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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.

Changing Environments

The examples given so far mainly pertain to protecting the cell or species and keeping the genome uncorrupted. But sometimes, in new situations, genetic changes are needed. 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)

Macroevolution

Adaptation to changing environments often requires only microevolution — evolution attainable with minor tweaking and optimizing of existing proteins. Macroevolution, by contrast, requires wholly new programs. It is best illustrated by example. Examples would include the first earthly appearances of [a long list]. These evolutionary features depend on the first deployment of genetic sequences that contain the programming for [the long list]. This first deployment requires (1) that the programming is available, and (2) that the regulatory system is appropriate for it and synchronized with it. First, where does the programming come from?

Horizontal Gene Transfer

is the whole story among bacteria
can be accelerated
can be initiated by the recipient species (
5). bacteria can kill to steal
"the amoeba replaced it with another gene with the same function from bacteria." (4)
virual infection can transform whole eukaryotic species in few generations (3.5)

Regulatory Changes

Reverse Transcription

Pseudogenes

Gene Conversion

for restoration, optimization or exploration

Miscellaneous

What'sNEW

A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication by Monica S. Guo, Diane L. Haakonsen et al., doi:10.1016/j.cell.2018.08.029, Cell, 04 Oct 2018.
10 Oct 2018: Elegant and precise genetic programs guide the forces that allow seemingly identical starting cells to develop into highly specialized entities....
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability by Mathias Munschauer et al., doi:10.1038/s41586-018-0453-z, Nature, 27 Aug 2018.
The organization of genome duplication is a critical determinant of the landscape of genome maintenance by Blanca Gómez-Escoda and Pei-Yun Jenny Wu, doi:10.1101/gr.224527.117, Genome Res., 22 Jun 2018.
RES complex is associated with intron definition and required for zebrafish early embryogenesis by Juan Pablo Fernandez, Miguel Angel Moreno-Mateos et al., PLoS Genet., 03 Jul 2018. ...long introns surrounding short exons are recognized and spliced through "exon definition" mechanisms....
Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG by Thomas Dodd et al., PNAS, online 21 May 2018. Our results show that DNA sculpting, dynamic glycosylase interactions, and stabilizing contacts collectively provide a powerful mechanism for the detection and discrimination of modified bases and epigenetic marks in DNA.
Dynamic Architecture of DNA Repair Complexes and the Synaptonemal Complex at Sites of Meiotic Recombination by Alexander Woglar and Anne M. Villeneuve, Cell, doi:10.1016/j.cell.2018.03.066, online 10 May 2018. Meiotic double-strand breaks (DSBs) are generated and repaired in a highly regulated manner to ensure formation of crossovers (COs) while also enabling efficient non-CO repair to restore genome integrity.
A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization by Maike M.K. Hansen, Winnie Y. Wen, Elena Ingerman et al., Cell, doi:10.1016/j.cell.2018.04.005, online 10 May 2018.
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock by Vinesh Vinayachandran et al., Genome Res., online 14 Feb 2018. Together, these findings reveal protein–genome interactions that are robustly reprogrammed in precise and uniform ways far beyond what is elicited by changes in gene expression.
Stable Intronic Sequence RNAs Engage in Feedback Loops by Jun Wei Pek, Trends in Genetics, online 01 Feb 2018. The use of sisRNAs as mediators for local feedback control may be a general phenomenon.
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock by Vinesh Vinayachandran et al., Genome Res., online 14 Feb 2018. Our findings reveal a precise positional organization of proteins bound at most genes, some of which rapidly reorganize within minutes of heat shock.
RNA Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates by William H. Palmer et al., doi:10.1534/genetics.117.300567, Genetics, 01 Feb 2018.
Protecting and Diversifying the Germline by Ryan J. Gleason et al., doi:10.1534/genetics.117.300208, Genetics, 01 Feb 2018.
Systematic discovery of antiphage defense systems in the microbial pangenome by Shany Doron, Sarah Melamed et al., doi:10.1126/science.aar4120, Science, 25 Jan 2018. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.
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....
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....
07 Apr 2016: ...molecular-resolution reconstruction of a central assembly of the human spliceosome.
28 Apr 2015: Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene.
30 Jan 2015: I guess we owe the evolution of pregnancy to what are effectively genomic parasites.
19 Jan 2015: ...Deliberate killing of nonimmune cells ...releases DNA and makes it accessible for HGT.
07 July 2014: ...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
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.
Enard D, Depaulis F, Crollius HR, "Human and Non-Human Primate Genomes Share Hotspots of Positive Selection" [link], PLoS Genet 6(2): e1000840. doi:10.1371/journal.pgen.1000840, online 5 Feb 2010. "Our results show that positive selection affecting the same genes independently in human and other primates is a common phenomenon and is not restricted to specific functions such as defence against pathogens or reproduction."
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?
03 Nov 1998: Two geneticists find evidence for "a predominating integration mechanism," that inserts acquired foreign genes into genomes in clustered fragments.

References

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.
3.5. Susumu Ohno, Evolution by Gene Duplication, Springer-Verlag Publishing Company, 1970. p 55.
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.
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