scholarly journals Molecular identification of methane monooxygenase and quantitative analysis of methanotrophic endosymbionts under laboratory maintenance inBathymodiolus platifronsfrom the South China Sea

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3565 ◽  
Author(s):  
Yan Sun ◽  
Minxiao Wang ◽  
Leilei Li ◽  
Li Zhou ◽  
Xiaocheng Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Deep Sea ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Methane Monooxygenase ◽  
Cold Seep ◽  
Type I ◽  
Laboratory Maintenance ◽  
The Impact ◽  
Methane Oxidization

Deep-sea mussels of the genusBathymodiolusare numerically dominant macrofauna in many cold seep and hydrothermal vent ecosystems worldwide, and they depend on organic carbon produced by symbionts present in the epithelial cells of the gills. AlthoughBathymodiolus platifronsrepresents typical methanotrophic endosymbiosis, our understanding of molecular mechanisms of methane oxidization and carbon fixation is still in its infancy. Moreover, the laboratory maintenance ofB. platifronsand the symbiont abundance dynamics during maintenance has not been reported. In the present study, we report the first systematic identification and phylogenetic analysis of three subunits of methane monooxygenase (pmoA, pmoB, and pmoC) obtained from the endosymbiotic bacteria found inB. platifrons. The coding sequences (CDS) of the three genes in theB. platifronsendosymbiont were 750, 1,245, and 753 bp, encoding 249, 414, and 250 amino acids, respectively. Sequence alignment and phylogenetic analysis revealed that the symbiont ofB. platifronsbelongs to the type I methanotrophs. In order to clarify the impact of environmental methane on symbiont abundance, a 34-day laboratory maintenance experiment was conducted in whichB. platifronsindividuals were acclimatized to methane-present and methane-absent environments. Symbiont abundance was evaluated by calculating the relative DNA content of the methane monooxygenase gene using quantitative real-time PCR. We found that symbiont quantity immediately decreased from its initial level, then continued to gradually decline during maintenance. At 24 and 34 days of maintenance, symbiont abundance in the methane-absent environment had significantly decreased compared to that in the methane-present environment, indicating that the maintenance of symbionts relies on a continuous supply of methane. Our electron microscopy results validated the qPCR analysis. This study enriches our knowledge of the molecular basis and the dynamic changes of the methanotrophic endosymbiosis inB. platifrons, and provides a feasible model biosystem for further investigation of methane oxidization, the carbon fixation process, and environmental adaptations of deep-sea mussels.

scholarly journals Metabolic diversification of anaerobic methanotrophic archaea in a deep-sea cold seep

2020 ◽  
Vol 2 (4) ◽  
pp. 431-441
Author(s):  
Wen-Li Li ◽  
Yu-Zhi Wu ◽  
Guo-wei Zhou ◽  
Hui Huang ◽  
Yong Wang
Keyword(s):  
Carbon Dioxide ◽  
South China Sea ◽  
Carbon Metabolism ◽  
Deep Sea ◽  
Cold Seep ◽  
Cold Seeps ◽  
Sulfate Concentration ◽  
Novel Approach ◽  
Genes Encoding ◽  
Methane Oxidization

Abstract Anaerobic methanotrophic archaea (ANME) can assimilate methane and govern the greenhouse effect of deep-sea cold seeps. In this study, a total of 13 ANME draft genomes representing five ANME types (ANME-1a, ANME-1b, ANME-2a, ANME-2b and ANME-2c), in size between 0.8 and 1.8 Mbp, were obtained from the Jiaolong cold seep in the South China Sea. The small metagenome-assembled genomes (MAGs) contained all the essential pathways for methane oxidization and carbon dioxide fixation. All genes related to nitrate and sulfate reduction were absent from the MAGs, indicating their syntrophic dependence on partner organisms. Aside from acetate secretion and sugar storage, propanoate synthesis pathway, as an alternative novel carbon flow, was identified in all the MAGs and transcriptionally active. Regarding type-specific features of the MAGs, the genes encoding archaellum and bacteria-derived chemotaxis were specific to ANME-2, perhaps for fitness under fluctuation of methane and sulfate concentration flux. Our genomic and transcriptomic results strongly suggested that ANME could carry out simple carbon metabolism from C1 assimilation to C3 biosynthesis in the SCS cold seep, which casts light on a novel approach for synthetic biology.

scholarly journals Sphingosinithalassobacter tenebrarum sp. nov., isolated from a deep-sea cold seep

2020 ◽  
Vol 70 (10) ◽  
pp. 5561-5566 ◽  
Author(s):  
Rikuan Zheng ◽  
Chaomin Sun
Keyword(s):  
Phylogenetic Analysis ◽  
Deep Sea ◽  
Type Species ◽  
Cold Seep ◽  
Rrna Gene ◽  
Content Type ◽  
Ph Values ◽  
Link Type ◽  
Optimum Ph ◽  
Ubiquinone 10

A Gram-stain-negative, facultatively anaerobic, yellow-pigmented, non-motile, rod-shaped bacterium, designated zrk23T, was isolated from a deep-sea cold seep. The strain was characterized by a polyphasic approach to clarify its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences placed zrk23T within the genus Sphingosinithalassobacter and showed the highest similarity to Sphingosinithalassobacter portus FM6T (97.93 %). Growth occurs at temperatures from 16 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.5 (optimum, pH 7.0) and in 0–5.0 % (w/v) NaCl (optimum, 1.5 %). The major fatty acids were C16 : 0, C14 : 0 2-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified phosphoglycolipid, three unidentified glycolipids and three unidentified phospholipids. The G+C content of the genomic DNA was 64.69 %. The average nucleotide identity values between zrk23T and the most closely related available genome, of Sphingosinithalassobacter portus FM6T, was 82.21 %, indicating that zrk23T was clearly distinguished from S. portus . The analysis of genome sequence of zrk23T revealed that there were many genes associated with degradation of aromatic compounds existing in the genome of zrk23T. As a result of the combination of the results of phylogenetic analysis and phenotypic and chemotaxonomic data, zrk23T was considered to represent a novel species of the genus Sphingosinithalassobacter , for which the name Sphingosinithalassobacter tenebrarum sp. nov. is proposed. The type strain is zrk23T (=KCTC 72896T=MCCC 1K04416T).

scholarly journals Maribellus comscasis sp. nov., isolated from the deep-sea cold seep

2021 ◽  
Author(s):  
Rikuan Zheng ◽  
Chaomin Sun
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Deep Sea ◽  
Degradation Mechanism ◽  
Amino Acid Identity ◽  
Cold Seep ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Optimum Ph ◽  
Curved Rod

ABSTRACTA facultatively anaerobic, Gram-stain-negative, non-motile, curved rod-shaped bacterium, designated WC007T, was isolated from the deep-sea cold seep, P. R. China. Strain WC007T was found to grow at temperatures from 28 to 37 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-5.0% (w/v) NaCl (optimum, 1.0%). The major fatty acids (>10.0%) were iso-C15:0, C16:0, summed feature 3 and summed feature 8. The major isoprenoid quinone was MK-7. Predominant polar lipids were phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The G+C content of the genomic DNA was 38.38%. The average nucleotide identity (ANIb and ANIm), amino acid identity (AAI), the tetranucleotide signatures (Tetra) and in silico DNA-DNA hybridization (isDDH) similarities between the genome sequences of isolate WC007T and Maribellus luteus XSD2T were 70.11%, 84.94%, 71.0%, 0.92022 and 20.40%, respectively, indicating that strain WC007T was distinguished from M. luteus. Phylogenetic analysis based on 16S rRNA gene sequences placed strain WC007T within the genus Maribellus and showed the highest similarity to strain XSD2T (95.70%). In combination of the results of phylogenetic analysis and phenotypic and chemotaxonomic data, strain WC007T was considered to represent a novel species of the genus Maribellus, for which the name Maribellus comscasis sp. nov. is proposed. The type strain is WC007T (=KCTC 25169T = MCCC 1K04777T). The available of the genome sequence of strain WC007T would be helpful in understanding the degradation mechanism of difficult-to-degrade polysaccharides.

scholarly journals Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts

2019 ◽  
Vol 14 (1) ◽  
pp. 135-150 ◽  
Author(s):  
Yi Yang ◽  
Jin Sun ◽  
Yanan Sun ◽  
Yick Hang Kwan ◽  
Wai Chuen Wong ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Energy Use ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Energy Utilization ◽  
Host Cells ◽  
Host Bacterium ◽  
Immunity Genes ◽  
Weak Expression

Abstract Deep-sea hydrothermal vents and methane seeps are often densely populated by animals that host chemosynthetic symbiotic bacteria, but the molecular mechanisms of such host-symbiont relationship remain largely unclear. We characterized the symbiont genome of the seep-living siboglinid Paraescarpia echinospica and compared seven siboglinid-symbiont genomes. Our comparative analyses indicate that seep-living siboglinid endosymbionts have more virulence traits for establishing infections and modulating host-bacterium interaction than the vent-dwelling species, and have a high potential to resist environmental hazards. Metatranscriptome and metaproteome analyses of the Paraescarpia holobiont reveal that the symbiont is highly versatile in its energy use and efficient in carbon fixation. There is close cooperation within the holobiont in production and supply of nutrients, and the symbiont may be able to obtain nutrients from host cells using virulence factors. Moreover, the symbiont is speculated to have evolved strategies to mediate host protective immunity, resulting in weak expression of host innate immunity genes in the trophosome. Overall, our results reveal the interdependence of the tubeworm holobiont through mutual nutrient supply, a pathogen-type regulatory mechanism, and host-symbiont cooperation in energy utilization and nutrient production, which is a key adaptation allowing the tubeworm to thrive in deep-sea chemosynthetic environments.

scholarly journals Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

mSystems ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Ren-Mao Tian ◽  
Weipeng Zhang ◽  
Lin Cai ◽  
Yue-Him Wong ◽  
Wei Ding ◽  
...  
Keyword(s):  
Deep Sea ◽  
Carbon Fixation ◽  
Genome Reduction ◽  
Cold Seep ◽  
Cold Seeps ◽  
Symbiotic Relationship ◽  
Associated Bacteria ◽  
Sponge Body ◽  
Sulfur Oxidizing ◽  
Functional Features

ABSTRACT Sponges and their symbionts are important players in the biogeochemical cycles of marine environments. As a unique habitat within marine ecosystems, cold seeps have received considerable interest in recent years. This study explores the lifestyle of a new symbiotic SOB in a cold seep sponge. The results demonstrate that both this sponge symbiont and endosymbionts in deep-sea clams employ similar strategies of genome reduction. However, this bacterium has retained unique functions for immunity and defense. Thus, the functional features are determined by both the symbiotic relationship and host type. Moreover, analyses of the genome of an AOA suggest that microbes play different roles in biochemical cycles in the sponge body. Our findings provide new insights into invertebrate-associated bacteria in cold seep environments. As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a new deep-sea SOB group. Microscopic observations suggest that Gsub is probably an extracellular symbiont. Gsub has complete sulfide oxidation and carbon fixation pathways, suggesting a chemoautotrophic lifestyle. Comparative genomics with other sponge-associated SOB and free-living SOB revealed significant genome reduction in Gsub, characterized by the loss of genes for carbohydrate metabolism, motility, DNA repair, and osmotic stress response. Intriguingly, this scenario of genome reduction is highly similar to those of the endosymbionts in deep-sea clams. However, Gsub has retained genes for phage defense and protein secretion, with the latter potentially playing a role in interactions with the sponge host. In addition, we recovered the genome of an ammonia-oxidizing archaeon (AOA), which may carry out ammonia oxidation and carbon fixation within the sponge body. IMPORTANCE Sponges and their symbionts are important players in the biogeochemical cycles of marine environments. As a unique habitat within marine ecosystems, cold seeps have received considerable interest in recent years. This study explores the lifestyle of a new symbiotic SOB in a cold seep sponge. The results demonstrate that both this sponge symbiont and endosymbionts in deep-sea clams employ similar strategies of genome reduction. However, this bacterium has retained unique functions for immunity and defense. Thus, the functional features are determined by both the symbiotic relationship and host type. Moreover, analyses of the genome of an AOA suggest that microbes play different roles in biochemical cycles in the sponge body. Our findings provide new insights into invertebrate-associated bacteria in cold seep environments.

The Impact of Ultraviolet Radiation on Barrier Function in Human Skin: Molecular Mechanisms and Topical Therapeutics

2019 ◽  
Vol 25 (40) ◽  
pp. 5503-5511 ◽  
Author(s):  
Abdulaziz Alhasaniah ◽  
Michael J. Sherratt ◽  
Catherine A. O'Neill
Keyword(s):  
Ultraviolet Radiation ◽  
Barrier Function ◽  
Molecular Mechanisms ◽  
Transepidermal Water Loss ◽  
Protective Effects ◽  
Barrier Dysfunction ◽  
Epidermal Barrier ◽  
Positive Effects ◽  
Terrestrial Mammals ◽  
The Impact

A competent epidermal barrier is crucial for terrestrial mammals. This barrier must keep in water and prevent entry of noxious stimuli. Most importantly, the epidermis must also be a barrier to ultraviolet radiation (UVR) from the sunlight. Currently, the effects of ultraviolet radiation on epidermal barrier function are poorly understood. However, studies in mice and more limited work in humans suggest that the epidermal barrier becomes more permeable, as measured by increased transepidermal water loss, in response UVR, at doses sufficiently high to induce erythema. The mechanisms may include disturbance in the organisation of lipids in the stratum corneum (the outermost layer of the epidermis) and reduction in tight junction function in the granular layer (the first living layer of the skin). By contrast, suberythemal doses of UVR appear to have positive effects on epidermal barrier function. Topical sunscreens have direct and indirect protective effects on the barrier through their ability to block UV and also due to their moisturising or occlusive effects, which trap water in the skin, respectively. Some topical agents such as specific botanical extracts have been shown to prevent the loss of water associated with high doses of UVR. In this review, we discuss the current literature and suggest that the biology of UVR-induced barrier dysfunction, and the use of topical products to protect the barrier, are areas worthy of further investigation.

The Role of Vascular Aging in Atherosclerotic Plaque Development and Vulnerability

2019 ◽  
Vol 25 (29) ◽  
pp. 3098-3111 ◽  
Author(s):  
Luca Liberale ◽  
Giovanni G. Camici
Keyword(s):  
Atherosclerotic Plaque ◽  
Molecular Mechanisms ◽  
Driving Forces ◽  
Plaque Burden ◽  
Vascular Aging ◽  
Age Related ◽  
Plaque Development ◽  
Increased Risk ◽  
The Impact ◽  
Over Time

Background: The ongoing demographical shift is leading to an unprecedented aging of the population. As a consequence, the prevalence of age-related diseases, such as atherosclerosis and its thrombotic complications is set to increase in the near future. Endothelial dysfunction and vascular stiffening characterize arterial aging and set the stage for the development of cardiovascular diseases. Atherosclerotic plaques evolve over time, the extent to which these changes might affect their stability and predispose to sudden complications remains to be determined. Recent advances in imaging technology will allow for longitudinal prospective studies following the progression of plaque burden aimed at better characterizing changes over time associated with plaque stability or rupture. Oxidative stress and inflammation, firmly established driving forces of age-related CV dysfunction, also play an important role in atherosclerotic plaque destabilization and rupture. Several genes involved in lifespan determination are known regulator of redox cellular balance and pre-clinical evidence underlines their pathophysiological roles in age-related cardiovascular dysfunction and atherosclerosis. Objective: The aim of this narrative review is to examine the impact of aging on arterial function and atherosclerotic plaque development. Furthermore, we report how molecular mechanisms of vascular aging might regulate age-related plaque modifications and how this may help to identify novel therapeutic targets to attenuate the increased risk of CV disease in elderly people.

VDAC1 Mediated Anticancer Activity of Gallic Acid in Human Lung Adenocarcinoma A549 Cells

2018 ◽  
Vol 18 (2) ◽  
pp. 255-262 ◽  
Author(s):  
Aikebaier Maimaiti ◽  
Amier Aili ◽  
Hureshitanmu Kuerban ◽  
Xuejun Li
Keyword(s):  
Western Blot ◽  
Cell Viability ◽  
Gallic Acid ◽  
Molecular Mechanisms ◽  
A549 Cells ◽  
Dependent Manner ◽  
Lung Carcinoma Cells ◽  
Induced Apoptosis ◽  
The Impact

Aims: Gallic acid (GA) is generally distributed in a variety of plants and foods, and possesses cell growth-inhibiting activities in cancer cell lines. In the present study, the impact of GA on cell viability, apoptosis induction and possible molecular mechanisms in cultured A549 lung carcinoma cells was investigated. Methods: In vitro experiments showed that treating A549 cells with various concentrations of GA inhibited cell viability and induced apoptosis in a dose-dependent manner. In order to understand the mechanism by which GA inhibits cell viability, comparative proteomic analysis was applied. The changed proteins were identified by Western blot and siRNA methods. Results: Two-dimensional electrophoresis revealed changes that occurred to the cells when treated with or without GA. Four up-regulated protein spots were clearly identified as malate dehydrogenase (MDH), voltagedependent, anion-selective channel protein 1(VDAC1), calreticulin (CRT) and brain acid soluble protein 1(BASP1). VDAC1 in A549 cells was reconfirmed by western blot. Transfection with VDAC1 siRNA significantly increased cell viability after the treatment of GA. Further investigation showed that GA down regulated PI3K/Akt signaling pathways. These data strongly suggest that up-regulation of VDAC1 by GA may play an important role in GA-induced, inhibitory effects on A549 cell viability.

scholarly journals SARS-CoV-2 and the Nervous System: From Clinical Features to Molecular Mechanisms

2020 ◽  
Vol 21 (15) ◽  
pp. 5475 ◽  
Author(s):  
Manuela Pennisi ◽  
Giuseppe Lanza ◽  
Luca Falzone ◽  
Francesco Fisicaro ◽  
Raffaele Ferri ◽  
...  
Keyword(s):  
Nervous System ◽  
Molecular Mechanisms ◽  
Neuronal Damage ◽  
Neurological Complications ◽  
Neurological Manifestations ◽  
Wide Range ◽  
Inflammatory State ◽  
Acute Polyneuropathy ◽  
The Central Nervous System ◽  
The Impact

Increasing evidence suggests that Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) can also invade the central nervous system (CNS). However, findings available on its neurological manifestations and their pathogenic mechanisms have not yet been systematically addressed. A literature search on neurological complications reported in patients with COVID-19 until June 2020 produced a total of 23 studies. Overall, these papers report that patients may exhibit a wide range of neurological manifestations, including encephalopathy, encephalitis, seizures, cerebrovascular events, acute polyneuropathy, headache, hypogeusia, and hyposmia, as well as some non-specific symptoms. Whether these features can be an indirect and unspecific consequence of the pulmonary disease or a generalized inflammatory state on the CNS remains to be determined; also, they may rather reflect direct SARS-CoV-2-related neuronal damage. Hematogenous versus transsynaptic propagation, the role of the angiotensin II converting enzyme receptor-2, the spread across the blood-brain barrier, the impact of the hyperimmune response (the so-called “cytokine storm”), and the possibility of virus persistence within some CNS resident cells are still debated. The different levels and severity of neurotropism and neurovirulence in patients with COVID-19 might be explained by a combination of viral and host factors and by their interaction.

scholarly journals The impact of FGF19/FGFR4 signaling inhibition in antitumor activity of multi-kinase inhibitors in hepatocellular carcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hiroaki Kanzaki ◽  
Tetsuhiro Chiba ◽  
Junjie Ao ◽  
Keisuke Koroki ◽  
Kengo Kanayama ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Mechanisms ◽  
Kinase Inhibitors ◽  
Progression Free Survival ◽  
Erk Signaling ◽  
Enzyme Linked Immunosorbent Assay ◽  
Antitumor Effects ◽  
The Impact

AbstractFGF19/FGFR4 autocrine signaling is one of the main targets for multi-kinase inhibitors (MKIs). However, the molecular mechanisms underlying FGF19/FGFR4 signaling in the antitumor effects to MKIs in hepatocellular carcinoma (HCC) remain unclear. In this study, the impact of FGFR4/ERK signaling inhibition on HCC following MKI treatment was analyzed in vitro and in vivo assays. Serum FGF19 in HCC patients treated using MKIs, such as sorafenib (n = 173) and lenvatinib (n = 40), was measured by enzyme-linked immunosorbent assay. Lenvatinib strongly inhibited the phosphorylation of FRS2 and ERK, the downstream signaling molecules of FGFR4, compared with sorafenib and regorafenib. Additional use of a selective FGFR4 inhibitor with sorafenib further suppressed FGFR4/ERK signaling and synergistically inhibited HCC cell growth in culture and xenograft subcutaneous tumors. Although serum FGF19high (n = 68) patients treated using sorafenib exhibited a significantly shorter progression-free survival and overall survival than FGF19low (n = 105) patients, there were no significant differences between FGF19high (n = 21) and FGF19low (n = 19) patients treated using lenvatinib. In conclusion, robust inhibition of FGF19/FGFR4 is of importance for the exertion of antitumor effects of MKIs. Serum FGF19 levels may function as a predictive marker for drug response and survival in HCC patients treated using sorafenib.

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