Unique myoglobin adaptation to endothermy and flight since the origin of birds

Myoglobin (Mb) mediates oxygen diffusion and storage in muscle tissue and thus is important for the energy utilization and activity of animals. Birds generally have a high body temperature, and most species also possess the capability of powered flight. Both of these require high levels of aerobic metabolism. Within endothermic mammals, bats also independently evolved flight. Although the functional evolution of myoglobins in deep-diving amniote vertebrates has been well-studied, the functional evolution of myoglobin since the origins of both birds and bats is unclear. Here, with Mb-coding sequences from >200 extant amniote species, we reconstructed ancestral sequences to estimate the functional properties of myoglobin through amniote evolution. A dramatic change in net surface charge on myoglobin occurred during the origin of Aves, which might have been driven by positively selected amino acid substitutions that occurred on the lineage leading to all birds. However, in bats, no change in net surface charge occurred and instead, the Mb genes show evidence of strong purifying selection. The increased net surface charge on bird myoglobins implies an adaptation to flight-related endothermic and higher body temperatures, possibly by reducing harmful protein aggregations. Different from the findings of net surface charge, myoglobins of extant birds show lower stability compared with other amniotes, which probably accelerates the rate of oxygen utilization in muscles. In bats and other mammals, higher stability of Mb may be an alternative pathway for adaptation to endothermy, indicating divergent evolution of myoglobin in birds and bats.

A case for myoglobin-macromolecular rate theory applied to pseudo peroxidase kinetics

This study explores the well-known catalytic behavior of myoglobin as a pseudo-peroxidase by applying macromolecular rate theory (MMRT) to assess its temperature-dependent enzyme kinetics. While myoglobin is primarily recognized for its oxygen-binding properties in muscle tissues, with a characterized pseudo-peroxidase ability to catalyze the degradation of hydrogen peroxide in the presence of electron donors, the claim that myoglobin is actually a true peroxidase can be explored by analyzing the heat capacity changes (ΔCp ‡) in the catalyzed reaction at different temperatures and fitting the results to the expanded Eyring equation (MMRT equation). This research uses the MMRT equation to compare myoglobin's catalytic activity (a pseudo-peroxidase) with that of lactoperoxidase (a true peroxidase) and copper ions (a non-enzymatic catalyst) across a range of temperatures at pH 5, after which the biological catalysts are compared again at pH 7. By analyzing the ΔCp ‡ of these catalysts, it was found that myoglobin exhibits a significant catalytic contribution at both pH levels, suggesting a structural/vibrational or some other relatively significant transition during the reaction. The study's findings provide a new perspective into myoglobin's enzymatic role in peroxide decomposition and highlight the utility of MMRT in quantifying the contribution of polypeptide chains in enzyme-catalyzed peroxidase reactions. Additionally, our research notes the pH-dependence of myoglobin's catalytic efficiency compared to traditional peroxidases, offering implications for understanding its broader biological roles.

Postmortem Immunohistochemical Findings in Early Acute Myocardial Infarction: A Systematic Review

The diagnosis of early acute myocardial infarction is of particular importance in forensic practice considering the frequency of sudden cardiac death and the difficulty of positively identifying it through classical histological methods if survival is less than 6 h. This article aims to analyze potential immunohistochemical markers that could be useful in diagnosing acute myocardial infarction within the first 6 h of its onset. We conducted an extensive evaluation of the literature according to the PRISMA guidelines for reporting systematic literature reviews. We searched the Web of Science and PubMed databases from their inception to 2023 using the following keywords: "myocardial infarction" and "immunohistochemistry". Fifteen studies met the inclusion criteria. Immunohistochemical markers as complement factors and CD59, myoglobin, fibrinogen, desmin, tumor necrosis factor alpha (TNF-α), P-38, JNK (Jun N Terminal Kinase), transforming growth factor β1 (TGF-β1), cardiac troponins, fibronectin, H-FABP (heart fatty acid binding protein), dityrosine, fibronectin, CD15, IL-1β, IL-6, IL-15, IL-8, MCP-1, ICAM-1, CD18, and tryptase can be used to identify the first six hours of acute myocardial infarction. These markers are mostly studied in experimental animal models. It is necessary to conduct extensive studies on human myocardial tissue fragments, which will involve the analysis of several immunohistochemical markers and careful analysis of the available data on perimortem events, resuscitation, and postmortem intervals in the context of a uniform laboratory methodology.

A Novel Rabbit Anti-Myoglobin Monoclonal Antibody's Potential Application in Rhabdomyolysis Associated Acute Kidney Injury

Myoglobin (Mb) is the main constituent of vertebrate skeletal muscle and myocardium and plays an essential role in oxygen binding, storage, transport, and earliest disease diagnosis. This study focuses on preparing the novel recombinant rabbit anti-Mb monoclonal antibody and applying it to a diagnosis of Mb deposition in rhabdomyolysis-associated acute kidney injury (RM-AKI). The full-length coding sequence of rat Mb was cloned and expressed, and the high-quality and titer rabbit anti-Mb polyclonal antibodies were produced by the immunogen His-Mb fusion protein. A new hybridoma cell was obtained by hybridoma screening technology. With the help of DNA sequencing and a molecular clonal, anti-Mb monoclonal antibody heavy and light chains expression plasmid was constructed. Finally, the recombinant rabbit anti-Mb monoclonal antibody with extraordinarily high affinity (K_D = 1.21 pM) was obtained. Meanwhile, it had broad species reactivity (mouse, rat, human, and horse) and good tissue specificity (skeletal muscle and myocardium). It also had a very good performance in western blotting, immunohistochemistry, and immunofluorescence assay to detect the Mb level in the kidney, myocardium, and skeletal muscle of RM-AKI. This study will be significantly helpful for Mb-associated disease diagnosis, and pathogenesis exploration, and further may act as a neutralizing antibody for disease treatment.

Structural evolution of an amphibian-specific globin: A computational evolutionary biochemistry approach

Studies on the globin family are continuously revealing insights into the mechanisms of gene and protein evolution. The rise of a new globin gene type in Pelobatoidea and Neobatrachia (Amphibia:Anura) from an α-globin precursor provides the opportunity to investigate the genetic and physical mechanisms underlying the origin of new protein structural and functional properties. This amphibian-specific globin (globin A/GbA) discovered in the heart of Rana catesbeiana is a monomer. As the ancestral oligomeric state of α-globins is a homodimer, we inferred that the ancestral state was lost somewhere in the GbA lineage. Here, we combined computational molecular evolution with structural bioinformatics to determine the extent to which the loss of the homodimeric state is pervasive in the GbA clade. We also characterized the loci of GbA genes in Bufo bufo. We found two GbA clades in Neobatrachia. One was deleted in Ranidae, but retained and expanded to yield a new globin cluster in Bufonidae species. Loss of the ancestral oligomeric state seems to be pervasive in the GbA clade. However, a taxonomic sampling that includes more Pelobatoidea, as well as early Neobatrachia, lineages would be necessary to determine the oligomeric state of the last common ancestor of all GbA. The evidence presented here points out a possible loss of oligomerization in Pelobatoidea GbA as a result of amino acid substitutions that weaken the homodimeric state. In contrast, the loss of oligomerization in both Neobatrachia GbA clades was linked to independent deletions that disrupted many packing contacts at the homodimer interface.

Effect of Different Gas-Stunning Conditions on Heme Pigment Solutions and on the Color of Blood, Meat, and Small Intestine of Rabbits

The objectives of this study were to elucidate the effect of different high-concentration levels of inert gases (Ar and N2) on heme-pigment solutions and on the color of the blood, meat, and small intestine of rabbits; and to figure out the proper concentration level of inert gas (Ar or N2) for the complete stunning of the rabbit. To observe the changing of color attributes, a research study was conducted in the abattoir of the National Institute of Animal Science (NIAS), RDA, Republic of Korea. This experiment had 2 parts, (i) A trial on heme-pigment solutions (hemoglobin and myoglobin solution) was conducted in a gas chamber with different high-concentration levels of carbon dioxide, argon, nitrogen, and normal air; and (ii) a rabbit experiment was conducted—stunning with different high-concentration levels of carbon dioxide, argon, nitrogen, and the Halal method (non-stunning). A small-size digital gas chamber was used for this experiment (size: width 850 mm × depth 1350 mm). Artificial hemoglobin (Hb) and myoglobin (Mb) solutions were created from “porcine hemoglobin lyophilized powder” and “equine skeletal muscle myoglobin lyophilized powder”, respectively. In the heme-pigment solutions trial, 10 treatments were used: (i) 80% carbon dioxide (T1), (ii) 85% carbon dioxide (T2), (iii) 90% carbon dioxide (T3), (iv) 80% argon (T4), (v) 85% argon (T5), (vi) 90% argon (T6), (vii) 80% nitogen (T7), (viii) 85% nitogen (T8), (ix) 90% nitogen (T9), and (x) normal air (T10). Heme-pigment solutions (both Hb and Mb) were exposed with each treatment for four separate durations of time (30 s, 1 min, 2 min, and 4 min); and every sample (Hb and Mb) was exposed during each duration of time for 10 times (n = 10). In the rabbit experiment, seven treatments were used (i) 85% carbon dioxide (T1), (ii) 90% carbon dioxide (T2), (iii) 85% argon (T3), (iv) 90% argon (T4), (v) 96% nitrogen (T5), (vi) 98% nitogen (T6), and (vii) the Halal method (non-stunning) (T7). Forty-two rabbits (mixed-breed) were collected from the nearest commercial farm and randomly selected for a treatment group (n = 6). The average body weight was 2.3 kg. For stunning, each individual rabbit was separately kept in a gas chamber, after which each specific gas was used to fulfill the desired level in the pit. After reaching the desired level of concentration, rabbits were stunned within a very short time. It was observed that the time required for stunning in the T1, T2, T3, T4, T5 and T6 treatment was 79−82, 68−73, 97−103, 88−91, 164−173, and 108−115 s, respectively. In the case of the Halal method (non-stunning), as per the rules of Islam, rabbits were slaughtered without stunning. After slaughtering, in all treatments, the blood, meat, and small intestine of each animal were collected carefully and kept in a cool room in which the temperature was −2 °C, and after 24 h, the color attributes—lightness (L*), redness (a*), and yellowness (b*)—were measured via a Chroma Meter. It was found that in both experiments (trial on heme-pigment solutions and rabbit stunning), the color values (L*, a* and b*) showed a significant difference (p < 0.05) among the treatment groups. The CO2-treated groups showed high redness (a*) and low lightness (L*) and yellowness (b*), which indicated a dark-red color, and N2-treated groups showed high lightness (L*) and yellowness (b*) and low redness (a*), which implied a bright-red color. The effect of the Ar was in between the CO2- and N2-treated groups. These phenomena were observed both in the heme-pigment solutions (Hb and Mb) and in the blood, meat, and small intestine of the rabbits. N2-stunned animals fulfill the fundamental desire of consumers to purchase bright red-colored fresh meat. Therefore, in view of color attributes, consumer satisfaction, and animal welfare, N2 gas can be thought of as a valuable alternative to stunning. Considering the time required for complete stunning and desirable color attributes, a 98% concentration of N2 is best for rabbit stunning. As such, it could be used as a better option for the gas stunning of animals.

Transcriptomes of Clusterin- and S100B-transfected neuronal cells elucidate protective mechanisms against hypoxia and oxidative stress in the hooded seal (Cystophora cristata) brain

BACKGROUND

The hooded seal (Cystophora cristata) exhibits impressive diving skills and can tolerate extended durations of asphyxia, hypoxia and oxidative stress, without suffering from irreversible neuronal damage. Thus, when exposed to hypoxia in vitro, neurons of fresh cortical and hippocampal tissue from hooded seals maintained their membrane potential 4-5 times longer than neurons of mice. We aimed to identify the molecular mechanisms underlying the intrinsic neuronal hypoxia tolerance. Previous comparative transcriptomics of the visual cortex have revealed that S100B and clusterin (apolipoprotein J), two stress proteins that are involved in neurological disorders characterized by hypoxic conditions, have a remarkably high expression in hooded seals compared to ferrets. When overexpressed in murine neuronal cells (HN33), S100B and clusterin had neuroprotective effects when cells were exposed to hypoxia. However, their specific roles in hypoxia have remained largely unknown.

METHODS

In order to shed light on potential molecular pathways or interaction partners, we exposed HN33 cells transfected with either S100B, soluble clusterin (sCLU) or nuclear clusterin (nCLU) to normoxia, hypoxia and oxidative stress for 24 h. We then determined cell viability and compared the transcriptomes of transfected cells to control cells. Potential pathways and upstream regulators were identified via Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA).

RESULTS

HN33 cells transfected with sCLU and S100B demonstrated improved glycolytic capacity and reduced aerobic respiration at normoxic conditions. Additionally, sCLU appeared to enhance pathways for cellular homeostasis to counteract stress-induced aggregation of proteins. S100B-transfected cells sustained lowered energy-intensive synaptic signaling. In response to hypoxia, hypoxia-inducible factor (HIF) pathways were considerably elevated in nCLU- and sCLU-transfected cells. In a previous study, S100B and sCLU decreased the amount of reactive oxygen species and lipid peroxidation in HN33 cells in response to oxidative stress, but in the present study, these functional effects were not mirrored in gene expression changes.

CONCLUSIONS

sCLU and S100B overexpression increased neuronal survival by decreasing aerobic metabolism and synaptic signaling in advance to hypoxia and oxidative stress conditions, possibly to reduce energy expenditure and the build-up of deleterious reactive oxygen species (ROS). Thus, a high expression of CLU isoforms and S100B is likely beneficial during hypoxic conditions.

Structure-Function Relationships of Oxygen Transport Proteins in Marine Invertebrates Enduring Higher Temperatures and Deoxygenation

AbstractPredictions for climate change-to lesser and greater extents-reveal a common scenario in which marine waters are characterized by a deadly trio of stressors: higher temperatures, lower oxygen levels, and acidification. Ectothermic taxa that inhabit coastal waters, such as shellfish, are vulnerable to rapid and prolonged environmental disturbances, such as heatwaves, pollution-induced eutrophication, and dysoxia. Oxygen transport capacity of the hemolymph (blood equivalent) is considered the proximal driver of thermotolerance and respiration in many invertebrates. Moreover, maintaining homeostasis under environmental duress is inextricably linked to the activities of the hemolymph-based oxygen transport or binding proteins. Several protein groups fulfill this role in marine invertebrates: copper-based extracellular hemocyanins, iron-based intracellular hemoglobins and hemerythrins, and giant extracellular hemoglobins. In this brief text, we revisit the distribution and multifunctional properties of oxygen transport proteins, notably hemocyanins, in the context of climate change, and the consequent physiological reprogramming of marine invertebrates.

The More, the Merrier? Multiple Myoglobin Genes in Fish Species, Especially in Gray Bichir (Polypterus senegalus) and Reedfish (Erpetoichthys calabaricus)

The members of the globin superfamily are a classical model system to investigate gene evolution and their fates as well as the diversity of protein function. One of the best-known globins is myoglobin (Mb), which is mainly expressed in heart muscle and transports oxygen from the sarcolemma to the mitochondria. Most vertebrates harbor a single copy of the myoglobin gene, but some fish species have multiple myoglobin genes. Phylogenetic analyses indicate an independent emergence of multiple myoglobin genes, whereby the origin is mostly the last common ancestor of each order. By analyzing different transcriptome data sets, we found at least 15 multiple myoglobin genes in the polypterid gray bichir (Polypterus senegalus) and reedfish (Erpetoichthys calabaricus). In reedfish, the myoglobin genes are expressed in a broad range of tissues but show very different expression values. In contrast, the Mb genes of the gray bichir show a rather scattered expression pattern; only a few Mb genes were found expressed in the analyzed tissues. Both, gray bichir and reedfish possess lungs which enable them to inhabit shallow and swampy waters throughout tropical Africa with frequently fluctuating and low oxygen concentrations. The myoglobin repertoire probably reflects the molecular adaptation to these conditions. The sequence divergence, the substitution rate, and the different expression pattern of multiple myoglobin genes in gray bichir and reedfish imply different functions, probably through sub- and neofunctionalization during evolution.

Expression of Myoglobin in Normal and Cancer Brain Tissues: Correlation With Hypoxia Markers

Background

Myoglobin (MB) is increasingly recognized as a key player in cancer growth and metastasis. Low oxygen tensions, commonly associated with highly aggressive and recurrent cancers, have been shown to regulate its expression in several cancers such as lung, neck, prostate and breast cancer. However, it is not yet known whether it contributes to the growth and spread of brain cancers especially Glioblastoma multiforme (GBM).

Methods

Here we investigate the expression of MB, and its correlation with the hypoxia markers carbonic anhydrase IX (CAIX) and lactate dehydrogenase A (LDHA), in human tissue microarrays of multiple organ tumors, brain tumors, and GBM tumors, and their respective cancer-adjacent normal tissues. Correlation between MB protein expression and tumor grade was also assessed.

Results

We show that MB protein is expressed in a wide variety of cancers, benign tumors, cancer-adjacent normal tissues, hyperplastic tissue samples and normal brain tissue, and low oxygen tensions modulate MB protein expression in different brain cancers, including GBM. Enhanced nuclear LDHA immune-reactivity in GBM was also observed. Finally, we report for the first time a positive correlation between MB expression and brain tumor grade.

Conclusion

Our data suggest that hypoxia regulate MB expression in different brain cancers (including GBM) and that its expression is associated with a more aggressive phenotype as indicated by the positive correlation with the brain tumor grade. Additionally, a role for nuclear LDHA in promoting aggressive tumor phenotype is also suggested based on enhanced nuclear expression which was observed only in GBM.

The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes

The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.

Cell Culture Experiments Reveal that High S100B and Clusterin Levels may Convey Hypoxia-tolerance to the Hooded Seal (Cystophora cristata) Brain

While the brain of most mammals suffers from irreversible damage after only short periods of low oxygen levels (hypoxia), marine mammals are excellent breath-hold divers that have adapted to hypoxia. In addition to physiological adaptations, such as large oxygen storing capacity and strict oxygen economy during diving, the neurons of the deep-diving hooded seal (Cystophora cristata) have an intrinsic tolerance to hypoxia. We aim to understand the molecular basis of this neuronal hypoxia tolerance. Previously, transcriptomics of the cortex of the hooded seal have revealed remarkably high expression levels of S100B and clusterin (apolipoprotein J) when compared to the ferret, a non-diving carnivore. Both genes have much-debated roles in hypoxia and oxidative stress. Here, we evaluated the effects of S100B and of two isoforms of clusterin (soluble and nucleus clusterin) on the survival, metabolic activity and the amount of reactive oxygen species (ROS) in HN33 neuronal mouse cells exposed to hypoxia and oxidative stress. S100B and soluble clusterin had neuroprotective effects, with reduced ROS-levels and retention of normoxic energy status of cells during both stress conditions. The protective effects of nucleus clusterin were restricted to hypoxia. S100B and clusterin showed purifying selection in marine and terrestrial mammals, indicating a functional conservation across species. Immunofluorescence revealed identical cellular distributions of S100B and clusterin in mice, ferrets and hooded seals, further supporting the functional conservation. Taken together, our data suggest that the neuroprotective effects of all three proteins are exclusively facilitated by their increased expression in the brain of the hooded seal.

Lessons from the post-genomic era: Globin diversity beyond oxygen binding and transport

Vertebrate hemoglobin (Hb) and myoglobin (Mb) were among the first proteins whose structures and sequences were determined over 50 years ago. In the subsequent pregenomic period, numerous related proteins came to light in plants, invertebrates and bacteria, that shared the myoglobin fold, a signature sequence motif characteristic of a 3-on-3 α-helical sandwich. Concomitantly, eukaryote and bacterial globins with a truncated 2-on-2 α-helical fold were discovered. Genomic information over the last 20 years has dramatically expanded the list of known globins, demonstrating their existence in a limited number of archaeal genomes, a majority of bacterial genomes and an overwhelming majority of eukaryote genomes. In vertebrates, 6 additional globin types were identified, namely neuroglobin (Ngb), cytoglobin (Cygb), globin E (GbE), globin X (GbX), globin Y (GbY) and androglobin (Adgb). Furthermore, functions beyond the familiar oxygen transport and storage have been discovered within the vertebrate globin family, including NO metabolism, peroxidase activity, scavenging of free radicals, and signaling functions. The extension of the knowledge on globin functions suggests that the original roles of bacterial globins must have been enzymatic, involved in defense against NO toxicity, and perhaps also as sensors of O₂, regulating taxis away or towards high O₂ concentrations. In this review, we aimed to discuss the evolution and remarkable functional diversity of vertebrate globins with particular focus on the variety of non-canonical expression sites of mammalian globins and their according impressive variability of atypical functions.

Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles

Simple Summary

Oxygen-binding proteins that mediate oxygen-binding for storage and consumption, to reduce energy, are very diverse in fish, depending on their habitats. In the present study, oxygen-binding protein gene expression in the skeletal muscle of 25 diverse fish species was examined by a meta-transcriptomic approach. By using RNAseq data, this is the first study to examine the high level of myoglobin, one of the oxygen-binding proteins, transcripts in pacu and loach fish that might be related to their high tolerance for the oxygen-deficient environment. In addition, this study presents the power of the current method to compare the fish oxygen-binding protein expression and its putative gene expansion event.

Abstract

Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the skeletal muscle of 25 diverse fish species for the first time. RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. The genes encoding oxygen-binding proteins were then identified by the BLAST search, and the relative expression level of oxygen-binding protein genes was normalized by the RPKM (Reads per Kilobase Million) method. By performing expression profiling, hierarchy clustering, and principal component analysis, pacu and loach fish were noticed by their high myoglobin expression levels in skeletal muscle tissues among 25 diverse fish species. In conclusion, we demonstrated that meta-transcriptomic analysis of RNAseq data is an informative approach to compare the oxygen-binding protein expression and putative gene expansion event in fish.

Recent Insights into the Diversity and Evolution of Invertebrate Hemerythrins and Extracellular Globins

There are three broad groups of oxygen-transport proteins found in the haemolymph (blood) of invertebrates, namely the hemocyanins, the hemerythrins and the globins. Both hemerythrins and extracellular globins are iron-based proteins that are understudied when compared to the copper-containing hemocyanins. Recent evidence suggests that hemerythrins and (giant) extracellular globins (and their linker chains) are more widely distributed than previously thought and may have biological functions beyond oxygen transport and storage. Herein, we review contemporary literature of these often-neglected proteins with respect to their structural configurations on formation and ancestral states.

Genetic and functional diversity of the multiple lungfish myoglobins

It is known that the West African lungfish (Protopterus annectens) harbours multiple myoglobin (Mb) genes that are differentially expressed in various tissues and that the Mbs differ in their abilities to confer tolerance towards hypoxia. Here, we show that other lungfish species (Protopterus dolloi, Protopterus aethiopicus and Lepidosiren paradoxa) display a similar diversity of Mb genes and have orthologous Mb genes. To investigate the functional diversification of these genes, we studied the structures, O₂ binding properties and nitrite reductase enzymatic activities of recombinantly expressed P. annectens Mbs (PanMbs). CD spectroscopy and small-angle X-ray scattering revealed the typical globin-fold in all investigated recombinant Mbs, indicating a conserved structure. The highest O₂ affinity was measured for PanMb2 (P₅₀  = 0.88 Torr at 20 °C), which is mainly expressed in the brain, whereas the muscle-specific PanMb1 has the lowest O₂ affinity (P₅₀  = 3.78 Torr at 20 °C), suggesting that tissue-specific O₂ requirements have resulted in the emergence of distinct Mb types. Two of the mainly neuronally expressed Mbs (PanMb3 and PanMb4b) have the highest nitrite reductase rates. These data show different O₂ binding and enzymatic properties of lungfish Mbs, reflecting multiple subfunctionalisation and neofunctionalisation events that occurred early in the evolution of lungfish. Some Mbs may have also taken over the functions of neuroglobin and cytoglobin, which are widely expressed in vertebrates but appear to be missing in lungfish.

Globin E is a myoglobin-related, respiratory protein highly expressed in lungfish oocytes

Globins are a classical model system for the studies of protein evolution and function. Recent studies have shown that – besides the well-known haemoglobin and myoglobin – additional globin-types occur in vertebrates that serve different functions. Globin E (GbE) was originally identified as an eye-specific protein of birds that is distantly related to myoglobin. GbE is also present in turtles and the coelacanth but appeared to have been lost in other vertebrates. Here, we show that GbE additionally occurs in lungfish, the closest living relatives of the tetrapods. Each lungfish species harbours multiple (≥5) GbE gene copies. Surprisingly, GbE is exclusively and highly expressed in oocytes, with mRNA levels that exceed that of myoglobin in the heart. Thus, GbE is the first known oocyte-specific globin in vertebrates. No GbE transcripts were found in the ovary or egg transcriptomes of other vertebrates, suggesting a lungfish-specific function. Spectroscopic analysis and kinetic studies of recombinant GbE1 of the South American lungfish Lepidosiren paradoxa revealed a typical pentacoordinate globin with myoglobin-like O₂-binding kinetics, indicating similar functions. Our findings suggest that the multiple copies of GbE evolved to enhance O₂-supply in the developing embryo of lungfish, analogous to the embryonic and fetal haemoglobins of other vertebrates. In evolution, GbE must have changed its expression site from oocytes to eyes, or vice versa.

Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation

Background

Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life.

Results

Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1–2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish.

Conclusions

This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5355-9) contains supplementary material, which is available to authorized users.

Evidence for a Large Expansion and Subfunctionalization of Globin Genes in Sea Anemones

The globin gene superfamily has been well-characterized in vertebrates, however, there has been limited research in early-diverging lineages, such as phylum Cnidaria. This study aimed to identify globin genes in multiple cnidarian lineages, and use bioinformatic approaches to characterize the evolution, structure, and expression of these genes. Phylogenetic analyses and in silico protein predictions showed that all cnidarians have undergone an expansion of globin genes, which likely have a hexacoordinate protein structure. Our protein modeling has also revealed the possibility of a single pentacoordinate globin lineage in anthozoan species. Some cnidarian globin genes displayed tissue and development specific expression with very few orthologous genes similarly expressed across species. Our phylogenetic analyses also revealed that eumetazoan globin genes form a polyphyletic relationship with vertebrate globin genes. Overall, our analyses suggest that a Ngb-like and GbX-like gene were most likely present in the globin gene repertoire for the last common ancestor of eumetazoans. The identification of a large-scale expansion and subfunctionalization of globin genes in actiniarians provides an excellent starting point to further our understanding of the evolution and function of the globin gene superfamily in early-diverging lineages.

Discovery of Novel Hemocyanin-Like Genes in Metazoans

Among animals, two major groups of oxygen-binding proteins are found: proteins that use iron to bind oxygen (hemoglobins and hemerythrins) and two non-homologous hemocyanins that use copper. Although arthropod and mollusc hemocyanins bind oxygen in the same manner, they are distinct in their molecular structures. In order to better understand the range of natural variation in hemocyanins, we searched for them in a diverse array of metazoan transcriptomes by using bioinformatics tools to examine hemocyanin evolutionary history and to consequently revive the discussion about whether all metazoan hemocyanins shared a common origin with frequent losses or whether they originated separately after the divergence of Lophotrochozoa and Ecdysozoa. We confirm that the distribution of hemocyanin-like genes is more widespread than previously reported, including five putative novel mollusc hemocyanin genes in two annelid species from Chaetopteridae. For arthropod hemocyanins, 16 putative novel genes were retained, and the presence of arthropod hemocyanins in 11 annelid species represents a novel observation. Interestingly, Annelida is the lineage that presents the greatest repertoire of oxygen transport proteins reported to date, possessing all the main superfamily proteins, which could be explained partially by the immense variability of lifestyles and habitats. Work presented here contradicts the canonical view that hemocyanins are restricted to molluscs and arthropods, suggesting that the occurrence of copper-based blood pigments in metazoans has been underestimated. Our results also support the idea of the presence of oxygen carrier hemocyanins being widespread across metazoans with an evolutionary history characterized by frequent losses.

Broad Phylogenetic Occurrence of the Oxygen-Binding Hemerythrins in Bilaterians

Animal tissues need to be properly oxygenated for carrying out catabolic respiration and, as such, natural selection has presumably favored special molecules that can reversibly bind and transport oxygen. Hemoglobins, hemocyanins, and hemerythrins (Hrs) fulfill this role, with Hrs being the least studied. Knowledge of oxygen-binding proteins is crucial for understanding animal physiology. Hr genes are present in the three domains of life, Archaea, Bacteria, and Eukaryota; however, within Animalia, Hrs has been reported only in marine species in six phyla (Annelida, Brachiopoda, Priapulida, Bryozoa, Cnidaria, and Arthropoda). Given this observed Hr distribution, whether all metazoan Hrs share a common origin is circumspect. We investigated Hr diversity and evolution in metazoans, by employing in silico approaches to survey for Hrs from of 120 metazoan transcriptomes and genomes. We found 58 candidate Hr genes actively transcribed in 36 species distributed in 11 animal phyla, with new records in Echinodermata, Hemichordata, Mollusca, Nemertea, Phoronida, and Platyhelminthes. Moreover, we found that “Hrs” reported from Cnidaria and Arthropoda were not consistent with that of other metazoan Hrs. Contrary to previous suggestions that Hr genes were absent in deuterostomes, we find Hr genes present in deuterostomes and were likely present in early bilaterians, but not in nonbilaterian animal lineages. As expected, the Hr gene tree did not mirror metazoan phylogeny, suggesting that Hrs evolutionary history was complex and besides the oxygen carrying capacity, the drivers of Hr evolution may also consist of secondary functional specializations of the proteins, like immunological functions.

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.

Discovery and evolution of novel hemerythrin genes in annelid worms

BACKGROUND

Despite extensive study on hemoglobins and hemocyanins, little is known about hemerythrin (Hr) evolutionary history. Four subgroups of Hrs have been documented, including: circulating Hr (cHr), myohemerythrin (myoHr), ovohemerythrin (ovoHr), and neurohemerythrin (nHr). Annelids have the greatest diversity of oxygen carrying proteins among animals and are the only phylum in which all Hr subgroups have been documented. To examine Hr diversity in annelids and to further understand evolution of Hrs, we employed approaches to survey annelid transcriptomes in silico.

RESULTS

Sequences of 214 putative Hr genes were identified from 44 annelid species in 40 different families and Bayesian inference revealed two major clades with strong statistical support. Notably, the topology of the Hr gene tree did not mirror the phylogeny of Annelida as presently understood, and we found evidence of extensive Hr gene duplication and loss in annelids. Gene tree topology supported monophyly of cHrs and a myoHr clade that included nHrs sequences, indicating these designations are functional rather than evolutionary.

CONCLUSIONS

The presence of several cHrs in early branching taxa suggests that a variety of Hrs were present in the common ancestor of extant annelids. Although our analysis was limited to expressed-coding regions, our findings demonstrate a greater diversity of Hrs among annelids than previously reported.