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Sergey Melnikov, Kasidet Manakongtreecheep, Dieter Söll
Ribosomal proteins are indispensable components of a living cell, and yet their structures are remarkably diverse in different species. Here we use manually curated structural alignments to provide a comprehensive catalog of structural variations in homologous ribosomal proteins from bacteria, archaea, eukaryotes and eukaryotic organelles. By resolving numerous ambiguities and errors of automated structural and sequence alignments, we uncover a whole new class of structural variations, which reside within seemingly conserved segments of ribosomal proteins...
February 24, 2018: Molecular Biology and Evolution
Alvaro Orell, Vanessa Tripp, Victor Aliaga-Tobar, Sonja-Verena Albers, Vinicius Maracaja-Coutinho, Lennart Randau
Non-coding RNAs (ncRNA) are involved in essential biological processes in all three domains of life. The regulatory potential of ncRNAs in Archaea is, however, not fully explored. In this study, RNA-seq analyses identified a set of 29 ncRNA transcripts in the hyperthermophilic archaeon Sulfolobus acidocaldarius that were differentially expressed in response to biofilm formation. The most abundant ncRNA of this set was found to be resistant to RNase R treatment (RNase R resistant RNA, RrrR(+)) due to duplex formation with a reverse complementary RNA (RrrR(-))...
February 26, 2018: Nucleic Acids Research
Nina Gunde-Cimerman, Ana Plemenitaš, Aharon Oren
Hypersaline environments with salt concentrations up to NaCl saturation are inhabited by a great diversity of microorganisms belonging to the three domains of life. They all must cope with the low water activity of their environment, but different strategies exist to provide osmotic balance of the cells' cytoplasm with the salinity of the medium. One option used by many halophilic Archaea and a few representatives of the Bacteria is to accumulate salts, mainly KCl and to adapt the entire intracellular machinery to function in the presence of molar concentrations of salts...
February 26, 2018: FEMS Microbiology Reviews
Serina L Robinson, Jonathan P Badalamenti, Anthony G Dodge, Lambros J Tassoulas, Lawrence P Wackett
Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the fastest-growing isolate, Herbaspirillum sp. BH-1 and identified genes encoding putative biuret hydrolases (BHs). We purified and characterized a functional BH enzyme from Herbaspirillum sp. BH-1 and two other bacteria from divergent phyla...
March 12, 2018: Environmental Microbiology
Michael Hemkemeyer, Anja B Dohrmann, Bent T Christensen, Christoph C Tebbe
Genetic fingerprinting demonstrated in previous studies that differently sized soil particle fractions (PSFs; clay, silt, and sand with particulate organic matter (POM)) harbor microbial communities that differ in structure, functional potentials and sensitivity to environmental conditions. To elucidate whether specific bacterial or archaeal taxa exhibit preference for specific PSFs, we examined the diversity of PCR-amplified 16S rRNA genes by high-throughput sequencing using total DNA extracted from three long-term fertilization variants (unfertilized, fertilized with minerals, and fertilized with animal manure) of an agricultural loamy sand soil and their PSFs...
2018: Frontiers in Microbiology
Tao Zhou, Xingzhe Yao, Jinfeng Wang, Yingang Feng
Domain of unknown function 61 (DUF61) family proteins widely exist in archaea and the genes of DUF61 proteins in crenarchaea are in an operon containing two genes of box C/D RNA protein complexes. Here we report the solution NMR structure of DUF61 family member protein SSO0941, from the hyperthermophilic archaeon Sulfolobus solfataricus. SSO0941 has a rigid core structure and flexible N- and C-terminal regions as well as a negatively-charged independent C-terminal helix. The core structure consists of N- and C-terminal subdomains, in which the C-terminal subdomain shows significant structural similarity with several nucleic acid binding proteins...
March 8, 2018: Journal of Structural Biology
Natalia Alfaro, María Fdz-Polanco, Fernando Fdz-Polanco, Israel Díaz
The performance of a pilot ceramic membrane bioreactor for the bioconversion of H2 and CO2 to bioCH4 was evaluated in thermophilic conditions. The loading rate was between 10 and 30 m3  H2 /m3 reactor  d and the system transformed 95% of H2 fed. The highest methane yield found was 0.22 m3  CH4 /m3  H2 , close to the maximum stoichiometric value (0.25 m3  CH4 /m3  H2 ) thus indicating that archaeas employed almost all H2 transferred to produce CH4 . kL a value of 268 h-1 was reached at 30 m3  H2 /m3 reactor  d...
February 23, 2018: Bioresource Technology
Alyne Marem, Debora N Okamoto, Lilian C G Oliveira, Diego M Ruiz, Roberto A Paggi, Marcia Y Kondo, Iuri E Gouvea, Maria A Juliano, Rosana E de Castro, Luiz Juliano, Marcelo Y Icimoto
Nep (Natrialba magadii extracellular protease) is a halolysin-like peptidase secreted by the haloalkaliphilic archaeon Natrialba magadii. Many extracellular proteases have been characterized from archaea to bacteria as adapted to hypersaline environments retaining function and stability until 4.0 M NaCl. As observed in other secreted halolysins, this stability can be related to the presence of a C-terminal extension (CTE) sequence. In the present work, we compared the biochemical properties of recombinant Nep protease with the truncated form at the 134 amino acids CTE (Nep∆CTE), that was more active in 4 M NaCl than the non-truncated wild type enzyme...
March 7, 2018: International Journal of Biological Macromolecules
Carolina Díaz-Cárdenas, Angela Cantillo, Laura Yinneth Rojas, Tito Sandoval, Susana Fiorentino, Jorge Robles, Freddy A Ramos, María Mercedes Zambrano, Sandra Baena
The original version of this article (Diaz-Cardenas et al. 2017) unfortunately contained a mistake in Fig. 1. The pie chart of Fig. 1 should explain the distribution of the relative abundance of the Bacteria and Archaea strains isolated at Zipaquirá salt mine: Proteobacteria 39%; Actinobacteria 9%, Bacteroidetes 1%, Archaea 3% and Firmicutes 48% instead of NOMBRE DE CATEGORIA [PORCENTAJE]. The corrected Fig. 1 and caption are given below.
March 9, 2018: AMB Express
Frank Hille, Hagen Richter, Shi Pey Wong, Majda Bratovič, Sarah Ressel, Emmanuelle Charpentier
In bacteria and archaea, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system against phages and other foreign genetic elements. Here, we review the biology of the diverse CRISPR-Cas systems and the major progress achieved in recent years in understanding the underlying mechanisms of the three stages of CRISPR-Cas immunity: adaptation, crRNA biogenesis, and interference. The ecology and regulation of CRISPR-Cas in the context of phage infection, the roles of these systems beyond immunity, and the open questions that propel the field forward are also discussed...
March 8, 2018: Cell
Cindy J Castelle, Jillian F Banfield
The recent recovery of genomes for organisms from phyla with no isolated representative (candidate phyla) via cultivation-independent genomics enabled delineation of major new microbial lineages, namely the bacterial candidate phyla radiation (CPR), DPANN archaea, and Asgard archaea. CPR and DPANN organisms are inferred to be mostly symbionts, and some are episymbionts of other microbial community members. Asgard genomes encode typically eukaryotic systems, and their inclusion in phylogenetic analyses results in placement of eukaryotes as a branch within Archaea...
March 8, 2018: Cell
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No abstract text is available yet for this article.
March 8, 2018: Cell
Omar Federico Ordoñez, María Cecilia Rasuk, Mariana Noelia Soria, Manuel Contreras, María Eugenia Farías
Biofilms, microbial mats, and microbialites dwell under highly limiting conditions (high salinity, extreme aridity, pH, and elevated arsenic concentration) in the Andean Puna. Only recent pioneering studies have described the microbial diversity of different Altiplano lakes and revealed their unexpectedly diverse microbial communities. Arsenic metabolism is proposed to be an ancient mechanism to obtain energy by microorganisms. Members of Bacteria and Archaea are able to exploit arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite...
March 8, 2018: Microbial Ecology
Rabea Jesser, Juliane Behler, Christian Benda, Viktoria Reimann, Wolfgang R Hess
Specialized RNA endonucleases are critical for efficient activity of the CRISPR-Cas defense mechanisms against invading DNA or RNA. Cas6-type enzymes are the RNA endonucleases in many type I and type III CRISPR-Cas systems. These enzymes are diverse and critical residues involved in the recognition and cleavage of RNA substrates are not universally conserved. Cas6 endonucleases associated with the CRISPR-Cas subtypes I-A, I-B, I-C, I-E and I-F, as well as III-B have been studied from four archaea and three bacteria thus far...
March 8, 2018: RNA Biology
Jingwei Xu, Qiang He, Hong Li, Chun Yang, Yinliang Wang, Hainan Ai
Sewer system is an important source of methane formation and emission. Although some models were developed to predict methane production in sewers, the impact of microorganism amount was indicated indirectly. Here, seven laboratory scale sewers with varied wall-shear stresses were established. The biofilm thickness, microorganism amount, DO distribution, microorganism community in the biofilms and methane production in the sewers were measured. Based on experimental data, an empirical model was developed to directly describe the relationship between methane production, microorganism amount and wall-shear stress...
March 7, 2018: AMB Express
William H Lewis, Kacper M Sendra, T Martin Embley, Genoveva F Esteban
Many anaerobic ciliated protozoa contain organelles of mitochondrial ancestry called hydrogenosomes. These organelles generate molecular hydrogen that is consumed by methanogenic Archaea, living in endosymbiosis within many of these ciliates. Here we describe a new species of anaerobic ciliate, Trimyema finlayi n. sp., by using silver impregnation and microscopy to conduct a detailed morphometric analysis. Comparisons with previously published morphological data for this species, as well as the closely related species, Trimyema compressum , demonstrated that despite them being similar, both the mean cell size and the mean number of somatic kineties are lower for T...
2018: Frontiers in Microbiology
Alejandro Palomo, Anders G Pedersen, S Jane Fowler, Arnaud Dechesne, Thomas Sicheritz-Pontén, Barth F Smets
The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing bacteria (β-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonia oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira. Unlike canonical Nitrospira, comammox Nitrospira genomes lack genes for assimilatory nitrite reduction, suggesting that they have lost the potential to use external nitrite nitrogen sources...
March 7, 2018: ISME Journal
Yuying Deng, Zhenxing Huang, Wenquan Ruan, Hengfeng Miao, Wansheng Shi, Mingxing Zhao
Using lignocellulosic materials as substrates, ruminal microbiota were co-inoculated with anaerobic sludge at different loading rates (LR) to study the microbial community in the semi-continuous mode. The results indicated that the highest CH4 yield reached 0.22 L/g volatile solid at LR of 4 g/L/day, which obtained 56-58% of the theoretical value. In the steady stage with LR of 2-4 g/L/day and slurry recirculation, copies of total archaea increased. Especially the Methanobacteriales increased significantly (p < 0...
March 6, 2018: Applied Microbiology and Biotechnology
Diego Rivera Gelsinger, Jocelyne DiRuggiero
Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions...
March 5, 2018: Genes
Patricia Rojas, Nuria Rodriguez, Vicenta de la Fuente, Daniel Sánchez-Mata, Ricardo Amils, Jose Luis Sanz Martin
Soda lakes are inhabited by important haloalkaliphilic microbial communities that are well adapted to these extreme characteristics. The surface waters of the haloalkaline Mono Lake (CA, USA) are alkaline but, in contrast to its bottom waters, do not present high salinity. We have studied the microbiota present in the shoreline sediments of Mono Lake using next-generation sequencing techniques. The statistical indexes showed that Bacteria had a higher richness, diversity and evenness compared to Archaea. 17 phyla and 8 "candidate divisions", were identified among the Bacteria, with a predominance of the phyla <i>Firmicutes</i>, <i>Proteobacteria </i>and <i>Bacteroidetes</i>...
March 6, 2018: Canadian Journal of Microbiology
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