The current status of natural products from marine fungi and their potential as anti-infective agents

A growing number of marine fungi are the sources of novel and potentially life-saving bioactive secondary metabolites. Here, we have discussed some of these novel antibacterial, antiviral, antiprotozoal compounds isolated from marine-derived fungi and their possible roles in disease eradication. We have also discussed the future commercial exploitation of these compounds for possible drug development using metabolic engineering and post-genomics approaches.     

Hyaluronan and its catabolic products in tissue injury and repair.

Hyaluronan is an unbiquitous glycosaminoglycan present in most tissues. Under homeostatic conditions hyaluronan exists as a high molecular mass polymer that has important roles in tissue structural integrity. Under conditions of stress such as following tissue injury, hyaluronan becomes depolymerized and lower molecular mass polymers are generated. The biological properties of these hyaluronan fragments appear to be distinct from the larger precursor molecules. This review examines the biological role of hyaluronan fragments in tissue injury and repair.     

Plant carotenoid cleavage oxygenases and their apocarotenoid products

The oxidative cleavage of carotenoids leads to the production of apocarotenoids and is catalyzed by a family of carotenoid cleavage dioxygenases (CCDs). CCDs often exhibit substrate promiscuity, which probably contributes to the diversity of apocarotenoids found in nature. Biologically and commercially important apocarotenoids include the phytohormone abscisic acid, the visual and signaling molecules retinal and retinoic acid, and the aromatic volatile beta-ionone. Unexpected properties associated with the CCD catalytic products emphasize their role in many aspects of plant growth and development. For instance, CCD7 and CCD8 produce a novel, graft-transmissible hormone that controls axillary shoot growth in plants. Here, CCDs are discussed according to their roles in the biosynthesis of these products. Recent studies regarding their mechanism of action are also addressed.     

Radical SAM enzymes in the biosynthesis of sugar-containing natural products

Carbohydrates play a key role in the biological activity of numerous natural products. In many instances their biosynthesis requires radical mediated rearrangements, some of which are catalyzed by radical SAM enzymes. BtrN is one such enzyme responsible for the dehydrogenation of a secondary alcohol in the biosynthesis of 2-deoxystreptamine. DesII is another example that catalyzes a deamination reaction necessary for the net C4 deoxygenation of a glucose derivative en route to desosamine formation. BtrN and DesII represent the two most extensively characterized radical SAM enzymes involved in carbohydrate biosynthesis. In this review, we summarize the biosynthetic roles of these two enzymes, their mechanisms of catalysis, the questions that have arisen during these investigations and the insight they can offer for furthering our understanding of radical SAM enzymology. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.     

Natural products reveal cancer cell dependence on oxysterol-binding proteins

Cephalostatin 1, OSW-1, ritterazine B and schweinfurthin A are natural products that potently, and in some cases selectively, inhibit the growth of cultured human cancer cell lines. The cellular targets of these small molecules have yet to be identified. We have discovered that these molecules target oxysterol binding protein (OSBP) and its closest paralog, OSBP-related protein 4L (ORP4L)--proteins not known to be involved in cancer cell survival. OSBP and the ORPs constitute an evolutionarily conserved protein superfamily, members of which have been implicated in signal transduction, lipid transport and lipid metabolism. The functions of OSBP and the ORPs, however, remain largely enigmatic. Based on our findings, we have named the aforementioned natural products ORPphilins. Here we used ORPphilins to reveal new cellular activities of OSBP. The ORPphilins are powerful probes of OSBP and ORP4L that will be useful in uncovering their cellular functions and their roles in human diseases.     

Comparing Reference Charts

Reference charts are valuable tools for clinicians in their daily work on pediatric clinics. Reference charts are often constructed by smoothing techniques, and in this paper we present a newly developed non-parametric test for comparing these charts. We illustrate the method by an example. The worked example compares cross-sectional data on height in children from two Danish studies from 1970 and 1990, respectively. The test compares the average height over the range of ages for the two groups.     

The function of terpene natural products in the natural world

As the largest class of natural products, terpenes have a variety of roles in mediating antagonistic and beneficial interactions among organisms. They defend many species of plants, animals and microorganisms against predators, pathogens and competitors, and they are involved in conveying messages to conspecifics and mutualists regarding the presence of food, mates and enemies. Despite the diversity of terpenes known, it is striking how phylogenetically distant organisms have come to use similar structures for common purposes. New natural roles undoubtedly remain to be discovered for this large class of compounds, given that such a small percentage of terpenes has been investigated so far.     

Evidence that the two Escherichia coli groE morphogenetic gene products interact in vivo.

The Escherichia coli groEL and groES gene products are essential for both phage morphogenesis and bacterial growth. Although the gene products have been identified, their exact roles in these processes are not known. We have isolated mutations in the groEL gene that suppress defects in the groES gene. These intergenic suppressors were shown to map in the groEL gene by a variety of genetic and biochemical analyses. These results suggest that the two morphogenetic gene products interact in vivo and help to explain why mutations in either gene exhibit the same phenotype with respect to lambda head assembly and bacterial growth.     

DNA polymerase V allows bypass of toxic guanine oxidation products in vivo

Reactive oxygen and nitrogen radicals produced during metabolic processes, such as respiration and inflammation, combine with DNA to form many lesions primarily at guanine sites. Understanding the roles of the polymerases responsible for the processing of these products to mutations could illuminate molecular mechanisms that correlate oxidative stress with cancer. Using M13 viral genomes engineered to contain single DNA lesions and Escherichia coli strains with specific polymerase (pol) knockouts, we show that pol V is required for efficient bypass of structurally diverse, highly mutagenic guanine oxidation products in vivo. We also find that pol IV participates in the bypass of two spiroiminodihydantoin lesions. Furthermore, we report that one lesion, 5-guanidino-4-nitroimidazole, is a substrate for multiple SOS polymerases, whereby pol II is necessary for error-free replication and pol V for error-prone replication past this lesion. The results spotlight a major role for pol V and minor roles for pol II and pol IV in the mechanism of guanine oxidation mutagenesis.     

Symbiotic and dietary marine microalgae as a source of bioactive molecules–experience from natural products research

Cyanobacterial metabolites have proven to be invaluable as tools in thedissection of signal transduction pathways in mammalian cells and some arecurrently under clinical evaluation as drug candidates. It is now also realizedthat cyanobacteria are the true biosynthetic origin of many bioactive moleculesisolated from marine invertebrates; marine invertebrates may sequestercyanobacteria through diet or by symbiosis. This review discusses thedietary-derived cyanobacterial origin of the dolastatins, potent cytotoxiccompounds, originally isolated from the Indian Ocean sea hare,Dolabella auricularia. A discussion on the dietarydissemination of cyanobacterial metabolites through the marine food chain isalso presented. Reference to the metabolites isolated fromDysidea sponges is given to illustrate their origin fromsymbiotic cyanobacteria associated with this organism.     

Utility of Childhood BMI in the Prediction of Adulthood Disease: Comparison of National and International References

Objective: To determine whether the U.S. Centers for Disease Control and Prevention (CDC; CDC Reference) or International Obesity Task Force (IOTF; IOTF Reference) BMI cut‐off points for classifying adiposity status in children are more effective at predicting future health risk. Research Methods and Procedures: The sample (N = 1709) included 4‐ to 15‐year‐old (at baseline) boys and girls from the Bogalusa Heart Study. Overweight and obesity status were determined using both the CDC Reference and IOTF Reference BMI cut‐off points at baseline. The ability of childhood overweight and obesity, determined from the two BMI classification systems, to predict obesity and metabolic disorders in young adulthood (after a 13‐ to 24‐year follow‐up) was then compared. Results: Independently of the classification system employed to determine adiposity based on childhood BMI, the odds of being obese and having all of the metabolic disorders in young adulthood were significantly (p < 0.05) higher in the overweight and obese groups by comparison with the nonoverweight groups. Childhood overweight and obesity, determined by both the CDC Reference and IOTF Reference, had a low sensitivity and a high specificity for predicting obesity and metabolic disorders in young adulthood. Overweight and obesity as determined by the CDC Reference were slightly more sensitive and slightly less specific than the corresponding values based on the IOTF Reference. Discussion: Overweight and obesity during childhood, as determined by both the CDC and IOTF BMI cut‐off points, are strong predictors of obesity and coronary heart disease risk factors in young adulthood. The differences in the predictive capacity of the CDC Reference and IOTF Reference are, however, minimal.     

Large Neurological Component to Genetic Differences Underlying Biased Sperm Use in Drosophila

Sperm competition arises as a result of complex interactions among male and female factors. While the roles of some male factors are known, little is known of the molecules or mechanisms that underlie the female contribution to sperm competition. The genetic tools available for Drosophila allow us to identify, in an unbiased manner, candidate female genes that are critical for mediating sperm competition outcomes. We first screened for differences in female sperm storage and use patterns by characterizing the natural variation in sperm competition in a set of 39 lines from the sequenced Drosophila Genetic Reference Panel (DGRP) of wild-derived inbred lines. We found extensive female variation in sperm competition outcomes. To generate a list of candidate female genes for functional studies, we performed a genome-wide association mapping, utilizing the common single-nucleotide polymorphisms (SNPs) segregating in the DGRP lines. Surprisingly, SNPs within ion channel genes and other genes with roles in the nervous system were among the top associated SNPs. Knockdown studies of three candidate genes (para, Rab2, and Rim) in sensory neurons innervating the female reproductive tract indicate that some of these candidate female genes may affect sperm competition by modulating the neural input of these sensory neurons to the female reproductive tract. More extensive functional studies are needed to elucidate the exact role of all these candidate female genes in sperm competition. Nevertheless, the female nervous system appears to have a previously unappreciated role in sperm competition. Our results indicate that the study of female control of sperm competition should not be limited to female reproductive tract-specific genes, but should focus also on diverse biological pathways.     

Perspective: emerging evidence for signaling roles of mitochondrial anaplerotic products in insulin secretion

The importance of mitochondrial biosynthesis in stimulus secretion coupling in the insulin-producing beta-cell probably equals that of ATP production. In glucose-induced insulin secretion, the rate of pyruvate carboxylation is very high and correlates more strongly with the glucose concentration the beta-cell is exposed to (and thus with insulin release) than does pyruvate decarboxylation, which produces acetyl-CoA for metabolism in the citric acid cycle to produce ATP. The carboxylation pathway can increase the levels of citric acid cycle intermediates, and this indicates that anaplerosis, the net synthesis of cycle intermediates, is important for insulin secretion. Increased cycle intermediates will alter mitochondrial processes, and, therefore, the synthesized intermediates must be exported from mitochondria to the cytosol (cataplerosis). This further suggests that these intermediates have roles in signaling insulin secretion. Although evidence is quite good that all physiological fuel secretagogues stimulate insulin secretion via anaplerosis, evidence is just emerging about the possible extramitochondrial roles of exported citric acid cycle intermediates. This article speculates on their potential roles as signaling molecules themselves and as exporters of equivalents of NADPH, acetyl-CoA and malonyl-CoA, as well as alpha-ketoglutarate as a substrate for hydroxylases. We also discuss the "succinate mechanism," which hypothesizes that insulin secretagogues produce both NADPH and mevalonate. Finally, we discuss the role of mitochondria in causing oscillations in beta-cell citrate levels. These parallel oscillations in ATP and NAD(P)H. Oscillations in beta-cell plasma membrane electrical potential, ATP/ADP and NAD(P)/NAD(P)H ratios, and glycolytic flux are known to correlate with pulsatile insulin release. Citrate oscillations might synchronize oscillations of individual mitochondria with one another and mitochondrial oscillations with oscillations in glycolysis and, therefore, with flux of pyruvate into mitochondria. Thus citrate oscillations may synchronize mitochondrial ATP production and anaplerosis with other cellular oscillations.     

Mutually exclusive expression of sex-specific and non-sex-specific fruitless gene products in the Drosophila central nervous system

The fruitless gene of Drosophila produces multiple protein isoforms, which are classified into two major classes, sex-specific Fru proteins (FruM) and non-sex specific proteins (FruCOM). Whereas FruM proteins are expressed in ∼2000 neurons to masculinize their structure and function, little is known about FruCOM's roles. As an attempt to obtain clues to the roles of FruCOM, we compared expression patterns of FruCOM and FruM in the central nervous system at the late larval stage. We found that nearly all neuroblasts express FruCOM but not FruM, whereas a subset of ganglion mother cells and differentiated neurons express FruM but not FruCOM. It is inferred that FruCOM proteins support fundamental stem cell functions, contrasting to FruM proteins, which play major roles in sex-specific differentiation of neurons.     

New Components of Drosophila Leg Development Identified through Genome Wide Association Studies

The adult Drosophila melanogaster body develops from imaginal discs, groups of cells set-aside during embryogenesis and expanded in number during larval stages. Specification and development of Drosophila imaginal discs have been studied for many years as models of morphogenesis. These studies are often based on mutations with large developmental effects, mutations that are often lethal in embryos when homozygous. Such forward genetic screens can be limited by factors such as early lethality and genetic redundancy. To identify additional genes and genetic pathways involved in leg imaginal disc development, we employed a Genome Wide Association Study utilizing the natural genetic variation in leg proportionality found in the Drosophila Genetic Reference Panel fly lines. In addition to identifying genes already known to be involved in leg development, we identified several genes involved in pathways that had not previously been linked with leg development. Several of the genes appear to be involved in signaling activities, while others have no known roles at this time. Many of these uncharacterized genes are conserved in mammals, so we can now begin to place these genes into developmental contexts. Interestingly, we identified five genes which, when their function is reduced by RNAi, cause an antenna-to-leg transformation. Our results demonstrate the utility of this approach, integrating the tools of quantitative and molecular genetics to study developmental processes, and provide new insights into the pathways and networks involved in Drosophila leg development.     

Sequestered end products and enzyme regulation: the case of ornithine decarboxylase.

The polyamines (putrescine, spermidine, and spermine) are synthesized by almost all organisms and are universally required for normal growth. Ornithine decarboxylase (ODC), an initial enzyme of polyamine synthesis, is one of the most highly regulated enzymes of eucaryotic organisms. Unusual mechanisms have evolved to control ODC, including rapid, polyamine-mediated turnover of the enzyme and control of the synthetic rate of the protein without change of its mRNA level. The high amplitude of regulation and the rapid variation in the level of the protein led biochemists to infer that polyamines had special cellular roles and that cells maintained polyamine concentrations within narrow limits. This view was sustained in part because of our continuing uncertainty about the actual biochemical roles of polyamines. In this article, we challenge the view that ODC regulation is related to precise adjustment of polyamine levels. In no organism does ODC display allosteric feedback inhibition, and in three types of organism, bacteria, fungi, and mammals, the size of polyamine pools may vary radically without having a profound effect on growth. We suggest that the apparent stability of polyamine pools in unstressed cells is due to their being largely bound to cellular polyanions. We further speculate that allosteric feedback inhibition, if it existed, would be inappropriately responsive to changes in the small, freely diffusible polyamine pool. Instead, mechanisms that control the amount of the ODC protein have appeared in most organisms, and even these are triggered inappropriately by variation of the binding of polyamines to ionic binding sites. In fact, feedback inhibition of ODC might be maladaptive during hypoosmotic stress or at the onset of growth, when organisms appear to require rapid increases in the size of their cellular polyamine pools.     

Innovation and the regulation of products of agricultural biotechnology in the United States of America

The policy of the United States government is to seek regulatory approaches, consistent with applicable laws, that protect health and the environment while reducing unnecessary regulatory burdens and avoiding unjustifiably inhibiting innovation, stigmatizing new technologies, or creating unnecessary trade barriers [Adapted from the National Strategy for Modernizing the Regulatory System for Biotechnology Products, Product of the Emerging Technologies Interagency Policy Coordination Committee’s Biotechnology Working Group (OSTP 2016)]. U.S. agencies are focused on delivering health and environmental protection based on the best available science; establishing transparent, coordinated, predictable, and efficient regulatory practices across agencies; and promoting public confidence in the oversight of the products of biotechnology through clear and transparent public engagement [Adapted from the Task Force on Agriculture and Rural Prosperity Report (USDA 2017)]. U.S. agencies that regulate the products of agricultural biotechnology discuss regulatory approaches presented during the June 2018 OECD Conference on Genome Editing Applications in Agriculture, focusing on plants developed using genome editing.

     

On the evolution of functional secondary metabolites (natural products)

It is argued that organisms have evolved the ability to biosynthesize secondary metabolites (natural products) because of the selectional advantages they obtain as a result of the functions of the compounds. The clustering together of antibiotic biosynthesis, regulation, and resistance genes implies that these genes have been selected as a group and that the antibiotics function in antagonistic capacities in nature. Pleiotropic switching, the simultaneous expression of sporulation and antibiotic biosynthesis genes, is interpreted in terms of the defence roles of antibiotics. We suggest a general mechanism for the evolution of secondary metabolite biosynthesis pathways, and argue against the hypothesis that modern antibiotics had prebiotic effector functions, on the basis that it does not account for modern biosynthetic pathways.