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Wall JD, Zane GM, Juba TR, Kuehl JV, Ray J, Chhabra SR, Trotter VV, Shatsky M, De León KB, Keller KL, Bender KS, Butland G, Arkin AP, Deutschbauer AM. Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Microbiol Resour Announc 2021; 10:e00072-21. [PMID: 33737356 PMCID: PMC7975874 DOI: 10.1128/mra.00072-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.
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Affiliation(s)
- Judy D Wall
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Grant M Zane
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Thomas R Juba
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Jennifer V Kuehl
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Swapnil R Chhabra
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Valentine V Trotter
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Maxim Shatsky
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kara B De León
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Kimberly L Keller
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Kelly S Bender
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Gareth Butland
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics 2016; 15:1539-55. [PMID: 26873250 DOI: 10.1074/mcp.m115.054692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/31/2023] Open
Abstract
Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates. In addition, our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.
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Affiliation(s)
- Maxim Shatsky
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Simon Allen
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Barbara L Gold
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Nancy L Liu
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Thomas R Juba
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - Sonia A Reveco
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Dwayne A Elias
- the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Ramadevi Prathapam
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jennifer He
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Wenhong Yang
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Evelin D Szakal
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Haichuan Liu
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mary E Singer
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Jil T Geller
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Bonita R Lam
- the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Avneesh Saini
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Valentine V Trotter
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Steven C Hall
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Susan J Fisher
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Steven E Brenner
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; the Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, 94720
| | - Swapnil R Chhabra
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Terry C Hazen
- the Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, 37996; and
| | - Judy D Wall
- the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211
| | - H Ewa Witkowska
- the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143
| | - Mark D Biggin
- the Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - John-Marc Chandonia
- From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
| | - Gareth Butland
- the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Berleman JE, Allen S, Danielewicz MA, Remis JP, Gorur A, Cunha J, Hadi MZ, Zusman DR, Northen TR, Witkowska HE, Auer M. The lethal cargo of Myxococcus xanthus outer membrane vesicles. Front Microbiol 2014; 5:474. [PMID: 25250022 PMCID: PMC4158809 DOI: 10.3389/fmicb.2014.00474] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/22/2014] [Indexed: 11/13/2022] Open
Abstract
Myxococcus xanthus is a bacterial micro-predator known for hunting other microbes in a wolf pack-like manner. Outer membrane vesicles (OMVs) are produced in large quantities by M. xanthus and have a highly organized structure in the extracellular milieu, sometimes occurring in chains that link neighboring cells within a biofilm. OMVs may be a vehicle for mediating wolf pack activity by delivering hydrolytic enzymes and antibiotics aimed at killing prey microbes. Here, both the protein and small molecule cargo of the OMV and membrane fractions of M. xanthus were characterized and compared. Our analysis indicates a number of proteins that are OMV-specific or OMV-enriched, including several with putative hydrolytic function. Secondary metabolite profiling of OMVs identifies 16 molecules, many associated with antibiotic activities. Several hydrolytic enzyme homologs were identified, including the protein encoded by MXAN_3564 (mepA), an M36 protease homolog. Genetic disruption of mepA leads to a significant reduction in extracellular protease activity suggesting MepA is part of the long-predicted (yet to date undetermined) extracellular protease suite of M. xanthus.
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Affiliation(s)
- James E Berleman
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA ; School of Biology, St. Mary's College Moraga, CA, USA
| | - Simon Allen
- Department of Obstetrics, Gynecology and Reproductive Science, UCSF Sandler-Moore Mass Spectrometry Core Facility San Francisco, CA, USA
| | - Megan A Danielewicz
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jonathan P Remis
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Amita Gorur
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jack Cunha
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Masood Z Hadi
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Space Biosciences Division, Synthetic Biology Program, NASA Ames Research Center Moffett Field, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - David R Zusman
- Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA, USA
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - H Ewa Witkowska
- Department of Obstetrics, Gynecology and Reproductive Science, UCSF Sandler-Moore Mass Spectrometry Core Facility San Francisco, CA, USA
| | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. mBio 2014; 5:e01041-14. [PMID: 24865553 PMCID: PMC4045070 DOI: 10.1128/mbio.01041-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED The genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5' RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the D. alaskensis G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene Dde_3007 is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to O-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance. IMPORTANCE Sulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in Desulfovibrio alaskensis G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria.
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Fiévet A, Cascales E, Valette O, Dolla A, Aubert C. IHF is required for the transcriptional regulation of the Desulfovibrio vulgaris Hildenborough orp operons. PLoS One 2014; 9:e86507. [PMID: 24466126 PMCID: PMC3897727 DOI: 10.1371/journal.pone.0086507] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/10/2013] [Indexed: 01/08/2023] Open
Abstract
Transcriptional activation of σ(54)-dependent promoters is usually tightly regulated in response to environmental cues. The high abundance of potential σ(54)-dependent promoters in the anaerobe bacteria, Desulfovibrio vulgaris Hildenborough, reflects the high versatility of this bacteria suggesting that σ(54) factor is the nexus of a large regulatory network. Understanding the key players of σ(54)-regulation in this organism is therefore essential to gain insights into the adaptation to anaerobiosis. Recently, the D. vulgaris orp genes, specifically found in anaerobe bacteria, have been shown to be transcribed by the RNA polymerase coupled to the σ(54) alternative sigma factor. In this study, using in vitro binding experiments and in vivo reporter fusion assays in the Escherichia coli heterologous host, we showed that the expression of the divergent orp promoters is strongly dependent on the integration host factor IHF. Bioinformatic and mutational analysis coupled to reporter fusion activities and mobility shift assays identified two functional IHF binding site sequences located between the orp1 and orp2 promoters. We further determined that the D. vulgaris DVU0396 (IHFα) and DVU1864 (IHFβ) subunits are required to control the expression of the orp operons suggesting that they form a functionally active IHF heterodimer. Interestingly results obtained from the in vivo inactivation of DVU0396, which is required for orp operons transcription, suggest that several functionally IHF active homodimer or heterodimer are present in D. vulgaris.
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Affiliation(s)
- Anouchka Fiévet
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Eric Cascales
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Odile Valette
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Alain Dolla
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
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Krumholz LR, Wang L, Beck DAC, Wang T, Hackett M, Mooney B, Juba TR, McInerney MJ, Meyer B, Wall JD, Stahl DA. Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis. Microbiology (Reading) 2013; 159:2162-2168. [DOI: 10.1099/mic.0.063818-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lee R. Krumholz
- Institute for Energy and the Environment, University of Oklahoma, Norman, OK 73019, USA
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Luyao Wang
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - David A. C. Beck
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
- eScience Institute, University of Washington, Seattle, WA 98195, USA
| | - Tiansong Wang
- Center for Microbial Proteomics, University of Washington, Seattle, WA 98195, USA
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Murray Hackett
- Center for Microbial Proteomics, University of Washington, Seattle, WA 98195, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Brian Mooney
- Department of Biochemistry, University of Missouri, USA
| | | | - Michael J. McInerney
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Birte Meyer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
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Rapid transposon liquid enrichment sequencing (TnLE-seq) for gene fitness evaluation in underdeveloped bacterial systems. Appl Environ Microbiol 2013; 79:7510-7. [PMID: 24077707 DOI: 10.1128/aem.02051-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Whole-genome fitness analysis in microbes that uses saturating transposon mutagenesis combined with massively parallel sequencing (Tn-seq) is providing a measure of the contribution of each gene to a given growth condition. With this technique, gene fitness profiles and essential genes are discovered by simultaneous analyses of whether the absence of each gene product alters the growth kinetics of the bacterium. Here we modify the standard Tn-seq procedure to simplify and shorten the process by including delivery of the transposon through conjugation and liquid culture enrichment of the mutant pool, creating transposon liquid enrichment sequencing (TnLE-seq). To illustrate the success of these modifications and the robustness of the procedure, analyses of gene fitness of two cultures of the strictly anaerobic bacterium Desulfovibrio vulgaris Hildenborough were performed, with growth on lactate as the electron donor and sulfate as the electron acceptor. These data demonstrate reproducibility and provide a base condition for analysis of fitness changes in deletion mutants and in various growth conditions. The procedural modifications will facilitate the application of this powerful genetic analysis to microbes lacking a facile genetic system. Pilot studies produced 2.5×10(5) and 3.4×10(5) unique insertion mutants in the anaerobe Desulfovibrio vulgaris Hildenborough grown under typical laboratory conditions in rich medium. These analyses provided two similar high-resolution maps of gene fitness across the genome, and the method was also applied to growth in minimal medium. These results were also compared to the coverage obtained with a ca. 13,000-member cataloged transposon library constructed by sequencing transposon insertion sites in individual mutants.
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Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 2012; 9:999-1003. [PMID: 22941365 PMCID: PMC3816492 DOI: 10.1038/nmeth.2148] [Citation(s) in RCA: 837] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/04/2012] [Indexed: 12/15/2022]
Abstract
Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires elimination of systematic biases. We present a pipeline that integrates a strategy for mapping of sequencing reads and a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. We validate ICE (Iterative Correction and Eigenvector decomposition) on published Hi-C data, and demonstrate that eigenvector decomposition of the obtained maps provides insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes.
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Ramos AR, Keller KL, Wall JD, Pereira IAC. The Membrane QmoABC Complex Interacts Directly with the Dissimilatory Adenosine 5'-Phosphosulfate Reductase in Sulfate Reducing Bacteria. Front Microbiol 2012; 3:137. [PMID: 22536198 PMCID: PMC3333476 DOI: 10.3389/fmicb.2012.00137] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 03/22/2012] [Indexed: 01/20/2023] Open
Abstract
The adenosine 5′-phosphosulfate reductase (AprAB) is the enzyme responsible for the reduction of adenosine 5′-phosphosulfate (APS) to sulfite in the biological process of dissimilatory sulfate reduction, which is carried out by a ubiquitous group of sulfate reducing prokaryotes. The electron donor for AprAB has not been clearly identified, but was proposed to be the QmoABC membrane complex, since an aprBA–qmoABC gene cluster is found in many sulfate reducing and sulfur-oxidizing bacteria. The QmoABC complex is essential for sulfate reduction, but electron transfer between QmoABC and AprAB has not been reported. In this work we provide the first direct evidence that QmoABC and AprAB interact in Desulfovibrio spp., using co-immunoprecipitation, cross-linking Far-Western blot, tag-affinity purification, and surface plasmon resonance studies. This showed that the QmoABC–AprAB complex has a strong steady-state affinity (KD = 90 ± 3 nM), but has a transient character due to a fast dissociation rate. Far-Western blot identified QmoA as the Qmo subunit most involved in the interaction. Nevertheless, electron transfer from menaquinol analogs to APS through anaerobically purified QmoABC and AprAB could not be detected. We propose that this reaction requires the involvement of a third partner to allow electron flow driven by a reverse electron bifurcation process, i.e., electron confurcation. This process is deemed essential to allow coupling of APS reduction to chemiosmotic energy conservation.
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Affiliation(s)
- Ana Raquel Ramos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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