News: Gene's 'Selective Signature' Aids Detection Of Natural Selection In Microbial Evolution
- From: "Robert Karl Stonjek" <rstonjek@xxxxxxxxxxxxxx>
- Date: Thu, 20 Mar 2008 12:19:46 -0500 (EST)
Gene's 'Selective Signature' Aids Detection Of Natural Selection In
Microbial Evolution
ScienceDaily (Mar. 20, 2008) - Scientists at MIT have come up with a
mathematical approach for analyzing a protein simultaneously in a set of
ecologically distinct species to identify occurrences of natural selection
in an organism's evolution.
The new method determines the "selective signature" of a gene, that is, the
pattern of fast or slow evolution of that gene across a group of species,
and uses that signature to infer gene function or to map changes to
ecological shifts.
By reversing the usual order of inquiry-studying an organism, then trying to
identify which genes are involved in a particular function-the scientists
hope to hasten the understanding of microbial evolution by taking advantage
of the nearly 2,500 microbes already sequenced.
"By comparing across species, we looked for changes in genes that reflect
natural selection and then asked, 'How does this gene relate to the ecology
of the species it occurs in?'" said Eric Alm, the Doherty Assistant
Professor of Ocean Utilization in the Department of Civil and Environmental
Engineering. "The selective signature method also allows us to focus on a
single species and better understand the selective pressures on it."
"Our hope is that other researchers will take this tool and apply it to sets
of related species with fully sequenced genomes to understand the genetic
basis of that ecological divergence," said graduate student B. Jesse
Shapiro, who co-authored with Alm a paper published in the February issue of
PLoS Genetics.
Their work also suggests that evolution occurs on functional modules-genes
that may not sit together on the genome, but that encode proteins that
perform similar functions.
"When we see similar results across all the genes in a pathway, it suggests
the genomic landscape may be organized into functional modules even at the
level of natural selection," said Alm. "If that's true, it may be easier
than expected to understand the complex evolutionary pressures on a cell."
"In a single species, a whole set of genes in the same module tend to change
together," said Shapiro. "Identifying these changes brings us a step closer
to understanding the ecological basis of selection in a species and how
changes at the genetic level affect the organisms interactions with its
environment."
For example, in Idiomarina loihiensis, a marine bacterium that has adapted
to life near sulfurous hydrothermal vents in the ocean floor, the genes
involved in metabolizing sugar and the amino acid phenylalanine underwent
significant changes (over hundreds of millions of years) that may help the
bacterium obtain carbon from amino acids rather than from sugars, a
necessity for life in that ecological niche. In one of I. loihiensis' sister
species, Colwellia psychrerythraea, some of those same genes have been lost
altogether, an indication that sugar metabolism is no longer important for
Colwellia.
Shapiro and Alm focused on 744 protein families among 30 species of
gamma-proteobacteria that shared a common ancestor roughly 1 to 2 billion
years ago. These bacteria include the laboratory model organism E. coli, as
well as intracellular parasites of aphids, pathogens like the bacteria that
cause cholera, and soil and plant bacteria. They mapped the evolutionary
distance of each species from the ancestor and incorporated information
about the gene family (for instance, important proteins evolve more slowly
than less vital ones) and the normal rate of evolution in a particular
species' genome in order to determine a gene's selective signature.
"These are experiments we could never perform in a lab," said Alm. "But
Mother Nature has put genes into an environment and run an evolutionary
experiment over billions of years. What we're doing is mining that data to
see if genes that perform a similar function, say motility, evolve at the
same rate in different species. To the extent that they differ, it helps us
to understand how change in core genes drives functional divergence between
species across the tree of life."
This work is part of the Virtual Institute for Microbial Stress and
Survival. The research was also supported by additional grants from the U.S.
Department of Energy Genomics: GTL Program, the National Institutes of
Health, and a scholarship from the Natural Sciences and Engineering Research
Council of Canada.
Adapted from materials provided by Massachusetts Institute of Technology,
Department of Civil and Environmental Engineering.
Massachusetts Institute of Technology, Department of Civil and Environmental
Engineering (2008, March 20). Gene's 'Selective Signature' Aids Detection Of
Natural Selection In Microbial Evolution. ScienceDaily. Retrieved March 20,
2008, from http://www.sciencedaily.com/releases/2008/03/080318121556.htm
Posted by
Robert Karl Stonjek
.
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