Population Genetics of the Teleost Orange Roughy, Hoplostethus Atlanticus, and Insights into their Visual Adaptations to the Deep-Sea Environment

<p>The orange roughy, Hoplostethus atlanticus, has been one of the main targeted species in deep-sea fisheries worldwide. It occurs at depths of 450 – 1800 m and is abundant off the coasts of New Zealand, Australia, Namibia, Chile, and in the Northeast Atlantic Ocean. Like many other deep-sea fishes, orange roughy is vulnerable to over exploitation because they grow slow reaching maturity at about 30 years and live for more than 100 years. Their fecundity is low, which means they have low productivity. The individuals form predictable and dense spawning aggregations close to seamounts, plateaus and canyons. The trawl fishery for orange roughy started in seamounts around New Zealand in the late 1970s and progressively expanded off the coast of other countries and to the high seas (out of any Economic Exclusive Zone). Most stocks have been fished down to or below 30% pre-exploitation levels; as a consequence, fisheries have been closed or catches largely reduced. Currently, the only large scale fisheries operate off New Zealand. For effective fisheries management it is essential to define real biological units or “stocks”. There has been considerable research into the levels of population differentiation of orange roughy using a range of techniques at different geographic scales to attempt to differentiated stocks. However, there is no consensus about the level of connectivity among populations. In the present study, I investigated the levels of population differentiation in orange roughy using two types of neutral molecular markers at a global and fine-scales. Both markers revealed high levels of genetic diversity which is likely related with historically large population sizes. The analyses of 546 cytochrome c oxidase subunit I (COI) sequences revealed a lack of global genetic differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation was found between the Southern hemisphere sites and two Northeast Atlantic sites. Mismatch distribution and Bayesian analyses indicated the occurrence of expansion events in orange roughy during the Pleistocene period. A data set of nine microsatellite DNA loci genotyped from 812 individuals, showed a predominant lack of significant genetic differentiation across the Tasman Sea and at a fine-scale around New Zealand. At a global scale, differentiation was low but significant across the Southern hemisphere; and the highest values of differentiation were detected between the Southern hemisphere sites and the Northeast Atlantic Ocean. The predominant lack of differentiation at the regional and fine-scale and the low differentiation within the Southern hemisphere is probably the result of stepping-stone dispersal of long-lived adults that are able to spawn many times in their life. Most orange roughy studies have been oriented to fisheries aspects, but other kind of studies as the genetic divergence and phylogenetic relationships among Hoplostethus species are lacking. Using available COI sequences, I conducted a phylogenetic study including H. atlanticus, H. crassispinus, H. gigas, H. japonicus H. latus, and H. mediterraneus. As expected, the inter species divergence was much higher than the intra species divergence. Phylogenetics analyses showed that H. latus, H. crassispinus, H. japonicus, and H. mediterraneus form a separate clade from H. atlanticus and H. gigas. The position of H. gigas was not well defined with the nucleotide data. However, at the amino acid level, non-synonymous substitutions differentiated H. atlanticus from all the other species. This was correlated with morphological characteristics presented elsewhere. A candidate gene approach was attemped using the rhodopsin gene; however, there was almost no variation among partial sequences of individuals from distant sites. Instead, this gene was used to investigate the molecular basis for visual adaptations in orange roughy to the bathypelagic light environment. It is known that certain amino acid replacements in the rhodopsin gene of vertebrates shift the λmax value of the pigment to perceive different light conditions. To compare and identify critical amino acid sites that are known to be involved in spectral tuning, I obtained partial rhodopsin sequences of other 18 marine teleost habiting at different depths (1 – 1,175 m) and, thus, different light environments. A phylogenetic analysis was conducted to determine whether particular rhodopsin gene sequences correlate with the depths occupied by the species. I identified four critical amino acid replacements that have been involved in the spectral tuning of rod pigments. Orange roughy presented the same amino acid combination at two critical sites already reported for the deep-sea congener silver roughy, which was not found in any of the other species. This likely reflects an adaptation to the light available (i.e. bioluminescence) in the bathypelagic environment. The phylogeny was weakly related to the maximum depth of the species, probably because there are selectively neutral (i.e. inherited by ancestry) and non-neutral changes (i.e. influenced by natural selection) among the rhodopsin sequences of the species being considered.</p>

Population Genetics of the Teleost Orange Roughy, Hoplostethus Atlanticus, and Insights into their Visual Adaptations to the Deep-Sea Environment

<p>The orange roughy, Hoplostethus atlanticus, has been one of the main targeted species in deep-sea fisheries worldwide. It occurs at depths of 450 – 1800 m and is abundant off the coasts of New Zealand, Australia, Namibia, Chile, and in the Northeast Atlantic Ocean. Like many other deep-sea fishes, orange roughy is vulnerable to over exploitation because they grow slow reaching maturity at about 30 years and live for more than 100 years. Their fecundity is low, which means they have low productivity. The individuals form predictable and dense spawning aggregations close to seamounts, plateaus and canyons. The trawl fishery for orange roughy started in seamounts around New Zealand in the late 1970s and progressively expanded off the coast of other countries and to the high seas (out of any Economic Exclusive Zone). Most stocks have been fished down to or below 30% pre-exploitation levels; as a consequence, fisheries have been closed or catches largely reduced. Currently, the only large scale fisheries operate off New Zealand. For effective fisheries management it is essential to define real biological units or “stocks”. There has been considerable research into the levels of population differentiation of orange roughy using a range of techniques at different geographic scales to attempt to differentiated stocks. However, there is no consensus about the level of connectivity among populations. In the present study, I investigated the levels of population differentiation in orange roughy using two types of neutral molecular markers at a global and fine-scales. Both markers revealed high levels of genetic diversity which is likely related with historically large population sizes. The analyses of 546 cytochrome c oxidase subunit I (COI) sequences revealed a lack of global genetic differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation was found between the Southern hemisphere sites and two Northeast Atlantic sites. Mismatch distribution and Bayesian analyses indicated the occurrence of expansion events in orange roughy during the Pleistocene period. A data set of nine microsatellite DNA loci genotyped from 812 individuals, showed a predominant lack of significant genetic differentiation across the Tasman Sea and at a fine-scale around New Zealand. At a global scale, differentiation was low but significant across the Southern hemisphere; and the highest values of differentiation were detected between the Southern hemisphere sites and the Northeast Atlantic Ocean. The predominant lack of differentiation at the regional and fine-scale and the low differentiation within the Southern hemisphere is probably the result of stepping-stone dispersal of long-lived adults that are able to spawn many times in their life. Most orange roughy studies have been oriented to fisheries aspects, but other kind of studies as the genetic divergence and phylogenetic relationships among Hoplostethus species are lacking. Using available COI sequences, I conducted a phylogenetic study including H. atlanticus, H. crassispinus, H. gigas, H. japonicus H. latus, and H. mediterraneus. As expected, the inter species divergence was much higher than the intra species divergence. Phylogenetics analyses showed that H. latus, H. crassispinus, H. japonicus, and H. mediterraneus form a separate clade from H. atlanticus and H. gigas. The position of H. gigas was not well defined with the nucleotide data. However, at the amino acid level, non-synonymous substitutions differentiated H. atlanticus from all the other species. This was correlated with morphological characteristics presented elsewhere. A candidate gene approach was attemped using the rhodopsin gene; however, there was almost no variation among partial sequences of individuals from distant sites. Instead, this gene was used to investigate the molecular basis for visual adaptations in orange roughy to the bathypelagic light environment. It is known that certain amino acid replacements in the rhodopsin gene of vertebrates shift the λmax value of the pigment to perceive different light conditions. To compare and identify critical amino acid sites that are known to be involved in spectral tuning, I obtained partial rhodopsin sequences of other 18 marine teleost habiting at different depths (1 – 1,175 m) and, thus, different light environments. A phylogenetic analysis was conducted to determine whether particular rhodopsin gene sequences correlate with the depths occupied by the species. I identified four critical amino acid replacements that have been involved in the spectral tuning of rod pigments. Orange roughy presented the same amino acid combination at two critical sites already reported for the deep-sea congener silver roughy, which was not found in any of the other species. This likely reflects an adaptation to the light available (i.e. bioluminescence) in the bathypelagic environment. The phylogeny was weakly related to the maximum depth of the species, probably because there are selectively neutral (i.e. inherited by ancestry) and non-neutral changes (i.e. influenced by natural selection) among the rhodopsin sequences of the species being considered.</p>

Modification of the transglucosylation properties of α-glucosidases from Aspergillus oryzae and Aspergillus sojae via a single critical amino acid replacement

We constructed enzyme variants of the α-glucosidases from Aspergillus oryzae (AoryAgdS) and Aspergillus sojae (AsojAgdL) by mutating the amino acid residue at position 450. AoryAgdS_H450R acquired the ability to produce considerable amounts of α-1,6-transglucosylation products, whereas AsojAgdL_R450H changed to produce more α-1,3- and α-1,4-transglucosylation products than α-1,6-products. The 450th amino acid residue is critical for the transglucosylation of these α-glucosidases.

Critical Amino Acid Variants in HLA-DRB1 and -DQB1 Allotypes in the Development of Classical Type 1 Diabetes and Latent Autoimmune Diabetes in Adults in the Japanese Population

The effects of amino acid variants encoded by the human leukocyte antigen (HLA) class II on the development of classical type 1 diabetes (T1D) and latent autoimmune diabetes in adults (LADA) have not been fully elucidated. We retrospectively investigated the HLA-DRB1 and -DQB1 genes of 72 patients with classical T1D and 102 patients with LADA in the Japanese population and compared the frequencies of HLA-DRB1 and -DQB1 alleles between these patients and the Japanese populations previously reported by another institution. We also performed a blind association analysis with all amino acid positions in classical T1D and LADA, and compared the associations of HLA-DRB1 and -DQB1 amino acid positions in classical T1D and LADA. The frequency of DRß-Phe-13 was significantly higher and those of DRß-Arg-13 and DQß-Gly-70 were significantly lower in patients with classical T1D and LADA than in controls. The frequencies of DRß-His-13 and DQß-Glu-70 were significantly higher in classical T1D patients than in controls. The frequency of DRß-Ser-13 was significantly lower and that of DQß-Arg-70 was significantly higher in LADA patients than in controls. HLA-DRß1 position 13 and HLA-DQß1 position 70 could be critical amino acid positions in the development of classical T1D and LADA.

Revealing Insights into Natural Products Against mcr-1-Producing Bacteria

: Bacterial resistance has become a major global concern, affecting about 500,000 individuals in 22 countries. Thus, it is clear that Gram-negative bacteria have been receiving more attention in this scenario. These bacteria perform several resistance mechanisms, such as modifying lipid A from lipopolysaccharides as a product of the mcr-1 gene expression. This gene was initially identified in animals; however, it quickly spread to humans, spreading to 70 countries. Mcr-1 gene attributes resistance to polymyxin B and colistin, which are drugs established as the last alternative to combat Enterobacteriaceae bacteria. Notwithstanding the prevalence and lack of antibiotic therapies for such bacteria, this article aimed to compile information about natural compounds against the resistance attributed by this gene, including the activity of isolated colistin or its associations with other antibiotics. Among the studies that evaluated colistin's synergistic action with other compounds, azidothymidine and isoalantholactone stood out. On the other hand, the paenipeptin 1 analog showed satisfactory activities when associated with other antibiotics. Besides, it is worth mentioning that molecular docking results between ostole and eugenol toward phosphoethanolamine transferase MCR-1 revealed that these compounds could interact with critical amino acid residues for the catalytic action of this enzyme. Based on this, natural agents' role is evident against infections caused by mcr-1-positive bacteria, directly contributing to the development of new effective pharmacotherapies.

Binding Mechanism Elucidation of the Acute Respiratory Disease Causing Agent Adenovirus of Serotype 7 to Desmoglein-2

The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human adenoviruses, adenovirus of serotype 7 (HAdV7) is one of the most virulent serotypes. This virus regularly re-emerges in Asia and has just been the cause of several deaths in the United States. A critical step of the virus life cycle is the attachment of the knob domain of the fiber (HAd7K) to the cellular receptor desmoglein-2 (DSG2). Complexes between the fiber knob and two extracellular domains of DSG2 have been produced. Their characterization by biochemical and biophysical methods show that these two domains are sufficient for the interaction and that the trimeric HAd7K could accommodate up to three DSG2 receptor molecules. The cryo-electron microscopy (cryo-EM) structure of these complexes at 3.1 Å resolution confirmed the biochemical data, and allowed the identification of the critical amino acid residues for this interaction, which shows similarities with other DSG2 interacting adenoviruses, despite a low homology in the primary sequences.

The Mechanism of Bidirectional pH Taxis in Bacillus subtilis

ABSTRACT We investigated pH taxis in Bacillus subtilis. This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments. We next investigated the chemoreceptors involved in sensing pH gradients. We identified four chemoreceptors involved in sensing pH: McpA and TlpA for sensing acidic environments and McpB and TlpB for sensing alkaline ones. In addition, TlpA was found to also weakly sense alkaline environments. By analyzing chimeras between McpA and TlpB, the principal acid- and base-sensing chemoreceptors, we identified four critical amino acid residues—Thr199, Gln200, His273, and Glu274 on McpA and Lys199, Glu200, Gln273, and Asp274 on TlpB—involved in sensing pH. Swapping these four residues between McpA and TlpB converted the former into a base receptor and the latter into an acid receptor. Based on the results, we propose that disruption of hydrogen bonding between the adjacent residues upon pH changes induces signaling. Collectively, our results further our understanding of chemotaxis in B. subtilis and provide a new model for pH sensing in bacteria. IMPORTANCE Many bacteria can sense the pH in their environment and then use this information to direct their movement toward more favorable locations. In this study, we investigated the pH sensing mechanism in Bacillus subtilis. This bacterium preferentially migrates to neutral environments. It employs four chemoreceptors to sense pH. Two are involved in sensing acidic environments, and two are involved in sensing alkaline ones. To identify the mechanism for pH sensing, we constructed receptor chimeras of acid- and base-sensing chemoreceptors. By analyzing the responses of these chimeric receptors, we were able to identify four critical amino acid residues involved in pH sensing and propose a model for the pH sensing mechanism in B. subtilis.

Four chemoreceptors govern bidirectional pH taxis in Bacillus subtilis

ABSTRACTWe investigated pH taxis in Bacillus subtilis. This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments. We next investigated the chemoreceptors involved in sensing pH gradients. We found that four chemoreceptors are involved in sensing pH: McpA and TlpA for sensing acidic environments and McpB and TlpB for alkaline ones. In addition, TlpA was found to also weakly sense alkaline environments. By analyzing chimeras between McpA and TlpB, the principal acid and base-sensing chemoreceptors, we identified four critical amino-acid residues – Thr199, Gln200, His273, and Glu274 on McpA and Lys199, Glu200, Gln273, and Asp274 on TlpB – involved in sensing pH. Swapping these four residues between McpA and TlpB converted the former into a base receptor and the latter into an acid receptor. Based on the results, we propose that disruption of hydrogen bonding between the adjacent residues upon pH changes induces signaling. Collectively, our results further our understanding of chemotaxis in B. subtilis and provide a new model for pH sensing in bacteria.IMPORTANCEMany bacteria can sense the pH in their environment and then use this information to direct their movement towards more favorable locations. In this study, we investigated the pH sensing mechanism in Bacillus subtilis. This bacterium preferentially migrates to neutral environments. It employs four chemoreceptors to sense pH. Two are involved in sensing acidic environments and two are involved in sensing alkaline ones. To identify the mechanism for pH sensing, we constructed receptor chimeras of acid and base sensing chemoreceptors. By analyzing the response of these chimeric receptors, we were able to identify four critical amino-acid residues involved in pH sensing and propose a model for the pH sensing mechanism in B. subtilis.