scholarly journals New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

2014 ◽  
Vol 81 (4) ◽  
pp. 1338-1352 ◽  
Author(s):  
Kristina Lang ◽  
Jörg Schuldes ◽  
Andreas Klingl ◽  
Anja Poehlein ◽  
Rolf Daniel ◽  
...  

ABSTRACTThe recently discovered seventh order of methanogens, theMethanomassiliicoccales(previously referred to as “Methanoplasmatales”), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of “CandidatusMethanoplasma termitum” from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, “Ca. Methanoplasma termitum” lacks the entire pathway for CO2reduction to methyl coenzyme M and produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates thatMethanomassiliicoccalesemploy a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophicMethanosphaera stadtmanae. Instead, all strains possess a novel complex that is related to the F420:methanophenazine oxidoreductase (Fpo) ofMethanosarcinalesbut lacks an F420-oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog inMethanosaeta thermophila. Since allMethanomassiliicoccalesalso lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), we propose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin:heterodisulfide oxidoreductase. The dual function of heterodisulfide inMethanomassiliicoccales, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order.

2014 ◽  
Vol 80 (15) ◽  
pp. 4668-4676 ◽  
Author(s):  
Pengfei Liu ◽  
Yanxiang Yang ◽  
Zhe Lü ◽  
Yahai Lu

ABSTRACTMembers ofMethanocellalesare widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms' adaptation to low H2and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation ofMethanocella conradiiHZ254, a strain recently isolated from paddy field soil.M. conradiiwas grown in monoculture and syntrophically withPelotomaculum thermopropionicum(a propionate syntroph) orSyntrophothermus lipocalidus(a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F420-nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed inM. conradii. We propose thatMethanocellamethanogens cope with low H2and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formate-dependent methanogenesis.


2013 ◽  
Vol 79 (9) ◽  
pp. 2882-2890 ◽  
Author(s):  
Guillermo D. Repizo ◽  
Víctor S. Blancato ◽  
Pablo Mortera ◽  
Juke S. Lolkema ◽  
Christian Magni

ABSTRACTEnterococcus faecalisencodes a biotin-dependent oxaloacetate decarboxylase (OAD), which is constituted by four subunits:E. faecaliscarboxyltransferase subunit OadA (termedEf-A), membrane pumpEf-B, biotin acceptor proteinEf-D, and the novel subunitEf-H. Our results show that inE. faecalis, subunitsEf-A,Ef-D, andEf-H form a cytoplasmic soluble complex (termedEf-AHD) which is also associated with the membrane. In order to characterize the role of the novelEf-H subunit, coexpression ofoadgenes was performed inEscherichia coli, showing that this subunit is vital forEf-A andEf-D interaction. Diminished growth of theoadAandoadDsingle deletion mutants in citrate-supplemented medium indicated that the activity of the complex is essential for citrate utilization. Remarkably, theoadB-deficient strain was still capable of growing to wild-type levels but with a delay during the citrate-consuming phase, suggesting that the solubleEf-AHD complex is functional inE. faecalis.These results suggest that theEf-AHD complex is active in its soluble form, and that it is capable of interacting in a dynamic way with the membrane-boundEf-B subunit to achieve its maximal alkalinization capacity during citrate fermentation.


2015 ◽  
Vol 81 (12) ◽  
pp. 4098-4110 ◽  
Author(s):  
Binbin Sheng ◽  
Jing Xu ◽  
Yingxin Zhang ◽  
Tianyi Jiang ◽  
Sisi Deng ◽  
...  

ABSTRACTd-Lactate was identified as one of the few available organic acids that supported the growth ofGluconobacter oxydans621H in this study. Interestingly, the strain usedd-lactate as an energy source but not as a carbon source, unlike other lactate-utilizing bacteria. The enzymatic basis for the growth ofG. oxydans621H ond-lactate was therefore investigated. Although two putative NAD-independentd-lactate dehydrogenases, GOX1253 and GOX2071, were capable of oxidizingd-lactate, GOX1253 was the only enzyme able to support thed-lactate-driven growth of the strain. GOX1253 was characterized as a membrane-bound dehydrogenase with high activity towardd-lactate, while GOX2071 was characterized as a soluble oxidase with broad substrate specificity towardd-2-hydroxy acids. The latter used molecular oxygen as a direct electron acceptor, a feature that has not been reported previously ind-lactate-oxidizing enzymes. This study not only clarifies the mechanism for the growth ofG. oxydansond-lactate, but also provides new insights for applications of the important industrial microbe and the noveld-lactate oxidase.


2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3950-3957 ◽  
Author(s):  
Jerri E. Zilli ◽  
Alexandre C. Baraúna ◽  
Krisle da Silva ◽  
Sofie E. De Meyer ◽  
Eliane N. C. Farias ◽  
...  

Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247T, BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6 %) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S–23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05T ( = LMG 24129T) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium . Results of DNA–DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium . Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus Bradyrhizobium . Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247T ( = HAMBI 3599T).


2015 ◽  
Vol 81 (7) ◽  
pp. 2466-2473 ◽  
Author(s):  
Muhammad Farhan Ul-Haque ◽  
Bhagyalakshmi Kalidass ◽  
Alexey Vorobev ◽  
Bipin S. Baral ◽  
Alan A. DiSpirito ◽  
...  

ABSTRACTMethanotrophs can express a cytoplasmic (soluble) methane monooxygenase (sMMO) or membrane-bound (particulate) methane monooxygenase (pMMO). Expression of these MMOs is strongly regulated by the availability of copper. Many methanotrophs have been found to synthesize a novel compound, methanobactin (Mb), that is responsible for the uptake of copper, and methanobactin produced byMethylosinus trichosporiumOB3b plays a key role in controlling expression of MMO genes in this strain. As all known forms of methanobactin are structurally similar, it was hypothesized that methanobactin from one methanotroph may alter gene expression in another. WhenMethylosinus trichosporiumOB3b was grown in the presence of 1 μM CuCl2, expression ofmmoX, encoding a subunit of the hydroxylase component of sMMO, was very low.mmoXexpression increased, however, when methanobactin fromMethylocystissp. strain SB2 (SB2-Mb) was added, as did whole-cell sMMO activity, but there was no significant change in the amount of copper associated withM. trichosporiumOB3b. IfM. trichosporiumOB3b was grown in the absence of CuCl2, themmoXexpression level was high but decreased by several orders of magnitude if copper prebound to SB2-Mb (Cu-SB2-Mb) was added, and biomass-associated copper was increased. Exposure ofMethylosinus trichosporiumOB3b to SB2-Mb had no effect on expression ofmbnA, encoding the polypeptide precursor of methanobactin in either the presence or absence of CuCl2.mbnAexpression, however, was reduced when Cu-SB2-Mb was added in both the absence and presence of CuCl2. These data suggest that methanobactin acts as a general signaling molecule in methanotrophs and that methanobactin “piracy” may be commonplace.


2018 ◽  
Vol 47 (4) ◽  
pp. 350-359 ◽  
Author(s):  
Nivin M. Ahmed ◽  
Mostafa G. Mohamed ◽  
Reham H. Tammam ◽  
Mohamed R. Mabrouk

Purpose This study aims to apply novel anticorrosive pigments containing silica fume-phosphates (Si-Ph), which were prepared using core-shell technique by covering 80-90 per cent silica fume (core) with 10-20 per cent phosphates (shell) previously, to play dual functions simultaneously as anticorrosive pigments in coating formulations and as an anticorrosive admixture in concrete even if it is not present in the concrete itself. Two comparisons were held out to show the results of coatings on rebars containing core-shell pigments in concrete, and concrete admixtured with silica fume can perform a dual function as anticorrosive pigment and concrete admixture. The evaluation of corrosion protection efficiency of coatings containing core-shell pigments and those containing phosphates was performed. Design/methodology/approach Simple chemical techniques were used to prepare core-shell pigments, and their characterization was carried out in a previous work. These pigments were incorporated in solvent-based paint formulations based on epoxy resin. Different electrochemical techniques such as open-circuit potential and electrochemical impedance spectroscopy were used to evaluate the anticorrosive efficiency of the new pigments. Findings The electrochemical measurements showed that concrete containing coated rebars with core-shell pigments exhibited almost similar results to that of concrete admixtured with silica fume. Also, the anticorrosive performance of coatings containing Si-Ph pigments offered protection efficiency almost similar to that of phosphates, proving that these new pigments can perform both roles as anticorrosive pigment and concrete admixture. Originality/value Although the new Si-Ph pigments contain more than 80 per cent waste material, its performance can be compared to original phosphate pigments in the reinforced concrete.


2019 ◽  
Vol 85 (21) ◽  
Author(s):  
Meng Zhang ◽  
Tao Lu ◽  
Hans W. Paerl ◽  
Yiling Chen ◽  
Zhenyan Zhang ◽  
...  

ABSTRACT The frequency and intensity of cyanobacterial blooms are increasing worldwide. Interactions between toxic cyanobacteria and aquatic microorganisms need to be critically evaluated to understand microbial drivers and modulators of the blooms. In this study, we applied 16S/18S rRNA gene sequencing and metabolomics analyses to measure the microbial community composition and metabolic responses of the cyanobacterium Microcystis aeruginosa in a coculture system receiving dissolved inorganic nitrogen and phosphorus (DIP) close to representative concentrations in Lake Taihu, China. M. aeruginosa secreted alkaline phosphatase using a DIP source produced by moribund and decaying microorganisms when the P source was insufficient. During this process, M. aeruginosa accumulated several intermediates in energy metabolism pathways to provide energy for sustained high growth rates and increased intracellular sugars to enhance its competitive capacity and ability to defend itself against microbial attack. It also produced a variety of toxic substances, including microcystins, to inhibit metabolite formation via energy metabolism pathways of aquatic microorganisms, leading to a negative effect on bacterial and eukaryotic microbial richness and diversity. Overall, compared with the monoculture system, the growth of M. aeruginosa was accelerated in coculture, while the growth of some cooccurring microorganisms was inhibited, with the diversity and richness of eukaryotic microorganisms being more negatively impacted than those of prokaryotic microorganisms. These findings provide valuable information for clarifying how M. aeruginosa can potentially modulate its associations with other microorganisms, with ramifications for its dominance in aquatic ecosystems. IMPORTANCE We measured the microbial community composition and metabolic responses of Microcystis aeruginosa in a microcosm coculture system receiving dissolved inorganic nitrogen and phosphorus (DIP) close to the average concentrations in Lake Taihu. In the coculture system, DIP is depleted and the growth and production of aquatic microorganisms can be stressed by a lack of DIP availability. M. aeruginosa could accelerate its growth via interactions with specific cooccurring microorganisms and the accumulation of several intermediates in energy metabolism-related pathways. Furthermore, M. aeruginosa can decrease the carbohydrate metabolism of cooccurring aquatic microorganisms and thus disrupt microbial activities in the coculture. This also had a negative effect on bacterial and eukaryotic microbial richness and diversity. Microcystin was capable of decreasing the biomass of total phytoplankton in aquatic microcosms. Overall, compared to the monoculture, the growth of total aquatic microorganisms is inhibited, with the diversity and richness of eukaryotic microorganisms being more negatively impacted than those of prokaryotic microorganisms. The only exception is M. aeruginosa in the coculture system, whose growth was accelerated.


2019 ◽  
Vol 35 (2) ◽  
pp. 1-17
Author(s):  
Shai Rudin

Purpose This study aims to examine the responses and perceptions of Israeli Arab teachers toward multicultural and educational issues concerning Jewish–Arab relations. Design/methodology/approach This study is a qualitative research. The study included 44 novice Arab teachers, who teach Hebrew in the Arab sector and are currently studying toward their masters’ degree at a teacher education college in northern Israel. The teachers were asked to read the novel Nadia by Galila Ron Feder–Amit. Published in 1985, the novel describes the complex integration of Nadia, an Arab village girl, into a Jewish boarding school, and it is narrated in first person. After having read the novel, the teachers were requested to answer the writing task, which addressed the character of the protagonist, the issue of teaching the novel in the Jewish and Arabic educational systems and the anticipated responses of Jewish and Arab students to the novel. Findings Phenomenological analysis of the teachers’ responses found that the reading experience was complex and resulted in a variety of responses toward the protagonist. Some were based on identification and appreciation, while others on criticism and judgment of the heroine’s restraint vis-a-vis the racism that she was experiencing. However, most of the teachers demonstrated moral courage and thought that the novel should be taught, as they viewed it as a bridge leading to understanding between the two nations. The teachers anticipated conflicting responses of Jewish and Arab students to the novel, according to the students’ political views and values. Practical implications These findings indicate that the educational system should include political texts relating to the Jewish–Arab schism, especially texts that voice the Palestinian narrative. This view differs from the current situation in both sectors, whereby the tendency is to avoid political texts while ignoring the Palestinian narrative. Originality/value The study shows that the reading experience of a political novel affords various and often contrasting responses with the teachers facing the didactic challenges. The teachers who participated in the study anticipated complexity of the reading and teaching process, yet were not deterred by it, particularly in view of the novel’s messages – striving to understand the “other” and to bridge a discourse between the nations.


2011 ◽  
Vol 77 (9) ◽  
pp. 3023-3034 ◽  
Author(s):  
Ya-Jie Tang ◽  
Wei Zhao ◽  
Hong-Mei Li

ABSTRACTAccording to the structure of podophyllotoxin and its structure-function relationship, a novel tandem biotransformation process was developed for the directional modification of the podophyllotoxin structure to directionally synthesize a novel compound, 4-(2,3,5,6-tetramethylpyrazine-1)-4′-demethylepipodophyllotoxin (4-TMP-DMEP). In this novel tandem biotransformation process, the starting substrate of podophyllotoxin was biotransformed into 4′-demethylepipodophyllotoxin (product 1) with the demethylation of the methoxyl group at the 4′ position byGibberella fujikuroiSH-f13, which was screened out from Shennongjia prime forest humus soil (Hubei, China). 4′-Demethylepipodophyllotoxin (product 1) was then biotransformed into 4′-demethylpodophyllotoxone (product 2) with the oxidation of the hydroxyl group at the 4 position byAlternaria alternataS-f6, which was screened out from the gatheredDysosma versipellisplants in the Wuhan Botanical Garden, Chinese Academy of Sciences. Finally, 4′-demethylpodophyllotoxone (product 2) and ligustrazine were linked with a transamination reaction to synthesize the target product 4-TMP-DMEP (product 3) byAlternaria alternataS-f6. Compared with podophyllotoxin (i.e., a 50% effective concentration [EC50] of 529 μM), the EC50of 4-TMP-DMEP against the tumor cell line BGC-823 (i.e., 0.11 μM) was significantly reduced by 5,199 times. Simultaneously, the EC50of 4-TMP-DMEP against the normal human proximal tubular epithelial cell line HK-2 (i.e., 0.40 μM) was 66 times higher than that of podophyllotoxin (i.e., 0.006 μM). Furthermore, compared with podophyllotoxin (i.e., logP= 0.34), the water solubility of 4-TMP-DMEP (i.e., logP= 0.66) was significantly enhanced by 94%. For the first time, the novel compound 4-TMP-DMEP with superior antitumor activity was directionally synthesized from podophyllotoxin by the novel tandem biotransformation process developed in this work.


2014 ◽  
Vol 81 (3) ◽  
pp. 1024-1031 ◽  
Author(s):  
Bhagyalakshmi Kalidass ◽  
Muhammad Farhan Ul-Haque ◽  
Bipin S. Baral ◽  
Alan A. DiSpirito ◽  
Jeremy D. Semrau

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.


Sign in / Sign up

Export Citation Format

Share Document