A world of cytochrome P450s

The world we live in is a biosphere influenced by all organisms who inhabit it. It is also an ecology of genes, with some having rather startling effects. The premise put forth in this issue is cytochrome P450 is a significant player in the world around us. Life and the Earth itself would be visibly different and diminished without cytochrome P450s. The contributions to this issue range from evolution on the billion year scale to the colour of roses, from Darwin to Rachel Carson; all as seen through the lens of cytochrome P450.     

A study of the occurrence of regulator secondary structures in globular proteins

The distribution of regular secondary structures, viz. α-helices and β-strands, along the length of over 70 properties whose secondary structural details have been reported, has been analysed. The occurrence of these regular structures tends to be a maximum at the N- and C-termini. Our analysis suggests that both these free ends could possibly serve as nucleating centers for secondary structures and could play an important role in the folding of proteins.     

Intrinsically Unstructured Sequences in the mRNA 3ʹ UTR Reduce the Ability of Poly(A) Tail to Enhance Translation

The 5? cap and 3? poly(A) tail of mRNA are known to synergistically stimulate translation initiation via the formation of the cap?eIF4E?eIF4G?PABP?poly(A) complex. Most mRNA sequences have an intrinsic propensity to fold into extensive intramolecular secondary structures that result in short end-to-end distances. The inherent compactness of mRNAs might stabilize the cap?eIF4E?eIF4G?PABP?poly(A) complex and enhance cap-poly(A) translational synergy. Here, we test this hypothesis by introducing intrinsically unstructured sequences into the 5? or 3? UTRs of model mRNAs. We found that the introduction of unstructured sequences into the 3? UTR, but not the 5? UTR, decreases mRNA translation in cell-free wheat germ and yeast extracts without affecting mRNA stability. The observed reduction in protein synthesis results from the diminished ability of the poly(A) tail to stimulate translation. These results suggest that base pair formation by the 3? UTR enhances the cap-poly(A) synergy in translation initiation.     

Meiofaunal responses to nutrient additions in a Mediterranean stream

1. The effects of a moderate addition of nutrients (twofold N and threefold P) were examined during a 2‐year period to determine the response to nutrient addition in a meiofaunal community inhabiting sandy patches in a Mediterranean stream. 2. The pattern of meiofaunal assemblages exhibits a high degree of intra‐ and interannual variability. This pattern alternates between periods of hydrological stability and disturbances, such as floods and droughts, which is a characteristic of Mediterranean systems. 3. A before–after–control–impact (BACI) design was used to determine the outcome of the addition by comparing an upstream non‐enriched reach with an enriched downstream reach. Analysis of the study data by means of a nonparametric permutational procedure (permanova ) showed that fertilisation had a significant effect. Density and biomass values increased in the most abundant meiofaunal groups, including microcrustaceans, oligochaetes and chironomids. Microcrustaceans were the dominant group in the permanent meiofauna. 4. We also examined differences in microcrustacean secondary production in both reaches. Ostracods and cyclopoid copepods increased their secondary production in the impacted reach as a result of the nutrient addition. 5. Our study demonstrated that moderate nutrient enrichment can affect the biomass and production of stream meiofauna, but it is still unclear whether this effect was because of autotrophic or heterotrophic pathways.     

Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.     

The potential utility of postnatalskeletal developmental patterns in squamate phylogenetics

Postnatal patterns of skeletal development, includingthe sequence of appearance of ossification centres and the distributionof sesamoids, appear to be highly conserved species-level phenomenain squamates. As such, they are a potential source of charactersfor phylogenetic inquiry. These patterns, from 21 species representing14 crown squamate clades, form the basis for two analyses. In thefirst, the sequence of postnatal skeletal events is coded as charactersusing the sequence unit approach. This analysis reveals that thesequence of postnatal skeletal events might be useful for determiningrelationships at or above the level of crown clades, but not amongthem. The second analysis utilizes discrete data from postnatalskeletal development, such as the presence/absence of sesamoidsand the number of secondary centres in epiphyseal cartilages. Thesediscrete data appear capable of recovering the deeper divergenceswithin Squamata, but evolve too slowly to be informative at thelevel of crown clades. Thus, patterns of postnatal skeletal developmenthave the potential to help illuminate relationships throughout thesquamate tree. Further progress in this area will require the examinationof additional squamate species, the exploration of alternative codingschemes for developmental sequences, and comparable postnatal datafor Sphenodon .  © 2002 The Linnean Societyof London, Zoological Journal of the Linnean Society, 2002, 136 ,277−313.     

Fence-Line Contact Between Wild and Farmed Cervids in Colorado: Potential for Disease Transmission

Abstract: Direct and indirect contact between wild and farmed cervids along perimeter fences may play a role in transmission of diseases like chronic wasting disease (CWD), but no studies have quantified such interactions. At 9 high-fenced commercial elk (Cervus elaphus) farms in Colorado, USA, during October 2003 to January 2005, we used animal-activated video to estimate rates of fence-line use by wild cervids, rates of direct contact between farmed and wild cervids, and probability of direct contact when wild cervids were present. We recorded 8-fold-more wild elk per unit time than mule deer (Odocoileus hemionus) at fence lines. Depending on site, we recorded 0.66 to 46.90 wild elk per 1,000 hours of camera monitoring. We documented 77 interactions between wild and farmed elk involving naso-oral contact and no contact between wild mule deer and farmed elk. Rate of direct contact ranged from 0.00 to 1.92 direct contacts per 1,000 hours of camera monitoring among sites. Given recorded presence of wild elk, estimated probability of observing direct contact during a 2-minute video recording ranged from 0.00 to 0.11 among sites. Risk of direct contact was about 3.5 times greater for single woven-wire fence compared with offset electric fence attached to a single woven-wire fence. We observed no direct contact through double woven-wire fences. Because little is currently known about infection rates associated with infection mechanisms, we cannot infer a level of CWD infection risk from our results, but some form of double fencing should reduce potential for direct and indirect transmission of disease into or out of elk farms.