Gene regulatory evolution in cold-adapted fly populations neutralizes plasticity and may undermine genetic canalization

The relationships between adaptive evolution, phenotypic plasticity, and canalization remain incompletely understood. Theoretical and empirical studies have made conflicting arguments on whether adaptive evolution may enhance or oppose the plastic response. Gene regulatory traits offer excellent potential to study the relationship between plasticity and adaptation, and they can now be studied at the transcriptomic level. Here we take advantage of three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. We measure the transcriptome-wide plasticity in gene expression levels and alternative splicing (intron usage) between warm and cold laboratory environments. We find that suspected adaptive changes in both gene expression and alternative splicing tend to neutralize the ancestral plastic response. Further, we investigate the hypothesis that adaptive evolution can lead to decanalization of selected gene regulatory traits. We find strong evidence that suspected adaptive gene expression (but not splicing) changes in cold-adapted populations are more vulnerable to the genetic perturbation of inbreeding than putatively neutral changes. We find some evidence that these patterns may reflect a loss of genetic canalization accompanying adaptation, although other processes including hitchhiking recessive deleterious variants may contribute as well. Our findings augment our understanding of genetic and environmental effects on gene regulation in the context of adaptive evolution.

CHARACTERIZATION OF PREDICTED BACTERIAL COLD-ADAPTED LIPASE FROM SEAFOOD COLD STORAGE

Lipases constitute as top three most important group of enzymes along with carbohydrases and proteases, and are widely used in various industries. In particular, lipase that perform high activity at low temperatures, or referred as cold adapted lipase (CLPs) considered as attractive catalyst due to its activity at low temperature. This unique feature is the main advantage of cold adapted lipase utilization because it requires a low energy source that is correlated with lower production costs and energy. In addition, reactions occur in cold temperatures may result in better product quality. The purpose of this research was to perform screening and characterization of bacterial cold adapted lipase from seafood cold storage. Among 53 isolates, Kr_16_30, TI_37_14 and Kr_16_28 showed the highest activity with 4.12 U/mL; 3.87 U/mL and 3.21 U/mL, respectively. Isolates Kr_16_30 seemed to be typical cold adapted lipase with optimum temperature at 20°C and pH 7. Isolates Kr_16_28 performed highest lipolytic activity at 30°C while TI_37_14 suspected to be similar to typical mesophilic lipase with optimum temperature at 40°C. Species identification based on 16s rRDA sequencing revealed that isolates Kr_16 30 and Kr_16 28 are belong to genus Pseudomonas and Bacillus, repectively.

A First Glimpse on Cold-Adapted PCB-Oxidizing Bacteria in Edmonson Point Lakes (Northern Victoria Land, Antarctica)

Antarctic freshwater ecosystems are especially vulnerable to human impacts. Polychlorobiphenyls (PCBs) are persistent organic pollutants that have a long lifetime in the environment. Despite their use having either been phased out or restricted, they are still found in nature, also in remote areas. Once in the environment, the fate of PCBs is strictly linked to bacteria which represent the first step in the transfer of toxic compounds to higher trophic levels. Data on PCB-oxidizing bacteria from polar areas are still scarce and fragmented. In this study, the occurrence of PCB-oxidizing cold-adapted bacteria was evaluated in water and sediment of four coastal lakes at Edmonson Point (Northern Victoria Land, Antarctica). After enrichment with biphenyl, 192 isolates were obtained with 57 of them that were able to grow in the presence of the PCB mixture Aroclor 1242, as the sole carbon source. The catabolic gene bphA, as a proxy for PCB degradation potential, was harbored by 37 isolates (out of 57), mainly affiliated to the genera Salinibacterium, Arthrobacter (among Actinobacteria) and Pusillimonas (among Betaproteobacteria). Obtained results enlarge our current knowledge on cold-adapted PCB-oxidizing bacteria and pose the basis for their potential application as a valuable eco-friendly tool for the recovery of PCB-contaminated cold sites.

Industrial Applications of Enzymes From Extremophiles

Extremophilic microorganisms have developed a variety of molecular tactics to exist in extreme environments. Researchers are fascinated by extremophiles and unearth various enzymes from these fascinating microbes. Extremozymes are astonishing biocatalysts with distinctive properties of catalysis and stability under a multitude of daunting conditions of salt, pH, organic solvents, and temperature, which open up new possibilities for biocatalysis and biotransformation and outcompetes mesophilic counterparts. Biotechnological implications include simple, immobilized, as well as whole-cell applications. Stability in organic solvents adds to the asymmetric catalysis and thereby exemplifies the applicability of extremozymes and in fostering biobased economies. Marine, cold-adapted enzymes, and those that help in the removal of a toxic hazardous substance from the environment are obvious choices for food industries and bioremediation. The major area of application and research emphasis includes textile, detergents, food, dairy, agriculture, and environmental remediation.

Psychrophiles

Life on the Earth has evolved in the cold environments. Such cold habitats pose special challenges to the microbes in cold ecosystems, such as minimum metabolic activities, very limited nutrient availability, and often extreme conditions such as pH and salinity apart from temperature. Microbial communities surviving under these extreme conditions must have evolved complex structural and functional adaptations. Prokaryotic adaptations to cold environments are through physiological adaptations by increasing membrane fluidity through large amount of unsaturated fatty acids. These microbes also possess some cold adapted proteins whose steady state levels are maintained. They also produce certain compounds such as polyamines, sugars, polyols, amino acids, and some antifreeze proteins to protect themselves under freezing conditions. They also produce exopolymeric substances that promote adhesion of microbes to moist surfaces to induce biofilm formation which helps getting nutrients and protect the cells from harsh conditions. Antioxidants help destroying toxic reactive oxygen species.

Highly Stable, Cold-Active Aldehyde Dehydrogenase from the Marine Antarctic Flavobacterium sp. PL002

Stable aldehyde dehydrogenases (ALDH) from extremophilic microorganisms constitute efficient catalysts in biotechnologies. In search of active ALDHs at low temperatures and of these enzymes from cold-adapted microorganisms, we cloned and characterized a novel recombinant ALDH from the psychrotrophic Flavobacterium PL002 isolated from Antarctic seawater. The recombinant enzyme (F-ALDH) from this cold-adapted strain was obtained by cloning and expressing of the PL002 aldH gene (1506 bp) in Escherichia coli BL21(DE3). Phylogeny and structural analyses showed a high amino acid sequence identity (89%) with Flavobacterium frigidimaris ALDH and conservation of all active site residues. The purified F-ALDH by affinity chromatography was homotetrameric, preserving 80% activity at 4 °C for 18 days. F-ALDH used both NAD+ and NADP+ and a broad range of aliphatic and aromatic substrates, showing cofactor-dependent compensatory KM and kcat values and the highest catalytic efficiency (0.50 µM−1 s−1) for isovaleraldehyde. The enzyme was active in the 4–60 °C-temperature interval, with an optimal pH of 9.5, and a preference for NAD+-dependent reactions. Arrhenius plots of both NAD(P)+-dependent reactions indicated conformational changes occurring at 30 °C, with four(five)-fold lower activation energy at high temperatures. The high thermal stability and substrate-specific catalytic efficiency of this novel cold-active ALDH favoring aliphatic catalysis provided a promising catalyst for biotechnological and biosensing applications.

"Heat waves" experienced during larval life have species-specific consequences on life-history traits and sexual development in anuran amphibians

Extreme temperatures during heat waves can induce mass-mortality events, but can also exert sublethal negative effects by compromising life-history traits and derailing sexual development. Ectothermic animals may, however, also benefit from increased temperatures via enhanced physiological performance and the suppression of cold-adapted pathogens. Therefore, it is crucial to address how the intensity and timing of naturally occurring or human-induced heat waves affect life-history traits and sexual development in amphibians, to predict future effects of climate change and to minimise risks arising from the application of elevated temperature in disease mitigation. We raised agile frog (Rana dalmatina) and common toad (Bufo bufo) tadpoles at 19 °C and exposed them to a simulated heat wave of 28 or 30 °C for six days during one of three ontogenetic periods (early, mid or late larval development). In agile frogs, exposure to 30 °C during early larval development increased mortality. Regardless of timing, all heat-treatments delayed metamorphosis, and exposure to 30 °C decreased body mass at metamorphosis. Furthermore, exposure to 30 °C during any period and to 28 °C late in development caused female-to-male sex reversal, skewing sex ratios strongly towards males. In common toads, high temperature only slightly decreased survival and did not influence phenotypic sex ratio, while it reduced metamorph mass and length of larval development. Juvenile body mass measured two months after metamorphosis was not adversely affected by temperature treatments in either species. Our results indicate that heat waves may have devastating effects on amphibian populations, and the severity of these negative consequences, and sensitivity can vary greatly between species and with the timing and intensity of heat. Finally, thermal treatments against cold-adapted pathogens have to be executed with caution, taking into account the thermo-sensitivity of the species and the life stage of animals to be treated.

Selection-driven adaptation to the extreme Antarctic environment in the Emperor penguin

The eco-evolutionary history of penguins is profoundly influenced by their shift from temperate to cold environments. Breeding only in Antarctica during the winter, the Emperor penguin appears as an extreme outcome of this process, with unique features related to insulation, heat production and energy management. However, whether this species actually diverged from a less cold-adapted ancestor, thus more similar in ecology to its sister species, the King penguin, is still an open question. As the Antarctic niche shift likely resulted in vast changes in selective pressure experienced by the Emperor penguin, the identification and relative quantification of the genomic signatures of selection, unique to each of these sister species, could answer this question. Applying a suite of phylogeny-based methods on 7,651 orthologous gene alignments of seven penguins and 13 other birds, we identified a set of candidate genes showing significantly different selection regimes either in the Emperor or in the King penguin lineage. Our comparative approach unveils a more pervasive selection shift in the Emperor penguin, supporting the hypothesis that its extreme cold adaptation is a derived state from a more King penguin-like ecology. Among the candidate genes under selection in the Emperor penguin, four genes (TRPM8, LEPR, CRB1, and SFI1) were identified before in other cold adapted vertebrates, while, on the other hand, 161 genes can be assigned to functional pathways relevant to cold adaptation (e.g., cardiovascular system, lipid, fatty acid and glucose metabolism, insulation, etc.). Our results show that extreme cold adaptation in the Emperor penguin largely involved unique genetic options which, however, affect metabolic and physiological traits common to other cold-adapted homeotherms.