High-resolution habitat and bathymetry maps for 65,000 sq. km of Earth’s remotest coral reefs

Coral Reefs - With compelling evidence that half the world’s coral reefs have been lost over the last four decades, there is urgent motivation to understand where reefs are located and their...     

Constraints to growth of annual nettle (Urtica urens) in an elevated CO2 atmosphere: Decreased leaf area ratio and tissue N cannot be explained by ontogenetic drift or mineral N supply

Plant sterols differ from cholesterol in having an alkyl group at Δ-24, and, in the case of stigmasterol, also a Δ-22 double bond. The effects of 10 mol% of three plant sterols (campesterol, β -sitosterol, stigmasterol) and cholesterol on the molecular dynamics and phase behavior in multilamellar liposomes made from different phosphatidylcholine (PC) molecular species have been compared, utilizing the fluorescent probe Laurdan (2-dimethyl-amino-6-laurylnaphthalene). Laurdan reports the molecular mobility in the hydrophilic/hydrophobic interface of the membrane by determining the rate of dipolar relaxation of water molecules close to the glycerol backbone of PC. Our results showed that the Δ-24 alkyl group of plant sterols did not affect their ability to reduce molecular mobility in this region of the PC membranes. However, the plant sterols had a decreased capacity compared to cholesterol to inhibit formation of co-existing domains of gel and liquid-crystalline phases in membranes composed of equimolar dilauroyl-PC and dipalmitoyl-PC. The Δ-22 double bond present in stigmasterol decreased the ability of this sterol, compared to the other phytosterols, to reduce the molecular mobility at the hydrophobic/hydrophilic interface in membranes made of a saturated PC molecular species. However, in membranes made from 16:0/18:2-PC, a lipid species common in plant plasma membranes, stigmasterol was as efficient as other sterols in affecting the polarity and molecular mobility at the hydrophilic/hydrophobic interface of the membrane at 25°C, but was, in contrast to the other sterols, without effect at 0°C. Our results thus confirm as well as contradict the results of previous studies of the interactions between saturated PC and sterols, where other membrane regions were probed. The physiological relevance of the findings is discussed.     

Vif counteracts a cyclophilin A-imposed inhibition of simian immunodeficiency viruses in human cells

Vif is a primate lentiviral accessory protein that is crucial for viral infectivity. Vif counteracts the antiviral activity of host deaminases such as APOBEC3G and APOBEC3F. We now report a novel function of African green monkey simian immunodeficiency virus (SIVagm) Vif that promotes replication of SIVagm in human cells lacking detectable deaminase activity. We found that cyclophilin A (CypA) was excluded from wild-type SIV particles but was efficiently packaged into vif-deficient SIVagm virions. The presence of CypA in vif-defective SIVagm was correlated with reduced viral replication. Infection of CypA knockout Jurkat cells or treatment of Jurkat cells with cyclosporine A eliminated the Vif-sensitive inhibition and resulted in replication profiles that were similar for wild-type and vif-deficient SIVagm. Importantly, the inhibitory effect of CypA was restricted to virus-producing cells and was TRIM5alpha independent. The abilities of SIVagm Vif to inhibit encapsidation of CypA and to increase viral infectivity were shared by rhesus macaque SIV Vif and thus seem to be general properties of SIV Vif proteins. Exclusion of CypA from SIVagm particles was not associated with intracellular degradation, suggesting a mode of Vif action distinct from that proposed for APOBEC3G. This is the first report of a novel vif-sensitive antiviral activity of human CypA that may limit zoonotic transmission of SIV and the first demonstration of CypA encapsidation into a virus other than human immunodeficiency virus type 1.     

Family portraits: the enzymes behind benzylisoquinoline alkaloid diversity

Benzylisoquinoline alkaloids (BIAs) are a group of specialized metabolites found predominantly in the plant order Ranunculales. Approximately 2500 naturally occurring BIAs have been identified, many of which possess a variety of potent biological and pharmacological properties. The initial BIA skeleton is formed via condensation by a unique enzyme, norcoclaurine synthase, of the l-tyrosine derivatives dopamine and 4-hydroxyphenylacetaldehyde, yielding (S)-norcoclaurine as a central intermediate. The vast diversity of BIA structures is subsequently derived from (1) transformation of the basic BIA backbone by oxidative enzymes, particularly cytochromes P450 and FAD-linked oxidases, and (2) further structural and functional group modification by tailoring enzymes, which also include various reductases, dioxygenases, acetyltransferases, and carboxylesterases. Most of the biosynthetic enzymes responsible for the biosynthesis of major BIAs (i.e. morphine, noscapine, papaverine, and sanguinarine) in opium poppy (Papaver somniferum), and other compounds (e.g. berberine) in related plants, have been isolated and partially characterized. Diversity in BIA metabolism is driven by the modular and repetitive recruitment, and subsequent neo-functionalization, of a limited number of ancestral enzymes. In this review, BIA biosynthetic enzymes are discussed in the context of their respective families, facilitating exploration of common phylogeny and biochemical mechanisms.     

A structural study of the myristoylated N-terminus of ARF1

The effect of myristoylation on the 15-amino-acid peptide from the membrane-binding N-terminus of ADP ribosylation factor 1 (ARF1) was studied using neutron diffraction and circular dichroism. A previous study on the non-acylated form indicated that the peptide lies parallel to the membrane, at a shallow depth and in the vicinity of the phosphorylcholine headgroups. It was suggested that the helix does not extend past residue 12, an important consequence for the linking region of the ARF1 protein. In this paper, we show that the result of myristoylation is to increase the helical content reaching the peptide's C-terminus, resulting in the formation of a new hydrophobic face. This increased helicity may augment the entire protein's membrane-binding affinity, indicating that ARF1 effectively has two interdependent membrane-binding motifs.     

Large P body-like RNPs form in C. elegans oocytes in response to arrested ovulation, heat shock, osmotic stress, and anoxia and are regulated by the major sperm protein pathway

As Caenorhabditis elegans hermaphrodites age, sperm become depleted, ovulation arrests, and oocytes accumulate in the gonad arm. Large ribonucleoprotein (RNP) foci form in these arrested oocytes that contain RNA-binding proteins and translationally masked maternal mRNAs. Within 65 min of mating, the RNP foci dissociate and fertilization proceeds. The majority of arrested oocytes with foci result in viable embryos upon fertilization, suggesting that foci are not deleterious to oocyte function. We have determined that foci formation is not strictly a function of aging, and the somatic, ceh-18, branch of the major sperm protein pathway regulates the formation and dissociation of oocyte foci. Our hypothesis for the function of oocyte RNP foci is similar to the RNA-related functions of processing bodies (P bodies) and stress granules; here, we show three orthologs of P body proteins, DCP-2, CAR-1 and CGH-1, and two markers of stress granules, poly (A) binding protein (PABP) and TIA-1, appear to be present in the oocyte RNP foci. Our results are the first in vivo demonstration linking components of P bodies and stress granules in the germ line of a metazoan. Furthermore, our data demonstrate that formation of oocyte RNP foci is inducible in non-arrested oocytes by heat shock, osmotic stress, or anoxia, similar to the induction of stress granules in mammalian cells and P bodies in yeast. These data suggest commonalities between oocytes undergoing delayed fertilization and cells that are stressed environmentally, as to how they modulate mRNAs and regulate translation.     

The crystal structure of BlmI as a model for nonribosomal peptide synthetase peptidyl carrier proteins

Carrier proteins (CPs) play a critical role in the biosynthesis of various natural products, especially in nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymology, where the CPs are referred to as peptidyl‐carrier proteins (PCPs) or acyl‐carrier proteins (ACPs), respectively. CPs can either be a domain in large multifunctional polypeptides or standalone proteins, termed Type I and Type II, respectively. There have been many biochemical studies of the Type I PKS and NRPS CPs, and of Type II ACPs. However, recently a number of Type II PCPs have been found and biochemically characterized. In order to understand the possible interaction surfaces for combinatorial biosynthetic efforts we crystallized the first characterized and representative Type II PCP member, BlmI, from the bleomycin biosynthetic pathway from Streptomyces verticillus ATCC 15003. The structure is similar to CPs in general but most closely resembles PCPs. Comparisons with previously determined PCP structures in complex with catalytic domains reveals a common interaction surface. This surface is highly variable in charge and shape, which likely confers specificity for interactions. Previous nuclear magnetic resonance (NMR) analysis of a prototypical Type I PCP excised from the multimodular context revealed three conformational states. Comparison of the states with the structure of BlmI and other PCPs reveals that only one of the NMR states is found in other studies, suggesting the other two states may not be relevant. The state represented by the BlmI crystal structure can therefore serve as a model for both Type I and Type II PCPs. Proteins 2014; 82:1210–1218. © 2013 Wiley Periodicals, Inc.     

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss

Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic causes. The genomes of budding yeasts have been shaped by extensive reductive evolution, such as reduced genome sizes and the losses of metabolic capabilities. However, the extent and mechanisms of trait reacquisition after gene loss in yeasts have not been thoroughly studied. Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes. Unexpectedly, we detected multiple galactose-utilizing lineages that were deeply embedded within clades that underwent ancient losses of galactose utilization. We show that at least two, and possibly three, lineages reacquired the GAL pathway via yeast-to-yeast horizontal gene transfer. Our results show how trait reacquisition can occur tens of millions of years after an initial loss via horizontal gene transfer from distant relatives. These findings demonstrate that the losses of complex traits and even whole pathways are not always evolutionary dead-ends, highlighting how reversals to ancestral states can occur.