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Thread: Genes...How Many are Required?

  1. #1 Genes...How Many are Required? 
    Forum Radioactive Isotope zinjanthropos's Avatar
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    I hope I word this right but.....Is there a minimum quantity of genes that need to be present in a stretch of DNA to qualify it as part of a living organism? Can DNA carry only one gene in chain of genes, all being the same, and still be part of a living organism??


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    SHF
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    Blueprint for creating artificial life is discovered Minimum genes to support living organisms found - News - The Independent


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    Forum Radioactive Isotope zinjanthropos's Avatar
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    If according to the article the minimum number is 300-350 then I guess the next question would be why the switch goes on at that number? Can we currently observe chains under the 300 total in nature and if so where?
    All that belongs to human understanding, in this deep ignorance and obscurity, is to be skeptical, or at least cautious; and not to admit of any hypothesis, whatsoever; much less, of any which is supported by no appearance of probability...Hume
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    Forum Professor Zwolver's Avatar
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    Lol.. i'd say the minimum number of genes required would be less, if the lifeform was parasitic or symbiotic with another one..

    Why is it 300.. Well, if it has to maintain it's DNA, it'll have to read it (4genes), copy it (4genes), repair it(10genes). It's proteins have to be constructed (20genes), energy will have to be stored (4genes), RNA carriers for every aminoacid (256genes), actually one for every possible codon (except, which don't require one but have one anyway). Then it needs a way to produce fats (8genes), a way to destroy foreign DNA/RNA (8genes). And it needs things i forgot to mention (xxgenes).. thats about 300..

    Please do not take this post literally, i have not checked, i am just guessing .. This is, what i think is a probable makeup for a genome...
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    SHF
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    This is an interesting question. It popped back into my mind today. Some further looking around and we find the 300-350 postulated in the news article I posted previously is superseded (or subseded depending on how you look at it, and if we pretend subseded is a word).

    So the organism in the link of the previous post was M.genitalium. Here is a journal article on it (rather than a newspaper article like the previous link):

    Regulation of transcription by DNA supercoiling in Mycoplasma genitalium: global control in the smallest known self-replicating genome
    Charles J. Dorman
    Molecular Microbiology (2011) 81(2), 302–304

    In it is says: “The 580-kilo-base-pair genome of M. genitalium contains just 470 genes”

    (note that the 300-350 we were talking about before was in the news article which stated:
    “"The bottom line is that out of the just over 500 genes in M. genitalium - the simplest free-living organism there is - we found that between 300 and 350 genes seem to be essential for growth," Dr Fraser said.”)

    -----
    Just to note for eukaryotes:

    The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis
    Nicolas Corradi1,*,†, Jean-François Pombert1,*, Laurent Farinelli2, Elizabeth S. Didier3 & Patrick J. Keeling1
    naturecommunications | 1:77 | DOI: 10.1038/ncomms1082

    This paper states:
    “Overall, microsporid*ian nuclear genomes are the most reduced and compacted of any eukaryotic cell, including picoplankton and other obligately intracellular parasites such as Plasmodium, the agent of malaria.”

    “The remainder of the genome is relatively con*served in content, order and density, and indeed we find that the intergenic regions and the introns are remarkably well conserved at the sequence level, altogether suggesting that these chromosome ‘cores’ have reached a certain limit of reduction and additional sub*stantial changes to them are likely to be difficult.”

    “Altogether, 1,833 protein-coding genes were identified in the assembly. If complete, this would result in a coding capacity that is almost 10% smaller than that of E. cuniculi, and the smallest identified in a eukaryote.”


    -----
    Thought this was interesting also (it talks about an organism that uses base pairs with less nitrogen where possible (I guess the nitrogen supply, but not the carbon supply, is a rate-limiter for it). So there are ways of ‘simplifying’ the genome (with regard to your environment in this case because the biochemical burden is reduced) without necessarily having fewer genes. This link also notes that this organism (Pelagibacter) is self-sufficient unlike the M.genitalium (although the quote from Dr Fraser above says M.genitalium is free-living, so hmmm)

    BBC NEWS | Science/Nature | Ocean bug has 'smallest genome'

    “Humans have around 30,000 genes that determine everything from our eye colour to our sex but Pelagibacter has just 1,354, US biologists report in the journal Science.
    (…)
    Pelagibacter has even gone one step further. It has chosen where possible to use genetic letters - or base pairs - which use less nitrogen in their construction: nitrogen is a difficult nutrient for living things to obtain.
    (…)
    There are organisms with smaller genomes - Mycoplasma genitalium has about 400 genes. But these are all obligate parasites or symbionts, relying on other organisms to do the jobs they have abandoned. Pelagibacter is entirely self-sufficient.
    (…)
    There is a great deal of interest in finding out how few genes a living organism can get away with. Bio-entrepreneur Craig Venter is trying to create an artificial version of a bacterium, aiming for as few as 300 genes.
    (…)
    Stephen Giovannoni says the synthetic one will barely function. But Pelagibacter on the other hand, accounting for a quarter of all organisms in the ocean, is a shining example of Darwin's principle, the survival of the fittest.”


    -----

    This bacterium has 182 protein-coding genes:

    Smallest genome clocks in at 182 genes : Nature News

    “How small can a genome get and still run a living organism? Researchers now say that a symbiotic bacterium called Carsonella ruddii, which lives off sap-feeding insects, has taken the record for smallest genome with just 159,662 'letters' (or base pairs) of DNA and 182 protein-coding genes. At one-third the size of previously found 'minimal' organisms, it is smaller than researchers thought they would find.

    (…)
    It is generally thought that a minimal genome will need to include genes for replication and for protein synthesis, and probably also for making the enzymes needed to construct basic building blocks, such as amino acids, from chemicals available in the immediate environment.

    B. aphidicola challenges that idea, because it lacks the genes needed to make the essential amino acid tryptophan. Since the aphid hosts can't make this amino acid either, where does it come from? Latorre and her colleagues think it is supplied by a secondary symbiotic bacterium, showing just how interdependent these groups of organisms may become.
    "The work shows that all discussions of minimal genomes have to think about the environment in which the organism will live," says Siv Andersson, an evolutionary molecular biologist at the University of Uppsala in Sweden.

    C. ruddii seems even more extreme. "Its gene inventory seems insufficient for most biological processes that appear to be essential for bacterial life," write Atsushi Nakabachi at the University of Arizona in Tucson, Masahira Hattori at the University of Tokyo, Japan, and their colleagues. At the moment, the researchers are not sure how C. ruddii copes, although they speculate that some of the necessary genes may have been transferred over evolutionary time to the genomes of the host.

    That is precisely what is thought to have happened during the evolution of the compartments called mitochondria in our own cells, which are responsible for energy production. These are believed to have once been symbionts that lost all autonomy by relinquishing most of their genes to the host (mitochondria still have their own DNA).

    Andersson says that C. ruddii might be analogues of mitochondria, caught in the process of changing from separate but dependent organisms into structures that will be engulfed and incorporated into the host cells.”

    ---

    Then there is:
    What are the Smallest Genomes?
    “the smallest reported genome found outside an organelle was the Tremblaya genome, which has just 121 genes,”

    Although, this would not be considered as an independent organism (see: Complete genome sequence of "Candidatus Tremblay... [J Bacteriol. 2011] - PubMed - NCBI)

    ----

    Then we come to acellular ‘life’ genomes:
    Virus - Wikipedia, the free encyclopedia
    “The smallest viral genomes – the ssDNA circoviruses, family Circoviridae – code for only two proteins and have a genome size of only 2 kilobases”

    Complete Genome Sequence of a Highly Prevalent Porcine Circovirus 2 Isolated from Piglet Stool Samples in China
    “The genome of PCV2 strain JSTZ is a single-stranded DNA molecule comprising 1,767 bp, with a GC content of 48.33%. It contained at least three open reading frames (ORFs), encoding 2 major proteins. ORF1 encodes the replicase protein Rep; ORF2 encodes the viral capsid (cap) protein.”

    ---

    So…..
    if you can be an obligate parasite / symbiont, relying on host / other symbiont genome for some things, then you can have a smaller DNA (do you include these? Obviously this raises the point that many organisms are obligate parasites / symbionts – we, homo sapiens sapiens, need our gut flora for example) (could we include mitochondria or chloroplasts in the discussion? I suppose they are not considered as individual organisms so perhaps not, they are considered as organelles). [it was interesting in the paper on C.ruddii to read “C. ruddii might be analogues of mitochondria, caught in the process of changing from separate but dependent organisms into structures that will be engulfed and incorporated into the host cells”]

    Zwolver noted some of the possibly required gene types; I say possibly as some things, like DNA expression regulation can have non-coding regulation such as by coiling / state of winding (as noted in the first paper cited in this post. (the state of coiling being effected by such things as osmolality)

    Also it depends if you are asking about total number of genes or total bp (e.g. shorter gene sequences (exons), fewer/smaller intragenic regions, overlapping coding sequences, etc)

    I presume one of the key disadvantages of having a minimal genome is that (for want of a better phrase) it makes it harder to evolve (e.g. by gene duplication and divergence). Although, Pelagibacter seems to be doing well for its self. Another disadvantage would be limitations of function (but if you only need a few functions to thrive then so be it)
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