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In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.
Two classes of transcription terminators, Rho-dependent and Rho-independent, have been identified throughout prokaryotic genomes. These widely distributed sequences are responsible for triggering the end of transcription upon normal completion of gene or operon transcription, mediating early termination of transcripts as a means of regulation such as that observed in transcriptional attenuation, and to ensure the termination of runaway transcriptional complexes that manage to escape earlier terminators by chance, which prevents unnecessary energy expenditure for the cell.
Rho-dependent transcription terminators require a protein called Rho factor, which exhibits RNA helicase activity, to disrupt the mRNA-DNA-RNA polymerase transcriptional complex. Rho-dependent terminators are found in bacteria and phage. The Rho-dependent terminator occurs downstream of translational stop codons and consists of an unstructured, cytosine-rich sequence on the mRNA known as a Rho utilization site (rut) for which a consensus sequence has not been identified, and a downstream transcription stop point (tsp). The rut serves as a mRNA loading site and as an activator for Rho; activation enables Rho to efficiently hydrolyze ATP and translocate down the mRNA while it maintains contact with the rut site. Rho is able to catch up with the RNA polymerase, which is stalled at the downstream tsp sites. Contact between Rho and the RNA polymerase complex stimulates dissociation of the transcriptional complex through a mechanism involving allosteric effects of Rho on RNA polymerase.
Intrinsic transcription terminators or Rho-independent terminators require the formation of a self-annealing hairpin structure on the elongating transcript, which results in the disruption of the mRNA-DNA-RNA polymerase ternary complex. The terminator sequence in DNA contains a 20 basepair GC-rich region of dyad symmetry followed by a short poly-T tract or "T stretch" which is transcribed to form the terminating hairpin and a 7–9 nucleotide "U tract" respectively. The mechanism of termination is hypothesized to occur through a combination of direct promotion of dissociation through allosteric effects of hairpin binding interactions with the RNA polymerase and "competitive kinetics". The hairpin formation causes RNA polymerase stalling and destabilization, leading to a greater likelihood that dissociation of the complex will occur at that location due to an increased time spent paused at that site and reduced stability of the complex. Additionally, the elongation protein factor NusA interacts with the RNA polymerase and the hairpin structure to stimulate transcriptional termination.
In eukaryotic transcription of mRNAs, terminator signals are recognized by protein factors that are associated with the RNA polymerase II and which trigger the termination process. Once the poly-A signals are transcribed into the mRNA, the proteins cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CstF) transfer from the carboxyl terminal domain of RNA polymerase II to the poly-A signal. These two factors then recruit other proteins to the site to cleave the transcript, freeing the mRNA from the transcription complex, and add a string of about 200 A-repeats to the 3' end of the mRNA in a process known as polyadenylation. During these processing steps, the RNA polymerase continues to transcribe for several hundred to a few thousand bases and eventually dissociates from the DNA and downstream transcript through an unclear mechanism; there are two basic models for this event known as the torpedo and allosteric models.
After the mRNA is completed and cleaved off at the poly-A signal sequence, the left-over (residual) RNA strand remains bound to the DNA template and the RNA polymerase II unit, continuing to be transcribed. After this cleavage, a so-called exonuclease binds to the residual RNA strand and removes the freshly transcribed nucleotides one at a time (also called 'degrading' the RNA), moving towards the bound RNA polymerase II. This exonuclease is XRN2 (5'-3' Exoribonuclease 2) in humans. This model proposes that XRN2 proceeds to degrade the uncapped residual RNA from 5' to 3' until it reaches the RNA pol II unit. This causes the exonuclease to 'push off' the RNA pol II unit as it moves past it, terminating the transcription while also cleaning up the residual RNA strand.
Similar to Rho-dependent termination, XRN2 triggers the dissociation of RNA polymerase II by either pushing the polymerase off of the DNA template or pulling the template out of the RNA polymerase. The mechanism by which this happens remains unclear, however, and has been challenged not to be the sole cause of the dissociation.
In order to protect the transcribed mRNA from degradation by the exonuclease, a 5' cap is added to the strand. This is a modified guanine added to the front of mRNA, which prevents the exonuclease from binding and degrading the RNA strand. A 3' poly(A) tail is added to the end of a mRNA strand for protection from other exonucleases as well.
The allosteric model suggests that termination occurs due to the structural change of the RNA polymerase unit after binding to or losing some of its associated proteins, making it detach from the DNA strand after the signal. This would occur after the RNA pol II unit has transcribed the poly-A signal sequence, which acts as a terminator signal.
RNA polymerase is normally capable of transcribing DNA into single-stranded mRNA efficiently. However, upon transcribing over the poly-A signals on the DNA template, a conformational shift is induced in the RNA polymerase from the proposed loss of associated proteins from its carboxyl terminal domain. This change of conformation reduces RNA polymerase's processivity making the enzyme more prone to dissociating from its DNA-RNA substrate. In this case, termination is not completed by degradation of mRNA but instead is mediated by limiting the elongation efficiency of RNA polymerase and thus increasing the likelihood that the polymerase will dissociate and end its current cycle of transcription.
- Richardson, J. P. (1996). "Rho-dependent Termination of Transcription Is Governed Primarily by the Upstream Rho Utilization (rut) Sequences of a Terminator". Journal of Biological Chemistry. 271 (35): 21597–21603. doi:10.1074/jbc.271.35.21597. ISSN 0021-9258.
- Ciampi, MS. (Sep 2006). "Rho-dependent terminators and transcription termination". Microbiology. 152 (Pt 9): 2515–28. doi:10.1099/mic.0.28982-0. PMID 16946247.
- Epshtein, V; Dutta, D; Wade, J; Nudler, E (Jan 14, 2010). "An allosteric mechanism of Rho-dependent transcription termination". Nature. 463 (7278): 245–9. doi:10.1038/nature08669. PMC 2929367. PMID 20075920.
- von Hippel, P. H. (1998). "An Integrated Model of the Transcription Complex in Elongation, Termination, and Editing". Science. 281 (5377): 660–665. doi:10.1126/science.281.5377.660.
- Gusarov, Ivan; Nudler, Evgeny (1999). "The Mechanism of Intrinsic Transcription Termination". Molecular Cell. 3 (4): 495–504. doi:10.1016/S1097-2765(00)80477-3. ISSN 1097-2765.
- Santangelo, TJ.; Artsimovitch, I. (May 2011). "Termination and antitermination: RNA polymerase runs a stop sign". Nat Rev Microbiol. 9 (5): 319–29. doi:10.1038/nrmicro2560. PMC 3125153. PMID 21478900.
- Watson, J. (2008). Molecular Biology of the Gene. Cold Spring Harbor Laboratory Press. pp. 410–411. ISBN 978-0-8053-9592-1.
- Rosonina, Emanuel; Kaneko, Syuzo; Manley, James L. (2006-05-01). "Terminating the transcript: breaking up is hard to do". Genes & Development. 20 (9): 1050–1056. doi:10.1101/gad.1431606. ISSN 0890-9369. PMID 16651651.
- Luo, W.; Bartley D. (2004). "A ribonucleolytic rat torpedoes RNA polymerase II". Cell. 119 (7): 911–914. doi:10.1016/j.cell.2004.11.041. PMID 15620350.
- Luo, Weifei; Johnson, Arlen W.; Bentley, David L. (2006-04-15). "The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric–torpedo model". Genes & Development. 20 (8): 954–965. doi:10.1101/gad.1409106. ISSN 0890-9369. PMC 1472303. PMID 16598041.
You can either download the motif alignment or view it directly in your browser window. More...
You can download (or view in your browser) a text representation of a Rfam alignment in various formats:
- Gapped FASTA
- Ungapped FASTA
You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".
There are 247 Rfam families which match this motif.
This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...
To annotate the family with a motif model, the seed sequence was first filtered using a 0.9 fraction identity cut-off. The filtered seed was then scanned using Infernal cmscan (v1.1) with a concatenated CM file containing each of the motifs. Significance of hits between a seed sequence and the CM was based on a gathering threshold that was individually set for each motif. Only motifs where more than two and at least 10% of seed sequences scored higher than the gathering threshold were included for the next stage of processing. These subsets of motifs were then rescanned against the entire (non-filtered) seed to generate matches.
Number of Hits: the number of sequences in the family seed that score above the gathering threshold from motif.
Fraction of Hits: the fraction of sequences in the family seed that score above the gathering threshold from motif.
Sum of Bits: the sum of the bit scores of matches between the motif and the family seed sequence.
Image: plot illustrating where on the consensus secondary structure matches occur between seed sequences and the motif model.
|Original order||Family Accession||Family Description||Number of Hits||Fraction of Hits||Sum of Bits||Image|
|3||RF00018||CsrB/RsmB RNA family||35||0.921||660.3|
|3||RF00021||Spot 42 RNA||19||1.000||334.1|
|3||RF00028||Group I catalytic intron||2||0.167||58.9|
|3||RF00080||yybP-ykoY manganese riboswitch||5||0.172||66.4|
|3||RF00083||GlmZ RNA activator of glmS mRNA||18||0.857||248.8|
|3||RF00084||CsrC RNA family||4||1.000||110.1|
|3||RF00130||mir-192/215 microRNA precursor||19||0.463||297.5|
|3||RF00140||Alpha operon ribosome binding site||7||0.179||79.0|
|3||RF00143||mir-6 microRNA precursor||9||0.375||109.1|
|3||RF00166||PrrB/RsmZ RNA family||11||0.297||144.9|
|3||RF00229||Picornavirus internal ribosome entry site (IRES)||23||0.250||247.0|
|3||RF00257||mir-194 microRNA precursor family||12||0.414||133.2|
|3||RF00280||Small nucleolar RNA SNORD51||4||0.286||52.4|
|3||RF00304||Small nucleolar RNA Z279/snoR105/snoR108||2||0.100||24.8|
|3||RF00345||Small nucleolar RNA snoR1||2||0.154||23.0|
|3||RF00397||Small nucleolar RNA SNORA14||3||0.167||38.7|
|3||RF00424||Small Cajal body specific RNA 16||5||0.135||61.7|
|3||RF00488||Yeast U1 spliceosomal RNA||3||0.600||31.9|
|3||RF00506||Threonine operon leader||25||1.000||565.0|
|3||RF00512||Leucine operon leader||6||1.000||94.4|
|3||RF00513||Tryptophan operon leader||9||0.409||117.7|
|3||RF00514||Histidine operon leader||33||1.000||587.4|
|3||RF00515||PyrR binding site||26||0.634||373.2|
|3||RF00519||Makes More Granules Regulator RNA (mmgR)||81||0.931||1185.2|
|3||RF00540||Small nucleolar RNA psi18S-1854||4||0.250||48.9|
|3||RF00557||Ribosomal protein L10 leader||77||0.794||1238.8|
|3||RF00558||Ribosomal protein L20 leader||35||0.814||526.0|
|3||RF00563||Small nucleolar RNA SNORA53||4||0.143||53.6|
|3||RF00586||Small nucleolar RNA SNORA12||2||0.087||27.8|
|3||RF00598||Small nucleolar RNA SNORA76||4||0.182||48.7|
|3||RF00599||Small nucleolar RNA SNORA77||9||0.474||116.7|
|3||RF00600||Small nucleolar RNA SNORA79||4||0.160||49.0|
|3||RF01065||23S methyl RNA motif||7||0.368||99.0|
|3||RF01071||Ornate Large Extremophilic RNA||3||0.150||41.5|
|3||RF01227||Small nucleolar RNA snoR83||4||0.571||49.0|
|3||RF01231||Small nucleolar RNA snoR74||2||0.222||23.3|
|3||RF01241||Small nucleolar RNA SNORA81||12||0.429||136.6|
|3||RF01249||Small nucleolar RNA snR190||5||0.500||66.7|
|3||RF01264||Small nucleolar RNA snR83||4||0.800||65.6|
|3||RF01267||Small nucleolar RNA snR37||5||0.556||62.3|
|3||RF01270||Small nucleolar RNA snR84||2||0.333||21.0|
|3||RF01272||Small nucleolar RNA snR86||3||0.600||51.5|
|3||RF01395||isrL Hfq binding RNA||4||1.000||52.9|
|3||RF01401||rseX Hfq binding RNA||5||0.417||58.6|
|3||RF01402||STnc150 Hfq binding RNA||9||1.000||151.5|
|3||RF01407||STnc560 Hfq binding RNA||12||1.000||169.0|
|3||RF01408||sraL Hfq binding RNA||5||0.833||54.1|
|3||RF01419||Antisense RNA which regulates isiA expression||64||0.208||797.7|
|3||RF01456||Vibrio regulatory RNA of OmpA||11||1.000||163.7|
|3||RF01459||Listeria sRNA rliE||4||1.000||88.0|
|3||RF01470||Listeria sRNA rli38||15||0.750||271.4|
|3||RF01472||Listeria sRNA rli40||4||1.000||77.0|
|3||RF01473||Listeria sRNA rli41||6||1.000||66.3|
|3||RF01491||Listeria sRNA rli54||10||2.000||114.8|
|3||RF01670||Pseudomonas sRNA P17||3||1.000||35.5|
|3||RF01675||Pseudomonas sRNA CrcZ||5||0.263||60.6|
|3||RF01743||leu/phe leader RNA from Lactococcus||6||0.667||138.2|
|3||RF01769||Enterobacteria greA leader||3||0.120||32.2|
|3||RF01770||Gammaprotebacteria rimP leader||46||1.000||879.8|
|3||RF01771||Enterobacteria rnk leader||13||1.000||189.6|
|3||RF01772||Pseudomonas rnk leader||15||1.000||233.0|
|3||RF01773||Pseudomonas rpsL leader||9||1.000||122.7|
|3||RF01774||Rickettsia rpsL leader||7||1.000||108.9|
|3||RF01775||RNA S.aureus Orsay G||3||0.429||34.5|
|3||RF01796||Fumarate/nitrate reductase regulator sRNA||9||0.562||111.5|
|3||RF01808||MicX Vibrio cholerae sRNA||10||1.000||279.2|
|3||RF01816||RNA Staph. aureus A||3||0.429||37.6|
|3||RF01819||RNA Staph. aureus D||8||1.000||111.4|
|3||RF01820||RNA Staph. aureus E (RoxS)||11||0.733||148.6|
|3||RF01848||ACEA small nucleolar RNA U3||5||0.179||60.0|
|3||RF01859||Phenylalanine leader peptide||65||0.915||974.4|
|3||RF01882||Taurine upregulated gene 1 conserved region 1||15||0.714||182.1|
|3||RF01959||Archaeal small subunit ribosomal RNA||30||0.349||401.4|
|3||RF01960||Eukaryotic small subunit ribosomal RNA||31||0.341||574.8|
|3||RF02045||CDKN2B antisense RNA 1 convserved region 3||2||0.111||21.7|
|3||RF02053||Enterobacterial sRNA STnc430||6||0.857||127.8|
|3||RF02055||Enterobacterial sRNA STnc380||4||0.800||80.7|
|3||RF02057||Salmonella enterica sRNA STnc40||17||1.000||240.2|
|3||RF02060||Enterobacterial sRNA STnc410||3||0.214||36.5|
|3||RF02064||Enterobacterial sRNA STnc370||10||1.000||135.2|
|3||RF02065||Enterobacterial sRNA STnc340||3||0.750||57.8|
|3||RF02067||Salmonella enterica sRNA STnc310||4||0.500||74.0|
|3||RF02074||Enterobacterial sRNA STnc240||15||1.000||257.8|
|3||RF02075||Enterobacterial sRNA STnc230||4||0.364||47.3|
|3||RF02076||Gammaproteobacterial sRNA STnc100||8||0.333||106.8|
|3||RF02079||Enterobacterial sRNA STnc180||4||0.400||65.3|
|3||RF02082||Enterobacterial sRNA STnc540||3||1.000||69.6|
|3||RF02084||Enterobacteria sRNA STnc130||5||0.385||58.6|
|3||RF02096||mir-2973 microRNA precursor||2||0.286||21.9|
|3||RF02142||HOXA11 antisense RNA 1 conserved region 6||6||0.286||72.5|
|3||RF02143||Hydatidiform mole associated and imprinted conserved region 1||3||0.188||34.2|
|3||RF02190||ST7 overlapping transcript 4 conserved region 4||4||0.154||51.6|
|3||RF02225||Proteobacterial sRNA sX6||8||1.000||109.6|
|3||RF02230||Proteobacterial sRNA sX11||10||1.000||135.7|
|3||RF02241||Xanthomonadaceae sRNA Xoo2||3||1.000||46.7|
|3||RF02243||Proteobacterial sRNA Xoo8||4||1.000||49.6|
|3||RF02278||Betaproteobacteria toxic small RNA||47||0.922||747.2|
|3||RF02330||Tetrahymena snoRNA TtnuHACA23||2||1.000||23.8|
|3||RF02342||Alphaproteobacterial sRNA ar7||18||0.621||255.0|
|3||RF02343||Alphaproteobacterial sRNA ar9||16||0.571||256.3|
|3||RF02346||Alphaproteobacterial sRNA ar35||12||0.923||164.3|
|3||RF02351||Proteobacteria sRNA psRNA14||2||0.667||39.7|
|3||RF02353||Bradyrhizobiaceae sRNA BjrC68||11||0.917||146.3|
|3||RF02356||Alphaproteobacterial sRNA BjrC1505||23||0.920||319.0|
|3||RF02362||Cyanobacterial functional RNA 10||5||0.833||81.3|
|3||RF02363||Cyanobacterial functional RNA 11||4||1.000||51.7|
|3||RF02366||Cyanobacterial functional RNA 19||6||1.000||140.5|
|3||RF02370||Bacillus tryptophan operon leader||5||0.556||57.4|
|3||RF02379||Cia-dependent small RNA csRNA1||12||0.250||131.1|
|3||RF02384||FasX small RNA||3||0.375||31.1|
|3||RF02399||Nitrogen stress-induced RNA 1||6||0.353||76.6|
|3||RF02405||Pseudomonas sRNA P34||5||1.000||99.9|
|3||RF02409||Small nucleolar RNA snoR125||5||1.000||75.2|
|3||RF02410||Small nucleolar RNA snoR136||3||0.375||36.8|
|3||RF02411||Small nucleolar RNA snoR138||3||0.429||38.2|
|3||RF02419||Streptococcus sRNA Spd-sr37||3||0.120||31.5|
|3||RF02423||Burkholderia sRNA Bp1_Cand871_SIPHT||9||0.600||103.7|
|3||RF02424||Burkholderia sRNA Bp2_Cand287_SIPHT||9||0.643||99.6|
|3||RF02425||Streptococcus sRNA SpF01||10||0.769||156.4|
|3||RF02430||Streptococcus sRNA SpF19||3||1.000||42.3|
|3||RF02431||Streptococcus sRNA SpF22||3||0.136||35.7|
|3||RF02432||Streptococcus sRNA SpF25||18||0.900||300.1|
|3||RF02433||Streptococcus sRNA SpF36||4||1.000||101.4|
|3||RF02434||Streptococcus sRNA SpF39||13||1.000||278.9|
|3||RF02435||Streptococcus sRNA SpF41||2||0.222||33.9|
|3||RF02442||Streptococcus sRNA SpF66||9||1.000||144.4|
|3||RF02445||Streptococcus sRNA SpR14||3||0.600||32.6|
|3||RF02449||Bacillus sRNA ncr1015||16||1.000||300.4|
|3||RF02450||Bacillus sRNA ncr1175||4||1.000||78.3|
|3||RF02451||Bacillus sRNA ncr1241||4||0.500||53.3|
|3||RF02452||Bacillus sRNA ncr1575||20||0.690||257.6|
|3||RF02454||Bacillus sRNA ncr982||6||1.000||94.6|
|3||RF02495||Oppression of Hydrophobic ORF by sRNA||23||0.676||274.8|
|3||RF02502||Rhizobiales sRNA Atu_C8||26||0.963||339.2|
|3||RF02503||Rhizobiales sRNA Atu_C9||9||1.000||137.2|
|3||RF02524||Streptococcus sRNA sagA||6||1.000||101.0|
|3||RF02526||Streptococcus sRNA SSRC34||8||0.500||95.3|
|3||RF02543||Eukaryotic large subunit ribosomal RNA||37||0.420||871.6|
|3||RF02551||ABC transporter regulator||6||1.000||98.3|
|3||RF02574||Rickettsia sRNA 10||3||1.000||31.7|
|3||RF02630||Hfq-regulated sRNA 12||2||1.000||30.2|
|3||RF02631||Hfq-regulated sRNA 13||2||1.000||27.5|
|3||RF02713||Mycoplasma sRNA MCS4||5||1.000||90.5|
|3||RF02728||Haemophilus regulatory RNA responsive to iron||7||1.000||109.4|
|3||RF02732||Aggregatibacter sRNA JA04||5||0.833||90.1|
|3||RF02737||Soft rot Enterobacteriaceae Rev 13 asRNA||3||1.000||38.6|
|3||RF02744||Soft rot Enterobacteriaceae Rev 39 5'UTR||4||1.000||75.3|
|3||RF02767||Yersinia sRNA 186/sR026/CsrC||4||1.000||79.6|
|3||RF02834||Vibrio RNA VqmR||3||0.750||39.3|
|3||RF02837||Burkholderia RNA 7 (anti-hemB)||3||1.000||60.6|
|3||RF02838||Enterococcus sRNA 55||2||0.500||23.3|
|3||RF02842||Enterococcus sRNA A1||4||1.000||50.6|
|3||RF02844||Enterococcus sRNA A9||2||0.500||27.0|
|3||RF02845||Enterococcus sRNA 1C||2||1.000||51.0|
|3||RF02858||Actinobacillus sRNA 08||2||0.667||36.2|
|3||RF02859||Actinobacillus sRNA 11||2||1.000||36.8|
|3||RF02860||Actinobacillus sRNA 14||4||1.000||54.3|
|3||RF02863||Enterococcus sRNA 2410||2||0.667||45.7|
|3||RF02865||Burkholderia sRNA 1||4||1.000||53.8|
|3||RF02866||Burkholderia sRNA 16 (Bc_KC_sr1)||3||0.750||35.1|
|3||RF02867||Burkholderia sRNA 11||4||1.000||64.0|
|3||RF02868||Burkholderia sRNA 37||3||1.000||41.7|
|3||RF02870||Burkholderia sRNA 35||2||0.667||24.9|
|3||RF02875||Antisense to pHK01_035||3||1.000||31.4|
|3||RF02876||Antisense to pHK01_099||2||0.500||20.6|
This section shows the database cross-references that we have for this Rfam motif.
Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z Nucleic Acids Res. 2011;39:5845-52. RNIE: genome-wide prediction of bacterial intrinsic terminators. PUBMED:21478170
External database links
|External sites:|| 1: http://github.com/ppgardne/RNIE
Curation and motif details
This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.
|Seed source||Published; PMID:21478170|
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
|Covariance model||Download the Infernal CM for the motif here|