NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

Ba, Alex N Nguyen; Pogoutse, Anastassia K.; Provart, Nicholas J.; Moses, Alan M.

doi:10.1186/1471-2105-10-202

Cited by 587 publications

(444 citation statements)

References 26 publications

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“…In short, amino acid sequences for those proteins identified by MS were extracted from the SOL genomics protein database v. ITAG2.4 (Tomato Genome, 2012). This data set was subjected to predictnls (default settings) (Cokol et al ., 2000) and nlstradamus (two‐state model; posterior threshold 0.6) (Nguyen Ba et al ., 2009) to identify proteins with nuclear localization signals, and the Nucleolar Localization Sequence Detector ( nod ) (default settings) (Scott et al ., 2010, 2011) to identify proteins with nucleolar localization signals. Additionally, we used wolf psort (plant) (Horton et al ., 2007) and filtered all proteins marked as nuclear.…”

Section: Methodsmentioning

confidence: 99%

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

et al. 2017

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Summary Plant–pathogen interactions are complex associations driven by the interplay of host and microbe‐encoded factors. With secreted pathogen proteins (effectors) and immune signalling components found in the plant nucleus, this compartment is a battleground where susceptibility is specified. We hypothesized that, by defining changes in the nuclear proteome during infection, we can pinpoint vital components required for immunity or susceptibility.We tested this hypothesis by documenting dynamic changes in the tomato (Solanum lycopersicum) nuclear proteome during infection by the oomycete pathogen Phytophthora capsici. We enriched nuclei from infected and noninfected tissues and quantitatively assessed changes in the nuclear proteome. We then tested the role of candidate regulators in immunity through functional assays.We demonstrated that the host nuclear proteome dynamically changes during P. capsici infection. We observed that known nuclear immunity factors were differentially expressed and, based on this observation, selected a set of candidate regulators that we successfully implicated in immunity to P. capsici.Our work exemplifies a powerful strategy to gain rapid insight into important nuclear processes that underpin complex crop traits such as resistance. We have identified a large set of candidate nuclear factors that may underpin immunity to pathogens in crops.

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Section: Methodsmentioning

confidence: 99%

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

et al. 2017

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“…The SAUR36 protein contains a nuclear localization signal, 59-RRRS-62 (Supplemental Fig. S1), predicted by the NLStradamus program (Nguyen Ba et al, 2009). A GFP fusion protein confirms that the SAUR36 protein is targeted to the nucleus (Narsai et al, 2011).…”

Section: Auxin May Promote Leaf Senescence In Arabidopsismentioning

confidence: 96%

SAUR36, a SMALL AUXIN UP RNA Gene, Is Involved in the Promotion of Leaf Senescence in Arabidopsis

2012

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Small Auxin Up RNA genes (SAURs) are early auxin-responsive genes, but whether any of them are involved in leaf senescence is not known. Auxin, on the other hand, has been shown to have a role in leaf senescence. Some of the external application experiments indicated that auxin can inhibit leaf senescence, whereas other experiments indicated that auxin can promote leaf senescence. Here, we report the identification and characterization of an Arabidopsis (Arabidopsis thaliana) leaf senescenceassociated gene named SAG201, which is highly up-regulated during leaf senescence and can be induced by 1-naphthaleneacetic acid, a synthetic auxin. It encodes a functionally uncharacterized SAUR that has been annotated as SAUR36. Leaf senescence in transfer DNA insertion saur36 knockout lines was delayed as revealed by analyses of chlorophyll content, F v /F m ratio (a parameter for photosystem II activity), ion leakage, and the expression of leaf senescence marker genes. In contrast, transgenic Arabidopsis plants overexpressing SAUR36 (without its 39 untranslated region [UTR]) displayed an early leaf senescence phenotype. However, plants overexpressing SAUR36 with its 39 UTR were normal and did not exhibit the early-senescence phenotype. These data suggest that SAUR36 is a positive regulator of leaf senescence and may mediate auxin-induced leaf senescence and that the 39 UTR containing a highly conserved downstream destabilizes the SAUR36 transcripts in young leaves.

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“…Subcellular localization of proteins was performed using MultiLoc2 (Blum et al, 2009), and nucleus-localizing signals were identified using NLStradamus (Nguyen Ba et al, 2009). Protein secondary structures were predicted using PSIPRED (Bryson et al, 2005).…”

Section: Other Bioinformatics Tools Usedmentioning

confidence: 99%

The Mediator Complex in Plants: Structure, Phylogeny, and Expression Profiling of Representative Genes in a Dicot (Arabidopsis) and a Monocot (Rice) during Reproduction and Abiotic Stress

et al. 2011

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The Mediator (Med) complex relays regulatory information from DNA-bound transcription factors to the RNA polymerase II in eukaryotes. This macromolecular unit is composed of three core subcomplexes in addition to a separable kinase module. In this study, conservation of Meds has been investigated in 16 plant species representing seven diverse groups across the plant kingdom. Using Hidden Markov Model-based conserved motif searches, we have identified all the known yeast/metazoan Med components in one or more plant groups, including the Med26 subunits, which have not been reported so far for any plant species. We also detected orthologs for the Arabidopsis (Arabidopsis thaliana) Med32, -33, -34, -35, -36, and -37 in all the plant groups, and in silico analysis identified the Med32 and Med33 subunits as apparent orthologs of yeast/metazoan Med2/ 29 and Med5/24, respectively. Consequently, the plant Med complex appears to be composed of one or more members of 34 subunits, as opposed to 25 and 30 members in yeast and metazoans, respectively. Despite low similarity in primary Med sequences between the plants and their fungal/metazoan partners, secondary structure modeling of these proteins revealed a remarkable similarity between them, supporting the conservation of Med organization across kingdoms. Phylogenetic analysis between plant, human, and yeast revealed single clade relatedness for 29 Med genes families in plants, plant Meds being closer to human than to yeast counterparts. Expression profiling of rice (Oryza sativa) and Arabidopsis Med genes reveals that Meds not only act as a basal regulator of gene expression but may also have specific roles in plant development and under abiotic stress conditions.

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NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

Cited by 587 publications

References 26 publications

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

SAUR36, a SMALL AUXIN UP RNA Gene, Is Involved in the Promotion of Leaf Senescence in Arabidopsis

The Mediator Complex in Plants: Structure, Phylogeny, and Expression Profiling of Representative Genes in a Dicot (Arabidopsis) and a Monocot (Rice) during Reproduction and Abiotic Stress

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