Enzyme promiscuity: mechanism and applications

Introductory courses in biochemistry teach that enzymes are specific for their substrates and the reactions they catalyze. Enzymes diverging from this statement are sometimes called promiscuous. It has been suggested that relaxed substrate and reaction specificities can have an important role in enzyme evolution; however, enzyme promiscuity also has an applied aspect. Enzyme condition promiscuity has, for a long time, been used to run reactions under conditions of low water activity that favor ester synthesis instead of hydrolysis. Together with enzyme substrate promiscuity, it is exploited in numerous synthetic applications, from the laboratory to industrial scale. Furthermore, enzyme catalytic promiscuity, where enzymes catalyze accidental or induced new reactions, has begun to be recognized as a valuable research and synthesis tool. Exploiting enzyme catalytic promiscuity might lead to improvements in existing catalysts and provide novel synthesis pathways that are currently not available.     

Contrasting evolution of diversity at two disease-associated chicken genes

There have been significant evolutionary pressures on the chicken during both its speciation and its subsequent domestication by man. Infectious diseases are expected to have exerted strong selective pressures during these processes. Consequently, it is likely that genes associated with disease susceptibility or resistance have been subject to some form of selection. Two genes involved in the immune response (interferon-γ and interleukin 1-β) were selected for sequencing in diverse chicken populations from Pakistan, Sri Lanka, Bangladesh, Kenya, Senegal, Burkina Faso and Botswana, as well as six outgroup samples (grey, green, red and Ceylon jungle fowl and grey francolin and bamboo partridge). Haplotype frequencies, tests of neutrality, summary statistics, coalescent simulations and phylogenetic analysis by maximum likelihood were used to determine the population genetic characteristics of the genes. Networks indicate that these chicken genes are most closely related to the red jungle fowl. Interferon-γ had lower diversity and considerable coding sequence conservation, which is consistent with its function as a key inflammatory cytokine of the immune response. In contrast, the pleiotropic cytokine interleukin 1-β had higher diversity and showed signals of balancing selection moderated by recombination, yielding high numbers of diverse alleles, possibly reflecting broader functionality and potential roles in more diseases in different environments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

Androstenol – a Steroid Derived Odor Activates the Hypothalamus in Women

Background

Whether pheromone signaling exists in humans is still a matter of intense discussion. In the present study we tested if smelling of Androstenol, a steroid produced by the human body and reported to affect human behavior, may elicit cerebral activation. A further issue was to evaluate whether the pattern of activation resembles the pattern of common odors.

Methodology

PET measurements of regional cerebral blood flow (rCBF) were conducted in 16 healthy heterosexual women during passive smelling of Androstenol, four ordinary odors (OO), and odorless air (the base line condition).

Principal findings

Smelling Androstenol caused activation of a portion of the hypothalamus, which according to animal data mediates the pheromone triggered mating behavior. Smelling of OO, on the other hand, engaged only the classical olfactory regions (the piriform cortex, lateral amygdala, anterior insular and anterior cingulate cortex).

Conclusions

The observed pattern of activation is very similar to the pattern previously detected with 4,16-androstadien-3-one in heterosexual females. It suggests that several compounds released by human body may activate cerebral networks involved in human reproduction.     

Energy state of the liver during short-term and exhaustive exercise in C57BL/6J mice

A portal venous 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranoside infusion that results in hepatic 5-aminoimidazole-4-carboxamide-1-beta-D-ribosyl-5-monophosphate (ZMP) concentrations of approximately 4 micromol/g liver increases hepatic glycogenolysis and glucose output. ZMP is an AMP analog that mimics the regulatory actions of this nucleotide. The aim of this study was to measure hepatic AMP concentrations in response to increasing energy requirements to test the hypothesis that AMP achieves concentrations during exercise, consistent with a role in stimulation of hepatic glucose metabolism. Male C57BL/6J mice (27.4+/- 0.4 g) were subjected to 35 min of rest [sedentary (SED), n=8], underwent short-term (ST, 35 min) moderate (20 m/min, 5% grade) exercise (n=8), or underwent treadmill exercise under similar conditions but until exhaustion (EXH, n=8). Hepatic AMP concentrations were 0.82+/- 0.05, 1.17+/- 0.11, and 2.52+/- 0.16 micromol/g liver in SED, ST, and EXH mice, respectively (P< 0.05). Hepatic energy charge was 0.66+/- 0.01, 0.58+/- 0.02, and 0.33+/- 0.22 in SED, ST, and EXH mice, respectively (P< 0.05). Hepatic glycogen was 11.6+/- 1.0, 8.8+/- 2.2, and 0.0+/- 0.1 mg/g liver in SED, ST, and EXH mice, respectively (P< 0.05). Hepatic AMPK (Thr(172)) phosphorylation was 1.00+/- 0.14, 1.96+/- 0.16, and 7.44+/- 0.63 arbitrary units in SED, ST, and EXH mice, respectively (P< 0.05). Thus exercise increases hepatic AMP concentrations. These data suggest that the liver is highly sensitive to metabolic demands, as evidenced by dramatic changes in cellular energy indicators (AMP) and sensors thereof (AMP-activated protein kinase). In conclusion, AMP is sensitively regulated, consistent with it having an important role in hepatic metabolism.     

Altered Oceanic pH Impairs Mating Propensity in a Pipefish

Anthropogenic disturbance is currently altering the environment of terrestrial as well as aquatic organisms. Those changes affect a variety of animal behaviours, which in turn may cause changes in species interactions, population dynamics and evolutionary processes. In marine ecosystems, nutrient enrichment may elevate pH, while it is reduced by carbon dioxide‐induced ocean acidification. These two processes are not expected to balance one another but rather to affect the environment at different times and scales. We here show experimentally that an increase in water pH has a negative effect on mating propensity in the broad‐nosed pipefish Syngnathus typhle, whereas lowered pH did not elicit the same detrimental effect. This study provides, to our knowledge, the first evidence that mating propensity is impaired by an increase in pH, suggesting that anthropogenic nutrient enrichment in aquatic ecosystems may change the processes of sexual selection and population dynamics solely on the basis of altered water pH.     

Evaluating somatic tumor mutation detection without matched normal samples

Background

Observations of recurrent somatic mutations in tumors have led to identification and definition of signaling and other pathways that are important for cancer progression and therapeutic targeting. As tumor cells contain both an individual’s inherited genetic variants and somatic mutations, challenges arise in distinguishing these events in massively parallel sequencing datasets. Typically, both a tumor sample and a “normal” sample from the same individual are sequenced and compared; variants observed only in the tumor are considered to be somatic mutations. However, this approach requires two samples for each individual.

Results

We evaluate a method of detecting somatic mutations in tumor samples for which only a subset of normal samples are available. We describe tuning of the method for detection of mutations in tumors, filtering to remove inherited variants, and comparison of detected mutations to several matched tumor/normal analysis methods. Filtering steps include the use of population variation datasets to remove inherited variants as well a subset of normal samples to remove technical artifacts. We then directly compare mutation detection with tumor-only and tumor-normal approaches using the same sets of samples. Comparisons are performed using an internal targeted gene sequencing dataset (n = 3380) as well as whole exome sequencing data from The Cancer Genome Atlas project (n = 250). Tumor-only mutation detection shows similar recall (43–60%) but lesser precision (20–21%) to current matched tumor/normal approaches (recall 43–73%, precision 30–82%) when compared to a “gold-standard” tumor/normal approach. The inclusion of a small pool of normal samples improves precision, although many variants are still uniquely detected in the tumor-only analysis.

Conclusions

A detailed method for somatic mutation detection without matched normal samples enables study of larger numbers of tumor samples, as well as tumor samples for which a matched normal is not available. As sensitivity/recall is similar to tumor/normal mutation detection but precision is lower, tumor-only detection is more appropriate for classification of samples based on known mutations. Although matched tumor-normal analysis is preferred due to higher precision, we demonstrate that mutation detection without matched normal samples is possible for certain applications.