1
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Banta AB, Myers KS, Ward RD, Cuellar RA, Place M, Freeh CC, Bacon EE, Peters JM. A Targeted Genome-scale Overexpression Platform for Proteobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582922. [PMID: 38496613 PMCID: PMC10942329 DOI: 10.1101/2024.03.01.582922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, and basic research. Although CRISPRi knockdowns have been broadly applied in bacteria, options for genome-scale overexpression face key limitations. Here, we develop a facile approach for genome-scale gene overexpression in bacteria we call, "CRISPRtOE" (CRISPR transposition and OverExpression). We create a platform for comprehensive gene targeting using CRISPR-associated transposition (CAST) and show that transposition occurs at a higher frequency in non-transcribed DNA. We then demonstrate that CRISPRtOE can upregulate gene expression in Proteobacteria with medical and industrial relevance by integrating synthetic promoters of varying strength upstream of target genes. Finally, we employ CRISPRtOE screening at the genome-scale in Escherichia coli, recovering known antibiotic targets and genes with unexplored roles in antibiotic function. We envision that CRISPRtOE will be a valuable overexpression tool for antibiotic mode of action, industrial strain optimization, and gene function discovery in bacteria.
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Affiliation(s)
- Amy B. Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin S. Myers
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Rodrigo A. Cuellar
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Claire C. Freeh
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Emily E. Bacon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
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2
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Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022; 17:1518-1552. [PMID: 35478247 PMCID: PMC9189070 DOI: 10.1038/s41596-022-00692-9] [Citation(s) in RCA: 154] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment.
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Affiliation(s)
- Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lucas Kampman
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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3
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Zhou K, Litfin T, Solayman M, Zhao H, Zhou Y, Zhan J. High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing. Int J Biol Macromol 2022; 203:543-552. [PMID: 35120933 DOI: 10.1016/j.ijbiomac.2022.01.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Splitting a protein at a position may lead to self- or assisted-complementary fragments depending on whether two resulting fragments can reconstitute to maintain the native function spontaneously or require assistance from two interacting molecules. Assisted complementary fragments with high contrast are an important tool for probing biological interactions. However, only a small number of assisted-complementary split-variants have been identified due to manual, labour-intensive optimization of a candidate gene. Here, we introduce a technique for high-throughput split-protein profiling (HiTS) that allows fast identification of self- and assisted complementary positions by transposon mutagenesis, a rapamycin-regulated FRB-FKBP protein interaction pair, and deep sequencing. We test this technique by profiling three antibiotic-resistant genes (fosfomycin-resistant gene, fosA3, erythromycin-resistant gene, ermB, and chloramphenicol-resistant gene, catI). Self- and assisted complementary fragments discovered by the high-throughput technique were subsequently confirmed by low-throughput testing of individual split positions. Thus, the HiTS technique provides a quicker alternative for discovering the proteins with suitable self- and assisted-complementary split positions when combining with a readout such as fluorescence, bioluminescence, cell survival, gene transcription or genome editing.
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Affiliation(s)
- Kai Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Thomas Litfin
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Md Solayman
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Huijun Zhao
- Centre for Clean Environment and Energy, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
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4
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Abstract
TnSeq, or sequencing of transposon insertion libraries, has proven to be a valuable method for probing the functions of genes in a wide range of bacteria. TnSeq has found many applications for studying genes involved in core functions (such as cell division or metabolism), stress response, virulence, etc., as well as to identify potential drug targets. Two of the most commonly used transposons in practice are Himar1, which inserts randomly at TA dinucleotides, and Tn5, which can insert more broadly throughout the genome. These insertions cause putative gene function disruption, and clones with insertions in genes that cannot tolerate disruption (in a given condition) are eliminated from the population. Deep sequencing can be used to efficiently profile the surviving members, with insertions in genes that can be inferred to be non-essential. Data from TnSeq experiments (i.e. transposon insertion counts at specific genomic locations) is inherently noisy, making rigorous statistical analysis (e.g. quantifying significance) challenging. In this chapter, we describe Transit, a Python-based software package for analyzing TnSeq data that combines a variety of data processing tools, quality assessment methods, and analytical algorithms for identifying essential (or conditionally essential) genes.
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Affiliation(s)
- Thomas R Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX, USA.
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5
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Maynard LH, Smith O, Tilmans NP, Tham E, Hosseinzadeh S, Tan W, Leenay R, May AP, Paulk NK. Fast-Seq: A Simple Method for Rapid and Inexpensive Validation of Packaged Single-Stranded Adeno-Associated Viral Genomes in Academic Settings. Hum Gene Ther Methods 2020; 30:195-205. [PMID: 31855083 PMCID: PMC6919253 DOI: 10.1089/hgtb.2019.110] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Adeno-associated viral (AAV) vectors have shown great promise in gene delivery as evidenced by recent FDA approvals. Despite efforts to optimize manufacturing for good manufacturing practice (GMP) productions, few academic laboratories have the resources to assess vector composition. One critical component of vector quality is packaged genome fidelity. Errors in viral genome replication and packaging can result in the incorporation of faulty genomes with mutations, truncations, or rearrangements, compromising vector potency. Thus, sequence validation of packaged genome composition is an important quality control (QC), even in academic settings. We developed Fast-Seq, an end-to-end method for extraction, purification, sequencing, and data analysis of packaged single-stranded AAV (ssAAV) genomes intended for non-GMP preclinical environments. We validated Fast-Seq on ssAAV vectors with three different genome compositions (CAG-GFP, CAG-tdTomato, EF1α-FLuc), three different genome sizes (2.9, 3.6, 4.4 kb), packaged in four different capsid serotypes (AAV1, AAV2, AAV5, and AAV8), and produced using the two most common production methods (Baculovirus-Sf9 and human HEK293), from both common commercial vendors and academic core facilities supplying academic laboratories. We achieved an average genome coverage of >1,400 × and an average inverted terminal repeat coverage of >280 × , despite the many differences in composition of each ssAAV sample. When compared with other ssAAV next-generation sequencing (NGS) methods for GMP settings, Fast-Seq has several unique advantages: Tn5 transposase-based fragmentation rather than sonication, 125 × less input DNA, simpler adapter ligation, compatibility with commonly available inexpensive sequencing instruments, and free open-source data analysis code in a preassembled customizable Docker container designed for novices. Fast-Seq can be completed in 18 h, is more cost-effective than other NGS methods, and is more accurate than Sanger sequencing, which is generally only applied at 1-2 × sequencing depth. Fast-Seq is a rapid, simple, and inexpensive methodology to validate packaged ssAAV genomes in academic settings.
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Affiliation(s)
- Lucy H Maynard
- Chan Zuckerberg Biohub, Department of Genome Engineering, San Francisco, California
| | - Olivia Smith
- Chan Zuckerberg Biohub, Department of Genome Engineering, San Francisco, California
| | | | - Eleonore Tham
- Chan Zuckerberg Biohub, Department of Genome Engineering, San Francisco, California
| | - Shayan Hosseinzadeh
- Chan Zuckerberg Biohub, Department of Genome Engineering, San Francisco, California
| | - Weilun Tan
- Chan Zuckerberg Biohub, Department of Genome Engineering, San Francisco, California
| | - Ryan Leenay
- Chan Zuckerberg Biohub, Department of Genome Engineering, San Francisco, California
| | - Andrew P May
- Chan Zuckerberg Biohub, Department of Genome Engineering, San Francisco, California
| | - Nicole K Paulk
- Genome Engineering, Chan Zuckerberg Biohub, San Francisco, California.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California
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6
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Guerin K, Rego M, Bourges D, Ersing I, Haery L, Harten DeMaio K, Sanders E, Tasissa M, Kostman M, Tillgren M, Makana Hanley L, Mueller I, Mitsopoulos A, Fan M. A Novel Next-Generation Sequencing and Analysis Platform to Assess the Identity of Recombinant Adeno-Associated Viral Preparations from Viral DNA Extracts. Hum Gene Ther 2020; 31:664-678. [PMID: 32159396 PMCID: PMC7310222 DOI: 10.1089/hum.2019.277] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors are increasingly popular gene delivery tools in biological systems. They are safe and lead to high-level, long-term transgene expression. rAAV are available in multiple serotypes, natural or engineered, which enable targeting to a wide array of tissues and cell types. In addition, rAAVs are relatively easily produced in a well-equipped lab or obtained from a viral vector core facility. Unfortunately, there is no standardization of quality control assays beyond titering and purity assessments. Next-generation sequencing (NGS) can be used to identify rAAV preparations. Because the rAAV genome is single stranded, previous studies have assumed that rAAV genomes must be converted to double strands before NGS. We demonstrate that rAAV DNA extracts exist primarily as double-stranded species. We hypothesize that these molecules form from the natural base pairing of complementary [+] and [−] strands after DNA extraction and show that rAAV DNA extracts are sufficient templates for downstream NGS without the labor-intensive double-stranding step. Here, we provide a detailed protocol for the simple and rapid NGS of rAAV genomes from DNA extracts. With this protocol, users can quickly confirm the identity of an rAAV preparation and detect the presence of contaminating rAAV DNA. In addition, we share custom Python scripts that allow users to accurately determine the serotype and detect Cre-independent DNA recombination events in rAAV containing Lox sites within minutes. We have used these scripts to analyze more than 100 rAAV preparations. Although we focused on the detection of cross-contaminating rAAV DNA and recombination events, our Python scripts can be customized to detect other sequences or events, such as reverse packaging of plasmid backbone or DNA from the packaging cell line. We find that the NGS of rAAV DNA extracts, termed viral genome sequencing, is a simple and powerful method for rAAV validation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Melina Fan
- Addgene, Watertown, Massachusetts, USA
- Correspondence: Dr. Melina Fan, Addgene, 490 Arsenal Way, Suite 100, Watertown, MA 02472, USA.
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7
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Coyote-Maestas W, Nedrud D, Okorafor S, He Y, Schmidt D. Targeted insertional mutagenesis libraries for deep domain insertion profiling. Nucleic Acids Res 2020; 48:e11. [PMID: 31745561 PMCID: PMC6954442 DOI: 10.1093/nar/gkz1110] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/22/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Domain recombination is a key principle in protein evolution and protein engineering, but inserting a donor domain into every position of a target protein is not easily experimentally accessible. Most contemporary domain insertion profiling approaches rely on DNA transposons, which are constrained by sequence bias. Here, we establish Saturated Programmable Insertion Engineering (SPINE), an unbiased, comprehensive, and targeted domain insertion library generation technique using oligo library synthesis and multi-step Golden Gate cloning. Through benchmarking to MuA transposon-mediated library generation on four ion channel genes, we demonstrate that SPINE-generated libraries are enriched for in-frame insertions, have drastically reduced sequence bias as well as near-complete and highly-redundant coverage. Unlike transposon-mediated domain insertion that was severely biased and sparse for some genes, SPINE generated high-quality libraries for all genes tested. Using the Inward Rectifier K+ channel Kir2.1, we validate the practical utility of SPINE by constructing and comparing domain insertion permissibility maps. SPINE is the first technology to enable saturated domain insertion profiling. SPINE could help explore the relationship between domain insertions and protein function, and how this relationship is shaped by evolutionary forces and can be engineered for biomedical applications.
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Affiliation(s)
- Willow Coyote-Maestas
- Dept. of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Nedrud
- Dept. of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Steffan Okorafor
- Dept. of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yungui He
- Dept. of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel Schmidt
- Dept. of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455, USA
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8
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Zhou Y, Xu H, Wu H, Yu H, Zhou P, Qiu X, Zheng Z, Chen Q, Xu F, Li G, Zhou J, Cheng G, He W, Zou L, Wan Y. Streamlined Low-Input Transcriptomics through EASY-RNAseq. J Mol Biol 2019; 431:5075-5085. [DOI: 10.1016/j.jmb.2019.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022]
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9
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Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. BMC Bioinformatics 2019; 20:603. [PMID: 31752678 PMCID: PMC6873424 DOI: 10.1186/s12859-019-3156-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Background Deep sequencing of transposon mutant libraries (or TnSeq) is a powerful method for probing essentiality of genomic loci under different environmental conditions. Various analytical methods have been described for identifying conditionally essential genes whose tolerance for insertions varies between two conditions. However, for large-scale experiments involving many conditions, a method is needed for identifying genes that exhibit significant variability in insertions across multiple conditions. Results In this paper, we introduce a novel statistical method for identifying genes with significant variability of insertion counts across multiple conditions based on Zero-Inflated Negative Binomial (ZINB) regression. Using likelihood ratio tests, we show that the ZINB distribution fits TnSeq data better than either ANOVA or a Negative Binomial (in a generalized linear model). We use ZINB regression to identify genes required for infection of M. tuberculosis H37Rv in C57BL/6 mice. We also use ZINB to perform a analysis of genes conditionally essential in H37Rv cultures exposed to multiple antibiotics. Conclusions Our results show that, not only does ZINB generally identify most of the genes found by pairwise resampling (and vastly out-performs ANOVA), but it also identifies additional genes where variability is detectable only when the magnitudes of insertion counts are treated separately from local differences in saturation, as in the ZINB model.
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10
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Maynard LH, Smith O, Tilmans NP, Tham E, Hosseinzadeh S, Tan W, Leenay R, May AP, Paulk NK. Fast-Seq, a simple method for rapid and inexpensive validation of packaged ssAAV genomes in academic settings. Hum Gene Ther Methods 2019. [DOI: 10.1089/hum.2019.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Lucy H. Maynard
- The Chan Zuckerberg Initiative, 503506, Genome Engineering, San Francisco, California, United States
| | - Olivia Smith
- The Chan Zuckerberg Initiative, 503506, Genome Engineering, San Francisco, California, United States
| | - Nicolas P. Tilmans
- The Chan Zuckerberg Initiative, 503506, Genome Engineering, Palo Alto, California, United States
| | - Eleonore Tham
- The Chan Zuckerberg Initiative, 503506, Genome Engineering, San Francisco, California, United States
| | - Shayan Hosseinzadeh
- The Chan Zuckerberg Initiative, 503506, San Francisco, California, United States
| | - Weilun Tan
- The Chan Zuckerberg Initiative, 503506, San Francisco, California, United States
| | - Ryan Leenay
- The Chan Zuckerberg Initiative, 503506, Genome Engineering, San Francisco, California, United States
| | - Andrew P. May
- The Chan Zuckerberg Initiative, 503506, Genome Engineering, San Francisco, California, United States
| | - Nicole K. Paulk
- UCSF, 8785, Biochemistry and Biophysics, San Francisco, California, United States
- The Chan Zuckerberg Initiative, 503506, Genome Engineering, San Francisco, California, United States
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11
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Poulsen BE, Yang R, Clatworthy AE, White T, Osmulski SJ, Li L, Penaranda C, Lander ES, Shoresh N, Hung DT. Defining the core essential genome of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2019; 116:10072-10080. [PMID: 31036669 PMCID: PMC6525520 DOI: 10.1073/pnas.1900570116] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomics offered the promise of transforming antibiotic discovery by revealing many new essential genes as good targets, but the results fell short of the promise. While numerous factors contributed to the disappointing yield, one factor was that essential genes for a bacterial species were often defined based on a single or limited number of strains grown under a single or limited number of in vitro laboratory conditions. In fact, the essentiality of a gene can depend on both the genetic background and growth condition. We thus developed a strategy for more rigorously defining the core essential genome of a bacterial species by studying many pathogen strains and growth conditions. We assessed how many strains must be examined to converge on a set of core essential genes for a species. We used transposon insertion sequencing (Tn-Seq) to define essential genes in nine strains of Pseudomonas aeruginosa on five different media and developed a statistical model, FiTnEss, to classify genes as essential versus nonessential across all strain-medium combinations. We defined a set of 321 core essential genes, representing 6.6% of the genome. We determined that analysis of four strains was typically sufficient in P. aeruginosa to converge on a set of core essential genes likely to be essential across the species across a wide range of conditions relevant to in vivo infection, and thus to represent attractive targets for novel drug discovery.
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Affiliation(s)
- Bradley E Poulsen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Rui Yang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Anne E Clatworthy
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Tiantian White
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Sarah J Osmulski
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Li Li
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Cristina Penaranda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Deborah T Hung
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114;
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
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12
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Lewis L, Crawford GE, Furey TS, Rusyn I. Genetic and epigenetic determinants of inter-individual variability in responses to toxicants. CURRENT OPINION IN TOXICOLOGY 2017; 6:50-59. [PMID: 29276797 PMCID: PMC5739339 DOI: 10.1016/j.cotox.2017.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It is well established that genetic variability has a major impact on susceptibility to common diseases, responses to drugs and toxicants, and influences disease-related outcomes. The appreciation that epigenetic marks also vary across the population is growing with more data becoming available from studies in humans and model organisms. In addition, the links between genetic variability, toxicity outcomes and epigenetics are being actively explored. Recent studies demonstrate that gene-by-environment interactions involve both chromatin states and transcriptional regulation, and that epigenetics provides important mechanistic clues to connect expression-related quantitative trait loci (QTL) and disease outcomes. However, studies of Gene×Environment×Epigenetics further extend the complexity of the experimental designs and create a challenge for selecting the most informative epigenetic readouts that can be feasibly performed to interrogate multiple individuals, exposures, tissue types and toxicity phenotypes. We propose that among the many possible epigenetic experimental methodologies, assessment of chromatin accessibility coupled with total RNA levels provides a cost-effective and comprehensive option to sufficiently characterize the complexity of epigenetic and regulatory activity in the context of understanding the inter-individual variability in responses to toxicants.
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Affiliation(s)
- Lauren Lewis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology and Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Terrence S. Furey
- Department of Genetics, Department of Biology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas
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13
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Zhang F, Christiansen L, Thomas J, Pokholok D, Jackson R, Morrell N, Zhao Y, Wiley M, Welch E, Jaeger E, Granat A, Norberg SJ, Halpern A, C Rogert M, Ronaghi M, Shendure J, Gormley N, Gunderson KL, Steemers FJ. Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube. Nat Biotechnol 2017. [PMID: 28650462 DOI: 10.1038/nbt.3897] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Haplotype-resolved genome sequencing promises to unlock a wealth of information in population and medical genetics. However, for the vast majority of genomes sequenced to date, haplotypes have not been determined because of cumbersome haplotyping workflows that require fractions of the genome to be sequenced in a large number of compartments. Here we demonstrate barcode partitioning of long DNA molecules in a single compartment using "on-bead" barcoded tagmentation. The key to the method that we call "contiguity preserving transposition" sequencing on beads (CPTv2-seq) is transposon-mediated transfer of homogenous populations of barcodes from beads to individual long DNA molecules that get fragmented at the same time (tagmentation). These are then processed to sequencing libraries wherein all sequencing reads originating from each long DNA molecule share a common barcode. Single-tube, bulk processing of long DNA molecules with ∼150,000 different barcoded bead types provides a barcode-linked read structure that reveals long-range molecular contiguity. This technology provides a simple, rapid, plate-scalable and automatable route to accurate, haplotype-resolved sequencing, and phasing of structural variants of the genome.
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Affiliation(s)
- Fan Zhang
- Advanced Research Department, Illumina, San Diego, California, USA
| | | | - Jerushah Thomas
- Advanced Research Department, Illumina, San Diego, California, USA
| | - Dmitry Pokholok
- Advanced Research Department, Illumina, San Diego, California, USA
| | - Ros Jackson
- Technology Development Department, Illumina, Little Chesterford, Essex, UK
| | - Natalie Morrell
- Technology Development Department, Illumina, Little Chesterford, Essex, UK
| | - Yannan Zhao
- Technology Development, Illumina, San Diego, California, USA
| | - Melissa Wiley
- Technology Development, Illumina, San Diego, California, USA
| | - Emily Welch
- Technology Development, Illumina, San Diego, California, USA
| | - Erich Jaeger
- Gene Expression Department, Illumina, San Francisco, California, USA
| | - Ana Granat
- Gene Expression Department, Illumina, San Francisco, California, USA
| | - Steven J Norberg
- Advanced Research Department, Illumina, San Diego, California, USA
| | - Aaron Halpern
- Gene Expression Department, Illumina, San Francisco, California, USA
| | - Maria C Rogert
- Technology Development, Illumina, San Diego, California, USA
| | - Mostafa Ronaghi
- Advanced Research Department, Illumina, San Diego, California, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Niall Gormley
- Technology Development Department, Illumina, Little Chesterford, Essex, UK
| | | | - Frank J Steemers
- Advanced Research Department, Illumina, San Diego, California, USA
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14
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Schirmer M, D'Amore R, Ijaz UZ, Hall N, Quince C. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics 2016; 17:125. [PMID: 26968756 PMCID: PMC4787001 DOI: 10.1186/s12859-016-0976-y] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/02/2016] [Indexed: 11/17/2022] Open
Abstract
Background Illumina’s sequencing platforms are currently the most utilised sequencing systems worldwide. The technology has rapidly evolved over recent years and provides high throughput at low costs with increasing read-lengths and true paired-end reads. However, data from any sequencing technology contains noise and our understanding of the peculiarities and sequencing errors encountered in Illumina data has lagged behind this rapid development. Results We conducted a systematic investigation of errors and biases in Illumina data based on the largest collection of in vitro metagenomic data sets to date. We evaluated the Genome Analyzer II, HiSeq and MiSeq and tested state-of-the-art low input library preparation methods. Analysing in vitro metagenomic sequencing data allowed us to determine biases directly associated with the actual sequencing process. The position- and nucleotide-specific analysis revealed a substantial bias related to motifs (3mers preceding errors) ending in “GG”. On average the top three motifs were linked to 16 % of all substitution errors. Furthermore, a preferential incorporation of ddGTPs was recorded. We hypothesise that all of these biases are related to the engineered polymerase and ddNTPs which are intrinsic to any sequencing-by-synthesis method. We show that quality-score-based error removal strategies can on average remove 69 % of the substitution errors - however, the motif-bias remains. Conclusion Single-nucleotide polymorphism changes in bacterial genomes can cause significant changes in phenotype, including antibiotic resistance and virulence, detecting them within metagenomes is therefore vital. Current error removal techniques are not designed to target the peculiarities encountered in Illumina sequencing data and other sequencing-by-synthesis methods, causing biases to persist and potentially affect any conclusions drawn from the data. In order to develop effective diagnostic and therapeutic approaches we need to be able to identify systematic sequencing errors and distinguish these errors from true genetic variation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0976-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. .,Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA. .,University of Glasgow, School of Engineering, Oakfield Avenue, Glasgow, G12 8LT, UK.
| | - Rosalinda D'Amore
- University of Liverpool, Centre for Genomic Research, Crown Street, Liverpool, L69 7ZB, UK
| | - Umer Z Ijaz
- University of Glasgow, School of Engineering, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - Neil Hall
- University of Liverpool, Centre for Genomic Research, Crown Street, Liverpool, L69 7ZB, UK
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15
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Shapland EB, Holmes V, Reeves CD, Sorokin E, Durot M, Platt D, Allen C, Dean J, Serber Z, Newman J, Chandran S. Low-Cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process. ACS Synth Biol 2015; 4:860-6. [PMID: 25913499 DOI: 10.1021/sb500362n] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, next-generation sequencing (NGS) technology has greatly reduced the cost of sequencing whole genomes, whereas the cost of sequence verification of plasmids via Sanger sequencing has remained high. Consequently, industrial-scale strain engineers either limit the number of designs or take short cuts in quality control. Here, we show that over 4000 plasmids can be completely sequenced in one Illumina MiSeq run for less than $3 each (15× coverage), which is a 20-fold reduction over using Sanger sequencing (2× coverage). We reduced the volume of the Nextera tagmentation reaction by 100-fold and developed an automated workflow to prepare thousands of samples for sequencing. We also developed software to track the samples and associated sequence data and to rapidly identify correctly assembled constructs having the fewest defects. As DNA synthesis and assembly become a centralized commodity, this NGS quality control (QC) process will be essential to groups operating high-throughput pipelines for DNA construction.
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Affiliation(s)
- Elaine B. Shapland
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | - Victor Holmes
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | | | - Elena Sorokin
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | - Maxime Durot
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
- TOTAL New Energies USA, Inc., 5858 Horton Street, Suite 253, Emeryville, California 94608, United States
| | - Darren Platt
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | - Christopher Allen
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | - Jed Dean
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | - Zach Serber
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | - Jack Newman
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
| | - Sunil Chandran
- Amyris, Inc., 5885 Hollis, Suite
100, Emeryville, California 94608, United States
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16
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Lan JH, Yin Y, Reed EF, Moua K, Thomas K, Zhang Q. Impact of three Illumina library construction methods on GC bias and HLA genotype calling. Hum Immunol 2014; 76:166-75. [PMID: 25543015 DOI: 10.1016/j.humimm.2014.12.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 10/17/2014] [Accepted: 12/15/2014] [Indexed: 01/04/2023]
Abstract
Next-generation sequencing (NGS) is increasingly recognized for its ability to overcome allele ambiguity and deliver high-resolution typing in the HLA system. Using this technology, non-uniform read distribution can impede the reliability of variant detection, which renders high-confidence genotype calling particularly difficult to achieve in the polymorphic HLA complex. Recently, library construction has been implicated as the dominant factor in instigating coverage bias. To study the impact of this phenomenon on HLA genotyping, we performed long-range PCR on 12 samples to amplify HLA-A, -B, -C, -DRB1, and -DQB1, and compared the relative contribution of three Illumina library construction methods (TruSeq Nano, Nextera, Nextera XT) in generating downstream bias. Here, we show high GC% to be a good predictor of low sequencing depth. Compared to standard TruSeq Nano, GC bias was more prominent in transposase-based protocols, particularly Nextera XT, likely through a combination of transposase insertion bias being coupled with a high number of PCR enrichment cycles. Importantly, our findings demonstrate non-uniform read depth can have a direct and negative impact on the robustness of HLA genotyping, which has clinical implications for users when choosing a library construction strategy that aims to balance cost and throughput with data quality.
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Affiliation(s)
- James H Lan
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA; University of British Columbia, Clinician Investigator Program, Vancouver, BC, Canada
| | - Yuxin Yin
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Elaine F Reed
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Kevin Moua
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Kimberly Thomas
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
| | - Qiuheng Zhang
- UCLA Immunogenetics Center, Department of Pathology & Laboratory Medicine, Los Angeles, CA, USA
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17
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Characterization of plasmid pPO1 from the hyperacidophile Picrophilus oshimae. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:723604. [PMID: 21941462 PMCID: PMC3177234 DOI: 10.1155/2011/723604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/21/2011] [Indexed: 11/17/2022]
Abstract
Picrophilus oshimae and Picrophilus torridus are free-living, moderately thermophilic and acidophilic organisms from the lineage of Euryarchaeota. With a pH optimum of growth at pH 0.7 and the ability to even withstand molar concentrations of sulphuric acid, these organisms represent the most extreme acidophiles known. So far, nothing is known about plasmid biology in these hyperacidophiles. Also, there are no genetic tools available for this genus. We have mobilized the 7.6 Kbp plasmid from P. oshimae in E. coli by introducing origin-containing transposons and described the plasmid in terms of its nucleotide sequence, copy number in the native host, mode of replication, and transcriptional start sites of the encoded ORFs. Plasmid pPO1 may encode a restriction/modification system in addition to its replication functions. The information gained from the pPO1 plasmid may prove useful in developing a cloning system for this group of extreme acidophiles.
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18
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Abstract
Tn5 was one of the first transposons to be identified ( 10 ). As a result of Tn5's early discovery and its simple macromolecular requirements for transposition, the Tn5 system has been a very productive tool for studying the molecular mechanism of DNA transposition. These studies are of broad value because they offer insights into DNA transposition in general, because DNA transposition is a useful model with which to understand other types of protein-DNA interactions such as retroviral DNA integration and the DNA cleavage events involved in immunoglobulin gene formation, and because Tn5-derived tools are useful adjuncts in genetic experimentation.
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Affiliation(s)
- William S Reznikoff
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, Massachusetts 02543, USA.
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19
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Mealer R, Butler H, Hughes T. Functional fusion proteins by random transposon-based GFP insertion. Methods Cell Biol 2008; 85:23-44. [PMID: 18155457 DOI: 10.1016/s0091-679x(08)85002-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Fusions with fluorescent proteins are usually created by fusing the ends of two coding sequences. Appending the coding region of a fluorescent protein to the N- or C-terminus of another protein is typically the easiest way of creating a functional, fluorescent fusion protein. Another strategy involves placing the fluorescent protein in the middle of another protein. Such sandwich fusions are feasible, and there are many reasons for creating these fusion proteins. For example, sandwich fusions can be used to place two fluorescent proteins close to one another for optimization of a biosensor based on fluorescence resonance energy transfer, or they can be used to place the fluorescent protein in a region that moves during conformational changes of the host protein. Designing a sandwich fusion that produces a functional, fluorescent fusion protein is often challenging. This protocol describes an alternative approach. A simple, in vitro, transposon reaction is used to randomly insert the sequence encoding a fluorescent fusion protein into a target protein. This random labeling strategy makes it possible to create a small library of sandwich fusion proteins that can then be screened for activity. The approach makes it possible to test many possible solutions to the complex problem of building new biosensors.
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Affiliation(s)
- Robert Mealer
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana 59717, USA
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20
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Gradman RJ, Ptacin JL, Bhasin A, Reznikoff WS, Goryshin IY. A bifunctional DNA binding region in Tn5 transposase. Mol Microbiol 2007; 67:528-40. [PMID: 18086215 PMCID: PMC2229646 DOI: 10.1111/j.1365-2958.2007.06056.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Tn5 transposition is a complicated process that requires the formation of a highly ordered protein-DNA structure, a synaptic complex, to catalyse the movement of a sequence of DNA (transposon) into a target DNA. Much is known about the structure of the synaptic complex and the positioning of protein-DNA contacts, although many protein-DNA contacts remain largely unstudied. In particular, there is little evidence for the positioning of donor DNA and target DNA. In this communication, we describe the isolation and analysis of mutant transposases that have, for the first time, provided genetic and biochemical evidence for the stage-specific positioning of both donor and target DNAs within the synaptic complex. Furthermore, we have provided evidence that some of the amino acids that contact donor DNA also contact target DNA, and therefore suggest that these amino acids help define a bifunctional DNA binding region responsible for these two transposase-DNA binding events.
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Affiliation(s)
- Richard J Gradman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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21
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Kline KA, Criss AK, Wallace A, Seifert HS. Transposon mutagenesis identifies sites upstream of the Neisseria gonorrhoeae pilE gene that modulate pilin antigenic variation. J Bacteriol 2007; 189:3462-70. [PMID: 17307859 PMCID: PMC1855897 DOI: 10.1128/jb.01911-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gene conversion mediates the variation of virulence-associated surface structures on pathogenic microorganisms, which prevents host humoral immune responses from being effective. One of the best-studied gene conversion systems is antigenic variation (Av) of the pilin subunit of the Neisseria gonorrhoeae type IV pilus. To identify cis-acting DNA sequences that facilitate Av, the 700-bp region upstream of the pilin gene pilE was targeted for transposon mutagenesis. Four classes of transposon-associated mutations were isolated, distinguishable by their pilus-associated phenotypes: (i) insertions that did not alter Av or piliation, (ii) insertions that blocked Av, (iii) insertions that interfered with Av, and (iv) insertions that interfered with pilus expression and Av. Mutagenesis of the pilE promoter did not affect the frequency of Av, directly demonstrating that pilin Av is independent of pilE transcription. Two stretches of sequence upstream of pilE were devoid of transposon insertions, and some deletions in these regions were not recoverable, suggesting that they are essential for gonococcal viability. Insertions that blocked pilin Av were located downstream of the RS1 repeat sequence, and deletion of the region surrounding these insertions completely abrogated pilin Av, confirming that specific sequences 5' to pilE are essential for the recombination events underlying pilin Av.
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Affiliation(s)
- Kimberly A Kline
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 303 East Chicago Ave., Chicago, IL 60620, USA
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22
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Whitfield CR, Wardle SJ, Haniford DB. Formation, characterization and partial purification of a Tn5 strand transfer complex. J Mol Biol 2006; 364:290-301. [PMID: 17014865 DOI: 10.1016/j.jmb.2006.09.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 09/07/2006] [Accepted: 09/11/2006] [Indexed: 10/24/2022]
Abstract
DNA transposition reactions typically involve a strand transfer step wherein the transposon ends are covalently joined by the transposase protein to a short target site. There is very little known about the transposase-DNA interactions that direct this process, and thus our overall understanding of the dynamics of DNA transposition reactions is limited. Tn5 presents an attractive system for defining such interactions because it has been possible to solve the structure of at least one Tn5 transposition intermediate: a transpososome formed with pre-cleaved ends. However, insertion specificity in the Tn5 system is low and this has hampered progress in generating target-containing transpososomes that are homogeneous in structure (i.e. where a single target site is engaged) and therefore suitable for biochemical and structural analysis. We have developed a system where the Tn5 transpososome integrates almost exclusively into a single target site within a short DNA fragment. The key to establishing this high degree of insertion specificity was to use a target DNA with tandem repeats of a previously characterized Tn5 insertion hotspot. The target DNA requirements to form this strand transfer complex are evaluated. In addition, we show that target DNAs missing single phosphate groups at specific positions are better substrates for strand transfer complex formation relative to the corresponding unmodified DNA fragments. Moreover, utilization of missing phosphate substrates can increase the degree of target site selection. A method for concentrating and partially purifying the Tn5 strand transfer complex is described.
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Affiliation(s)
- Crystal R Whitfield
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1
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23
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Ason B, Knauss DJ, Balke AM, Merkel G, Skalka AM, Reznikoff WS. Targeting Tn5 transposase identifies human immunodeficiency virus type 1 inhibitors. Antimicrob Agents Chemother 2005; 49:2035-43. [PMID: 15855529 PMCID: PMC1087639 DOI: 10.1128/aac.49.5.2035-2043.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 10/12/2004] [Accepted: 12/29/2004] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) type 1 (HIV-1) integrase is an underutilized drug target for the treatment of HIV infection. One limiting factor is the lack of costructural data for use in the rational design or modification of integrase inhibitors. Tn5 transposase is a structurally well characterized, related protein that may serve as a useful surrogate. However, little data exist on inhibitor cross-reactivity. Here we screened 16,000 compounds using Tn5 transposase as the target and identified 20 compounds that appear to specifically inhibit complex assembly. Six were found to also inhibit HIV-1 integrase. These compounds likely interact with a highly conserved region presumably within the catalytic core. Most promising, several cinnamoyl derivatives were found to inhibit HIV transduction in cells. The identification of integrase inhibitors from a screen using Tn5 transposase as the target illustrates the utility of Tn5 as a surrogate for HIV-1 integration even though the relationship between the two systems is limited to the active site architecture and catalytic mechanism.
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Affiliation(s)
- Brandon Ason
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA
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