Staphylococcus aureus haem biosynthesis and acquisition pathways are linked through haem monooxygenase IsdG.

Haem is an essential cofactor in central metabolic pathways in the vast majority of living systems. Prokaryotes acquire haem via haem biosynthesis pathways, and some also utilize haem uptake systems, yet it remains unclear how they balance haem requirements with the paradox that free haem is toxic. Here, using the model pathogen Staphylococcus aureus, we report that IsdG, one of two haem oxygenase enzymes in the haem uptake system, inhibits the formation of haem via the internal haem biosynthesis route. More specifically, we show that IsdG decreases the activity of ferrochelatase and that the two proteins interact both in vitro and in vivo. Further, a bioinformatics analysis reveals that a significant number of haem biosynthesis pathway containing organisms possess an IsdG-homologue and that those with both biosynthesis and uptake systems have at least two haem oxygenases. We conclude that IsdG-like proteins control intracellular haem levels by coupling the two pathways. IsdG is thus a target for the treatment of S. aureusinfections.

The structure, function and properties of sirohaem decarboxylase--an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway.

Some bacteria and archaea synthesize haem by an alternative pathway, which involves the sequestration of sirohaem as a metabolic intermediate rather than as a prosthetic group. Along this pathway the two acetic acid side-chains attached to C12 and C18 are decarboxylated by sirohaem decarboxylase, a heterodimeric enzyme composed of AhbA and AhbB, to give didecarboxysirohaem. Further modifications catalysed by two related radical SAM enzymes, AhbC and AhbD, transform didecarboxysirohaem into Fe-coproporphyrin III and haem respectively. The characterization of sirohaem decarboxylase is reported in molecular detail. Recombinant versions of Desulfovibrio desulfuricans, Desulfovibrio vulgaris and Methanosarcina barkeri AhbA/B have been produced and their physical properties compared. The D. vulgaris and M. barkeri enzyme complexes both copurify with haem, whose redox state influences the activity of the latter. The kinetic parameters of the D. desulfuricans enzyme have been determined, the enzyme crystallized and its structure has been elucidated. The topology of the enzyme reveals that it shares a structural similarity to the AsnC/Lrp family of transcription factors. The active site is formed in the cavity between the two subunits and a AhbA/B-product complex with didecarboxysirohaem has been obtained. A mechanism for the decarboxylation of the kinetically stable carboxyl groups is proposed.

Recent advances in the biosynthesis of modified tetrapyrroles: the discovery of an alternative pathway for the formation of heme and heme d 1.

Hemes (a, b, c, and o) and heme d 1 belong to the group of modified tetrapyrroles, which also includes chlorophylls, cobalamins, coenzyme F430, and siroheme. These compounds are found throughout all domains of life and are involved in a variety of essential biological processes ranging from photosynthesis to methanogenesis. The biosynthesis of heme b has been well studied in many organisms, but in sulfate-reducing bacteria and archaea, the pathway has remained a mystery, as many of the enzymes involved in these characterized steps are absent. The heme pathway in most organisms proceeds from the cyclic precursor of all modified tetrapyrroles uroporphyrinogen III, to coproporphyrinogen III, which is followed by oxidation of the ring and finally iron insertion. Sulfate-reducing bacteria and some archaea lack the genetic information necessary to convert uroporphyrinogen III to heme along the "classical" route and instead use an "alternative" pathway. Biosynthesis of the isobacteriochlorin heme d 1, a cofactor of the dissimilatory nitrite reductase cytochrome cd 1, has also been a subject of much research, although the biosynthetic pathway and its intermediates have evaded discovery for quite some time. This review focuses on the recent advances in the understanding of these two pathways and their surprisingly close relationship via the unlikely intermediate siroheme, which is also a cofactor of sulfite and nitrite reductases in many organisms. The evolutionary questions raised by this discovery will also be discussed along with the potential regulation required by organisms with overlapping tetrapyrrole biosynthesis pathways.

Molecular hijacking of siroheme for the synthesis of heme and d1 heme.

Modified tetrapyrroles such as chlorophyll, heme, siroheme, vitamin B(12), coenzyme F(430), and heme d(1) underpin a wide range of essential biological functions in all domains of life, and it is therefore surprising that the syntheses of many of these life pigments remain poorly understood. It is known that the construction of the central molecular framework of modified tetrapyrroles is mediated via a common, core pathway. Herein a further branch of the modified tetrapyrrole biosynthesis pathway is described in denitrifying and sulfate-reducing bacteria as well as the Archaea. This process entails the hijacking of siroheme, the prosthetic group of sulfite and nitrite reductase, and its processing into heme and d(1) heme. The initial step in these transformations involves the decarboxylation of siroheme to give didecarboxysiroheme. For d(1) heme synthesis this intermediate has to undergo the replacement of two propionate side chains with oxygen functionalities and the introduction of a double bond into a further peripheral side chain. For heme synthesis didecarboxysiroheme is converted into Fe-coproporphyrin by oxidative loss of two acetic acid side chains. Fe-coproporphyrin is then transformed into heme by the oxidative decarboxylation of two propionate side chains. The mechanisms of these reactions are discussed and the evolutionary significance of another role for siroheme is examined.

Revaluating forest drought experiments according to future precipitation patterns, ecosystem carbon and decomposition rate responses: A meta-analysis.

Moisture availability is a strong determinant of decomposition rates in forests worldwide. Climate models suggest that many terrestrial ecosystems are at risk from future droughts, suggesting moisture limiting conditions will develop across a range of forests worldwide. The impacts of increasing drought conditions on forest carbon (C) fluxes due to shifts in organic matter decay rates may be poorly characterised due to limited experimental research. To appraise this question, we conducted a meta-analysis of forest drought experiment studies worldwide, examining spatial limits, knowledge gaps and potential biases. To identify limits to experimental knowledge, we projected the global distribution of forest drought experiments against spatially modelled estimates of (i) future precipitation change, (ii) ecosystem total above-ground C and (iii) soil C storage. Our assessment, involving 115 individual experimental study locations, found a mismatch between the distribution of forest drought experiments and regions with higher levels of future drought risk and C storage, such as Central America, Amazonia, the Atlantic Forest of Brazil, equatorial Africa and Indonesia. Decomposition rate responses in litter and soil were also relatively under-studied, with only 30 experiments specifically examining the potential experimental impacts of drought on C fluxes from soil or litter. We propose new approaches for engaging experimentally with forest drought research, utilising standardised protocols to appraise the impacts of drought on the C cycle, while targeting the most vulnerable and relevant forests.

Reducing topical drug waste in ophthalmic surgery: multisociety position paper.

This position article on reducing topical drug waste with ophthalmic surgery was written by the Ophthalmic Instrument Cleaning and Sterilization Task Force, comprising representatives of the ASCRS, American Academy of Ophthalmology, American Glaucoma Society, and Outpatient Ophthalmic Surgery Society. Drug waste significantly increases the costs and carbon footprint of ophthalmic surgery. Surgical facilities should be permitted to use topical drugs in multidose containers on multiple patients until the manufacturer's labeled date of expiration, if proper guidelines are followed. Surgical patients requiring a topical medication not used for other patients should be allowed to bring that partially used medication home for postoperative use. These recommendations are based on published evidence and clarification of policies from multiple regulatory and accrediting agencies with jurisdiction over surgical facilities. Surveys suggest that most ambulatory surgery centers and hospitals performing cataract surgery are wasting topical drugs unnecessarily.

Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution.

Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences lower than 0.05% relative abundance). Comparable findings were made across local, regional, and global data sets and when using shotgun metagenomic markers. Altogether, these findings suggest that bacteria exhibit strong biogeographic patterns, but these signals can be obscured by methodological limitations. We advocate various innovations, including using zeta diversity, to advance the study of microbial biogeography.IMPORTANCE It is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in sampling design, sequence processing, and diversity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is driven by selection due to factors such as local soil characteristics. Altogether, these findings suggest that the processes underpinning diversity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil biodiversity.

Biotechnological Advances in Bacterial Microcompartment Technology.

Bacterial microcompartments (BMCs) represent proteinaceous macromolecular nanobioreactors that are found in a broad range of bacteria, and which are associated with either anabolic or catabolic processes. They consist of a semipermeable outer shell that packages a central metabolic enzyme or pathway, providing both enhanced flux and protection against toxic intermediates. Recombinant production of BMCs has led to their repurposing with the incorporation of altogether new pathways. Deconstructing BMCs into their component parts has shown that some individual shell proteins self-associate into filaments that can be further modified into a cytoplasmic scaffold, or cytoscaffold, to which enzymes/proteins can be targeted. BMCs therefore represent a modular system that is highly suited for engineering biological systems for useful purposes.

Scleral patch graft calcification and erosion following Molteno implant surgery.

A case of dystrophic calcification of a scleral patch graft and conjunctival tissue erosion 17 years following the implantation ofa Molteno drainage device is described.

The effect of cutaneous prostaglandin application on nail growth, nail brittleness, and intraocular pressure.

BACKGROUND: Bimatoprost has known adnexal activity and was observed to increase nail growth at two clinical centers. OBJECTIVES: In this randomized, double-blinded, placebo-controlled pilot study, we examine the effect of bimatoprost (Lumigan 0.01%), applied bid to the proximal nail fold on nail growth, nail brittleness, and intraocular pressure. METHODS: Bimatoprost drops were placed on the proximal nail folds of 45 subjects on one hand (medication group) and vehicle drops to the other hand (control group). Baseline and final nail growth measurements, Goldmann applanation tensions of both eyes, and photos at 30 days were performed. Nail brittleness was subjectively graded. RESULTS: For the 38 subjects completing the study, the final mean nail growth of the hands, the net individual nail growth of the digits (excluding chipped nails), nail brittleness, and eye pressure readings were NS at P<.05. Photos revealed no increased hirsutism, but one subject with increased skin pigmentation. The drops were well tolerated without adverse effects. Nail chipping was a limitation of the study. CONCLUSIONS: Despite the negative results in this pilot study on nail growth and brittleness, further studies with higher bimatoprost concentration (0.03%) are warranted. We recommend monitoring nail growth by etching or marking the nail rather than measuring the full nail length due to our chipped nail findings.

Construction of Recombinant Pdu Metabolosome Shells for Small Molecule Production in Corynebacterium glutamicum.

Bacterial microcompartments have significant potential in the area of industrial biotechnology for the production of small molecules, especially involving metabolic pathways with toxic or volatile intermediates. Corynebacterium glutamicum is an established industrial workhorse for the production of amino acids and has been investigated for the production of diamines, dicarboxylic acids, polymers and biobased fuels. Herein, we describe components for the establishment of bacterial microcompartments as production chambers in C. glutamicum. Within this study, we optimized genetic clusters for the expression of the shell components of the Citrobacter freundii propanediol utilization (Pdu) bacterial compartment, thereby facilitating heterologous compartment production in C. glutamicum. Upon induction, transmission electron microscopy images of thin sections from these strains revealed microcompartment-like structures within the cytosol. Furthermore, we demonstrate that it is possible to target eYFP to the empty microcompartments through C-terminal fusions with synthetic scaffold interaction partners (PDZ, SH3 and GBD) as well as with a non-native C-terminal targeting peptide from AdhDH (Klebsiella pneumonia). Thus, we show that it is possible to target proteins to compartments where N-terminal targeting is not possible. The overproduction of PduA alone leads to the construction of filamentous structures within the cytosol and eYFP molecules are localized to these structures when they are N-terminally fused to the P18 and D18 encapsulation peptides from PduP and PduD, respectively. In the future, these nanotube-like structures might be used as scaffolds for directed cellular organization and pathway enhancement.

Combining field experiments and predictive models to assess potential for increased plant diversity to climate-proof intensive agriculture.

Agricultural production systems face increasing threats from more frequent and extreme weather fluctuations associated with global climate change. While there is mounting evidence that increased plant community diversity can reduce the variability of ecosystem functions (such as primary productivity) in the face of environmental fluctuation, there has been little work testing whether this is true for intensively managed agricultural systems. Using statistical modeling techniques to fit environment-productivity relationships offers an efficient means of leveraging hard-won experimental data to compare the potential variability of different mixtures across a wide range of environmental contexts. We used data from two multiyear field experiments to fit climate-soil-productivity models for two pasture mixtures under intensive grazing-one composed of two drought-sensitive species (standard), and an eight-species mixture including several drought-resistant species (complex). We then used these models to undertake a scoping study estimating the mean and coefficient of variation (CV) of annual productivity for long-term climate data covering all New Zealand on soils with low, medium, or high water-holding capacity. Our results suggest that the complex mixture is likely to have consistently lower CV in productivity, irrespective of soil type or climate regime. Predicted differences in mean annual productivity between mixtures were strongly influenced by soil type and were closely linked to mean annual soil water availability across all soil types. Differences in the CV of productivity were only strongly related to interannual variance in water availability for the lowest water-holding capacity soil. Our results show that there is considerable scope for mixtures including drought-tolerant species to enhance certainty in intensive pastoral systems. This provides justification for investing resources in a large-scale distributed experiment involving many sites under different environmental contexts to confirm these findings.

Effect of bio-engineering on size, shape, composition and rigidity of bacterial microcompartments.

Bacterial microcompartments (BMCs) are proteinaceous organelles that are found in a broad range of bacteria and are composed of an outer shell that encases an enzyme cargo representing a specific metabolic process. The outer shell is made from a number of different proteins that form hexameric and pentameric tiles, which interact to allow the formation of a polyhedral edifice. We have previously shown that the Citrobacter freundii BMC associated with 1,2-propanediol utilization can be transferred into Escherichia coli to generate a recombinant BMC and that empty BMCs can be formed from just the shell proteins alone. Herein, a detailed structural and proteomic characterization of the wild type BMC is compared to the recombinant BMC and a number of empty BMC variants by 2D-gel electrophoresis, mass spectrometry, transmission electron microscopy (TEM) and atomic force microscopy (AFM). Specifically, it is shown that the wild type BMC and the recombinant BMC are similar in terms of composition, size, shape and mechanical properties, whereas the empty BMC variants are shown to be smaller, hollow and less malleable.

Linking climate suitability, spread rates and host-impact when estimating the potential costs of invasive pests.

Biosecurity agencies need robust bioeconomic tools to help inform policy and allocate scarce management resources. They need to estimate the potential for each invasive alien species (IAS) to create negative impacts, so that relative and absolute comparisons can be made. Using pine processionary moth (Thaumetopoea pityocampa sensu lato) as an example, these needs were met by combining species niche modelling, dispersal modelling, host impact and economic modelling. Within its native range (the Mediterranean Basin and adjacent areas), T. pityocampa causes significant defoliation of pines and serious urticating injuries to humans. Such severe impacts overseas have fuelled concerns about its potential impacts, should it be introduced to New Zealand. A stochastic bioeconomic model was used to estimate the impact of PPM invasion in terms of pine production value lost due to a hypothetical invasion of New Zealand by T. pityocampa. The bioeconomic model combines a semi-mechanistic niche model to develop a climate-related damage function, a climate-related forest growth model, and a stochastic spread model to estimate the present value (PV) of an invasion. Simulated invasions indicate that Thaumetopoea pityocampa could reduce New Zealand's merchantable and total pine stem volume production by 30%, reducing forest production by between NZ$1,550 M to NZ$2,560 M if left untreated. Where T. pityocampa is controlled using aerial application of an insecticide, projected losses in PV were reduced, but still significant (NZ$30 M to NZ$2,210 M). The PV estimates were more sensitive to the efficacy of the spray program than the potential rate of spread of the moth. Our novel bioeconomic method provides a refined means of estimating potential impacts of invasive alien species, taking into account climatic effects on asset values, the potential for pest impacts, and pest spread rates.

Proteomic analysis of whey and casein proteins in early milk from the marsupial Trichosurus vulpecula, the common brushtail possum.

Whey and casein proteins representing the first and second halves of the early lactation phase in the common brushtail possum (Trichosurus vulpecula) have been compared by two dimensional gel electrophoresis. Nine components of whey were differentially expressed during early lactation, including proteins identified as cathepsin B, clusterin, late lactation protein, lysozyme, ganglioside M2 activator and neutrophil gelatinase-associated lipocalin. A major novel protein, termed very early lactation protein (VELP), was identified in whey. Partial amino acid sequence data obtained from VELP did not appear to match any other reported protein sequence. VELP was shown to be an acidic glycoprotein of 20-30 kDa which exists as a homodimer. In the casein fraction, kappa-casein appeared to be differentially post-translationally modified during early lactation and fragments of beta-casein were relatively more abundant at the earlier lactation stage.

Characterization of bovine seminal plasma by proteomics.

Previous investigations of bovine seminal plasma (BSP) have revealed the identities of the three major proteins, BSP-PDC109, BSP-A3 and BSP-30 kDa, which together constitute about half of the total protein, as well as about 30 of the minor proteins. Analyses of BSP by 2-DE have revealed about 250 protein spots, suggesting that much of the BSP proteome remains undescribed. In this study, BSP has been analyzed by 2-D LC-based and SDS-PAGE-based proteomic methods. Ninety-nine proteins were identified, including 49 minor proteins that have not previously been described in seminal plasma of any species.

Human colostrum: identification of minor proteins in the aqueous phase by proteomics.

Human colostrum is an important source of protective, nutritional and developmental factors for the newborn. We have investigated the low abundance proteins in the aqueous phase of human colostrum, after depletion of the major proteins secretory IgA, lactoferrin, alpha-lactalbumin and HSA by immunoabsorption, using 2-D LC and gel-based proteomic methods. One hundred and fifty-one proteins were identified, 83 of which have not been previously reported in human colostrum, or milk. This is the first comprehensive proteomic analysis of human colostrum produced during the first 48 h of lactation.