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Fosdick  Suspended Member (Idle past 5529 days) Posts: 1793 From: Upper Slobovia Joined: |
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Author | Topic: What about those jumping genes? | ||||||||||||||||||||||||
Fosdick  Suspended Member (Idle past 5529 days) Posts: 1793 From: Upper Slobovia Joined: |
crash wrote:
...But the idea of finding HGT's in genomic sequences without a mechanism that makes it a lot more likely seems astronomical to me.
But what about those mariner elements? Maybe transposons (on steroids?) are the mechanisms you're looking for. If they work for genes, then why not genomes? The OP article speaks to a whole genome jumping from prokaryotes to eukaryotes. That makes a jump from insects to humans look trivial by comparison.
The classical models of molecular phylogeny don't have much room for HGT.
Do you think they should? I do. ”HM
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crashfrog Member (Idle past 1495 days) Posts: 19762 From: Silver Spring, MD Joined: |
Maybe transposons (on steroids?) are the mechanisms you're looking for. Back to the same problems with naked DNA wandering around an organism's body. If a retrovirus is the simplest possible chemical structure that can get DNA from one cell to another reliably, the idea of naked DNA doing it seems unfeasible.
Do you think they should? I do. Yeah, I do, too. For right now I think the problem is that HGT, if it's found to be common, is going to cast a lot of doubt on constructed phylogenies. Possibly a lot more doubt than is justified. No reason to stop looking for HGT, of course, but it's a good reason to refrain from a conclusion of HGT until one is very, very sure.
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Fosdick  Suspended Member (Idle past 5529 days) Posts: 1793 From: Upper Slobovia Joined: |
Back to the same problems with naked DNA wandering around an organism's body. If a retrovirus is the simplest possible chemical structure that can get DNA from one cell to another reliably, the idea of naked DNA doing it seems unfeasible.
Naked DNA transfer is an interesting concept. Do you know of any mariner elements or transposons (if they are categorically different) that are able to operate apart from viral activity? ”HM
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crashfrog Member (Idle past 1495 days) Posts: 19762 From: Silver Spring, MD Joined: |
Do you know of any mariner elements or transposons (if they are categorically different) that are able to operate apart from viral activity? I'm afraid I don't.
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molbiogirl Member (Idle past 2670 days) Posts: 1909 From: MO Joined: |
After having read the brief "news report" in New Scientist, I tried to track down the paper. I haven't had any luck.
Do you have a link? If Andy Brass et. al. weren't able to publish their results, the tsetse/human HGT thing isn't worth discussing.
HM writes: Do you know of any mariner elements or transposons (if they are categorically different... You seem a bit confused. A mariner element is a transposon. maTA Clade of Transposons Intermediate Between mariner and Tc1 | Molecular Biology and Evolution | Oxford Academic
The mariner transposon of Drosophila mauritiana and the Tc1 transposable element (TE) of Caenorhabditis elegans are members of a superfamily of class II TEs that are found in a large number of organisms, ranging from fungi to vertebrates. Mariner elements are very small ...
Mariner elements are generally about 1.3 kb long and share "low overall sequence identity" between species.
Despite a low overall sequence identity (16%) across the superfamily (Robertson 1995), the transposases share several functional and predicted structural characters that suggest they are derived from a common ancestor (Plasterk et. al. 1999). Given this low sequence identity, it doesn't seem likely that Mariner sequences transfer "whole" to their host.
HM writes: ...that are able to operate apart from viral activity? Just to be clear. Transposons are similar to viruses, but it isn't fair to say that they "operate (with) viral activity".
wiki writes: (Transposons) are similar to viruses. Viruses and transposons share features in their genome structure and biochemical abilities. Transposons may confer benefit to their hosts, but it is generally thought that they are selfish DNA parasites. Transposons notoriously confer antibiotic resistance (and that is of benefit to the host) and they may have evolved into useful cellular "tools" for eukaryotes (telomerase and RAG1/RAG2).
Transposons link.
Telomerase, the enzyme essential for maintaining chromosome length, is closely related to the reverse transcriptase of LINEs and may have evolved from it. RAG-1 and RAG-2. The proteins encoded by these genes are needed to assemble the repertoire of antibodies and T-cells receptors (TCRs) used by the adaptive immune system. The mechanism resembles that of the cut and paste method of Class II transposons , and the RAG genes may have evolved from them. If so, the event occurred some 450 million years ago when the jawed vertebrates evolved from jawless ancestors. Only jawed vertebrates have an adaptive immune system and the RAG-1 and RAG-2 genes that make it possible. HM writes: Maybe transposons (on steroids?) are the mechanisms you're looking for. If they work for genes, then why not genomes? We are well aware of the mechanism for Class II TE transposition. Are you suggesting that a Class II TE (mariner) is responsible for moving an entire tsetse fly genome into a host? If you are able to provide support for that assertion, I would like to see it. Edited by molbiogirl, : No reason given.
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Fosdick  Suspended Member (Idle past 5529 days) Posts: 1793 From: Upper Slobovia Joined: |
molbiogirl asks:
After having read the brief "news report" in New Scientist, I tried to track down the paper. I haven't had any luck. Do you have a link?
Only the one I posted to the abstract of the article. But I have a hard copy of the article somewhere in my files (I'm watching the Seahawks right now so I'm going to go dig for it).
You seem a bit confused. A mariner element is a transposon.
Thanks. I wasn't entirely sure.
Just to be clear. Transposons are similar to viruses, but it isn't fair to say that they "operate (with) viral activity".
Thanks again. With you and crashfrog around I'll finally get things straight.
Are you suggesting that a Class II TE (mariner) is responsible for moving an entire tsetse fly genome into a host?
No. Only fly genes. The only time I referenced whole-genome transfer was with respect to the OP artcile. ”HM
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molbiogirl Member (Idle past 2670 days) Posts: 1909 From: MO Joined: |
No. Only fly genes. The only time I referenced whole-genome transfer was with respect to the OP artcile. From the article you cited:
In a project for the Ministry of Agriculture, Fisheries and Food, Andy Brass and two colleagues at the University of Manchester compared the DNA of 80 000 different organisms, using over five million sequences. They found seven pairs of similar mariner sequences. For instance, 83 per cent of the sequence in the tsetse fly "Glossina palpalis", a blood-sucker that spreads human sleeping sickness, was the same as a sequence in humans. Such a close match is "strong suggestive evidence" that mariner has moved between tsetse flies and humans, Brass says. The transfer occurred recently in evolutionary terms, he thinks, although it is not clear whether mariner jumped from the fly to humans or vice versa. The author is pointing out that flies and humans have the mariner gene in common. Not that a fly gene is in the human genome. Gueiros-Filho F J, Beverley S M. Science. Trans kingdom transposition of the Drosophila element mariner within the protozoan Leishmania 1997;276:1716-1719.
Transposons of the mariner/Tc1 family are ubiquitous elements of eukaryotic genomes, occurring in virtually every taxon examined (1-3). Phylogenetic studies of mariner elements have provided compelling evidence for the occurrence of horizontal transfer across species during evolution, traversing distances as far as that separating insects and flatworms. HGT is just interspecific transfer of DNA.
wiki writes: Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved. wiki writes: While horizontal gene transfer is well-known among bacteria, it is only within the past 10 years that its occurrence has become recognized among higher plants and animals. The scope for horizontal gene transfer is essentially the entire biosphere, with bacteria and viruses serving both as intermediaries for gene trafficking and as reservoirs for gene multiplication and recombination (the process of making new combinations of genetic material). Here's how HGT happens in prokaryotes:
wiki writes: * Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA). This process is relatively common in bacteria, but less common in eukaryotes. * Transduction, the process in which bacterial DNA is moved from one bacterium to another by a bacterial virus (a bacteriophage, commonly called a phage). * Bacterial conjugation, a process in which a living bacterial cell transfers genetic material through cell-to-cell contact. In other words, the fly and the human could have gotten the mariner TE from some common bacterial virus. Edited by molbiogirl, : fixed grammar
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Fosdick  Suspended Member (Idle past 5529 days) Posts: 1793 From: Upper Slobovia Joined: |
molbiogirl,
Thank you for that contribution. I think what you have written above pretty much dispells my fantasy about tsetse-fly genes hopping over into the human genome. It was fun while it lasted, but your argument is compelling. ...So much for genetic transmorgrification. ”HM
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crashfrog Member (Idle past 1495 days) Posts: 19762 From: Silver Spring, MD Joined: |
Thank you for that contribution. Seconded. A fascinatingly informative series of posts. Kudos!
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Buzsaw Inactive Member |
I use a lot more than faith for debating creationism at EvC, in fact a lot more non-faith arguments for my ideology. Just as in secularist arguments I'm constantly required to document things etc just like you people are. This thread may not be the place to debate this and I won't because I'm not capable, but I grab onto all I can which supports my ideology to any degree. So if HGT should become imperically substantiated I still understand it as a problem for accredited science creationists to address. Frankly as a Biblical creationist I'm pleased to see that it is debatable.
BUZSAW B 4 U 2 C Y BUZ SAW. The immeasurable present is forever consuming the eternal future and extending the infinite past.
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molbiogirl Member (Idle past 2670 days) Posts: 1909 From: MO Joined: |
FYI, buz.
HGT happens all the time. In bacteria and invertebrates. The only thing that was "debatable" on this thread was the transfer of eukaryotic DNA. And that was mostly just a misunderstanding. Turns out no fly genes were found in the human genome. Btw. Thanks Crash. Thanks HM. My pleasure.
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Buzsaw Inactive Member |
OK Mobiogirl, thanks. Perhaps then so long as it's not observed in higher life forms CF and HM are right that it has little or no relevance to the creationism/evolution debate.
BUZSAW B 4 U 2 C Y BUZ SAW. The immeasurable present is forever consuming the eternal future and extending the infinite past.
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molbiogirl Member (Idle past 2670 days) Posts: 1909 From: MO Joined: |
Buz, HGT has happened in eukaryotes.
The mitochondria. The chloroplast. Telomerase. RAG1 and RAG2 (important to antibodies and T cells). And that's just off the top of my head. Were I to research the question a bit, I am certain I could provide further examples of HGT in eukaryotes.
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Fosdick  Suspended Member (Idle past 5529 days) Posts: 1793 From: Upper Slobovia Joined: |
molbiogirl, you wrote:
The only thing that was "debatable" on this thread was the transfer of eukaryotic DNA. And that was mostly just a misunderstanding. Turns out no fly genes were found in the human genome. You and crashfrog seem to be astute in this business of HGT. I am neither astute nor in the business, but I read enough about it to be dangerous (at least to my own credibility). I have been reading Frederic Bushman's Lateral DNA Transfer/Mechanisms and Consequences (2002), in which he asserts "Our own DNA is a complex composite of imported sequences and mobile genetic parasites..." (p. xiii), and he speaks of "genes floating on a sea of retrotransposons" (pp. 239-275). Boy, does that ignite my imagination! Bushman uses the term "lateral DNA transfer" instead of HGT. Have either of you read his works? He appears to be a leader in this area at the Salk Institute. In Chapter 19 of his book he pursues the question: "DNA Transposons of Eukaryotes: Mariners Sailing to Survive?" In that pursuit he observes (p. 282): "Consider the cecropia family of Tc1/mariner elements, named for the giant silk worm moth Hyalophora cecropia, in which the first family member was found (Fig. 9.7) [see below]. Members of this family have been found in insects, flatworms, a hydra, and humans."
"Figure 9.7. Sequence relationship among mariner elements of the cecropia subfamily. Note that a human element clusters with several insects, whereas a prosimian sequence clusters in a different part of the tree with other insects." (p. 282) I don't know, crash and molbiogirl, those bug genes look pretty jumpy to me. ”HM
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molbiogirl Member (Idle past 2670 days) Posts: 1909 From: MO Joined: |
But where did Hyalophora cecropia get the mariner element?
It was first identified in a moth, but no one (that I've found) indicates where this transposon originated. Btw. Transposons are 45% of your genome.
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