Biography of Jeffrey L. Bennetzen

Jeffrey L. Bennetzen, a genetics professor at the University of Georgia in Athens, has spent his career teasing out the intricacies of plant genomes with respect to their gene number, arrangement, and evolutionary traits. He says he has studied maize, wheat, barley, rice, and sorghum as models, “primarily because they have well defined phylogenetic relationships that provide the opportunity to determine genetic changes that have occurred between genomes. We can estimate the approximate time that their common ancestors diverged.

Rice Genomes

Bennetzen's work has earned him several awards, including election to the National Academy of Sciences in 2004. In his Inaugural Article (1), published in this issue of PNAS, Bennetzen, along with his colleague Jianxin Ma, determined some of the genetic changes that have occurred in rice (or Oryza) over the past 640,000 years. His analysis focuses on two subspecies of rice, indica and japonica, and the DNA changes that caused a dramatic growth and divergence between their two genomes. The sequences between genes in both subspecies appear to have a high rate of divergence, indicating a point mutation rate for transposable elements at least 2-fold greater than the rate of synonymous base substitutions (i.e., mutations that do not change the amino acids that are encoded). Bennetzen and Ma also report that, although a huge number of deletions have occurred, these genomes have grown over time by the amplification of retrotransposons. Furthermore, regions prone to frequent insertions and deletions exhibited higher levels of point mutations. “These results indicate a highly dynamic rice genome with competing processes for the generation and removal of genetic variation,” the researchers conclude.

Figure 1.

Jeffrey L. Bennetzen

Bennetzen's work allows scientists to manipulate genomes more effectively, resulting in a more realistic transgene environment in genetically engineered plants. His work also allows comparative analysis of genomes and subsequent identification of genes that will improve crops. For example, Bennetzen points out that maize evolved in locations where drought is usually not the major constraint for survival. However, the genome of maize, especially with regard to gene content and order, is closely related to that of sorghum, which evolved in a drought-prone environment. “So, if I were looking for genes that might improve maize drought tolerance, I'd look to sorghum, try to isolate the appropriate genes, and put them in maize. And they'd probably work because sorghum and maize usually employ the same pathways,” Bennetzen said.

Yeast Endeavors

Bennetzen began making significant scientific contributions early in his career. He obtained his undergraduate degree in biology at the University of California at San Diego in 1974. Then, as a graduate student at the University of Washington in Seattle, he helped clone, sequence, and map the transcripts for the yeast alcohol dehydrogenase (adh1) gene (2,3). This promoter is still widely used in the genetic manipulation of yeast.

Bennetzen credits several people with helping him develop his scientific acumen throughout his career, including his graduate adviser at the University of Washington, Ben Hall. “I've had the good fortune of working with a number of people who were really deep thinkers—they made science an intellectual pursuit.” His efforts with Hall, whom he calls “a pioneer in the study of genome structure, evolution, and expression,” helped provide the first description of codon bias in yeast and Escherichia coli genomes. The findings indicate that all yeast genes show a distinct preference for codons that are highly complementary to the major cellular isoacceptor tRNA species and that this bias was greatest for the most highly expressed genes. In the case of yeast, the favored codons numbered 25 of 61 possible codons. “This work suggested that translation is most efficient if tRNAs are abundant for the codons used,” Bennetzen noted. He also pointed out that the work influenced genetic engineering of yeast by helping to identify the codons that would allow the most efficient translation of proteins. Of his contributions, this codon bias study, published in The Journal of Biological Chemistry (4), is one of his most heavily referenced and influential contributions.

While a graduate student, Bennetzen also became interested in transposable elements, both due to their intrinsic ability to alter genomes and gene expression and for an idea he had that they could be used, as a transposon tag, to clone genes. After completing a one-year shared postdoctoral position between Virginia Walbot's laboratory at Washington University in St. Louis and Michael Freeling's group at the University of California in Berkeley, Bennetzen took a position in industry with the International Plant Research Institute in San Carlos, CA. While there, he applied his previous knowledge of the yeast adh1 gene to clone the maize adh1 gene. This was the first step toward isolating various transposons that were inserted in alleles of this gene. Subsequently, he cloned and sequenced the first active transposable element from plants, Mutator, or Mu1, of maize (5).

Transposon Transition

To pursue more academic research, Bennetzen left industry and took a position in 1983 as assistant professor at Purdue University in West Lafayette, Indiana. There, he started exploring the intricacies of transposable elements, their specificities, and their epigenetic regulation. “We found, for example, that Mutator transposable elements preferred to insert into genes and that they were regulated by a process associated with DNA methylation,” he said (6).

Bennetzen also began work on plant disease resistance genes as possible targets for transposon tagging. He discovered that the locus of the rust resistance Rp1 gene of maize was highly unstable because of a process of unequal recombination (7). According to Bennetzen, this gene complex has turned out to be “exceedingly interesting because of its hyperevolution; nonetheless, it has been recalcitrant to isolation by transposon tagging.”

His next endeavor was to create a genetic map of sorghum. Colleagues of Bennetzen's at Purdue University wanted a genome map to further study and improve the crop trough genetic manipulation. Bennetzen predicted that developing the genetic map of sorghum would be easy because they already had a genetic map of maize, a close relative to sorghum. He expected that maize DNA probes would hybridize well, and they would not only derive a genetic map for sorghum but would also allow comparison of the two plants' genetic maps. As expected, the resulting sorghum genetic map (8) had significant stretches of collinearity with the maize genetic map, and the field of comparative mapping in grasses was born. In fact, because the maps of these and other cereals demonstrated such collinearity, Bennetzen and Freeling proposed that grasses could be studied as if they were a single species. “This is sometimes called the unified grass genome, or grasses as a single genome, and the concept has been used pretty frequently as a research tool.”

One of Bennetzen's next major contributions, in 1996, involved sequencing a 240-kb block of DNA flanking maize adh1 (9). Within this region, nested intergene retrotransposons were identified as the major component of the maize genome. “This finding demonstrated the incredible abundance of these elements within maize and their ability to minimize mutational effects by the fact that they rarely insert into genes,” Bennetzen said, noting that this is his most heavily referenced plant paper. “Subsequently, the same thing has been seen to varying degrees in other plant genomes.” He also discovered that retrotransposons comprise more than 70% of the maize genome and that they amplified in the maize genome within the last 6 million years, with most of the increase in the last 3 million years (10).

Genome Exploration

In the last few years Bennetzen has been conducting comparative sequencing of the adh1 region and other regions in many different plant species. “We've found that the area between genes is not conserved at all and also that the genes themselves are quite often rearranged—in fact, often 5% or more of the genes are rearranged in order and orientation within 10 million years,” he said. According to Bennetzen, grass genomes are unstable. He has recently shown that maize, an ancient tetraploid, lost most of its extra genes (11). “About 12 million years ago, maize went through a polyploidization event,” he said, “and, in that 12 million years, we've shown that over 50% of those extra genes have been removed.”

A challenge ahead for Bennetzen is to determine the mechanistic basis of genome structure—in particular, the actual events that are taking place and to what extent these events determine genome structure. “We know natural selection is a factor. But we also know that many of these changes occur even in the absence of any obvious selection. In any given organism, the genome is organized differently, so we expect that there is going to be a tremendous amount of functional variation derived from the structural variation, and it will be interesting to see what that is,” he said. Bennetzen predicts that, within the next decade, much more is going to be understood about how genome structure is affecting function. “Our biggest limitation at the moment is a shortage of genomic sequence and gene function data from a broad spectrum of phylogenetically appropriate plants,” he said. To help remedy this problem, Bennetzen has developed gene enrichment and mapping technologies for greatly decreasing the cost of complex genome sequencing, and he is now using this as part of a pilot study to sequence the maize genome (12).

Bennetzen is energized by having so much genomic sequence at his disposal.

Bennetzen will continue on the maize sequencing project as the Norman and Doris Giles Eminent Scholar Chair in Molecular Biology and Functional Genomics at the University of Georgia's department of genetics, where he relocated in 2003. As his group generates and annotates more sequence data, Bennetzen hopes to continue to extrapolate the phylogenetic connections between plant species, much like the indica and japonica work published in his PNAS Inaugural Article (1). Bennetzen is energized by having so much genomic sequence at his disposal. “I think I became interested in the study of genome components because the technology is incredibly powerful. The limitation is your creativity and not your ability to get some finicky technique to work,” he noted. “I've found out—although I don't like to admit this to my students—that by far my most productive times are when I'm working least. What you do with your hands is of relatively minor significance. It's what you do in your head that's important.”