Abstract：
:Riboswitches are RNA-based regulatory devices that mediate ligand-dependent control of gene expression. However, there has been limited success in rationally designing riboswitches. Moreover, most previous riboswitches are confined to a particular gene and only perform one-way regulation. Here, we used a library screening strategy for efficient creation of ON and OFF riboswitches of lacI on the chromosome of Escherichia coli. We then engineered a riboswitch-LacP hybrid device to achieve portable gene control in response to theophylline and IPTG. Moreover, this device regulated target expression in a 'two-way' manner: the default state of target expression was ON; the expression was switched off by adding theophylline and restored to the ON state by adding IPTG without changing growth medium. We showcased the portability and two-way regulation of this device by applying it to the small RNA CsrB and the RpoS protein. Finally, the use of the hybrid device uncovered an inhibitory role of RpoS in acetate assimilation, a function which is otherwise neglected using conventional genetic approaches. Overall, this work establishes a portable riboswitch-LacP device that achieves sequential OFF-and-ON gene regulation. The two-way control of gene expression has various potential scientific and biotechnological applications and helps reveal novel gene functions.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Jin Y,Huang JDdoi
10.1093/nar/gkr609subject
Has Abstractpub_date
2011-10-01 00:00:00pages
e131issue
19eissn
0305-1048issn
1362-4962pii
gkr609journal_volume
39pub_type
杂志文章abstract：:Genomic meta-analysis to combine relevant and homogeneous studies has been widely applied, but the quality control (QC) and objective inclusion/exclusion criteria have been largely overlooked. Currently, the inclusion/exclusion criteria mostly depend on ad-hoc expert opinion or naïve threshold by sample size or platfo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1071
更新日期：2012-01-01 00:00:00
abstract：:Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecul...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky765
更新日期：2018-11-16 00:00:00
abstract：:DNA binding of heat shock factor 2 (HSF2) is induced during hemin-induced differentiation of human erythroleukemia cell line K562. To identify the transcriptional activation and the regulatory domains of HSF2, we constructed a series of deletion derivatives fused to the yeast GAL4 DNA binding domain and analyzed their...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.11.2580
更新日期：1998-06-01 00:00:00
abstract：:This report documents the error rate in a commercially distributed subset of the IMAGE Consortium mouse cDNA clone collection. After isolation of plasmid DNA from 1189 bacterial stock cultures, only 62. 2% were uncontaminated and contained cDNA inserts that had significant sequence identity to published data for the o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.2.582
更新日期：2001-01-15 00:00:00
abstract：:We previously proposed that the first enzyme for histidine biosynthesis in Salmonellatyphimurium plays a role in regulating expression of the histidine operon and that in order to play this role the enzyme must form a complex with histidyl-tRNA. Among the many observations that led to these conclusions were 1) that re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.7.881
更新日期：1974-07-01 00:00:00
abstract：:The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson-Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1124
更新日期：2008-03-01 00:00:00
abstract：:The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv260
更新日期：2015-04-30 00:00:00
abstract：:Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw930
更新日期：2016-11-16 00:00:00
abstract：:Reverse transcription in retroviruses and retrotransposons requires nucleic acid chaperones, which drive the rearrangement of nucleic acid conformation. The nucleic acid chaperone properties of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid (NC) protein have been extensively studied, and nucleic acid agg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr726
更新日期：2012-01-01 00:00:00
abstract：:Apicoplast, an essential organelle of human malaria parasite Plasmodium falciparum contains a ∼35 kb circular genome and is a possible target for therapy. Proteins required for the replication and maintenance of the apicoplast DNA are not clearly known. Here we report the presence of single-stranded DNA binding protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq565
更新日期：2010-11-01 00:00:00
abstract：:IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl958
更新日期：2007-01-01 00:00:00
abstract：:Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.22.4495
更新日期：1996-11-15 00:00:00
abstract：:Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We hav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg049
更新日期：2003-01-01 00:00:00
abstract：:Uridylation-dependent RNA decay is a widespread eukaryotic pathway modulating RNA homeostasis. Terminal uridylyltransferases (Tutases) add untemplated uridyl residues to RNA 3'-ends, marking them for degradation by the U-specific exonuclease Dis3L2. In Schizosaccharomyces pombe, Cid1 uridylates a variety of RNAs. In t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz043
更新日期：2019-04-08 00:00:00
abstract：:In kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g)RNAs. Currently popular mechanisms for the editing process envisage a series of consecutive 'cut-and-paste' reactions, carried out by a compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.14.2950
更新日期：2001-07-15 00:00:00
abstract：:Intrinsic energetic and solvation factors contributing to the unusual structural and biochemical properties of N3'-phosphoramidate DNA analogs have been re-examined using a combination of quantum mechanical and molecular dynamics methods. Evaluation of the impact of the N3'-H substitution was performed via comparison ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.15.3219
更新日期：2001-08-01 00:00:00
abstract：:The thyroid hormone receptor alpha (THRA or c-erbA-1) gene belongs to a family of genes which encode nuclear receptors for various hydrophobic ligands such as steroids, vitamin D, retinoic acid and thyroid hormones. These receptors are composed of several domains important for hormone-binding, DNA-binding, dimerizatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.5.1105
更新日期：1991-03-11 00:00:00
abstract：:A role for BRCA1 in the direct and indirect regulation of transcription is well established. However, a comprehensive view of the degree to which BRCA1 impacts transcriptional regulation on a genome-wide level has not been defined. We performed genome-wide expression profiling and ChIP-chip analysis, comparison of whi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr679
更新日期：2011-12-01 00:00:00
abstract：:The cnjC gene from the protozoan Tetrahymena thermophila was completely sequenced. The deduced gene product was found to have significant sequence similarity to the yeast and prokaryotic RNA polymerase subunits involved with subunit assembly. Since cnjC is active only during the sexual stage (conjugation) of Tetrahyme...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.10.2953
更新日期：1990-05-25 00:00:00
abstract：:Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf062
更新日期：2002-06-15 00:00:00
abstract：:The expression of thymidine kinase in fungi, which normally lack this enzyme, will greatly aid the study of DNA metabolism and provide useful drug-sensitive phenotypes. The herpes simplex virus type-1 thymidine kinase gene ( tk ) was expressed in Neurospora crassa. tk was expressed as a fusion to N.crassa arg-2 regula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.12.2389
更新日期：1997-06-15 00:00:00
abstract：:A search of sequence information in the GenBank files shows that tracts of 15-30 contiguous purines are greatly overrepresented in all eukaryotic species examined, ranging from yeast to human. Such an overabundance does not occur in prokaryotic sequences. The large increase in the number of oligopurine tracts cannot b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.4.689
更新日期：1995-02-25 00:00:00
abstract：:Modified bases, such as O6-methylguanines, are produced in cells exposed to alkylating agents and cause apoptosis. In human cells treated with N-methyl-N-nitrosourea, we detected a protein complex composed of MutSalpha, MutLalpha and PCNA on damaged DNA by immunoprecipitation method using chromatin extracts, in which ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki878
更新日期：2005-10-04 00:00:00
abstract：:The combination of RNA interference (RNAi) with the tetracycline-controlled transcription activation (tet) system promises to become a powerful method for conditional gene inactivation in cultured cells and in whole organisms. Here, we tested critical sequence elements that originated from miRNA mR-30 for optimal effi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq616
更新日期：2010-09-01 00:00:00
abstract：:The bacteriophage Mu A and B genes, which lie adjacent to each other and are colinear on the phage genome, encode proteins that catalyze efficient transposition of Mu DNA. We show that the molar ratio of A and B proteins is approximately 1:20 in extracts prepared after induction of cells containing a Mu lysogen or a p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.23.11285
更新日期：1988-12-09 00:00:00
abstract：:A new method for evaluating some complex characteristics of the primary structure of E.coli promoters is proposed. The method, of nonparametric statistical significance, selects important conserved single-base positions in combination with 2-base coupling relations of identity and complementarity. The extended consens...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.12.4799
更新日期：1989-06-26 00:00:00
abstract：:RNA interference represents a potent intervention for cancer treatment but requires a robust delivery agent for transporting gene-modulating molecules, such as small interfering RNAs (siRNAs). Although numerous molecular approaches for siRNA delivery are adequate in vitro, delivery to therapeutic targets in vivo is li...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz900
更新日期：2019-12-02 00:00:00
abstract：:The E. coli single-stranded binding protein (SSB) has been demonstrated in vitro to be involved in a number of replicative, DNA renaturation, and protective functions. It was shown previously that SSB can interact with exonuclease I to stimulate the hydrolysis of single-stranded DNA. We demonstrate here that E. coli S...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.2.247
更新日期：1994-01-25 00:00:00
abstract：:The evolution of regulatory networks in Bacteria has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations fas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa162
更新日期：2020-05-07 00:00:00
abstract：:We have previously shown that integration of a polyoma vector containing rodent repetitive elements into rat cellular DNA is non-random (Wallenburg et al. J. Virol. 50: 678-683). Junctions between the polyoma vector and the host DNA occur in the repetitive sequences of the vector about ten times more frequently than w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.19.7849
更新日期：1987-10-12 00:00:00
