A5045663522- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Epigenetics and DNA Methylation
- Ubiquitin and proteasome pathways
- Protist diversity and phylogeny
- Biochemical and Molecular Research
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Legume Nitrogen Fixing Symbiosis
- Vibrio bacteria research studies
- Enzyme Structure and Function
- DNA Repair Mechanisms
- Aquaculture disease management and microbiota
- Plant Virus Research Studies
- Chromosomal and Genetic Variations
- Peptidase Inhibition and Analysis
- Microbial Community Ecology and Physiology
- Advanced Semiconductor Detectors and Materials
- Semiconductor Quantum Structures and Devices
- Bioinformatics and Genomic Networks
- Plant-Microbe Interactions and Immunity
- Escherichia coli research studies
National Center for Biotechnology Information
2015-2024
National Institutes of Health
2015-2024
United States National Library of Medicine
2023
Canadian Standards Association
2014
Institute of Electrical and Electronics Engineers
2014
University of Michigan
2012
University of Alabama at Birmingham
2005
Stowers Institute for Medical Research
2005
Biotechnology Institute
2005
University of Maryland, Baltimore
2005
Methylation Mediation of cytosine bases, 5-methylcytosine (5mC), in DNA plays an important regulatory role mammalian genomes. patterns are often inherited across generations, but they can also be dynamic, suggesting that active demethylation pathways exist. One such pathway, best characterized plants, involves the removal 5mC base, and its replacement by C, via a repair mechanism. Kriaucionis Heintz (p. 929 , published online 16 April) now show that, as well genomes, there significant...
The apicomplexan Cryptosporidium parvum is an intestinal parasite that affects healthy humans and animals, causes unrelenting infection in immunocompromised individuals such as AIDS patients. We report the complete genome sequence of C. parvum, type II isolate. Genome analysis identifies extremely streamlined metabolic pathways a reliance on host for nutrients. In contrast to Plasmodium Toxoplasma, lacks apicoplast its genome, possesses degenerate mitochondrion has lost genome. Several novel...
Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific They characterized by a remarkable diversity C-terminal domains generated recombination with standalone toxin-coding cassettes. Prior analysis revealed striking nuclease deaminase among the modules. We systematically investigated using comparative genomics, sequence structure...
Modified bases in nucleic acids present a layer of information that directs biological function over and beyond the coding capacity conventional bases. While large number modified have been identified, many enzymes generating them still remain to be discovered. Recently, members 2-oxoglutarate- iron(II)-dependent dioxygenase superfamily, which modify diverse substrates from small molecules biopolymers, were predicted subsequently confirmed catalyze oxidative modification acids. Of these, two...
The tripartite DENN module, comprised of a N-terminal longin domain, followed by DENN, and d-DENN domains, is GDP-GTP exchange factor (GEFs) for Rab GTPases, which are regulators practically all membrane trafficking events in eukaryotes. Using sequence structure analysis we identify multiple novel homologs the many can be traced back to ancestral eukaryote. These findings provide unexpected leads regarding key cellular processes such as autophagy, vesicle-vacuole interactions, chromosome...
Cyclic di- and linear oligo-nucleotide signals activate defenses against invasive nucleic acids in animal immunity; however, their evolutionary antecedents are poorly understood. Using comparative genomics, sequence structure analysis, we uncovered a vast network of systems defined by conserved prokaryotic gene-neighborhoods, which encode enzymes generating such nucleotides or alternatively processing them to yield potential signaling molecules. The nucleotide-generating include several...
Instead of the immunoglobulin-type antigen receptors jawed vertebrates, jawless fish have variable lymphocyte (VLRs), which consist leucine-rich repeat (LRR) modules. Somatic diversification VLR gene is shown here to occur through a multistep assembly LRR modules randomly selected from large bank flanking cassettes. The predicted concave surface lined with hypervariable positively residues, and computational analysis suggests repertoire about 10(14) unique receptors. Lamprey immunized...
We report an in-depth computational study of the protein sequences and structures superfamily archaeo-eukaryotic primases (AEPs). This analysis greatly expands range diversity AEPs reveals unique active site shared by all members this superfamily. In particular, it is shown that eukaryotic nucleo-cytoplasmic large DNA viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses mimivirus, encode a distinct family, which also includes herpesvirus whose relationship to has not...
Abstract Background Acetylcholine receptor type ligand-gated ion channels (ART-LGIC; also known as Cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such acetylcholine, serotonin, glycine, GABA, glutamate and histamine, Zn 2+ ions. They play central role in fast synaptic signaling animal nervous systems so far have not been found outside Metazoa. Results Using sensitive sequence-profile searches we identified homologs ART-LGICs several...
With a protein structure comparison, an iterative database search with sequence profiles, and multiple-alignment analysis, we show that two domains the helix-grip fold, star-related lipid-transfer (START) domain of MLN64 birch allergen, are homologous. They define large, previously underappreciated superfamily call START superfamily. In addition to classical primarily involved in eukaryotic signaling mediated by lipid binding antigen family consists plant proteins implicated stress/pathogen...
The apicomplexans Plasmodium and Cryptosporidium have developed distinctive adaptations via lineage-specific gene loss innovation in the process of diverging from a common parasitic ancestor. two lineages acquired distinct but overlapping sets surface protein adhesion domains typical animal proteins, no case do they share multidomain architectures identical to animals. , not possesses an animal-type O -linked glycosylation pathway, along with >30 predicted proteins having mucin-like...
The use of nucleases as toxins for defense, offense or addiction selfish elements is widely encountered across all life forms. Using sensitive sequence profile analysis methods, we characterize a novel superfamily (the SUKH superfamily) that unites diverse group proteins including Smi1/Knr4, PGs2, FBXO3, SKIP16, Syd, herpesviral US22, IRS1 and TRS1, their bacterial homologs. contextual present evidence the members this are potential immunity variety toxin systems also include recently...
Microbial infection of the amniotic fluid is a significant cause fetal injury, preterm birth, and newborn infections. Group B Streptococcus (GBS) an important human bacterial pathogen associated with neonatal mortality. Although GBS has been isolated from women in labor, mechanisms utero remain unknown. Previous studies indicated that are unable to invade epithelial cells (hAECs), which represent last barrier cavity fetus. We show invades hAECs strains lacking hemolysin repressor CovR/S...
WRKY and GCM1 are metal chelating DNA-binding domains (DBD) which share a four stranded fold. Using sensitive sequence searches, we show that this WRKY–GCM1 fold is also shared by the FLYWCH Zn-finger domain DBDs of two classes Mutator-like element (MULE) transposases. We present evidence they stabilizing core, suggests possible origin from BED finger-like intermediate was in turn ultimately derived C2H2 domain. Through systematic study phyletic pattern, superfamily widespread...
The deaminase-like fold includes, in addition to nucleic acid/nucleotide deaminases, several catalytic domains such as the JAB domain, and others involved nucleotide ADP-ribose metabolism. Using sensitive sequence structural comparison methods, we develop a comprehensive natural classification of show that its ancestral version was likely operate on nucleotides or acids. Consequently, present evidence specific group are possess DNA repair function, distinct from previously known...
Ubiquitin (Ub)-mediated signaling is one of the hallmarks all eukaryotes. Prokaryotic homologs Ub (ThiS and MoaD) E1 ligases have been studied in relation to sulfur incorporation reactions thiamine molybdenum/tungsten cofactor biosynthesis. However, there no evidence for entire protein modification systems with Ub-like proteins deconjugation by deubiquitinating enzymes prokaryotes. Hence, evolutionary assembly eukaryotic Ub-signaling apparatus remains unclear.We systematically analyzed...