HIGHLIGHTS

IN BRIEF

M ICROB IAL GENOM ICS

I cant live without you

PLANT GENETICS

In terms of the publicity it generates, the Minimal Genome Project

Craig Venters latest endeavour, which aims to synthesize a working
bacterial genome from scratch threatens to rival Celeras race with the
publicly funded Human Genome Project. However, it is an important
collaboration between European and Japanese scientists to systematically
inactivate Bacillus subtilis genes that has generated the most reliable list, so
far, of genes that are essential for a minimal genome to work.
To inactivate genes, Kobayashi et al. inserted nonreplicating plasmids
into target genes by a single crossover recombination. Shorter genes, which
are difficult to inactivate in this way, were replaced with a gene that could be
selected for. A gene was viewed as potentially essential if it was not possible
to get a viable strain when it was inactivated or replaced. It was confirmed as
essential if the growth of a strain became IPTG-dependent when the
expression of the gene was under the control of an IPTG-inducible promoter.
From a total of 4,101 annotated B. subtilis genes, 271 are essential for
bacterial growth, 150 of which were identified for the first time in this
study. Approximately half of these essential genes are involved in DNA and
RNA metabolism, and protein synthesis.
Genes that are required for the cell envelope, shape and division,
account for about one-fifth of the total essential genes most are involved
in cell-wall synthesis.
All of these groups of essential genes fall into the category of the usual
suspects on the basis of previous work. However, the fact that most of
the genes in the EmbdenMeyerhofParnas (EMP) pathway, which
provides the energy and building blocks for the bacterial cell, are essential
is a big surprise.
The rich medium used for these experiments should circumvent the
need for the EMP pathway, and we know that at least part of the pathway
can be bypassed through an alternative biochemical route. So, the fact that
EMP genes are vital for bacterial growth indicates that the enzymes they
encode have other new and essential roles.
The authors produce a list of the essential genes identified in B. subtilis
one of the best-studied bacteria which is relevant to the entire
bacterial kingdom; homologues for ~80% are present in a wide range of
bacteria and 49% have eukaryote homologues. Their comparative analyses
also indicate that in smaller bacterial genomes there is a preferential loss of
essential genes that are involved in the cell envelope, shape, division and
respiration. So, smaller bacterial genomes probably have a smaller set of
essential genes; that is, it is possible to build, maintain and reproduce a cell
compartment in a simpler way than that used in bacteria with larger
genomes, such as B. subtilis.
Any list of essential genes must be viewed in terms of their nutritional
and environmental context. The list would be much longer if cells were
grown in a minimal medium or in the natural environment of B. subtilis.
Similarly, the list would be lengthened if it included families of genes that
encode essential functions, in which any one paralogous gene can execute a
particular essential function. Such genes would be undetected in this study
because only a single gene is inactivated in each strain.
So, although building a working bacterial genome from scratch is a
fascinating project, the extent to which it will help us to understand how
genomes work in situ is debatable.
Nick Campbell
References and links
ORIGINAL RESEARCH PAPER Kobayashi, K. et al. Essential Bacillus subtilis genes. Proc. Natl Acad.

Sci. USA 100, 46784683 (2003)

NATURE REVIEWS | GENETICS

ICE1: a regulator of cold-induced transcriptome and

freezing tolerance in Arabidopsis.
Chinnusamy, V. et al. Genes Dev. 17, 10431054 (2003)

In many plants, exposure to low temperatures can induce the expression of genes that confer tolerance to freezing. Chinnusamy et al.
have identified a new upstream regulator of this process in
Arabidopsis a MYC-like bHLH transcription factor, called inducer
of CBF expression 1 (ICE1). ice1 mutants are more sensitive to freezing, whereas overexpression of this gene enhances freezing tolerance.
ICE1 binds to the promoters and activates the transcription of CBF
transcription factors that, in turn, switch on the expression of the
structural genes that are responsible for freezing tolerance.
EVOLUT ION

Directional selection has shaped the oral jaws of Lake

Malawi cichlid fishes.
Albertson, R. C. et al. Proc. Natl Acad. Sci. USA 100, 52525257 (2003)

Cichlid fishes have undergone parallel explosive radiations in three

large East African lakes, but direct molecular evidence of how these
marked examples of sympatric speciation arose has remained elusive. Albertson et al. use QTL analysis to show that strong divergent
selection has occurred on genomic regions that are responsible for
functionally important differences in feeding structures this
might explain rapid parallel diversification in cichlids.
EVOLUT ION

The evolutionary origin of complex features.

Lenski, R. E., Ofria, C., Pennock, R. T. & Adami, C. Nature 424, 139144 (2003)

Studies of the evolution of complex features, such as the eye, rarely

encompass all of the genetic and developmental mechanisms
involved. Lenski et al. show that digital organisms computer programs that replicate, mutate and compete in a computational environment can model the origin of traits through random mutation and natural selection. By tracing the genealogy of a logic
function, with no missing links, they illustrate how complex traits
can evolve by the modification of existing structures.
HUMAN GENETICS

Epigenetic abnormalities associated with a

chromosome 18(q21-q22) inversion and a Gilles de la
Tourette syndrome phenotype.
State, W. et al. Proc. Natl Acad. Sci. USA 100, 46844689 (2003)

Gilles de la Tourette syndrome (GTS) is an inherited disorder, but no

genes involved in disease etiology have been identified. State and colleagues map a rearrangement on chromosome 18q that is present in
a group of GTS patients, and discover increased replication asynchrony with delayed replication timing across a 500-kb interval.
Their results indicate that long-range functional dysregulation of
genes in this region might be associated with the GTS phenotype.

VOLUME 4 | JUNE 2003 | 4 0 5

2003 Nature Publishing Group