NEW YORK, March 20 - Researchers have recently called into question the Human Genome Project's assertion that 223 genes in its draft sequence of the human genome were laterally transferred from bacteria to a vertebrate ancestor of humans.
In its paper, "Initial Sequencing and Analysis of the Human Genome," which was published in the February 15th issue of Nature , the project's authors pointed out 223 proteins that have “significant similarity to proteins from bacteria, but no comparable similarity to proteins from yeast, worm, fly and mustard weed, or indeed from any other (nonvertebrate) eukaryote.” The most “parsimonious” explanation for this finding, the authors stated, “was that these genes entered the vertebrate (or prevertebrate) lineage by horizontal transfer from bacteria.”
But Steven Salzberg, senior director of bioinformatics at The Institute for Genomic Research, told GenomeWeb that he does not accept this horizontal bacteria-vertebrate transfer explanation.
“If you’ve done this kind of analysis, you see that what [the consortium did] isn’t valid,” Salzberg said.
Salzberg and his colleagues at TIGR, who collaborated with Celera in its publication of the human genome draft sequence in Science , have begun a careful reexamination of the human sequence data put out separately by the HGP and Celera.
Salzberg said one reason for this reexamination was the potential impact that an erroneous finding of gene transfer could have on the public’s perception of genomics.
“I think it’s a particularly dangerous claim they’re making, because it’s been picked up in the press that bacteria transfer genes into us, and people might speculate - although no evidence exists to support this - that GMOs [genetically modified organisms] could transfer their genes into humans,” Salzberg said.
Prominent newspapers across the country, including The New York Times , ran stories highlighting the claim that a number of genes had been transferred from bacteria to humans.
So far Salzberg has found one E. coli contaminant in the original data analyzed by the consortium for purposes of the Nature paper. He also came across approximately eight genes in GenBank that researchers at TIGR identified as probable malaria genes mistakenly entered into the database.
Ewan Birney of the European Bioinformatics Institute confirmed these findings, and said both the malaria genes and the E. coli contaminant were removed from Ensembl 8.0, the latest annotated human protein set released by EBI.
Ensembl 8.0 contains 2,000 fewer entries than the previous release, due to the fact that some “genes” in the previous release were found to be parts of one longer gene, and were combined to reflect this finding, Salzberg said.
Despite these revisions, Birney emphatically stated in an e-mail to GenomeWeb that the bacterial-human gene transfers could not be attributed to contamination “as we used experimental evidence to confirm this.”
The HGP's researchers combed the sequence to remove any sequence that was basically identical to known bacterial DNA, and then designed PCR primers for 35 of these genes to verify that they could be detected directly in human sequence.
In support of Birney's claim, Eric Lander, director of the Whitehead Institute/ MIT Center for Genome Research, wrote in an e-mail to GenomeWeb: “The authors were quite concerned to be sure that these sequences did not represent contamination from any source. Thus, we insisted that a large sample be tested by direct PCR of human DNA. As we state in the paper, this rules out that any substantial fraction are due to contamination, although it is always possible that a small number are contaminants.”
However, even if contamination is not an explanation for the appearance of bacterial gene homologs in the human genome, the transfer explanation does not comport with previous work on prokaryote-eukaryote transfer, according to Russell Doolittle, a microbiologist at University of California San Diego, who has researched the evolution of bacterial genomes.
“I think there are legitimate cases of transfer of genes from bacteria to eukaryotes, but they are very rare and the criteria for establishing them has to be examined very carefully,” said Doolittle. “The field as a whole has come up with about a dozen prokaryote-eukaryote transfers, of which there is agreement on half a dozen.”
Doolittle added that these prokaryote-eukaryote gene transfers generally occur between a select number of related bacteria and a small number of eukaryotes. For example, he said, certain antibiotic synthesis genes are found in both selected fungi and in certain bacteria.
In the Nature paper, by contrast, the authors said they were unable to identify a preferred bacterial source for the laterally transferred genes, and presented a long and varied list of probable bacterial sources for the transferred genes as well as other vertebrates in which the genes have been found.
Because of this lack of specific pathway from bacterium to vertebrate, Doolittle said he believes a more plausible explanation is that the genes found in both bacteria and humans were also initially present in lower eukaryotes, and were sloughed off during the evolution of the yeast, worm, fly, and mustard seed.
“The other phenomenon they didn’t consider is the rate variation,” added Salzberg. “Different genes mutate at different rates.” Some of the invertebrate genes could have mutated to the extent that they were no longer identifiable using a BLAST search, he said.
Doolittle also suggested that the researchers might not have been using sufficiently sensitive tools to detect homologies between human and invertebrate genes. “I think this was an artifact of their search mechanism,” Doolittle said.