The focus of research in the Giovannoni laboratory is molecular and genetic analysis of fruit ripening and related signal transduction systems with emphasis on the relationship of fruit ripening to nutritional quality. We are also involved in development of tools for genomics of the Solanaceae including participation in the International Tomato Sequencing Project. We employ several experimental systems but the majority of our work involves the use of tomato. The broad objectives of the lab include deciphering the underlying molecular basis of components of ripening regulation conserved through evolution and how these regulatory networks coordinate ripening events including those related to quality and nutritional content.
Experimental approaches include: 1) positional cloning of loci known via mutation to harbor genes necessary for normal fruit development and ripening, and 2) isolation of candidate ripening regulatory genes based on expression pattern or relationship to ripening-related signal transduction systems (e.g. ethylene, light), and functional analysis in transgenic plants.
Learning the genetic basis of fruit ripening could significantly impact the quality and availability of certain foods. This knowledge would be particularly useful in countries where food spoilage due to over-ripening is a cause of hunger.
Jim Giovannoni’s laboratory at BTI is working to understand the process by focusing on the genes and regulatory networks that control fruit ripening in tomato – knowledge that will have applications in other plants such as pepper, peach, pineapple, banana, strawberry and melon. Because many fruits ripen in response to the release of the hormone ethylene, understanding the mechanism that controls the plant’s sensitivity to ethylene can lead to basic knowledge about the ripening process.
In studying mutant tomato plants that produce only unripe tomatoes,Giovannoni’s team discovered an alteration in a gene called Gr, or Greenripe, that causes overproduction of a certain protein in the fruit that decreases the fruit’s sensitivity to ethylene. So, though the plants produce ethylene in normal amounts, the fruit does not respond to it and, therefore, fails to ripen. Being able to control the production of this protein,which would make the fruit under- or over-sensitive to ethylene, could lead to the ability to speed or delay the ripening process.
Giovannoni further found that overproduction of the Gr protein throughout the plant has no effect on any part of the plant except the fruit. This discovery is important because it indicates there are constituents specific to the fruit involved in its response to ethylene.
The next step in the research is to develop transgenic tomato plants in which the Gr gene has been“knocked out,” or disabled, so that the plants are no longer able to produce the Gr protein. This work will demonstrate whether or not normal Gr expression plays a significant role in ripening. Giovannoni predicts that these plants will be highly sensitive to ethylene and will, therefore, ripen early.
The ability to control the ripening process by controlling the ethylene response could lead to fruit, such as strawberry, papaya and even tomato, that have a longer shelf life. Because ripening is directly related to fruit flavor, texture and nutrient content, these discoveries could lead to higher quality food as well.
Most scientific exploration is much less telegenic than planting a flag on the moon or tracking whales on the high seas. Molecular biology is no exception: its giant leaps usually appear as lines on gels or colored dots on microarrays. But when Jim Giovannoni, Joyce Van Eck, and their collaborators proposed an international endeavor to sequence the tomato genome, they drummed up support by promising countries a prize befitting the occasion: the chance to put their flag on one of tomato's 12 chromosomes..
This will be the first fruit or vegetable genome sequenced. The sequence will yield information not only about tomato and other members of the Solanaceae (nightshade) family, including potato, pepper, eggplant, but also other related species such as coffee and sunflower. But the potential agricultural benefits weren't enough to entice some nations to participate, so the U.S. team structured their proposal so that each country would be in charge of sequencing a discrete piece of the genome. “If these countries had each given a little money to the project, they wouldn't have gotten much credit,” Giovannoni explained. “This way, each of them can point to a chromosome and say, ‘we did that.’'”
The U.S. team—made up of Giovannoni and Van Eck at BTI, two labs at Cornell, and one at Colorado State University—got funding late in 2004 to lay the foundation for the project. Soon afterward, labs and funding agencies in nine other countries each agreed to take on a chromosome. Tackling the project this way ruled out shotgun sequencing, in which the genome is cut into small pieces and sequenced, with the sequence information then pieced together into the complete genetic code. Instead, the U.S. team would have to cut the genome into larger DNA segments and find out which chromosomes those segments belonged to before they were sequenced. Fortunately, previous studies had shown that most tomato genes are clustered near the ends of chromosomes in areas called euchromatin islands. So the team made the project more manageable by concentrating on these islands, leaving out vast stretches of DNA with little useful genetic information.
Giovannoni believes the information contained in the euchromatin will help his lab learn more about fruit ripening and nutritional quality in tomato. His lab's role in the sequencing is to isolate the DNA and break it up into large chunks. They then paste the chunks into vectors for US collaborators and labs overseas to use.
Van Eck manages the project, communicating with researchers around the world, coordinating shipments of DNA, and writing reports. She also edits the SOL Newsletter, which keeps interested researchers apprised of sequencing progress and other information of interest to the Solanaceae community. And she runs the outreach component of the sequencing project, including a summer bioinformatics internship that blends biology and computer science. She hopes the completed sequence will yield information helpful to her work on antioxidant accumulation in potatoes.
Giovannoni and Van Eck’s U.S. collaborators determine where and on which chromosome each section of DNA belongs, and later process the sequence information from abroad and make it available on a Web site. The team recently submitted a proposal to the National Science Foundation to sequence the three remaining tomato chromosomes, and if all goes well, the tomato genome should be unlocked sometime in 2008. In addition to helping scientists understand economically important nightshades, the sequence should yield clues to the puzzle of how such genetically similar plants evolved very diverse traits.
Most shoppers in America have access to a wide selection of fresh fruits and vegetables year-round, but these rarely measure up to home grown varieties. “In general, things are harvested very prematurely so that they have the shelf life and the firmness to survive shipping,” Giovannoni explains. “What's always lost in that tradeoff is taste, appearance, aroma—things that are associated with quality.”
To make store-bought fruit more palatable, agricultural scientists need a better understanding of how fruits “decide” when and how much to ripen. Giovannoni’s lab studies tomatoes and other plants to find the genes responsible for that decision. In 2004 they discovered several such genes, including two that may play a role in a broad range of species. The lab is now working to find similar genes that cooperate with these genes to regulate ripening and associated quality characteristics.
Giovannoni’s group also participates in a broader effort, with others at BTI and in nine foreign countries, to map and sequence the tomato genome. The completed genome will represent a giant step toward unlocking tomato's inner workings, just as the Human Genome Project did for people. In a related project, the lab uses microarrays and computer analysis to learn how groups of genes switch on and off at the right time at each stage of ripening. This eagle's eye view of the dynamics of development enables them to compare the process across different species, and to pick out genes that may control the timing of ripening.
