Evolutionary Rewiring

Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

By Ruth Williams | February 26, 2015

Pseudomonas fluorescensWIKIMEDIA, RIRAQ25Bacteria that lack a vital protein for growing flagella—tail-like structures that enable the microbes to swim—can attain flagella in as little as four days given enough pressure to evolve, according to a paper published in Science today (February 26). Furthermore, this fast fix evolves in nearly the same way in each independent strain: through the repurposing of a distantly related protein.

“This is a fascinating set of evolution experiments,” wrote evolutionary biologist Richard Lenski of Michigan State University in an e-mail to The Scientist. “Their experiments show how a biological function—in this case, flagellar motility in Pseudomonas fluorescens—can re-evolve after the deletion of a seemingly critical gene. The bacteria regained motility not by reacquiring the lost gene . . . but instead by mutations in other genes that put their products to new uses.”

There are still some big unanswered questions about evolution, such as “how major evolutionary changes take place,” said Austin Hughes of the University of South Carolina who, like Lenski, was not involved in the work. “It relates to the old debates going way back between gradualism and saltation,” Hughes said. That is, whether evolution occurs in small steps or giant leaps. Another question is whether evolution can ever be—even remotely—predictable, said study coauthor Louise Johnson of the University of Reading in the U.K. “The received wisdom has always been that evolution is sort of tinkering and not necessarily finding a good path,” said Johnson, “so it’s often thought that the direction evolution is going to choose is going to be highly random.”

Johnson and her colleagues have now discovered, however, that not only can giant evolutionary leaps happen, but they can do so in a reproducible way. Interestingly, the team didn’t set out to study such profound, long-standing questions. Rather, she said, the investigations came about because PhD student and coauthor Abdullah Alsohim “made a bit of a mistake.”

Alsohim’s original project had been to investigate how a lack of flagella impacts the ability of the soil bacteria P. fluorescens to colonize plant roots and help the plants grow. The bugs had been engineered to lack fleQ, which encodes a key transcriptional regulator of flagella genes. But “he left the plates to incubate much longer than intended, and [the bacteria] began to swim again,” said Johnson. “We were startled.”

There was another shock to come: each bacterial strain that regained its swimming ability—first slow, then fast—did so via essentially the same evolutionary process. The team sequenced the genomes of different slow- and fast-swimming strains and discovered that all of the slow swimmers had mutations in genes that would directly or indirectly increase expression of a nitrogen regulatory protein called NtrC. Furthermore, all of the fast swimmers had mutations in the gene for NtrC itself.

NtrC shares 30 percent amino acid identity with FleQ, suggesting the proteins may be able to minimally cross-react with each other’s target genes. Sure enough, the researchers determined that the initial mutations, which ramped up NtrC levels, enabled a minor upregulation of FleQ’s target genes. The second mutations to NtrC itself then improved the protein’s interaction with the FleQ targets, boosting their expression, and the bacteria’s ability to swim.

The results highlight the importance of gene duplication in evolution, said Hughes, and the ability of the resulting diverged proteins to “moonlight” in roles aside from their main function. Indeed, said Jeff Barrick of the University of Texas in Austin who was not involved in the work, such cross-talk gives organisms “greater robustness,” allowing them “to restore a function even though they are missing a genetic part.”

But while the re-evolved flagella enabled the bacteria to access food supplies at the farthest reaches of the Petri dish, the ability came at a price. “The bacteria that became much better at swimming were much worse at nitrogen regulation,” said Johnson. However, she added, “sometimes the advantage can be so great that it’s worth paying that cost because otherwise you die.”

T.B. Taylor et al., “Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system,” Science, 347:1014-17, 2015.

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Avatar of: James V. Kohl

James V. Kohl

Posts: 532

February 27, 2015

Re: "...repurposing of a distantly related protein."

1) The "repurposing" is nutrient-dependent and pheromone-controlled.

2) The repurposing exemplifies how ecological variation leads to nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize DNA in the organized genomes of species from microbes to man.

See how important it is to understand genomic stability in the context of "repurposing." Biocontainment of genetically modified organisms by synthetic protein design. See also the importance of Combating Evolution to Fight Disease.

Lenski and many others have been on the wrong side of this fight for several decades.

Re: "The results highlight the importance of gene duplication..."

Gene duplication is nutrient-dependent. Fixation of amino acid substitutions that stabilize the genome is controlled by the physiology of reproduction, which is controlled by the metabolism of nutrients to species-specific pheromones.

The RNA-mediated fixation of amino acid substitutions links metabolic networks to genetic networks. That fact explains why Church's group has taken great care to address other facts that link physics, chemistry, and conserved molecular mechanisms to cell type proliferation, which theorists tend to attribute to mutations and evolution.

For constast to the claims of theorists, Christ and others: The Pharmacology of Regenerative Medicine are also attempting to link "... the salient features of diverse fields of research—ranging from materials chemistry and functionalized biomaterials to stem cells, organ/tissue regeneration, wound healing, and development biology..."

Accurate representations of nutrient-dependent biologically-based cause and effect during life history transistions also can be viewed in the context of heterochronic parabiosis, which links fixed amino acid substitutions in red blood cells to the delivery of nutrients to every cell in organisms with a circulatory system.

Mutations perturb the molecular mechanisms of the delivery system, which typically prevent sepsis caused by E. coli or other microbes that ecologically adapt to higher body temperatures than can be maintained by immunocompromised mammals (e.g., like your grandmother who may have died from complications of a urinary tract infection in the context of evolutionary theory).

Avatar of: spritrig


Posts: 6

February 27, 2015



A Novel Linear Plasmid Mediates Flagellar Variation in SalmonellaTyphi


Avatar of: Pieter Snotter

Pieter Snotter

Posts: 1

Replied to a comment from James V. Kohl made on February 27, 2015

March 5, 2015

"RNA-mediated amino acid substitutions that stabilize DNA" - Interesting, never heard of this. where can i read more about it? 

"Fixation of amino acid substitutions that stabilize the genome" I do not understand this. Can you be more concrete?

I cannot make sense of the remaining of your text in relation to the journal article.  it seems not related with the contebnt of the article at all?


March 11, 2015

The article refers to the observed phenomenon as being a result of "cross-talk" and quotes Jeff Barrick as saying this provides the organisms with "greater robustness" that allows them "to restore a function even though they are missing a genetic part." Then where is the evolution headlined in this piece? Viewed from an engineering perspective, these bacteria are provided with a carefully engineered backup system much like moderrn spacecraft, aircraft and computers. 

Avatar of: James V. Kohl

James V. Kohl

Posts: 532

Replied to a comment from Forrest M. Mims III made on March 11, 2015

April 22, 2015

The 'backup system' appears to protect against the damage caused by viruses and viral microRNAs that perturb the biophysically constrained chemistry of nutrient-dependent protein folding and reproduction in species from microbes to humans.

See: Viruses and cell type differentiation

Avatar of: James V. Kohl

James V. Kohl

Posts: 532

Replied to a comment from James V. Kohl made on April 22, 2015

September 17, 2015

Bats frequently come into contact with infectious diseases, but rarely suffer from them

The octopus genome sequencing linked the conserved molecular mechanisms of cell type differentiation that are required to keep viruses from contributing to genomic entropy. Other studies have linked marine invertebrates to terrestrial invertebrates and  vertebrates via conserved molecular epigenetics, but evolutionary theorists continue to report their findings in the context of neo-Darwinian nonsense.

Avatar of: James V. Kohl

James V. Kohl

Posts: 532

January 1, 2017

See also: RNA Sequences Don’t Predict In Vivo Transcript Structure

Interactions between nucleotides can turn sections of transcripts into loops, bends, and knots, some of which have regulatory functions in the cell.

The predictable energy-dependent interactions link natural selection for codon optimaility to healthy longevity. They have not been considered in the context of virus-driven energy theft, which has since been linked from viral latency to all pathology.

Epigenetics and Genetics of Viral Latency

... viral latency is responsible for life-long pathogenesis and mortality risk...

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