The dawn of synthetic genomics

The first month of 2008 was unusually quiet in terms of microbial genome sequencing. Still, even the relatively short list of newly released genomes includes several interesting environmental microorganisms, such as the anoxygenic phototroph Chloroflexus aurantiacus, the toxic bloom-forming cyanobacterium Microcystis aeruginosa, and the methylotroph Methylobacterium extorquens (Table 1). However, arguably the biggest news was the announcement by J. Craig Venter and colleagues that they ‘have synthesized a 582 970 bp Mycoplasma genitalium genome’ (Gibson et al., 2008). The authors used chemically synthesized oligonucleotides ~50 nucleotides in length to assemble ‘cassettes’ 5–7 kb in length, then to join them by in vitro recombination to produce intermediate assemblies, gradually increasing in size. Finally, four 144 kb pieces were cloned in Escherichia coli as bacterial artificial chromosomes, transferred into yeast and assembled into a full-length genome. The genome of the resulting strain, named M. genitalium JCVI-1.0, was virtually identical to the genome of the original strain M. genitalium G37. It was not immediately clear whether this technically very challenging and truly monumental work had any purpose beyond just serving as a proof of principle. However, J. C. Venter and colleagues have a record of overcoming enormous technical challenges and launching entirely new areas of biotechnology. It might be simply too early right now to ask them to explain the future of this work. In any case, the era of synthetic biology has officially begun and who knows what kind of molecules people will be synthesizing 10 or 20 years from now. Returning to the present-day problems, scientists at the Northwest Fisheries Center have sequenced the genome of Renibacterium salmoninarum, the causative agent of bacterial kidney disease (kidney granulomatosis) in salmonid fish. Renibacterium salmoninarum is a moderately psychrophilic actinobacterium that grows optimally at 15–18°C (Sanders and Fryer, 1980; Fryer and Sanders, 1981). It can survive for several days in fresh or sea water before infecting new fish. In addition, R. salmoninarum populates ovarian liquid of infected female fish and can be vertically transmitted to their eggs. The disease was first detected in 1930s in salmon from the river Dee and was initially referred to as ‘Dee disease’. It took more than 20 years to cultivate the organism and recognize its similarity to corynebacteria. The disease still remains poorly understood owing largely to the extremely slow growth of R. salmoninarum in pure culture (Hirvelä-Koski, 2008). The genome data are expected to help identify R. salmoninarum virulence factors, vaccine candidates and design improved diagnostic tests. Chloroflexus aurantiacus is a facultatively aerobic phototrophic gliding filamentous bacterium, first isolated from the Hakone hot spring area west of Tokyo, Japan (Pierson and Castenholz, 1974). It is the best-studied representative of the phylum Chloroflexi, also referred to as Green non-sulfur bacteria, and a popular model organism for studying anoxygenic photosynthesis and autotrophic CO2 assimilation pathways (Stackebrandt et al., 1996; Herter et al., 2001). Chloroflexi are an early branching bacterial phylum that has retained certain unique properties, including very unusual cell walls (Meissner et al., 1988). These organisms are particularly important for understanding the evolution of photosynthesis. In contrast to anoxygenic phototrophs that belong to green sulfur bacteria (Chlorobi), C. aurantiacus encodes photosynthetic reaction centre of type II, similar to the Photosystem II found in cyanobacteria and green plants, as well as in phototrophic proteobacteria. Accordingly, Chloroflexi have been proposed to be the original phototrophs (Oyaizu et al., 1987). An alternative, less exciting variant simply implied that Chloroflexi have acquired their photosynthetic machinery via lateral gene transfer from ancestral cyanobacteria (Mulkidjanian et al., 2006). The sequencing of C. aurantiacus genome has had a long history. The first version, consisting of 1142 contigs, was deposited in GenBank back in 2002. In 2005, the number of contigs was reduced to 77, and remained at that stage for more *For correspondence. E-mail [email protected]; Tel. (+1) 301 435 5910; Fax (+1) 301 435 7793. Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. Environmental Microbiology (2008) 10(4), 821–825 doi:10.1111/j.1462-2920.2008.01581.x