BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria

Abstract

Gram-negative bacteria utilize secretion systems to export substrates into their surrounding environment or directly into neighboring cells. These substrates are proteins that function to promote bacterial survival: by facilitating nutrient collection, disabling competitor species or, for pathogens, to disable host defenses. Following a rapid development of computational techniques, a growing number of substrates have been discovered and subsequently validated by wet lab experiments. To date, several online databases have been developed to catalogue these substrates but they have limited user options for in-depth analysis, and typically focus on a single type of secreted substrate. We therefore developed a universal platform, BastionHub, that incorporates extensive functional modules to facilitate substrate analysis and integrates the five major Gram-negative secreted substrate types (i.e. from types I-IV and VI secretion systems). To our knowledge, BastionHub is not only the most comprehensive online database available, it is also the first to incorporate substrates secreted by type I or type II secretion systems. By providing the most up-to-date details of secreted substrates and state-of-the-art prediction and visualized relationship analysis tools, BastionHub will be an important platform that can assist biologists in uncovering novel substrates and formulating new hypotheses. BastionHub is freely available at http://bastionhub.erc.monash.edu/.

Graphical Abstract

BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria.

Figure 1.

General framework of BastionHub illustrating the interconnecting modules that provide standard substrate investigation modules (right panel) and advanced functional modules (left panels). Solid lines indicate procedures within each functional model that operate as an independent toolkit, while dotted lines highlight interactions between different functional modules as interconnecting pipelines.

Figure 2.

Distribution of the 2366 validated secreted substrates catalogued in BastionHub. The doughnut chart illustrates the proportion of each type of secreted substrate. Each subgraph shows the species distribution for that secretion type as a proportion (pie chart) or by total numbers (bar chart).

Figure 3.

Standard investigation modules of BastionHub: the Browse page (A), the Search page and its results page (B), the Statistics page (C), the Download page (D) and the Detailed information page (E).

Figure 4.

Advanced functional modules of BastionHub: the prediction input (A) and results pages (B, C), and the relationship analysis input (D) and results pages (E–G). The yellow arrows represent the interactions between modules within the BastionHub pipelines.