More Data Allows Cross-Species Comparison
Although important elements of the human and mouse genome projects have been
published and a sense of completion prevails, there remains much detail work
to be done on both projects. This month, a team led by Haoyi Wang of Miami University
in Oxford, Ohio, elegantly dissects the conservation of one cluster of highly
duplicated genes across the two species. The team simultaneously resolves the
sequence of one of the many remaining ambiguous regions of the mouse genome,
finds new insights into evolution, and provides new tools for future work aimed
at understanding how the cytochrome P450 (CYP) system works in the mouse model
system, which is used heavily in research related to human health [EHP 111:1835-1842].
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Of mice and men. New research
maps the structure of the mouse Cyp2 gene cluster that encodes the P450
enzymes responsible for metabolizing many xenobiotics. These new data will
enable scientists to make cross-species comparisons to the previously sequenced
human CYP2 analog.
image credit: Top to bottom: Arnold
Greenwell/EHP; Protein Data Bank |
Filling in the genomes' finest details, especially in regions with only slightly
differentiated copies of the same information, will take far longer than the
initial large-scale sequencing projects did. But it's a necessary task: in active
clusters of duplicated genes, where repeated near-copies of the same sequence
in the same region of DNA encode functional products, the genes are so similar
that it is hard to be sure that the sequenced DNA has been assembled in the
right order. Like putting together puzzle pieces of nearly the same shape and
pattern, sequence assembly in repetitive regions can easily go astray. Furthermore,
not knowing the exact sequence in such a region can confound efforts to reliably
identify, knock out, or clone genes of interest for further study with biochemistry
and genetics.
The CYP superfamily of genes is conserved across kingdoms, from the
bacteria, plants, and fungi to the higher eukaryotes. It encodes a wide range
of heme-thiolate monooxygenases, enzymes that carry a molecule of the pigment
heme. Some of these enzymes catalyze specific oxidation reactions that detoxify
a panoply of environmental compounds and drugs. Members of the CYP family
are also involved in the metabolism of eicosanoids, steroids, and fatty acids.
Because the superfamily's conserved genes are also heavily duplicated within
a given species, they provide an excellent system for examining how species,
given the basic building blocks of the gene family, copy and rearrange the genes
and thereby accumulate a set of enzymes appropriate for their own needs. The
diversity is impressive. When sequencing is combined with other information,
mice are shown to have 189 CYP genes and pseudogenes, and humans to have
115.
In 2001, principal investigator Susan M.G. Hoffman published the structure
of a cluster of 13 genes from the CYP2 family in humans. This month in
EHP, she, Wang, and colleagues lay out the pattern of the corresponding
cluster in mice, and they are working on similar analyses in other species.
The CYP2 genes are a substantial group, the largest P450 family in the
mammals, with 15 subfamilies containing dozens of genes so far identified. Biochemical
assays have shown that the CYP2 enzymes, together, are able to metabolize many
chemicals, including more than half of all frequently prescribed drugs, as well
as some steroids and arachidonic acid, the major precursor of several classes
of signal molecules including the prostaglandins.
Wang and Hoffman's group combined work at the computer and at the bench to
accurately assemble the mouse Cyp2 cluster, located on chromosome 7,
and to compare it with the CYP2 cluster on human chromosome 19. Their
new assembly solves the published sequence's gaps within the cluster, allowing
them to identify new genes that had been fragmented or left out in earlier assemblies.
At the same time, they have used cloned genomic DNA to painstakingly patch together
an improved fine-structure physical map of the region.
Together, the reassembly and the new map have generated a more accurate picture
of genes in the cluster. Coupled with the group's similar work with the related
human CYP2 gene cluster, the mouse mapping data show how--although not
why--the two species have expanded their CYP2 genes in the time since
evolution separated them. The authors write, "This comparison should enable
researchers to better utilize the mouse as a model system for the study of these
CYP genes in humans and in other mammals."
Victoria McGovern |