Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors

Wang, Jiawei; Yang, Bingjiao; Leier, André; Marquez‐Lago, Tatiana T.; Hayashida, Morihiro; Rocker, Andrea; Zhang, Yanju; Akutsu, Tatsuya; Chou, Kuo‐Chen; Strugnell, Richard A.; Song, Jiangning; Lithgow, Trevor

doi:10.1093/bioinformatics/bty155

Cited by 107 publications

(73 citation statements)

References 51 publications

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“…Bayesian inference analysis was computed using MrBayes software (v3.2.6) [28] under a LG+I+G+F substitution model for 10 5 generations, burn-in 25%. Amino acid sequences were also analyzed with the T3S effector prediction programs SIEVE [29], pEffect [30], EffectiveT3 [31] and ModLab T3S [32], as well as the T4S effector prediction programs T4SEpre [33] and T4 EffPred [31], and the T6SS predictor tools Bastion6 [34] and SecReT6 [35]. Amino acid sequences for L. pneumophila VipE, Salmonella enterica SopE and Legionella londiniensis Hcp were used as positive controls for the T3SS, T4SS, and T6SS effector predictors, respectively.…”

Section: In Silico P Salmonis Hsp60 Amino Acid Sequence Analysesmentioning

confidence: 99%

Subcellular Location of Piscirickettsia salmonis Heat Shock Protein 60 (Hsp60) Chaperone by Using Immunogold Labeling and Proteomic Analysis

et al. 2020

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Piscirickettsia salmonis is the causative bacterial agent of piscirickettsiosis, a systemic fish disease that significantly impacts the Chilean salmon industry. This bacterium possesses a type IV secretion system (T4SS), several proteins of the type III secretion system (T3SS), and a single heat shock protein 60 (Hsp60/GroEL). It has been suggested that due to its high antigenicity, the P. salmonis Hsp60 could be surface-exposed, translocated across the membrane, and (or) secreted into the extracellular matrix. This study tests the hypothesis that P. salmonis Hsp60 could be located on the bacterial surface. Immunogold electron microscopy and proteomic analyses suggested that although P. salmonis Hsp60 was predominantly associated with the bacterial cell cytoplasm, Hsp60-positive spots also exist on the bacterial cell envelope. IgY antibodies against P. salmonis Hsp60 protected SHK-1 cells against infection. Several bioinformatics approaches were used to assess Hsp60 translocation by the T4SS, T3SS, and T6SS, with negative results. These data support the hypothesis that small amounts of Hsp60 must reach the bacterial cell surface in a manner probably not mediated by currently characterized secretion systems, and that they remain biologically active during P. salmonis infection, possibly mediating adherence and (or) invasion.

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Section: In Silico P Salmonis Hsp60 Amino Acid Sequence Analysesmentioning

confidence: 99%

Subcellular Location of Piscirickettsia salmonis Heat Shock Protein 60 (Hsp60) Chaperone by Using Immunogold Labeling and Proteomic Analysis

et al. 2020

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“…Upstream to this gene, there is another small protein (138 amino acids) containing a DUF2195 annotated as STM14_0335 , which encodes a predicted Sec signal peptide sequence for periplasmic localization (Figure S1A) (Almagro Armenteros et al, 2019). Bastion6 software prediction (Wang et al, 2018) indicates that STM14_0336 could be a T6SS effector (score 0.758). To test whether STM14_0336 and STM14_0335 are a bona fide effector/immunity pair we cloned these genes in compatible vectors under the control of different promoters.…”

Section: Resultsmentioning

confidence: 99%

A Superfamily of T6SS Antibacterial Effectors Displaying L,D-carboxypeptidase Activity Towards Peptidoglycan

Sibinelli-Sousa

Hespanhol

Nicastro

et al. 2020

Preprint

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SummaryType VI secretion systems (T6SSs) are contractile nanomachines used by bacteria to inject toxic effectors into competitors. The identity and mechanism of many effectors remain unknown. We characterized a Salmonella SPI-6 T6SS antibacterial effector called Tae5STM (type VI amidase effector 5). Tae5STM is toxic in target-cell periplasm and is neutralized by its cognate immunity protein (Tai5STM). Microscopy analysis revealed that cells expressing the effector stop dividing and lose cell envelope integrity. Bioinformatic analysis uncovered similarities between Tae5STM and the catalytic domain of L,D-transpeptidase. Point mutations on conserved catalytic histidine and cysteine residues abrogated toxicity. Biochemical assays revealed that Tae5STM displays L,D-carboxypeptidase activity, cleaving peptidoglycan tetrapeptides between meso-diaminopimelic acid3 and D-alanine4. Phylogenetic analysis showed that Tae5STM homologs constitutes a new superfamily of T6SS-associated amidase effectors distributed among α-, β- and γ-proteobacteria. This work expands our current knowledge about bacterial effectors used in interbacterial competition.

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“…81,82 However, validation of MIX reliability was done against Bastion6, the first machine-learning tool that promises accurate prediction of T6SS effectors. 83 MIX motif ability in the identification of T6SS effectors or importance for translocation and effector function was very low. 83 On the other hand, Nguyen et al used the poorly rated marker and reported 57 novel MIX T6SS effectors and two identified T6SS phospholipases.…”

Section: Pipelines Currently Assisting the Discovery Of Antieukaryotimentioning

confidence: 99%

Antieukaryotic Type Six Secretion System Virulence Factors of Bacteria

Maphosa¹,

Motaung²,

Moleleki³

2020

Preprint

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The type 6 protein secretion system (T6SS) is prevalently utilized by Gram-negative bacteria to compete for resources and space. Upon activation, toxic effectors from this secretion system are translocated into the competitor prokaryote or eukaryote in a contact-dependent manner. While much has been reported on T6SS-mediated prokaryotic competition, very little is understood about the mechanisms of bacterial interactions with eukaryotic hosts. Likewise, many virulent T6SS effectors are known to be antibacterial. In recent years, however, evidence has emerged on numerous T6SS effectors that interact with related immunity proteins in a range of eukaryotic hosts. Insights into how this effector-immunity pairing alters the physiological responses of the recipient organism might provide opportunities relating to the T6SS agricultural and biotherapeutic applications. We, therefore, summarize the impacts of the T6SS effectors with a special focus on bacterial interactions with animals, plants, and fungi. We further briefly discuss pipelines that are currently used to characterize antieukaryotic T6SS effectors.

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Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 107 publications

References 51 publications

Subcellular Location of Piscirickettsia salmonis Heat Shock Protein 60 (Hsp60) Chaperone by Using Immunogold Labeling and Proteomic Analysis

Subcellular Location of Piscirickettsia salmonis Heat Shock Protein 60 (Hsp60) Chaperone by Using Immunogold Labeling and Proteomic Analysis

A Superfamily of T6SS Antibacterial Effectors Displaying L,D-carboxypeptidase Activity Towards Peptidoglycan

Antieukaryotic Type Six Secretion System Virulence Factors of Bacteria

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