scholarly journals Aerobic H2respiration enhances metabolic flexibility of methanotrophic bacteria

2016 ◽  
Author(s):  
Carlo R. Carere ◽  
Kiel Hards ◽  
Karen M. Houghton ◽  
Jean F. Power ◽  
Ben McDonald ◽  
...  
Keyword(s):  
Soil Microorganisms ◽  
Hydrogen Gas ◽  
Environmental Adaptation ◽  
Metabolic Flexibility ◽  
General Strategy ◽  
Methanotrophic Bacteria ◽  
Mixotrophic Growth ◽  
Methanotrophic Bacterium ◽  
Genes Encoding ◽  
Membrane Bound

AbstractMethanotrophic bacteria are important soil biofilters for the climate-active gas methane. The prevailing opinion is that these bacteria exclusively metabolise single-carbon, and in limited instances, short-chain hydrocarbons for growth. This specialist lifestyle juxtaposes metabolic flexibility, a key strategy for environmental adaptation of microorganisms. Here we show that a methanotrophic bacterium from the phylum Verrucomicrobia oxidises hydrogen gas (H2) during growth and persistence.Methylacidiphilumsp. RTK17.1 expresses a membrane-bound hydrogenase to aerobically respire molecular H2at environmentally significant concentrations. While H2oxidation did not support growth as the sole electron source, it significantly enhanced mixotrophic growth yields under both oxygen-replete and oxygen-limiting conditions and was sustained in non-growing cultures starved for methane. We propose that H2is consumed by this bacterium for mixotrophic growth and persistence in a manner similar to other non-methanotrophic soil microorganisms. We have identified genes encoding oxygen-tolerant uptake hydrogenases in all publicly-available methanotroph genomes, suggesting that H2oxidation serves a general strategy for methanotrophs to remain energised in chemically-limited environments.

scholarly journals Craniofacial Diseases Caused by Defects in Intracellular Trafficking

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 726
Author(s):  
Chung-Ling Lu ◽  
Jinoh Kim
Keyword(s):  
Endoplasmic Reticulum ◽  
Membrane Proteins ◽  
Intracellular Trafficking ◽  
Critical Role ◽  
Treatment Strategies ◽  
Soluble Proteins ◽  
Genes Encoding ◽  
Membrane Bound ◽  
Signaling Receptors ◽  
Craniofacial Morphogenesis

Cells use membrane-bound carriers to transport cargo molecules like membrane proteins and soluble proteins, to their destinations. Many signaling receptors and ligands are synthesized in the endoplasmic reticulum and are transported to their destinations through intracellular trafficking pathways. Some of the signaling molecules play a critical role in craniofacial morphogenesis. Not surprisingly, variants in the genes encoding intracellular trafficking machinery can cause craniofacial diseases. Despite the fundamental importance of the trafficking pathways in craniofacial morphogenesis, relatively less emphasis is placed on this topic, thus far. Here, we describe craniofacial diseases caused by lesions in the intracellular trafficking machinery and possible treatment strategies for such diseases.

scholarly journals Competition between Metals for Binding to Methanobactin Enables Expression of Soluble Methane Monooxygenase in the Presence of Copper

2014 ◽  
Vol 81 (3) ◽  
pp. 1024-1031 ◽  
Author(s):  
Bhagyalakshmi Kalidass ◽  
Muhammad Farhan Ul-Haque ◽  
Bipin S. Baral ◽  
Alan A. DiSpirito ◽  
Jeremy D. Semrau
Keyword(s):  
Methane Monooxygenase ◽  
High Specificity ◽  
Copper Uptake ◽  
Content Type ◽  
Soluble Methane Monooxygenase ◽  
Sds Page ◽  
Genes Encoding ◽  
Key Factor ◽  
Membrane Bound

ABSTRACTIt is well known that copper is a key factor regulating expression of the two forms of methane monooxygenase found in proteobacterial methanotrophs. Of these forms, the cytoplasmic, or soluble, methane monooxygenase (sMMO) is expressed only at low copper concentrations. The membrane-bound, or particulate, methane monooxygenase (pMMO) is constitutively expressed with respect to copper, and such expression increases with increasing copper. Recent findings have shown that copper uptake is mediated by a modified polypeptide, or chalkophore, termed methanobactin. Although methanobactin has high specificity for copper, it can bind other metals, e.g., gold. Here we show that inMethylosinus trichosporiumOB3b, sMMO is expressed and active in the presence of copper if gold is also simultaneously present. Such expression appears to be due to gold binding to methanobactin produced byM. trichosporiumOB3b, thereby limiting copper uptake. Such expression and activity, however, was significantly reduced if methanobactin preloaded with copper was also added. Further, quantitative reverse transcriptase PCR (RT-qPCR) of transcripts of genes encoding polypeptides of both forms of MMO and SDS-PAGE results indicate that both sMMO and pMMO can be expressed when copper and gold are present, as gold effectively competes with copper for binding to methanobactin. Such findings suggest that under certain geochemical conditions, both forms of MMO may be expressed and activein situ. Finally, these findings also suggest strategies whereby field sites can be manipulated to enhance sMMO expression, i.e., through the addition of a metal that can compete with copper for binding to methanobactin.

Streptococcus salivarius Isolates of Varying Acid Tolerance Exhibit F1F0-ATPase Conservation

2021 ◽  
pp. 1-4
Author(s):  
Lauren L. Allen ◽  
Nicholas C.K. Heng ◽  
Geoffrey R. Tompkins
Keyword(s):  
Molecular Structure ◽  
Amino Acid ◽  
Acid Tolerance ◽  
Mutans Streptococci ◽  
Streptococcus Salivarius ◽  
Synonymous Substitutions ◽  
Carious Lesions ◽  
Genes Encoding ◽  
Atpase Subunits ◽  
Membrane Bound

Genes encoding the subunits of the membrane-bound F<sub>1</sub>F<sub>0</sub>-ATPase (responsible for exporting protons from the cytoplasm and contributing to acid tolerance) were sequenced for 24 non-mutans streptococci isolated from carious lesions. Isolates, mostly <i>Streptococcus salivarius</i>, displayed a continuum of acid tolerance thresholds ranging from pH 4.55 to 3.39, but amino acid alignments of F<sub>1</sub>F<sub>0</sub>-ATPase subunits revealed few non-synonymous substitutions and these were unrelated to acid tolerance. Thus, the F<sub>1</sub>F<sub>0</sub>-ATPase is highly-conserved among <i>S. salivarius</i> isolates despite varying acid tolerance thresholds, supporting the contention that acid tolerance is determined by the level of gene/protein expression rather than variation in molecular structure.

scholarly journals pH Homeostasis and Sodium Ion Pumping by Multiple Resistance and pH Antiporters in Pyrococcus furiosus

2021 ◽  
Vol 12 ◽  
Author(s):  
Dominik K. Haja ◽  
Michael W. W. Adams
Keyword(s):  
Pyrococcus Furiosus ◽  
Gas Production ◽  
Hydrogen Gas ◽  
Sodium Ion ◽  
Redox Activity ◽  
Deletion Strain ◽  
Multiple Resistance ◽  
Ph Homeostasis ◽  
Membrane Bound ◽  
Ion Pumping

Multiple Resistance and pH (Mrp) antiporters are seven-subunit complexes that couple transport of ions across the membrane in response to a proton motive force (PMF) and have various physiological roles, including sodium ion sensing and pH homeostasis. The hyperthermophilic archaeon Pyrococcus furiosus contains three copies of Mrp encoding genes in its genome. Two are found as integral components of two respiratory complexes, membrane bound hydrogenase (MBH) and the membrane bound sulfane sulfur reductase (MBS) that couple redox activity to sodium translocation, while the third copy is a stand-alone Mrp. Sequence alignments show that this Mrp does not contain an energy-input (PMF) module but contains all other predicted functional Mrp domains. The P. furiosus Mrp deletion strain exhibits no significant changes in optimal pH or sodium ion concentration for growth but is more sensitive to medium acidification during growth. Cell suspension hydrogen gas production assays using the deletion strain show that this Mrp uses sodium as the coupling ion. Mrp likely maintains cytoplasmic pH by exchanging protons inside the cell for extracellular sodium ions. Deletion of the MBH sodium-translocating module demonstrates that hydrogen gas production is uncoupled from ion pumping and provides insights into the evolution of this Mrp-containing respiratory complex.

scholarly journals Oxygen reduction in the strict anaerobe Desulfovibrio vulgaris Hildenborough: characterization of two membrane-bound oxygen reductases

Microbiology ◽  
2011 ◽  
Vol 157 (9) ◽  
pp. 2720-2732 ◽  
Author(s):  
O. Lamrabet ◽  
L. Pieulle ◽  
C. Aubert ◽  
F. Mouhamar ◽  
P. Stocker ◽  
...  
Keyword(s):  
Electron Donor ◽  
Desulfovibrio Vulgaris ◽  
Strictly Anaerobic ◽  
Quinol Oxidase ◽  
Genes Encoding ◽  
Oxygen Reductase ◽  
Membrane Bound ◽  
Carbon Monoxide Binding ◽  
Cellular Compartments ◽  
Encoding Genes

Although Desulfovibrio vulgaris Hildenborough (DvH) is a strictly anaerobic bacterium, it is able to consume oxygen in different cellular compartments, including extensive periplasmic O2 reduction with hydrogen as electron donor. The genome of DvH revealed the presence of cydAB and cox genes, encoding a quinol oxidase bd and a cytochrome c oxidase, respectively. In the membranes of DvH, we detected both quinol oxygen reductase [inhibited by heptyl-hydroxyquinoline-N-oxide (HQNO)] and cytochrome c oxidase activities. Spectral and HPLC data for the membrane fraction revealed the presence of o-, b- and d-type haems, in addition to a majority of c-type haems, but no a-type haem, in agreement with carbon monoxide-binding analysis. The cytochrome c oxidase is thus of the cc(o/b)o 3 type, a type not previously described. The monohaem cytochrome c 553 is an electron donor to the cytochrome c oxidase; its encoding gene is located upstream of the cox operon and is 50-fold more transcribed than coxI encoding the cytochrome c oxidase subunit I. Even when DvH is grown under anaerobic conditions in lactate/sulfate medium, the two terminal oxidase-encoding genes are expressed. Furthermore, the quinol oxidase bd-encoding genes are more highly expressed than the cox genes. The cox operon exhibits an atypical genomic organization, with the gene coxII located downstream of coxIV. The occurrence of these membrane-bound oxygen reductases in other strictly anaerobic Deltaproteobacteria is discussed.

scholarly journals Engineering Hydrogen Gas Production from Formate in a Hyperthermophile by Heterologous Production of an 18-Subunit Membrane-bound Complex

2013 ◽  
Vol 289 (5) ◽  
pp. 2873-2879 ◽  
Author(s):  
Gina L. Lipscomb ◽  
Gerrit J. Schut ◽  
Michael P. Thorgersen ◽  
William J. Nixon ◽  
Robert M. Kelly ◽  
...  
Keyword(s):  
Gas Production ◽  
Hydrogen Gas ◽  
Heterologous Production ◽  
Membrane Bound

scholarly journals Functional Analyses of a Putative, Membrane-Bound, Peroxisomal Protein Import Mechanism from the Apicomplexan Protozoan Toxoplasma gondii

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 434
Author(s):  
Alison Mbekeani ◽  
Will Stanley ◽  
Vishal Kalel ◽  
Noa Dahan ◽  
Einat Zalckvar ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Protein Import ◽  
Fluorescent Protein ◽  
Metabolic Energy ◽  
Peroxisomal Protein ◽  
Genes Encoding ◽  
Peroxisomal Targeting ◽  
Membrane Bound ◽  
Green Fluorescent

Peroxisomes are central to eukaryotic metabolism, including the oxidation of fatty acids—which subsequently provide an important source of metabolic energy—and in the biosynthesis of cholesterol and plasmalogens. However, the presence and nature of peroxisomes in the parasitic apicomplexan protozoa remains controversial. A survey of the available genomes revealed that genes encoding peroxisome biogenesis factors, so-called peroxins (Pex), are only present in a subset of these parasites, the coccidia. The basic principle of peroxisomal protein import is evolutionarily conserved, proteins harbouring a peroxisomal-targeting signal 1 (PTS1) interact in the cytosol with the shuttling receptor Pex5 and are then imported into the peroxisome via the membrane-bound protein complex formed by Pex13 and Pex14. Surprisingly, whilst Pex5 is clearly identifiable, Pex13 and, perhaps, Pex14 are apparently absent from the coccidian genomes. To investigate the functionality of the PTS1 import mechanism in these parasites, expression of Pex5 from the model coccidian Toxoplasma gondii was shown to rescue the import defect of Pex5-deleted Saccharomyces cerevisiae. In support of these data, green fluorescent protein (GFP) bearing the enhanced (e)PTS1 known to efficiently localise to peroxisomes in yeast, localised to peroxisome-like bodies when expressed in Toxoplasma. Furthermore, the PTS1-binding domain of Pex5 and a PTS1 ligand from the putatively peroxisome-localised Toxoplasma sterol carrier protein (SCP2) were shown to interact in vitro. Taken together, these data demonstrate that the Pex5–PTS1 interaction is functional in the coccidia and indicate that a nonconventional peroxisomal import mechanism may operate in the absence of Pex13 and Pex14.

scholarly journals Transcript Analysis of Genes Encoding a Family 61 Endoglucanase and a Putative Membrane-Anchored Family 9 Glycosyl Hydrolase from Phanerochaete chrysosporium

2002 ◽  
Vol 68 (11) ◽  
pp. 5765-5768 ◽  
Author(s):  
Amber Vanden Wymelenberg ◽  
Stuart Denman ◽  
Diane Dietrich ◽  
Jennifer Bassett ◽  
Xiaochun Yu ◽  
...  
Keyword(s):  
Phanerochaete Chrysosporium ◽  
Glycoside Hydrolase ◽  
Glycosyl Hydrolase ◽  
Thermobifida Fusca ◽  
Glycoside Hydrolase Family ◽  
Transcript Analysis ◽  
Transcript Levels ◽  
Genes Encoding ◽  
Membrane Bound ◽  
Hydrolase Family

ABSTRACT Phanerochaete chrysosporium cellulase genes were cloned and characterized. The cel61A product was structurally similar to fungal endoglucanases of glycoside hydrolase family 61, whereas the cel9A product revealed similarities to Thermobifida fusca Cel9A (E4), an enzyme with both endo- and exocellulase characteristics. The fungal Cel9A is apparently a membrane-bound protein, which is very unusual for microbial cellulases. Transcript levels of both genes were substantially higher in cellulose-grown cultures than in glucose-grown cultures. These results show that P. chrysosporium possesses a wide array of conventional and unconventional cellulase genes.

Patterns of evolutionary conservation in the nesprin genes highlight probable functionally important protein domains and isoforms

2008 ◽  
Vol 36 (6) ◽  
pp. 1359-1367 ◽  
Author(s):  
Jennifer G. Simpson ◽  
Roland G. Roberts
Keyword(s):  
Nuclear Envelope ◽  
Expressed Sequence Tag ◽  
Sequence Data ◽  
Actin Binding ◽  
Structural Elements ◽  
Spectrin Repeat ◽  
Protein Protein Interaction ◽  
Common Structure ◽  
Genes Encoding ◽  
Membrane Bound

The nesprins [also known as SYNEs (synaptic nuclear envelope proteins)] are a family of type II transmembrane proteins implicated in the tethering of membrane-bound organelles and in the genetic aetiology of cerebellar ataxia and Emery–Dreifuss muscular dystrophy. They are characterized by a common structure of an SR (spectrin repeat) rod domain and a C-terminal transmembrane KLS (klarsicht)/KASH [klarsicht/ANC-1 (anchorage 1)/SYNE homology] domain which interacts with SUN [Sad1p/UNC (uncoordinated)-84] proteins in the nuclear envelope; most nesprins also have N-terminal actin-binding CH (calponin homology) domains. The genes encoding the three vertebrate nesprins (five in bony fish) and the small transmembrane actin-binding protein calmin are related to each other by ancient duplications and rearrangements. In the present paper, we collate sequence data for nesprins and calmins across the vertebrate clade and use these to study evolutionary constraints acting on their genes. We show that the rod domains of the larger nesprins are composed almost entirely of unbroken SR-like structures (74 in nesprin-1 and 56 in nesprin-2) and that these range from poorly conserved purely structural elements to highly conserved regions with a presumed protein–protein interaction function. The analysis suggests several interesting regions for future study. We also assess the evolutionary and EST (expressed sequence tag) expression support for nesprin isoforms, both known and novel; our findings suggest that substantial reassessment is required.

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