|
Diversity-generating Retroelement
Diversity-generating retroelements (DGRs) are a family of retroelements that were first found in '' Bordetella phage (BPP-1)'', and since been found in bacteria (e.g.''Treponema denticola'' ''and Legionella pneumophila''), Archaea, Archaean viruses (e.g. ANMV-1), temperate phages (e.g. Hankyphage and CrAss-like phage), and lytic phages. DGRs benefit their host by mutating particular regions of specific target proteins, for instance, phage tail fiber in BPP-1, lipoprotein in legionella ''pneumophila'' ( the pathogen behind Legionnaires disease), and TvpA in ''Treponema denticola (oral-associated periopathogen)'.'' An error-prone reverse transcriptase is responsible for generating these hypervariable regions in target proteins (Mutagenic retrohoming). In mutagenic retrohoming, a mutagenized cDNA (containing substantial A to N mutations) is reverse transcribed from a template region (TR), and is replaced with a segment similar to the template region called variable region (VR). Acces ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Retroelements
Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the reverse transcription process using an RNA transposition intermediate. Through reverse transcription, retrotransposons amplify themselves quickly to become abundant in eukaryotic genomes such as maize (49–78%) and humans (42%). They are only present in eukaryotes but share features with retroviruses such as HIV, for example, discontinuous reverse transcriptase-mediated extrachromosomal recombination. These retrotransposons are regulated by a family of short non-coding RNAs termed as PIWI -element induced wimpy testisinteracting RNAs (piRNAs). piRNA is a recently discovered class of ncRNAs, which are in the length range of ~24-32 nucleotides. Initially, piRNAs were described as repeat-associated siRNAs (rasiRNAs) because of their ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bordetella Virus BPP1
''Rauchvirus'' is a genus of viruses in the order ''Caudovirales'', in the family ''Podoviridae ''Podoviridae'' is a family of bacteriophage in the order ''Caudovirales'' often associated with T-7 like phages. There are 130 species in this family, assigned to 3 subfamilies and 52 genera. This family is characterized by having very short, n ...''. Bacteria serve as natural hosts. The genus contains only one species: ''Bordetella virus BPP1''. Structure Viruses in ''Rauchvirus'' are non-enveloped, with icosahedral and head-tail geometries, and T=7 symmetry. The diameter is around 67 nm. Genomes are linear, around 42kb in length, and usually encodes about 50 proteins. The ''Bordetella'' phages of this genus contains an RNA-directed DNA polymerase which plays a role in tropism. The genomes are linear, terminally redundant, and circularly with approximately 40. There are 53 proteins, and genes are arrayed in two transcriptional units, one on the negative strand, which is inv ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Treponema Denticola
''Treponema denticola'' is a Gram-negative, obligate anaerobic, motile and highly proteolytic spirochete bacterium. It is one of four species of oral spirochetes to be reliably cultured, the others being ''Treponema pectinovorum, Treponema socranskii'' and ''Treponema vincentii''''. T. denticola'' dwells in a complex and diverse microbial community within the oral cavity and is highly specialized to survive in this environment. ''T. denticola'' is associated with the incidence and severity of human periodontal disease. ''Treponema denticola'' is one of three bacteria that form the Red Complex, the other two being ''Porphyromonas gingivalis'' and ''Tannerella forsythia''. Together they form the major virulent pathogens that cause chronic periodontitis. Having elevated ''T. denticola'' levels in the mouth is considered one of the main etiological agents of periodontitis. ''T. denticola'' is related to the syphilis-causing obligate human pathogen, ''Treponema pallidum'' subsp. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Legionella Pneumophila
''Legionella pneumophila'' is a thin, aerobic, pleomorphic, flagellated, non-spore-forming, Gram-negative bacterium of the genus ''Legionella''. ''L. pneumophila'' is the primary human pathogenic bacterium in this group and is the causative agent of Legionnaires' disease, also known as legionellosis. In nature, ''L. pneumophila'' infects freshwater and soil amoebae of the genera ''Acanthamoeba'' and ''Naegleria''. The mechanism of infection is similar in amoeba and human cells. Characterization ''L. pneumophila'' is a Gram-negative, non-encapsulated, aerobic bacillus with a single, polar flagellum often characterized as being a coccobacillus. It is aerobic and unable to hydrolyse gelatin or produce urease. It is also non- fermentative. ''L. pneumophila'' is neither pigmented nor does it autofluoresce. It is oxidase- and catalase-positive, and produces beta-lactamase. ''L. pneumophila'' colony morphology is gray-white with a textured, cut-glass appearance; it also requires cyst ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat, square cells of ''Haloquadratum walsbyi''. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phage
A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes (e.g. MS2) and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. Viruses are the most abundant biological entity in the water column of the world's oceans, and the second largest component of biomass ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CrAssphage
CrAss-like phage are a bacteriophage (virus that infects bacteria) family that was discovered in 2014 by cross assembling reads in human fecal metagenomes. In silico comparative genomics and taxonomic analysis have found that crAss-like phages represent a highly abundant and diverse family of viruses. CrAss-like phage were predicted to infect bacteria of the ''Bacteroidota'' phylum and the prediction was later confirmed when the first crAss-like phage (crAss001) was isolated on a ''Bacteroidota'' host (''B. intestinalis'') in 2018. The presence of crAss-like phage in the human gut microbiota is not yet associated with any health condition. Discovery The crAss (cross-assembly) software used to discover the first crAss-like phage, p-crAssphage (prototypical-crAssphage), relies on cross assembling reads from multiple metagenomes obtained from the same environment. The goal of cross-assembly is that unknown reads from one metagenome align with known reads, or reads that have similarity ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reverse Transcriptase
A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, and by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes. Contrary to a widely held belief, the process does not violate the flows of genetic information as described by the classical central dogma, as transfers of information from RNA to DNA are explicitly held possible. Retroviral RT has three sequential biochemical activities: RNA-dependent DNA polymerase activity, ribonuclease H (RNase H), and DNA-dependent DNA polymerase activity. Collectively, these activities enable the enzyme to convert single-stranded RNA into double-stranded cDNA. In retroviruses and retrotransposons, this cDNA can then integrate into the host genom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hypervariable Region
A hypervariable region (HVR) is a location within nuclear DNA or the D-loop of mitochondrial DNA in which base pairs of nucleotides repeat (in the case of nuclear DNA) or have substitutions (in the case of mitochondrial DNA). Changes or repeats in the hypervariable region are highly polymorphic. Mitochondrial There are two MITOCHONDRIAL hypervariable regions used in human mitochondrial genealogical DNA testing. HVR1 is considered a "low resolution" region and HVR2 is considered a "high resolution" region. Getting HVR1 and HVR2 DNA tests can help determine one's haplogroup. In the revised Cambridge Reference Sequence of the human mitogenome, the most variable sites of HVR1 are numbered 16024-16383 (this subsequence is called HVR-I), and the most variable sites of HVR2 are numbered 57-372 (''i.e.,'' HVR-II) and 438-574 (''i.e.,'' HVR-III).''PhyloTree mt''"Annotated mtDNA reference sequences: revised Cambridge Reference Sequence (rCRS)" Retrieved on 4 February 2016. In some bony f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Faecalibacterium Prausnitzii
''Faecalibacterium'' is a genus of bacteria. Its sole known species, ''Faecalibacterium prausnitzii'' is gram-positive, mesophilic, rod-shaped, anaerobic and is one of the most abundant and important commensal bacteria of the human gut microbiota. It is non-spore forming and non-motile. These bacteria produce butyrate and other short-chain fatty acids through the fermentation of dietary fiber. History Formerly considered to be a member of ''Fusobacterium'', the bacterium is named in honor of German bacteriologist Otto Prausnitz. In 2002, it was proposed to be reclassified as its own genus, ''Faecalibacterium'', containing the species ''Faecalibacterium prausnitzii'', as phylogenetic analysis from isolates showed it to be only distantly related to ''Fusobacterium'', and a closer member of Clostridium cluster IV. Genetics ''Faecalibacterium prausnitzii'' has a genome 2,868,932 bp long and has a GC-content of 56.9%. The bacterium has been found to have 2,707 coding sequences, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Retron
A retron is a distinct DNA sequence found in the genome of many bacteria species that codes for reverse transcriptase and a unique single-stranded DNA/RNA hybrid called multicopy single-stranded DNA (msDNA). Retron msr RNA is the non-coding RNA produced by retron elements and is the immediate precursor to the synthesis of msDNA. The retron msr RNA folds into a characteristic secondary structure that contains a conserved guanosine residue at the end of a stem loop. Synthesis of DNA by the retron-encoded reverse transcriptase (RT) results in a DNA/RNA chimera which is composed of small single-stranded DNA linked to small single-stranded RNA. The RNA strand is joined to the 5′ end of the DNA chain via a 2′–5′ phosphodiester linkage that occurs from the 2′ position of the conserved internal guanosine residue. Sequence and structure Retron elements are about 2 kb long. They contain a single operon controlling the synthesis of an RNA transcript carrying three loci, ''msr' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mobile Genetic Elements
Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In humans, approximately 50% of the genome is thought to be MGEs. MGEs play a distinct role in evolution. Gene duplication events can also happen through the mechanism of MGEs. MGEs can also cause mutations in protein coding regions, which alters the protein functions. These mechanisms can also rearrange genes in the host genome generating variation. These mechanism can increase fitness by gaining new or additional functions. An example of MGEs in evolutionary context are that virulence factors and antibiotic resistance genes of MGEs can be transported to share genetic code with neighboring bacteria. However, MGEs can also decrease fitness by introducing disease-causing alleles or mutations. The set of MGEs in an organism is called a mobilome, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
.jpg "Click for more on -> Archaea")
