Evolutionary Genomics

Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Cooper, T. et al. Proc. Natl Acad. Sci. 100, 1072–1077 (2003)

Parallel changes in independent evolutionary lineages in response to an environmental challenge are clear indicators of adaptive evolution. Cooper et al. used DNA macroarrays to examine the changes in gene-expression in two lineages of E. coli in response to a glucose-limiting medium. The authors go on to identify a specific mutation accounting for many of the 59 genes that changed expression in parallel, raising the possibility that this might provide a general strategy for identifying the genes involved in adaptation.

Plant Genetics

Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Huang, C. et al. Nature 5 February 2003 (10.1038/nature01435)

We know that plant chloroplast genes can move to the nuclear genome, but how often does this happen? To answer this question, Huang et al. engineered tobacco-chloroplast genomes with a gene that confers kanamycin resistance only if it is transferred to the nucleus. The authors found 16 out of 250,000 plants with independent nuclear insertions: a rate high enough to significantly impact nuclear genome organization and gene function, and to have implications for the design of genetically modified crops.

Genomics

Ringlike structure of the Deinococcus radiodurans genome: a key to radioresistance? Levin-Zaidman S. et al. Science 299, 254–256 (2003)

D. radiodurans can withstand ionizing radiation at doses that are lethal to all other organisms. In this paper, Levin-Zaidman et al. describe the unusual 'toroidal' conformation of its genome. This tightly packed structure might confer resistance to ionizing radiation by enabling broken DNA strands to be held together tightly and facilitating template-independent repair.

Technology

A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Zazopoulos, E. A. et al. Nature Biotech. 21, 187–190 (2003)

Taking advantage of the fact that bacterial metabolic genes are clustered, Zazopoulos et al. developed a high-throughput method for identifying metabolic loci independently of their expression. First, using a genomic library, the authors generated 700-bp random genome-sequence tags (GSTs). Second, GSTs of interest were identified on the basis of sequence homology to the biosynthetic genes that are present in microbial databases. Selected GSTs were then used as probes to identify new metabolic genes (and their neighbours) from individual cosmids or BACs.