Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog.

Abstract:

:Serine phosphorylation is a key post-translational modification that regulates diverse biological processes. Powerful analytical methods have identified thousands of phosphorylation sites, but many of their functions remain to be deciphered. A key to understanding the function of protein phosphorylation is access to phosphorylated proteins, but this is often challenging or impossible. Here we evolve an orthogonal aminoacyl-tRNA synthetase/tRNACUA pair that directs the efficient incorporation of phosphoserine (pSer (1)) into recombinant proteins in Escherichia coli. Moreover, combining the orthogonal pair with a metabolically engineered E. coli enables the site-specific incorporation of a nonhydrolyzable analog of pSer. Our approach enables quantitative decoding of the amber stop codon as pSer, and we purify, with yields of several milligrams per liter of culture, proteins bearing biologically relevant phosphorylations that were previously challenging or impossible to access--including phosphorylated ubiquitin and the kinase Nek7, which is synthetically activated by a genetically encoded phosphorylation in its activation loop.

journal_name

Nat Chem Biol

journal_title

Nature chemical biology

authors

Rogerson DT,Sachdeva A,Wang K,Haq T,Kazlauskaite A,Hancock SM,Huguenin-Dezot N,Muqit MM,Fry AM,Bayliss R,Chin JW

doi

10.1038/nchembio.1823

subject

Has Abstract

pub_date

2015-07-01 00:00:00

pages

496-503

issue

7

eissn

1552-4450

issn

1552-4469

pii

nchembio.1823

journal_volume

11

pub_type

杂志文章
  • Heterogeneity in the chemistry, structure and function of plant cell walls.

    abstract::Higher plants resist the forces of gravity and powerful lateral forces through the cumulative strength of the walls that surround individual cells. These walls consist mainly of cellulose, noncellulosic polysaccharides and lignin, in proportions that depend upon the specific functions of the cell and its stage of deve...

    journal_title:Nature chemical biology

    pub_type: 杂志文章,评审

    doi:10.1038/nchembio.439

    authors: Burton RA,Gidley MJ,Fincher GB

    更新日期:2010-10-01 00:00:00

  • Secondary structure reshuffling modulates glycosyltransferase function at the membrane.

    abstract::Secondary structure refolding is a key event in biology as it modulates the conformation of many proteins in the cell, generating functional or aberrant states. The crystal structures of mannosyltransferase PimA reveal an exceptional flexibility of the protein along the catalytic cycle, including β-strand-to-α-helix a...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1694

    authors: Giganti D,Albesa-Jové D,Urresti S,Rodrigo-Unzueta A,Martínez MA,Comino N,Barilone N,Bellinzoni M,Chenal A,Guerin ME,Alzari PM

    更新日期:2015-01-01 00:00:00

  • Primary amines protect against retinal degeneration in mouse models of retinopathies.

    abstract::Vertebrate vision is initiated by photoisomerization of the visual pigment chromophore 11-cis-retinal and is maintained by continuous regeneration of this retinoid through a series of reactions termed the retinoid cycle. However, toxic side reaction products, especially those involving reactive aldehyde groups of the ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.759

    authors: Maeda A,Golczak M,Chen Y,Okano K,Kohno H,Shiose S,Ishikawa K,Harte W,Palczewska G,Maeda T,Palczewski K

    更新日期:2011-12-25 00:00:00

  • Insights into mucopolysaccharidosis I from the structure and action of α-L-iduronidase.

    abstract::Mucopolysaccharidosis type I (MPS I), caused by mutations in the gene encoding α-L-iduronidase (IDUA), is one of approximately 70 genetic disorders collectively known as the lysosomal storage diseases. To gain insight into the basis for MPS I, we crystallized human IDUA produced in an Arabidopsis thaliana cgl mutant. ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1357

    authors: Bie H,Yin J,He X,Kermode AR,Goddard-Borger ED,Withers SG,James MN

    更新日期:2013-11-01 00:00:00

  • Nitric oxide activates TRP channels by cysteine S-nitrosylation.

    abstract::Transient receptor potential (TRP) proteins form plasma-membrane cation channels that act as sensors for diverse cellular stimuli. Here, we report a novel activation mechanism mediated by cysteine S-nitrosylation in TRP channels. Recombinant TRPC1, TRPC4, TRPC5, TRPV1, TRPV3 and TRPV4 of the TRPC and TRPV families, wh...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio821

    authors: Yoshida T,Inoue R,Morii T,Takahashi N,Yamamoto S,Hara Y,Tominaga M,Shimizu S,Sato Y,Mori Y

    更新日期:2006-11-01 00:00:00

  • Small molecule-triggered Cas9 protein with improved genome-editing specificity.

    abstract::Directly modulating the activity of genome-editing proteins has the potential to increase their specificity by reducing activity following target locus modification. We developed Cas9 nucleases that are activated by the presence of a cell-permeable small molecule by inserting an evolved 4-hydroxytamoxifen-responsive i...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1793

    authors: Davis KM,Pattanayak V,Thompson DB,Zuris JA,Liu DR

    更新日期:2015-05-01 00:00:00

  • Serine is a new target residue for endogenous ADP-ribosylation on histones.

    abstract::ADP-ribosylation (ADPr) is a biologically and clinically important post-translational modification, but little is known about the amino acids it targets on cellular proteins. Here we present a proteomic approach for direct in vivo identification and quantification of ADPr sites on histones. We have identified 12 uniqu...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2180

    authors: Leidecker O,Bonfiglio JJ,Colby T,Zhang Q,Atanassov I,Zaja R,Palazzo L,Stockum A,Ahel I,Matic I

    更新日期:2016-12-01 00:00:00

  • Optogenetic control of kinetochore function.

    abstract::Kinetochores act as hubs for multiple activities during cell division, including microtubule interactions and spindle checkpoint signaling. Each kinetochore can act autonomously, and activities change rapidly as proteins are recruited to, or removed from, kinetochores. Understanding this dynamic system requires tools ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2456

    authors: Zhang H,Aonbangkhen C,Tarasovetc EV,Ballister ER,Chenoweth DM,Lampson MA

    更新日期:2017-10-01 00:00:00

  • Determinants of amyloid fibril degradation by the PDZ protease HTRA1.

    abstract::Excessive aggregation of proteins has a major impact on cell fate and is a hallmark of amyloid diseases in humans. To resolve insoluble deposits and to maintain protein homeostasis, all cells use dedicated protein disaggregation, protein folding and protein degradation factors. Despite intense recent research, the und...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1931

    authors: Poepsel S,Sprengel A,Sacca B,Kaschani F,Kaiser M,Gatsogiannis C,Raunser S,Clausen T,Ehrmann M

    更新日期:2015-11-01 00:00:00

  • Discovery of MRSA active antibiotics using primary sequence from the human microbiome.

    abstract::Here we present a natural product discovery approach, whereby structures are bioinformatically predicted from primary sequence and produced by chemical synthesis (synthetic-bioinformatic natural products, syn-BNPs), circumventing the need for bacterial culture and gene expression. When we applied the approach to nonri...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2207

    authors: Chu J,Vila-Farres X,Inoyama D,Ternei M,Cohen LJ,Gordon EA,Reddy BV,Charlop-Powers Z,Zebroski HA,Gallardo-Macias R,Jaskowski M,Satish S,Park S,Perlin DS,Freundlich JS,Brady SF

    更新日期:2016-12-01 00:00:00

  • A PHGDH inhibitor reveals coordination of serine synthesis and one-carbon unit fate.

    abstract::Serine is both a proteinogenic amino acid and the source of one-carbon units essential for de novo purine and deoxythymidine synthesis. In the canonical pathway of glucose-derived serine synthesis, Homo sapiens phosphoglycerate dehydrogenase (PHGDH) catalyzes the first, rate-limiting step. Genetic loss of PHGDH is tox...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2070

    authors: Pacold ME,Brimacombe KR,Chan SH,Rohde JM,Lewis CA,Swier LJ,Possemato R,Chen WW,Sullivan LB,Fiske BP,Cho S,Freinkman E,Birsoy K,Abu-Remaileh M,Shaul YD,Liu CM,Zhou M,Koh MJ,Chung H,Davidson SM,Luengo A,Wang AQ,

    更新日期:2016-06-01 00:00:00

  • Structure and function of the bacterial decapping enzyme NudC.

    abstract::RNA capping and decapping are thought to be distinctive features of eukaryotes. The redox cofactor NAD was recently discovered to be attached to small regulatory RNAs in bacteria in a cap-like manner, and Nudix hydrolase NudC was found to act as a NAD-decapping enzyme in vitro and in vivo. Here, crystal structures of ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2132

    authors: Höfer K,Li S,Abele F,Frindert J,Schlotthauer J,Grawenhoff J,Du J,Patel DJ,Jäschke A

    更新日期:2016-09-01 00:00:00

  • Identifying polyglutamine protein species in situ that best predict neurodegeneration.

    abstract::Polyglutamine (polyQ) stretches exceeding a threshold length confer a toxic function to proteins that contain them and cause at least nine neurological disorders. The basis for this toxicity threshold is unclear. Although polyQ expansions render proteins prone to aggregate into inclusion bodies, this may be a neuronal...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.694

    authors: Miller J,Arrasate M,Brooks E,Libeu CP,Legleiter J,Hatters D,Curtis J,Cheung K,Krishnan P,Mitra S,Widjaja K,Shaby BA,Lotz GP,Newhouse Y,Mitchell EJ,Osmand A,Gray M,Thulasiramin V,Saudou F,Segal M,Yang XW,Masliah

    更新日期:2011-10-30 00:00:00

  • Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes.

    abstract::Mammals that degrade uric acid are not affected by gout or urate kidney stones. It is not fully understood how they convert uric acid into the much more soluble allantoin. Until recently, it had long been thought that urate oxidase was the only enzyme responsible for this conversion. However, detailed studies of the m...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio768

    authors: Ramazzina I,Folli C,Secchi A,Berni R,Percudani R

    更新日期:2006-03-01 00:00:00

  • Programmable and printable Bacillus subtilis biofilms as engineered living materials.

    abstract::Bacterial biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional mater...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-018-0169-2

    authors: Huang J,Liu S,Zhang C,Wang X,Pu J,Ba F,Xue S,Ye H,Zhao T,Li K,Wang Y,Zhang J,Wang L,Fan C,Lu TK,Zhong C

    更新日期:2019-01-01 00:00:00

  • Calcium Green FlAsH as a genetically targeted small-molecule calcium indicator.

    abstract::Intracellular Ca(2+) regulates numerous proteins and cellular functions and can vary substantially over submicron and submillisecond scales, so precisely localized fast detection is desirable. We have created a approximately 1-kDa biarsenical Ca(2+) indicator, called Calcium Green FlAsH (CaGF, 1), to probe [Ca(2+)] su...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2007.4

    authors: Tour O,Adams SR,Kerr RA,Meijer RM,Sejnowski TJ,Tsien RW,Tsien RY

    更新日期:2007-07-01 00:00:00

  • Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5.

    abstract::A 2.4-Å-resolution X-ray crystal structure of the carrier-protein-independent halogenase WelO5 in complex with its welwitindolinone precursor substrate, 12-epi-fischerindole U, reveals that the C13 chlorination target is proximal to the anticipated site of the oxo group in a presumptive cis-halo-oxo-iron(IV) (haloferr...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2112

    authors: Mitchell AJ,Zhu Q,Maggiolo AO,Ananth NR,Hillwig ML,Liu X,Boal AK

    更新日期:2016-08-01 00:00:00

  • How proteins bind macrocycles.

    abstract::The potential utility of synthetic macrocycles (MCs) as drugs, particularly against low-druggability targets such as protein-protein interactions, has been widely discussed. There is little information, however, to guide the design of MCs for good target protein-binding activity or bioavailability. To address this kno...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1584

    authors: Villar EA,Beglov D,Chennamadhavuni S,Porco JA Jr,Kozakov D,Vajda S,Whitty A

    更新日期:2014-09-01 00:00:00

  • The evolving interface between synthetic biology and functional metagenomics.

    abstract::Nature is a diverse and rich source of bioactive pathways or novel building blocks for synthetic biology. In this Perspective, we describe the emerging research field in which metagenomes are functionally interrogated using synthetic biology. This approach substantially expands the set of identified biological activit...

    journal_title:Nature chemical biology

    pub_type: 杂志文章,评审

    doi:10.1038/s41589-018-0100-x

    authors: van der Helm E,Genee HJ,Sommer MOA

    更新日期:2018-08-01 00:00:00

  • Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA.

    abstract::RNA G-quadruplex (G4) structures are thought to affect biological processes, including translation and pre-mRNA splicing, but it is not possible at present to demonstrate that they form naturally at specific sequences in long functional RNA molecules. We developed a new strategy, footprinting of long 7-deazaguanine-su...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2228

    authors: Weldon C,Behm-Ansmant I,Hurley LH,Burley GA,Branlant C,Eperon IC,Dominguez C

    更新日期:2017-01-01 00:00:00

  • miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction.

    abstract::Identifying the interaction partners of noncoding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA crosslinking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-crosslinking and Argonaute 2 i...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1713

    authors: Imig J,Brunschweiger A,Brümmer A,Guennewig B,Mittal N,Kishore S,Tsikrika P,Gerber AP,Zavolan M,Hall J

    更新日期:2015-02-01 00:00:00

  • A PCBP1-BolA2 chaperone complex delivers iron for cytosolic [2Fe-2S] cluster assembly.

    abstract::Hundreds of cellular proteins require iron cofactors for activity, and cells express systems for their assembly and distribution. Molecular details of the cytosolic iron pool used for iron cofactors are lacking, but iron chaperones of the poly(rC)-binding protein (PCBP) family play a key role in ferrous ion distributi...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/s41589-019-0330-6

    authors: Patel SJ,Frey AG,Palenchar DJ,Achar S,Bullough KZ,Vashisht A,Wohlschlegel JA,Philpott CC

    更新日期:2019-09-01 00:00:00

  • A reactivity-based probe of the intracellular labile ferrous iron pool.

    abstract::Improved methods for studying intracellular reactive Fe(II) are of significant interest for studies of iron metabolism and disease-relevant changes in iron homeostasis. Here we describe a highly selective reactivity-based probe in which a Fenton-type reaction with intracellular labile Fe(II) leads to unmasking of the ...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.2116

    authors: Spangler B,Morgan CW,Fontaine SD,Vander Wal MN,Chang CJ,Wells JA,Renslo AR

    更新日期:2016-09-01 00:00:00

  • A chemical inhibitor of jasmonate signaling targets JAR1 in Arabidopsis thaliana.

    abstract::Jasmonates are lipid-derived plant hormones that regulate plant defenses and numerous developmental processes. Although the biosynthesis and molecular function of the most active form of the hormone, (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile), have been unraveled, it remains poorly understood how the diversity of bioac...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1591

    authors: Meesters C,Mönig T,Oeljeklaus J,Krahn D,Westfall CS,Hause B,Jez JM,Kaiser M,Kombrink E

    更新日期:2014-10-01 00:00:00

  • A stand-alone adenylation domain forms amide bonds in streptothricin biosynthesis.

    abstract::The streptothricin (ST) antibiotics, produced by Streptomyces bacteria, contain L-β-lysine ((3S)-3,6-diaminohexanoic acid) oligopeptides as pendant chains. Here we describe three unusual nonribosomal peptide synthetases (NRPSs) involved in ST biosynthesis: ORF 5 (a stand-alone adenylation (A) domain), ORF 18 (containi...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1040

    authors: Maruyama C,Toyoda J,Kato Y,Izumikawa M,Takagi M,Shin-ya K,Katano H,Utagawa T,Hamano Y

    更新日期:2012-09-01 00:00:00

  • Transcriptional recorder.

    abstract:: ...

    journal_title:Nature chemical biology

    pub_type: 评论,杂志文章

    doi:10.1038/s41589-018-0174-5

    authors: Song Y

    更新日期:2018-12-01 00:00:00

  • Cholesterol modulates glycolipid conformation and receptor activity.

    abstract::We document a new dimension of surface recognition in which communication is controlled through the collective behavior of lipids. Membrane cholesterol induces a tilt in glycolipid receptor headgroup, resulting in loss of access for ligand binding. This property appears to organize erythrocyte blood group presentation...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.551

    authors: Lingwood D,Binnington B,Róg T,Vattulainen I,Grzybek M,Coskun U,Lingwood CA,Simons K

    更新日期:2011-05-01 00:00:00

  • A propofol binding site on mammalian GABAA receptors identified by photolabeling.

    abstract::Propofol is the most important intravenous general anesthetic in current clinical use. It acts by potentiating GABAA (γ-aminobutyric acid type A) receptors, but where it binds to this receptor is not known and has been a matter of some debate. We synthesized a new propofol analog photolabeling reagent whose biological...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.1340

    authors: Yip GM,Chen ZW,Edge CJ,Smith EH,Dickinson R,Hohenester E,Townsend RR,Fuchs K,Sieghart W,Evers AS,Franks NP

    更新日期:2013-11-01 00:00:00

  • Scaffold composition and biological relevance of screening libraries.

    abstract::The chemical scaffolds from which screening libraries are built have strong influence on the libraries' utility for screening campaigns. Here we present analysis of the scaffold composition of several types of commercially available screening collections and compare those compositions to those of drugs and drug candid...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio0807-442

    authors: Shelat AA,Guy RK

    更新日期:2007-08-01 00:00:00

  • Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem.

    abstract::Biodiversity, or the relative abundance of species, measures the persistence of an ecosystem. To better understand its modulation, we analyzed the spatial and temporal dynamics of a synthetic, chemical-mediated ecosystem that consisted of two engineered Escherichia coli populations. Depending on the specific experimen...

    journal_title:Nature chemical biology

    pub_type: 杂志文章

    doi:10.1038/nchembio.244

    authors: Song H,Payne S,Gray M,You L

    更新日期:2009-12-01 00:00:00