“细菌—人类水平基因转移”的争论结束

[编者的话]

在今年发布的人类基因组测序报告中提出大约有200个基因是从细菌水平转移到人类中来的。但是，这一结论目前看来是不够严谨的、存在着重大的偏差---实际数字远低于原来的预期。在近期的science杂志上，生物信息学家重新研究了这一问题，认为原来的结论需要校正，而最近的nature杂志上的相关文章进一步支持了这一观点。

Bacteria aren't as free and easy with their genes as some would have us believe. Genes have not hopped directly from bacteria to humans but were inherited from common ancestors, say researchers, whose evidence is now settling an evolutionary row and allaying fears about genetically modified organisms1,2.

The human genome sequence contained some real surprises. The public sequencing consortium's announcement that at least 113 genes were likely to have jumped into the genome by 'horizontal transfer' from bacteria caused a particular stir3.

But the assertion left evolutionary biologists sceptical. Now two research teams in the United States have produced evidence to rebut the claim.

The original analysis assumed that genes shared by humans and bacteria, but not by non-vertebrates such as fruit flies, yeast, roundworms and mustard weed, are candidates for horizontal gene transfer.

But other organisms could have had the gene and then lost it, points out Jonathan Eisen of The Institute for Genomic Research in Rockville, Maryland. "It's a common event in evolution," he says.

To back up this theory, Eisen and his colleagues re-analysed the sequence data, increasing the number of species in the comparison1. In many cases, similar genes were found in non-vertebrates such as parasites, sponges and fungi, ruling out direct horizontal transfer from bacteria to vertebrates.

But the gold standard for establishing whether horizontal gene transfer has occurred is drawing up evolutionary trees to trace a candidate gene's inheritance, admits Eisen.

Now publication of these trees has settled the matter. Drawn up for 28 of the candidate horizontal transfer genes, the trees reveal that almost all the genes are also found in other distant ancestors. So say Michael Stanhope and his colleagues at GlaxoSmithKline in Pennsylvania2.

"Our study searches a more thorough representation of sequences," explains Stanhope - from slime mould to mosquito. A gene's presence in humans can therefore be explained by descent through common ancestors, he says.

Bacteria frequently exchange genes, including those for antibiotic resistance, even between distant species. But horizontal transfer from bacteria to vertebrates or other multicellular organisms is very rare.

Such a gene leap would have to take place from bacteria into either eggs or sperm, and the gene would need to be incorporated into the genome to be passed on to subsequent generations. "It's an extraordinary event," says Stanhope - so it seemed unfeasible that it could have occurred 113 times.

"It's a tempest in a teapot," says Russell Doolittle, an evolutionary biologist at the University of California, San Diego, of the scientific squabble. He says that the current spate of results is simply "putting the record straight".

And it's an important record to set straight - the teams hope that besides pacifying unhappy scientists, public fears about horizontal gene transfer from genetically modified organisms will be allayed by their findings. "We don't find any evidence for it," says Stanhope.

References

Salzberg, S.L., White, O., Peterson, AJ. & Eisen, J.A.Micorobila genes in the human genome: lateral transfer or gene loss?. Science, 292, 1903 - 1906, (2001).

Stanhope, M.J. et al.Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates.. Nature, 411, 940 - 944, (2001).

International Human Genome Sequencing Consortium.Initial sequencing and analysis of the human genome. Nature, 409, 860 - 921, (2001).