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  • transcription
  • The integrated protein index (IPI) shows significant similarity with fly, worm and yeast proteomes, particularly for proteins involved in metabolism, DNA replication, transcription and translations, protein folding and degradation. (biomedcentral.com)
  • To this end, a bacterial expression clone may include a ribosome binding site (Shine-Dalgarno sequence) to enhance translation of the gene of interest's mRNA, a transcription termination sequence, or, in eukaryotes, specific sequences to promote the post-translational modification of the protein product. (wikipedia.org)
  • Given these clues and knowledge that bactera transcribe (see Transcription (genetics)) proteins starting with N-Formylmethionine whereas eukaryotic cells mostly initiate protein synthesis with non-formylated methionine, Schiffmann, Corcoran, and Wahl theorized and then showed that N-formyl-methionine and a series N-formyl-methionyl dipeptides and tripeptides stimulated the chemotaxis of neutrophils isolated from rabbit peritoneal exudates as well as of macrophages isolated from guinea pig peritoneal exudates. (wikipedia.org)
  • When injected into plants, these proteins can enter the nucleus of the plant cell, bind plant promoter sequences, and activate transcription of plant genes that aid in bacterial infection. (wikipedia.org)
  • Such engineered TAL effectors have been used to create artificial transcription factors that can be used to target and activate or repress endogenous genes in tomato, Arabidopsis thaliana, and human cells. (wikipedia.org)
  • In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. (wikipedia.org)
  • It is orchestrated by transcription factors and other proteins working in concert to finely tune the amount of RNA being produced through a variety of mechanisms. (wikipedia.org)
  • Most importantly is the idea of combinatorial control, which is that any given gene is likely controlled by a specific combination of factors to control transcription. (wikipedia.org)
  • Much of the early understanding of transcription came from prokaryotic organisms, although the extent and complexity of transcriptional regulation is greater in eukaryotes. (wikipedia.org)
  • Prokaryotic transcription is governed by three main sequence elements: Promoters are elements of DNA that may bind RNA polymerase and other proteins for the successful initiation of transcription directly upstream of the gene. (wikipedia.org)
  • Operators recognize repressor proteins that bind to a stretch of DNA and inhibit the transcription of the gene. (wikipedia.org)
  • Positive control elements that bind to DNA and incite higher levels of transcription While these means of transcriptional regulation also exist in eukaryotes, the transcriptional landscape is significantly more complicated both by the number of proteins involved as well as by the presence of introns and the packaging of DNA into histones. (wikipedia.org)
  • The transcription of a basic prokaryotic gene is dependent on the strength of its promoter and the presence of activators or repressors. (wikipedia.org)
  • This means that transcriptional regulation in the form of protein repressors and positive control elements can either increase or decrease transcription. (wikipedia.org)
  • This strategy of control is distinct from eukaryotic transcription, whose basal state is to be off and where co-factors required for transcription initiation are highly gene dependent. (wikipedia.org)
  • Sigma factors are specialized bacterial proteins that bind to RNA polymerases and orchestrate transcription initiation. (wikipedia.org)
  • Sigma factors act as mediators of sequence-specific transcription, such that a single sigma factor can be used for transcription of all housekeeping genes or a suite of genes the cell wishes to express in response to some external stimuli such as stress. (wikipedia.org)
  • Transcription and translation of genes have been reported to occur in spatially segregated locations within the cell, which is otherwise characteristic of eukaryotic but not prokaryotic cells. (wikipedia.org)
  • evolutionary
  • In the mid-1980s, Syvanen predicted that lateral gene transfer existed, had biological significance, and was involved in shaping evolutionary history from the beginning of life on Earth. (wikipedia.org)
  • genome
  • The genome-wide average GC content is 41%, but regional variations confirm a correlation between GC content and gene density. (biomedcentral.com)
  • The genes within these chromosomes are the cell's nuclear genome and are structured in such a way to promote cell function. (wikipedia.org)
  • In a hypothetical example, the factors A and B might regulate a distinct set of genes from the combination of factors A and C. This combinatorial nature extends to complexes of far more than two proteins, and allows a very small subset (less than 10%) of the genome to control the transcriptional program of the entire cell. (wikipedia.org)
  • Apart from its original function in bacterial immunity, the Cas9 protein has been heavily utilized as a genome engineering tool to induce site-directed double strand breaks in DNA. (wikipedia.org)
  • Alongside zinc finger nucleases and TALEN proteins, Cas9 is becoming a prominent tool in the field of genome editing. (wikipedia.org)
  • The Lokiarchaeum composite genome consists of 5,381 protein coding genes. (wikipedia.org)
  • Both proteins are encoded on the same operon within the bacterial genome. (wikipedia.org)
  • Escherichia
  • Three of these genes, from Mycobacterium smegmatis , Corynebacterium glutamicum , and Halobacterium salinarum , were cloned and functionally expressed in Escherichia coli . (asm.org)
  • Functional studies demonstrated that, despite the structural and amino acid sequence differences from bacterial SSBs, Orf14(bIL67) protein complements the conditional lethal ssb-1 mutation of Escherichia coli. (sigmaaldrich.com)
  • Type I, exemplified by the hemolysin secretion system of Escherichia coli , is a rather simple exporter that is based on only three proteins, one of which belongs to the ABC transporters. (antievolution.org)
  • unlike
  • Unlike other proteins involved in DNA metabolism, the RecA/Rad51 family forms a helical nucleoprotein filament on DNA. (wikipedia.org)
  • sequence
  • Multidrug transporters are ubiquitous proteins, and, based on amino acid sequence similarities, they have been classified into several families. (asm.org)
  • Although the sequence similarity of these proteins is low (∼20% identity), their folds are highly similar. (asm.org)
  • We have performed a large scale phylogenetic analysis and pairwise sequence comparisons of SSB proteins from different phyla. (sigmaaldrich.com)
  • The N-terminal fMet is removed from majority of proteins, both host and recombinant, by a sequence of two enzymatic reactions. (wikipedia.org)
  • The first group, headed by Adam Bogdanove, broke this code computationally by searching for patterns in protein sequence alignments and DNA sequences of target promoters. (wikipedia.org)
  • The second group deduced the code through molecular analysis of the TAL effector AvrBs3 and its target DNA sequence in the promoter of a pepper gene activated by AvrBs3. (wikipedia.org)
  • Then the normal translation will translate the tm-RNA codons sequence that will provide a particular tag which signifies that the protein is incomplete. (wikipedia.org)
  • A four-amino acid sequence motif - GYVG, glycine-tyrosine-valine-glycine - conserved in hslU ATPases and located on the inner surface of the assembled pore dramatically accelerates the degradation of some proteins, and is required for the degradation of others. (wikipedia.org)
  • sequences
  • The average coding sequences of human genes (1,340 bp) are similar to worms and flies , although they are spread out over larger regions (due to larger introns, on average 3.3 kb). (biomedcentral.com)
  • These proteins can bind promoter sequences in the host plant and activate the expression of plant genes that aid bacterial infection. (wikipedia.org)
  • These proteins are interesting to researchers both for their role in disease of important crop species and the relative ease of retargeting them to bind new DNA sequences. (wikipedia.org)
  • The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins. (wikipedia.org)
  • cellular
  • The gulf between the cellular organizations of eukaryotes and prokaryotes is all the more striking because no intermediates have been found. (royalsocietypublishing.org)
  • FMLP led to the first discovery of a leukocyte receptor for a chemotactic factor, defined three different types of FMLP receptors that have complimentary and/or opposing effects on inflammatory responses as well as many other activities, and helped define the stimulus-response coupling mechanisms by which diverse chemotactic factors and their G protein coupled receptors induce cellular function. (wikipedia.org)
  • The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of gene expression, and responses to oxidative stress. (wikipedia.org)
  • homologues
  • The high-resolution structures of the bacterial homologues provided an invaluable insight on many aspects of substrate recognition and transport through biological channels. (asm.org)
  • membrane
  • A comparison with other proteins in the family suggests the existence of a potential ion pair in the membrane domain. (asm.org)
  • Mechanistic understanding of membrane proteins is limited by the difficulties in obtaining structural data. (asm.org)
  • These problems stem mainly from difficulties in expressing, purifying, and crystallizing membrane proteins. (asm.org)
  • Although the interior of the nucleus does not contain any membrane-bound sub compartments, its contents are not uniform, and a number of sub-nuclear bodies exist, made up of unique proteins, RNA molecules, and particular parts of the chromosomes. (wikipedia.org)
  • Before the discovery of the ubiquitin proteasome system, protein degradation in cells was thought to rely mainly on lysosomes, membrane-bound organelles with acidic and protease-filled interiors that can degrade and then recycle exogenous proteins and aged or damaged organelles. (wikipedia.org)
  • The analysis revealed several genes with cell membrane-related functions. (wikipedia.org)
  • In eukaryotes, the function of these shared proteins include cell membrane deformation, cell shape formation, and a dynamic protein cytoskeleton. (wikipedia.org)
  • The repertoire of membrane-related functions of Lokiarchaeum suggests that the common ancestor to the eukaryotes might be an intermediate step between the prokaryotic cells, devoid of subcellular structures, and the eukaryotic cells, which harbor many organelles. (wikipedia.org)
  • At low surface area-to-volume ratios the diffusion of nutrients and waste products across the bacterial cell membrane limits the rate at which microbial metabolism can occur, making the cell less evolutionarily fit. (wikipedia.org)
  • Since the cell wall is required for bacterial survival, but is absent in some eukaryotes, several antibiotics (notably the penicillins and cephalosporins) stop bacterial infections by interfering with cell wall synthesis, while having no effects on human cells which have no cell wall only a cell membrane. (wikipedia.org)
  • distinct
  • Here we identified for the first time a group of phages encoded SSBs which are clearly distinct from their bacterial counterparts. (sigmaaldrich.com)
  • This was shown in 1978 to be composed of several distinct protein chains, a novelty among proteases at the time. (wikipedia.org)
  • molecular
  • The proteasome subcomponents are often referred to by their Svedberg sedimentation coefficient (denoted S). The proteasome most exclusively used in mammals is the cytosolic 26S proteasome, which is about 2000 kilodaltons (kDa) in molecular mass containing one 20S protein subunit and two 19S regulatory cap subunits. (wikipedia.org)
  • histones
  • Cell nuclei contain most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. (wikipedia.org)
  • Later work on modification of histones led to the identification of an unexpected covalent modification of the histone protein by a bond between a lysine side chain of the histone and the C-terminal glycine residue of ubiquitin, a protein that had no known function. (wikipedia.org)
  • structures
  • The high-resolution structures of two bacterial MFS proteins were solved: LacY, the lactose permease ( 1 ), and GlpT, the phosphate, glycerol 3-phosphate antiporter ( 10 ). (asm.org)
  • These α subunits are controlled by binding to "cap" structures or regulatory particles that recognize polyubiquitin tags attached to protein substrates and initiate the degradation process. (wikipedia.org)
  • While all bacterial cell walls (with a few exceptions e.g. extracellular parasites such as Mycoplasma) contain peptidoglycan, not all cell walls have the same overall structures. (wikipedia.org)
  • mammalian
  • Eukaryotes usually have a single nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei, and a few others have many. (wikipedia.org)
  • endogenous
  • Bacterial circadian rhythms, like other circadian rhythms, are endogenous "biological clocks" that have the following three characteristics: (a) in constant conditions (i.e. constant temperature and either constant light {LL} or constant darkness {DD}) they oscillate with a period that is close to, but not exactly, 24 hours in duration, (b) this "free-running" rhythm is temperature compensated, and (c) the rhythm will entrain to an appropriate environmental cycle. (wikipedia.org)
  • extracellular
  • Active, ATP-dependent, likely receptor-mediated import of extracellular proteins has been observed under laboratory conditions, although it is of unknown functional significance. (wikipedia.org)
  • recognize
  • Interference (or 'Immunity')- Interference involves the crRNAs within a multi-protein complex called CASCADE, which can recognize and specifically base-pair with regions of inserting complementary foreign DNA. (wikipedia.org)
  • bind
  • Polymorphonuclear cells can bind proteins starting with fMet, and use them to initiate the attraction of circulating blood leukocytes and then stimulate microbicidal activities such as phagocytosis. (wikipedia.org)
  • inject
  • They inject a number of effector proteins, including TAL effectors, into the plant via their type III secretion system. (wikipedia.org)
  • operon
  • The promoter region of the operon encoding HslU and HslV contains a stem-loop structure which is necessary for gene expression. (wikipedia.org)
  • clones
  • Expression cloning is a technique in DNA cloning that uses expression vectors to generate a library of clones, with each clone expressing one protein. (wikipedia.org)
  • proteasome
  • The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein. (wikipedia.org)
  • Later, the ATP-dependent proteolytic complex that was responsible for ubiquitin-dependent protein degradation was discovered and was called the 26S proteasome. (wikipedia.org)
  • HslV and hslU genes have also been identified in some eukaryotes, although these also require the constitutively expressed proteasome for survival. (wikipedia.org)
  • Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes. (wikipedia.org)
  • regulate
  • The transcriptional and translational signals may be synthetically created to make the expression of the gene of interest easier to regulate. (wikipedia.org)
  • fMet
  • The prototypical fMet-containing oligopeptide is N-Formylmethionine-leucyl-phenylalanine (FMLP) which activates leukocytes and other cell types by binding with these cells' formyl peptide receptor 1 (FPR1) and formyl peptide receptor 2 (FPR2) G protein coupled receptors (see also formyl peptide receptor 3). (wikipedia.org)
  • fMet-containing oligopeptides and proteins also function in other physiological and pathological responses. (wikipedia.org)
  • oligopeptides
  • The studies cited above lead to the eventual cloning of the human Formyl peptide receptor 1, a G protein coupled receptor that binds FMLP and other formylated oligopeptides to mediate their stimulatory actions on human and rabbit neutrophils. (wikipedia.org)
  • degradation
  • Proteins are tagged for degradation with a small protein called ubiquitin. (wikipedia.org)
  • It was then discovered that a previously identified protein associated with proteolytic degradation, known as ATP-dependent proteolysis factor 1 (APF-1), was the same protein as ubiquitin. (wikipedia.org)
  • Role of the GYVG pore motif of HslU ATPase in protein unfolding and translocation for degradation by HslV peptidase. (wikipedia.org)
  • nucleus
  • The nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression-the nucleus is, therefore, the control center of the cell. (wikipedia.org)
  • structural
  • Complex internal structure resembling a liquid crystal has been reported, with some structural similarities to the chromatin of eukaryotes such as dinoflagellates. (wikipedia.org)
  • molecules
  • The pores cross both nuclear membranes, providing a channel through which larger molecules must be actively transported by carrier proteins while allowing free movement of small molecules and ions. (wikipedia.org)
  • Movement of large molecules such as proteins and RNA through the pores is required for both gene expression and the maintenance of chromosomes. (wikipedia.org)
  • Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. (wikipedia.org)
  • In prokaryotes, the primary function of the cell wall is to protect the cell from internal turgor pressure caused by the much higher concentrations of proteins and other molecules inside the cell compared to its external environment. (wikipedia.org)
  • species
  • Typical examples include: coccus (spherical) bacillus (rod-like) spiral(DNA-like) filamentous (elongated) Cell shape is generally characteristic of a given bacterial species, but can vary depending on growth conditions. (wikipedia.org)