Team:Hong Kong HKUST/riboregulator/regulatory RNAs catalog

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Revision as of 16:04, 30 May 2015



Catalog for regulatory RNAs

Over the years, the number of regulatory RNAs in Part Registry has steadily increased over time and many has been made available to end users. Based on different mode actions and natures of regulatory RNAs, they can be grouped into different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing regulatory RNAs. Some of them are grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them.Over the years, the number of non-coding RNAs in Part Registry has increased steadily over time and many have been made available to end users. More than 400 entries in the Part Registry are related to RNA devices (updated 25-12-2014). Based on different mode of actions and natures of non-coding RNAs (ncRNAs), they can be grouped under different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing ncRNAs. Some of them are simply grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them. For example, BBa_K145013, which is a part for antisense LuxI, could be used to add an extra layer of control to the widely utilized quorum sensing Lux pathway but it has not been extensively reused. It is likely that Part Registry users are unaware of its existence because there has yet to be an information hub for ncRNA.

We would like to solve this problem by designing a list of category tags as well as a guideline, so that automated display of non-coding RNAs by the function can be facilitated. By doing so, we hope that we can assist other users to find and use those parts efficiently. Ultimately we want to facilitate the implementation of the philosophy of Part Registry, which is to get and give (and share), through a better organization of ncRNA parts in the registry.

This page was written in compliance with Part Registry's format for general Catalog Pages. Currently, the information is uploaded manually because we have yet to submit our suggestions to iGEM HQ. Upon approval, we will tag existing regulatory RNAs and complete the page. Being part of the cross-cohort "Project Riboregulator", the page is far from complete and is expected to take shape by Summer 2015. We welcome and encourage constant update and adoption of this page in the future.


For more information on categorized ncRNAs on this page, please refer to A Guideline for Categorization of non-coding RNA In Part Registry.

Riboregulator

Riboregulators regulate translation by two elements: a cis-repressive sequence upstream of RBS, and a trans-activating RNA. In absence of the latter, the cis-repressive sequence promotes formation of a hairpin at the RBS. With the RBS locked up, translation cannot take place.. Trans-activating RNA, when introduced, can form complementary bases to cis-repressive sequence, promotes disassembly of the hairpin, and expose the RBS for ribosomal binding, allowing translation to occur.

Designer Part Number Description
Delft 2009 BBa_K175029 Weak lock
Delft 2009 BBa_K175030 Key for lcok of weak RBS
Delft 2009 BBa_K175030 Medium lock
Delft 2009 BBa_K175030 Key for Medium lock
Delft 2009 BBa_K175034 (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030
Delft 2009 BBa_K175034 Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032
Caltech 2007 BBa_I759015 cis3-repressed, tet-regulated YFP
Caltech 2007 BBa_I759016 cis4-repressed, tet-regulated YFP
Caltech 2007 BBa_I759020 cis8-repressed, tet-regulated YFP
Caltech 2007 BBa_I759027 cis3-repressed, tet-regulated Q
Caltech 2007 BBa_I759028 cis4-repressed, tet-regulated Q
Caltech 2007 BBa_I759014 (cis2-repressed, tet-regulated YFP
Caltech 2007 BBa_I759017 cis5-repressed, tet-regulated YFP
Caltech 2007 BBa_I759018 cis6-repressed, tet-regulated YFP
Caltech 2007 BBa_I759019 cis7-repressed, tet-regulated YFP
Caltech 2007 BBa_I759013 cis1-repressed, tet-regulated YFP
Caltech 2007 BBa_I759032 Ptet_cis1_YFP
Caltech 2007 BBa_I759034 Ptet_cis2_YFP
Caltech 2007 BBa_I759036 Ptet_cis3_YFP
Caltech 2007 BBa_I759038 Ptet_cis4_YFP
Caltech 2007 BBa_I759040 Ptet_cis5_YFP
Caltech 2007 BBa_I759042 Ptet_cis6_YFP
Caltech 2007 BBa_I759044 Ptet_cis7_YFP
Caltech 2007 BBa_I759046 Ptet_cis8_YFP
Caltech 2007 BBa_I759023 pBAD-trans2
Caltech 2007 BBa_I759022 pBAD-trans1
Caltech 2007 BBa_I759024 pBAD-trans3
Caltech 2007 BBa_I759025 pBAD-trans4
Caltech 2007 BBa_I759026 pBAD-trans5
Peking 2007 BBa_I714070 R0040-J23078-pTet-Lock3
Peking 2007 BBa_I714080 [R0040][J23078][E0040][B0015]
Peking 2007 BBa_I714081 R0040-J01010-E0040-B0015
Peking 2007 BBa_I714037 R751+ C600 E.coli cells with traI-R751 knockout
Peking 2007 BBa_I714074 R0010-J23066-pLac-Key3-DblTerm Uses Lock and Key 3 from berkeley
K.U. Leuven 2008 BBa_K145215 FILTER Key (TetR promoter + key)
K.U. Leuven 2008 BBa_K145216 FILTER T7 RNA pol Lock from berkeley
K.U. Leuven 2008 BBa_K145217 FILTER Complete The two previous together
K.U. Leuven 2008 BBa_K145220 INVERTED TIMER
K.U. Leuven 2008 BBa_K145225 RESET lactonase
K.U. Leuven 2008 BBa_K145300 Lactonase controlled by key/lock
K.U. Leuven 2008 BBa_K145301 lacI controlled by key/lock
K.U. Leuven 2008 BBa_K145302 luxI generator controlled by key/lock
K.U. Leuven 2008 BBa_K145303 GFP generator controlled by key/lock
K.U. Leuven 2008 BBa_K145003 T7 PoPS -> RiboKey 3d
K.U. Leuven 2008 BBa_K145004 T7 PoPS + RiboLock |> LuxI
K.U. Leuven 2008 BBa_K145005 T7 PoPS + PR -> cI
K.U. Leuven 2008 BBa_K145216 FILTER T7 RNA pol
K.U. Leuven 2008 BBa_K145251 OLD RESET lactonase
K.U. Leuven 2008 BBa_K145253 OLD INVERTIMER Part 1
K.U. Leuven 2008 BBa_K145255 NEW INVERTIMER part 1
K.U. Leuven 2008 BBa_K145264 test FILTER (new)
K.U. Leuven 2008 BBa_K145265 test FILTER (old)
K.U. Leuven 2008 BBa_K145271 GFP regulated by AND-gate
K.U. Leuven 2008 BBa_K145272 GFP regulated by AND-gate
K.U. Leuven 2008 BBa_K145275 T7 polymerase generator under TetR repressible promoter (filter)
K.U. Leuven 2008 BBa_K145276 T7 polymerase generator under TetR repressible promoter
K.U. Leuven 2008 BBa_K145277 T7 DNA polymerase regulated by lock
K.U. Leuven 2008 BBa_K145278 T7 DNA polymerase regulated by [lock3d]
K.U. Leuven 2009 BBa_K238004 Vanillin synthesis
K.U. Leuven 2009 BBa_K238006 Short version of vanillin synthesis
K.U. Leuven 2009 BBa_K238012 short version II of vanillin synthesis
Groningen 2011 BBa_K607005 short version II of vanillin synthesis
Groningen 2011 BBa_K607000 PhybB_taRNA
VictoriaBC 2009 BBa_K235010 [K145303] (ribokey-controlled GFP generator)
VictoriaBC 2009 BBa_K235000 [R0010][J23066] (pLac+ribokey+stop)
VictoriaBC 2009 BBa_K235001 [J23102][J23066] (constitutive promoter+ribokey+stop)
VictoriaBC 2009 BBa_K235009 [J23102][J23032] (constitutive promoter+ribolocked RBS)
VictoriaBC 2009 BBa_K235011 [K235009][K235005] (ribokey-controlled mCherry generator)
VictoriaBC 2009 BBa_K235013 [K145303][K235000] (ribokey-mediated pLac-controlled GFP reporter)
VictoriaBC 2009 BBa_K235014 [K145303][K235001] (ribokey-mediated GFP generator)
VictoriaBC 2009 BBa_K235016 [I0500][J23032] (pAra+ribolocked RBS)
VictoriaBC 2009 BBa_K235019 [K235016][K235003] (ribokey-mediated pAra-controlled lambda repressor generator)
VictoriaBC 2009 BBa_K235021 [K235009][K235003] (ribokey-mediated lambda repressor generator)
VictoriaBC 2009 BBa_K235022 [K235018][K235019] (mCherry generator, pAra-controlled ribokey-mediated signal inversion)
VictoriaBC 2009 BBa_K235024 [K235018][K235021] (mCherry generator, ribokey-mediated signal inversion)
VictoriaBC 2009 BBa_K235025 [K235022][K235000] (NAND gate, pAra and pLac input signal control, mCherry output signal)
VictoriaBC 2009 BBa_K235026 [K235022][K235001] (NAND gate control test, pLac positive control)
VictoriaBC 2009 BBa_K235027 [K235024][K235000] (NAND gate control test, arabinose positive control)
VictoriaBC 2009 BBa_K235028 [K235024][K235001] (NAND gate control test, positive control)
Melborne2008 BBa_K085000 (lacI)promoter->key3c
Melborne2008 BBa_K085002 pTet->lock3d->GFP
Calgary 2007 BBa_I737003 OmpF controlled RNA Key
Calgary 2007 BBa_I737006 Temperature induced repression/activation of an RNA key
Calgary 2007 BBa_I737005 AHL and RNA lock controlled AraC

RNA Aptamer

An RNA aptamer can fold into a tertiary confirmation that binds with strong affinity and high specificity to small molecules through non-Watson-Crick base pairing.

Designer Part Number Description

CRISPR

CRISPR/Cas RNAs are guiding RNAs that direct Cas proteins to their spacers. They can be a 2-subunit RNA comprising CRISPR RNA (crRNA) and trans-acting crRNA (tracrRNA). They can also be a single guide RNA by fusing the above 2 functional domains together through RNA linkers. They associate with Cas proteins or their derivatives and guide them to DNA containing complementary sequence to crRNA.

Designer Part Number Description

RNA-IN / RNA-OUT

RNA-IN RNA-OUT regulates translation on the RNA level. RNA-IN is located upstream of RBS whereas RNA-OUT is a small ncRNA which is form complementary base-pairing with RNA-IN. In the presence of the RNA-OUT, RNA-IN will hybridize with RNA-OUT and block the RBS and the start codon, with the RBS locked up, translation cannot take place.

Designer Part Number Description

RNA interference (RNAi)

Small interfering RNAs (siRNAs) and micro RNAs (miRNAs) function through the RNA interference (RNAi) pathway. siRNAs are usually produced by "dicing" exogenous, long double stranded RNA into 21-nucleotides small fragments. Whereas miRNAs usually have an endogenous origin and started as hairpin transcripts. Processed siRNAs or miRNAs associates with Argonaute in the RNA-induced silencing complex (RISC). The complex then search for RNA targets using the siRNA/miRNA, and in most cases degrades the latter, resulting in inhibition or reduction of gene expression.

Designer Part Number Description

Riboswitch

A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an on or off manner. Riboswitches usually contain sensor domains that bind small molecules and regulatory domains that regulate gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation. on or off manner. Riboswitches usually contain sensor domains for binding of small molecules and regulatory domains for gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation.

Designer Part Number Description

Ribozyme

A ribozyme is an RNA molecule with intrinsic catalytic activity, which are usually cleavage or ligation activities.

Designer Part Number Description

Aptazyme

RNA aptazymes, as the name suggests, are RNAs that carry properties o both aptamers and ribozymes. They are capable of sensing small molecules. Ribozyme-mediated cleavage is triggered upon ligand binding.

• For a part to be qualified as an apatazyme, the aptamer domain and the ribozyme domain should be functionally coupled. An RNA that contains aptamer domains and ribozyme domains without functional relationships is merely a composite RNA device.

Designer Part Number Description

pT181

The pT181-RNAI is a special class of ncRNAs derived from elements in the Staphylococcus aureus pathogenicity plasmid pT181. A specific 5’ UTR region would normally form an anti-termination loop. pT181-RNAI, when introduced, induces formation of a premature terminator loop instead, which results in early termination an incompletely transcribed mRNA.

Designer Part Number Description

Complex

This tag describes ncRNA BioBricks containing 2 or more ncRNAs..

Designer Part Number Description

Target sequence

This tag describes with segments of ncRNAs that are purposefully designed to serve as recognizable targets by other ncRNAs.

Designer Part Number Description

Other

This tag describes ncRNAs that do not belong to any types of ncRNA listed above

Designer Part Number Description

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