scholarly journals The Expanded Universe of Prokaryotic Argonaute Proteins

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Sergei Ryazansky ◽  
Andrey Kulbachinskiy ◽  
Alexei A. Aravin
Keyword(s):  
Rna Interference ◽  
Nucleic Acid ◽  
Genome Engineering ◽  
Bacterial Species ◽  
Host Cells ◽  
Bacterial Strains ◽  
Domains Of Life ◽  
Genomic Studies ◽  
Basic Biology

ABSTRACT Members of the ancient family of Argonaute (Ago) proteins are present in all domains of life. The common feature of Ago proteins is the ability to bind small nucleic acid guides and use them for sequence-specific recognition—and sometimes cleavage—of complementary targets. While eukaryotic Ago (eAgo) proteins are key players in RNA interference and related pathways, the properties and functions of these proteins in archaeal and bacterial species have just started to emerge. We undertook comprehensive exploration of prokaryotic Ago (pAgo) proteins in sequenced genomes and revealed their striking diversity in comparison with eAgos. Many pAgos contain divergent variants of the conserved domains involved in interactions with nucleic acids, while having extra domains that are absent in eAgos, suggesting that they might have unusual specificities in the nucleic acid recognition and cleavage. Many pAgos are associated with putative nucleases, helicases, and DNA binding proteins in the same gene or operon, suggesting that they are involved in target processing. The great variability of pAgos revealed by our analysis opens new ways for exploration of their functions in host cells and for their use as potential tools in genome editing. IMPORTANCE The eukaryotic Ago proteins and the RNA interference pathways they are involved in are widely used as a powerful tool in research and as potential therapeutics. In contrast, the properties and functions of prokaryotic Ago (pAgo) proteins have remained poorly understood. Understanding the diversity and functions of pAgos holds a huge potential for discovery of new cellular pathways and novel tools for genome manipulations. Only few pAgos have been characterized by structural or biochemical approaches, while previous genomic studies discovered about 300 proteins in archaeal and eubacterial genomes. Since that time the number of bacterial strains with sequenced genomes has greatly expanded, and many previously sequenced genomes have been revised. We undertook comprehensive analysis of pAgo proteins in sequenced genomes and almost tripled the number of known genes of this family. Our research thus forms a foundation for further experimental characterization of pAgo functions that will be important for understanding of the basic biology of these proteins and their adoption as a potential tool for genome engineering in the future.

scholarly journals The expanded universe of prokaryotic Argonaute proteins

2018 ◽  
Author(s):  
Sergei Ryazansky ◽  
Andrey Kulbachinskiy ◽  
Alexei A. Aravin
Keyword(s):  
Rna Interference ◽  
Nucleic Acid ◽  
Horizontal Gene Transfer ◽  
Bacterial Species ◽  
Dna Binding Proteins ◽  
Host Cells ◽  
Argonaute Proteins ◽  
Key Players ◽  
Domains Of Life ◽  
The Common

AbstractThe members of the ancient family of Argonaute (Ago) proteins are present in all domains of life. The common feature of Ago proteins is the ability to bind small nucleic acid guides and use them for sequence-specific recognition – and sometimes cleavage – of complementary targets. While eukaryotic Ago (eAgo) proteins are key players in RNA interference and related pathways, the properties and functions of these proteins in archaeal and bacterial species have just started to emerge. We undertook comprehensive exploration of prokaryotic Ago (pAgo) proteins in sequenced genomes and almost tripled the number of previously analyzed genes of this family. In comparison with eAgos, pAgos are highly diverse and have likely spread by horizontal gene transfer. Many pAgos contain divergent variants of the conserved domains involved in interactions with nucleic acids and in target cleavage, while having extra domains that are absent in eAgos, suggesting that they might have unusual specificities in the nucleic acid recognition and processing. Many pAgos, including catalytically inactive variants, are associated with putative nucleases, helicases and DNA binding proteins in the same gene or operon, suggesting that they are involved in DNA processing. The great diversity of pAgos revealed by our analysis opens new ways for exploration of their functions in host cells and their use as potential tools in genome editing.

scholarly journals Characterization of gtf, a Glucosyltransferase Gene in the Genomes of Pediococcus parvulus and Oenococcus oeni, Two Bacterial Species Commonly Found in Wine

2008 ◽  
Vol 74 (13) ◽  
pp. 4079-4090 ◽  
Author(s):  
Marguerite Dols-Lafargue ◽  
Hyo Young Lee ◽  
Claire Le Marrec ◽  
Alain Heyraud ◽  
Gérard Chambat ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Oenococcus Oeni ◽  
Mobile Elements ◽  
The Other ◽  
Bacterial Strains ◽  
Model Medium ◽  
Polysaccharide Synthesis

ABSTRACT “Ropiness” is a bacterial alteration in wines, beers, and ciders, caused by β-glucan-synthesizing pediococci. A single glucosyltransferase, Gtf, controls ropy polysaccharide synthesis. In this study, we show that the corresponding gtf gene is also present on the chromosomes of several strains of Oenococcus oeni isolated from nonropy wines. gtf is surrounded by mobile elements that may be implicated in its integration into the chromosome of O. oeni. gtf is expressed in all the gtf + strains, and β-glucan is detected in the majority of these strains. Part of this β-glucan accumulates around the cells forming a capsule, while the other part is liberated into the medium together with heteropolysaccharides. Most of the time, this polymer excretion does not lead to ropiness in a model medium. In addition, we show that wild or recombinant bacterial strains harboring a functional gtf gene (gtf +) are more resistant to several stresses occurring in wine (alcohol, pH, and SO2) and exhibit increased adhesion capacities compared to their gtf mutant variants.

scholarly journals Regulation of Hypercompetence in Legionella pneumophila

2004 ◽  
Vol 186 (12) ◽  
pp. 3814-3825 ◽  
Author(s):  
Jessica A. Sexton ◽  
Joseph P. Vogel
Keyword(s):  
Legionella Pneumophila ◽  
Bacterial Species ◽  
Single Species ◽  
Great Promise ◽  
Dna Uptake ◽  
Bacterial Strains ◽  
Aerobic Growth ◽  
Laboratory Conditions ◽  
Normal Laboratory

ABSTRACT Although many bacteria are known to be naturally competent for DNA uptake, this ability varies dramatically between species and even within a single species, some isolates display high levels of competence while others seem to be completely nontransformable. Surprisingly, many nontransformable bacterial strains appear to encode components necessary for DNA uptake. We believe that many such strains are actually competent but that this ability has been overlooked because standard laboratory conditions are inappropriate for competence induction. For example, most strains of the gram-negative bacterium Legionella pneumophila are not competent under normal laboratory conditions of aerobic growth at 37°C. However, it was previously reported that microaerophilic growth at 37°C allows L. pneumophila serogroup 1 strain AA100 to be naturally transformed. Here we report that another L. pneumophila serogroup 1 strain, Lp02, can also be transformed under these conditions. Moreover, Lp02 can be induced to high levels of competence by a second set of conditions, aerobic growth at 30°C. In contrast to Lp02, AA100 is only minimally transformable at 30°C, indicating that Lp02 is hypercompetent under these conditions. To identify potential causes of hypercompetence, we isolated mutants of AA100 that exhibited enhanced DNA uptake. Characterization of these mutants revealed two genes, proQ and comR, that are involved in regulating competence in L. pneumophila. This approach, involving the isolation of hypercompetent mutants, shows great promise as a method for identifying natural transformation in bacterial species previously thought to be nontransformable.

scholarly journals Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces

2011 ◽  
Vol 78 (2) ◽  
pp. 511-518 ◽  
Author(s):  
Yohei Watanabe ◽  
Fumiko Nagai ◽  
Masami Morotomi
Keyword(s):  
Bacterial Species ◽  
Short Chain Fatty Acids ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Gi Tract ◽  
Bacterial Strains ◽  
High Sequence Identity ◽  
Healthy Human ◽  
Content Type

ABSTRACTIsolation, cultivation, and characterization of the intestinal microorganisms are important for understanding the comprehensive physiology of the human gastrointestinal (GI) tract microbiota. Here, we isolated two novel bacterial strains, YIT 12067Tand YIT 12068, from the feces of healthy human adults. Phylogenetic analysis indicated that they belonged to the same species and were most closely related toPhascolarctobacterium faeciumACM 3679T, with 91.4% to 91.5% 16S rRNA gene sequence similarities, respectively. Substrate availability tests revealed that the isolates used only succinate; they did not ferment any other short-chain fatty acids or carbohydrates tested. When these strains were cocultured with the xylan-utilizing and succinate-producing bacteriumParaprevotella xylaniphilaYIT 11841T, in medium supplemented with xylan but not succinate, their cell numbers became 2 to 3 orders of magnitude higher than those of the monoculture; succinate became undetectable, and propionate was formed. Database analysis revealed that over 200 uncultured bacterial clones from the feces of humans and other mammals showed high sequence identity (>98.7%) to YIT 12067T. Real-time PCR analysis also revealed that YIT 12067T-like bacteria were present in 21% of human fecal samples, at an average level of 3.34 × 108cells/g feces. These results indicate that YIT 12067T-like bacteria are distributed broadly in the GI tract as subdominant members that may adapt to the intestinal environment by specializing to utilize the succinate generated by other bacterial species. The phylogenetic and physiological properties of YIT 12067Tand YIT 12068 suggest that these strains represent a novel species, which we have designatedPhascolarctobacterium succinatutenssp. nov.

scholarly journals THE IDENTIFICATION, PRODUCTION AND CHARACTERIZATION OF NATTOKINASE, BACTERIOCIN FROM BACTERIAL SPECIES

2019 ◽  
Vol 2 (4) ◽  
pp. 91
Author(s):  
Lal Krishna
Keyword(s):  
Enzyme Activity ◽  
Bacillus Subtilis ◽  
Pathogenic Bacteria ◽  
Blood Clot ◽  
Bacterial Species ◽  
Antagonistic Activity ◽  
Bacterial Strains ◽  
Wide Range

The study was aimed at identification, production and characterization of nattokinase, bacteriocin from bacterial species. Nattokinase and bacteriocins finds a wide range of applications in Pharmaceutical industry, health care and medicine. Nattokinase is a highly active fibrinolytic enzyme secreted by Bacillus subtilis and bacteriocins are proteinaceous toxins produced by Lactobacillus to inhibit the growth of closely related bacterial strains. Bacillus subtilis and Lactobacillus isolates shown positive results to microscopic, biochemical analysis.  The nattokinase and bacteriocins were produced by optimizing the media. The enzymes were purified by ammonium sulfate precipitation and HPLC. The enzyme activity for nattokinase was found at 7 mg/ml, pH 8.0 and temperature 48 ºC and the enzyme activity for bacteriocin was found at 3.9 mg/ml, pH 6.5 and temperature 30 °C. Bacteriocins from Lactobacillus showed good antagonistic activity against pathogenic bacteria. Nattokinase from Bacillus subtilis played a significant role in thrombolytic and anti-coagulation at in vitro. The results indicated that the pure enzyme has a potential in dissolving blood clot.

scholarly journals Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages

2021 ◽  
Author(s):  
Alexander J Meeske ◽  
Matthew C Johnson ◽  
Logan T Hille ◽  
Benjamin P Kleinstiver ◽  
Joseph Bondy-Denomy
Keyword(s):  
Nucleic Acid ◽  
Rna Cleavage ◽  
Nucleic Acid Binding ◽  
Bacterial Strains ◽  
Bioinformatics Analyses ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Bona Fide ◽  
Adaptive Immune Systems

CRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements, like bacteriophages and plasmids. To overcome CRISPR immunity, phages have evolved diverse families of anti-CRISPR proteins (Acrs), each of which inhibits the nucleic acid binding or cleavage activities of specific Cas protein families. Recently, Lin et al. (2020) described the discovery and characterization of 7 different Acr families (AcrVIA1-7) that inhibit type VI-A CRISPR systems, which use the nuclease Cas13a to perform RNA-guided RNA cleavage. In this Matters Arising article, we detail several inconsistencies that question the results reported in the Lin et al. (2020) study. These include inaccurate bioinformatics analyses, as well as reported experiments involving bacterial strains that are impossible to construct. The authors were unable to provide their published strains with which we might reproduce their experiments. We independently tested the Acr sequences described in Lin et al. (2020) in two different Cas13 inhibition assays, but could not detect anti-CRISPR activity. Taken together, our data and analyses prompt us to question the claim that AcrVIA1-7 reported in Lin et al. are bona fide type VI anti-CRISPR proteins.

scholarly journals Characterization of Two Unique Cold-Active Lipases Derived from a Novel Deep-Sea Cold Seep Bacterium

2021 ◽  
Vol 9 (4) ◽  
pp. 802
Author(s):  
Chenchen Guo ◽  
Rikuan Zheng ◽  
Ruining Cai ◽  
Chaomin Sun ◽  
Shimei Wu
Keyword(s):  
Deep Sea ◽  
Bacterial Species ◽  
Deep Ocean ◽  
Cold Seep ◽  
Bacterial Strains ◽  
E Coli ◽  
Cold Active ◽  
Genes Encoding ◽  
Potential Inhibitors

The deep ocean microbiota has unexplored potential to provide enzymes with unique characteristics. In order to obtain cold-active lipases, bacterial strains isolated from the sediment of the deep-sea cold seep were screened, and a novel strain gcc21 exhibited a high lipase catalytic activity, even at the low temperature of 4 °C. The strain gcc21 was identified and proposed to represent a new species of Pseudomonas according to its physiological, biochemical, and genomic characteristics; it was named Pseudomonas marinensis. Two novel encoding genes for cold-active lipases (Lipase 1 and Lipase 2) were identified in the genome of strain gcc21. Genes encoding Lipase 1 and Lipase 2 were respectively cloned and overexpressed in E. coli cells, and corresponding lipases were further purified and characterized. Both Lipase 1 and Lipase 2 showed an optimal catalytic temperature at 4 °C, which is much lower than those of most reported cold-active lipases, but the activity and stability of Lipase 2 were much higher than those of Lipase 1 under different tested pHs and temperatures. In addition, Lipase 2 was more stable than Lipase 1 when treated with different metal ions, detergents, potential inhibitors, and organic solvents. In a combination of mutation and activity assays, catalytic triads of Ser, Asp, and His in Lipase 1 and Lipase 2 were demonstrated to be essential for maintaining enzyme activity. Phylogenetic analysis showed that both Lipase 1 and Lipase 2 belonged to lipase family III. Overall, our results indicate that deep-sea cold seep is a rich source for novel bacterial species that produce potentially unique cold-active enzymes.

scholarly journals High-Quality Nucleic Acid Isolation from Hard-to-Lyse Bacterial Strains Using PMAP-36, a Broad-Spectrum Antimicrobial Peptide

2021 ◽  
Vol 22 (8) ◽  
pp. 4149
Author(s):  
Hye-sun Cho ◽  
Munjeong Choi ◽  
Yunjung Lee ◽  
Hyoim Jeon ◽  
Byeongyong Ahn ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Broad Spectrum ◽  
Bacterial Species ◽  
Rna Isolation ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
High Quality ◽  
Nucleic Acid Isolation

The efficiency of existing cell lysis methods to isolate nucleic acids from diverse bacteria varies depending on cell wall structures. This study tested a novel idea of using broad-spectrum antimicrobial peptides to improve the lytic efficiency of hard-to-lyse bacteria and characterized their differences. The lysis conditions of Staphylococcus aureus using recombinant porcine myeloid antimicrobial peptide 36 (PMAP-36), a broad-spectrum pig cathelicidin, was optimized, and RNA isolation was performed with cultured pellets of ten bacterial species using various membranolytic proteins. Additionally, three other antimicrobial peptides, protegrin-1 (PG-1), melittin, and nisin, were evaluated for their suitability as the membranolytic agents of bacteria. However, PMAP-36 use resulted in the most successful outcomes in RNA isolation from diverse bacterial species. The amount of total RNA obtained using PMAP-36 increased by ~2-fold compared to lysozyme in Salmonella typhimurium. Streptococci species were refractory to all lytic proteins tested, although the RNA yield from PMAP-36 treatment was slightly higher than that from other methods. PMAP-36 use produced high-quality RNA, and reverse transcription PCR showed the efficient amplification of the 16S rRNA gene from all tested strains. Additionally, the results of genomic DNA isolation were similar to those of RNA isolation. Thus, our findings present an additional option for high quality and unbiased nucleic acid isolation from microbiomes or challenging bacterial strains.

scholarly journals Glaciochemistry and pigment producing ability of bacteria from roof of the world, the glaciers of Karakoram, Pakistan

2021 ◽  
Author(s):  
Noor Hassan ◽  
Muhammad Rafiq ◽  
Abdul Haleem ◽  
Aamir Ali Shah ◽  
Fariha Hasan
Keyword(s):  
Bacterial Species ◽  
Rpob Gene ◽  
Mountain Range ◽  
Bacterial Strains ◽  
Mountain Ranges ◽  
The World ◽  
Alternative Sources ◽  
Geochemical Analyses ◽  
Pigmented Bacteria

Abstract The Karakoram Mountain Range (KMR) is one of the largest mountain ranges in the world, with ~ 37% of its area glaciated. Here, we present the geochemistry of ice, sediment and meltwaters sampled from Ghulmet, Ghulkin and Hopar glaciers of the Karakoram Range, Pakistan, in addition to the first information on the diversity of pigmented bacteria evaluated using culture-dependent techniques. Geochemical analyses revealed Ca2+ and SO42− to be the most abundant cation and anion species across all glacial samples, respectively. Total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) were found in the sediments of all glaciers studied in current research. Bacterial species were capable of producing a variety of different pigments, including alloxanthin, astaxanthin, bacterioruberin, β-carotene, 19'-hexanoyloxyfucoxanthin, peridinin, violacein and zeaxanthin. Culturable bacterial diversity was studied using two molecular biomarkers, 16S rRNA and rpoB gene, with a total of 82 bacterial strains representing 25 genera identified across all glacial samples. This study provides the first characterization of glacier-associated, pigment-producing bacterial communities from the KMR. Findings are important for considerations of alternative sources of conventional pigment production in industrial fields.

Cultivation and characterization of symbiotic bacteria from the gut of Reticulitermes chinensis

2016 ◽  
Vol 1 (1) ◽  
pp. 3 ◽  
Author(s):  
Hao Fang ◽  
Wen Chen ◽  
Baojun Wang ◽  
Xiaojuan Li ◽  
Shuang-Jiang Liu ◽  
...  
Keyword(s):  
Cellulose Degradation ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Symbiotic Bacteria ◽  
Nitrogen Recycling ◽  
Bacterial Strains ◽  
High Sequence Similarity

The complex symbiotic relationship between wood-feeding termites and microorganisms inhabiting their intestinal tracts is a fascinating phenomenon in nature. To understand the physiological functions of symbiotic micro-organisms, bacteria were isolated from the gut homogenate of Reticulitermes chinensis with different media and culture conditions. Under aerobic conditions, 105 bacterial strains were isolated with 1/5 LB medium, 1/3 TSB medium and a modified basal mineral medium, MM-4. Most dominant isolates were bacteria in the genera Bacillus (27.6%) and Lactococcus (21.9%). Under anaerobic conditions, 60 bacterial strains were isolated with 1/5 LB medium, 1/3 TSB medium and a modified Peptone-Yeast medium. The predominant isolates were bacteria in the genus Enterobacter (41.7%) and Citrobacter (33.3%). Many of these bacterial isolates shared high sequence similarity (>98%) in 16S rRNA genes to bacterial clones obtained from the same termite and the other wood-feeding termites or cockroaches. Several bacterial species such as Deinococcus and Gryllotalpicola were isolated from termite gut for the first time. Characterization of these isolates showed that (i) most of Enterobacteriaceae and Lactococcus strains were able to hydrolyze uric acid; and (ii) many of the Bacillus and Streptomyces strains presented endo-β-1,4-glucanase activity. The preliminary results of this work gave us hints of possible functions of symbiotic bacteria in nitrogen recycling and cellulose degradation in the gut of wood-feeding termites

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