Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons
Abstract
ABSTRACT Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5andmarinertransposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with any transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq withEscherichia coli,Phaeobacter inhibens,Pseudomonas stutzeri,Shewanella amazonensis, andShewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. InP. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbonmore »
- Authors:
-
- Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Physical Biosciences Division.
- Lawrence Berkeley National Laboratory, Walnut Creek, CA (United States). Joint Genome Institute.
- Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Life Sciences Division.
- Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Physical Biosciences Division; Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1215637
- Alternate Identifier(s):
- OSTI ID: 1512190
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 6; Journal Issue: 3; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Wetmore, Kelly M., Price, Morgan N., Waters, Robert J., Lamson, Jacob S., He, Jennifer, Hoover, Cindi A., Blow, Matthew J., Bristow, James, Butland, Gareth, Arkin, Adam P., and Deutschbauer, Adam. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. United States: N. p., 2015.
Web. doi:10.1128/mBio.00306-15.
Wetmore, Kelly M., Price, Morgan N., Waters, Robert J., Lamson, Jacob S., He, Jennifer, Hoover, Cindi A., Blow, Matthew J., Bristow, James, Butland, Gareth, Arkin, Adam P., & Deutschbauer, Adam. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. United States. https://doi.org/10.1128/mBio.00306-15
Wetmore, Kelly M., Price, Morgan N., Waters, Robert J., Lamson, Jacob S., He, Jennifer, Hoover, Cindi A., Blow, Matthew J., Bristow, James, Butland, Gareth, Arkin, Adam P., and Deutschbauer, Adam. Tue .
"Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons". United States. https://doi.org/10.1128/mBio.00306-15. https://www.osti.gov/servlets/purl/1215637.
@article{osti_1215637,
title = {Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons},
author = {Wetmore, Kelly M. and Price, Morgan N. and Waters, Robert J. and Lamson, Jacob S. and He, Jennifer and Hoover, Cindi A. and Blow, Matthew J. and Bristow, James and Butland, Gareth and Arkin, Adam P. and Deutschbauer, Adam},
abstractNote = {ABSTRACT Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5andmarinertransposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with any transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq withEscherichia coli,Phaeobacter inhibens,Pseudomonas stutzeri,Shewanella amazonensis, andShewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. InP. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putatived-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling. IMPORTANCEA large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are too laborious to be applied to hundreds of experimental conditions across multiple bacteria. Here, we describe an approach, random bar code transposon-site sequencing (RB-TnSeq), which greatly simplifies the measurement of gene fitness by using bar code sequencing (BarSeq) to monitor the abundance of mutants. We performed 387 genome-wide fitness assays across five bacteria and identified phenotypes for over 5,000 genes. RB-TnSeq can be applied to diverse bacteria and is a powerful tool to annotate uncharacterized genes using phenotype data.},
doi = {10.1128/mBio.00306-15},
journal = {mBio (Online)},
number = 3,
volume = 6,
place = {United States},
year = {Tue May 12 00:00:00 EDT 2015},
month = {Tue May 12 00:00:00 EDT 2015}
}
Web of Science
Figures / Tables:
Works referenced in this record:
Single-Cell Dynamics Reveals Sustained Growth during Diauxic Shifts
journal, April 2013
- Boulineau, Sarah; Tostevin, Filipe; Kiviet, Daniel J.
- PLoS ONE, Vol. 8, Issue 4
Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions
journal, November 2011
- Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.
- PLoS Genetics, Vol. 7, Issue 11
Genetic analysis of pigment biosynthesis in Xanthobacter autotrophicus Py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria
journal, September 2002
- Larsen, Rachel; Wilson, Marlena; Guss, Adam
- Archives of Microbiology, Vol. 178, Issue 3
Metabolic niche of a prominent sulfate-reducing human gut bacterium
journal, July 2013
- Rey, F. E.; Gonzalez, M. D.; Cheng, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 33
Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries
journal, November 2011
- Goodman, Andrew L.; Wu, Meng; Gordon, Jeffrey I.
- Nature Protocols, Vol. 6, Issue 12
BLAT---The BLAST-Like Alignment Tool
journal, March 2002
- Kent, W. J.
- Genome Research, Vol. 12, Issue 4
Quantitative phenotyping via deep barcode sequencing
journal, July 2009
- Smith, A. M.; Heisler, L. E.; Mellor, J.
- Genome Research, Vol. 19, Issue 10
Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli
journal, September 2006
- Joyce, A. R.; Reed, J. L.; White, A.
- Journal of Bacteriology, Vol. 188, Issue 23
Carbohydrate Catabolism in Phaeobacter inhibens DSM 17395, a Member of the Marine Roseobacter Clade
journal, May 2014
- Wiegmann, Katharina; Hensler, Michael; Wöhlbrand, Lars
- Applied and Environmental Microbiology, Vol. 80, Issue 15
At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies
journal, December 2005
- Ashelford, K. E.; Chuzhanova, N. A.; Fry, J. C.
- Applied and Environmental Microbiology, Vol. 71, Issue 12
Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis
journal, January 2012
- Klein, Brian A.; Tenorio, Elizabeth L.; Lazinski, David W.
- BMC Genomics, Vol. 13, Issue 1
Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples
journal, May 2010
- Smith, A. M.; Heisler, L. E.; St. Onge, R. P.
- Nucleic Acids Research, Vol. 38, Issue 13
Gene Annotation and Drug Target Discovery in Candida albicans with a Tagged Transposon Mutant Collection
journal, October 2010
- Oh, Julia; Fung, Eula; Schlecht, Ulrich
- PLoS Pathogens, Vol. 6, Issue 10
Towards an Informative Mutant Phenotype for Every Bacterial Gene
journal, August 2014
- Deutschbauer, A.; Price, M. N.; Wetmore, K. M.
- Journal of Bacteriology, Vol. 196, Issue 20
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009
- Langmead, Ben; Trapnell, Cole; Pop, Mihai
- Genome Biology, Vol. 10, Issue 3
Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes
journal, January 2000
- Goryshin, Igor Y.; Jendrisak, Jerry; Hoffman, Les M.
- Nature Biotechnology, Vol. 18, Issue 1
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006
- Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
- Molecular Systems Biology, Vol. 2, Article No. 2006.0008
Phenotypic Landscape of a Bacterial Cell
journal, January 2011
- Nichols, Robert J.; Sen, Saunak; Choo, Yoe Jin
- Cell, Vol. 144, Issue 1
Cost-Benefit Tradeoffs in Engineered lac Operons
journal, May 2012
- Eames, M.; Kortemme, T.
- Science, Vol. 336, Issue 6083
Genomic encyclopedia of sugar utilization pathways in the Shewanella genus
journal, January 2010
- Rodionov, Dmitry A.; Yang, Chen; Li, Xiaoqing
- BMC Genomics, Vol. 11, Issue 1
Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action
journal, January 2010
- Hillenmeyer, Maureen E.; Ericson, Elke; Davis, Ronald W.
- Genome Biology, Vol. 11, Issue 3
The Comprehensive Microbial Resource
journal, January 2001
- Peterson, J. D.
- Nucleic Acids Research, Vol. 29, Issue 1
Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures
journal, April 2014
- Lee, A. Y.; St. Onge, R. P.; Proctor, M. J.
- Science, Vol. 344, Issue 6180
Variation among Desulfovibrio Species in Electron Transfer Systems Used for Syntrophic Growth
journal, December 2012
- Meyer, B.; Kuehl, J.; Deutschbauer, A. M.
- Journal of Bacteriology, Vol. 195, Issue 5
A universal TagModule collection for parallel genetic analysis of microorganisms
journal, May 2010
- Oh, Julia; Fung, Eula; Price, Morgan N.
- Nucleic Acids Research, Vol. 38, Issue 14
Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms
journal, May 2013
- van Opijnen, Tim; Camilli, Andrew
- Nature Reviews Microbiology, Vol. 11, Issue 7
Why Does Escherichia coli Grow More Slowly on Glucosamine than on N-Acetylglucosamine? Effects of Enzyme Levels and Allosteric Activation of GlcN6P Deaminase (NagB) on Growth Rates
journal, April 2005
- Alvarez-Anorve, L. I.; Calcagno, M. L.; Plumbridge, J.
- Journal of Bacteriology, Vol. 187, Issue 9
Indirect and suboptimal control of gene expression is widespread in bacteria
journal, January 2013
- Price, Morgan N.; Deutschbauer, Adam M.; Skerker, Jeffrey M.
- Molecular Systems Biology, Vol. 9, Issue 1
A fine scale phenotype-genotype virulence map of a bacterial pathogen
journal, July 2012
- van Opijnen, T.; Camilli, A.
- Genome Research, Vol. 22, Issue 12
Rapid Transposon Liquid Enrichment Sequencing (TnLE-seq) for Gene Fitness Evaluation in Underdeveloped Bacterial Systems
journal, September 2013
- Fels, Samuel R.; Zane, Grant M.; Blake, Sean M.
- Applied and Environmental Microbiology, Vol. 79, Issue 23
Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
journal, September 2009
- van Opijnen, Tim; Bodi, Kip L.; Camilli, Andrew
- Nature Methods, Vol. 6, Issue 10
Functional profiling of the Saccharomyces cerevisiae genome
journal, July 2002
- Giaever, Guri; Chu, Angela M.; Ni, Li
- Nature, Vol. 418, Issue 6896
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
journal, October 2009
- Langridge, G. C.; Phan, M. -D.; Turner, D. J.
- Genome Research, Vol. 19, Issue 12
Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung
journal, September 2009
- Gawronski, J. D.; Wong, S. M. S.; Giannoukos, G.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 38
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
journal, January 2011
- Haas, B. J.; Gevers, D.; Earl, A. M.
- Genome Research, Vol. 21, Issue 3
Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20
journal, May 2014
- Kuehl, Jennifer V.; Price, Morgan N.; Ray, Jayashree
- mBio, Vol. 5, Issue 3
Harnessing Single Cell Sorting to Identify Cell Division Genes and Regulators in Bacteria
journal, April 2013
- Burke, Catherine; Liu, Michael; Britton, Warwick
- PLoS ONE, Vol. 8, Issue 4
SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation
journal, July 2020
- Zoch, Ansgar; Auchynnikava, Tania; Berrens, Rebecca V.
- Nature, Vol. 584, Issue 7822
Identification and Characterization of a Novel FosA7 Member from Fosfomycin-Resistant Escherichia coli Clinical Isolates from Canadian Hospitals
journal, December 2020
- Milner, Kieran A.; Bay, Denice C.; Alexander, David
- Antimicrobial Agents and Chemotherapy, Vol. 65, Issue 1
The S-Phase Cyclin Clb5 Promotes rRNA Gene (rDNA) Stability by Maintaining Replication Initiation Efficiency in rDNA
journal, April 2021
- Goto, Mayuko; Sasaki, Mariko; Kobayashi, Takehiko
- Molecular and Cellular Biology, Vol. 41, Issue 5
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium
journal, April 2021
- González-Pech, Raúl A.; Stephens, Timothy G.; Chen, Yibi
- BMC Biology, Vol. 19, Issue 1
Works referencing / citing this record:
Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis
journal, October 2018
- Lakemeyer, Markus; Zhao, Weining; Mandl, Franziska A.
- Angewandte Chemie International Edition, Vol. 57, Issue 44
Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016
- Garst, Andrew D.; Bassalo, Marcelo C.; Pines, Gur
- Nature Biotechnology, Vol. 35, Issue 1, p. 48-55
Emerging and evolving concepts in gene essentiality
journal, October 2017
- Rancati, Giulia; Moffat, Jason; Typas, Athanasios
- Nature Reviews Genetics, Vol. 19, Issue 1
Rhizobia: from saprophytes to endosymbionts
journal, January 2018
- Poole, Philip; Ramachandran, Vinoy; Terpolilli, Jason
- Nature Reviews Microbiology, Vol. 16, Issue 5
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance
journal, June 2018
- Wang, Tianmin; Guan, Changge; Guo, Jiahui
- Nature Communications, Vol. 9, Issue 1
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria
journal, January 2019
- Mutalik, Vivek K.; Novichkov, Pavel S.; Price, Morgan N.
- Nature Communications, Vol. 10, Issue 1
Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes
journal, December 2019
- Thibault, Derek; Jensen, Paul A.; Wood, Stephen
- Nature Communications, Vol. 10, Issue 1
DABs are inorganic carbon pumps found throughout prokaryotic phyla
journal, August 2019
- Desmarais, John J.; Flamholz, Avi I.; Blikstad, Cecilia
- Nature Microbiology, Vol. 4, Issue 12
CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria
journal, October 2019
- Wang, Gaoyan; Zhao, Zhiying; Ke, Jing
- Nature Microbiology, Vol. 4, Issue 12
Mutant phenotypes for thousands of bacterial genes of unknown function
journal, May 2018
- Price, Morgan N.; Wetmore, Kelly M.; Waters, R. Jordan
- Nature, Vol. 557, Issue 7706
Genetic dissection of interspecific differences in yeast thermotolerance
journal, October 2018
- Weiss, Carly V.; Roop, Jeremy I.; Hackley, Rylee K.
- Nature Genetics, Vol. 50, Issue 11
A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis
journal, March 2019
- Li, Xiaobo; Patena, Weronika; Fauser, Friedrich
- Nature Genetics, Vol. 51, Issue 4
Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
journal, May 2018
- Jahn, Leonie Johanna; Porse, Andreas; Munck, Christian
- Scientific Reports, Vol. 8, Issue 1
Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production
journal, April 2019
- Savitskaya, Judy; Protzko, Ryan J.; Li, Francesca-Zhoufan
- Scientific Reports, Vol. 9, Issue 1
The essential gene set of a photosynthetic organism
journal, October 2015
- Rubin, Benjamin E.; Wetmore, Kelly M.; Price, Morgan N.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 48
Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA
journal, July 2018
- Welkie, David G.; Rubin, Benjamin E.; Chang, Yong-Gang
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 30
Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast
journal, September 2019
- Helmann, Tyler C.; Deutschbauer, Adam M.; Lindow, Steven E.
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 38
Novel approaches in function-driven single-cell genomics
journal, June 2017
- Doud, Devin F. R.; Woyke, Tanja
- FEMS Microbiology Reviews, Vol. 41, Issue 4
A putative RND-type efflux pump, H239_3064, contributes to colistin resistance through CrrB in Klebsiella pneumoniae
journal, February 2018
- Cheng, Yi-Hsiang; Lin, Tzu-Lung; Lin, Yi-Tsung
- Journal of Antimicrobial Chemotherapy, Vol. 73, Issue 6
There is no hiding if you Seq: recent breakthroughs in Pseudomonas aeruginosa research revealed by genomic and transcriptomic next-generation sequencing
journal, February 2020
- Valli, Richard X. E.; Lyng, Mark; Kirkpatrick, Clare L.
- Journal of Medical Microbiology, Vol. 69, Issue 2
Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater
preprint, September 2018
- Hentchel, Kristy L.; Ruiz, Leila M. Reyes; Curtis, Patrick D.
- The ISME Journal
Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits
posted_content, August 2018
- Mutalik, Vivek K.; Novichkov, Pavel S.; Price, Morgan N.
- bioRxiv
A genome-wide algal mutant library reveals a global view of genes required for eukaryotic photosynthesis
posted_content, November 2018
- Li, Xiaobo; Patena, Weronika; Fauser, Friedrich
- bioRxiv
Brucella periplasmic protein EipB is a molecular determinant of cell envelope integrity and virulence
posted_content, March 2019
- Herrou, Julien; Willett, Jonathan W.; Fiebig, Aretha
- bioRxiv
Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria
posted_content, September 2019
- Shiver, Anthony L.; Culver, Rebecca; Deutschbauer, Adam M.
- Nature Protocols
Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans -acting effects influencing species-dependent essential genes
journal, January 2019
- Sanchez, Monica R.; Payen, Celia; Cheong, Frances
- Genome Research, Vol. 29, Issue 3
The bare necessities: Uncovering essential and condition‐critical genes with transposon sequencing
journal, February 2019
- Shields, Robert C.; Jensen, Paul A.
- Molecular Oral Microbiology, Vol. 34, Issue 2
Brucella Periplasmic Protein EipB Is a Molecular Determinant of Cell Envelope Integrity and Virulence
journal, April 2019
- Herrou, Julien; Willett, Jonathan W.; Fiebig, Aretha
- Journal of Bacteriology, Vol. 201, Issue 12
Genome-Wide Transposon Screen of a Pseudomonas syringae mexB Mutant Reveals the Substrates of Efflux Transporters
journal, October 2019
- Helmann, Tyler C.; Ongsarte, Caitlin L.; Lam, Jennifer
- mBio, Vol. 10, Issue 5
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression
journal, November 2019
- Subramaniyam, Siddharth; DeJesus, Michael A.; Zaveri, Anisha
- BMC Bioinformatics, Vol. 20, Issue 1
Essential genome of Campylobacter jejuni
journal, August 2017
- Mandal, Rabindra K.; Jiang, Tieshan; Kwon, Young Min
- BMC Genomics, Vol. 18, Issue 1
Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes
journal, September 2017
- Lau, Billy T.; Ji, Hanlee P.
- BMC Genomics, Vol. 18, Issue 1
New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions
journal, May 2020
- De Meur, Quentin; Deutschbauer, Adam; Koch, Matthias
- BMC Microbiology, Vol. 20, Issue 1
Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC
journal, October 2018
- Eng, Thomas; Demling, Philipp; Herbert, Robin A.
- Microbial Cell Factories, Vol. 17, Issue 1
Genome-wide identification of bacterial plant colonization genes
journal, September 2017
- Cole, Benjamin J.; Feltcher, Meghan E.; Waters, Robert J.
- PLOS Biology, Vol. 15, Issue 9
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
journal, January 2018
- Price, Morgan N.; Zane, Grant M.; Kuehl, Jennifer V.
- PLOS Genetics, Vol. 14, Issue 1
High-throughput interaction screens illuminate the role of c-di-AMP in cyanobacterial nighttime survival
journal, April 2018
- Rubin, Benjamin E.; Huynh, TuAnh Ngoc; Welkie, David G.
- PLOS Genetics, Vol. 14, Issue 4
A Comparison of the Costs and Benefits of Bacterial Gene Expression
journal, October 2016
- Price, Morgan N.; Wetmore, Kelly M.; Deutschbauer, Adam M.
- PLOS ONE, Vol. 11, Issue 10
Genomics Approaches to Deciphering Natural Transformation in Cyanobacteria
journal, June 2019
- Wendt, Kristen E.; Pakrasi, Himadri B.
- Frontiers in Microbiology, Vol. 10
Challenges and Approaches in Microbiome Research: From Fundamental to Applied
journal, August 2018
- Sergaki, Chrysi; Lagunas, Beatriz; Lidbury, Ian
- Frontiers in Plant Science, Vol. 9
An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism
journal, June 2020
- Thompson, Mitchell G.; Blake-Hedges, Jacquelyn M.; Pereira, Jose Henrique
- Nature Communications, Vol. 11, Issue 1
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
journal, May 2000
- Datsenko, K. A.; Wanner, B. L.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645
Enhancements and modifications of primer design program Primer3
journal, March 2007
- Koressaar, T.; Remm, M.
- Bioinformatics, Vol. 23, Issue 10
A Comparison of the Costs and Benefits of Bacterial Gene Expression
journal, July 2016
- Price, Morgan N.; Wetmore, Kelly M.; Deutschbauer, Adam M.
- PLOS ONE
Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA
journal, June 2018
- Welkie, David G.; Rubin, Benjamin E.; Chang, Yong-Gang
- Proceedings of the National Academy of Sciences
Statistical Analysis of Variability in TnSeq Data Across Conditions Using Zero-Inflated Negative Binomial Regression
posted_content, August 2019
- Subramaniyam, Siddharth; Zaveri, Anisha; DeJesus, Michael A.
- bioRxiv
H2S: A Universal Defense Against Antibiotics in Bacteria
journal, November 2011
- Shatalin, K.; Shatalina, E.; Mironov, A.
- Science, Vol. 334, Issue 6058
A Carbonic Anhydrase Pseudogene Sensitizes Select Brucella Lineages to Low CO 2 Tension
journal, November 2019
- Varesio, Lydia M.; Willett, Jonathan W.; Fiebig, Aretha
- Journal of Bacteriology, Vol. 201, Issue 22
Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC
text, January 2018
- Eng, Thomas; Demling, Philipp; Herbert, Robin A.
- RWTH Aachen University
Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution
journal, February 2020
- Jasinska, Weronika; Manhart, Michael; Lerner, Jesse
- Nature Ecology & Evolution, Vol. 4, Issue 3
Genome-wide identification of bacterial plant colonization genes
text, January 2017
- Gaoyan, Wang,; M., Ryan, Elizabeth; Meredith, McDonald,
- The University of North Carolina at Chapel Hill University Libraries
Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria
journal, May 2021
- Shiver, Anthony L.; Culver, Rebecca; Deutschbauer, Adam M.
- Nature Protocols, Vol. 16, Issue 6
Genome-wide transposon screen of a Pseudomonas syringae mexB mutant reveals the substrates of efflux transporters
posted_content, July 2019
- Helmann, Tyler C.; Ongsarte, Caitlin L.; Lam, Jennifer
- mBio
Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater
journal, October 2018
- Hentchel, Kristy L.; Reyes Ruiz, Leila M.; Curtis, Patrick D.
- The ISME Journal, Vol. 13, Issue 2
Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution
text, January 2020
- Weronika, Jasinska,; Michael, Manhart,; Jesse, Lerner,
- ETH Zurich
Figures / Tables found in this record: