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Author Sean B. Carroll mentions that there are about 500 genes common to all organisms. They have to do with the essential DNA machinery and so forth. What are these genes? Where can I read more about this fascinating concept? When you google immortal genes you get mentions of Sean B. Carroll. What term do others use for these genes?

"When we compare the genomes of Archaea, bacteria, fungi, plants, and animals, we find about 500 genes that exist in all domains of life... The functions of immortal genes are central... processes such as decoding DNA ... and making proteins. All forms of life have depended on these genes since the origin of complex DNA-encoded life early in Earth's history." (Making of the Fittest, pg 79)

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    $\begingroup$ I've not heard the term. However, "Housekeeping genes" are genes that are always turned on as a basic function of being alive. $\endgroup$ – Karl Kjer Jan 19 '18 at 14:23
  • $\begingroup$ That’s the term you get when a physicist writes about biology. $\endgroup$ – canadianer Jan 19 '18 at 16:32
  • $\begingroup$ Please provide a reference with a preferably a link for Carroll's statement. Otherwise your question is unclear. $\endgroup$ – David Jan 19 '18 at 17:13
  • $\begingroup$ Ok I added quote from his book. I would LOVE some details on what these genes are or what term others use for them. $\endgroup$ – user39663 Jan 19 '18 at 20:16
  • $\begingroup$ In order to expand my answer (did you read it?) in an appropriate manner, could you indicate how much biochemistry you know. For example, can you think of 100+ genes that would be required for ribosomal protein synthesis in any organism? Do you know what replication, transcription and translation are? Have you heard of glycolysis. If your answer is generally "no" then the expansion of my answer will need to be different from if it is yes. $\endgroup$ – David Jan 20 '18 at 14:29
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Introduction

I believe that Sean B. Caroll is confusing:

• the minimum number of genes required for a viable organism

with

• those genes that are present in all organisms — so called ‘immortal genes’

I will deal with each in turn.

The minimum number of genes required for a viable organism

I have not read the book from which the quotation is taken. From its context and my knowledge I think that the author is mistakenly interpreting ‘the minimum number of genes required for a viable organism’ as ‘the genes present in all organisms’. This is because he seems to be referring to work from the laboratory of Craig Ventner on engineering mycoplasma.

Mycoplasma are among the smallest organisms capable of independent life. They have a genome of about 500 coding sequences, but as parasitic organisms they devotes some of these genes to their parasitic mode of life, while they lack others that the host provides.

The number of 500 may actually be too high: a figure of 300 is quoted in this description, who had plans of Ventner’s plans to build an organism containing a minimal genome containing only such essential genes. There is more on this in a Wikipedia article entitled Mycoplasma laboratorium. It should be noted that the word “immortal” does not appear in either account.

‘Les Immortels’ — genes present in all organisms

The poster would like a list of those genes essential to life, but I know of no such list. How would one go about composing one?

First, one has to set the rules. Do parasites, such as mycoplasma, which are dependent on their host organism, count? Do human beings count? We require amino acids and vitamins, but obtain them from food rather than synthesizing them ourselves. So although it is necessary that a self-sufficient organism have the enzymes for synthesizing the 20 amino acids of the genetic code, these are not all present in humans. I would suggest that we have to restrict ‘les immortels’ to self-sufficient organisms.

Second, one has to decide whether one is talking about a set of genes for accomplishing a function, or individual genes with a structural relationship in all living things that suggests a common identity. For example all cellular organisms (i.e. excluding viruses) must have ribosomes to synthesize proteins, but the protein complement of those ribosomes differs among organisms. Thus, the ribosomal proteins necessary to engineer a minimal mycoplasma may differ from those present in a bacterium such as Escherichia coli, and will certainly not be common to humans. I would suggest we would have to go for the latter.

Having made this decision, one would get a team of undergraduate students to take all the genes in the genome of E. coli (or even of a mycoplasma) and perform BLAST searches to see whether they are present in representative organisms. Unfortunately I am no longer in a position to torment undergraduate students in this way, so I will have to start a list myself and encourage others to add to (or subtract from) it.

The List — a start

The genes for DNA replication, transcription of RNA and protein synthesis constitute the low hanging fruit her. My area is (used to be) protein synthesis, so I will start there:

Protein Synthesis

Large and small subunit and 5S ribosomal RNAs (3)

Ribosomal proteins (≤32)

Protein synthesis factors — EF1, EF2, IF1 and possibly others

Aminoacyl tRNA synthetases (20?)

tRNAs? — but all that is conserved is probably the anticodon (and sometimes not even that)

Accessory enzymes for protein synthesis:

Pseudouridine synthase

rRNA methylases?

DNA synthesis

B-family DNA polymerases?

RNA synthesis

? Evolutionarily related, but complicated because of multi-subunit nature

But if DNA synthesis is a problem, the reactions leading from RNA to DNA are surely not:

Enzymes of nucleotide metabolism

Ribonucleotide reductase (two subunits)

Thymidylate synthase

Uracil DNA-glycosylase?

Tetrahydrofolate reductase?

Enzymes for interconversion of nucleotides — Adenylate kinase? Nucleoside-diphosphate kinase?

Metabolism

This requires some work. One cannot specify either aerobic or anaerobic metabolsm, but in either case one needs oxido-reducto enzymes. Enzymes of hexose metabolism — hexokinase? Enzymes to metabolize key intermediates like glutamate and glutamine, and enzymes for introducing different groups in synthetic processes. This could make an interesting crowd-sourced project, or, failing that, a game for your next Biochemistry Christmas Party.

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    $\begingroup$ Aren't the number of genes common to all organisms and the number required in a minimal organism different concepts? Related, sure, but different. $\endgroup$ – Jack Aidley Mar 21 '18 at 14:13
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    $\begingroup$ @JackAidley — They are indeed. However, it is Sean Carroll — to whom the poster refers — who is confusing the two and actually refering to the number in a minimal organism. I tried to make that clear in my answer. Thus, a minimum set of genes might require 50 ribosomal proteins (say) but it may be possible to identify only a half a dozen (if that) that are common to all organisms. Likewise a system for replication and transcription is required, but the divergence between eukaryotes and prokaryotes may be such as to exclude common components (not my field). $\endgroup$ – David Mar 21 '18 at 15:15
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    $\begingroup$ I would be happier if you included that in your answer directly. $\endgroup$ – Jack Aidley Mar 21 '18 at 15:41
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    $\begingroup$ I have now edited my answer to address the valid point made by @JackAidley. The original answer was more directed to the poster and the extent of his biochemical knowledge, but the purpose of SE Biology is to provide answers of general utility, so the current answer refers to aspects of biochemistry with which the naive reader may not be familiar. The partial list is new. I realize it is scanty, but it is better than nothing, and nothing is what was there before. $\endgroup$ – David Mar 21 '18 at 23:00
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It seems likely that Carroll's claim is untrue, in fact there are a much smaller number of genes shared between organisms and genes that provide core functions appear to have independent evolutionary histories in many cases (source).

It is unfortunate that Carroll does not provide a reference for this claim, so I do not know where he was getting his data from but the book was written in 2006 which is the infancy of whole genome sequencing so that may be the cause for the error. But, even so, by 2003 evidence was pointing to a much smaller number, and even the earliest genome comparison papers (e.g. here) weren't finding conservation on the scale suggested by Carroll.

So, rather than "around 500" immortal genes, it appears that there is a much smaller number of genes that both common to all life and share evolutionary history, perhaps 30 or so and, remember, these numbers can only ever go down as we sequence more species so it's entirely possible that it will turn out that there are no genes that are universal and share common evolutionary histories in all organisms.

You may wonder how this can happen when there are so many core functions that a cell must surely have to function. The answer appears to be that new genes able to perform these functions evolve, perhaps specialised to operate under particular conditions, and - for a time - the organism carries both versions of the gene until eventually losing the original gene in some lineages. You can see this pattern of evolution in organisms where an enzyme is known in two forms and some carry one or the other, while some carry both (here's detail on one such example).

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