The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.     

Shell composition has no net impact on large-scale evolutionary patterns in mollusks

A major suspected bias in the fossil record of skeletonized groups is variation in preservability owing to differences in shell composition. However, despite extensive changes in shell composition over the 500-million-year history of marine bivalves, genus duration and shell composition show few significant relationships, and of those, virtually all are contrary to bias from preferential loss of highly reactive shell types. Distortion of large-scale temporal patterns in marine bivalves owing to preservability is thus apparently weak or randomly distributed, which increases the likelihood that observed patterns in this and other shelled groups carry a strong biological signal.     

PKA type IIalpha holoenzyme reveals a combinatorial strategy for isoform diversity

The catalytic (C) subunit of cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is inhibited by two classes of regulatory subunits, RI and RII. The RII subunits are substrates as well as inhibitors and do not require adenosine triphosphate (ATP) to form holoenzyme, which distinguishes them from RI subunits. To understand the molecular basis for isoform diversity, we solved the crystal structure of an RIIalpha holoenzyme and compared it to the RIalpha holoenzyme. Unphosphorylated RIIalpha(90-400), a deletion mutant, undergoes major conformational changes as both of the cAMP-binding domains wrap around the C subunit's large lobe. The hallmark of this conformational reorganization is the helix switch in domain A. The C subunit is in an open conformation, and its carboxyl-terminal tail is disordered. This structure demonstrates the conserved and isoform-specific features of RI and RII and the importance of ATP, and also provides a new paradigm for designing isoform-specific activators or antagonists for PKA.     

On the origin of bacterial resistance to penicillin: comparison of a beta-lactamase and a penicillin target

Structural data are now available for comparing a penicillin target enzyme, the D-alanyl-D-alanine-peptidase from Streptomyces R61, with a penicillin-hydrolyzing enzyme, the beta-lactamase from Bacillus licheniformis 749/C. Although the two enzymes have distinct catalytic properties and lack relatedness in their overall amino acid sequences except near the active-site serine, the significant similarity found by x-ray crystallography in the spatial arrangement of the elements of secondary structure provides strong support for earlier hypotheses that beta-lactamases arose from penicillin-sensitive D-alanyl-D-alanine-peptidases involved in bacterial wall peptidoglycan metabolism.     

Interpretation of recent Southern Hemisphere climate change

Climate variability in the high-latitude Southern Hemisphere (SH) is dominated by the SH annular mode, a large-scale pattern of variability characterized by fluctuations in the strength of the circumpolar vortex. We present evidence that recent trends in the SH tropospheric circulation can be interpreted as a bias toward the high-index polarity of this pattern, with stronger westerly flow encircling the polar cap. It is argued that the largest and most significant tropospheric trends can be traced to recent trends in the lower stratospheric polar vortex, which are due largely to photochemical ozone losses. During the summer-fall season, the trend toward stronger circumpolar flow has contributed substantially to the observed warming over the Antarctic Peninsula and Patagonia and to the cooling over eastern Antarctica and the Antarctic plateau.     

Hepatic glucose sensing via the CREB coactivator CRTC2

Chronic hyperglycemia contributes to the development of diabetes-associated complications. Increases in the concentration of circulating glucose activate the hexosamine biosynthetic pathway (HBP) and promote the O-glycosylation of proteins by O-glycosyl transferase (OGT). We show that OGT triggered hepatic gluconeogenesis through the O-glycosylation of the transducer of regulated cyclic adenosine monophosphate response element-binding protein (CREB) 2 (TORC2 or CRTC2). CRTC2 was O-glycosylated at sites that normally sequester CRTC2 in the cytoplasm through a phosphorylation-dependent mechanism. Decreasing amounts of O-glycosylated CRTC2 by expression of the deglycosylating enzyme O-GlcNAcase blocked effects of glucose on gluconeogenesis, demonstrating the importance of the HBP in the development of glucose intolerance.     

Long-Term Variable Rate Lime and Phosphorus Application for Piedmont No-Till Field Crops

Variable rate (VR) fertilizer application is a paradigm with potential to improve input efficiency and farm profitability. It is widely marketed by commercial applicators in the southeastern US. However, field studies comparing VR with traditional management have not demonstrated consistent, positive results. The objectives of this study were: (1) to determine the soil impact, crop response and economic potential of VR phosphorus (P) and lime application in a North Carolina Piedmont no-till field crop system using intensive soybean [Glycine max (L.) Merr.] production and (2) to economically evaluate alternatives to standard commercial grid soil sampling for directing VR P and lime. A 23-ha long-term no-till field in the SE Piedmont was divided into 0.4ha plots assigned to either VR or uniform P and lime application. Grid soil sampling and VR P and lime application were done prior to four crops over 3 years: full season soybean, wheat (Triticum aestivum L.)–double cropped soybean, and full season soybean. Soil test P, pH and crop yield response to VR P were inconsistent. Soil pH in areas with low pH initially did increase in response to VR lime, but it took two to three applications to bring all of these areas to the target pH. Once VR-liming raised initially low soil pH to levels close to target, yield of soybean, but not wheat, were up to 0.74Mgha^–1 higher than with uniform lime. Even with significantly higher soybean yields associated with VR lime, 3 years of grid sampling and VR application were not profitable compared to uniform application. The results indicated that VR lime could be profitable if the initial grid sampling data were used either for 2 consecutive years, or if it was used to restrict future grid sampling to specific areas requiring further VR lime.     

Hsp90 potentiates the rapid evolution of new traits: drug resistance in diverse fungi

Hsp90 is a molecular chaperone for many signal transducers and may influence evolution by releasing previously silent genetic variation in response to environmental change. In fungi separated by approximately 800 million years of evolution, Hsp90 potentiated the evolution of drug resistance in a different way, by enabling new mutations to have immediate phenotypic consequences. Resistance was abrogated by Hsp90 inhibitors and by febrile temperatures, suggesting new therapeutic strategies and a clinical benefit of fever. During selection in a human host, drug resistance that was initially Hsp90-dependent evolved toward independence. Thus, Hsp90 can act in diverse ways to couple environmental contingency to the emergence and fixation of new traits.