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Robust Software Management in Genomes What'sNEW >

If evolution works by cosmic ancestry, it must depend on robust software management within genomes. For an example of this capability, many bacteria are able to form dormant endospores in response to environmental threats. The endospore has a multi-layered protective outer coat, reduced water content, and can resist hazards like starvation, freezing, drought, vacuum, high pressure, acceleration and most poisons. With no metabolism, an endospore may remain viable for millenia, millions of years, possibly indefinitely. And when safe conditions are restored, the cell may return to active life again within minutes. Many genetically directed changes in the cell underlie the conversion from vegetative growth to sporulation (1).

Some of this capability has analogies in our familiar digital world, as when a portable computer runs low on battery power and automatically launches a shutdown routine. But the endospore is more analogous to the computer repackaged into its original protective shipping carton, somehow effected by robust software management.

Some bacteria, like Deinococcus radiodurans, have a very impressive capability to repair their genomes after the DNA has been severly fragmented by radiation. This reminds us of the "Defrag" function on most computers, but with something analogous to syntax- and spell-check included. (1.5)

These features of bacteria are matched by simlar capabilities among eukaryotes, where the genome exists in two nearly identical versions, so there's a backup copy. When a eukaryotic cell replaces a broken gene with the backup version, it's called "gene conversion" (2), an excellent example of robust software management.

Heat shock proteins, found in prokaryotes as well, are quickly produced when the cell experiences a sudden rise in temperature. (2.5) More examples include double strand break repair, gene duplication, the generation of intronless paralogs, not to mention meiosis.

New Environments

The examples given so far mainly pertain to protecting the cell or species and keeping the genome uncorrupted. But sometimes, in new situations, new genetic programming is needed. And there is plenty of evidence that programs can be optimized to suit changed conditions. A familiar example is the color vision of coelacanths, living 200 meters underwater where only dim blue light is available. In each of two color-receptors, only two amino acids are changed from the orthologous receptors in species living in brighter light. Each of these changes could be accomplished by one nucleotide substitution, not forbiddingly unlikely. Examples of similar optimization are everywhere in the tree of life.

Of course, random nucleotide substitutions are usually harmful and sometimes fatal. Therefore, it would be better if the tinkering were minimized until a need arises. There is programming to effect this. The phenomenon is called "adaptive mutation." By one account, ...the newly identified mutases, present in all cells, produce mutations only when a genetic or metabolic stress triggers their induction and activation. (2.6)

It would also help if the mutations were focussed on the appropriate nucleotides only, the ones needing to change. Indeed, "directed mutation" often confines the point mutations to positions where they may be useful. Among prokaryotes, diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. ...Crucially, the reverse transcriptase (RT) used is error-prone at template adenine bases, but has high fidelity at other template bases.... Massive and low-risk protein diversification offers clear advantages to any organism. (4.5)


Regulatory Changes

Horizontal Gene Transfer

is the whole story among bacteria
can be accelerated
can be initiated by the recipient species (
bacteria can kill to steal
"the amoeba replaced it with another gene with the same function from bacteria."(4)


DNA mismatch repair preferentially protects genes from mutation by Eric J. Belfield, Zhong Jie Ding et al., doi:10.1101/gr.219303.116, Genome Res., 12 Dec 2017.
Structural basis for the initiation of eukaryotic transcription-coupled DNA repair by Jun Xu et al., Nature, 30 Nov 2017.
Mismatch repair prefers exons by Dashiell J Massey and Amnon Koren, Nature Genetics, Dec 2017.
Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation by Katja R. Kasimatis and Patrick C. Phillips, G3, online 21 Nov 2017.
Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae by Rui Bai, Chuangye Yan, Ruixue Wan et al., Cell, 16 Nov 2017.
The Mobile World of Transposable Elements by Caryn Navarro, Trends in Genetics, Nov 2017.
23 Aug 2017: ...a different code embedded in histone marks....
Quantifying the mechanisms of domain gain in animal proteins by Marija Buljan, Adam Frankish and Alex Bateman, doi:10.1186/gb-2010-11-7-r74; and commentary: How do proteins gain new domains? by Joseph A Marsh and Sarah A Teichmann, doi:10.1186/gb-2010-11-7-126, Genome Biology, 15 Jul 2010.
15 Jul 2017: Several studies have suggested that TE [transposable element] insertions have contributed to the rewiring and evolution of regulatory networks by recruiting multiple genes into the same regulatory circuit.
06 Jul 2017: How bacteria remember and defend against harmful viruses.
22 May 2017: ...ERVL LTRs provide molecular mechanisms for stochastically scanning, rewiring, and recycling genetic information on an extraordinary scale.
24 Jul2016: A cell's deciphering arsenal....
28 Apr 2015: Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene.
19 Jan 2015: ...Deliberate killing of nonimmune cells ...releases DNA and makes it accessible for HGT.
07 July 2014: There is also compelling evidence that not only may mutations be non-random but horizontal gene transfer too need not be random.
20 Dec 2012: Evolution: A View from the 21st Century by James A. Shapiro
9 May 2006: The structure of a bacterial enzyme that inserts mobile gene cassettes has been resolved by French biochemists and geneticists.
24 Mar 2005: Plants can overwrite unhealthy genes.
28 Feb 2005: Can pre-existing genetic programs be pieced together?


1. Michael T. Madigan, John M. Martinko and Jack Parker, Brock Biology of Microorganisms, 8th ed., 1997. p 97.
1.5. Michael J. Daly and Kenneth W. Minton, "
Resistance to Radiation," Science, 24 November 1995.
2. Bruce Alberts et al., The Molecular Biology of the Cell, 3rd ed., 1994. p 268.
2.5. James D. Watson et al., The Molecular Biology of the Gene, 4th ed., 1987. p 485.
2.6. Miroslav Radman. "Enzymes of evolutionary change," doi:10.1038/44738, Nature, 28 October 1999.
3. Shozo Yokoyama et al., " Adaptive evolution of color vision of the Comoran coelacanth...," PNAS, 25 May 1999.
4. Eva C. M. Nowack et al., "Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora", PNAS, online 10 Oct 2016.
4.5. Blair G. Paul et al., "Targeted diversity generation by intraterrestrial archaea and archaeal viruses", doi:10.1038/ncomms7585, n 6585 v 6, Nature Communications, 23 Mar 2015.
5. Gary M. Dunny, "The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signalling, gene transfer, complexity and evolution" doi:10.1098/rstb.2007.2043, Phil. Trans. R. Soc. B, 29 Jul 2007.

Related CA Webpages

What Is Life? includes the suggestion, A Cell Is Like a Computer.
Why Sexual Reproduction? includes a section titled, Gene Conversion.
Viruses and Other Gene Transfer Mechanisms is relevant.
How is it Possible? has earlier refences for adaptive and directed mutation.
COSMIC ANCESTRY | Quick Guide | Site Search | Next | by Brig Klyce | All Rights Reserved