Tandem fluorescent protein timers for in vivo analysis of protein dynamics.

Abstract:

:The functional state of a cell is largely determined by the spatiotemporal organization of its proteome. Technologies exist for measuring particular aspects of protein turnover and localization, but comprehensive analysis of protein dynamics across different scales is possible only by combining several methods. Here we describe tandem fluorescent protein timers (tFTs), fusions of two single-color fluorescent proteins that mature with different kinetics, which we use to analyze protein turnover and mobility in living cells. We fuse tFTs to proteins in yeast to study the longevity, segregation and inheritance of cellular components and the mobility of proteins between subcellular compartments; to measure protein degradation kinetics without the need for time-course measurements; and to conduct high-throughput screens for regulators of protein turnover. Our experiments reveal the stable nature and asymmetric inheritance of nuclear pore complexes and identify regulators of N-end rule–mediated protein degradation.

journal_name

Nat Biotechnol

journal_title

Nature biotechnology

authors

Khmelinskii A,Keller PJ,Bartosik A,Meurer M,Barry JD,Mardin BR,Kaufmann A,Trautmann S,Wachsmuth M,Pereira G,Huber W,Schiebel E,Knop M

doi

10.1038/nbt.2281

subject

Has Abstract

pub_date

2012-06-24 00:00:00

pages

708-14

issue

7

eissn

1087-0156

issn

1546-1696

pii

nbt.2281

journal_volume

30

pub_type

杂志文章
  • Statistical pattern matching facilitates the design of polyvalent inhibitors of anthrax and cholera toxins.

    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

    authors: Rai P,Padala C,Poon V,Saraph A,Basha S,Kate S,Tao K,Mogridge J,Kane RS

    更新日期:2006-05-01 00:00:00

  • Prospects for plant-derived antibacterials.

    abstract::Can weakly active phytochemicals be combined synergistically to produce new antibacterial treatments? ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1206-1504

    authors: Lewis K,Ausubel FM

    更新日期:2006-12-01 00:00:00

  • Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions.

    abstract::Antifreeze proteins (AFPs) are found in cold-adapted organisms and have the unusual ability to bind to and inhibit the growth of ice crystals. However, the underlying molecular basis of their ice-binding activity is unclear because of the difficulty of studying the AFP-ice interaction directly and the lack of a common...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1224

    authors: Doxey AC,Yaish MW,Griffith M,McConkey BJ

    更新日期:2006-07-01 00:00:00

  • A policy approach to the development of molecular diagnostic tests.

    abstract::Efficiently generating evidence of clinical utility is a major challenge for ensuring clinical adoption of valuable diagnostics. A new approach to reimbursement in the United States offers a balance between evidence and incentives for molecular diagnostic tests. ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1110-1157

    authors: Schulman KA,Tunis SR

    更新日期:2010-11-01 00:00:00

  • Systems strategies for developing industrial microbial strains.

    abstract::Industrial strain development requires system-wide engineering and optimization of cellular metabolism while considering industrially relevant fermentation and recovery processes. It can be conceptualized as several strategies, which may be implemented in an iterative fashion and in different orders. The key challenge...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,评审

    doi:10.1038/nbt.3365

    authors: Lee SY,Kim HU

    更新日期:2015-10-01 00:00:00

  • Directed evolution of proteins by exon shuffling.

    abstract::Evolution of eukaryotes is mediated by sexual recombination of parental genomes. Crossovers occur in random, but homologous, positions at a frequency that depends on DNA length. As exons occupy only 1% of the human genome and introns about 24%, by far most of the crossovers occur between exons, rather than inside. The...

    journal_title:Nature biotechnology

    pub_type: 杂志文章,评审

    doi:10.1038/88084

    authors: Kolkman JA,Stemmer WP

    更新日期:2001-05-01 00:00:00

  • Microscale culture of human liver cells for drug development.

    abstract::Tissue function depends on hierarchical structures extending from single cells ( approximately 10 microm) to functional subunits (100 microm-1 mm) that coordinate organ functions. Conventional cell culture disperses tissues into single cells while neglecting higher-order processes. The application of semiconductor-dri...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1361

    authors: Khetani SR,Bhatia SN

    更新日期:2008-01-01 00:00:00

  • Engineering soluble proteins for structural genomics.

    abstract::Structural genomics has the ambitious goal of delivering three-dimensional structural information on a genome-wide scale. Yet only a small fraction of natural proteins are suitable for structure determination because of bottlenecks such as poor expression, aggregation, and misfolding of proteins, and difficulties in s...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt732

    authors: Pédelacq JD,Piltch E,Liong EC,Berendzen J,Kim CY,Rho BS,Park MS,Terwilliger TC,Waldo GS

    更新日期:2002-09-01 00:00:00

  • Profiling alternative splicing on fiber-optic arrays.

    abstract::The human transcriptome is marked by extensive alternative mRNA splicing and the expression of many closely related genes, which may be difficult to distinguish using standard microarray techniques. Here we describe a sensitive and specific assay for parallel analysis of mRNA isoforms on a fiber-optic microarray platf...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0402-353

    authors: Yeakley JM,Fan JB,Doucet D,Luo L,Wickham E,Ye Z,Chee MS,Fu XD

    更新日期:2002-04-01 00:00:00

  • A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples.

    abstract::Comparing diverse single-cell RNA sequencing (scRNA-seq) datasets generated by different technologies and in different laboratories remains a major challenge. Here we address the need for guidance in choosing algorithms leading to accurate biological interpretations of varied data types acquired with different platfor...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/s41587-020-00748-9

    authors: Chen W,Zhao Y,Chen X,Yang Z,Xu X,Bi Y,Chen V,Li J,Choi H,Ernest B,Tran B,Mehta M,Kumar P,Farmer A,Mir A,Mehra UA,Li JL,Moos M Jr,Xiao W,Wang C

    更新日期:2020-12-21 00:00:00

  • Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.

    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

    authors: Ding J,Adiconis X,Simmons SK,Kowalczyk MS,Hession CC,Marjanovic ND,Hughes TK,Wadsworth MH,Burks T,Nguyen LT,Kwon JYH,Barak B,Ge W,Kedaigle AJ,Carroll S,Li S,Hacohen N,Rozenblatt-Rosen O,Shalek AK,Villani AC,Regev

    更新日期:2020-06-01 00:00:00

  • Selective amplification of protein-coding regions of large sets of genes using statistically designed primer sets.

    abstract::We describe a novel approach to design a set of primers selective for large groups of genes. This method is based on the distribution frequency of all nucleotide combinations (octa- to decanucleotides), and the combined ability of primer pairs, based on these oligonucleotides, to detect genes. By analyzing 1000 human ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0796-857

    authors: López-Nieto CE,Nigam SK

    更新日期:1996-07-01 00:00:00

  • At the heart of genetic testing.

    abstract::Genetic testing for rare heart conditions might someday expand to more common cardiac ailments. Already there are signs testing is dramatically changing how some conditions are treated and doctors' definition of who a patient is. Stephen Strauss reports. ...

    journal_title:Nature biotechnology

    pub_type: 新闻

    doi:10.1038/nbt1010-1003

    authors: Strauss S

    更新日期:2010-10-01 00:00:00

  • A signal sequence trap based on a constitutively active cytokine receptor.

    abstract::Targeting of secreted and cell-surface proteins to the cell membrane is mediated by a short hydrophobic stretch of amino acids, termed the signal sequence. We have developed a method that detects signal sequences in cDNA fragments based on their ability to redirect a constitutively active mutant of a cytokine receptor...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/8666

    authors: Kojima T,Kitamura T

    更新日期:1999-05-01 00:00:00

  • Tumor refractoriness to anti-VEGF treatment is mediated by CD11b+Gr1+ myeloid cells.

    abstract::Vascular endothelial growth factor (VEGF) is an essential regulator of normal and abnormal blood vessel growth. A monoclonal antibody (mAb) that targets VEGF suppresses tumor growth in murine cancer models and human patients. We investigated cellular and molecular events that mediate refractoriness of tumors to anti-a...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1323

    authors: Shojaei F,Wu X,Malik AK,Zhong C,Baldwin ME,Schanz S,Fuh G,Gerber HP,Ferrara N

    更新日期:2007-08-01 00:00:00

  • Blockade of CD2-LFA-3 interactions protects human skin allografts in immunodeficient mouse/human chimeras.

    abstract::A human skin allograft injury model in immunodeficient mice, engrafted with human peripheral blood mononuclear cells from a different donor, has been used to test whether reagents that block human T cell CD2 interactions with its principal ligand, LFA-3 (CD58), can inhibit immune reactions in vivo. In this model, huma...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0897-759

    authors: Sultan P,Schechner JS,McNiff JM,Hochman PS,Hughes CC,Lorber MI,Askenase PW,Pober JS

    更新日期:1997-08-01 00:00:00

  • Prevention of systemic lupus erythematosus in MRL/lpr mice by administration of an immunoglobulin-binding peptide.

    abstract::Systemic lupus erythematosus (SLE) is a multisystem chronic inflammatory disease of unknown etiology that affects many organs, including the kidney. The presence of multiple autoantibodies and other immunological abnormalities point to basic defects in immunoregulatory controls that normally maintain self-tolerance. T...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/77296

    authors: Marino M,Ruvo M,De Falco S,Fassina G

    更新日期:2000-07-01 00:00:00

  • Visualizing lipid-formulated siRNA release from endosomes and target gene knockdown.

    abstract::A central hurdle in developing small interfering RNAs (siRNAs) as therapeutics is the inefficiency of their delivery across the plasma and endosomal membranes to the cytosol, where they interact with the RNA interference machinery. With the aim of improving endosomal release, a poorly understood and inefficient proces...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3298

    authors: Wittrup A,Ai A,Liu X,Hamar P,Trifonova R,Charisse K,Manoharan M,Kirchhausen T,Lieberman J

    更新日期:2015-08-01 00:00:00

  • Human embryonic stem cell-derived cardiomyocytes restore function in infarcted hearts of non-human primates.

    abstract::Pluripotent stem cell-derived cardiomyocyte grafts can remuscularize substantial amounts of infarcted myocardium and beat in synchrony with the heart, but in some settings cause ventricular arrhythmias. It is unknown whether human cardiomyocytes can restore cardiac function in a physiologically relevant large animal m...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.4162

    authors: Liu YW,Chen B,Yang X,Fugate JA,Kalucki FA,Futakuchi-Tsuchida A,Couture L,Vogel KW,Astley CA,Baldessari A,Ogle J,Don CW,Steinberg ZL,Seslar SP,Tuck SA,Tsuchida H,Naumova AV,Dupras SK,Lyu MS,Lee J,Hailey DW,Reinec

    更新日期:2018-08-01 00:00:00

  • Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations.

    abstract::The ability to detect single protein molecules in blood could accelerate the discovery and use of more sensitive diagnostic biomarkers. To detect low-abundance proteins in blood, we captured them on microscopic beads decorated with specific antibodies and then labeled the immunocomplexes (one or zero labeled target pr...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1641

    authors: Rissin DM,Kan CW,Campbell TG,Howes SC,Fournier DR,Song L,Piech T,Patel PP,Chang L,Rivnak AJ,Ferrell EP,Randall JD,Provuncher GK,Walt DR,Duffy DC

    更新日期:2010-06-01 00:00:00

  • Generation of oligodendroglial cells by direct lineage conversion.

    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

    authors: Yang N,Zuchero JB,Ahlenius H,Marro S,Ng YH,Vierbuchen T,Hawkins JS,Geissler R,Barres BA,Wernig M

    更新日期:2013-05-01 00:00:00

  • Integration and expression of the high-molecular-weight glutenin subunit 1Ax1 gene into wheat.

    abstract::The unique bread-making characteristic of wheat flour is closely related to the elasticity and extensibility of the gluten proteins stored in the starchy endosperm, particularly the high-molecular-weight glutenin subunits (HMW-GS), which are important in determining gluten and dough elasticity. The quality of wheat cu...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0996-1155

    authors: Altpeter F,Vasil V,Srivastava V,Vasil IK

    更新日期:1996-09-01 00:00:00

  • Engineered off-the-shelf therapeutic T cells resist host immune rejection.

    abstract::Engineered T cells are effective therapies against a range of malignancies, but current approaches rely on autologous T cells, which are difficult and expensive to manufacture. Efforts to develop potent allogeneic T cells that are not rejected by the recipient's immune system require abrogating both T- and natural kil...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/s41587-020-0601-5

    authors: Mo F,Watanabe N,McKenna MK,Hicks MJ,Srinivasan M,Gomes-Silva D,Atilla E,Smith T,Ataca Atilla P,Ma R,Quach D,Heslop HE,Brenner MK,Mamonkin M

    更新日期:2021-01-01 00:00:00

  • Reversible permeabilization of plasma membranes with an engineered switchable pore.

    abstract::By using an engineered, self-assembling, proteinaceous, 2-nm pore equipped with a metal-actuated switch, a technique to reversibly permeabilize the plasma membrane to small molecules (approximately 1000 Da) has been developed. We have demonstrated the dose-dependent permeabilization of fibroblasts by pores designed to...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt0397-278

    authors: Russo MJ,Bayley H,Toner M

    更新日期:1997-03-01 00:00:00

  • Reengineering a receptor footprint of adeno-associated virus enables selective and systemic gene transfer to muscle.

    abstract::Reengineering the receptor footprints of adeno-associated virus (AAV) isolates may yield variants with improved properties for clinical applications. We generated a panel of synthetic AAV2 vectors by replacing a hexapeptide sequence in a previously identified heparan sulfate receptor footprint with corresponding resid...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.1599

    authors: Asokan A,Conway JC,Phillips JL,Li C,Hegge J,Sinnott R,Yadav S,DiPrimio N,Nam HJ,Agbandje-McKenna M,McPhee S,Wolff J,Samulski RJ

    更新日期:2010-01-01 00:00:00

  • Efficient proximity labeling in living cells and organisms with TurboID.

    abstract::Protein interaction networks and protein compartmentalization underlie all signaling and regulatory processes in cells. Enzyme-catalyzed proximity labeling (PL) has emerged as a new approach to study the spatial and interaction characteristics of proteins in living cells. However, current PL methods require over 18 h ...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.4201

    authors: Branon TC,Bosch JA,Sanchez AD,Udeshi ND,Svinkina T,Carr SA,Feldman JL,Perrimon N,Ting AY

    更新日期:2018-10-01 00:00:00

  • Homology-driven genome editing in hematopoietic stem and progenitor cells using ZFN mRNA and AAV6 donors.

    abstract::Genome editing with targeted nucleases and DNA donor templates homologous to the break site has proven challenging in human hematopoietic stem and progenitor cells (HSPCs), and particularly in the most primitive, long-term repopulating cell population. Here we report that combining electroporation of zinc finger nucle...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3408

    authors: Wang J,Exline CM,DeClercq JJ,Llewellyn GN,Hayward SB,Li PW,Shivak DA,Surosky RT,Gregory PD,Holmes MC,Cannon PM

    更新日期:2015-12-01 00:00:00

  • Plant viral genes in DNA idiotypic vaccines activate linked CD4+ T-cell mediated immunity against B-cell malignancies.

    abstract::DNA delivery of tumor antigens can activate specific immune attack on cancer cells. However, antigens may be weak, and immune capacity can be compromised. Fusion of genes encoding activating sequences to the tumor antigen sequence facilitates promotion and manipulation of effector pathways. Idiotypic determinants of B...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/90816

    authors: Savelyeva N,Munday R,Spellerberg MB,Lomonossoff GP,Stevenson FK

    更新日期:2001-08-01 00:00:00

  • A high-quality catalog of the Drosophila melanogaster proteome.

    abstract::Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanog...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt1300

    authors: Brunner E,Ahrens CH,Mohanty S,Baetschmann H,Loevenich S,Potthast F,Deutsch EW,Panse C,de Lichtenberg U,Rinner O,Lee H,Pedrioli PG,Malmstrom J,Koehler K,Schrimpf S,Krijgsveld J,Kregenow F,Heck AJ,Hafen E,Schlapbach R

    更新日期:2007-05-01 00:00:00

  • A calcium- and light-gated switch to induce gene expression in activated neurons.

    abstract::Despite recent advances in optogenetics, it remains challenging to manipulate gene expression in specific populations of neurons. We present a dual-protein switch system, Cal-Light, that translates neuronal-activity-mediated calcium signaling into gene expression in a light-dependent manner. In cultured neurons and br...

    journal_title:Nature biotechnology

    pub_type: 杂志文章

    doi:10.1038/nbt.3902

    authors: Lee D,Hyun JH,Jung K,Hannan P,Kwon HB

    更新日期:2017-09-01 00:00:00