Microbial diversity in extreme environments

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(4), P. 219 - 235

Published: Nov. 9, 2021

Language: Английский

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Accurate and complete genomes from metagenomes

Genome Research, Journal Year: 2020, Volume and Issue: 30(3), P. 315 - 333

Published: March 1, 2020

Genomes are an integral component of the biological information about organism; thus, more complete genome, informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, first reported sequences manually curated to completion. However, bottleneck imposed by requirement for isolates precluded genomic insights vast majority microbial life. Shotgun sequencing communities, referred initially as community genomics subsequently genome-resolved metagenomics, can circumvent this limitation obtaining metagenome-assembled (MAGs); but gaps, local assembly errors, chimeras, contamination fragments other limit value these genomes. Here, we discuss genome curation improve and, in some cases, achieve (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably very complex systems such soil sediment. Through analysis 7000 published isolate genomes, verify cumulative GC skew combination with metrics establish sequence accuracy. The identified potential misassemblies reference isolated bacteria repeat that likely gave rise them. We methods could be implemented bioinformatic approaches ensure metabolic evolutionary analyses based on high-quality

Language: Английский

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Pharokka: a fast scalable bacteriophage annotation tool

Bioinformatics, Journal Year: 2022, Volume and Issue: 39(1)

Published: Dec. 1, 2022

Abstract Summary In recent years, there has been an increasing interest in bacteriophages, which led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, is a need for rapid and consistent annotation tool dedicated bacteriophages. Existing tools either are not designed specifically bacteriophages or web- email-based require significant manual curation, makes their integration into bioinformatic pipelines challenging. Pharokka was created provide that annotates genomes easily, rapidly consistently with standards compliant outputs. Moreover, requires only two lines code install use takes under 5 min run average 50-kb genome. Availability implementation implemented Python available as bioconda package using ‘conda -c pharokka’. The source on GitHub (https://github.com/gbouras13/pharokka). tested Linux-64 MacOSX machines Windows Linux Virtual Machine.

Language: Английский

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Structure of the bacterial ribosome at 2 Å resolution

eLife, Journal Year: 2020, Volume and Issue: 9

Published: Sept. 14, 2020

Using cryo-electron microscopy (cryo-EM), we determined the structure of Escherichia coli 70S ribosome with a global resolution 2.0 Å. The maps reveal unambiguous positioning protein and RNA residues, their detailed chemical interactions, modifications. Notable features include first examples isopeptide thioamide backbone substitutions in ribosomal proteins, former likely conserved all domains life. also extensive solvation small (30S) subunit, interactions A-site P-site tRNAs, mRNA, antibiotic paromomycin. models bacterial presented here now allow deeper phylogenetic analysis components including structural conservation to level solvation. high quality should enable future analyses basis for translation aid development robust tools cryo-EM modeling refinement.

Language: Английский

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A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(23)

Published: June 3, 2021

Significance Mechanisms of many human chronic diseases involve abnormal action the immune system and/or altered metabolism. The microbiome, an important regulator metabolic and immune-related phenotypes, has been shown to be associated with or participate in development a variety diseases. Viruses bacteria (i.e., “phages”) are ubiquitous mysterious, several studies have that phages exert great control over behavior—and misbehavior—of their host bacteria. This study uses techniques discover analyze 45,000 viruses bodies. abundance 2,000 specific is found correlate common

Language: Английский

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Noncanonical Roles of tRNAs: tRNA Fragments and Beyond

Annual Review of Genetics, Journal Year: 2020, Volume and Issue: 54(1), P. 47 - 69

Published: Aug. 25, 2020

As one of the most abundant and conserved RNA species, transfer RNAs (tRNAs) are well known for their role in reading codons on messenger translating them into proteins. In this review, we discuss noncanonical functions tRNAs. These include tRNAs as precursors to novel small molecules derived from tRNAs, also called tRNA-derived fragments, that across species have diverse different biological processes, including regulating protein translation, Argonaute-dependent gene silencing, more. Furthermore, biosynthesis other regulatory pathways, nutrient sensing, splicing, transcription, retroelement regulation, immune response, apoptosis, is reviewed. Genome organization sequence variation tRNA genes discussed light functions. Lastly, recent applications genome editing microbiome sequencing.

Language: Английский

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Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: 48(4), P. 2000 - 2012

Published: Dec. 13, 2019

CRISPR-Cas systems provide prokaryotes with adaptive immune functions against viruses and other genetic parasites. In contrast to all types of systems, type IV has remained largely overlooked. Here, we describe a previously uncharted diversity gene cassettes, primarily encoded by plasmid-like elements from diverse prokaryotic taxa. Remarkably, via comprehensive analysis their CRISPR spacer content, these were found exhibit strong bias towards the targeting plasmids. Our data indicate that have diverged those host-related adopt role in mediating conflicts between Furthermore, find evidence for cross-talk certain I co-exist intracellularly, thus providing simple answer enigmatic absence adaptation modules. Collectively, our results lead expansion reclassification novel insights into biological function evolution elusive systems.

Language: Английский

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Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(8), P. 2366 - 2378

Published: March 1, 2021

Abstract In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse but little is about infecting these microorganisms. Here, we probed metagenomes from seven geographically across global oceans assess viral diversity, virus–host interaction, virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons inhabiting other ecosystems reveal that seep harbour considerable unexplored diversity. Most display high degrees endemism fluid flux being one main drivers community composition. silico predictions linked 14.2% populations many belonging poorly understood candidate bacterial archaeal phyla. Lysis was predicted be a predominant lifestyle based lineage-specific virus/host abundance ratios. Metabolic prokaryotic genomes AMGs suggest influence hydrocarbon biodegradation at seeps, as well carbon, sulfur nitrogen cycling via virus-induced mortality and/or augmentation. Overall, findings diversity biogeography indicate how may manipulate ecology biogeochemistry.

Language: Английский

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Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria

Annual Review of Genetics, Journal Year: 2020, Volume and Issue: 54(1), P. 93 - 120

Published: Aug. 28, 2020

Prokaryotes have developed numerous defense strategies to combat the constant threat posed by diverse genetic parasites that endanger them. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas loci guard their hosts with an adaptive immune system against foreign nucleic acids. Protection starts immunization phase, in which pieces of invader's genome, known as spacers, are captured and integrated into CRISPR locus after infection. Next, during targeting spacers transcribed RNAs (crRNAs) guide CRISPR-associated (Cas) nucleases destroy DNA or RNA. Here we describe many different molecular mechanisms how they interconnected phase through a third CRISPR-Cas response: primed spacer acquisition. In this Cas proteins direct crRNA-guided acquisition additional achieve more rapid robust population.

Language: Английский

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A Review on the Mechanism and Applications of CRISPR/Cas9/Cas12/Cas13/Cas14 Proteins Utilized for Genome Engineering

Molecular Biotechnology, Journal Year: 2022, Volume and Issue: 65(3), P. 311 - 325

Published: Sept. 27, 2022

Language: Английский

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