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What can baker’s yeast reveal about genetic processes?
Beatrice Jin
Beatrice Jin

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Eric Alani says, “Most of the basic molecular processes like transcription and translation are highly conserved between brewer’s yeast and higher eukaryotes.”
Beatrice Jin/Frank DiMeo
Beatrice Jin/Frank DiMeo

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The Alani lab studies DNA mismatch repair in which enzymes act as "spell checkers," identifying and fixing errors in the DNA code after replication and recombination.
Beatrice Jin/Frank DiMeo
Beatrice Jin/Frank DiMeo

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Alani’s biochemistry and genetics expertise combined with colleague Charles Aquadro’s knowledge of population genetics further advance DNA mismatch repair research.
Beatrice Jin/Frank DiMeo
Beatrice Jin/Frank DiMeo

DNA Spell Checkers

by Lauren Cahoon Roberts

Some of the most important questions about our own genetic processes may lie within a lump of bread dough. Eric Alani, Molecular Biology and Genetics, uses baker’s yeast to examine key DNA "spell-checking" molecules and their role in genetic replication, evolution, and disease.

Alani credits his career path to both a natural fascination with science and good timing. “I was going to college at a time when recombinant DNA technology and molecular biology were coming of age and gave you new tools to study new fields,” he says. “Suddenly, studying basic molecular processes in a cell became feasible.”

As a graduate student at Harvard, Alani worked under visionary molecular and cellular biologist Nancy Kleckner who at the time was starting a new project in her lab—understanding how chromosomes recombine during meiosis in brewer’s yeast. This project would serve as Alani’s introduction to a biological system that he would continue to analyze to this day. “Most of the basic molecular processes like transcription and translation are highly conserved between brewer’s yeast and higher eukaryotes,” says Alani. He became fascinated with the crucial step in meiosis known as crossing over, in which pairs of chromosomes, one from “Mom” and the other from “Dad,” recombine and segregate to form gametes-eggs or sperm. This process enables greater genetic diversity through a "reshuffling" of the parents’ genes. Alani studied how breaks in “Mom” or “Dad” chromosomes initiate the crossing-over process, a key step that was not fully understood until he examined it closely.

How the Spell-Checking System Works

Now at Cornell, Alani’s research focuses on repair and recombination, using genetic and biochemical approaches to tackle these questions. In particular, the Alani lab studies a process called DNA mismatch repair (MMR), in which enzymes act as "spell checkers," identifying and fixing errors in the DNA code after replication and recombination. “These proteins ensure that the error rate when a cell replicates its DNA is one hundred to a thousand-fold lower than if the spell-checker system was not in place,” says Alani. The two main proteins that initiate this process in MMR are called MSH (MutS homolog) and MLH (MutL homolog) family proteins. When either of these proteins is mutated in humans, it can result in a predisposition to a hereditary form of colon cancer, known as HNPCC. “Why a process like MMR, that’s seen in every other cell, would lead primarily to colon cancer is not quite known today,” says Alani.

The lab examines how the cells' spell-checker machinery has been co-opted by the meiosis process to help facilitate chromosome crossover.

His lab is currently pursuing a project that examines how the cells' spell-checker machinery has been co-opted by the meiosis process to help facilitate the crossing over between chromosomes. “But how that process works is not understood,” says Alani. “We’ve purified this protein and we’ve found it can cut a very specific form of DNA, but we don’t understand how it does this and who it talks to.” So, to start piecing the puzzle together, Alani and graduate student Najla Al-Sweel are using genetics to “beat up this protein, mutate it, and see which regions are critical,” says Alani.

Collaborating to Understand Genetic Incompatibilities

The Alani lab is also collaborating with colleague Charles Aquadro’s lab on another project that combines Alani’s structural and functional biochemistry and genetics expertise with Aquadro’s knowledge of population genetics to better understand how incompatibilities between MMR gene partners could promote adaptation to a stress condition. “About 10 years ago we created a model to explain some curious results obtained when analyzing the function of the MLH1 mismatch repair gene. We identified a mutation in the MLH1 gene that did not cause a defect in MMR when it was introduced into the same background that the gene was derived from. However, if the mutant MLH1 gene was introduced into a yeast strain that was from a different genetic background, a complete defect in MMR was observed.” Over the past 10 years, Alani and Aquadro have investigated this phenomenon. “It’s tied to epistasis—interactions between gene variants that can result in novel defects,” says Alani. “Such a phenomenon can explain why an individual could suffer from a disease while another person with the same mutation is unaffected.”

Through extensive screening of yeast genes from around the world, Aquadro and Alani have pieced together how this incompatibility works—why one gene mutation in one background is silent, yet not in another. “We believe such a mechanism can enable a cell to acquire mutations that allow it to better adapt to stressful environments. Working with graduate student Duyen Bui, we have recently shown that this mechanism does in fact work in the lab. We are now testing our hypothesis that subsequent matings in nature can also eliminate the mutagenic incompatibility but preserve the genetic changes that promoted adaptation,” says Alani.