Abstract:
:Heterologous pathways used in metabolic engineering may produce intermediates toxic to the cell. Dynamic control of pathway enzymes could prevent the accumulation of these metabolites, but such a strategy requires sensors, which are largely unknown, that can detect and respond to the metabolite. Here we applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product. We apply this approach to regulate farnesyl pyrophosphate (FPP) production in the isoprenoid biosynthetic pathway in Escherichia coli. This strategy improved production of amorphadiene, the final product, by twofold over that from inducible or constitutive promoters, eliminated the need for expensive inducers, reduced acetate accumulation and improved growth. We extended this approach to another toxic intermediate to demonstrate the broad utility of identifying novel sensor-regulator systems for dynamic regulation.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Dahl RH,Zhang F,Alonso-Gutierrez J,Baidoo E,Batth TS,Redding-Johanson AM,Petzold CJ,Mukhopadhyay A,Lee TS,Adams PD,Keasling JDdoi
10.1038/nbt.2689subject
Has Abstractpub_date
2013-11-01 00:00:00pages
1039-46issue
11eissn
1087-0156issn
1546-1696pii
nbt.2689journal_volume
31pub_type
杂志文章abstract::Numerous biological processes involve the recognition of a specific pattern of binding sites on a target protein or surface. Although ligands displayed by disordered scaffolds form stochastic rather than specific patterns, theoretical models predict that recognition will occur between patterns that are characterized b...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1204
更新日期:2006-05-01 00:00:00
abstract::Transplantation of oligodendrocyte precursor cells (OPCs) is a promising potential therapeutic strategy for diseases affecting myelin. However, the derivation of engraftable OPCs from human pluripotent stem cells has proven difficult and primary OPCs are not readily available. Here we report the generation of induced ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2564
更新日期:2013-05-01 00:00:00
abstract::The basics of determining valuation will help you to understand what criteria matter most for investors. ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:
更新日期:2004-08-01 00:00:00
abstract::Paralleling the diversity of genetic and protein activities, pathologic human tissues also exhibit diverse radiographic features. Here we show that dynamic imaging traits in non-invasive computed tomography (CT) systematically correlate with the global gene expression programs of primary human liver cancer. Combinatio...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1306
更新日期:2007-06-01 00:00:00
abstract::Therapeutic ex vivo T-cell expansion is limited by low rates and T-cell products of limited functionality. Here we describe a system that mimics natural antigen-presenting cells (APCs) and consists of a fluid lipid bilayer supported by mesoporous silica micro-rods. The lipid bilayer presents membrane-bound cues for T-...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.4047
更新日期:2018-02-01 00:00:00
abstract::Academic researchers have regularly ignored patents on key technologies as a strategy to maneuver around patent thickets and freedom-to-operate issues, but they may be more at risk than they realize. ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1107-1225
更新日期:2007-11-01 00:00:00
abstract::We describe a simple technology used to cure an established metastatic disease. Intradermal injection of plasmid DNA encoding a transcriptionally targeted cytotoxic gene, along with hsp70, not only promoted tissue-specific, inflammatory killing of normal melanocytes, but also induced a CD8(+) T-cell-dependent, antigen...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1007
更新日期:2004-09-01 00:00:00
abstract::Development of a cell therapy for diabetes would be greatly aided by a renewable supply of human beta-cells. Here we show that pancreatic endoderm derived from human embryonic stem (hES) cells efficiently generates glucose-responsive endocrine cells after implantation into mice. Upon glucose stimulation of the implant...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1393
更新日期:2008-04-01 00:00:00
abstract::Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt.4022
更新日期:2017-12-01 00:00:00
abstract::Efficient delivery of small interfering (si)RNA to specific cell populations in vivo remains a formidable challenge to its successful therapeutic application. We show that siRNA synthetically linked to a CpG oligonucleotide agonist of toll-like receptor (TLR)9 targets and silences genes in TLR9(+) myeloid cells and B ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.1564
更新日期:2009-10-01 00:00:00
abstract::Debates on patenting DNA must evolve to reflect the global decline in filings and regional disparities in patenting activity. ...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt0207-185
更新日期:2007-02-01 00:00:00
abstract::Escherichia coli-based artificial chromosomes have become important tools for physical mapping and sequencing in various genome projects. The lack of a general method to modify these large bacterial clones, however, has limited their utility in functional studies. We developed a simple method to modify bacterial artif...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0997-859
更新日期:1997-09-01 00:00:00
abstract::The advent of in vitro DNA amplification has enabled rapid acquisition of genomic information. We present here an analogous technique for protein detection, in which the coordinated and proximal binding of a target protein by two DNA aptamers promotes ligation of oligonucleotides linked to each aptamer affinity probe....
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0502-473
更新日期:2002-05-01 00:00:00
abstract::Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. Although tens of thousands of phosphorylation sites have been identified in human cells, approaches to determine the functional importance of each phosphosite are lacking. Here, we manually cu...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-019-0344-3
更新日期:2020-03-01 00:00:00
abstract::In most tree-breeding programs worldwide, increasing the trees' growth rates and stem volumes and shortening their rotation times are important aims. Such trees would yield more biomass per unit area. Here we show that overexpressing a key regulatory gene in the biosynthesis of the plant hormone gibberellin (GA) in hy...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/77355
更新日期:2000-07-01 00:00:00
abstract::MicroRNAs (miRNAs) are increasingly implicated in the regulation of metastasis. Despite their potential as targets for anti-metastatic therapy, miRNAs have only been silenced in normal tissues of rodents and nonhuman primates. Therefore, the development of effective approaches for sequence-specific inhibition of miRNA...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.1618
更新日期:2010-04-01 00:00:00
abstract::CRISPR-Cas9-based genetic screens are a powerful new tool in biology. By simply altering the sequence of the single-guide RNA (sgRNA), one can reprogram Cas9 to target different sites in the genome with relative ease, but the on-target activity and off-target effects of individual sgRNAs can vary widely. Here, we use ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3437
更新日期:2016-02-01 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Nature biotechnology
pub_type: 已发布勘误
doi:10.1038/s41587-019-0167-2
更新日期:2019-07-01 00:00:00
abstract::The identification of co-regulated genes and their transcription-factor binding sites (TFBS) are key steps toward understanding transcription regulation. In addition to effective laboratory assays, various computational approaches for the detection of TFBS in promoter regions of coexpressed genes have been developed. ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt802
更新日期:2003-04-01 00:00:00
abstract::Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3267
更新日期:2015-07-01 00:00:00
abstract::Detection of mutations and damaged DNA bases is important for the early diagnosis of genetic disease. Here we describe an electrocatalytic method for the detection of single-base mismatches as well as DNA base lesions in fully hybridized duplexes, based on charge transport through DNA films. Gold electrodes modified w...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/80301
更新日期:2000-10-01 00:00:00
abstract::The scale and capabilities of single-cell RNA-sequencing methods have expanded rapidly in recent years, enabling major discoveries and large-scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single-cell and/or si...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0465-8
更新日期:2020-06-01 00:00:00
abstract::Cells isolated from the embryonic, neonatal, and adult rodent central nervous system divide in response to epidermal growth factor (EGF) and fibroblast growth factor 2 (FGF-2), while retaining the ability to differentiate into neurons and glia. These cultures can be grown in aggregates termed neurospheres, which conta...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/88158
更新日期:2001-05-01 00:00:00
abstract::The site-specific recombinases FLP and Cre are useful for genomic engineering in many living systems. Manipulation of their enzymatic properties offers a means to improve their applicability in different host organisms. We chose to manipulate the thermolability of FLP recombinase. A lacZ-based recombination assay in E...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0798-657
更新日期:1998-07-01 00:00:00
abstract::The adoptive transfer of antigen-specific cytotoxic T lymphocytes (CTLs) is a promising therapeutic approach for a number of diseases. To overcome the difficulty in generating specific CTLs, we established stable artificial antigen-presenting cells (AAPCs) that can be used to stimulate T cells of any patient of a give...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/74455
更新日期:2000-04-01 00:00:00
abstract::The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single ce...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3880
更新日期:2017-07-01 00:00:00
abstract::Recombinant adeno-associated viruses (rAAVs) are commonly used vehicles for in vivo gene transfer. However, the tropism repertoire of naturally occurring AAVs is limited, prompting a search for novel AAV capsids with desired characteristics. Here we describe a capsid selection method, called Cre recombination-based AA...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3440
更新日期:2016-02-01 00:00:00
abstract::Can new approaches for deriving human stem cells circumnavigate existing patents that dominate embryonic stem cell intellectual property? ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0406-411
更新日期:2006-04-01 00:00:00
abstract::Single-molecule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduced accuracy in homonucleotide stretches. We now combine the CsgG nanopore with the 35-residue N-terminal region of its extracellular interaction partner CsgF to produce a dual-constriction pore with improved...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0570-8
更新日期:2020-12-01 00:00:00
abstract::Dietary omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs), docosahexaenoic acid (DHA, C22:6) and eicosapentaenoic acid (EPA, C20:5) are usually derived from marine fish. Although production of both EPA and DHA has been engineered into land plants, including Arabidopsis, Camelina sativa and Brassica juncea, nei...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3585
更新日期:2016-08-01 00:00:00