SignalP 5.0 improves signal peptide predictions using deep neural networks

Armenteros, José Juan Almagro; Tsirigos, Konstantinos D.; Sønderby, Casper Kaae; Petersen, Thomas Nordahl; Winther, Ole; Brunak, Søren; Heijne, Gunnar von; Nielsen, Henrik

doi:10.1038/s41587-019-0036-z

Cited by 3,632 publications

(2,664 citation statements)

References 46 publications

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“…Signal peptide cleavage sites were predicted by the SignalP 5.0 server (http://www.cbs.dtu.dk/services/SignalP/) (Almagro Armenteros et al, ). Densitometric analysis of the protein band on Western blot was performed using ImageJ (Schneider, Rasband, & Eliceiri, ).…”

Section: Methodsmentioning

confidence: 99%

Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO₂ capture and utilization

Moon

Joon

2019

Biotech & Bioengineering

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Carbonic anhydrase (CA) is a diffusion‐limited enzyme that rapidly catalyzes the hydration of carbon dioxide (CO2). CA has been proposed as an eco‐friendly yet powerful catalyst for CO2 capture and utilization. A bacterial whole‐cell biocatalyst equipped with periplasmic CA provides an option for a cost‐effective CO2‐capturing system. However, further utilization of the previously constructed periplasmic system has been limited by its relatively low activity and stability. Herein, we engineered three genetic components of the periplasmic system for the construction of a highly efficient whole‐cell catalyst: a CA‐coding gene, a signal sequence, and a ribosome‐binding site (RBS). A stable and halotolerant CA (hmCA) from the marine bacterium Hydrogenovibrio marinus was employed to improve both the activity and stability of the system. The improved secretion and folding of hmCA and increased membrane permeability were achieved by translocation via the Sec‐dependent pathway. The engineering of RBS strength further enhanced whole‐cell activity by improving both the secretion and folding of hmCA. The newly engineered biocatalyst displayed 5.7‐fold higher activity and 780‐fold higher stability at 60°C compared with those of the previously constructed periplasmic system, providing new opportunities for applications in CO2 capture and utilization.

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Section: Methodsmentioning

confidence: 99%

Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO₂ capture and utilization

Moon

Joon

2019

Biotech & Bioengineering

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“…PKS and FAS genes. The presence of signal peptides was determined using SignalP predictor (http://www.cbs.dtu.dk/ services/SignalP) (Emanuelsson et al, 1999;Armenteros et al, 2019). DeepLoc-1.0 (http://www.cbs.dtu.dk/services/ DeepLoc-1.0) was used to predict the subcellular localization of the PKS and FAS proteins (Armenteros et al, 2017).…”

Section: Rna Extraction and Sequencingmentioning

confidence: 99%

Transcriptomic investigation into polyketide toxin synthesis in Ostreopsis (Dinophyceae) species

Verma

Kohli

Harwood

et al. 2019

Environmental Microbiology

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Summary In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth. Their ecological success may be related to their production of complex toxic polyketide compounds. Ostreopsis species produce potent palytoxin‐like compounds (PLTX), which are associated with human skin and eye irritations, and illnesses through the consumption of contaminated seafood. To investigate the genetic basis of PLTX‐like compounds, we sequenced and annotated transcriptomes from two PLTX‐producing Ostreopsis species; O. cf. ovata, O. cf. siamensis, one non‐PLTX producing species, O. rhodesae and compared them to a close phylogenetic relative and non‐PLTX producer, Coolia malayensis. We found no clear differences in the presence or diversity of ketosynthase and ketoreductase transcripts between PLTX producing and non‐producing Ostreopsis and Coolia species, as both groups contained >90 and > 10 phylogenetically diverse ketosynthase and ketoreductase transcripts, respectively. We report for the first‐time type I single‐, multi‐domain polyketide synthases (PKSs) and hybrid non‐ribosomal peptide synthase/PKS transcripts from all species. The long multi‐modular PKSs were insufficient by themselves to synthesize the large complex polyether backbone of PLTX‐like compounds. This implies that numerous PKS domains, including both single and multi‐, work together on the biosynthesis of PLTX‐like and other related polyketide compounds.

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“…31,39 To investigate the ability of miropin to interact with proteases in the extracellular environment, we preincubated plasmin with increasing amounts of washed T. forsythia cell suspension and OMVs, and then measured the residual activity. 31,39 To investigate the ability of miropin to interact with proteases in the extracellular environment, we preincubated plasmin with increasing amounts of washed T. forsythia cell suspension and OMVs, and then measured the residual activity.…”

Section: Omv-released Miropin Can Inhibit Plasminmentioning

confidence: 99%

Plasmin inhibition by bacterial serpin: Implications in gum disease

et al. 2019

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Tannerella forsythia is a periodontopathogen that expresses miropin, a protease inhibitor in the serpin superfamily. In this study, we show that miropin is also a specific and efficient inhibitor of plasmin; thus, it represents the first proteinaceous plasmin inhibitor of prokaryotic origin described to date. Miropin inhibits plasmin through the formation of a stable covalent complex triggered by cleavage of the Lys 368 -Thr 369 (P2-P1) reactive site bond with a stoichiometry of inhibition of 3.8 and an association rate constant (k ass ) of 3.3 × 10 5 M −1 s −1 . The inhibition of the fibrinolytic activity of plasmin was nearly as effective as that exerted by α 2 -antiplasmin. Miropin also acted in vivo by reducing blood loss in a mice tail bleeding assay. Importantly, intact T. forsythia cells or outer membrane vesicles, both of which carry surface-associated miropin, strongly inhibited plasmin. In intact bacterial cells, the antiplasmin activity of miropin protects envelope proteins from plasmin-mediated degradation. In summary, in the environment of periodontal pockets, which are bathed in gingival crevicular fluid consisting of 70% of blood plasma, an abundance of T. forsythia in the bacterial biofilm can cause local inhibition of fibrinolysis, which could have possible deleterious effects on the tooth-supporting structures of the periodontium. K E Y W O R D Sfibrinolysis, plasmin, periodontitis, serpin, Tannerella forsythia 620 |

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SignalP 5.0 improves signal peptide predictions using deep neural networks

Cited by 3,632 publications

References 46 publications

Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO₂ capture and utilization

Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO₂ capture and utilization

Transcriptomic investigation into polyketide toxin synthesis in Ostreopsis (Dinophyceae) species

Plasmin inhibition by bacterial serpin: Implications in gum disease

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SignalP 5.0 improves signal peptide predictions using deep neural networks

Cited by 3,632 publications

References 46 publications

Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO2 capture and utilization

Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO2 capture and utilization

Transcriptomic investigation into polyketide toxin synthesis in Ostreopsis (Dinophyceae) species

Plasmin inhibition by bacterial serpin: Implications in gum disease

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Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO₂ capture and utilization

Engineering the genetic components of a whole‐cell catalyst for improved enzymatic CO₂ capture and utilization