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 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 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 Occurrence ofBordetellaInfection in Pigs in Northern India

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Sandeep Kumar ◽  
Bhoj R. Singh ◽  
Monika Bhardwaj ◽  
Vidya Singh
Keyword(s):  
Plasmid Profile ◽  
Antigen Detection ◽  
Bordetella Bronchiseptica ◽  
Atrophic Rhinitis ◽  
Serum Samples ◽  
Northern India ◽  
Antimicrobial Sensitivity ◽  
Nasal Swabs ◽  
Species Specific ◽  
Almost All

Bordetella bronchisepticainfection causing atrophic rhinitis in pigs is reported from almost all countries. In the present study, occurrence ofBordetellainfection in apparently healthy pigs was determined in 392 pigs sampled to collect 358 serum samples and 316 nasal swabs from Northern India by conventional bacterioscopy, detection of antigen with multiplex polymerase chain reaction (mPCR), and detection of antibodies with microagglutination test (MAT) and enzyme linked immune-sorbent assay (ELISA).Bordetella bronchisepticacould be isolated from six (1.92%) nasal swabs. Although isolates varied significantly in their antimicrobial sensitivity, they had similar plasmid profile. The genus specific and species specific amplicons were detected from 8.2% and 4.4% nasal swabs using mPCR withalcgene (genus specific) andflagene andfim2 gene (species specific) primers, respectively. Observations revealed that there may be other bordetellae infecting pigs because about 50% of the samples positive using mPCR for genus specific amplicons failed to confirm presence ofB. bronchiseptica. Of the pig sera tested with MAT and ELISA forBordetellaantibodies, 67.6% and 86.3% samples, respectively, were positive. For antigen detection mPCR was more sensitive than conventional bacterioscopy while for detection of antibodies neither of the two tests (MAT and ELISA) had specificity in relation to antigen detection. Study indicated high prevalence of infection in swine herds in Northern India.

scholarly journals FAME (v1.0): a simple module to simulate the effect of planktonic foraminifer species-specific habitat on their oxygen isotopic content

2018 ◽  
Vol 11 (9) ◽  
pp. 3587-3603 ◽  
Author(s):  
Didier M. Roche ◽  
Claire Waelbroeck ◽  
Brett Metcalfe ◽  
Thibaut Caley
Keyword(s):  
Late Holocene ◽  
Simple Module ◽  
Climatic Conditions ◽  
Model Data ◽  
Planktonic Foraminifer ◽  
Planktonic Foraminifers ◽  
Oxygen Isotopic ◽  
Species Specific ◽  
Almost All ◽  
Multiproxy Approach

Abstract. The oxygen-18 to oxygen-16 ratio recorded in fossil planktonic foraminifer shells has been used for over 50 years in many geoscience applications. However, different planktonic foraminifer species generally yield distinct signals, as a consequence of their specific living habitats in the water column and along the year. This complexity is usually not taken into account in model–data integration studies. To overcome this shortcoming, we developed the Foraminifers As Modeled Entities (FAME) module. The module predicts the presence or absence of commonly used planktonic foraminifers and their oxygen-18 values. It is only forced by hydrographic data and uses a very limited number of parameters, almost all derived from culture experiments. FAME performance is evaluated using the Multiproxy Approach for the Reconstruction of the Glacial Ocean surface (MARGO) Late Holocene planktonic foraminifer calcite oxygen-18 and abundance datasets. The application of FAME to a simple cooling scenario demonstrates its utility to predict changes in planktonic foraminifer oxygen-18 to oxygen-16 ratio in response to changing climatic conditions.

scholarly journals A bacteriophage infecting Mesorhizobium species has a prolate capsid and shows similarities to a family of Caulobacter crescentus phages

2020 ◽  
pp. 1-14
Author(s):  
K.M. Damitha Gunathilake ◽  
Anupama P. Halmillawewa ◽  
Keith D. MacKenzie ◽  
Benjamin J. Perry ◽  
Christopher K. Yost ◽  
...  
Keyword(s):  
Caulobacter Crescentus ◽  
Gc Content ◽  
Nucleotide Metabolism ◽  
Gene Arrangement ◽  
Modular Organization ◽  
Trna Genes ◽  
Direct Repeats ◽  
Structural Genes ◽  
Replication Mechanism ◽  
Replication Module

Mesorhizobium phage vB_MloS_Cp1R7A-A1 was isolated from soil planted with chickpea in Saskatchewan. It is dissimilar in sequence and morphology to previously described rhizobiophages. It is a B3 morphotype virus with a distinct prolate capsid and belongs to the tailed phage family Siphoviridae. Its genome has a GC content of 60.3% and 238 predicted genes. Putative functions were predicted for 57 genes, which include 27 tRNA genes with anticodons corresponding to 18 amino acids. This represents the highest number of tRNA genes reported yet in a rhizobiophage. The gene arrangement shows a partially modular organization. Most of the structural genes are found in one module, whereas tRNA genes are in another. Genes for replication, recombination, and nucleotide metabolism form the third module. The arrangement of the replication module resembles the replication module of Enterobacteria phage T5, raising the possibility that it uses a recombination-based replication mechanism, but there is also a suggestion that a T7-like replication mechanism could be used. Phage termini appear to be long direct repeats of just over 12 kb in length. Phylogenetic analysis revealed that Cp1R7A-A1 is more closely related to PhiCbK-like Caulobacter phages and other B3 morphotype phages than to other rhizobiophages sequenced thus far.

scholarly journals Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jian Zeng ◽  
Yan Wang ◽  
Ju Zhang ◽  
Shixing Yang ◽  
Wen Zhang
Keyword(s):  
Gc Content ◽  
Cloacal Swab ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Viral Metagenomics ◽  
Toxin Gene ◽  
Microbial Genomes ◽  
The Family ◽  
Zonula Occludens Toxin ◽  
Reference Strains

AbstractMembers of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.

scholarly journals Molecular Analysis of VanA Outbreak ofEnterococcus faeciumin Two Warsaw Hospitals: The Importance of Mobile Genetic Elements

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Ewa Wardal ◽  
Katarzyna Markowska ◽  
Dorota Żabicka ◽  
Marta Wróblewska ◽  
Małgorzata Giemza ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Molecular Data ◽  
Multidrug Resistant ◽  
Common Source ◽  
Hospital Acquired Infections ◽  
Vancomycin Resistant ◽  
Clonal Variability ◽  
Almost All ◽  
Hospital Acquired ◽  
Vntr Analysis

Vancomycin-resistantEnterococcus faeciumrepresents a growing threat in hospital-acquired infections. Two outbreaks of this pathogen from neighboring Warsaw hospitals have been analyzed in this study. Pulsed-field gel electrophoresis (PFGE) ofSmaI-digested DNA, multilocus VNTR analysis (MLVA), and multilocus sequence typing (MLST) revealed a clonal variability of isolates which belonged to three main lineages (17, 18, and 78) of nosocomialE. faecium. All isolates were multidrug resistant and carried several resistance, virulence, and plasmid-specific genes. Almost all isolates shared the same variant of Tn1546transposon, characterized by the presence of insertion sequence ISEf1and a point mutation in thevanAgene. In the majority of cases, this transposon was located on 50 kb or 100 kb pRUM-related plasmids, which lacked, however, theaxe-txetoxin-antitoxin genes. 100 kb plasmid was easily transferred by conjugation and was found in various clonal backgrounds in both institutions, while 50 kb plasmid was not transferable and occurred solely in MT159/ST78 strains that disseminated clonally in one institution. Although molecular data indicated the spread of VRE between two institutions or a potential common source of this alert pathogen, epidemiological investigations did not reveal the possible route by which outbreak strains disseminated.

scholarly journals Raw Sewage Harbors Diverse Viral Populations

mBio ◽  
2011 ◽  
Vol 2 (5) ◽  
Author(s):  
Paul G. Cantalupo ◽  
Byron Calgua ◽  
Guoyan Zhao ◽  
Ayalkibet Hundesa ◽  
Adam D. Wier ◽  
...  
Keyword(s):  
Genetic Material ◽  
Viral Diversity ◽  
Emerging Pathogens ◽  
Viral Genomes ◽  
Untreated Wastewater ◽  
Virus Diversity ◽  
Double Stranded Dna ◽  
Large Numbers ◽  
Ideal System ◽  
Species Specific

ABSTRACTAt this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity.IMPORTANCEAt this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that the viral universe is far more vast and diverse than previously suspected.

scholarly journals Hsp70 targets Hsp100 chaperones to substrates for protein disaggregation and prion fragmentation

2012 ◽  
Vol 198 (3) ◽  
pp. 387-404 ◽  
Author(s):  
Juliane Winkler ◽  
Jens Tyedmers ◽  
Bernd Bukau ◽  
Axel Mogk
Keyword(s):  
Protein Aggregates ◽  
Specific Targeting ◽  
Terminal Domain ◽  
Independent Association ◽  
Species Specific ◽  
Almost All ◽  
Hsp100 Chaperones

Hsp100 and Hsp70 chaperones in bacteria, yeast, and plants cooperate to reactivate aggregated proteins. Disaggregation relies on Hsp70 function and on ATP-dependent threading of aggregated polypeptides through the pore of the Hsp100 AAA+ hexamer. In yeast, both chaperones also promote propagation of prions by fibril fragmentation, but their functional interplay is controversial. Here, we demonstrate that Hsp70 chaperones were essential for species-specific targeting of their Hsp100 partner chaperones ClpB and Hsp104, respectively, to heat-induced protein aggregates in vivo. Hsp70 inactivation in yeast also abrogated Hsp104 targeting to almost all prions tested and reduced fibril mobility, which indicates that fibril fragmentation by Hsp104 requires Hsp70. The Sup35 prion was unique in allowing Hsp70-independent association of Hsp104 via its N-terminal domain, which, however, was nonproductive. Hsp104 overproduction even outcompeted Hsp70 for Sup35 prion binding, which explains why this condition prevented Sup35 fragmentation and caused prion curing. Our findings indicate a conserved mechanism of Hsp70–Hsp100 cooperation at the surface of protein aggregates and prion fibrils.

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