plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters.


:Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic loci: biosynthetic gene clusters (BGCs). Here, we introduce plantiSMASH, a versatile online analysis platform that automates the identification of candidate plant BGCs. Moreover, it allows integration of transcriptomic data to prioritize candidate BGCs based on the coexpression patterns of predicted biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis to study the evolutionary conservation of each cluster. Applied on 48 high-quality plant genomes, plantiSMASH identifies a rich diversity of candidate plant BGCs. These results will guide further experimental exploration of the nature and dynamics of gene clustering in plant metabolism. Moreover, spurred by the continuing decrease in costs of plant genome sequencing, they will allow genome mining technologies to be applied to plant natural product discovery. The plantiSMASH web server, precalculated results and source code are freely available from


Nucleic Acids Res


Nucleic acids research


Kautsar SA,Suarez Duran HG,Blin K,Osbourn A,Medema MH




Has Abstract


2017-07-03 00:00:00














  • Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo.

    abstract::Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Malik I,Qiu C,Snavely T,Kaplan CD

    更新日期:2017-05-05 00:00:00

  • A sequence motif in many polymerases.

    abstract::A 15-residue sequence motif has been found in many polymerases from various species and involving DNA and RNA dependence and product. The motif is characterized by a Tyr-Gly-Asp-(Thr)-Asp core flanked by hydrophobic spans five residues in length. An mRNA maturase segment is also suggested to display the motif pattern....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Argos P

    更新日期:1988-11-11 00:00:00

  • The human U1 snRNA promoter and enhancer do not direct synthesis of messenger RNA.

    abstract::We examined the ability of the 5' flanking region sequences of a human U1 RNA gene to direct synthesis of functional mRNA. When fused to chloramphenicol acetyltransferase (CAT) coding region sequences, the upstream sequences of the U1 gene were able to stimulate the synthesis of functional CAT mRNA in 293 cells but no...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dahlberg JE,Schenborn ET

    更新日期:1988-07-11 00:00:00

  • The swi4+ gene of Schizosaccharomyces pombe encodes a homologue of mismatch repair enzymes.

    abstract::The swi4+ gene of Schizosaccharomyces pombe is involved in termination of copy-synthesis during mating-type switching. The gene was cloned by functional complementation of a swi4 mutant transformed with a genomic library. Determination of the nucleotide sequence revealed an open reading frame of 2979 nucleotides which...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fleck O,Michael H,Heim L

    更新日期:1992-05-11 00:00:00

  • Transcription reinitiation rate: a potential role for TATA box stabilization of the TFIID:TFIIA:DNA complex.

    abstract::Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional compl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yean D,Gralla JD

    更新日期:1999-02-01 00:00:00

  • Oct-2 regulates CD36 gene expression via a consensus octamer, which excludes the co-activator OBF-1.

    abstract::The POU domain transcription factor, Oct-2, is essential for the B cell-specific expression of CD36 in mouse B cells. In order to determine how Oct-2 mediates expression of CD36 in B cells, we cloned and analysed the mouse CD36 promoter. In contrast to the human CD36 promoter, the mouse promoter contains a consensus o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shore P,Dietrich W,Corcoran LM

    更新日期:2002-04-15 00:00:00

  • PLK1 targets CtIP to promote microhomology-mediated end joining.

    abstract::Proper DNA double-strand break (DSB) repair is essential for maintaining genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism, which introduces mutations at break sites and contributes to chromosomal translocations and telomere fusions, thus driving carcinogenesis. Mitotic kin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang H,Qiu Z,Liu B,Wu Y,Ren J,Liu Y,Zhao Y,Wang Y,Hao S,Li Z,Peng B,Xu X

    更新日期:2018-11-16 00:00:00

  • A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability.

    abstract::The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end gu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shi W,Ye HQ,Deng CL,Li R,Zhang B,Gong P

    更新日期:2020-02-20 00:00:00

  • A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae.

    abstract::The relationship between the similarity of expression patterns for a pair of genes and interaction of the proteins they encode is demonstrated both for the simple genome of the bacteriophage T7 and the considerably more complex genome of the yeast Saccharomyces cerevisiae. Statistical analysis of large-scale gene expr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grigoriev A

    更新日期:2001-09-01 00:00:00

  • OMA 2011: orthology inference among 1000 complete genomes.

    abstract::OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Altenhoff AM,Schneider A,Gonnet GH,Dessimoz C

    更新日期:2011-01-01 00:00:00

  • The Borrelia burgdorferi telomere resolvase, ResT, anneals ssDNA complexed with its cognate ssDNA-binding protein.

    abstract::Spirochetes of the genus Borrelia possess unusual genomes that consist in a linear chromosome and multiple linear and circular plasmids. The linear replicons are terminated by covalently closed hairpin ends, referred to as hairpin telomeres. The hairpin telomeres represent a simple solution to the end-replication prob...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Huang SH,Kobryn K

    更新日期:2016-06-20 00:00:00

  • The conformation of adenovirus VAI-RNA in solution.

    abstract::The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Monstein HJ,Philipson L

    更新日期:1981-09-11 00:00:00

  • Gene disruption and gene replacement in Streptomyces via single stranded DNA transformation of integration vectors.

    abstract::For the isolation of single stranded plasmid DNA, various E. coli and E. coli-Streptomyces shuttle plasmids were equipped with the phage f1 replication origin. The transformation of some representative Streptomyces species with plasmid vectors occurred irrespective of whether single or double stranded DNA was used. In...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hillemann D,Pühler A,Wohlleben W

    更新日期:1991-02-25 00:00:00

  • Overexpression of eIF5 or its protein mimic 5MP perturbs eIF2 function and induces ATF4 translation through delayed re-initiation.

    abstract::ATF4 is a pro-oncogenic transcription factor whose translation is activated by eIF2 phosphorylation through delayed re-initiation involving two uORFs in the mRNA leader. However, in yeast, the effect of eIF2 phosphorylation can be mimicked by eIF5 overexpression, which turns eIF5 into translational inhibitor, thereby ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kozel C,Thompson B,Hustak S,Moore C,Nakashima A,Singh CR,Reid M,Cox C,Papadopoulos E,Luna RE,Anderson A,Tagami H,Hiraishi H,Slone EA,Yoshino KI,Asano M,Gillaspie S,Nietfeld J,Perchellet JP,Rothenburg S,Masai H,W

    更新日期:2016-10-14 00:00:00

  • Impairing the production of ribosomal RNA activates mammalian target of rapamycin complex 1 signalling and downstream translation factors.

    abstract::Ribosome biogenesis is a key process for maintaining protein synthetic capacity in dividing or growing cells, and requires coordinated production of ribosomal proteins and ribosomal RNA (rRNA), including the processing of the latter. Signalling through mammalian target of rapamycin complex 1 (mTORC1) activates all the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu R,Iadevaia V,Averous J,Taylor PM,Zhang Z,Proud CG

    更新日期:2014-04-01 00:00:00

  • Ligation-independent cloning of PCR products (LIC-PCR).

    abstract::A new procedure has been developed for the efficient cloning of complex PCR mixtures, resulting in libraries exclusively consisting of recombinant clones. Recombinants are generated between PCR products and a PCR-amplified plasmid vector. The procedure does not require the use of restriction enzymes, T4 DNA ligase or ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Aslanidis C,de Jong PJ

    更新日期:1990-10-25 00:00:00

  • Role of RNA structure in non-homologous recombination between genomic molecules of brome mosaic virus.

    abstract::Brome mosaic virus (BMV) is a tripartite genome, positive-sense RNA virus of plants. Previously it was demonstrated that local hybridization between BMV RNAs (RNA-RNA heteroduplex formation) efficiently promotes non-homologous RNA recombination. In addition, studies on the role of the BMV polymerase in RNA recombinati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Figlerowicz M

    更新日期:2000-04-15 00:00:00

  • From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data.

    abstract::Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bottini S,Hamouda-Tekaya N,Tanasa B,Zaragosi LE,Grandjean V,Repetto E,Trabucchi M

    更新日期:2017-05-19 00:00:00

  • Functional analysis of the tobacco mosaic virus tRNA-like structure in cytoplasmic gene regulation.

    abstract::The 3'-untranslated region (UTR) of tobacco mosaic virus (TMV), which terminates in a tRNA-like structure, functionally substitutes for a poly(A) tail in both plant and animal cells. The addition of the TMV 3'-UTR to chimeric mRNA constructs increases their expression up to 100-fold, increasing both translational effi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gallie DR,Feder JN,Schimke RT,Walbot V

    更新日期:1991-09-25 00:00:00

  • Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa.

    abstract::In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) act as post-transcriptional regulators during carbon catabolite repression (CCR). In this regard Crc is required for full-fledged Hfq-mediated translational repression of catabolic genes. RNAseq based transcriptome anal...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sonnleitner E,Wulf A,Campagne S,Pei XY,Wolfinger MT,Forlani G,Prindl K,Abdou L,Resch A,Allain FH,Luisi BF,Urlaub H,Bläsi U

    更新日期:2018-02-16 00:00:00

  • Highly conserved sequences in the 3' untranslated region of mRNAs coding for homologous proteins in distantly related species.

    abstract::Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yaffe D,Nudel U,Mayer Y,Neuman S

    更新日期:1985-05-24 00:00:00

  • Ligation with T4 RNA ligase of an oligodeoxyribonucleotide to covalently-linked cross-sectional base-pair analogues of short, normal, and long dimensions.

    abstract::Compounds that are covalent analogues of nucleic acid base pairs of normal, long, and short C1' to C1' dimensions [B. Devadas and N.J. Leonard (1990) J. Am. Chem. Soc., 112, 3125-3135.] have been added to the oligodeoxyribonucleotide d(A)6 with bacteriophage T4 RNA ligase as a prelude to placing them at defined loci w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Petric A,Bhat B,Leonard NJ,Gumport RI

    更新日期:1991-02-11 00:00:00

  • Cabeza, a Drosophila gene encoding a novel RNA binding protein, shares homology with EWS and TLS, two genes involved in human sarcoma formation.

    abstract::We have previously described a partial Drosophila cDNA, clone P19, which bears homology to members of the RNA recognition motif (RRM) family of proteins [Haynes et al. (1987) Proc. Natl. Acad. Sci. USA, 84, 1819-1823]. RNA binding as well as involvement in RNA processing has been demonstrated for some RRM proteins. We...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stolow DT,Haynes SR

    更新日期:1995-03-11 00:00:00

  • Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.

    abstract::The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Komatsu S,Kojima K,Suzuki K,Ozaki K,Higo K

    更新日期:2004-01-01 00:00:00

  • Molecular characterization of Mybbp1a as a co-repressor on the Period2 promoter.

    abstract::The circadian clock comprises transcriptional feedback loops of clock genes. Cryptochromes are essential components of the negative feedback loop in mammals as they inhibit CLOCK-BMAL1-mediated transcription. We purified mouse CRY1 (mCRY1) protein complexes from Sarcoma 180 cells to determine their roles in circadian ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hara Y,Onishi Y,Oishi K,Miyazaki K,Fukamizu A,Ishida N

    更新日期:2009-03-01 00:00:00

  • JAFA: a protein function annotation meta-server.

    abstract::With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress in automated protei...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Friedberg I,Harder T,Godzik A

    更新日期:2006-07-01 00:00:00

  • Ab initio gene identification in metagenomic sequences.

    abstract::We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhu W,Lomsadze A,Borodovsky M

    更新日期:2010-07-01 00:00:00

  • Specific-primer-directed DNA sequencing using automated fluorescence detection.

    abstract::Automated fluorescence-based DNA sequence analysis offers the possibility to undertake very large scale sequencing projects. Directed strategies, such as the specific-primer-directed sequencing approach ('gene walking'), should prove useful in such projects. Described herein is a study involving the use of this approa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kaiser RJ,MacKellar SL,Vinayak RS,Sanders JZ,Saavedra RA,Hood LE

    更新日期:1989-08-11 00:00:00

  • Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks.

    abstract::Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rageul J,Park JJ,Jo U,Weinheimer AS,Vu TTM,Kim H

    更新日期:2019-05-07 00:00:00

  • Release of promoter-proximal paused Pol II in response to histone deacetylase inhibition.

    abstract::A correlation between histone acetylation and transcription has been noted for a long time, but little is known about what step(s) in the transcription cycle is influenced by acetylation. We have examined the immediate transcriptional response to histone deacetylase (HDAC) inhibition, and find that release of promoter...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vaid R,Wen J,Mannervik M

    更新日期:2020-05-21 00:00:00