Iddo Friedberg, PhDBioinformatics and Computational Biology

Iowa State University

@iddux

Finding Bacteriocins using BOA

Antibiotic resistanceWHO (2014): “A problem so serious that it threatens the achievements of modern medicine... A post-antibiotic era, in which common infections and minor injuries can kill, far from being an apocalyptic fantasy, is instead a very real possibility for the 21st century.”

Antibiotic Resistance

Nature Chemical Biology 3, 541 - 548 (2007)

Decline in Antiobiotic Approval

Avoiding antbiotic resistance

● Using less antibiotics● Narrow-spectrum

drugs● Harvest more

natural compounds

The Wide World of Bacteriocins

Antimicrobial Peptides

Nisin A

Microcin B17

Berninamycin A

Microcin J25

Bacteriocin AS-48

Virulence Factors

Streptolysin SListeriolysin SClostridiolysin S

CylLL + CylLS

Signaling Peptides

RNPP/Rgg

Agr

Gly-Gly

Bacteriocins AntibioticsSynthesis Ribosomal Secondary metabolite

Bioactivity spectra Mostly narrow Mostly broad

Intensity of bioactivity

Active at nano-to-micro molar range

Active at micro-to-milli molar range

Proteolytic enzyme degradability

High Moderate-to-none

Thermal stability High Low

Active pH range Wide Narrow

Possible mechanism of target cell developing resistance

Adaptation through changes in cell membrane composition

Genetically transferable determinant that inactivates the active compound

Mode of action Pore formation, inhibition of cell wall biosynthesis

Cell membrane or intercellular targets, inhibition cell wall biosynthesis

A B T C I P R K F E G

A B T C I P R K F E G

A B T C I P R K F E G

NisB

NisC

NisT

NisP

A B T C I P R K F E G

NisB

NisC

NisT

NisP

A B T C I P R K F E G

NisB

NisC

NisT

NisP

A B T C I P R K F E G

NisB

NisC

NisT

NisP

A B T C I P R K F E G

NisB

NisC

NisT

NisP

NisF

NisF

NisE

NisG

NisI

A B T C I P R K F E G

NisB

NisC

NisT

NisP

NisF

NisF

NisE

NisG

NisI

NisK

NisR

A B T C I P R K F E G

NisB

NisC

NisT

NisP

NisF

NisF

NisE

NisG

NisI

NisK

NisR

A B T C I P R K F E G

NisB

NisC

NisT

NisP

NisF

NisF

NisE

NisG

NisI

NisK

NisR

Looking for more bacteriocins

Looking for more bacteriocins

?

Bacteriocins may not be homologous, or even detectable as ORFs

So how do we find more bacteriocins?

Antimicrobial Peptides

Nisin A

Microcin B17

Berninamycin A

Microcin J25

Bacteriocin AS-48

Virulence Factors

Streptolysin SListeriolysin SClostridiolysin S

CylLL + CylLS

Signaling Peptides

RNPP/Rgg

Agr

Gly-Gly

?

Use the homologs we have: genomic-context

BOA

Bacteriocin Operon Associator

LC-Set BAGEL BOA

Bacteriocin Operon Associator

LC-Set BAGEL

BLAST vs. GenBank

BOA

Bacteriocin Operon Associator

LC-Set BAGEL

BLAST vs. GenBank

Within 50kb of toxin gene

BOA

Bacteriocin Operon Associator

LC-Set BAGEL

BLAST vs. GenBank

Within 50kb of toxin gene

pHMM

HMMER

pHMM pHMM pHMM pHMM

BOA

Bacteriocin Operon Associator

LC-Set BAGEL

BLAST vs. GenBank

Within 50kb of toxin gene

pHMM

HMMER

pHMM pHMM pHMM pHMM

Clique Filter

BOA

Bacteriocin Operon Associator

The Clique Filter

Approving cliques

Yes

No

The Clique Filter

BAGEL v. BOA

Gene Blocks Found

Method Found

BAGEL 453

BOA + Toxin genes 1,003

BOA – Toxin genes 83

Top 3 Genomes: Different EcosystemsStreptococcus equi Streptomyces griseus Leifsonia xyli

Summing Up

● Annotated genbank files with all predicted bacteriocin blocks are available

● Need more curated bacteriocin blocks for training● Explore use of feature vectors with different

combinations / weights of context genes● Feed into experiments ← → and back● https://github.com/idoerg/BOA● Paper & data in production BMC Bioinformatics● http://arxiv.org/abs/1510.06008

Thanks

Jamie Morton

Stefan Freed Shaun Lee

Bioinformatics & Computational Biology PhD Program

● Well-established program, since 2000● Strengths in: genomics, structural bioinformatics, evolution,

bioengineering● NSF Training grant in plant phenomics● $$$ from: Graduate College, Vice Provost Presidential Initiative

Fellowships; Students take part in major plant and pharmaceutical company internships

● Recent Big Data presidential initiative faculty hires in metagenomics, phylogenetics, protein function prediction & more.

● Apply by February 15

Join the Friedberg Lab

http://iddo-friedberg.net

Biosynthesis of Bacteriocins

Gabrielsen et al. J. Bacteriol. 2014;196:911-919

Streptococcus equi 6

Streptomyces griseus 6

Lefsonia xyli 5

Pusillimonas sp. 4

Rhodosprillum rubrum 4

Streptococcus salivarius

4

Stretomyces sp. 4

Streptomyces pratensis

4

Symbiobacterium thermophilum

4

Thermotoga neopolitana

4

Sterptococcus equi (8)

Biosynthesis of Bacteriocins

Gabrielsen et al. J. Bacteriol. 2014;196:911-919