PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

Hu, James C.; Sherlock, Gavin; Siegele, Deborah A.; Aleksander, Suzi; Ball, Catherine A.; Demeter, János; Gouni, Sushanth; Holland, Timothy A.; Karp, Peter D.; Lewis, John E.; Liles, Nathan; McIntosh, Brenley K.; Mi, Huaiyu; Muruganujan, Anushya; Wymore, Farrell; Thomas, Paul D.

doi:10.1093/nar/gkt1203

Cited by 21 publications

(10 citation statements)

References 45 publications

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“…1C we mapped the V. fischeri genes that were orthologs of essential genes in E. coli MG1655, the organism for which the best curated list of essential genes exists (13). Most E. coli essential genes mapped to the clusters with no or relatively few transposon counts in V. fischeri (175 of the 230 orthologs encoded in V. fischeri), supporting their assignment as putative essential genes in V. fischeri.…”

Section: Resultsmentioning

confidence: 69%

Global discovery of colonization determinants in the squid symbiontVibrio fischeri

Brooks

Gyllborg

Cronin

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

102

120

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Animal epithelial tissue becomes reproducibly colonized by specific environmental bacteria. The bacteria (microbiota) perform critical functions for the host's tissue development, immune system development, and nutrition; yet the processes by which bacterial diversity in the environment is selected to assemble the correct communities in the host are unclear. To understand the molecular determinants of microbiota selection, we examined colonization of a simplified model in which the light organ of Euprymna scolopes squid is colonized exclusively by Vibrio fischeri bacteria. We applied highthroughput insertion sequencing to identify which bacterial genes are required during host colonization. A library of over 41,000 unique transposon insertions was analyzed before and after colonization of 1,500 squid hatchlings. Mutants that were reproducibly depleted following squid colonization represented 380 genes, including 37 that encode known colonization factors. Validation of select mutants in defined competitions against the wild-type strain identified nine mutants that exhibited a reproducible colonization defect. Some of the colonization factors identified included genes predicted to influence copper regulation and secretion. Other mutants exhibited defects in biofilm development, which is required for aggregation in host mucus and initiation of colonization. Biofilm formation in culture and in vivo was abolished in a strain lacking the cytoplasmic chaperone DnaJ, suggesting an important role for protein quality control during the elaboration of bacterial biofilm in the context of an intact host immune system. Overall these data suggest that cellular stress responses and biofilm regulation are critical processes underlying the reproducible colonization of animal hosts by specific microbial symbionts.H umans and other animals are often sterile before birth, from which point they immediately proceed to acquire environmental bacteria (1). The bacteria that reproducibly colonize animal hosts are critical for host tissue development, immune system development, and nutrient acquisition. The selection process by which the functional symbionts take residence in the animal from among the great diversity of environmental microbes is poorly understood, so model systems have been especially valuable to examine how specific patterns of colonization are shaped by the genetic makeup of the bacteria and the host environment (2).The light organ of the Hawaiian bobtail squid, Euprymna scolopes, is colonized exclusively by the Gram-negative luminous bacterium Vibrio fischeri. The host inhabits seawater containing 10 6 bacteria per milliliter, with V. fischeri comprising at most 0.02% of the environmental population (3). E. scolopes hatch without symbionts, but then rapidly acquire environmental bacteria and proceed to select for V. fischeri in a "winnowing" process that ensures colonization by only the specific symbiont (4). The squid-Vibrio system thus presents an opportunity to investigate the processes that underlie acquisition of s...

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Section: Resultsmentioning

confidence: 69%

Global discovery of colonization determinants in the squid symbiontVibrio fischeri

Brooks

Gyllborg

Cronin

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

102

120

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“…A separate issue is the benefits of using the hierarchical structure in the ontology of the different levels of detail used to describe GCs. Efforts such as those of COLOMBOS and PortEco, dealing with repositories of microarray experimental data, use either use previous ontologies or develop their own ( 10 , 11 ). Thanks to an initial collaboration with the COLOMBOS team, we are using their descriptions as an alternative dictionary of conditions within ODIN (See Figure 1 ).…”

Section: Resultsmentioning

confidence: 99%

Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12

Gama-Castro¹,

Rinaldi²,

López-Fuentes³

et al. 2014

Database

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Given the current explosion of data within original publications generated in the field of genomics, a recognized bottleneck is the transfer of such knowledge into comprehensive databases. We have for years organized knowledge on transcriptional regulation reported in the original literature of Escherichia coli K-12 into RegulonDB (http://regulondb.ccg.unam.mx), our database that is currently supported by >5000 papers. Here, we report a first step towards the automatic biocuration of growth conditions in this corpus. Using the OntoGene text-mining system (http://www.ontogene.org), we extracted and manually validated regulatory interactions and growth conditions in a new approach based on filters that enable the curator to select informative sentences from preprocessed full papers. Based on a set of 48 papers dealing with oxidative stress by OxyR, we were able to retrieve 100% of the OxyR regulatory interactions present in RegulonDB, including the transcription factors and their effect on target genes. Our strategy was designed to extract, as we did, their growth conditions. This result provides a proof of concept for a more direct and efficient curation process, and enables us to define the strategy of the subsequent steps to be implemented for a semi-automatic curation of original literature dealing with regulation of gene expression in bacteria. This project will enhance the efficiency and quality of the curation of knowledge present in the literature of gene regulation, and contribute to a significant increase in the encoding of the regulatory network of E. coli.RegulonDB Database URL: http://regulondb.ccg.unam.mxOntoGene URL: http://www.ontogene.org

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“…The weight of total proteins per cell was estimated by dividing the amount of proteins per unit volume of cell culture, which was measured using the Lowry method with BSA as standards after trichloroacetic acid precipitation, by the number of cells per unit volume, which was measured by counting colony-forming units after serial dilution. The absolute synthesis rates listed in Table S1 are also available through PortEco (Hu et al, 2014). …”

Section: Methodsmentioning

confidence: 99%

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

Burkhardt

Gross

et al. 2014

Cell

1,178

102

1,412

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Quantitative views of cellular functions requires precise measures of rates of biomolecule production, especially proteins—the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resultant E. coli dataset transforms our understanding of the extent to which protein synthesis is precisely controlled to optimize function and efficiency. Members of multi-protein complexes are made in precise proportion to their stoichiometry, whereas components of functional modules are produced differentially according to their hierarchical role. Estimates of absolute protein abundance also reveal principles used to optimize design. These include how the level of different types of transcription factors is optimized for rapid response, and how a metabolic pathway (methionine biosynthesis) balances production cost with activity requirements. Our studies reveal how general principles, important both for understanding natural systems and for synthesizing new ones, emerge from quantitative analyses of protein synthesis.

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PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

Cited by 21 publications

References 45 publications

Global discovery of colonization determinants in the squid symbiontVibrio fischeri

Global discovery of colonization determinants in the squid symbiontVibrio fischeri

Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

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