Kyle K. Biggar

Non-histone protein methylation as a regulator of cellular signalling and function

Methylation of Lys and Arg residues on non-histone proteins has emerged as a prevalent post-translational modification and as an important regulator of cellular signal transduction mediated by the MAPK, WNT, BMP, Hippo and JAK–STAT signalling pathways. Crosstalk between methylation and other types of post-translational modifications, and between histone and non-histone protein methylation frequently occurs and affects cellular functions such as chromatin remodelling, gene transcription, protein synthesis, signal transduction and DNA repair. With recent advances in proteomic techniques, in particular mass spectrometry, the stage is now set to decode the methylproteome and define its functions in health and disease.

The emerging roles of microRNAs in the molecular responses of metabolic rate depression

Metabolic rate depression is an important survival strategy for many animal species and a common element of hibernation, torpor, estivation, anoxia and diapause. Studies of the molecular mechanisms that regulate reversible transitions to and from hypometabolic states have identified principles of regulatory control. These control mechanisms are conserved among biologically diverse organisms and include the coordinated reduction of specific groups of key regulatory enzymes or proteins in the cell, a process likely driven by microRNA target repression/degradation. The present review focuses on a growing area of research in hypometabolism and mechanisms involving the rapid and reversible control of translation facilitated by microRNAs. The analysis draws primarily from current research on three animal models: hibernating mammals, anoxic turtles and freeze-tolerant frogs (with selected examples from multiple other sources). Here, we demonstrate a link between metabolic rate depression, a well-documented response to periods of environmental stress, and microRNA expression. Microarray-based expression profiles and PCR-driven studies have revealed that specific microRNAs are induced in response to environmental stress. Selected members of this group decrease pro-apoptotic signaling, reduce muscle wasting and reduce protein translation, whereas other members contribute to cell cycle arrest and mitogen-activated protein kinase signaling. Many of the same microRNAs are frequently deregulated in numerous disease pathologies and, hence, the hypometabolism model could provide a novel approach for the treatment of stroke and heart attack in humans.

MicroRNA regulation below zero: Differential expression of miRNA-21 and miRNA-16 during freezing in wood frogs ☆

Natural freeze tolerance depends on numerous biochemical adaptations that address the multiple stresses imposed on cells by freezing and preserves viability by suppressing energy-expensive cell functions in the frozen state. We hypothesized that microRNAs, small non-coding RNA transcripts that bind to mRNA, could act to establish rapid biological controls that aid the reorganization of metabolic priorities for freezing survival. Selected microRNA species (miR-16 and miR-21) were evaluated using RT-PCR in liver and skeletal muscle of wood frogs (Rana sylvatica) comparing controls (5 degrees C acclimated) with animals frozen for 24h at -3 degrees C. Levels of miR-21 increased significantly during freezing by 1.5-fold and 1.3-fold in liver and skeletal muscle, respectively. MiR-16 transcripts also rose significantly by 1.5-fold in liver of frozen frogs but fell by 50% in skeletal muscle. Protein levels of Dicer, a type III RNase that is responsible for mature microRNA processing in the cytoplasm, were unchanged in liver and decreased significantly by 50% in muscle. This data provides the first report of differential regulation of microRNA species in a freeze tolerant vertebrate and suggest a mechanism for rapid, yet reversible, gene silencing when animals transition into the frozen state.

MicroRNA regulation in extreme environments: differential expression of microRNAs in the intertidal snail Littorina littorea during extended periods of freezing and anoxia.

Several recent studies of vertebrate adaptation to environmental stress have suggested roles for microRNAs (miRNAs) in regulating global suppression of protein synthesis and/or restructuring protein expression patterns. The present study is the first to characterize stress-responsive alterations in the expression of miRNAs during natural freezing or anoxia exposures in an invertebrate species, the intertidal gastropod Littorina littorea. These snails are exposed to anoxia and freezing conditions as their environment constantly fluctuates on both a tidal and seasonal basis. The expression of selected miRNAs that are known to influence the cell cycle, cellular signaling pathways, carbohydrate metabolism and apoptosis was evaluated using RT-PCR. Compared to controls, significant changes in expression were observed for miR-1a-1, miR-34a and miR-29b in hepatopancreas and for miR-1a-1, miR-34a, miR-133a, miR-125b, miR-29b and miR-2a in foot muscle after freezing exposure at −6 °C for 24 h (P < 0.05). In addition, in response to anoxia stress for 24 h, significant changes in expression were also observed for miR-1a-1, miR-210 and miR-29b in hepatopancreas and for miR-1a-1, miR-34a, miR-133a, miR-29b and miR-2a in foot muscle (P < 0.05). Moreover, protein expression of Dicer, an enzyme responsible for mature microRNA processing, was increased in foot muscle during freezing and anoxia and in hepatopancreas during freezing. Alterations in expression of these miRNAs in L. littorea tissues may contribute to organismal survival under freezing and anoxia.

Evidence for cell cycle suppression and microRNA regulation of cyclin D1 during anoxia exposure in turtles

The red-eared slider turtle (Trachemys scripta elegans) has a well-developed natural tolerance for oxygen deprivation that derives from biochemical adaptations, including anoxia-induced suppression of metabolic rate. We hypothesized that mechanisms that suppress ATP-expensive cell cycle activity would contribute significantly to establishing the hypometabolic state during anaerobiosis. Cyclin D1 is a critical regulator of the G1 phase of the cell cycle and is regarded as key to initiating cell proliferation. The relative protein expression of cyclin D1 was analyzed in both whole-cell and nuclear fractions of liver, kidney and skeletal muscle from turtles exposed to 5 or 20 h of submergence anoxia. Expression of cyclin D1 in both total and nuclear fractions decreased significantly under anoxia in liver and kidney as compared with aerobic controls, but no significant change occurred in muscle. The relative phosphorylation state of cyclin D1 (threonine 286) was also unchanged during anoxia in all tissues. Since phosphorylation of threonine 286 is necessary for proteasomal degradation of cyclin D1, this implies that an alternative mechanism is responsible for cyclin D1 suppression in anoxia. Levels of cyclin D1 mRNA transcripts did not change under anoxia in any tissue, so a post-transcriptional method of regulation was implicated. Analysis of the 3’UTR of cyclin D1 showed the presence of both an AU-rich region and a conserved binding site for microRNA-16-1 and microRNA-15a. Levels of both microRNAs increased in liver and kidney (but not in muscle) under anoxic conditions, implicating microRNA inhibition of mRNA translation as the mechanism underlying the suppression of cyclin D1 protein levels in the anoxic turtle.

Differential Expression of Mature MicroRNAs Involved in Muscle Maintenance of Hibernating Little Brown Bats, Myotis lucifugus: A Model of Muscle Atrophy Resistance

Muscle wasting is common in mammals during extended periods of immobility. However, many small hibernating mammals manage to avoid muscle atrophy despite remaining stationary for long periods during hibernation. Recent research has highlighted roles for short non-coding microRNAs (miRNAs) in the regulation of stress tolerance. We proposed that they could also play an important role in muscle maintenance during hibernation. To explore this possibility, a group of 10 miRNAs known to be normally expressed in skeletal muscle of non-hibernating mammals were analyzed by RT-PCR in hibernating little brown bats, Myotis lucifugus. We then compared the expression of these miRNAs in euthermic control bats and bats in torpor. Our results showed that compared to euthermic controls, significant, albeit modest (1.2–1.6 fold), increases in transcript expression were observed for eight mature miRNAs, including miR-1a-1, miR-29b, miR-181b, miR-15a, miR-20a, miR-206 and miR-128-1, in the pectoral muscle of torpid bats. Conversely, expression of miR-21 decreased by 80% during torpor, while expression of miR-107 remained unaffected. Interestingly, these miRNAs have been either validated or predicted to affect multiple muscle-specific factors, including myostatin, FoxO3a, HDAC4 and SMAD7, and are likely involved in the preservation of pectoral muscle mass and functionality during bat hibernation.

HIF-1α regulation in mammalian hibernators: role of non-coding RNA in HIF-1α control during torpor in ground squirrels and bats

A potential role for non-coding RNAs, miR-106b and antisense hypoxia inducible transcription factor-1 (HIF-1α), in HIF-1α regulation during mammalian hibernation was investigated in two species, the thirteen-lined ground squirrel (Ictidomys tridecemlineatus) and the little brown bat (Myotis lucifugus). Both species showed differential regulation of HIF-1α during hibernation. HIF-1α protein levels increased significantly in skeletal muscle of both species when animals entered torpor, as well as in bat liver. HIF-1α mRNA levels correlated with the protein increase in bat skeletal muscle and liver but not in squirrel skeletal muscle. Antisense HIF-1α transcripts were identified in skeletal muscle of both hibernators. The expression of antisense HIF-1α was reduced in skeletal muscle of torpid bats compared with euthermic controls, suggesting that release of inhibition by the antisense RNA contributes to regulating HIF-1α translation in this tissue during torpor. The expression of miR-106b, a microRNA associated with HIF-1α regulation, also decreased during torpor in both skeletal muscle and liver of bats and in ground squirrel skeletal muscle. These data present the first evidence that non-coding RNA provides novel post-transcriptional mechanisms of HIF-1α regulation when hibernators descend into deep cold torpor, and also demonstrate that these mechanisms are conserved in two divergent mammalian orders (Rodentia and Chiroptera).

Amplification and sequencing of mature microRNAs in uncharacterized animal models using stem–loop reverse transcription–polymerase chain reaction

Expression of mature microRNA (miRNA) transcripts can be easily measured in many established animal model systems but is difficult to evaluate using conventional methods in new and uncharacterized animal models. In this study, we were able to expand an existing protocol to evaluate miRNA expression in both vertebrate and invertebrate animals for which mature miRNAs remain unsequenced. This method allows the researcher to sequence reverse transcription-polymerase chain reaction products, validating miRNA-specific amplification and providing the opportunity to add to the current body of knowledge of miRNA annotation.

Perspectives in Cell Cycle Regulation: Lessons from an Anoxic Vertebrate

The ability of an animal, normally dependent on aerobic respiration, to suspend breathing and enter an anoxic state for long term survival is clearly a fascinating feat, and has been the focus of numerous biochemical studies. When anoxia tolerant turtles are faced with periods of oxygen deprivation, numerous physiological and biochemical alterations take place in order to facilitate vital reductions in ATP consumption. Such strategies include reversible post-translational modifications as well as the implementation of translation and transcription controls facilitating metabolic depression. Although it is clear that anoxic survival relies on the suppression of ATP consuming processes, the state of the cell cycle in anoxia tolerant vertebrates remain elusive. Several anoxia tolerant invertebrate and embryonic vertebrate models display cell cycle arrest when presented with anoxic stress. Despite this, the cell cycle has not yet been characterized for anoxia tolerant turtles. Understanding how vertebrates respond to anoxia can have important clinical implications. Uncontrollable cellular proliferation and hypoxic tumor progression are inescapably linked in vertebrate tissues. Consequentially, the molecular mechanisms controlling these processes have profound clinical consequences. This review article will discuss the theory of cell cycle arrest in anoxic vertebrates and more specifically, the control of the retinoblastoma pathway, the molecular markers of cell cycle arrest, the activation of checkpoint kinases, and the possibility of translational controls implemented by microRNAs.

Real-time protein unfolding: a method for determining the kinetics of native protein denaturation using a quantitative real-time thermocycler

Protein stability can be monitored by many different techniques. However, these protocols are often lengthy, consume large amounts of protein, and require expensive and specialized instruments. Here we present a new protocol to analyze protein unfolding kinetics using a quantified real-time thermocycler. This technique enables the analysis of a wide range of denaturants (and their interactions with temperature change) on protein stability in a multi-well platform, where samples can be run in parallel under virtually identical conditions and with highly sensitive detection. Using this set-up, researchers can evaluate the half-maximal rate of protein denaturation (K(nd)), maximum rate of denaturation (D(max)), and the cooperativity of individual denaturants in protein unfolding (µ-coefficient). Both lysozyme and hexokinase are used as model proteins and urea as a model denaturant to illustrate this new method and the kinetics of protein unfolding that it provides. Overall, this method allows the researcher to explore a large number of denaturants, at either constant or variable temperatures, within the same assay, providing estimates of denaturation kinetics that have been previously inaccessible.