Archaeal genomes genome proteins genes bacterial. Medical search. Frequent questions

RefSeq prokaryotic genomes and proteins are now annotated with Gene Ontology (GO) terms. (nih.gov)
Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. (harvard.edu)
We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes. (biomedcentral.com)
Further, we demonstrate that the majority of genes in prokaryotic genomes can be reconstructed uniquely using very short reads even if the genomes themselves cannot. (biomedcentral.com)
Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. (biomedcentral.com)
We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance. (biomedcentral.com)
The avoidance of orthodox Type II R-M system recognition sites in prokaryotic genomes is a widespread phenomenon. (biomedcentral.com)

GO terms are now associated with coding sequence (CDS) features on newly-submitted genomes (See Figure 1). (nih.gov)

Eukaryotic 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. (darkenergybiosphere.org)
Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. (biomedcentral.com)
Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. (biomedcentral.com)
There are two major, distinct forms of regulatory small RNAs involved in eukaryotic gene silencing: small interfering (si) RNAs and micro (mi) RNAs. (biomedcentral.com)
This important lipid component of bacterial inner membranes is not found in the membranes of eukaryotic cells-except for the inner membranes of mitochondria. (reasons.org)
Molecular motors are important features of eukaryotic cells that are formed by a variety of protein types. (icr.org)
Instead, they noted that 'we provide an integrative and robust classification, useful for future genomic and functional studies on this crucial eukaryotic gene family. (icr.org)
Endosymbiotic origin and differential loss of eukaryotic genes. (avcr.cz)
P.1604 left column 2nd paragraph: 'Timing of the appearance of eubacterial genes in eukaryotic genomes is another way to attempt to distinguish between different hypotheses about the origin of the pro-eukaryotic genome. (harvard.edu)
Well-known examples are the eukaryotic and archaeal histones that wrap DNA and the nucleoid-associated proteins in bacteria and archaea that bend and bridge DNA. (universiteitleiden.nl)
Thus, an automated approach is required for advancing our understanding of the evolution and diversity of these systems and for finding new candidates for genome engineering in eukaryotic models. (uni-freiburg.de)

or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. (darkenergybiosphere.org)
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. (darkenergybiosphere.org)
Our understanding of the ecology of oral microbes surged thanks to the Human Microbiome Project (HMP) [ 20 ], which generated extensive sequencing data from 9 oral sites sampled from 200 healthy individuals and over 300 reference genomes for bacteria isolated from the human oral cavity. (biomedcentral.com)
In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. (nature.com)
Bacteriophages (phages), viruses that infect and replicate within bacteria, are important in both natural and human microbiomes because they prey on bacterial hosts, mediate horizontal gene transfer, alter host metabolism and redistribute bacterially derived compounds via host cell lysis 1 . (nature.com)
MCCUTCHEON, John P. Functional horizontal gene transfer from bacteria to eukaryotes. (avcr.cz)
Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora. (avcr.cz)
In bacteria and archaea the genome is not membrane enclosed and "free floating" yet centrally positioned in the cytoplasm, whereas in eukaryotes the genome is located in a dedicated organelle, the nucleus and surrounded by the nuclear membrane. (universiteitleiden.nl)
It is remodeled actively in eukaryotes by motor enzymes that can move or displace nucleosomes, in addition to remodeling mechanisms more ubiquitous in bacteria and archaea that are based on the interplay between multiple architectural proteins. (universiteitleiden.nl)
Models suggest that in bacteria and archaea there are direct effects of physicochemical factors such as osmolarity, temperature and pH on the action of chromatin proteins, in addition to indirect effects by modulating the expression ratios of different types of chromatin proteins. (universiteitleiden.nl)
These results highlight the potential impact of gene regulation in the adaptation of bacteria to the different habitats through the distribution of their regulatory potential among specific functions, and point to critical environmental factors that challenge the growth of any microbial community. (biomedcentral.com)
A notable example is the replacement of an original multi-subunit bacteria-like RNA polymerase (inherited from the proto-mitochondrial ancestor and still encoded in certain jakobid - but no other - mitochondrial genomes) by a single-subunit bacteriophage T3/T7-like RNA polymerase, which directs mitochondrial transcription in virtually all eukaryotes [ 24 ]. (biomedcentral.com)
Previous studies have suggested that the bacteria-derived mitochondria would be the optimal place for nitrogenase production, and many of the genes encoding nitrogenase subunits have been successfully expressed in yeast mitochondria, but the resulting complex lacked the essential metal cofactor. (plantae.org)
Streamlining Regulon Identification in Bacteria Regulons are a group of genes that can be turned on or off by the same regulatory protein. (doe.gov)
Additional findings include some of the earliest-evolved sulfite reductases in bacteria, identification of a novel protein unique to sulfate-reducing bacteria, and a key sulfite reductase gene in putatively symbiotic candidate phyla radiation (CPR) bacteria. (berscience.org)
15-) using a local database for identification of all viruses, bacteria and archaeal genomes extracted from the NCBI refseq database (downloaded 15/04/2017). (cdc.gov)

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. (darkenergybiosphere.org)
Three of the six up-regulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, ZnuC1) suggesting involvement of s479 in regulation of zinc transport. (uni-stuttgart.de)
Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. (nature.com)
The recently reported phage genomes range up to 735 kb in length and encode a diversity of genes involved in transcription and translation, as well as genes that may augment host metabolism 2 . (nature.com)
Scientists believe that the study of genes that encode the proteins for molecular motors will help solve the mysteries of evolution. (icr.org)
Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. (uni-bielefeld.de)
4,000 genomes, they identified 123 near-complete genomes that encode dissimilatory sulfite reductases involved in sulfate reduction. (berscience.org)

The Z curve method proved superior because while sequence analysis creates a phylogenetic tree based solely on coding sequences in the genome, the Z curve method analyzed the entire genome. (wikipedia.org)
With these technologies, the complete genome sequences of thousands of organisms have been determined, including those of many individual humans. (ddw-online.com)
For many scientists, the next step is to begin to manipulate these genome sequences for a variety of specific goals, including analysis of gene function, creating models of human disease, generating better models for drug discovery and, ultimately, human gene therapy. (ddw-online.com)
strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. (frontiersin.org)
All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)
For example, sequences observed twice as often as expected probably occur twice in the genome. (biomedcentral.com)
Researchers had hoped to find that matters would be clarified by myosin proteins derived from the DNA sequences of different single-celled eukaryotes, such as flagellated protozoa (protozoa with a whip-like tail), amoeboid protozoa, and algae. (icr.org)
It was suggested that both estimates relate to the same event, fusion between an archaebacterium and a eubacterium, and the shift in the appearance time of bacterial genes to the present day was merely due to involvement in the analysis of mitochondrial and α-proteobacterial sequences. (harvard.edu)
Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. (biomedcentral.com)
A couple of key findings were that gene sequences did not predict successful protein expression, solubility and activity, and that the successful strategy involved expressing genes from the extreme thermophile Methanothermobacter thermautotrophicus , which might account for the proteins' greater stability in a heterologous system. (plantae.org)
This might be that when we get the DNA sequence, translate it into its corresponding amino acid sequence, our best shot then is to compare it to the existing protein sequences in the databases to know how it looks like what and thus predict its function. (egybio.net)
If two protein sequences look the same, there's a chance, not a guarantee, that they have the same function, because if there's a one amino acid difference, they may have different substrates and thus different functions. (egybio.net)
MTase methylates specific DNA sequences (recognition sites) in the host genome. (biomedcentral.com)
Identification and analysis of informative single nucleotide polymorphisms in 16S rRNA gene sequences of the Bacillus cereus group. (cdc.gov)

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. (darkenergybiosphere.org)
1 Instead of finding a pattern of evolving myosin 'motor' genes (simple to complex) as life seemingly became more advanced, they found that the highest numbers of different types of myosin genes were found in single-celled eukaryotes. (icr.org)
The authors stated, 'The number of myosin genes varies markedly between lineages [types of eukaryotes],' and 'holozoan genomes, as well as some amoebozoans and heterokonts, have the highest numbers of myosins of all eukaryotes. (icr.org)
The role of foreign genes in the evolution of eukaryotes is, however, much less well-understood. (avcr.cz)

The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. (uni-bielefeld.de)
The phylogenetic analysis of the strain was based on 16S rRNA gene sequencing and showed that Paenibacillus sp. (asm.org)

Interestingly, s479 is not only encoded next to CRISPR-cas genes but the mature s479 contains a crRNA-like 5´ handle and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. (uni-stuttgart.de)
CRISPRloci provides an automated and comprehensive in silico characterization of CRISPR-Cas system on bacterial and archaeal genomes. (uni-freiburg.de)
Background: CRISPR-Cas genes are extraordinarily diverse and evolve rapidly when compared to other prokaryotic genes. (uni-freiburg.de)
With the rapid increase in newly sequenced archaeal and bacterial genomes, manual identification of CRISPR-Cas systems is no longer viable. (uni-freiburg.de)
Results: We introduce CRISPRcasIdentifier, a new machine learning-based tool that combines regression and classification models for the prediction of potentially missing proteins in instances of CRISPR-Cas systems and the prediction of their respective subtypes. (uni-freiburg.de)
In contrast to other available tools, CRISPRcasIdentifier can both detect cas genes and extract potential association rules that reveal functional modules for CRISPR-Cas systems. (uni-freiburg.de)

The Z-curve method has been used in many different areas of genome research, such as replication origin identification,, ab initio gene prediction,isochore identification,genomic island identification and comparative genomics. (wikipedia.org)
The GO terms on Pfams (protein families) are derived from the pfam2go mappings , while those on TIGRFAMs were inherited from The Institute for Genomic Research (TIGR) and reviewed in the past 6 months, and those on NCBIFAMs and BlastRules were added manually by NCBI experts. (nih.gov)
CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. (frontiersin.org)
In the present study, we searched the unreported phage genomic fragments from this lake for genes involved in methane oxidation. (nature.com)

The comparative studies of the potential protein content in many of these datasets have already provided interesting examples of specific functions that correlate with specific characteristics of the environment. (biomedcentral.com)
We describe a new computational method for the targeted discovery of functional modules of plant biomass-degrading protein families, based on their co-occurrence patterns across genomes and metagenome datasets, and the strength of association of these modules with the genomes of known degraders. (biomedcentral.com)
Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs. (cdc.gov)

Viruses are also considered to be potential reservoirs of antibiotic resistance genes (ARGs) and the delivery agents for horizontal gene transfer (HGT) of ARGs in the environment [ 7 , 12 ]. (biomedcentral.com)
Horizontal gene transfer: building the web of life. (avcr.cz)
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries. (cdc.gov)

Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. (biomedcentral.com)
It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems. (biomedcentral.com)
It is no longer debatable that viral, bacterial, and archaeal genomes have been forged by foreign genes for several billion years. (avcr.cz)

Researchers analyzed the intergenic distances in 50 completely sequenced bacterial and archaeal genomes using the COG database (primary source) to limit the study to pairs of robustly predicted genes. (harvard.edu)

Analysis of the Z curve has also been shown to be able to predict if a gene contains introns, Experiments have shown that the Z curve can be used to identify the replication origin in various organisms. (wikipedia.org)
which is found in almost all organisms and which sometimes contains operon structures in bacterial genomes. (easyomics.org)
The genetic information stored in the DNA of organisms from all three domains of life is folded into a structure that is compact, yet functionally organised in a way that permits genome activity. (universiteitleiden.nl)
An emerging theme in the field is how genome organisation in unicellular organisms is affected by cellular environment and growth conditions. (universiteitleiden.nl)
Until now, sulfate reduction was believed to be restricted to organisms from select bacterial and archael phyla. (berscience.org)
They used genome-resolved metagenomics to discover roles in sulfur cycling for organisms from 16 microbial phyla not previously associated with this process. (berscience.org)
Sulfate reduction, an important anaerobic metabolism, impacts carbon, nitrogen, and hydrogen transformations in numerous environments across the planet and is known to be restricted to organisms from selected bacterial and archaeal phyla. (berscience.org)

Colonization of the gut starts just after birth when pioneering species interact, through surface receptors, with gut cells to promote the expression of a specific set of host genes and favour the colonization of commensal microorganisms [6]. (deepdyve.com)
Taking the density of regulatory sites in promoters as a measure of the potential and complexity of gene regulation, we found it to be quantitatively the same in all three environments, despite their different physico-chemical conditions and species composition. (biomedcentral.com)
This allows, for the first time, to search for the molecular and genetic basis of adaptation through the comparison and the study of genomes of different species sharing the same environment, and of similar species living in different conditions. (biomedcentral.com)

We are embarking on this adventure and starting to place terms from the Biological Process, Molecular Function and Cellular Component ontologies to genomes and proteins we annotate with the Prokaryotic Genome Annotation Pipeline (PGAP). (nih.gov)
Figure 1: Excerpt from the RefSeq record for NZ_CP091650.1 , a Klebsiella pneumoniae genome, showing the annotation of the the katG gene, with Molecular Function GO terms GO:0004096 and GO:0004601 and Biological Process GO term GO:0006979 . (nih.gov)
It is a full suite for CRISPR locus characteriztion that includes CRISPR array orientation, detection of conserved leaders, cas gene annotation and subtype classification. (uni-freiburg.de)
High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology. (cdc.gov)

One of the genes lost by Hodgkinia encodes the translational Release Factor TF2 that recognizes UGA as a stop codon and terminates the protein at that point. (asmblog.org)
It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. (mdpi.com)
Or, if we're really lucky, we can make a guess - based on sequence similarity - that this gene, for example, encodes for a "hydrolase", but just a hydrolase with no clue about the exact biochemical pathways it's involved in or its substrate. (egybio.net)

Recruiting metagenomic short reads using single-copy core genes, Donati et al. (biomedcentral.com)
A phenomenon that has recently come to light via metagenomic studies is the prominence of phages with genomes that are much larger than the average size of ~55 kilobases (kb) predicted based on current genome databases 2 . (nature.com)
It has been shown in a number of metagenomic studies that the addition and removal of specific genes have allowed microbiomes to adapt to specific environmental conditions by losing and gaining specific functions. (biomedcentral.com)
More recently, metagenomic studies have gone beyond the sequencing of DNA and the counting of genes, and have incorporated techniques and protocols to detect, measure and analyze their transcriptome. (biomedcentral.com)
The authors used genome-resolved metagenomic analyses to determine the metabolic potential of microorganisms from six complex marine and terrestrial environments. (berscience.org)

In contrast, the microbial metabolomes, intestinal element and metal profiles, the diversity of bacterial, archaeal and fungal microbial communities were not significantly affected. (frontiersin.org)
Novel cellulolytic enzymes have been discovered in microbial genomes and metagenomes of microbial communities. (biomedcentral.com)
Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)

Since Hodgkinia has but two genes encoding DNA polymerase subunits, it might serve as a simplified model system for investigating this. (asmblog.org)
Genes corresponding to a B-family type polymerase ('polB') and an HNH nuclease ('HNH') are marked. (elifesciences.org)

Augmentation of bacterial energy generation by auxiliary metabolic genes has been reported for phages with smaller genomes. (nature.com)
Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. (biomedcentral.com)
In addition, viruses have been shown to regulate the metabolic processes of ecosystems by encoding auxiliary metabolic genes (AMGs) [ 11 ]. (biomedcentral.com)

Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
Functional prediction analyses suggested that ArsR M is a difunctional protein with transcriptional regulation and methyltransferase activities. (biomedcentral.com)
The observed progressive decrease in defecation frequency and concomitant increase in the electrical conductivity (EC) preceded or took place in absence of significant changes at the taxonomic, functional gene, metabolome and intestinal metal profile levels. (frontiersin.org)
From approximately 6.4 million family annotations for 2,884 microbial genomes, and 332 taxonomic bins from 18 metagenomes, we identified 5 functional modules that are distinctive for plant biomass degraders, which we term "plant biomass degradation modules" (PDMs). (biomedcentral.com)
On average, 70% of the families of each PDM were found to map to gene clusters in known degraders, which served as an additional confirmation of their functional relationships. (biomedcentral.com)
Functional modules of protein families that are involved in different aspects of plant cell wall degradation can be inferred from co-occurrence patterns across (meta-)genomes with a probabilistic topic model. (biomedcentral.com)
2022) Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica . (doe.gov)

Recent multi-omics studies have revealed the heterogeneity and complexity of tumor features such as their genetic mutations, transcriptome, proteins, and signaling pathways. (rsc.org)
However, the identification of relevant genes without known homologs, and the elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain challenging. (biomedcentral.com)
1) DNA sequencing is getting faster and cheaper in a rate that is exceeding our ability to understand the function or the biochemical pathways of every single gene sequenced. (egybio.net)

Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. (frontiersin.org)
The presence of a PDM in a genome or taxonomic metagenome bin furthermore allowed us to accurately predict the ability of any particular organism to degrade plant biomass. (biomedcentral.com)
They can also be used to predict the plant biomass degradation ability for a genome or taxonomic bin. (biomedcentral.com)

In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. (rsc.org)
In addition to the host regulatory mechanisms response to disease, the microbiome can make changes to the expression of the host features such as their genes, proteins, and/or PTMs. (rsc.org)
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)

The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. (biomedcentral.com)

2014. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. (nih.gov)

This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)
In order to expand our understanding of how recombination might influence virus variation during the course of adaptation, we focused on large DNA viruses, in which rapidly evolving populations can simultaneously harbor both adaptive gene copy number variation and beneficial single nucleotide variants (SNVs) at the same locus. (elifesciences.org)
Soil Virus Offers Insight into Maintaining Microorganisms Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health. (doe.gov)
The resulting contigs were scanned against several BLAST ( 12 ) pre-generated databases downloaded from NCBI ( nt , tsa_nt , ref_prok_rep_genomes , ref_viruses_rep_genomes , and vector - downloaded 15/04/2017). (cdc.gov)

90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus , Methylocystis and Methylobacter spp. (nature.com)

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein", PLOS ONE , vol. 8, 2013, : e57487. (uni-bielefeld.de)

R-M systems are widely spread among prokaryotes: they have been found or predicted with computational methods in the vast majority of bacterial and archaeal genomes [ 13 ]. (biomedcentral.com)

A number of specific and general insights into mitochondrial genome evolution follow from these data. (biomedcentral.com)

The gene encoding ArsR/methyltransferase fusion protein, arsR M , was amplified and expressed in Escherichia coli BL21 (DE3), and this strain showed resistance to arsenic in the present of 0.25-6 mM As(III), aresenate, or pentavalent roxarsone. (biomedcentral.com)
The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. (uni-stuttgart.de)
Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. (uni-stuttgart.de)
Upregulation of these genes in the deletion strain was confirmed by northern blot and proteome analyses. (uni-stuttgart.de)
Determination of the DNA genome sequence of this strain has been or is being determined either in whole or in part. (nih.gov)
Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. (uni-bielefeld.de)
The pure culture of the bacterial strain was grown under aerobic conditions on tryptic soy broth agar plates. (asm.org)
Genome Sequence of a Candidate World Health Organization Reference Strain of Zika Virus for Nucleic Acid Testing. (cdc.gov)

According to this idea, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a "host" microbe. (reasons.org)

Mitochondrial DNA may also lose genes whose functions are substituted for by unrelated genes encoded in the nucleus. (biomedcentral.com)

Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. (biomedcentral.com)

Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. (elifesciences.org)

In fact, this is the basis of currently used methods that link gene surveys to metabolic predictions of community function. (berscience.org)

The latter are DNA-binding modules found in natural transcription factor proteins. (ddw-online.com)
Genome folding is tightly interconnected with transcription, with genes in certain regions being silenced, while others are highly transcribed. (universiteitleiden.nl)
Our interest lies in understanding how architectural proteins act on DNA and how they regulate transcription. (universiteitleiden.nl)
Our current aim is to obtain an integrated picture of the interplay between spatial genome organization and DNA transactions in general and transcription in specific. (universiteitleiden.nl)
Thus genome organisation and transcription regulation are likely intimately coupled. (universiteitleiden.nl)
As transcription of many genes and operons responds to environmental changes and as these are often mediated by chromatin proteins, it is expected that 1) the architectural interplay of such proteins and/or 2) their direct response to physicochemical changes determines loop formation and dissolution leading to altered transcription levels. (universiteitleiden.nl)
More importantly, we are using and developing new approaches to investigate genome organisation and its coupling to transcription in vivo. (universiteitleiden.nl)
This work includes a huge amount of sequencing data, including ATAC-seq (transposase-accessible chromatin sequencing) chromatin accessibility landscape, DAP-seq for 32 maize transcription factor genome-wide binding sites, 9 ChiP-seq for histone features, and loop analysis by HiC and HiChiP. (plantae.org)
RIViT-seq technology could speed up associating transcription factors with their target genes. (doe.gov)

CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. (frontiersin.org)
The PDMs were linked to 81 gene clusters in genomes of known lignocellulose degraders, including previously described clusters of lignocellulolytic genes. (biomedcentral.com)

Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. (biomedcentral.com)
Thus we can give an upper bound on how well an assembler could possibly reconstruct a genome given reads of a certain length. (biomedcentral.com)
Finishing monkeypox genomes from short reads: assembly analysis and a neural network method. (cdc.gov)

This folded structure including the associated architectural proteins is referred to as chromatin. (universiteitleiden.nl)
Remodeling of chromatin is also mediated by chemical modifications of the DNA, the architectural proteins that shape it or physicochemical cues. (universiteitleiden.nl)
Also, my group is investigating the (architectural) interplay between different types of chromatin proteins in vitro (Laurens et al. (universiteitleiden.nl)
In addition to dissecting these mechanistic aspects of gene regulation, we are interested in the roles and physiological consequences of the products of genes regulated by chromatin proteins. (universiteitleiden.nl)
The chromatin landscape is key in the regulation of gene expression. (plantae.org)

Genome Med, Sep 7, 2016. (cdc.gov)

The association of the cas genes with CRISPR and, especially, the presence, in CRISPR units, of unique inserts homologous to phage and plasmid genes make us abandon this hypothesis. (biomedcentral.com)
In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. (nature.com)
Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. (nature.com)
Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. (nature.com)
Restriction-modification (R-M) systems were discovered and characterized as bacterial systems defending cells from an invasion of foreign DNA, e.g. , phage DNA [ 1 , 2 ]. (biomedcentral.com)

Because of the hierarchical nature of the Gene Ontologies, these annotations will help the comparison of gene content across genomes at variable levels of specificity and eventually allow GO term enrichment analysis. (nih.gov)
The requirement for a total of 6-12 fingers, each of which binds three base pairs, provides enough specificity to address a unique sequence in a genome as complex as the three billion base pairs of human DNA. (ddw-online.com)

Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. (biomedcentral.com)
In this paper, we study an idealized instance of the short-read assembly problem and attempt to estimate the ability of these technologies to reconstruct genomes. (biomedcentral.com)

It uses a modified form of the "universal" genetic code, a version that has turned up before in some mitochondrial lineages and Mycoplasma, all of which exhibit genome reduction and low GC content too. (asmblog.org)
Instead, Hodgkinia tells us that it is genome reduction, not low GC%, that is driving this shift in its genetic code. (asmblog.org)
Presumably, the endosymbiont gradually evolved into an organelle through a process referred to as genome reduction. (reasons.org)
This reduction resulted when genes from the endosymbiont's genome were transferred into the genome of the host organism. (reasons.org)

But it is not known whether and how the regulation of gene expression also contributes to adaptation. (biomedcentral.com)

The biological system is complex with many regulatory features such as DNA, mRNA, proteins, metabolites, and epigenetic features such as DNA methylation and histone post-translational modifications (PTMs). (rsc.org)
I will start with this talk by Dr. Richard Roberts , who received the Nobel Prize in Physiology or Medicine in 1993 for the discovery of split genes and mRNA splicing in 1977. (egybio.net)

Sequencing has also shown that mitochondrial genomes have, to variable extents, undergone a streamlining process ("reductive evolution" [ 20 ]), leading to a marked loss of coding capacity compared to that of their closest eubacterial relatives. (biomedcentral.com)

For 15 draft genomes of a cow rumen metagenome, we used cross-referencing to confirmed cellulolytic enzymes to validate that the PDMs identified plant biomass degraders within a complex microbial community. (biomedcentral.com)

Bacterial and archaeal genomes with GO terms in RefSeq! (nih.gov)
They will progressively appear on genomes that are already in RefSeq as these get reannotated (about once a year). (nih.gov)
We expect all RefSeq genomes to have some GO terms by the spring of 2023. (nih.gov)
We also added GO terms to 65 million non-redundant RefSeq proteins (with the WP_ prefix) that are named after a Protein Family Model with one or more GO terms. (nih.gov)
Figure 2: Excerpt from the RefSeq record for KatG protein WP_004180028.1 , with Molecular Function GO terms GO:0004096 and GO:0004601 and Biological Process GO term GO:0006979 on the protein feature. (nih.gov)

It is proposed that unique inserts of CRISPR, some of which are homologous to fragments of bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by base-pairing with the target mRNAs and promoting their degradation or translation shutdown. (biomedcentral.com)

The Z curve (or Z-curve) method is a bioinformatics algorithm for genome analysis. (wikipedia.org)
Our analysis uncovered a mechanism of adaptive SNV homogenization reminiscent of gene conversion, which is actively driven by selection. (elifesciences.org)
Through a data-independent acquisition analysis of protein profiles of noncapacitated sperms, normal capacitated sperms and SP-EVs treated capacitated sperms, we identified that EZRIN was one of the active proteins that participated in SP-EVs and sperms interaction. (bvsalud.org)
The analysis gives an upper-bound on the performance of genome assemblers for de novo reconstruction of genomes across a wide range of read lengths. (biomedcentral.com)
Despite these simplifying assumptions, it is important to conduct an analysis of the fundamental challenge of assembly -- the repeat structure of the genome -- free of the biases or limitations of any particular sequencing technology. (biomedcentral.com)
While the sequencing of metagenomes provides an overview of the genes present in specific environments that can potentially play a role in adaptation, the analysis of expression provides a more precise picture of what functions are expressed and active in a particular moment of the environment. (biomedcentral.com)

Gene duplication is long recognized as a potential source of genetic innovation ( Ohno, 1970 ). (elifesciences.org)
There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. (nature.com)
Origin of an alternative genetic code in the ex-tremely small and GC-rich genome of a bacterial symbiont. (asmblog.org)

However, the result of a study published in the journal Genome Biology and Evolution has only served to support the predictions of special creation-that unique variants of cellular complexity and innovation exist at all levels of life. (icr.org)
Genome Biology and Evolution. (icr.org)

The simplicity of design and the publication of several modular assembly schemes have led to the rapid adoption of TALENs for genome engineering. (ddw-online.com)

While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. (uni-stuttgart.de)

Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)

They see the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles. (reasons.org)
We investigate the activity of these proteins in vitro as well as in vivo using biochemical and state-of-the-art biophysical approaches. (universiteitleiden.nl)

primary source] showed that archaeal genes appeared in Eukarya about 2.3 billion years ago (Bya) while eubacterial genes appeared 2.1 Bya. (harvard.edu)
These data confirm that the mitochondrial genome originated from a eubacterial (specifically α-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome. (biomedcentral.com)

The distributional patterns of microbial genes suggested Dead Sea community trends in mono- and divalent cation metabolisms as well as in transposable elements. (nature.com)
So, how did the authors explain the incredible complexity found across the spectrum of life in myosin gene content that had no clear evolutionary patterns? (icr.org)
They explained it by 1) convergence (the sudden and simultaneous appearance of a gene with no evolutionary patterns in different taxa), 2) lineage-specific expansions (different myosin gene complements found in different creatures), and 3) gene losses (missing genes that evolutionists thought should have been there). (icr.org)

According to the experimental results, CRISPRcasIdentifier presented the best Cas protein identification and subtype classification performance. (uni-freiburg.de)

Anatomy5

Organisms22

Chemicals and Drugs19

Analytical, Diagnostic and Therapeutic Techniques and Equipment11

Phenomena and Processes53

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science10

Health Care1

Prokaryotic genomes7

Coding sequence1

Eukaryotic11

Bacteria17

Encode7

Sequences14

Eukaryotes4

Phylogenetic2

CRISPR-Cas6

Genomic4

Datasets3

Horizontal gene tra3

Viral3

Completely sequenced1

Organisms7

Species3

Annotation4

Encodes3

Metagenomic5

Microbial communities3

Polymerase2

Auxiliary metabolic genes3

Functional7

Pathways3

Taxonomic3

Microbiome3

Foreign genes1

Plastid1

Viruses4

Phylogenetically1

Genomics1

Prokaryotes1

Insights1

Strain8

Single-celled1

Mitochondrial DNA1

Analyses1

Nucleotide1

Metabolic1

Transcription9

Clusters2

Reads4

Chromatin5

20161

Phage5

Specificity2

Reconstruct2

Reduction4

Regulation1

MRNA2

Reductive1

Enzymes1

RefSeq5

Bacteriophage1

Analysis6

Genetic3

Biology2

Assembly1

Structures1

Recombination1

Biochemical2

Eubacterial2

Patterns3

Identification1