Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella

Science ◽  
2006 ◽  
Vol 313 (5784) ◽  
pp. 236-238 ◽  
Author(s):  
W. W. Navarre
Keyword(s):  
Gc Content ◽  
Foreign Dna

scholarly journals The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Sergey A. Shmakov ◽  
Vassilii Sitnik ◽  
Kira S. Makarova ◽  
Yuri I. Wolf ◽  
Konstantin V. Severinov ◽  
...  
Keyword(s):  
Dark Matter ◽  
Gc Content ◽  
Common Source ◽  
Microbial Genomes ◽  
Viral Genomes ◽  
Genetic Elements ◽  
Foreign Dna ◽  
Species Specific ◽  
Almost All ◽  
Defense Function

ABSTRACT Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR “dark matter.” We performed a comprehensive analysis of the spacers from all CRISPR- cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. IMPORTANCE The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match any sequences in the current databases, and of these, only a minority correspond to known parasitic elements. We show that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome. We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements.

scholarly journals CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa

2020 ◽  
Author(s):  
Rachel M. Wheatley ◽  
R. Craig MacLean
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gc Content ◽  
Adaptive Immune System ◽  
Opportunistic Pathogen ◽  
Adaptive Immune ◽  
Foreign Dna ◽  
Integrative Conjugative Elements ◽  
Major Target

AbstractCRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged an important model system for understanding CRISPR-Cas function. Across the diversity of P. aeruginosa, active CRISPR-Cas systems are associated with smaller genomes and a reduced GC content, suggesting that CRISPR-Cas inhibits the acquisition of foreign DNA. Although phage are the major target of CRISPR-Cas spacers, more than 80% of isolates with an active CRISPR-Cas system have spacers that target integrative conjugative elements (ICE) or the conserved conjugative transfer machinery used by plasmids and ICE. Consistent with these results, genomes containing active CRISPR-Cas systems harbor a lower abundance of both prophage and ICE. Crucially, spacers in genomes with active CRISPR-Cas systems map to ICE and phage that are integrated into the chromosomes of closely related genomes lacking CRISPR-Cas immunity, providing direct evidence that CRISPR-Cas constrains horizontal gene transfer in these lineages. In conclusion, we find that CRISPR-Cas acts as an important constraint to horizontal gene transfer, suggesting that CRISPR-Cas may constrain the ability of this pathogen to adapt to new niches and stressors.

scholarly journals An updated assembly strategy helps parsing the cryptic mitochondrial genome evolution in plants

2021 ◽  
Author(s):  
Yanlei Feng ◽  
Xiaoguo Xiang ◽  
Zhixi Fu ◽  
Xiaohua Jin
Keyword(s):  
Large Scale ◽  
Gc Content ◽  
Comparative Genomic ◽  
Genomic Analyses ◽  
Evolutionary Trajectories ◽  
Mitochondrial Genome Evolution ◽  
Foreign Dna ◽  
Almost All ◽  
Horizontal Transfers ◽  
Main Chromosome

AbstractAlthough plant mitogenomes are small in size, their variations are no less than any other complex genomes. They are under rapid structure and size changes. These characters make the assembly a great challenge. This caused two intertwined problems, a slow growth of known mitogenomes and a poor knowledge of their evolution. In many species, mitogenome becomes the last genome that undeciphered. To have a better understanding of these two questions, we developed a strategy using short sequencing reads and combining current tools and manual steps to get high quality mitogenomes. This strategy allowed us to assembled 23 complete mitogenomes from 5 families in Fagales. Our large-scale comparative genomic analyses indicated the composition of mitogenomes is very mosaic that “horizontal transfers” can be from almost all taxa in seed plants. The largest mitogenome contains more homologous DNA with other Fagales, rather than unique sequences. Besides of real HGTs, sometimes mitovirus, nuclear insertions and other third-part DNA could also produce HGT-like sequences, accounting partially for the unusual evolutionary trajectories, including the cryptic size expansion in Carpinus. Mitochondrial plasmid was also found. Its lower GC content indicates that it may be only an interphase of a foreign DNA before accepting by the main chromosome. Our methods and results provide new insights into the assembly and mechanisms of mitogenome evolution.

scholarly journals The CRISPR spacer space is dominated by sequences from the species-specific mobilome

2017 ◽  
Author(s):  
Sergey A. Shmakov ◽  
Vassilii Sitnik ◽  
Kira S. Makarova ◽  
Yuri I. Wolf ◽  
Konstantin V. Severinov ◽  
...  
Keyword(s):  
Dark Matter ◽  
Gc Content ◽  
Common Source ◽  
Direct Repeats ◽  
Microbial Genomes ◽  
Viral Genomes ◽  
Perfect Correlation ◽  
Foreign Dna ◽  
Species Specific ◽  
Almost All

The CRISPR-Cas is the prokaryotic adaptive immunity system that stores memory of past encounters with foreign DNA in spacers that are inserted between direct repeats in CRISPR arrays 1,2. Only for a small fraction of the spacers, homologous sequences, termed protospacers, are detectable in viral, plasmid or microbial genomes 3,4. The rest of the spacers remain the CRISPR “dark matter”. We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1 to about 19% of the spacers (∼7% global average). Among the detected protospacers, the majority, typically, 80 to 90%, originate from viral genomes, and among the rest, the most common source are genes integrated in microbial chromosomes but involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC-content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes show a nearly perfect correlation and are almost identical. Given the near absence of self-targeting spacers, these findings are best compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes.

scholarly journals CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa

2020 ◽  
Author(s):  
Rachel M. Wheatley ◽  
R. Craig MacLean
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gc Content ◽  
Adaptive Immune System ◽  
Opportunistic Pathogen ◽  
Evolutionary Mechanisms ◽  
Foreign Dna ◽  
Integrative Conjugative Elements ◽  
Major Target

AbstractCRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged as an important model system for understanding CRISPR-Cas function. Across the diversity of P. aeruginosa, active CRISPR-Cas systems are associated with smaller genomes and higher GC content, suggesting that CRISPR-Cas inhibits the acquisition of foreign DNA. Although phage is the major target of CRISPR-Cas spacers, more than 80% of isolates with an active CRISPR-Cas system have spacers that target integrative conjugative elements (ICE) or the conserved conjugative transfer machinery used by plasmids and ICE. Consistent with these results, genomes containing active CRISPR-Cas systems harbour a lower abundance of both prophage and ICE. Crucially, spacers in genomes with active CRISPR-Cas systems map to ICE and phage that are integrated into the chromosomes of closely related genomes lacking CRISPR-Cas immunity. We propose that CRISPR-Cas acts as an important constraint to horizontal gene transfer, and the evolutionary mechanisms that ensure its maintenance or drive its loss are key to the ability of this pathogen to adapt to new niches and stressors.

scholarly journals Diatom centromeres suggest a mechanism for nuclear DNA acquisition

2017 ◽  
Vol 114 (29) ◽  
pp. E6015-E6024 ◽  
Author(s):  
Rachel E. Diner ◽  
Chari M. Noddings ◽  
Nathan C. Lian ◽  
Anthony K. Kang ◽  
Jeffrey B. McQuaid ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Gc Content ◽  
Nuclear Genome ◽  
Artificial Chromosomes ◽  
Conserved Sequence ◽  
Foreign Dna ◽  
Sequence Requirements ◽  
Simple Sequence ◽  
Dna Acquisition

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequence features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.

Introduction of foreign DNA into walled plant cells via liposomes injected into the vacuole: a preliminary study

1990 ◽  
Vol 79 (1) ◽  
pp. 184-189
Author(s):  
W. J. Lucas ◽  
A. Lansing ◽  
J. R. de Wet ◽  
V. Walbot
Keyword(s):  
Plant Cells ◽  
Preliminary Study ◽  
Foreign Dna
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