On optima: The case of myoglobin-facilitated oxygen diffusion

Examining the role of oxygen-binding proteins on the early evolution of multicellularity

Oxygen availability is a key factor in the evolution of multicellularity, as larger and more sophisticated organisms often require mechanisms allowing efficient oxygen delivery to their tissues. One such mechanism is the presence of oxygen-binding proteins, such as globins and hemerythrins, which arose in the ancestor of bilaterian animals. Despite their importance, the precise mechanisms by which oxygen-binding proteins influenced the early stages of multicellular evolution under varying environmental oxygen levels are not yet clear. We addressed this knowledge gap by heterologously expressing the oxygen binding proteins myoglobin and myohemerythrin in snowflake yeast, a model system of simple, undifferentiated multicellularity. These proteins increased the depth and rate of oxygen diffusion, increasing the fitness of snowflake yeast growing aerobically. Experiments show that, paradoxically, oxygen-binding proteins confer a greater fitness benefit for larger organisms under high, not low, O2 conditions. We show via biophysical modeling that this is because facilitated diffusion is more efficient when oxygen is abundant, transporting a greater quantity of O2 which can be used for metabolism. By alleviating anatomical diffusion limitations to oxygen consumption, the evolution of O2-binding proteins in the oxygen-rich Neoproterozoic may have been a key breakthrough enabling the evolution of increasingly large, complex multicellular metazoan lineages.

Defining Physiological Normoxia for Improved Translation of Cell Physiology to Animal Models and Humans

The extensive oxygen gradient between the air we breathe (Po₂ ~21 kPa) and its ultimate distribution within mitochondria (as low as ~0.5-1 kPa) is testament to the efforts expended in limiting its inherent toxicity. It has long been recognized that cell culture undertaken under room air conditions falls short of replicating this protection in vitro. Despite this, difficulty in accurately determining the appropriate O₂ levels in which to culture cells, coupled with a lack of the technology to replicate and maintain a physiological O₂ environment in vitro, has hindered addressing this issue thus far. In this review, we aim to address the current understanding of tissue Po₂ distribution in vivo and summarize the attempts made to replicate these conditions in vitro. The state-of-the-art techniques employed to accurately determine O₂ levels, as well as the issues associated with reproducing physiological O₂ levels in vitro, are also critically reviewed. We aim to provide the framework for researchers to undertake cell culture under O₂ levels relevant to specific tissues and organs. We envisage that this review will facilitate a paradigm shift, enabling translation of findings under physiological conditions in vitro to disease pathology and the design of novel therapeutics.

Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes

Carbohydrates are biological blocks participating in diverse and crucial processes both at cellular and organism levels. They protect individual cells, establish intracellular interactions, take part in the immune reaction and participate in many other processes. Glycosylation is considered as one of the most important modifications of proteins and other biologically active molecules. Still, the data on the enzymatic machinery involved in the carbohydrate synthesis and processing are scattered, and the advance on its study is hindered by the vast bulk of accumulated genetic information not supported by any experimental evidences for functions of proteins that are encoded by these genes. In this article, we present novel instruments for statistical analysis of glycomes in taxa. These tools may be helpful for investigating carbohydrate-related enzymatic activities in various groups of organisms and for comparison of their carbohydrate content. The instruments are developed on the Carbohydrate Structure Database (CSDB) platform and are available freely on the CSDB web-site at http://csdb.glycoscience.ru.

Database URL: http://csdb.glycoscience.ru

Myoglobin oxygen affinity in aquatic and terrestrial birds and mammals

Myoglobin (Mb) is an oxygen binding protein found in vertebrate skeletal muscle, where it facilitates intracellular transport and storage of oxygen. This protein has evolved to suit unique physiological needs in the muscle of diving vertebrates that express Mb at much greater concentrations than their terrestrial counterparts. In this study, we characterized Mb oxygen affinity (P50) from 25 species of aquatic and terrestrial birds and mammals. Among diving species, we tested for correlations between Mb P50 and routine dive duration. Across all species examined, Mb P50 ranged from 2.40 to 4.85 mmHg. The mean P50 of Mb from terrestrial ungulates was 3.72±0.15 mmHg (range 3.70-3.74 mmHg). The P50 of cetaceans was similar to terrestrial ungulates ranging from 3.54 to 3.82 mmHg, with the exception of the melon-headed whale, which had a significantly higher P50 of 4.85 mmHg. Among pinnipeds, the P50 ranged from 3.23 to 3.81 mmHg and showed a trend for higher oxygen affinity in species with longer dive durations. Among diving birds, the P50 ranged from 2.40 to 3.36 mmHg and also showed a trend of higher affinities in species with longer dive durations. In pinnipeds and birds, low Mb P50 was associated with species whose muscles are metabolically active under hypoxic conditions associated with aerobic dives. Given the broad range of potential globin oxygen affinities, Mb P50 from diverse vertebrate species appears constrained within a relatively narrow range. High Mb oxygen affinity within this range may be adaptive for some vertebrates that make prolonged dives.

Rice ( Oryza) hemoglobins

Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O ₂, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O ₂. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O ₂-transport, O ₂-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs.

Vibrational dynamics of oxygenated heme proteins

Advanced spectroscopic techniques coupled with DFT calculations reveal the vibrational dynamics of the iron in stable dioxygen complexes with myoglobin and with a mutant engineered to model the catalytic site of heme-copper oxidases. The unprecedented level of detail will constrain computational modelling of reactions with oxygen.

Modeling of intracellular transport and compartmentation

The complexity and internal organization of mammalian cells as well as the regulation of intracellular transport processes has increasingly moved into the focus of investigation during the past two decades. Advanced staining and microscopy techniques help to shed light onto spatial cellular compartmentation and regulation, increasing the demand for improved modeling techniques. In this chapter, we summarize recent developments in the field of quantitative simulation approaches and frameworks for the description of intracellular transport processes. Special focus is therefore laid on compartmented and spatiotemporally resolved simulation approaches. The processes considered include free and facilitated diffusion of molecules, active transport via the microtubule and actin filament network, vesicle distribution, membrane transport, cell cycle-dependent cell growth and morphology variation, and protein production. Commercially and freely available simulation packages are summarized as well as model data exchange and harmonization issues.

Neuroglobin, cytoglobin, and myoglobin contribute to hypoxia adaptation of the subterranean mole rat Spalax

The subterranean mole rat Spalax is an excellent model for studying adaptation of a mammal toward chronic environmental hypoxia. Neuroglobin (Ngb) and cytoglobin (Cygb) are O(2)-binding respiratory proteins and thus candidates for being involved in molecular hypoxia adaptations of Spalax. Ngb is expressed primarily in vertebrate nerves, whereas Cygb is found in extracellular matrix-producing cells and in some neurons. The physiological functions of both proteins are not fully understood but discussed with regard to O(2) supply, the detoxification of reactive oxygen or nitrogen species, and apoptosis protection. Spalax Ngb and Cygb coding sequences are strongly conserved. However, mRNA and protein levels of Ngb in Spalax brain are 3-fold higher than in Rattus norvegicus under normoxia. Importantly, Spalax expresses Ngb in neurons and additionally in glia, whereas in hypoxia-sensitive rodents Ngb expression is limited to neurons. Hypoxia causes an approximately 2-fold down-regulation of Ngb mRNA in brain of rat and mole rat. A parallel regulatory response was found for myoglobin (Mb) in Spalax and rat muscle, suggesting similar functions of Mb and Ngb. Cygb also revealed an augmented normoxic expression in Spalax vs. rat brain, but not in heart or liver, indicating distinct tissue-specific functions. Hypoxia induced Cygb transcription in heart and liver of both mammals, with the most prominent mRNA up-regulation (12-fold) in Spalax heart. Our data suggest that tissue globins contribute to the remarkable tolerance of Spalax toward environmental hypoxia. This is consistent with the proposed cytoprotective effect of Ngb and Cygb under pathological hypoxic/ischemic conditions in mammals.

Regulation of myoglobin expression

Myoglobin is a well-characterized, cytoplasmic hemoprotein that is expressed primarily in cardiomyocytes and oxidative skeletal muscle fibers. However, recent studies also suggest low-level myoglobin expression in various non-muscle tissues. Prior studies incorporating molecular, pharmacological, physiological and transgenic technologies have demonstrated that myoglobin is an essential oxygen-storage hemoprotein capable of facilitating oxygen transport and modulating nitric oxide homeostasis within cardiac and skeletal myocytes. Concomitant with these studies, scientific investigations into the transcriptional regulation of myoglobin expression have been undertaken. These studies have indicated that activation of key transcription factors (MEF2, NFAT and Sp1) and co-activators (PGC-1alpha) by locomotor activity, differential intracellular calcium fluxes and low intracellular oxygen tension collectively regulate myoglobin expression. Future studies focused on tissue-specific transcriptional regulatory pathways and post-translational modifications governing myoglobin expression will need to be undertaken. Finally, further studies investigating the modulation of myoglobin expression under various myopathic processes may identify myoglobin as a novel therapeutic target for the treatment of various cardiac and skeletal myopathies.

Myoglobin's old and new clothes: from molecular structure to function in living cells

Myoglobin, a mobile carrier of oxygen, is without a doubt an important player central to the physiological function of heart and skeletal muscle. Recently, researchers have surmounted technical challenges to measure Mb diffusion in the living cell. Their observations have stimulated a discussion about the relative contribution made by Mb-facilitated diffusion to the total oxygen flux. The calculation of the relative contribution, however, depends upon assumptions, the cell model and cell architecture, cell bioenergetics, oxygen supply and demand. The analysis suggests that important differences can be observed whether steady-state or transient conditions are considered. This article reviews the current evidence underlying the evaluation of the biophysical parameters of myoglobin-facilitated oxygen diffusion in cells, specifically the intracellular concentration of myoglobin, the intracellular diffusion coefficient of myoglobin and the intracellular myoglobin oxygen saturation. The review considers the role of myoglobin in oxygen transport in vertebrate heart and skeletal muscle, in the diving seal during apnea as well as the role of the analogous leghemoglobin of plants. The possible role of myoglobin in intracellular fatty acid transport is addressed. Finally, the recent measurements of myoglobin diffusion inside muscle cells are discussed in terms of their implications for cytoarchitecture and microviscosity in these cells and the identification of intracellular impediments to the diffusion of proteins inside cells. The recent experimental data then help to refine our understanding of Mb function and establish a basis for future investigation.

Are animal models as good as we think?

Models have been a tool of science at least since the 18th century and serve a variety of purposes from focusing abstract thoughts to representing scaled down version of things for study. Generally, animal models are needed when it is impractical or unethical to study the target animal. Biologists have taken modeling by analogy beyond most other disciplines, deriving the relationship between model and target through evolution. The "unity in diversity" concept suggests that homology between model and target foretells functional similarities. Animal model studies have been invaluable for elucidating general strategies, pathways, processes and guiding the development of hypotheses to test in target animals. The vast majority of animals used as models are used in biomedical preclinical trials. The predictive value of those animal studies is carefully monitored, thus providing an ideal dataset for evaluating the efficacy of animal models. On average, the extrapolated results from studies using tens of millions of animals fail to accurately predict human responses. Inadequacies in experimental designs may account for some of the failure. However, recent discoveries of unexpected variation in genome organization and regulation may reveal a heretofore unknown lack of homology between model animals and target animals that could account for a significant proportion of the weakness in predictive ability. A better understanding of the mechanisms of gene regulation may provide needed insight to improve the predictability of animal models.