Delective Signature of Genes

Genetic sequencing allows MIT scientists to examine natural selection through the selective signature of a gene across a range of microbial species. This new method of analysis identifies the selective signature of genes, the pattern of differences in genetic sequences that indicates the rate of change or evolution of that gene across species. The signature is then used to infer gene function or to compare specific genetic change to ecological shifts.

* DNA Sequencing *

The term DNA sequencing applies to a variety of biochemical methods that are used to determine the order of nucleotide bases (adenine, guanine, cytosine, and thymine) in deoxyribonucleic acid (DNA).

Researchers have been sequencing DNA and identifying genes since the early 1970’s, and since that time, have developed numerous methods for more rapidly sequencing genomes.

Since DNA is the blueprint for an organism’s structural and functional makeup, decoding DNA sequences is useful in advancing research of fundamental biological processes, and has wide applications including health care, forensics and evolutionary biology.

* MIT’s Selective Signature *

The new twist of the MIT research is its focus on comparing variation in specific sets of genes across various organisms and then relating those genetic differences to environmental pressures that may have resulted in the observed genetic divergence over time.

“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.”

* Comparing Patterns of Natural Selection *

Eric Alm and B. Jesse Shapiro co-authored the paper “Comparing Patterns of Natural Selection across Species Using Selective Signatures”, recently published in the February issue of PLoS Genetics.

In their research, the authors show how variation in protein evolutionary rates can be used to estimate the types of natural selection and intensity of selective pressure acting on genes across different species.

By identifying genes that show unusually rapid and slow evolution for 744 core protein families in 30 proteobacterial species, they were able to determine selective signatures (patterns of fast or slow evolution across species) of genes.

* Gene That Function Together Evolve Together *

Selective signatures are useful tools, since they can reveal a profile of selection across species predictive of gene function, meaning that pairs of genes with similar selective signatures are more likely to be involved in the same cellular function. These genes that function together, evolve together.

An example the researchers provide is of Idiomarina loihiensis, a deep sea bacterium that thrives around sulfurous hydrothermal vents. The carbon source available in this unusual ecological niche is amino acid-based, rather than from sugars. Idiomarina’s glycolysis and phenylalanine metabolism genes show rapid evolution, reflecting an ecological shift in carbon source from sugars to amino acids. A close relative of I. loihiensis, Colwellia psychrerythraea, has completely lost genes for sugar metabolism.

* Evolution of Functional Modules *

Alms and Shapiro’s work also suggests that evolution occurs in functional modules; not necessarily genes that are located next to each other on the genome, but rather genes that encode proteins that perform similar functions.

By examining functional modules of genetic sequences, scientists can compare the rate of evolution of genes that perform similar functions in different species. The differences in the rate of genetic change can help scientists see specific examples of how genetic changes drive functional divergence between species across the entire tree of life.

For more information on this research, see the original article on ” Genetic Signature and Patterns of Natural Selection”.