive.

SSB, single stranded binding protein, binds specifically to single stranded DNA (duh!) in the replication fork, at replication origins, and on single stranded intermediates in DNA recombination and repair. It specifically interacts with one or more components in each of these essential processes. Finding an unrelated protein that performs the same function is unexpected (though you learn that in biology there are almost always exceptions), but more importantly, provides information that can help to map out the deep roots of the Archaea. A figure of a cluster analysis of SSB proteins can be found here (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208561/figure/pone-0026942-g001/).

This organism, T. tenax is an interesting critter (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024222#pone.0 024222.s009). It can grow as a heterotroph, using organic compounds for carbon and energy (e.g., sugars, etc.) and releasing CO2 by running the TCA cycle in the oxidative direction. But, it can also grow as an autotroph, fixing CO2 for its carbon needs by oxidizing H2 as its source of reducing power for energy. Although it appears capable of using the reductive (reverse TCA cycle) to fix CO2, it may bypass part of the cycle through a pathway starting with succinate. In both these lifestyles, sulfur is the ultimate electron acceptor. Analysis of the evolutionary history of these metabolic genes will also help to get an idea of the metabolic capacity available at the emergence of the Archaea. Since one leading model proposes that life emerged either from deep sea hydrothermal vents (goolge Lost City) or at terrestrial hydrothermal fields, sequences of isolates like this critter from places like Icelandic fumaroles will increase our understanding of early evolution and how such critters live. We may call them extremophiles, but to them, we might be the extremophile.

There is still much that is unknown at the early stages of life. The close relationship between the macromolecular machinery of Archaea and Eukaryotes suggests a common evolutionary history, but an extant Archaeal ancestor has not been found. Instead, each lineage contributes at least a few genes to the Eukaryotic core. Sequencing of more organisms is necessary. Indeed, there are whole clades that have been identified by their ribosomal RNA sequence for which there are no isolates that can be grown. You have to be able to grow an organism to be able to get a full genomic sequence. This situation is not unique to the Archaea, fewer than 1 % of the Bacterial organisms identified by environmental sequences have been cultured.

Ara Pacis
2012-Jun-13, 05:19 AM
After thinking about it, I wonder if anyone knows if plasmids can have anything to do with gene transfers in the organisms in question.

Selfsim
2012-Jun-13, 06:03 AM
So thanks kindly for that information there syzygy42 .. very informative … your contribution helps a lot to better understand the importance, (or otherwise), of this discovery.

A couple of thoughts come to mind. Firstly, gene duplications and deletions can occur within the same organism. So, lateral or horizontal gene transfer, may not necessarily have to be the sole origin of this particular change (??), although, as you point out, it is within the core group of ubiquitous genes within the clade (??). Am I reading this the right way ? Perhaps all this just pushes the split between organisms within the clade, further backwards in time ?

It seems in this case, SSB is required to inhibit premature annealing during polymerase chain reactions or during renaturation of DNA/RNA, so it is clearly a fundamental necessary function.

Secondly, in general, it also seems that there's lots of redundancy present in the way particular proteins are expressed. Whilst the function of annealing seems vital, I'm left wondering whether some seemingly so-called 'non-functional pseudogenes', might play a role in making the substitution of SSB in this particular organism ?

Your comment about whole clades for which there are no isolates which can be grown, is a timely reminder about what an early stage we are at, and how much more there is for us to know about our own 'universal' model of life.

Very interesting and thanks again for your post.

Regards

syzygy42
2012-Jun-13, 06:25 AM
After thinking about it, I wonder if anyone knows if plasmids can have anything to do with gene transfers in the organisms in question.

I am not that familiar with gene transfer in Archaea, but one sure route is by viruses. A virus has been isolated and/or its DNA is found integrated in the genome of every prokaryotic cell that anyone has looked at. Another name for these viruses is bacteriophage for Bacteria and archaeophage for Archaea. There are about 10^31 phage on Earth (~1 million/ml of water from basically any source). Roger Hendrix calculated that if you took all of them and lined them up end to end, a back of the envelope estimate is that they would stretch out for 200 million light years (I haven't done the calculation myself). Phage can carry genes around from one organism to another since their DNA packaging system does not have 100 % fidelity: occasionally they will package some chromosomal DNA. Just thinking back to one of the papers I read on T. tenax, it has a system that is used for defense against phage infection.

I am most familiar with the gene transfer between E. coli and its relatives. In addition to phage, you have as you say plasmids, some of which carry genes that transfer the plasmid DNA from one cell to another, and the recipient cell need not even be closely related. Another way is that when a phage infects a cell, the final step is the cell bursts open, releasing phage and chromosomal DNA that can be directly taken up by another cell. On top of that, there are transposable elements (jumping genes), that can move from one place in a chromosome to another or to another DNA such as a plasmid or phage. Occasionally, they can pick up a gene and move them to a phage or plasmid. When they get in another cell, they can move the gene from the phage or plasmid into the chromosome. One other element is called an integron, a whole collection of genes that can move from one cell to another. The interesting thing is that it only expresses one gene at a time and randomly rearranges itself to express another gene. Sort of like pressing the random shuffle button.

Phage are interesting creatures and are very ancient. One model is that a phage invented DNA and this is what triggered the move from an RNA/protein world to a DNA/RNA/protein world. Fascinating stuff.

Cheers

syzygy42
2012-Jun-13, 05:22 PM
A couple of thoughts come to mind. Firstly, gene duplications and deletions can occur within the same organism. So, lateral or horizontal gene transfer, may not necessarily have to be the sole origin of this particular change (??), although, as you point out, it is within the core group of ubiquitous genes within the clade (??). Am I reading this the right way ? Perhaps all this just pushes the split between organisms within the clade, further backwards in time ?

It seems in this case, SSB is required to inhibit premature annealing during polymerase chain reactions or during renaturation of DNA/RNA, so it is clearly a fundamental necessary function.

Secondly, in general, it also seems that there's lots of redundancy present in the way particular proteins are expressed. Whilst the function of annealing seems vital, I'm left wondering whether some seemingly so-called 'non-functional pseudogenes', might play a role in making the substitution of SSB in this particular organism ?

When I first read the link in the OP, I thought, "So what?" I had not read anything about SSB in a long time. I thought it was a pretty boring protein, acting like a buffer to keep ssDNA from folding back upon itself. Well a quick tour through the recent literature quashed that notion: I did not know about its extensive interaction with the different replication and repair machinery. Perhaps it's just years of reading news articles about science that I automatically filter out words like "surprising" and "novel". I once had a conversation with the guy who wrote the algorithm that finds related abstracts in PubMed. In addition to removing common English words from the search, he also had to remove "surprising" and "novel" and a few others as well :). Well after looking doing a few searches myself, I actually think that using the word novel here is one of those rare instances where it is appropriate.

So the question is where did this version of SSB come from? Your basic ideas of gene duplication and pseudogenes are fundamentally sound. Indeed, in Eukaryotes these sorts of mechanisms are at work. However, the situation in Bacteria, and I assume Archaea, is fundamentally different. Duplication of a segment of DNA is an unstable situation: it is quickly removed by homologous recombination. In fact, to maintain a duplication, you either have to disable the recombination system or you have to have a selection for the overexpression (increased synthesis) of the duplicated gene. Once the selection is removed, cells quickly revert back to their original single copy state.

Redundancy of function, as you point out, is an important consideration to take into account. However, when you look at the different systems in the cell and ask where you find genes with redundant functions, what you find is somewhat counter-intuitive -- at least for me it was. I naively thought that you would find redundancy in the genes encoding an essential function, for example as being a part of the DNA replication apparatus. In fact, the situation is exactly the opposite: for the set of ubiquitous core genes, you do not find any redundancy (i.e. two different genes encoding the proteins with the same or overlapping functions). As you move away from this core, you find some redundancy in central carbon, amino acid and lipid metabolism, usually in the form of isozymes (enzymes with the same catalytic function) that differ in the molecules that regulate their function. You find the most redundancy, in systems that feed products into the core metabolism. These are the systems that directly interact with the environment to transport nutrients, adapt to stressful conditions, and obtain energy.

A useful analogy is the peripheral genes are like the different clothing and tools that you use for different activities: you can often substitute one for another. You are then like the core genes, irreplaceable. Why might this be an advantage for bacteria? Mutations in the core genes that affect their function confer a selective disadvantage, and these mutants are rapidly lost from the population. Thus, the core genes represent a stable system. Outside of the core, what you find is a modular system in which a group of genes can encode a function such as a metabolic pathway or a system that can deal with environmental stress. An extreme example of this is there are bacteriophage that carry all of the genes necessary for photosynthesis. They can infect a non-photosynthetic bacterium and integrate into its chromosome. This bacterium can now perform photosynthesis. It is in these where you find the most variation between strains of the same "species". For strains that are called E. coli, you can find as much as 30 % of the genes that are found in only one strain. The classical notion of species has been replaced with a model in which an extended core of genes comprising the essential functions and a core metabolism are relatively stable with set of auxiliary genes whose precise composition is strain dependent. The auxiliary genes are the ones that most often undergo lateral gene transfer. The take home message here is that the E. coli strains that have inhabited your gut since you were born are very different than the E. coli that you read about in the news.

Returning to SSB, where did the ThermoDBP come from? I can think of two possibilities: (1) it did not "replace" the canonical SSB but has been there from the beginning of the radiation of the clade from the other Archaea, or (2) it acquired ThermoDBP much later in the evolutionary history of the clade. If the first possibility is true, then examination of this clade will help in discerning early evolutionary events. If the second is true, while it may reduce the importance of this clade in discerning deep history, it leaves the problem of where did it originate? and how did it "replace" the canonical SSB?

One possibility for the replacement model is that ThermoDBP was brought in by a phage. Many dsDNA viruses encode their own SSB and these are at best distantly related to the canonical SSB. Sometimes a phage encoded SSB can substitute, at least partially, for the host SSB. One can imagine a scenario in which the ThermoDBP was brought in by this mechanism and was able to replace the host SSB. The interesting thought I had was that it could be a combination of the two possibilities. Phage are thought to have developed DNA first and sparked the transition from the RNA/protein world to the DNA/RNA/protein world. It is possible that this clade acquired ThermoDBP in this transition. Of course, these are thoughts that are coming off the top of my head so take them with a grain of salt.

Fun stuff

Cheers

transreality
2012-Jun-14, 03:07 AM
Why would it strengthen the case you mention ?



Given lateral transfer of genes, and 3.4 billion years it is quite likely that the most advantageous gene would be found in particular environments. If SSD is a modification of ThermoDBP, and the relic of the earlier gene is found only where it is advantageous, and that highly specific environment is hot acidic water, then it is not unreasonable to suppose that gene originally arose in such an environment. This gene provides for a very basic function for the operation of DNA so it can be expected to be in use not long after actual abiogenesis. There are basically three scenarios for abiogenesis; in hot water, in cool water and in ice. The hot water possibility includes undersea volcanic vents by convention, but other volcanic systems are possible. So if not pointing at the actual event, it at least demonstrates that very early life may have been comfortable in what is a marginal environment now.

transreality
2012-Jun-14, 03:30 AM
Given lateral transfer of genes, and 3.4 billion years it is quite likely that the most advantageous gene would be found in particular environments. If SSD is a modification of ThermoDBP, and the relic of the earlier gene is found only where it is advantageous

Actually, having read the paper (http://research-repository.st-andrews.ac.uk/handle/10023/2108), I can see that ThermoDBP is a non-orthologous replacement for SSD, that is, it is not a modification.

syzygy42
2012-Jun-14, 03:49 AM
Actually, having read the paper (http://research-repository.st-andrews.ac.uk/handle/10023/2108), I can see that ThermoDBP is a non-orthologous replacement for SSD, that is, it is not a modification.

Thanks for the link!

agingjb
2012-Jun-14, 08:10 AM
The apparently interchangeable use of "gene" and "protein" puzzles me.

syzygy42
2012-Jun-14, 03:32 PM
The apparently interchangeable use of "gene" and "protein" puzzles me.

I am sorry if I have contributed to your confusion, and indeed it can be confusing. It is usually the "gene" part that gets people mixed up because it has different meanings in different contexts, and there is no single consistent definition that you can apply everywhere. In the context of evolution of proteins, "gene" here refers to what is called a "structural gene": the sequence of DNA that encodes a protein through the genetic code. In Bacteria and Archaea, decoding the DNA sequence is fairly straight forward. DNA has a four letter alphabet: ACGT. Proteins are synthesized in two steps: First, the DNA sequence is copied to make mRNA whose sequence is identical to one of the strands of DNA except U replaces T, a process called transcription. Second, the ribosome reads the sequence of the mRNA and synthesizes a protein whose sequence is determined by the sequence of the mRNA. The code is made up of 64 triplets called codons that specify 20 amino acids and three stop codons. One of the codons pulls double duty acting as a start signal, or start codon, and as a normal codon. Once the ribosome determines the position of the start site, it reads the code and synthesizes a protein with an amino acid sequence that matches the sequence of the codons. This process is analogous to how a computer reads ASCII code and turns it into something that you can read.

The essential point to remember about this process is that it is the same in all organisms*. Thus, if we can determine the DNA sequence of an organism, we can accurately predict what genes are present and what proteins they encode. Since the DNA --> Protein sequence is invariant, it is easy to mix "gene" and "protein". Also, since there are 61 codons encoding 20 amino acids, the code is redundant with up to 6 different codons representing 1 amino acid. The consequence of this is that different DNA sequences can code for the same protein sequence. So when people say that they analyzed the DNA sequence of your favorite organism, they are taking the DNA sequence and converting it into protein sequence which is then compared to the sequences of other proteins.

The other confusing part is the word "function". After being synthesized, proteins then participate in the processes of the cell. If a protein participates in a process, then people say protein X functions in process Y. Often, the verb "to function" is converted into a noun "function", thus protein X's function is to ..... Because of the direct correspondence between structural gene DNA sequence and protein sequence, often the function of a protein is assigned to a gene.

The last term to wrap your brain around is expression. This refers to the whole process from gene to protein. When a gene is expressed, this means that the protein is synthesized -- in more colloquial terms people say the gene is "turned on".

I wish that I could point you to a web resource that could help, but I haven't run across something that is detailed enough to know what is going on and accurate enough in its descriptions to be consistent with more detailed models. If you feel confused, you are not alone. Many biology majors carry significant misconceptions into their upper level classes. Getting students to "unlearn" things is the most difficult task of advanced level teaching.

Hope this helps.

Cheers

*there are always exceptions.

agingjb
2012-Jun-14, 04:03 PM
Sorry, I was too brief and not brief enough. I'm moderately familiar with the concepts of genotype and phenotype, and when I read:

"A gene previously thought to be present in all life on earth has been found missing in life near volcanoes.

The protein, thought to be one of the fundamental building blocks of life, is not present in certain volcanic single cell organisms. "

my reaction is: fog.

syzygy42
2012-Jun-14, 06:50 PM
Here, the writer has used both gene and protein to represent a function and switched, probably unconsciously when moving from one sentence to the next. Another issue is that in trying to present the story as a mystery to be solved (a typical approach for biological presentations) in a succinct manner, the context that explains the mystery is absent. It is partially provided later on, but by that time the fog has descended.

Given the headline and subject matter, perhaps a little context would have been useful. Such as



Common to all life are the processes of DNA replication and repair, a complex dance of dozens of protein components. It is then surprising to find organisms that appeared to be missing the gene that encodes one of the key components, single-stranded binding protein (SSB). The scientists then looked to see whether SSB's function had been replaced by another protein. Indeed, they identified the protein and the gene that encodes it. They report ...blah, blah, blah


I don't know if that reads any better, but it's the best I can do before I am yet again distracted by a football match :D.

Ara Pacis
2012-Jun-16, 08:59 AM
It seems to me that the real question here is whether it is conceivable that the Archaea as opposed to the Eubacteria could conceivably represent different discrete origins of life, whether on Earth or one or both as a result of panspermia. I gather the weight of scientific thought is that they represent divergent clades from a common ancestor. Marc Kaufman, in First Contact, notes how evidence, if and when it materializes, of a "second origin," either on Earth that managed to survive in parallel, or elsewhere, would shoot down the argument that life could be a spectacularly unlikely occurrence, which might have occurred only the one time, here on Earth. Obviously, if it happened twice anywhere near here, the argument that it likely happened elsewhere in the universe, over and over again, and that it is indeed probably common, would be strengthened.

Not really. The Copernican Principle is not a law of nature. If the circumstances for abiogenesis are relatively rare, it would seem to me that proper conditions in time and space would be more likely to allow multiple instances to appear. It would merely move the constraint from "chance assembly" to "proper conditions" which could still be very tightly constrained. However, the genesis of one gene doesn't mean much. I'd be more impressed and swayed if we found "life" that didn't even use the same biochemistry on earth. Do we expect another abiogenesis to use DNA?

publiusr
2012-Jun-16, 06:16 PM
I wonder if work could be done to see how the gene/protein responds to high pressures, or the sudden release of pressure.

syzygy42
2012-Jun-16, 10:58 PM
It seems to me that the real question here is whether it is conceivable that the Archaea as opposed to the Eubacteria could conceivably represent different discrete origins of life, whether on Earth or one or both as a result of panspermia. I gather the weight of scientific thought is that they represent divergent clades from a common ancestor.

You raise a very interesting question. For a while, both the scientific and popular literature have used the term Last Universal Common Ancestor (LUCA), there are a few problems with a common ancestor. First, when evolutionary trees are determined by examining one protein at a time, each individual protein has a fairly consistent root, or common ancestor. However, the roots of the different trees are inconsistent with one another. Eugene Koonin has called this "the forest of life". This makes inferring the genetic makeup of a single common ancestor extremely difficult and raises the possibility that extant organism evolved from not one but a set of organisms.

The second problem with the concept of a singular LUCA is the difference between the compositions of the membranes: Bacteria have cytoplasmic membranes composed of phospholipids in which a fatty acid with a straight unbranched lipid (or fatty) portion is linked to glycerol through a ester linkage. In contrast, Archaeal phospholipids differ in several important ways. (1) The lipid portion is based upon isoprenoid repeats that can be branched and contain different cyclic structures. (2) The lipid and glycerol are joined by an ether linkage. (3) The glycerol is a different stereochemical enantiomer. It is difficult to come up with a model in which an organism evolves a completely different membrane system.

It is unclear as to how these membrane systems evolved in the first place. Membranes in both domains are complicated structures that function to maintain a stable internal environment. To do so, they must maintain a proton gradient (high concentration outside) to transport ions and small molecules in and out of the cell. Additionally, cells that respire use the proton gradient to generate ATP through the membrane ATPase. This has led some to propose that these functions were a late innovation. Others propose that the development of functional membranes necessarily preceded development of free living organisms. In this model, evolution of the transcription, translation and replication machinery occurred in situ within cavities found in geological structures, such as warm deep sea ocean vents or in terrestrial geothermal fields. Within these structures, the two different systems segregated and each evolved different membrane systems. Thus our common ancestor may not be an organism as we commonly perceive but may be a chemical system existing within an ancient geological structure.


Originally Posted by Ara Pacis

Do we expect another abiogenesis to use DNA?

Interesting question. I have read recently that someone was able to synthesize DNA with two additional bases and a commonly used DNA polymerase could replicate this substrate and faithfully insert the new bases. Thus, it is possible that a DNA/RNA molecule could contain a different set of bases from the canonical ACGT/ACGU. As to the possibility of different information molecules with alternative backbone structures and bases analogs, I would speculate that such alternative biochemistries would be the norm and would depend upon the specific environment from which they emerged. Some effort has been made to construct such molecules with some success (a molecule with its ribose switched for another moiety), but besides study of such an organism, I have no idea how one could constrain the parameter space needed to practically explore the question.

These questions do raise the issue of "weird" life living a parallel existence here on Earth. I think Paul Davies was the first to put the idea forward in the literature. The argument rests upon the fact that most of our knowledge of the makeup of the microbial world is dependent upon PCR to amplify DNA sequences or upon shotgun cloning of isolated DNA. Thus if an organism had different bases or backbone, we would not have detected it with these methods. A second genesis here on Earth is a possibility, though remote, and researchers need to keep it in the back of their minds. Because who knows?


Originally Posted by publiusr

I wonder if work could be done to see how the gene/protein responds to high pressures, or the sudden release of pressure.

You are definitely thinking along the right track. How the environment shapes the genetic makeup of organisms and how they respond to different environmental stresses are recurring questions in these studies. I have not seen any literature regarding pressure, but I am certain that some exists.

Cheers

Ara Pacis
2012-Jun-17, 04:30 AM
You raise a very interesting question. For a while, both the scientific and popular literature have used the term Last Universal Common Ancestor (LUCA), there are a few problems with a common ancestor. First, when evolutionary trees are determined by examining one protein at a time, each individual protein has a fairly consistent root, or common ancestor. However, the roots of the different trees are inconsistent with one another. Eugene Koonin has called this "the forest of life". This makes inferring the genetic makeup of a single common ancestor extremely difficult and raises the possibility that extant organism evolved from not one but a set of organisms.

It is unclear as to how these membrane systems evolved in the first place. Membranes in both domains are complicated structures that function to maintain a stable internal environment. To do so, they must maintain a proton gradient (high concentration outside) to transport ions and small molecules in and out of the cell. Additionally, cells that respire use the proton gradient to generate ATP through the membrane ATPase. This has led some to propose that these functions were a late innovation. Others propose that the development of functional membranes necessarily preceded development of free living organisms. In this model, evolution of the transcription, translation and replication machinery occurred in situ within cavities found in geological structures, such as warm deep sea ocean vents or in terrestrial geothermal fields. Within these structures, the two different systems segregated and each evolved different membrane systems. Thus our common ancestor may not be an organism as we commonly perceive but may be a chemical system existing within an ancient geological structure.

Interesting question. I have read recently that someone was able to synthesize DNA with two additional bases and a commonly used DNA polymerase could replicate this substrate and faithfully insert the new bases. Thus, it is possible that a DNA/RNA molecule could contain a different set of bases from the canonical ACGT/ACGU. As to the possibility of different information molecules with alternative backbone structures and bases analogs, I would speculate that such alternative biochemistries would be the norm and would depend upon the specific environment from which they emerged. Some effort has been made to construct such molecules with some success (a molecule with its ribose switched for another moiety), but besides study of such an organism, I have no idea how one could constrain the parameter space needed to practically explore the question.


These questions do raise the issue of "weird" life living a parallel existence here on Earth. I think Paul Davies was the first to put the idea forward in the literature. The argument rests upon the fact that most of our knowledge of the makeup of the microbial world is dependent upon PCR to amplify DNA sequences or upon shotgun cloning of isolated DNA. Thus if an organism had different bases or backbone, we would not have detected it with these methods. A second genesis here on Earth is a possibility, though remote, and researchers need to keep it in the back of their minds. Because who knows?Would the former statements then not be considered a second abiogenesis even if two or more differing organisms developed out of the same community primordial soup. Does that mean then that the only way we could define a second abiogenesis is life with a radically different chemistry?

syzygy42
2012-Jun-17, 05:34 PM
Would the former statements then not be considered a second abiogenesis even if two or more differing organisms developed out of the same community primordial soup. Does that mean then that the only way we could define a second abiogenesis is life with a radically different chemistry?

For me, it's difficult to sharply define terms like "second genesis". It's sort of like trying to define what a gene is. Compare the glossaries of any textbook and you will find many definitions that emphasize one concept or another. I became acutely aware of this when I first read Dawkins' "The Selfish Gene". It was only after I had read about half the book before I started to get a grasp on what he meant. Partly it was a separation in time since he wrote it in the 1970s before much of anything was known at the molecular level about genes. In his classical perspective, genes, mutations and phenotypes were rather abstract concepts developed largely from genetic experiments and theories of population genetics. The neo-Darwinian synthesis continues to be developed as we understand more about how cells, organisms, populations and ecosystems function. Similarly, trying to come up with a definition of abiogenesis at this time may be a bit premature -- our experimental and theoretical knowledge is too primitive and subject to revision to define sharp boundaries.

For me, I look at the development of life as a continuous process: geochemistry -> synthesis of organic molecules -> development of a metabolism -> RNA replication -> RNA directed peptide synthesis -> development of the genetic code -> evolution of the first set of genes -> transition to DNA as the carrier of genetic information -> independent organisms. This is but a mere sketch focusing on the development of the information system. Parallel to this is the development of the metabolism and physical compartmentalization capable of sustaining the replication of the information system.

If one temporarily puts aside the timing of the emergence of what we would recognize as a free-living cell and concentrates on the similarities among the three domains, the model of a common origin is strongly supported. The structure and sequences of ribosomal RNA and proteins is conserved across the three domains. Moreover, identical structures within the ribosomes perform the same functions and interact with a conserved set of proteins in all three domains. Most importantly, the genetic code is universal. In contrast, the enzymes responsible for the copying of genetic information from RNA to RNA, from DNA to RNA, and from DNA to DNA are much more diverse with regard to their evolutionary histories. Among these, only the core catalytic structure of the cellular DNA-dependent-RNA-polymerases is strongly conserved throughout the three domains. Indeed, the catalytic subunit of the replicative DNA polymerases from Bacteria is unrelated to those found in Archaea and Eukaryotes. It is for these reasons that I favor the view that the ribosome and its associated factors form the foundation upon which all extant life was built.

In thinking about what might constitute a second genesis, I look to the most difficult process: development of the genetic code. Thus, finding an organism that has a substantially different code and uses a different set of amino acids (though there will be some in common) would for me be a significant finding, even if it were based upon familiar DNA and RNA templates. But at this early stage, I prefer to keep my theoretical framework flexible because having models that are too restrictive prevents one from exploring new conceptual landscapes.

Paul Wally
2012-Jun-17, 08:44 PM
I'm wondering, a planet with two landlocked oceans would present an interesting case. If such a planet has life and abiogenesis starts in the ocean, then if it happens easily then there should be two evolutionary trees, but if it doesn't happen easily then if life starts off in the one ocean then it must first evolve onto land and then back into the other ocean.
It is perhaps, because Earth has only one big ocean that we seem to have only one evolutionary tree. Just a thought. :)

Colin Robinson
2012-Jun-18, 12:57 AM
I'm wondering, a planet with two landlocked oceans would present an interesting case. If such a planet has life and abiogenesis starts in the ocean, then if it happens easily then there should be two evolutionary trees, but if it doesn't happen easily then if life starts off in the one ocean then it must first evolve onto land and then back into the other ocean.
It is perhaps, because Earth has only one big ocean that we seem to have only one evolutionary tree. Just a thought. :)

It's an interesting scenario. A planet with 2 or more landlocked oceans might be more like to experience multiple evolutionary trees... On the other hand...

For me, the phrase "evolve onto land" conjures up pictures (from childhood) of fish turning into frogs etc... But presumably, long before there were amphibians or even insects on land, microbes would have spread (via watercourses, air-born droplets, or dry spores) to everywhere on the planet with an energy source and a bit of moisture. So I wonder whether it would be that difficult for a microbial population from one land-locked ocean to "infect" another?

syzygy42
2012-Jun-18, 03:12 PM
Paul & Colin,

You raise a question that I have not seen adequately addressed: How local was the emergence of free living organisms?

Regardless of the specific model for the emergence of life, it seems unlikely that the postulated conditions were confined to a small area. It is then possible that alternative pathways of development were explored in many different locations, with alternative free living organisms emerging contemporaneously. Since we can only see the winners, was the first game of Risk played out by our microbial ancestors?

With regard to the spread of microbes, ice cores from around the world contain microbes living in the ice. The most robust communities reside in sea ice and glaciers close to the coast. Amazingly, photosynthetic bacteria have also been found in the remote Vostok ice cores, presumably blown in from the distant ocean.

Interesting thoughts.

publiusr
2012-Jun-18, 06:02 PM
I have not seen any literature regarding pressure, but I am certain that some exists.

Cheers

One would hope, but my guess is that most work done on organic chemistry is done in shirtsleeve conditions at one atmospheric pressure. Fine for life that already exists, but not if you want to do work on origins. I seem to remember different types of hot ices that exist due to pressure. What about carbon compounds. Let's say some ice has some organics and impacts--that would be one step. Subduction another, vorticity out of a smoker or release from volcanism another.

All things that are hard on scientists who want a nice 72 degrees in the lab. Oil cracking stations may have something interesting to researchers--or maybe even welding equipment--who knows?

Ara Pacis
2012-Jun-18, 07:05 PM
I recall reading recently that there is some thought that life may have happened before and survived the Giant Impact that formed the moon, and that not all of the earth was covered in a magma ocean. If the GIH is true, I wonder if we'll be able to find remains on moon rocks.

syzygy42
2012-Jun-18, 08:42 PM
Ara Pacis,

I've sometimes thought that in the distant future, the best evidence for the conditions of early life would be found in the ejecta from the Late Heavy Bombardment either on the Moon or Mars.

Jens
2012-Jun-19, 04:49 AM
The second problem with the concept of a singular LUCA is the difference between the compositions of the membranes: Bacteria have cytoplasmic membranes composed of phospholipids in which a fatty acid with a straight unbranched lipid (or fatty) portion is linked to glycerol through a ester linkage. In contrast, Archaeal phospholipids differ in several important ways.

It's interesting that you mention this, because I happened to go to a lecture a couple of weeks ago where the speaker was talking about that issue. I'm not a specialist by any means, so I may wrong on the details, but I think he was saying that the archaea have lipids with a different chirality than those of both bacteria and eukaryotes, and yet it is believed evolutionarily that both the bacteria and eukaryotes branched off from archaea. So it almost sounds like the chirality changed happened twice. I think he was suggesting that maybe originally it was mixed, and that later they became unified and just happened to fall two one way and one the other.

Nereid
2012-Jun-19, 02:28 PM
Awesome thread, awesome discovery! :clap:


These questions do raise the issue of "weird" life living a parallel existence here on Earth. I think Paul Davies was the first to put the idea forward in the literature. The argument rests upon the fact that most of our knowledge of the makeup of the microbial world is dependent upon PCR to amplify DNA sequences or upon shotgun cloning of isolated DNA.

Is this the "shadow biosphere"WP (http://en.wikipedia.org/wiki/Shadow_biosphere), or closely related?


The code is made up of 64 triplets called codons that specify 20 amino acids and three stop codons.

I thought I read somewhere that there are 22 amino acids in use across the three domains (though one is found only in the archaea?), and that the codons are not universal, in the sense that a given triplet always codes for the same amino acid (or start or stop), beyond one pulling double duty. If so, how does the biochemical machinery "know" what to do, when a codon may mean more than one amino acid (or a start or a stop)?

ShinAce
2012-Jun-19, 04:30 PM
A lecture I attended a few months ago was about 'traffic flow' in ribosomes making proteins. Even though there are multiple codons for a single amino acid, some are faster than others. If a protein requires a slow codon at the end of the chain, you'll often find a slow codon at the beginning near the start codon. This bottleneck at the beginning helps keep the traffic flowing smoothly down the rest of the chain and helps extra ribosomes from latching onto the start codon where they will sit idly for some time.

It was a shame that it was given to physics students who missed the point entirely. I did get lots of time to speak to the presenter as a result. Despite his work, he wanted to focus on the role of protein folding.

The lecture was titled "effeciency in protein synthesis" so everyone thought it would be about energy. And it was. Too many ribosomes stuck on a strand of rna is not efficient use of resources.

Edit: sorry nereid, I misread what you wrote. Make note that ribosomes are not 100% universal, thankfully. That's why we have antibiotics.

syzygy42
2012-Jun-20, 03:25 AM
I'm not a specialist by any means, so I may wrong on the details, but I think he was saying that the archaea have lipids with a different chirality than those of both bacteria and eukaryotes, and yet it is believed evolutionarily that both the bacteria and eukaryotes branched off from archaea. So it almost sounds like the chirality changed happened twice. I think he was suggesting that maybe originally it was mixed, and that later they became unified and just happened to fall two one way and one the other.

You heard correctly: one of the main differences between the lipids is the glycerol phosphate used to attach the fatty acids (Bacteria) or fatty alcohols (Archaea). Bacteria (and Eukaryotes) use glycerol-3-phosphate and Archaea use glycerol-1-phosphate. These are stereoisomers with a chiral center making them mirror images of each other. There are two arguments against his mixing suggestion. The first is based upon the observation that fatty acid and membrane synthesis in modern Bacteria (e.g., E. coli have around 20 genes involved in this process). I would imagine that Archaea have a similar number of genes. Thus, it seems unlikely that a common ancestor to both domains carried duplicate membrane biosynthetic systems. The second, and this is just recall from a talk, is that the two different kinds of phospholipids cannot form a functional membrane. Take the second reason under advisement: I have yet to find a citation in which someone has actually done the experiments.

You raise a very good point. While our probes into the evolutionary history of genes have made stupendous advances in the past decade with a deluge of data, our knowledge of the development of cell structure and function is sparse. The most prevalent model for the development of the Eukaryotic cell is that it descended from a symbiotic merger of Bacterial and Archaeal cells, with the Bacteria donating most of the metabolic genes and the Archaea donating most of the informational genes (i.e., replication, transcription, translation). The devil is in the details: there are about a half dozen different models with each emphasizing a different aspect.


Originally Posted by Nereid

Is this the "shadow biosphere"WP, or closely related?

Yep. The idea has been tarnished by the arsenic fiasco. When I heard about the NASA news conference, I was excited and hoped an announcement of some such creature. I had been thinking about the shadow biosphere for a while, so when I watched the news conference and read the paper, I was very disappointed :(.


Originally Posted by Nereid

If so, how does the biochemical machinery "know" what to do, when a codon may mean more than one amino acid (or a start or a stop)?

In biology, there are always exceptions, and as you point out, the universal code is not quite so universal. For the most part, there are a few oddball organisms out there who have slightly rearranged their code for their genomic genes. Mitochondria and, I assume, chloroplasts have codes that have substantial differences from the "universal" one. This is not surprising since their translation system only needs to be good enough, thereby tolerating some changes. This is not to say that there is no selective pressure on the mitochondrial genes.

There is one exception that is found throughout the three domains: a stop codon is used to code for selenocysteine in a few genes. The mechanism of how this is accomplished is very different from the normal translation process. First, a serine-tRNASer is modified to make selenocyteine-tRNASer, replacing the oxygen with selenium. This Sel-tRNASer is delivered to the ribosome using a specific protein that substitutes for the factor that delivers aa-tRNA. Additionally, a sequence in the mRNA is required to signal, "Insert the Sel-tRNASer at this stop codon." About half a dozen different proteins participate in this process. It's so rare that this is generally ignored unless one is examining a gene in which this is known to happen.



Originally Posted by ShinAce

It was a shame that it was given to physics students who missed the point entirely. I did get lots of time to speak to the presenter as a result. Despite his work, he wanted to focus on the role of protein folding.

Twas a shame, but I can understand why he may have chosen to emphasize that aspect of his research in his talk. He might of thought that kinetic modelling of translation would be more interesting for the students -- at least more accessible if they had ever taken a biology course. Protein folding is a difficult subject with a lot of history, structural detail, thermodynamics and modelling. Nevertheless, control of translation elongation rate is important in protein folding. If you take a protein and denature it by heating or chemical treatment (i.e., turn a protein from folded to unfolded) and then try to get it to refold back into its original functional form, many never do. They fold into a non-functional form which is stuck at an energy minimum. For some of these proteins, people have demonstrated that the ribosome translates some specific codon, or codon pairs, slowly. This allows time for the nascent protein that is just emerging from the ribosome to make a critical fold. Translate those codons too quickly and the following protein segment can interact with the unfolded segment, preventing proper folding.

I am happy to see that there is renewed interest in translation. Once the basic mechanisms were worked out, many people left the field to get into the mechanisms of transcription control, which became easier and easier with the new DNA technologies. Several labs did continue to develop the system, and now it is apparent that there is a whole bunch of interesting biology going on.

A similar thing goes on in transcription in which RNA polymerase will initiate transcription, transcribe a short distance and pause from seconds to hours, preventing new initiation from taking place. For those genes where RNA polymerase pauses for an extended period, they can be turned on by a trans-acting factor binding to the paused complex, releasing the pause, and allowing transcription of the gene.