How Prochlorococcus bacteria use nitrogen sparingly in their proteins

Organisms use proteins to perform an enormous range of functions that are essential for life. Proteins are usually composed of 20 different kinds of amino acids that each contain between one and four nitrogen atoms. In aggregate, the nitrogen atoms that are bound in proteins typically account for a substantial fraction of the nitrogen in a cell. Many organisms obtain the nitrogen that they use to make proteins from the environment, where its availability can vary greatly. These observations prompt the question: can environmental nitrogen scarcity lead to adaptive evolution in the nitrogen content of proteins? In this issue, Gilbert & Fagan (2011) address this question in the marine cyanobacteria Prochlorococcus, examining a variety of ways in which cells might be thrifty with nitrogen when making proteins. They show that different Prochlorococcus strains vary substantially in the average nitrogen content of their encoded proteins and relate this variation to nitrogen availability in different marine habitats and to genomic base composition (GC content). They also consider biases in the nitrogen content of different kinds of proteins. In most Prochlorococcus strains, a group of proteins that are commonly induced during nitrogen stress are poor in nitrogen relative to other proteins, probably reflecting selection for reduced nitrogen content. In contrast, ribosomal proteins are nitrogen rich relative to other Prochlorococcus proteins, and tend to be down‐regulated during nitrogen limitation. This suggests the possibility that decaying ribosomal proteins act as a source of nitrogen‐rich amino acids during periods of nitrogen stress. This work contributes to our understanding of how nutrient limitation might lead to adaptive variation in the composition of proteins and signals that marine microbes hold great promise for testing hypotheses about protein elemental costs in the future.     

Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure

Elevated temperatures resulting from climate change pose a clear threat to reef-building corals; however, the traits that might influence corals' survival and dispersal during climate change remain poorly understood. Global gene expression profiling is a powerful hypothesis-forming tool that can help elucidate these traits. Here, we applied a novel RNA-Seq protocol to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef-building coral Acropora millepora. This analysis of a single full-sibling family revealed contrasting responses between short- (4-h) and long-term (5-day) exposures to elevated temperatures. Heat shock proteins were up-regulated only in the short-term treatment, while the long-term treatment induced the down-regulation of ribosomal proteins and up-regulation of genes associated with ion transport and metabolism (Ca(2+) and CO(3)(2-)). We also profiled responses to settlement cues using a natural cue (crustose coralline algae, CCA) and a synthetic neuropeptide (GLW-amide). Both cues resulted in metamorphosis, accompanied by differential expression of genes with known developmental roles. Some genes were regulated only by the natural cue, which may correspond to the recruitment-associated behaviour and morphology changes that precede metamorphosis under CCA treatment, but are bypassed under GLW-amide treatment. Validation of these expression profiles using qPCR confirmed the quantitative accuracy of our RNA-Seq approach. Importantly, qPCR analysis of different larval families revealed extensive variation in these responses depending on genetic background, including qualitative differences (i.e. up-regulation in one family and down-regulation in another). Future studies of gene expression in corals will have to address this genetic variation, which could have important adaptive consequences for corals during global climate change.