BY KRISTA CONGER

Sequencing the human genome will likely be hailed as one of the great scientific accomplishments of all time. After the celebrating, however, many people may wonder what practical value can come from deciphering the strings of letters that make up our DNA. But Stanford researchers have already plunged into the wealth of data provided by this and other whole genome sequencing projects.

"Having the gene sequence information is part of what I call the 'toolbox' of cell biology," said Richard Scheller, PhD, professor of molecular and cellular physiology. "In addition to being able to make general conclusions about the genes, this information allows us to make antibodies against the protein, or to mutate the gene and express it in a cell. So identifying the genes also provides us with reagents to dissect the ways in which cells work."

Scheller is particularly interested in teasing apart the complex ways in which molecular traffic is directed inside a cell. By comparing amino acid sequences between yeast, fruit flies, worms and humans, researchers in his lab have identified previously unknown proteins involved in this process. They have used the newly identified genes to infer general principles about how proteins move from one place to another and how the process may have been modified during evolution.

He and his team published the results of their work in Monday's issue of Nature along with several other papers relating to sequencing the human genome.

The interior of the eukaryotic cell ­ cells other than bacteria ­ is divided into specialized compartments separated from the cellular soup by membranes. Molecules are shuttled from one compartment to another by vesicles ­ small capsules that bud from the surface of one compartment and fuse with another to deliver their contents.

Proteins embedded in membrane walls specify which molecular passengers will go along for the ride when a vesicle buds off; they also help select a particular landing pad from the many potential partners within the cell. These "trafficking" proteins can be categorized into specific families based on their amino acid sequences.

Researchers know that the roles of the trafficking families remain the same in organisms ranging from yeast to humans. But they didn't know whether the number of family members remained constant between species. Such a comparison would give a snapshot of evolution ­ families whose ranks had expanded in a particular species may indicate more complex trafficking pathways in that organism. But it's not possible to ascertain whether all members of a protein family have been identified without knowing the organism's entire genomic sequence.

Scheller's lab used recently published whole genome sequences of yeast, fruit fly, worms and humans to analyze four protein families involved in vesicle transport. They used a computer algorithm to search the databases for matches between known family members and the predicted amino acid sequences of the known genes in the four organisms. When a potential match was made, the computer assigned a similarity score to the new protein based on a number of variables. Those with scores above a pre-designated cutoff point were classified as members of the same family as the protein specified in the database search.

The idea was that even though different species have slight variations in the sequences, the overall family resemblance is great enough to allow scientists to pick them out of the crowd of genes when an organism's entire genomic sequence
is known.

In addition to picking out known family members, the searches revealed several new proteins, particularly in humans. The researchers speculate that the larger protein families in humans are necessary to handle the complex vesicle trafficking in mammals. For example, a protein family known as "Rabs" increased in size relative to another family, the "SNAREs," as the researchers progressed up the evolutionary ladder from yeast to humans.

"In yeast there are more SNAREs than Rabs. In worms and flies the numbers are similar, and there are many more Rabs than SNAREs in humans," Scheller said.

The team found this interesting because Rabs are primarily regulatory molecules, moderating and directing vesicle traffic in the cell. Higher numbers of Rabs may indicate that more regulation is needed to ensure that mammalian proteins arrive safely at their intended destinations, said the researchers.

The sequence similarity searches led to another discovery: the SNARE family, which helps the vesicle first dock and then fuse with the target compartment, can be subdivided into four smaller groups. Scheller's team found that one member from each group is necessary to form the three-dimensional structure that allows the two membranes to fuse and then deliver the vesicle contents to the interior of the new compartment.

"Now we know that you need one from each category to mediate a membrane fusion event," Scheller said. The lab members are planning to study both the SNARE and the Rab family members in greater detail, he added.

Scheller's research team included postdoctoral fellows Jason Bock, PhD; Hugo Matern, PhD; and Andrew Peden, PhD. Bock, the lead author of the paper, was a graduate student in Scheller's lab when the work was performed.