Rapid cold hardening increases axonal Na+/K+-ATPase activity and enhances performance of a visual motion detection circuit in Locusta migratoria.

Rapid cold hardening (RCH) is a type of phenotypic plasticity that delays the occurrence of chill coma in insects. Chill coma is mediated by a spreading depolarization of neurons and glia in the CNS, triggered by a failure of ion homeostasis. We used biochemical and electrophysiological approaches in the locust, Locusta migratoria, to test the hypothesis that the protection afforded by RCH is mediated by activation of the Na+/K+-ATPase (NKA) in neural tissue. RCH did not affect NKA activity measured in a biochemical assay of homogenized thoracic ganglia. However, RCH hyperpolarized the axon of a visual interneuron (DCMD) and increased the amplitude of an activity-dependent hyperpolarization (ADH) shown previously to be blocked by ouabain. RCH also improved performance of the visual circuitry presynaptic to DCMD to minimize habituation and increase excitability. We conclude that RCH enhances in situ NKA activity in the nervous system but also affects other neuronal properties that promote visual processing in locusts.

Utilizing comparative models in biomedical research.

This review serves as an introduction to a Special Issue of Comparative Biochemistry and Physiology, focused on using non-human models to study biomedical physiology. The concept of a model differs across disciplines. For example, several models are used primarily to gain an understanding of specific human pathologies and disease states, whereas other models may be focused on gaining insight into developmental or evolutionary mechanisms. It is often the case that animals initially used to gain knowledge of some unique biochemical or physiological process finds foothold in the biomedical community and becomes an established model. The choice of a particular model for biomedical research is an ongoing process and model validation must keep pace with existing and emerging technologies. While the importance of non-mammalian models, such as Caenorhabditis elegans, Drosophila melanogaster, Danio rerio and Xenopus laevis, is well known, we also seek to bring attention to emerging alternative models of both invertebrates and vertebrates, which are less established but of interest to the comparative biochemistry and physiology community.

WITHDRAWN: Utilizing comparative models in biomedical research.

The Publisher regrets that this article is an accidental duplication of an article that has already been published in Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, Volume 255, 2021, 110593, https://doi.org/10.1016/j.cbpb.2021.110593. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.

Measuring enzyme activities in crude homogenates: Na+/K+-ATPase as a case study in optimizing assays.

In this review of assays of Na+/K+-ATPase (NKA), we explore the choices made by researchers assaying the enzyme to investigate its role in physiological regulation. We survey NKA structure and function in the context of how it is typically assayed, and how technical choices influence what can be said about the enzyme. In comparing different methods for extraction and assay of NKA, we identified a series of common pitfalls that compromise the veracity of results. We include experimental work to directly demonstrate how choices in detergents, salts and substrates influence NKA activities measured in crude homogenates. Our review of assay approaches integrates what is known from enzymology, biomedical physiology, cell biology and evolutionary biology, offering a more robust method for assaying the enzyme in meaningful ways, identifying caveats and future directions to explore its structure and function. The goal is to provide the sort of background on the enzyme that should be considered in exploring the function of the enzyme in comparative physiology.

Getting the most out of reductionist approaches in comparative biochemistry and physiology.

This review serves as an introduction to a Special Issue of CBP focused on the use of reductionist approaches to explore questions in comparative biochemistry and physiology of animals. An overarching goal for research is to provide new insight and knowledge to advance the field. The significance of the research is dependent upon utilizing the most appropriate approach to get the most reliable data, which requires being knowledgeable about the experimental system and its limitations. It is not a trivial task to decide which level of biological organization is best suited to answer the question of interest, because each choice is a balance between strengths and weaknesses. Reporting caveats and limitations is perceived to detract from the definitiveness and value of a study, and so these are typically avoided, or included begrudgingly to appease a reviewer. Reductionist approaches are most valuable when the results can be translated to other biological levels of organization, providing physiological context for the work. Such extensions must also be accompanied by the appropriate assumptions and caveats arising from both the experimental system or its translation to higher levels of biological organization. In preparing this review, we seek to encourage authors to share the weaknesses and caveats in their approaches, and address the challenges associated with demonstrating the relevance of a reductionist approach to higher levels of organization.

Special issue on aquaculture: New opportunities to address global food supply for comparative biochemistry and physiology.

This article serves as an introduction to a Virtual Special Issue of Comparative Biochemistry and Physiology (CBP) focused on aquaculture. CBP has not traditionally had a focus on aquaculture, and the Editors sought to use this Special Issue to identify opportunities for synergy between traditional comparative physiology and applied physiology, such as aquaculture. Each of the four CBP journals has a dedicated special issue, with manuscripts that span the breadth of vertebrate and invertebrate species cultured around the globe. This overview is intended to identify the major themes of the submissions, as well as articulate a vision for the types of aquaculture-focused research that are well suited for CBP publications.

Sensing and responding to energetic stress: Evolution of the AMPK network.

AMP-activated protein kinase is an enzyme that mediates communication between cellular energy status and diverse effector proteins, particularly those that play roles in determining the metabolic phenotype. By phosphorylating metabolic enzymes, transcriptional regulators and proteins involved in cellular structure, it can modify energy metabolism in both the short term and long term. Its basic features are highly conserved, with homologues in all eukaryotes. Gene and/or genome duplications endowed early vertebrates with paralogs of AMPK subunits, though the nature of their subfunctionalization remains uncertain, even in mammals. While most research focuses on the role of the enzyme in human health, a great deal can be learned from comparative studies targeting non-traditional model animals. Fish, in particular, are interesting models because of the diversity in the metabolic properties and complex relationships between metabolism and environmental challenges. In this review, we examine what is known about AMPK structure and function though the lens of comparative physiology, looking for opportunities to better understand how this vital energy sensor has evolved in animals.

Subfunctionalization of COX4 paralogs in fish.

Cytochrome c oxidase (COX) subunit 4 has two paralogs in most vertebrates. The mammalian COX4-2 gene is hypoxia responsive, and the protein has a disrupted ATP-binding site that confers kinetic properties on COX that distinguish it from COX4-1. The structure-function of COX4-2 orthologs in other vertebrates remains uncertain. Phylogenetic analyses suggest the two paralogs arose in basal vertebrates, but COX4-2 orthologs diverged faster than COX4-1 orthologs. COX4-1/4-2 protein levels in tilapia tracked mRNA levels across tissues, and did not change in hypoxia, arguing against a role for differential post-translational regulation of paralogs. The heart, and to a lesser extent the brain, showed a size-dependent shift from COX4-1 to COX4-2 (transcript and protein). ATP allosterically inhibited both velocity and affinity for oxygen in COX assayed from both muscle (predominantly COX4-2) and gill (predominantly COX4-1). We saw some evidence of cellular and subcellular discrimination of COX4 paralogs in heart. In cardiac ventricle, some non-cardiomyocyte cells were COX positive but lacked detectible COX4-2. Within heart, the two proteins partitioned to different mitochondrial subpopulations. Cardiac subsarcolemmal mitochondria had mostly COX4-1 and intermyofibrillar mitochondria had mostly COX4-2. Collectively, these data argue that, despite common evolutionary origins, COX4-2 orthologs of fish show unique patterns of subfunctionalization with respect to transcriptional and posttranslation regulation relative to the rodents and primates that have been studied to date.

Evaluating the role of NRF-1 in the regulation of the goldfish COX4-1 gene in response to temperature.

Cold acclimation in fish typically increases muscle mitochondrial enzymes. In mammals, stressors that increase mitochondrial content are mediated though transcriptional regulators, including nuclear respiratory factor-1 (NRF-1). Focusing on the goldfish gene for cytochrome c oxidase (COX) subunit 4-1, we analysed the regulatory regions in various contexts to identify a mechanistic link between NRF-1 and cold-induced mitochondrial proliferation. Promoter analysis implicated two putative NRF-1 sites: one in the proximal promoter and a second in exon 1, which encodes the 5' untranslated region (5'-UTR). Transfection into mouse myoblasts showed that deletion of a region that included the proximal NRF-1 site reduced promoter activity by 30%; however, mutagenesis of the specific sequence had no effect. Thermal sensitivity analyses performed in rainbow trout gonadal fibroblasts (RTG-2) showed no effect of temperature (4 vs 19°C) on reporter gene expression. Likewise, reporters injected into muscle of thermally acclimated goldfish (4 vs 26°C) showed no elevation in expression. There was no difference in thermal responses of COX4-1 promoter reporters constructed from homologous regions of eurythermal goldfish and stenothermal zebrafish genes. NRF-1 chromatin immunoprecipitation of thermally acclimated goldfish muscle showed no temperature effect on NRF-1 binding to either the proximal promoter or 5'-UTR. It remains possible that the cold-induced upregulation of COX4-1 expression is a result of NRF-1 binding to distal regulatory regions or through indirect effects on other transcription factors. However, the proximal promoter does not appear to play a role in mediating the thermal response of the COX4-1 gene in fish.

mRNA degradation: an underestimated factor in steady-state transcript levels of cytochrome c oxidase subunits?

Steady-state mRNA levels are determined by synthesis and degradation; however, changes in mRNA levels are usually attributed to transcription. For cytochrome c oxidase (COX), cold acclimation typically leads to an increase in COX activity while transcript levels for the nuclear-encoded subunits change non-stoichiometrically. Whether those patterns are caused by differences in subunit transcription rates, decay rates or both was not known. We assessed decay rates of transcripts for COX subunits, including representatives that decreased, increased in parallel with COX or increased in excess of COX. Low temperature reduced the decay rate of all transcripts; however, COX subunits displayed higher thermal sensitivity than housekeeping genes. The lower decay rates for COX transcripts might explain some of their increase in response to cold acclimation. The reason for the exaggerated transcript response of two subunits (COX6B-1 and COX7A-2) may be due to decreased decay. However, decay rate differences could not explain the patterns seen with another subunit that did not change in mRNA level with thermal acclimation (COX6A-2). Further, the decay patterns differed between two thermal acclimation experiments, which may explain some of the heterogeneity seen in fish studies. The differences in decay rates suggest that the lack of stoichiometry in mRNA levels is exacerbated by post-transcriptional mechanisms. Collectively, these results suggest that temperature-induced differences in COX subunit mRNA levels and deviations from stoichiometry between them may partially arise from subunit-specific sensitivities to degradation. We suggest that all subunits are controlled by transcription, and that exaggerated responses of some subunits are due to reduced decay rates.

Metabolism in the age of 'omes'.

Much research in comparative physiology is now performed using 'omics' tools and many results are interpreted in terms of the effects of changes in gene expression on energy metabolism. However, 'metabolism' is a complex phenomenon that spans multiple levels of biological organization. In addition rates and directions of flux change dynamically under various physiological circumstances. Within cells, message level cannot be equated with protein level because multiple mechanisms are at play in the 'regulatory hierarchy' from gene to mRNA to enzyme protein. This results in many documented instances wherein change in mRNA levels and change in enzyme levels are unrelated. It is also known from metabolic control analysis that the influence of single steps in pathways on flux is often small. Flux is a system property and its control tends to be distributed among multiple steps. Consequently, change in enzyme levels cannot be equated with change in flux. Approaches developed by Hans Westerhoff and colleagues, called 'hierarchical regulation analysis', allow quantitative determination of the extent to which 'hierarchical regulation', involving change in enzyme level, and 'metabolic regulation', involving the modulation of the activity of preexisting enzyme, regulate flux. We outline these approaches and provide examples to show their applicability to problems of interest to comparative physiologists.

Transcriptional regulation of temperature-induced remodeling of muscle bioenergetics in goldfish.

Central to mammalian mitochondrial biogenesis is the transcriptional master regulator peroxisome proliferator-activated receptor (PPAR)-γ coactivator-1α (PGC-1α), and a network of DNA-binding proteins it coactivates. We explored the role of this pathway in muscle mitochondrial biogenesis in response to thermal acclimation in goldfish (Carassius auratus). We investigated the transcriptional response of PGC-1α, PGC-1ß, and their antagonist the nuclear receptor interacting protein 1 (RIP140), as well as the mRNA and protein patterns of DNA-binding proteins that bind PGC-1, including nuclear respiratory factors (NRF) 1 and 2, retinoid X receptor α (RXRα), estrogen-related receptor α (ERRα), thyroid receptor α-1 (TRα-1), PPARα, and PPARß/δ, and the host cell factor 1 (HCF1), which links PGC-1 and NRF-2. Cold-acclimated (4°C) fish had higher COX activities (4.5-fold) and COX4-1 mRNA levels (3.5-fold per total RNA; 6.5-fold per gram tissue) than warm-acclimated (32°C) fish. The transcription factor patterns were profoundly influenced by changes in RNA per gram tissue (2-fold higher in cold fish) and nuclear protein content (2-fold higher in warm fish). In cold-acclimated fish, mRNA per gram tissue was elevated for PGC-1ß, RIP140, NRF-1, HCF1, NRF-2α, NRF-2ß-2, ERRα, PPAR ß/δ, and RXRα, but other transcriptional regulators either did not change (PGC-1α, PPARα) or even decreased (TRα-1). Nuclear protein levels in cold-acclimated fish were higher only for NRF-1; other proteins were either unaffected (NRF-2α, ERRα) or decreased (NRF-2ß1/2, TRα, RXRα). Collectively, these data support the role for NRF-1 in regulating cold-induced mitochondrial biogenesis in goldfish, with effects mediated by PGC-1ß, rather than PGC-1α.

Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: the importance of taxon-sampling in codon-based models.

While endothermy is ubiquitous in birds and mammals, it is not exclusive to these most recently arisen vertebrate classes. The ability to warm specific organs and/or tissues above ambient temperature (regional endothermy) has evolved at least three times in phylogentically discrete fish lineages: lamnid sharks (Lamnidae), tunas (Scombridae) and billfishes (Istiophoridae and Xiphidae). Given the links between endothermy and metabolic rate, we looked for evidence of convergent molecular evolution in mtDNA-encoded cytochrome c oxidase (COX) subunits in each of these discrete lineages. We found no evidence that the endothermic phenotype in fishes is driven or accompanied by molecular convergence. Though we found little evidence for positively-selected sites in any of the lineages in any subunit, the conclusions were sensitive to the choice of maximum-likelihood model. Several sites identified by Naïve Empirical Bayes (NEB) were not found when Bayes Empirical Bayes (BEB) was employed. As well, conclusions were profoundly influenced by taxon-sampling. Several of the putative sites of positive selection in COX II were no longer apparent as we augmented taxon sampling. The lack of convergent molecular evolution in these remarkable taxa, combined with the profound influence of model choice and taxon sampling provide a cautionary note on the use of rates of non-synonymous to synonymous mutations (dN/dS) to explore questions of the evolution of physiological function.

Coordination of cytochrome c oxidase gene expression in the remodelling of skeletal muscle.

Many fish species respond to low temperature by inducing mitochondrial biogenesis, reflected in an increase in activity of the mitochondrial enzyme cytochrome c oxidase (COX). COX is composed of 13 subunits, three encoded by mitochondrial (mt)DNA and 10 encoded by nuclear genes. We used real-time PCR to measure mRNA levels for the 10 nuclear-encoded genes that are highly expressed in muscle. We measured mRNA levels in white muscle of three minnow species, each at two temperatures: zebrafish (Danio rerio) acclimated to 11 and 30°C, goldfish (Carassius auratus) acclimated to 4 and 35°C, and northern redbelly dace (Chrosomus eos) collected in winter and summer. We hypothesized that temperature-induced changes in COX activity would be paralleled by COX nuclear-encoded subunit transcript abundance. However, we found mRNA for COX subunits showed pronounced differences in thermal responses. Though zebrafish COX activity did not change in the cold, the transcript levels of four subunits decreased significantly (COX5A1, 60% decrease; COX6A2, 70% decrease; COX6C, 50% decrease; COX7B, 55% decrease). Treatments induced changes in COX activity in both dace (2.9 times in winter fish) and goldfish (2.5 times in cold fish), but the response in transcript levels was highly variable. Some subunits failed to increase in one (goldfish COX7A2, dace COX6A2) or both (COX7B, COX6B2) species. Other transcripts increased 1.7-100 times. The most cold-responsive subunits were COX4-1 (7 and 21.3 times higher in dace and goldfish, respectively), COX5A1 (13.9 and 5 times higher), COX6B1 (6 and 10 times higher), COX6C (11 and 4 times higher) and COX7C (13.3 and 100 times higher). The subunits that most closely paralleled COX increases in the cold were COX5B2 (dace 2.5 times, goldfish 1.7 times) and COX6A2 (dace 4.1 times, goldfish 1.7 times). Collectively, these studies suggest that COX gene expression is not tightly coordinated during cold-induced mitochondrial remodelling in fish muscle. Further, they caution against arguments about the importance of transcriptional regulation based on measurement of mRNA levels of select subunits of multimeric proteins.

Origins of variation in muscle cytochrome c oxidase activity within and between fish species.

Mitochondrial content, central to aerobic metabolism, is thought to be controlled by a few transcriptional master regulators, including nuclear respiratory factor 1 (NRF-1), NRF-2 and peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α). Though well studied in mammals, the mechanisms by which these factors control mitochondrial content have been less studied in lower vertebrates. We evaluated the role of these transcriptional regulators in seasonal changes in white muscle cytochrome c oxidase (COX) activity in eight local fish species representing five families: Centrarchidae, Umbridae, Esocidae, Gasterosteidae and Cyprinidae. Amongst centrarchids, COX activity was significantly higher in winter for pumpkinseed (2-fold) and black crappie (1.3-fold) but not bluegill or largemouth bass. In esociforms, winter COX activity was significantly higher in central mudminnow (3.5-fold) but not northern pike. COX activity was significantly higher in winter-acclimatized brook stickleback (2-fold) and northern redbelly dace (3-fold). Though mudminnow COX activity increased in winter, lab acclimation to winter temperatures did not alter COX activity, suggesting a role for non-thermal cues. When mRNA was measured for putative master regulators of mitochondria, there was little evidence for a uniform relationship between COX activity and any of NRF-1, NRF-2α or PGC-1α mRNA levels Collectively, these studies argue against a simple temperature-dependent mitochondrial response ubiquitous in fish, and suggest that pathways which control mitochondrial content in fish may differ in important ways from those of the better studied mammals.

Intra- and inter-specific variation in metabolic gene expression in relationship to environmental hypoxia.

In this study, we explored how environmental oxygen levels affect the metabolic phenotype of sympatric sunfish known to differ in their hypoxia tolerance. We examined bluegill (Lepomis macrochirus) and pumpkinseed (Lepomis gibbosus), two species commonly found in the same water bodies, though pumpkinseed are considered more hypoxia tolerant, and survive in hypoxic lakes that exclude bluegill. Freshly caught Lake Opinicon pumpkinseed possessed significantly higher glycolytic enzyme activities (PGI, ALD, GAPDH, ENO, and LDH) than bluegill, but after holding the fish in an oxygenated environment for 7days, pumpkinseed glycolytic enzymes (PGI, ALD, and LDH) and mRNA (LDHA and HIF1α) declined to bluegill's levels. When glycolytic enzymes and mRNA were compared in pumpkinseed populations from seven lakes, only Penyck Lake pumpkinseed had significantly elevated glycolytic enzyme activity that did not diminish with normoxic holding. The levels of mRNA for LDHA and HIF1α did not differ between lakes and did not change in response to normoxic holding in the Penyck Lake fish. Collectively, these studies on sunfish show that hypoxia tolerance contributes to ecological niche specialization between species, and provides an example of a population that has adapted chronically elevated glycolytic enzyme activity independent of current dissolved oxygen in the water.

Plasticity of oxidative metabolism in variable climates: molecular mechanisms.

Converting food to chemical energy (ATP) that is usable by cells is a principal requirement to sustain life. The rate of ATP production has to be sufficient for housekeeping functions, such as protein synthesis and maintaining membrane potentials, as well as for growth and locomotion. Energy metabolism is temperature sensitive, and animals respond to environmental variability at different temporal levels, from within-individual to evolutionary timescales. Here we review principal molecular mechanisms that underlie control of oxidative ATP production in response to climate variability. Nuclear transcription factors and coactivators control expression of mitochondrial proteins and abundance of mitochondria. Fatty acid and phospholipid concentrations of membranes influence the activity of membrane-bound proteins as well as the passive leak of protons across the mitochondrial membrane. Passive proton leak as well as protein-mediated proton leak across the inner mitochondrial membrane determine the efficacy of ATP production but are also instrumental in endothermic heat production and as a defense against reactive oxygen species. Both transcriptional mechanisms and membrane composition interact with environmental temperature and diet, and this interaction between diet and temperature in determining mitochondrial function links the two major environmental variables that are affected by changing climates. The limits to metabolic plasticity could be set by the production of reactive oxygen species leading to cellular damage, limits to substrate availability in mitochondria, and a disproportionally large increase in proton leak over ATP production.

Modular evolution of PGC-1alpha in vertebrates.

In mammals, the peroxisome proliferator activated receptor (PPAR)gamma coactivator-1alpha (PGC-1alpha) is a central regulator of mitochondrial gene expression, acting in concert with nuclear respiratory factor-1 (NRF-1) and the PPARs. Its role as a "master regulator" of oxidative capacity is clear in mammals, but its role in other vertebrates is ambiguous. In lower vertebrates, although PGC-1alpha seems to play a role in coordinating the PPARalpha axis as in mammals, it does not appear to be involved in NRF-1 regulation of mitochondrial content. To evaluate the evolutionary patterns of this coactivator in fish and mammals, we investigated the evolutionary trajectories of PGC-1alpha homologs in representative vertebrate lineages. A phylogeny of the PGC-1 paralogs suggested that the family diversified through repeated genome duplication events early in vertebrate evolution. Bayesian and maximum likelihood phylogenetic reconstructions of PGC-1alpha in representative vertebrate species revealed divergent evolutionary dynamics across the different functional domains of the protein. Specifically, PGC-1alpha exhibited strong conservation of the activation/PPAR interaction domain across vertebrates, whereas the NRF-1 and MEF2c interaction domains experienced accelerated rates of evolution in actinopterygian (fish lineages) compared to sarcopterygians (tetrapod lineages). Furthermore, analysis of the amino acid sequence of these variable domains revealed successive serine- and glutamine-rich insertions within the teleost lineages, with important ramifications for PGC-1alpha function in these lineages. Collectively, these results suggest modular evolution of the PGC-1alpha protein in vertebrates that could allow for lineage-specific divergences in the coactivating capabilities of this regulator.

Scaling of muscle metabolic enzymes: an historical perspective.

In this paper, we take an historical approach to reviewing research into the patterns of metabolic enzymes in muscle in relation to body size, focusing on mitochondrial enzymes. One of the first studies on allometric scaling of muscle enzymes was published in an early issue of this journal (George and Talesara, 1961 Comp. Biochem. Physiol. 3: 267-273). These researchers studied a number of locally available birds and a bat, measuring the activity of the mitochondrial enzyme succinate dehydrogenase in relation to body mass and muscle structure. Though the phenomenon of allometric scaling of metabolism was well recognized even 50 years earlier, this study was one of the first to explore the enzymatic underpinnings of the metabolic patterns in different animals. In this review, we begin by considering the George and Talesara study in the context of this early era in metabolic biochemistry and comparative physiology. We review subsequent studies in the last 50 years that continued the comparative analysis of enzyme patterns in relation to body size in diverse experimental models. This body of work identified a recurrent (though not ubiquitous) reciprocal relationship between oxidative and glycolytic enzymes. In the last 10 years, studies have focused on identifying the molecular mechanisms that determine the muscle metabolic enzyme phenotype.