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I know there is extensive research into the taxonomy and evolution of protein domains and many connections are, and are continuing to be, found between numerous domains. However, as far as I can see, new domains always arise from preexisting ones. I have seen no paper, in any field, showing the development of a new protein domain from a random piece of DNA which just mutates a start codon and synthesizes a new protein with no apparent function. I know this is theoretically possible but has anyone seen any evidence it has happened in any form of life in any geological period of time? OR are there some other mechanisms that could generate novel domains from non-coding DNA that I have overlooked when searching the journals?

My thinking is that, if de novo protein domain generation doesn't occurr, does it mean that all protein domains are a kind of "progeny" of a single domain that arose at the onset of life as we know it (or maybe even was the first lifeform on Earth). It seems very strange to me that this hasn't been pointed out by now since it's a relatively simple deduction. Thus, I'm asking either for a reference paper showing evidence for the evolution of de novo protein domains from a random piece of DNA that somehow managed to turn into a gene or for a reference to a paper discussing the idea that all proteins originate from a common ancestor existing at the onset of life and even, possibly, a single domain as old as life itself?

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  • $\begingroup$ You're right, it doesn't work this way. Which is why you've never seen a paper on it. "I'm asking either for a reference paper showing evidence for the evolution of de novo protein domain unknown by now from a random piece of DNA that somehow managed to turn into a gene" You won't get one; that's not how it happens. $\endgroup$
    – anongoodnurse
    Commented Sep 25, 2017 at 16:35
  • $\begingroup$ Then how does it happens @anongoodnurse? Please, explain how we can get a brand new protein domain and even possible new family of domains if there is no previous domain it came from? As far as I know all domains come from previous domains, all genes evolved from previous genes and all proteins from previous proteins. But if that is true does it mean all domains, all proteins, all genes, the entire biodiversity evolved from a single ancestor gene, which coded a single ancestor protein and may be it had a single ancestor domain? Am I right on track or am I missing out something important here? $\endgroup$
    – Yordan Yordanov
    Commented Sep 25, 2017 at 16:59
  • $\begingroup$ I've trimmed down your question a little bit, I hope it's still okay for you. I think it is interesting and will try and look for some literature. $\endgroup$
    – canadianer
    Commented Sep 26, 2017 at 17:19
  • $\begingroup$ Yes, there is no problem. I think it's better this way, too. :) I hope I could know do novel domains rise from random pieces of DNA or all proteins and genes just like the cells they are in come from a single ancestor? Of course we could speculate about LUCA containing all the genes necessary for the entire biodiversity but even then the question remains: Did LUCA itself had its genes and proteins evolved from a single gene with a single protein and may be a single domain? I'm thrilled to know could we trace all biodiversity to just one molecule, even more-to just one domain? $\endgroup$
    – Yordan Yordanov
    Commented Sep 26, 2017 at 19:58

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Yes. Novel protein domains can arise de novo in nature. The evidence is quite solid as those new domains show all the expected mutation patterns and statistical properties (expected for something evolving from DNA that doesn't yet encode for a domain). E.g.: see the following meta-analysis, which also describes how those new domains behave relative to older ones, and how they integrate into proteins: Toll-Riera et Mar Alba 2013, BMC Evolutionary Biology, "Emergence of novel domains in proteins": https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-47

If you are additionally interested in new genes, the following mini-review: http://www.sciencedirect.com/science/article/pii/S0960982214001547#bib20 .

If you are additionally interested in in-vitro evolution, which is directly observable within the life-span of single humans, the following review: http://www.sciencedirect.com/science/article/pii/S0022175904001309

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  • $\begingroup$ The link is dead for the first article. Could you write the titles/authors/etc for these articles? $\endgroup$
    – canadianer
    Commented Sep 28, 2017 at 0:09
  • $\begingroup$ Maybe the link isn't dead but rather my useless network is acting up. In any case, full citations would be appreciated. $\endgroup$
    – canadianer
    Commented Sep 28, 2017 at 0:38
  • $\begingroup$ note that presently NPG appears to have server problems (even nature.com is down), which also applies to the journal above. $\endgroup$
    – tsttst
    Commented Sep 28, 2017 at 4:19
  • $\begingroup$ @tsttst, if you could provide a list of the journals you targeted in your search and can provide me with a list of keywords I would give the price to you. It would be also useful if you can name the search engine you used. My background is in theoretical biology and the origins of Life, so, I'm not really good at genetics and modern fields connected to proteomics and may be have been using the wrong keywords, so, if you can tell me the 2 lists-of related journals and keywords I will be greatly thankful. I wish to know how to search better and if you can help me I will vote for your answer. $\endgroup$
    – Yordan Yordanov
    Commented Sep 29, 2017 at 19:02
  • $\begingroup$ @YordanYordanov: I knew that the topics covered by links 2 and 3 would exist and concluded that they would be thematically close, if something on de novo evolution of domains existed. Since the latter seems to be a fascinating and important topic I concluded that it would be covered tangentially by reviews on topic of link 2 and 3. Thus I looked for first review in google scholar on topic 2 within a good journal ( main npg or cell press ) and would read it - hoping to satisfy my and your curiosity on topic 1. Indeed the first review would contain cognate citation towards specialist article. $\endgroup$
    – tsttst
    Commented Sep 30, 2017 at 2:06

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