The Flexible Genome of Acidophilic Prokaryotes

2021 ◽  
pp. 231-266
Author(s):  
Simon Beard ◽  
Francisco J. Ossandon ◽  
Douglas E. Rawlings ◽  
Raquel Quatrini
Keyword(s):  
Flexible Genome

scholarly journals Properties and abundance of overlapping genes in viruses

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Timothy E Schlub ◽  
Edward C Holmes
Keyword(s):  
Genome Structure ◽  
Virus Genome ◽  
Overlapping Genes ◽  
Genome Database ◽  
Dna Viruses ◽  
Virus Family ◽  
Flexible Genome ◽  
Gene Overlap ◽  
Reference Genomes ◽  
Rna And Dna

Abstract Overlapping genes are commonplace in viruses and play an important role in their function and evolution. However, aside from studies on specific groups of viruses, relatively little is known about the extent and nature of gene overlap and its determinants in viruses as a whole. Here, we present an extensive characterisation of gene overlap in viruses through an analysis of reference genomes present in the NCBI virus genome database. We find that over half the instances of gene overlap are very small, covering <10 nt, and 84 per cent are <50 nt in length. Despite this, 53 per cent of all viruses still contained a gene overlap of 50 nt or larger. We also investigate several predictors of gene overlap such as genome structure (single- and double-stranded RNA and DNA), virus family, genome length, and genome segmentation. This revealed that gene overlap occurs more frequently in DNA viruses than in RNA viruses, and more frequently in single-stranded viruses than in double-stranded viruses. Genome segmentation is also associated with gene overlap, particularly in single-stranded DNA viruses. Notably, we observed a large range of overlap frequencies across families of all genome types, suggesting that it is a common evolutionary trait that provides flexible genome structures in all virus families.

scholarly journals Rapid evolutionary turnover of mobile genetic elements drives microbial resistance to viruses

2021 ◽  
Author(s):  
Fatima Aysha Hussain ◽  
Javier Dubert ◽  
Joseph Elsherbini ◽  
Mikayla Murphy ◽  
David VanInsberghe ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Bacterial Genome ◽  
Mobile Genetic Elements ◽  
Bacterial Strains ◽  
Genomic Features ◽  
Genetic Elements ◽  
Flexible Genome ◽  
In The Wild ◽  
Putative Phage ◽  
Resistance To Viruses

AbstractAlthough it is generally accepted that viruses (phages) drive bacterial evolution, how these dynamics play out in the wild remains poorly understood. Here we show that the arms race between phages and their hosts is mediated by large and highly diverse mobile genetic elements. These phage-defense elements display exceedingly fast evolutionary turnover, resulting in differential phage susceptibility among clonal bacterial strains while phage receptors remain invariant. Protection afforded by multiple elements is cumulative, and a single bacterial genome can harbor as many as 18 putative phage-defense elements. Overall, elements account for 90% of the flexible genome amongst closely related strains. The rapid turnover of these elements demonstrates that phage resistance is unlinked from other genomic features and that resistance to phage therapy might be as easily acquired as antibiotic resistance.

scholarly journals A Flexible Genome-Scale SARS-CoV-2 Clone Resource

2020 ◽  
Author(s):  
Dae-Kyum Kim ◽  
Jennifer J. Knapp ◽  
Da Kuang ◽  
Aditya Chawla ◽  
Patricia Cassonnet ◽  
...  
Keyword(s):  
Antiviral Agents ◽  
Health Crisis ◽  
Major Health ◽  
Coding Sequences ◽  
Global Pandemic ◽  
The World ◽  
Flexible Genome ◽  
Widespread Availability ◽  
Genome Scale ◽  
Rapid Transfer

The world is facing a major health crisis, the global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus, for which no approved antiviral agents or vaccines are currently available. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available via Addgene. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.

scholarly journals Genome-engineering with CRISPR-Cas9 in the mosquitoAedes aegypti

2014 ◽  
Author(s):  
Kathryn E Kistler ◽  
Leslie B Vosshall ◽  
Benjamin J Matthews
Keyword(s):  
Genome Engineering ◽  
Germ Line ◽  
Dna Binding Protein ◽  
Model Organisms ◽  
Homing Endonucleases ◽  
Loss Of Function ◽  
Dna Base ◽  
Different Types ◽  
Flexible Genome ◽  
Repair Mechanisms

The mosquitoAedes aegyptiis a potent vector of the Chikungunya, yellow fever, and Dengue viruses, which result in hundreds of millions of infections and over 50,000 human deaths per year. Loss-of-function mutagenesis inAe. aegyptihas been established with TALENs, ZFNs, and homing endonucleases, which require the engineering of DNA-binding protein domains to generate target specificity for a particular stretch of genomic DNA. Here, we describe the first use of the CRISPR-Cas9 system to generate targeted, site-specific mutations inAe. aegypti. CRISPR-Cas9 relies on RNA-DNA base-pairing to generate targeting specificity, resulting in cheaper, faster, and more flexible genome-editing reagents. We investigate the efficiency of reagent concentrations and compositions, demonstrate the ability of CRISPR-Cas9 to generate several different types of mutations via disparate repair mechanisms, and show that stable germ-line mutations can be readily generated at the vast majority of genomic loci tested. This work offers a detailed exploration into the optimal use of CRISPR-Cas9 inAe. aegyptithat should be applicable to non-model organisms previously out of reach of genetic modification.

scholarly journals Marine-freshwater prokaryotic transitions require extensive changes in the proteome

2019 ◽  
Author(s):  
Pedro J. Cabello-Yeves ◽  
Francisco Rodriguez-Valera
Keyword(s):  
Core Genome ◽  
Ion Concentration ◽  
Microbial Genomes ◽  
Bacterial Phyla ◽  
The Core ◽  
Marine Habitats ◽  
Flexible Genome ◽  
Freshwater Habitats ◽  
Protein Location ◽  
Marine Salt

AbstractThe comparison of microbial genomes found in either freshwater or marine habitats indicated that in some cases (SynechococcusandCa. Pelagibacter) there were notable differences in the global isoelectric point (pI) of proteins. We have analysed global metagenomic proteomes and have added more prokaryotes to extend the pI comparison. Without exception, in a set that included archaea and multiple bacterial phyla, the proteome pI distribution varied, with more acidic values in marine and neutral/basic in freshwater microbes. Four pairs of highly related prokaryotes of marine and freshwater origin revealed marked differences manifested mostly in the residues located at the protein surface. This study has also shown that the magnitude of the change depended on protein location (secreted > cytoplasmic > transmembrane) and affected proteins encoded at both core and flexible genome. Our results point to a very extensive variation taking place in microbes when they move from marine (salt-rich) to freshwater habitats. These adaptations would require long evolutionary times to produce changes involving many genes in the core genome. They also point to significant differences in the physiology, probably at the level of membrane functioning, bioenergetics, intracellular ion concentration and pH (or all of them).

scholarly journals Long read metagenomics, the next step?

2020 ◽  
Author(s):  
Jose M. Haro-Moreno ◽  
Mario López-Pérez ◽  
Francisco Rodríguez-Valera
Keyword(s):  
Error Rate ◽  
Population Genomics ◽  
Short Read ◽  
Short Reads ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Oxford Nanopore ◽  
Flexible Genome ◽  
Long Read ◽  
Generation Sequencing

ABSTRACTBackgroundThird-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, 2nd generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in allowing assembly of microbes with high microdiversity or retrieving the flexible (adaptive) compartment of prokaryotic genomes.ResultsHere we have used different 3rd generation techniques to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared Oxford Nanopore and PacBio last generation technologies with the classical approach using Illumina short reads followed by assembly. PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. Long reads allow efficient direct retrieval of complete genes (473M/Tb) and operons before assembly, facilitating annotation and compensates the limitations of short reads or short-read assemblies. MetaSPAdes was the most appropriate assembly program when used in combination with short reads. The assemblies of the long reads allow also the reconstruction of much more complete metagenome-assembled genomes, even from microbes with high microdiversity. The flexible genome of reconstructed MAGs is much more complete and allows rescuing more adaptive genes.ConclusionsFor most applications of metagenomics, from community structure analysis to ecosystem functioning, long-reads should be applied whenever possible. Particularly for in-silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be used from raw reads, before a computing-demanding (and potentially artefactual) assembly step.

scholarly journals Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus

2019 ◽  
Vol 116 (32) ◽  
pp. 15774-15783 ◽  
Author(s):  
Claudio Hidalgo-Cantabrana ◽  
Yong Jun Goh ◽  
Meichen Pan ◽  
Rosemary Sanozky-Dawes ◽  
Rodolphe Barrangou
Keyword(s):  
Genome Editing ◽  
Fluorescent Protein ◽  
Stop Codon ◽  
Mucosal Vaccine ◽  
Green Fluorescent Protein Gene ◽  
Type I ◽  
Lactobacillus Crispatus ◽  
Class 1 ◽  
Flexible Genome ◽  
Green Fluorescent

CRISPR-Cas systems are now widely used for genome editing and transcriptional regulation in diverse organisms. The compact and portable nature of class 2 single effector nucleases, such as Cas9 or Cas12, has facilitated directed genome modifications in plants, animals, and microbes. However, most CRISPR-Cas systems belong to the more prevalent class 1 category, which hinges on multiprotein effector complexes. In the present study, we detail how the native type I-E CRISPR-Cas system, with a 5′-AAA-3′ protospacer adjacent motif (PAM) and a 61-nucleotide guide CRISPR RNA (crRNA) can be repurposed for efficient chromosomal targeting and genome editing in Lactobacillus crispatus, an important commensal and beneficial microbe in the vaginal and intestinal tracts. Specifically, we generated diverse mutations encompassing a 643-base pair (bp) deletion (100% efficiency), a stop codon insertion (36%), and a single nucleotide substitution (19%) in the exopolysaccharide priming-glycosyl transferase (p-gtf). Additional genetic targets included a 308-bp deletion (20%) in the prophage DNA packaging Nu1 and a 730-bp insertion of the green fluorescent protein gene downstream of enolase (23%). This approach enables flexible alteration of the formerly genetically recalcitrant species L. crispatus, with potential for probiotic enhancement, biotherapeutic engineering, and mucosal vaccine delivery. These results also provide a framework for repurposing endogenous CRISPR-Cas systems for flexible genome targeting and editing, while expanding the toolbox to include one of the most abundant and diverse systems found in nature.

scholarly journals Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics

2021 ◽  
Vol 12 ◽  
Author(s):  
Jose M. Haro-Moreno ◽  
Mario López-Pérez ◽  
Francisco Rodriguez-Valera
Keyword(s):  
Water Column ◽  
Error Rate ◽  
Population Genomics ◽  
Enhanced Recovery ◽  
Third Generation ◽  
Long Reads ◽  
Flexible Genome ◽  
Long Read ◽  
Second Generation Sequencing ◽  
Generation Sequencing

Third-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, second-generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in the assembly of microbes with high microdiversity and retrieval of the flexible (adaptive) fraction of prokaryotic genomes. Here, we have used a third-generation technique to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared PacBio Sequel II with the classical approach using Illumina Nextseq short reads followed by assembly to study the metagenome. Long reads allow for efficient direct retrieval of complete genes avoiding the bias of the assembly step. Besides, the application of long reads on metagenomic assembly allows for the reconstruction of much more complete metagenome-assembled genomes (MAGs), particularly from microbes with high microdiversity such as Pelagibacterales. The flexible genome of reconstructed MAGs was much more complete containing many adaptive genes (some with biotechnological potential). PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. For most applications of metagenomics, from community structure analysis to ecosystem functioning, long reads should be applied whenever possible. Specifically, for in silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be analyzed from raw reads before a computationally demanding (and potentially artifactual) assembly step.

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