Functional and computational analysis of amino acid patterns predictive of type III secretion system substrates in Pseudomonas syringae.

PloS One
Lisa M SchechterEric Sakk

Abstract

Bacterial type III secretion systems (T3SSs) deliver proteins called effectors into eukaryotic cells. Although N-terminal amino acid sequences are required for translocation, the mechanism of substrate recognition by the T3SS is unknown. Almost all actively deployed T3SS substrates in the plant pathogen Pseudomonas syringae pathovar tomato strain DC3000 possess characteristic patterns, including (i) greater than 10% serine within the first 50 amino acids, (ii) an aliphatic residue or proline at position 3 or 4, and (iii) a lack of acidic amino acids within the first 12 residues. Here, the functional significance of the P. syringae T3SS substrate compositional patterns was tested. A mutant AvrPto effector protein lacking all three patterns was secreted into culture and translocated into plant cells, suggesting that the compositional characteristics are not absolutely required for T3SS targeting and that other recognition mechanisms exist. To further analyze the unique properties of T3SS targeting signals, we developed a computational algorithm called TEREE (Type III Effector Relative Entropy Evaluation) that distinguishes DC3000 T3SS substrates from other proteins with a high sensitivity and specificity. Although TEREE did not e...Continue Reading

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Citations

Aug 5, 2015·Journal of Biomolecular Structure & Dynamics·R PrathivirajP Chellapandi
Apr 13, 2017·Environmental Microbiology·Yueming HuYejun Wang
Apr 27, 2021·Computational and Structural Biotechnology Journal·Xinjie HuiYejun Wang

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Datasets Mentioned

BETA
GMI1000

Methods Mentioned

BETA
phosphotransferase
electrophoresis
PCR
ELISA

Software Mentioned

SIEVE
T3SS
BPBAac
TEREE
TMpred

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