scholarly journals Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes

2022 ◽  
Author(s):  
Fabai Wu ◽  
Daan R. Speth ◽  
Alon Philosof ◽  
Antoine Crémière ◽  
Aditi Narayanan ◽  
...  
Keyword(s):  
Viral Genome ◽  
Scaling Laws ◽  
Continuous Process ◽  
Mobile Elements ◽  
Gene Repertoire ◽  
Bacterial Gene ◽  
Size Dependent ◽  
Sequence Of Events ◽  
A Genome ◽  
Eukaryotic Genomes

AbstractEukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation–decentralized innovation–hierarchical import model that accounts for the emergence of eukaryotic complexity.

scholarly journals The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes

2015 ◽  
Vol 32 (6) ◽  
pp. 835-842 ◽  
Author(s):  
Filippo Utro ◽  
Valeria Di Benedetto ◽  
Davide F.V. Corona ◽  
Raffaele Giancarlo
Keyword(s):  
Closed Form ◽  
Dna Sequence ◽  
Chemical Properties ◽  
Supplementary Information ◽  
Information Theoretic ◽  
Nucleosome Organization ◽  
A Genome ◽  
Intrinsic Complexity ◽  
Mathematical Formulas ◽  
Eukaryotic Genomes

Abstract Motivation: Thanks to research spanning nearly 30 years, two major models have emerged that account for nucleosome organization in chromatin: statistical and sequence specific. The first is based on elegant, easy to compute, closed-form mathematical formulas that make no assumptions of the physical and chemical properties of the underlying DNA sequence. Moreover, they need no training on the data for their computation. The latter is based on some sequence regularities but, as opposed to the statistical model, it lacks the same type of closed-form formulas that, in this case, should be based on the DNA sequence only. Results: We contribute to close this important methodological gap between the two models by providing three very simple formulas for the sequence specific one. They are all based on well-known formulas in Computer Science and Bioinformatics, and they give different quantifications of how complex a sequence is. In view of how remarkably well they perform, it is very surprising that measures of sequence complexity have not even been considered as candidates to close the mentioned gap. We provide experimental evidence that the intrinsic level of combinatorial organization and information-theoretic content of subsequences within a genome are strongly correlated to the level of DNA encoded nucleosome organization discovered by Kaplan et al. Our results establish an important connection between the intrinsic complexity of subsequences in a genome and the intrinsic, i.e. DNA encoded, nucleosome organization of eukaryotic genomes. It is a first step towards a mathematical characterization of this latter ‘encoding’. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: [email protected].

scholarly journals The Essential Human Cytomegalovirus Proteins pUL77 and pUL93 Are Structural Components Necessary for Viral Genome Encapsidation

2016 ◽  
Vol 90 (13) ◽  
pp. 5860-5875 ◽  
Author(s):  
Eva Maria Borst ◽  
Rudolf Bauerfeind ◽  
Anne Binz ◽  
Thomas Min Stephan ◽  
Sebastian Neuber ◽  
...  
Keyword(s):  
Human Cytomegalovirus ◽  
Viral Genome ◽  
Fluorescent Protein ◽  
Unit Length ◽  
Start Codon ◽  
Nuclear Targeting ◽  
Reading Frame ◽  
A Genome ◽  
Genome Encapsidation ◽  
Insight Into

ABSTRACTSeveral essential viral proteins are proposed to participate in genome encapsidation of human cytomegalovirus (HCMV), among them pUL77 and pUL93, which remain largely uncharacterized. To gain insight into their properties, we generated an HCMV mutant expressing a pUL77-monomeric enhanced green fluorescent protein (mGFP) fusion protein and a pUL93-specific antibody. Immunoblotting demonstrated that both proteins are incorporated into capsids and virions. Conversely to data suggesting internal translation initiation sites within the UL93 open reading frame (ORF), we provide evidence that pUL93 synthesis commences at the first start codon. In infected cells, pUL77-mGFP was found in nuclear replication compartments and dot-like structures, colocalizing with capsid proteins. Immunogold labeling of nuclear capsids revealed that pUL77 is present on A, B, and C capsids. Pulldown of pUL77-mGFP revealed copurification of pUL93, indicating interaction between these proteins, which still occurred when capsid formation was prevented. Correct subnuclear distribution of pUL77-mGFP required pUL93 as well as the major capsid protein (and thus probably the presence of capsids), but not the tegument protein pp150 or the encapsidation protein pUL52, demonstrating that pUL77 nuclear targeting occurs independently of the formation of DNA-filled capsids. When pUL77 or pUL93 was missing, generation of unit-length genomes was not observed, and only empty B capsids were produced. Taken together, these results show that pUL77 and pUL93 are capsid constituents needed for HCMV genome encapsidation. Therefore, the task of pUL77 seems to differ from that of its alphaherpesvirus orthologue pUL25, which exerts its function subsequent to genome cleavage-packaging.IMPORTANCEThe essential HCMV proteins pUL77 and pUL93 were suggested to be involved in viral genome cleavage-packaging but are poorly characterized both biochemically and functionally. By producing a monoclonal antibody against pUL93 and generating an HCMV mutant in which pUL77 is fused to a fluorescent protein, we show that pUL77 and pUL93 are capsid constituents, with pUL77 being similarly abundant on all capsid types. Each protein is required for genome encapsidation, as the absence of either pUL77 or pUL93 results in a genome packaging defect with the formation of empty capsids only. This distinguishes pUL77 from its alphaherpesvirus orthologue pUL25, which is enriched on DNA-filled capsids and exerts its function after the viral DNA is packaged. Our data for the first time describe an HCMV mutant with a fluorescent capsid and provide insight into the roles of pUL77 and pUL93, thus contributing to a better understanding of the HCMV encapsidation network.

scholarly journals Gene-dependent yeast cell death pathway requires AP-3 vesicle trafficking leading to vacuole membrane permeabilization

2021 ◽  
Author(s):  
Zachary D Stolp ◽  
Madhura Kulkarni ◽  
Yining Liu ◽  
Chengzhang Zhu ◽  
Alizay Jalisi ◽  
...  
Keyword(s):  
Cell Death ◽  
Yeast Cell ◽  
Vesicle Trafficking ◽  
Membrane Integrity ◽  
Time Lapse ◽  
Membrane Permeabilization ◽  
Cell Death Pathway ◽  
Sequence Of Events ◽  
A Genome ◽  
Lysosome Membrane

Unicellular eukaryotes are suggested to undergo self-inflicted destruction. However, molecular details are sparse by comparison to the mechanisms of cell death known for human cells and animal models. Here we report a molecular pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization and cell death. Following exposure to heat-ramp conditions, a model of environmental stress, we observed that yeast cell death occurs over several hours, suggesting an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 adaptor complex. AP-3 promotes stress-induced cell death through its Arf1-GTPase-dependent vesicle trafficking function, which is required to transport and install proteins on the vacuole/lysosome membrane, including a death-promoting protein kinase Yck3. Time-lapse microscopy revealed a sequence of events where AP-3-dependent vacuole permeability occurs hours before the loss of plasma membrane integrity. An AP-3-dependent cell death pathway appears to be conserved in the human pathogen Cryptococcus neoformans.

scholarly journals Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering

2019 ◽  
Author(s):  
Joël Klein ◽  
Manon Neilen ◽  
Marcel van Verk ◽  
Guido Van den Ackerveken ◽  
Bas E. Dutilh
Keyword(s):  
Downy Mildew ◽  
Dna Isolation ◽  
Spinacia Oleracea ◽  
Gene Repertoire ◽  
Phylogenetic Distance ◽  
Annotate Orfs ◽  
A Genome ◽  
Spinach Downy Mildew ◽  
Insight Into ◽  
Spinach Leaves

Peronospora effusa (previously known as  P. farinosa f. sp. spinaciae, and here referred to as Pfs) is an obligate biotrophic oomycete that causes downy mildew on spinach (Spinacia oleracea). To combat this destructive disease resistant cultivars are continually bred. However, new Pfs races rapidly break the employed resistance genes. To get insight into the gene repertoire of Pfs and identify infection-related genes, the genome of the first reference race, Pfs1, was sequenced, assembled, and annotated. Due to the obligate biotrophic nature of this pathogen, material for DNA isolation can only be collected from infected spinach leaves that, however, also contain many other microorganisms. The obtained sequences are, therefore, considered a metagenome. To filter and obtain Pfs sequences we utilized the CAT tool to taxonomically annotate ORFs residing on long sequences of a genome pre-assembly. This study is the first to show that CAT filtering performs well on eukaryotic contigs. Based on the taxonomy, determined on multiple ORFs, contaminating long sequences and corresponding reads were removed. Filtered reads were re-assembled to provide a clean and improved Pfs genome sequence of 32.40 Mbp consisting of 8,635 scaffolds. Transcript sequencing of a range of infection time points aided the prediction of a total of 13,277 gene models, including 99 RXLR(-like) effector, and 14 putative Crinkler genes. Comparative analysis identified common features in the secretomes of different obligate biotrophic oomycetes, regardless of their phylogenetic distance. Their secretomes are generally smaller, compared to hemibiotrophic and necrotrophic oomycete species. We observe a reduction in proteins involved cell wall degradation, in Nep1-like proteins (NLPs), proteins with PAN/apple domains, and host translocated effectors. The genome of Pfs1 will be instrumental in studying downy mildew virulence and for understanding the molecular adaptations by which new isolates break spinach resistance.

Size-dependent magnetic and inductive heating properties of Fe3O4 nanoparticles: scaling laws across the superparamagnetic size

2018 ◽  
Vol 20 (18) ◽  
pp. 12879-12887 ◽  
Author(s):  
Jeotikanta Mohapatra ◽  
Fanhao Zeng ◽  
Kevin Elkins ◽  
Meiying Xing ◽  
Madhav Ghimire ◽  
...  
Keyword(s):  
Iron Oxide ◽  
Fe3o4 Nanoparticles ◽  
Absorption Rate ◽  
Scaling Laws ◽  
Specific Absorption Rate ◽  
Nanoparticle Size ◽  
Inductive Heating ◽  
Specific Absorption ◽  
Size Dependent

An efficient heat activating mediator with an enhanced specific absorption rate (SAR) value is attained via control of the iron oxide (Fe3O4) nanoparticle size from 3 to 32 nm.

scholarly journals Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jeanne Wilbrandt ◽  
Bernhard Misof ◽  
Kristen A. Panfilio ◽  
Oliver Niehuis
Keyword(s):  
Structural Properties ◽  
Gene Structure ◽  
Comparative Studies ◽  
Gene Repertoire ◽  
Manual Annotation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gene Sets ◽  
A Genome ◽  
Gene Models

Abstract Background The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. Results Our results show that the subset of genes chosen for manual annotation by a research community (3.5–7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species’ gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. Conclusions In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.

scholarly journals The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0139075 ◽  
Author(s):  
Abdel Belkorchia ◽  
Cyrielle Gasc ◽  
Valérie Polonais ◽  
Nicolas Parisot ◽  
Nicolas Gallois ◽  
...  
Keyword(s):  
Gene Repertoire ◽  
Eukaryotic Genomes

scholarly journals Transposable elements activity reveals punctuated patterns of speciation in mammals

2016 ◽  
Author(s):  
Marco Ricci ◽  
Valentina Peona ◽  
Etienne Guichard ◽  
Cristian Taccioli ◽  
Alessio Boattini
Keyword(s):  
Transposable Elements ◽  
Adaptive Radiation ◽  
Essential Role ◽  
Relative Rate ◽  
Mammalian Species ◽  
Punctuated Equilibria ◽  
A Genome ◽  
Eukaryotic Genomes

ABSTRACTTransposable elements (TEs) play an essential role in shaping eukaryotic genomes and generating variability. Our “Cold Genome” hypothesis postulates that speciation and TEs activity are strongly related in mammals. In order to test this hypothesis, we created two new parameters: the Density of Insertion (DI) and the Relative Rate of Speciation (RRS). The DI is the ratio between the number of TE insertions in a genome and its size, whereas the RRS is a conditional parameter designed to identify potential speciation bursts. Thus, by analyzing TEs insertions in mammals, we defined the genomes as “hot” (low DI) and “cold” (high DI). Then, comparing TEs activity among 16 intra-order pairs of mammalian species, 4 superorders of Eutheria and 29 taxonomical families of the whole Mammalia class, we showed that taxa with positive RRS correlate with “hot” genomes, whereas taxa with negative RRS correlate with “cold” genomes. In addition, our study supports the “Punctuated Equilibria” theory in mammals for both adaptive radiation and stasis.

scholarly journals Mobile genetic element insertions drive antibiotic resistance across pathogens

2019 ◽  
Author(s):  
Matthew G. Durrant ◽  
Michelle M. Li ◽  
Ben Siranosian ◽  
Ami S. Bhatt
Keyword(s):  
Antibiotic Resistance ◽  
De Novo ◽  
Bacterial Species ◽  
Mobile Element ◽  
Mobile Genetic Elements ◽  
Mobile Elements ◽  
Genetic Elements ◽  
Element Insertion ◽  
A Genome ◽  
Mobile Element Insertion

AbstractMobile genetic elements contribute to bacterial adaptation and evolution; however, detecting these elements in a high-throughput and unbiased manner remains challenging. Here, we demonstrate ade novoapproach to identify mobile elements from short-read sequencing data. The method identifies the precise site of mobile element insertion and infers the identity of the inserted sequence. This is an improvement over previous methods that either rely on curated databases of known mobile elements or rely on ‘split-read’ alignments that assume the inserted element exists within the reference genome. We apply our approach to 12,419 sequenced isolates of nine prevalent bacterial pathogens, and we identify hundreds of known and novel mobile genetic elements, including many candidate insertion sequences. We find that the mobile element repertoire and insertion rate vary considerably across species, and that many of the identified mobile elements are biased toward certain target sequences, several of them being highly specific. Mobile element insertion hotspots often cluster near genes involved in mechanisms of antibiotic resistance, and such insertions are associated with antibiotic resistance in laboratory experiments and clinical isolates. Finally, we demonstrate that mutagenesis caused by these mobile elements contributes to antibiotic resistance in a genome-wide association study of mobile element insertions in pathogenicEscherichia coli. In summary, by applying ade novoapproach to precisely identify mobile genetic elements and their insertion sites, we thoroughly characterize the mobile element repertoire and insertion spectrum of nine pathogenic bacterial species and find that mobile element insertions play a significant role in the evolution of clinically relevant phenotypes, such as antibiotic resistance.

scholarly journals Basis of specificity for a conserved and promiscuous chromatin remodeling protein

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Drake A Donovan ◽  
Johnathan G Crandall ◽  
Vi N Truong ◽  
Abigail L Vaaler ◽  
Thomas B Bailey ◽  
...  
Keyword(s):  
Specific Factor ◽  
Spacing Factor ◽  
Genome Wide ◽  
A Genome ◽  
Acidic Residues ◽  
Physical Interactions ◽  
Specific Factors ◽  
Barrier Model ◽  
Eukaryotic Genomes

Eukaryotic genomes are organized dynamically through the repositioning of nucleosomes. Isw2 is an enzyme that has been previously defined as a genome-wide, non-specific nucleosome spacing factor. Here, we show that Isw2 instead acts as an obligately targeted nucleosome remodeler in vivo through physical interactions with sequence-specific factors. We demonstrate that Isw2- recruiting factors use small and previously uncharacterized epitopes, which direct Isw2 activity through highly conserved acidic residues in the Isw2 accessory protein Itc1. This interaction orients Isw2 on target nucleosomes, allowing for precise nucleosome positioning at targeted loci. Finally, we show that these critical acidic residues have been lost in the Drosophila lineage, potentially explaining the inconsistently characterized function of Isw2-like proteins. Altogether, these data suggest an 'interacting barrier model' where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays.

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