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Effects of CO2 and H2 limitations on Methanococcus maripaludis.

Hydrogenotrophic methanogens play a key role in anaerobic ecosystems by catalyzing the bioconversion of hydrogen (H2) and carbon dioxide (CO … on donor vs electron acceptor results in distinctly different revival behaviors in the methanogenic Archaea, Methanococcus maripaludis. Methanogens play a crucial role in the global carbon cycle, participating in the anaerobic breakdown of organic matter to methane and carbon dioxide. They are also of biotechnological significance, being central to anaero …

De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis.

Cobalamin is an essential cofactor in all domains of life, yet its biosynthesis is restricted to some bacteria and archaea. Mycobacterium smegmatis, an environmental saprophyte frequently used as surrogate for the obligate human pathogen M. tuberculosis, carries approximately 30 genes predicted to be involved in de novo cobalamin biosynthesis. M. smegmatis also encodes multiple cobalamin-dependent enzymes, including MetH, a methionine synthase that catalyzes the final reaction in methionine biosynthesis. In addition to metH, M. smegmatis possesses a cobalamin-independent methionine synthase, m…

Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment.

BACKGROUND: The structure and function of bacterial nucleoid are controlled by histone-like proteins of HU/IHF family, omnipresent in bacteria and also founding archaea and some eukaryotes.HU protein binds dsDNA without sequence specificity and avidly binds DNA structures with propensity to be inclined such as forks, three/four-way junctions, nicks, overhangs and DNA bulges. Sequence comparison of thousands of known histone-like proteins from diverse bacteria phyla reveals relation between HU/IHF sequence, DNA-binding properties and other protein features. METHODOLOGY AND PRINCIPAL FINDINGS: …

Ectopic overexpression of Plasmodium falciparum DNA-/RNA-binding Alba proteins misregulates virulence gene homeostasis during asexual blood development.

Alba domain-containing proteins are ubiquitously found in archaea and eukaryotes. By binding to either DNA, RNA, or DNA:RNA hybrids, these proteins function in genome stabilization, chromatin organization, gene regulation, and/or translational modulation. In the malaria parasite Plasmodium falciparum, six Alba domain proteins PfAlba1-6 have been described, of which PfAlba1 has emerged as a "master regulator" of translation during parasite intra-erythrocytic development (IED). Given that a tight control of gene expression is especially important during IED, when malaria pathogenesis manifests, …

Functional Nitrogenase Cofactor Maturase NifB in Mitochondria and Chloroplasts of Nicotiana benthamiana.

Engineering plants to synthesize nitrogenase and assimilate atmospheric N2 will reduce crop dependency on industrial N fertilizers. This tec … n (for NifB function), were expressed in Nicotiana benthamiana chloroplasts and mitochondria. Three archaeal NifB proteins accumulated at high levels in soluble fractions of chloroplasts (Methanosarcina acetivorans and Methanocaldococcus infernus) or mitochondria (M. infernus and Methanothermobacter thermautotrophicus). These NifB proteins were shown to a …

Coenzyme F420-Dependent Glucose-6-Phosphate Dehydrogenase-Coupled Polyglutamylation of Coenzyme F420 in Mycobacteria.

Coenzyme F420 plays a key role in the redox metabolisms of various archaea and bacteria, including Mycobacterium tuberculosis In M. tuberculosis, F420-dependent reactions have been linked to several virulence factors. F420 carries multiple glutamate residues in the side chain, forming F420-n species (n, number of glutamate residues), and the length of this side chain impacts cellular physiology. M. tuberculosis strains with F420 species carrying shorter side chains exhibit resistance to delamanid and pretomanid, two new tuberculosis (TB) drugs. Thus, the process of polyglutamylation of F420 is…

Freshwater bacteria release methane as a byproduct of phosphorus acquisition.

UNLABELLED: Freshwater lakes emit large amounts of methane, some of which is produced in oxic surface waters. Two potential pathways for aer … rce of the methane can vary: it is the end product of the energy-conserving pathway in methanogenic archaea, which predominantly live in anoxic sediments or waters, but have also been identified in some oxic freshwater environments. More recently, methane release from small organic molecules has been observed in oxic marine environments. Here we show that …

The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction.

Helicases often achieve functional specificity through utilization of unique structural features incorporated into an otherwise conserved core. The archaeal Rad3 (xeroderma pigmentosum group D protein (XPD)) helicase is a prototypical member of the Rad3 family, distinct from other related (superfamily II) SF2 enzymes because of a unique insertion containing an iron-sulfur (FeS) cluster. This insertion may represent an auxiliary domain responsible for modifying helicase activity or for conferring specificity for selected DNA repair intermediates. The importance of the FeS cluster for the fine-t…

An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette.

CRISPR-Cas is an adaptive immune system that allows bacteria to inactivate mobile genetic elements. Approximately 50% of bacteria harbor CRI … h other defense systems. IMPORTANCE CRISPR-Cas is an adaptive immune system protecting bacteria and archaea against mobile genetic elements such as phages. In strains of Staphylococcus aureus, CRISPR-Cas is rare, but when present, it is located within the SCCmec element, which encodes resistance to methicillin and other β-lactam antibiotics. We show that …

A human ortholog of archaeal DNA repair protein Hef is defective in Fanconi anemia complementation group M.

Fanconi anemia is a genetic disease characterized by genomic instability and cancer predisposition. Nine genes involved in Fanconi anemia ha … tion group (FA-M). FAAP250 or FANCM has sequence similarity to known DNA-repair proteins, including archaeal Hef, yeast MPH1 and human ERCC4 or XPF. FANCM can dissociate DNA triplex, possibly owing to its ability to translocate on duplex DNA. FANCM is essential for monoubiquitination of FANCD2 and becomes hyperphosphorylated in response to DNA damage. Our …

Swertia chirayita ameliorates MAFLD by improving intestinal microenvironment and hepatic lipogenesis.

ETHNOPHARMACOLOGICAL RELEVANCE: Metabolic-associated fatty liver disease (MAFLD) is emerging as a very serious threat to human health. The s … stration helped reestablish the dysregulation of multiple types of gut microbiota (bacteria, fungi, archaea, and viruses) in MAFLD rats. It improved microbial diversity, community composition, and transkingdom correlations. In addition, SC enhanced gut barrier function by raising the amount of butyric acid, acetic acid, and propionic acid and upregulating …

Lessons from Natural Product Total Synthesis: Macrocyclization and Postcyclization Strategies.

Macrocyclic natural products are plentiful in the bacteria, archaea, and eukaryote domains of life. For the significant advantages that they provide to the producing organisms, evolution has learned how to implement various types of macrocyclization reactions into the different biosynthetic pathways and how to effect them with remarkable ease. Mankind greatly benefits from nature's pool, not least because naturally occurring macrocycles or derivatives thereof serve as important drugs for the treatment of many serious ailments.In stark contrast, macrocyclization reactions are usually perceived …

Nucleotide sequences of the arb genes, which control beta-glucoside utilization in Erwinia chrysanthemi: comparison with the Escherichia coli bgl operon and evidence for a new beta-glycohydrolase family including enzymes from eubacteria, archeabacteria, and humans.

The phytopathogenic bacterium Erwinia chrysanthemi, unlike other members of the family Enterobacteriaceae, is able to metabolize the beta-glucosides, arbutin, and salicin. A previous genetic analysis of the E. chrysanthemi arb genes, which mediate beta-glucoside metabolism, suggested that they were homologous to the Escherichia coli K-12 bgl genes. We have now determined the nucleotide sequence of a 5,065-bp DNA fragment containing three genes, arbG, arbF, and arbB. Deletion analysis, expression in minicell systems, and comparison with sequences of other proteins suggest that arbF and arbB enc

Effects of methane inhibitors on ruminal fermentation and microbial composition in vitro using inoculum from phenotypically high- and low-enteric-methane-emitting cows.

The objective of this study was to investigate the interaction of ruminal inoculum type (obtained from high- or low-CH4-emitting-phenotype c … re was no significant INOC × AMC interaction for estimates of methanogenic activity of methanogenic archaea. Inoculum from low-CH4-phenotype cows resulted in higher gene copy number of Methanobrevibacter ruminantium and Methanosphaera stadtmanae. In the bacterial community, 22 taxa had a significant interaction with INOC. Each AMC differentially affected …

All-in-One CO2 Capture and Transformation: Lessons from Formylmethanofuran Dehydrogenases.

Carbon-one-unit (C1) feedstocks are generally used in the chemical synthesis of organic molecules, such as solvents, drugs, polymers, and fu … he formylmethanofuran dehydrogenase (abbreviated as FMD).FMDs are multienzymatic complexes found in archaea that capture CO2 as a formyl group branched on the amine moiety of the methanofuran (MFR) cofactor. This overall reaction leading to formyl-MFR production does not require ATP hydrolysis as compared to the CO2-fixing microbes relying on the reductiv …

[Cephalometry study of craniofacial and upper airway in boys with OSAS].

BACKGROUND: Methanogenic archaea are of importance to the global C-cycle and to biological methane (CH4) production through anaerobic digestion and pure culture. Here, the individual and combined effects of copper (Cu), zinc (Zn), acetate, and propionate on the metabolism of the autotrophic, hydrogenotrophic methanogen Methanococcus maripaludis S2 were investigated. Cu, Zn, acetate, and propionate may interfere directly and indirectly with the acetyl-CoA synthesis and biological CH4 production. Thus, these compounds can compromise or improve the performance of M. maripaludis, an organism which…

Effects of elemental sulfur on the metabolism of the deep-sea hyperthermophilic archaeon Thermococcus strain ES-1: characterization of a sulfur-regulated, non-heme iron alcohol dehydrogenase.

The strictly anaerobic archaeon Thermococcus strain ES-1 was recently isolated from near a deep-sea hydrothermal vent. It grows at temperatures up to 91 degrees C by the fermentation of peptides and reduces elemental sulfur (S(o)) to H2S. It is shown here that the growth rates and cell yields of strain ES-1 are dependent upon the concentration of S(o) in the medium, and no growth was observed in the absence of S(o). The activities of various catabolic enzymes in cells grown under conditions of sufficient and limiting S(o) concentrations were investigated. These enzymes included alcohol dehydro

Восстановление ТРНС последнего универсального общего пастора (Общества) на пути к восстановлению системы перевода Древних.

Реконструирование ансестральной последовательности (АСР) было использовано для изучения эволюции переводческой системы путем определения последовательности tRNA в "Last Archaeal Common Ancestor" (LACA), "Last Bacterial Common Ancestor" (LBCA) и "Last Universal Common Ansancestor" (LUCA), которые в наших предыдущих исследованиях назывались "Общество". Составное филогенетическое дерево, взятое из реконструированных последовательности ТРНА, выявило топологию, отличную от ранее выведенных аминоачил-тРНА синтетазы (АРС). Такая непоследовательность может отражать изменения в структурных особенностях…

[Significance and effects of prenatal and postnatal microbiome in the period of early individual development and options for interventional treatment].

Összefoglaló. A humán mikrobiom az emberi szervezetben és az emberi testfelszínen élő mikrobaközösségek összessége, amelyek többsége a gyomo … gastrointestinal tract. These microbe communities contain many and varied bacteria, fungi, viruses, archaea and protozoa. This microbial community or microbiota in the host is largely reciprocal and takes care of nutrient metabolism in the gut, calibrates metabolism, teaches the immune system, maintains community integrity, and protects against pathogens. …

Структура и состав микробных сообществ в водной толще Южного залива Мексики и обнаружение предполагаемых микроорганизмов, деградирующих углеводороды.

В ходе этого исследования была проведена оценка сообщества бактериопланктонов и его связи с экологическими переменными, включая общую концентрацию нефтяных углеводородов (ТПГ), в районе шельфа Юкатан в Южном заливе Мексики. Анализ разнообразия бета на основе последовательности 16S rRNA показал различия в структуре общины бактериопланктона между участками отбора проб. ПЕРМАНОВА указала, что эти изменения могут быть связаны главным образом с глубокими изменениями (см.5 в адрес 180 m), концентрация растворенного кислорода (2.06 в адрес 5.93 мг L-1), и концентрация хлорофилла (0.184 в адрес 7.65 м

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… In addition, the presence of Oleibacter , AGEAN‐169, and the highest relative abundances of Alteromonas ( Gamma‐proteobacteria ), the marine group ZD0417 ( Gamma‐proteobacteria ), as well as three unassigned genera of Archaea of the class Thermoplasmata . … According to the SIMPER analysis (Figure 6 ), some of the characteristic taxa of cluster two included ASVs from the classes Marine Group I (Archaea), Thermoplasmata (Archaea), Phycisphaerae , Planctomycetacia , Nitrospira and Nitrospinia . …