In Nature this week, an international team reports on a genomic, transcriptomic, and proteomic study of the Pacific oyster, Crassostrea gigas. Sequencing the oyster's genome revealed a number of polymorphisms and repetitive sequences that allow the mollusks to survive environmental stresses. Meanwhile, a proteomic review of oyster shell samples revealed that shell formation is far more complex than previously thought, and requires assembly and modification steps achieved by specific cell types in collaboration with exosomes.
Elsewhere, a group of researchers from Michigan State University and collaborators describe the process by which Escherichia coli evolved aerobic citrate utilization, a novel trait that allows the bacteria to use citrate as an energy source. Combining full-genome sequencing with evolutionary replay experiments to follow the trait over more than 30,000 generations, the team determined that the trait required the evolution of a potentiating genetic background that allowed actualization mutations to occur. "Finally, novel functions often emerge in rudimentary forms that must be refined to exploit the ecological opportunities. This three-step process — in which potentiation makes a trait possible, actualization makes the trait manifest, and refinement makes it effective — is probably typical of many new functions."
Finally, over in Nature Biotechnology, investigators from the University of California, Berkeley, describe a process by which the physical separation of genetic elements such as RNA and DNA at the transcript level can enable the programming of predictable genetic systems. They developed a synthetic RNA-processing platform using the bacterial clustered regularly interspaced short palindromic repeat, or CRISPR, pathway, and show that "efficient and specific cleavage of precursor mRNA enables reliable and predictable regulation of multigene operons." Additionally, they show that CRISPR-based RNA cleavage is effective for regulation in bacteria, archaea, and eukaryotes. The data suggest that "programmable RNA processing using CRISPR offers a general approach for creating context-free genetic elements and can be readily used in the bottom-up construction of increasingly complex biological systems in a plug-and-play manner."