1
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Lee JH, Ma R, Nguyen L, Khan S, Qader M, Mpofu E, Shetye G, Krull NK, Augustinović M, Omarsdottir S, Cho S, Franzblau SG, Murphy BT. Discovery of a New Antibiotic Demethoxytetronasin Using a Dual-Sided Agar Plate Assay (DAPA). ACS Infect Dis 2023; 9:1593-1601. [PMID: 37450563 PMCID: PMC10426401 DOI: 10.1021/acsinfecdis.3c00171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 07/18/2023]
Abstract
For over a century, researchers have cultured microorganisms together on solid support─typically agar─in order to observe growth inhibition via antibiotic production. These simple bioassays have been critical to both academic researchers that study antibiotic production in microorganisms and to the pharmaceutical industry's global effort to discover drugs. Despite the utility of agar assays to researchers around the globe, several limitations have prevented their widespread adoption in advanced high-throughput compound discovery and dereplication campaigns. To address a list of specific shortcomings, we developed the dual-sided agar plate assay (DAPA), which exists in a 96-well plate format, allows microorganisms to compete through opposing sides of a solid support in individual wells, is amenable to high-throughput screening and automation, is reusable, and is low-cost. Herein, we validate the use of DAPA as a tool for drug discovery and show its utility to discover new antibiotic natural products. From the screening of 217 bacterial isolates on multiple nutrient media against 3 pathogens, 55 hits were observed, 9 known antibiotics were dereplicated directly from agar plugs, and a new antibiotic, demethoxytetronasin (1), was isolated from a Streptomyces sp. These results demonstrate that DAPA is an effective, accessible, and low-cost tool to screen, dereplicate, and prioritize bacteria directly from solid support in the front end of antibiotic discovery pipelines.
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Affiliation(s)
- Jung-Ho Lee
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Rui Ma
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Linh Nguyen
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
of Marine Biochemistry, Vietnam Academy
of Science and Technology, Nghiado, Caugiay, Hanoi 11307, Vietnam
| | - Shahebraj Khan
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Mallique Qader
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Enock Mpofu
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Nyssa K. Krull
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Mario Augustinović
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Sesselja Omarsdottir
- Faculty
of Pharmaceutical Sciences, University of
Iceland, Hagi, Hofsvallagata 53, Reykjavík IS-107, Iceland
| | - Sanghyun Cho
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Brian T. Murphy
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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2
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Kümpel C, Grein F, Dahl C. Fluorescence Microscopy Study of the Intracellular Sulfur Globule Protein SgpD in the Purple Sulfur Bacterium Allochromatium vinosum. Microorganisms 2023; 11:1792. [PMID: 37512964 PMCID: PMC10386293 DOI: 10.3390/microorganisms11071792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/01/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
When oxidizing reduced sulfur compounds, the phototrophic sulfur bacterium Allochromatium vinosum forms spectacular sulfur globules as obligatory intracellular-but extracytoplasmic-intermediates. The globule envelope consists of three extremely hydrophobic proteins: SgpA and SgpB, which are very similar and can functionally replace each other, and SgpC which is involved in the expansion of the sulfur globules. The presence of a fourth protein, SgpD, was suggested by comparative transcriptomics and proteomics of purified sulfur globules. Here, we investigated the in vivo function of SgpD by coupling its carboxy-terminus to mCherry. This fluorescent protein requires oxygen for chromophore maturation, but we were able to use it in anaerobically growing A. vinosum provided the cells were exposed to oxygen for one hour prior to imaging. While mCherry lacking a signal peptide resulted in low fluorescence evenly distributed throughout the cell, fusion with SgpD carrying its original Sec-dependent signal peptide targeted mCherry to the periplasm and co-localized it exactly with the highly light-refractive sulfur deposits seen in sulfide-fed A. vinosum cells. Insertional inactivation of the sgpD gene showed that the protein is not essential for the formation and degradation of sulfur globules.
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Affiliation(s)
- Carolin Kümpel
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
| | - Fabian Grein
- Institut für Pharmazeutische Mikrobiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 16, D-53115 Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Meckenheimer Allee 168, D-53115 Bonn, Germany
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3
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Cho H, Ren Z, Divaris K, Roach J, Lin BM, Liu C, Azcarate-Peril MA, Simancas-Pallares MA, Shrestha P, Orlenko A, Ginnis J, North KE, Zandona AGF, Ribeiro AA, Wu D, Koo H. Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries. Nat Commun 2023; 14:2919. [PMID: 37217495 PMCID: PMC10202936 DOI: 10.1038/s41467-023-38346-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.
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Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Ren
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffrey Roach
- UNC Information Technology Services and Research Computing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chuwen Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miguel A Simancas-Pallares
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Poojan Shrestha
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Orlenko
- Artificial Intelligence Innovation Lab, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeannie Ginnis
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hyun Koo
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Csibra E, Stan GB. Absolute protein quantification using fluorescence measurements with FPCountR. Nat Commun 2022; 13:6600. [PMID: 36329019 PMCID: PMC9633595 DOI: 10.1038/s41467-022-34232-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
This paper presents a generalisable method for the calibration of fluorescence readings on microplate readers, in order to convert arbitrary fluorescence units into absolute units. FPCountR relies on the generation of bespoke fluorescent protein (FP) calibrants, assays to determine protein concentration and activity, and a corresponding analytical workflow. We systematically characterise the assay protocols for accuracy, sensitivity and simplicity, and describe an 'ECmax' assay that outperforms the others and even enables accurate calibration without requiring the purification of FPs. To obtain cellular protein concentrations, we consider methods for the conversion of optical density to either cell counts or alternatively to cell volumes, as well as examining how cells can interfere with protein counting via fluorescence quenching, which we quantify and correct for the first time. Calibration across different instruments, disparate filter sets and mismatched gains is demonstrated to yield equivalent results. It also reveals that mCherry absorption at 600 nm does not confound cell density measurements unless expressed to over 100,000 proteins per cell. FPCountR is presented as pair of open access tools (protocol and R package) to enable the community to use this method, and ultimately to facilitate the quantitative characterisation of synthetic microbial circuits.
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Affiliation(s)
- Eszter Csibra
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
| | - Guy-Bart Stan
- grid.7445.20000 0001 2113 8111Department of Bioengineering, Imperial College Centre for Synthetic Biology (IC-CSynB), Imperial College London, London, SW7 2AY UK
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5
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Wakamatsu T, Mizobuchi S, Mori F, Futagami T, Terada T, Morono Y. Construction of Aerobic/Anaerobic-Substrate-Induced Gene Expression Procedure for Exploration of Metagenomes From Subseafloor Sediments. Front Microbiol 2022; 12:726024. [PMID: 35095779 PMCID: PMC8793675 DOI: 10.3389/fmicb.2021.726024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/17/2021] [Indexed: 11/13/2022] Open
Abstract
Substrate-induced gene expression (SIGEX) is a high-throughput promoter-trap method. It is a function-based metagenomic screening tool that relies on transcriptional activation of a reporter gene green fluorescence protein (gfp) by a metagenomic DNA library upon induction with a substrate. However, its use is limited because of the relatively small size of metagenomic DNA libraries and incompatibility with screening metagenomes from anaerobic environments. In this study, these limitations of SIGEX were addressed by fine-tuning metagenome DNA library construction protocol and by using Evoglow, a green fluorescent protein that forms a chromophore even under anaerobic conditions. Two metagenomic libraries were constructed for subseafloor sediments offshore Shimokita Peninsula (Pacific Ocean) and offshore Joetsu (Japan Sea). The library construction protocol was improved by (a) eliminating short DNA fragments, (b) applying topoisomerase-based high-efficiency ligation, (c) optimizing insert DNA concentration, and (d) column-based DNA enrichment. This led to a successful construction of metagenome DNA libraries of approximately 6 Gbp for both samples. SIGEX screening using five aromatic compounds (benzoate, 3-chlorobenzoate, 3-hydroxybenzoate, phenol, and 2,4-dichlorophenol) under aerobic and anaerobic conditions revealed significant differences in the inducible clone ratios under these conditions. 3-Chlorobenzoate and 2,4-dichlorophenol led to a higher induction ratio than that for the other non-chlorinated aromatic compounds under both aerobic and anaerobic conditions. After the further screening of induced clones, a clone induced by 3-chlorobenzoate only under anaerobic conditions was isolated and characterized. The clone harbors a DNA insert that encodes putative open reading frames of unknown function. Previous aerobic SIGEX attempts succeeded in the isolation of gene fragments from anaerobes. This study demonstrated that some gene fragments require a strict in vivo reducing environment to function and may be potentially missed when screened by aerobic induction. The newly developed anaerobic SIGEX scheme will facilitate functional exploration of metagenomes from the anaerobic biosphere.
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Affiliation(s)
- Taisuke Wakamatsu
- Agricultural Sciences, Graduate School of Integrated Arts and Sciences, Kochi University, Kōchi, Japan
| | - Saki Mizobuchi
- Agricultural Sciences, Graduate School of Integrated Arts and Sciences, Kochi University, Kōchi, Japan
| | - Fumiaki Mori
- Geomicrobiology Group, Kochi Institute for Core Smaple Research, Japan Agency for Marine-Earth Science and Technology, Kōchi, Japan
| | - Taiki Futagami
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | | | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Smaple Research, Japan Agency for Marine-Earth Science and Technology, Kōchi, Japan
- *Correspondence: Yuki Morono,
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6
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Ochi K, Tokuda M, Yanagiya K, Suzuki-Minakuchi C, Nojiri H, Yuki M, Ohkuma M, Kimbara K, Shintani M. Oxygen concentration affects frequency and range of transconjugants for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1. Biosci Biotechnol Biochem 2021; 85:1005-1015. [PMID: 33580688 DOI: 10.1093/bbb/zbaa118] [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: 12/01/2020] [Accepted: 12/20/2020] [Indexed: 11/12/2022]
Abstract
The frequency of transconjugants were compared for the incompatibility (Inc) P-1 and P-7 plasmids pBP136 and pCAR1 under aerobic and anaerobic conditions. Filter mating assays were performed with one donor strain and one recipient strain using different donors of Pseudomonas and recipient strains, including Pseudomonas, Pantoea, and Buttiauxella. Under anaerobic condition, frequencies of transconjugants for both plasmids were 101-103-fold lower than those under aerobic condition regardless of whether aerobically or anaerobically grown donors and recipients were used. To compare the transconjugant ranges under aerobic and anaerobic conditions, conjugation was performed between the donor of pBP136 and recipient bacteria extracted from environmental samples. Several transconjugants were uniquely obtained from each aerobic or anaerobic condition. Our findings indicate that a plasmid can differently spread among bacteria depending on the oxygen concentrations of the environment.
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Affiliation(s)
- Kentaro Ochi
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Maho Tokuda
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kosuke Yanagiya
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | | | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kazuhide Kimbara
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
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7
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Anderson NT, Weyant KB, Mukherjee A. Characterization of flavin binding in oxygen-independent fluorescent reporters. AIChE J 2020; 66. [PMID: 34305141 DOI: 10.1002/aic.17083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescent proteins based on light, oxygen, and voltage (LOV) sensing photoreceptors are among the few reporter gene technologies available for studying living systems in oxygen-free environments that render reporters based on the green fluorescent protein nonfluorescent. LOV reporters develop fluorescence by binding flavin mononucleotide (FMN), which they endogenously obtain from cells. As FMN is essential to cell physiology as well as for determining fluorescence in LOV proteins, it is important to be able to study and characterize flavin binding in LOV reporters. To this end, we report a method for reversibly separating FMN from two commonly used LOV reporters to prepare stable and soluble apoproteins. Using fluorescence titration, we measured the equilibrium dissociation constant for binding with all three cellular flavins: FMN, flavin adenine dinucleotide, and riboflavin. Finally, we exploit the riboflavin affinity of apo LOV reporters, identified in this work, to develop a fluorescence turn-on biosensor for vitamin B2.
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Affiliation(s)
- Nolan T. Anderson
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
| | - Kevin B. Weyant
- Smith School of Chemical & Biomolecular Engineering Cornell University Ithaca New York 14853 USA
| | - Arnab Mukherjee
- Department of Chemical Engineering University of California Santa Barbara California 93106 USA
- Department of Chemistry University of California Santa Barbara California 93106 USA
- Neuroscience Research Institute University of California Santa Barbara California 93106 USA
- Center for Bioengineering University of California Santa Barbara California 93106 USA
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8
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Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals. Int J Mol Sci 2020; 21:ijms21207639. [PMID: 33076477 PMCID: PMC7589590 DOI: 10.3390/ijms21207639] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.
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9
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Ozbakir HF, Anderson NT, Fan KC, Mukherjee A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjug Chem 2020; 31:293-302. [PMID: 31794658 PMCID: PMC7033020 DOI: 10.1021/acs.bioconjchem.9b00688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.
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Affiliation(s)
- Harun F. Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Nolan T. Anderson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kang-Ching Fan
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry, University of California, Santa Barbara, California 93106, United States
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California, Santa Barbara, California 93106, United States
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10
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The physiology and biotechnology of dark fermentative biohydrogen production. Biotechnol Adv 2018; 36:2165-2186. [DOI: 10.1016/j.biotechadv.2018.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 02/02/2023]
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11
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Wakamatsu T, Morono Y, Futagami T, Terada T, Nishikawa S, Morisawa T, Ohshita K, Inagaki F, Ashiuchi M. Metal-ion-induced expression of gene fragments from subseafloor micro-organisms in the Kumano forearc basin, Nankai Trough. J Appl Microbiol 2018; 125:1396-1407. [PMID: 30080957 DOI: 10.1111/jam.14061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 06/30/2018] [Accepted: 07/23/2018] [Indexed: 12/30/2022]
Abstract
AIMS Using substrate-induced gene-expression (SIGEX) screening on subseafloor sediment samples from the Nankai Trough, Japan, we identified gene fragments showing an induction response to metal ions. METHODS AND RESULTS Environmental DNA libraries in Escherichia coli host cells were tested by the addition of metal ions (Ni2+ , Co2+ , Ga3+ or Mo6+ ), followed by cell sorting of clones exhibiting green fluorescence upon co-expression of green fluorescence protein downstream of the inserted gene fragments. One clone displayed Ni2+ -specific induction, three clones displayed Ga3+ -specific induction and three clones displayed an induction response to multiple metal ions. DNA sequence analysis showed that a variety of genes showed induction responses in the screened clones. CONCLUSIONS Using the SIGEX approach, we retrieved gene fragments with no previously identified response to metal ions that exhibited metal-ion-induced expression. This method has the potential to promote exploration of gene function through gene-induction response. SIGNIFICANCE AND IMPACT OF THE STUDY We successfully linked gene-induction response with sequence information for gene fragments of previously unknown function. The SIGEX-based approach exhibited the potential to identify genetic function in unknown gene pools from the deep subseafloor biosphere, as well as novel genetic components for future biotechnological applications.
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Affiliation(s)
- T Wakamatsu
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Kochi, Japan
| | - Y Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kochi, Japan.,Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC, Kanagawa, Japan
| | - T Futagami
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
| | - T Terada
- Marine Works Japan Ltd, Kanagawa, Japan
| | - S Nishikawa
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Kochi, Japan
| | - T Morisawa
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Kochi, Japan
| | - K Ohshita
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Kochi, Japan
| | - F Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kochi, Japan.,Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC, Kanagawa, Japan.,Research and Development Center for Ocean Drilling Science, Kanagawa, Japan
| | - M Ashiuchi
- Agricultural Science, Graduate School of Integrated Arts and Sciences, Kochi University, Kochi, Japan
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12
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Anjum M, Madsen JS, Espinosa-Gongora C, Jana B, Wiese M, Nielsen DS, Sørensen SJ, Moodley A, Bortolaia V, Guardabassi L. A culture-independent method for studying transfer of IncI1 plasmids from wild-type Escherichia coli in complex microbial communities. J Microbiol Methods 2018; 152:18-26. [PMID: 30030013 DOI: 10.1016/j.mimet.2018.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 11/25/2022]
Abstract
IncI1 plasmids play a central role in the transfer of antimicrobial resistance genes among Enterobacteriaceae in animals and humans. Knowledge on the dynamics of IncI1 plasmid transfer is limited, mainly due to lack of culture-independent methods that can quantify donor strain survival and plasmid transfer in complex microbial communities. The aim of this study was to develop a culture-independent method to study the dynamics of IncI1 plasmids transfer by fluorescence-activated cell sorting. We genetically modified three wild-type Escherichia coli of animal (n = 2) and human (n = 1) origin carrying blaCMY-2 or blaCTX-M-1 on two epidemic IncI1 plasmids (pST12 and pST7). Non-coding regions on the chromosome and on the IncI1 plasmid of each strain were tagged with mCherry (red) and GFPmut3 (green) fluorescent proteins, respectively, using lambda recombineering. A gene cassette expressing mCherry and lacIq was inserted into the chromosome, whereas the plasmid was marked with a GFPmut3 cassette with LacIq repressible promoter. Therefore, gfpmut3 was repressed in donor strains but expressed in recipient strains acquiring the plasmids. We demonstrated that genetic engineering of the strains did not affect the growth rate and plasmid transfer-ability in filter and broth matings. A proof-of-concept experiment using the CoMiniGut, an in vitro model of the colon, proved the validity of our method for studying the survival of wild-type E. coli and horizontal transfer of IncI1 plasmids under different pH and oxygen conditions. The dual-labeling method by fluorescent proteins is useful to determine persistence of exogenous E. coli and transfer dynamics of IncI1 plasmids in microbial communities.
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Affiliation(s)
- Mehreen Anjum
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Jonas Stenløkke Madsen
- Department of Biology, University of Copenhagen 1, Building: 1-1-215, 2100 København Ø, Denmark
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Bimal Jana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Maria Wiese
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Dennis Sandris Nielsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, University of Copenhagen 1, Building: 1-1-215, 2100 København Ø, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs. Lyngby, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1-20, 1870 Frederiksberg C, Denmark.
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The Protease ClpXP and the PAS Domain Protein DivL Regulate CtrA and Gene Transfer Agent Production in Rhodobacter capsulatus. Appl Environ Microbiol 2018; 84:AEM.00275-18. [PMID: 29625982 DOI: 10.1128/aem.00275-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/29/2018] [Indexed: 01/01/2023] Open
Abstract
Several members of the Rhodobacterales (Alphaproteobacteria) produce a conserved horizontal gene transfer vector, called the gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system used to study GTA biology is the Rhodobacter capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls the production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that dysregulation of the CckA-ChpT-CtrA phosphorelay either by the loss of the PAS domain protein DivL or by substitution of the autophosphorylation residue of the hybrid histidine kinase CckA decreased CtrA phosphorylation and greatly increased RcGTA protein production in R. capsulatus We show that the loss of the ClpXP protease or the three C-terminal residues of CtrA results in increased CtrA levels in R. capsulatus and identify ClpX(P) to be essential for the maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in the RhodobacteralesIMPORTANCE Members of the Rhodobacterales are abundant in ocean and freshwater environments. The conserved GTA produced by many Rhodobacterales may have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay; however, several questions about GTA regulation remain. Our identification that a short DivL homologue and ClpXP regulate CtrA in R. capsulatus extends the model of CtrA regulation from Caulobacter crescentus to a member of the Rhodobacterales We found that the magnitude of RcGTA production greatly depends on DivL and CckA kinase activity, adding yet another layer of regulatory complexity to RcGTA. RcGTA is known to undergo CckA-dependent maturation, and we extend the understanding of this process by showing that the ClpX chaperone is required for formation of tailed, DNA-containing particles.
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Pinilla-Redondo R, Riber L, Sørensen SJ. Fluorescence Recovery Allows the Implementation of a Fluorescence Reporter Gene Platform Applicable for the Detection and Quantification of Horizontal Gene Transfer in Anoxic Environments. Appl Environ Microbiol 2018; 84:e02507-17. [PMID: 29330182 PMCID: PMC5835726 DOI: 10.1128/aem.02507-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 12/20/2017] [Indexed: 02/02/2023] Open
Abstract
The study of horizontal gene transfer (HGT) in microbial communities has been revolutionized by significant advances in cultivation-independent methods based on fluorescence reporter gene technologies. Recently, the combination of these novel approaches with flow cytometry has presented itself as one of the most powerful tools to study the spread of mobile genetic elements (MGEs) in the environment. However, the use of fluorescent markers, like green fluorescent protein (GFP) and mCherry, is limited by environmental constraints, such as oxygen availability and pH levels, that affect the correct maturation of their fluorophores. Few studies have characterized the effects of such environmental conditions in a systematic way, and the sheer amount of distinct protein variants requires each system to be examined in an individual fashion. The lack of efficient and reliable markers to monitor HGT in anaerobic environments, coupled to the abundance of ecologically and clinically relevant oxygen-deprived niches in which bacteria thrive, calls for the urgent development of suitable tools that permit its study. In an attempt to devise a process that allows the implementation of the mentioned dual-labeling system to anoxic milieus, the aerobic fluorescence recovery of mCherry and GFPmut3, as well as the effect of pH on their fluorescence intensities, was studied. The findings present a solution to an intrinsic problem that has long hampered the utilization of this system, highlight its pH limitations, and provide experimental tools that will help broaden its horizon of application to other fields.IMPORTANCE Many anaerobic environments, like the gastrointestinal tract, anaerobic digesters, and the interiors of dense biofilms, have been shown to be hotspots for horizontal gene transfer (HGT). Despite the increasing wealth of reports warning about the alarming spread of antibiotic resistance determinants, to date, HGT studies mainly rely on cultivation-based methods. Unfortunately, the relevance of these studies is often questionable, as only a minor fraction of bacteria can be cultivated. A recently developed approach to monitoring the fate of plasmids in microbial communities is based on a fluorescence dual-labeling system and allows the bypassing of cultivation. However, the fluorescent proteins on which it is founded are constrained by pH levels and by their strict dependence on oxygen for the maturation of their fluorophores. This study focused on the development and validation of an appropriate aerobic fluorescence recovery (AFR) method for this platform, as this embodies the missing technical link impeding its implementation in anoxic environments.
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Affiliation(s)
| | - Leise Riber
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
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15
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Landete JM, Medina M, Arqués JL. Fluorescent reporter systems for tracking probiotic lactic acid bacteria and bifidobacteria. World J Microbiol Biotechnol 2016; 32:119. [PMID: 27263014 DOI: 10.1007/s11274-016-2077-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/27/2016] [Indexed: 12/19/2022]
Abstract
In the last two decades, there has been increasing evidence supporting the role of the intestinal microbiota in health and disease, as well as the use of probiotics to modulate its activity and composition. Probiotic bacteria selected for commercial use in foods, mostly lactic acid bacteria and bifidobacteria, must survive in sufficient numbers during the manufacturing process, storage, and passage through the gastro-intestinal tract. They have several modes of action and it is crucial to unravel the mechanisms underlying their postulated beneficial effects. To track their survival and persistence, and to analyse their interaction with the gastro-intestinal epithelia it is essential to discriminate probiotic strains from endogenous microbiota. Fluorescent reporter proteins are relevant tools that can be exploited as a non-invasive marker system for in vivo real-time imaging in complex ecosystems as well as in vitro fluorescence labelling. Oxygen is required for many of these reporter proteins to fluoresce, which is a major drawback in anoxic environments. However, some new fluorescent proteins are able to overcome the potential problems caused by oxygen limitations. The current available approaches and the benefits/disadvantages of using reporter vectors containing fluorescent proteins for labelling of bacterial probiotic species commonly used in food are addressed.
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Affiliation(s)
- José M Landete
- Dpto. de Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, 28040, Madrid, Spain
| | - Margarita Medina
- Dpto. de Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, 28040, Madrid, Spain
| | - Juan L Arqués
- Dpto. de Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, 28040, Madrid, Spain.
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16
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Abstract
Here we describe protocols for using the red fluorescent protein mCherryOpt in Clostridium difficile. The protocols can be readily adapted to similar fluorescent proteins (FPs), such as green fluorescent protein (GFP) and cyan fluorescent protein (CFP). There are three critical considerations for using FPs in C. difficile. (1) Choosing the right color: Blue and (especially) red are preferred because C. difficile exhibits considerable yellow-green autofluorescence. (2) Codon optimization: Most FP genes in general circulation have a GC content of ~60 %, so they are not well expressed in low-GC bacteria. (3) Fixing anaerobically grown cells prior to exposure to O2: The FPs under consideration here are non-fluorescent when produced anaerobically because O2 is required to introduce double bonds into the chromophore. Fixation prevents C. difficile cells from becoming degraded during the several hours required for chromophore maturation after cells are exposed to air. Fixation can probably be omitted for studies in which maintaining cellular architecture is not important, such as using mCherryOpt to monitor gene expression.
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Affiliation(s)
- Eric M Ransom
- Department of Microbiology, University of Iowa, 51 Newton Rd, 3-372 Bowen Science Building, Iowa City, IA, 52242, USA
- Johne's Testing Center, School of Veterinary Medicine, Madison, WI, USA
| | - David S Weiss
- Department of Microbiology, University of Iowa, 51 Newton Rd, 3-372 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Craig D Ellermeier
- Department of Microbiology, University of Iowa, 51 Newton Rd, 3-372 Bowen Science Building, Iowa City, IA, 52242, USA.
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17
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Use of anaerobic green fluorescent protein versus green fluorescent protein as reporter in lactic acid bacteria. Appl Microbiol Biotechnol 2015; 99:6865-77. [DOI: 10.1007/s00253-015-6770-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 01/09/2023]
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18
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Mukherjee A, Weyant KB, Agrawal U, Walker J, Cann IKO, Schroeder CM. Engineering and characterization of new LOV-based fluorescent proteins from Chlamydomonas reinhardtii and Vaucheria frigida. ACS Synth Biol 2015; 4:371-7. [PMID: 25881501 DOI: 10.1021/sb500237x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Flavin-based fluorescent proteins (FbFPs) are a new class of fluorescent reporters that exhibit oxygen-independent fluorescence, which is a key advantage over the green fluorescent protein. Broad application of FbFPs, however, has been generally hindered by low brightness. To maximize the utility of FbFPs, there is a pressing need to expand and diversify the limited FbFP library through the inclusion of bright and robust variants. In this work, we use genome mining to identify and engineer two new FbFPs (CreiLOV and VafLOV) from Chlamydomonas reinhardtii and Vaucheria frigida. We show that CreiLOV is a thermostable, photostable, and fast-maturing monomeric reporter that outperforms existing FbFPs in brightness and operational pH range. Furthermore, we show that CreiLOV can be used to monitor dynamic gene expression in Escherichia coli. Overall, our work introduces CreiLOV as a robust addition to the FbFP repertoire and highlights genome mining as a powerful approach to engineer improved FbFPs.
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Affiliation(s)
- Arnab Mukherjee
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kevin B. Weyant
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Utsav Agrawal
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joshua Walker
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Isaac K. O. Cann
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles M. Schroeder
- Department of Chemical & Biomolecular Engineering, ‡Department of Microbiology, §Institute for Genomic Biology, ∥Department of Animal Sciences, ⊥Energy Biosciences Institute, #Center for Biophysics and Quantitative Biology, ∇Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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19
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Ransom EM, Ellermeier CD, Weiss DS. Use of mCherry Red fluorescent protein for studies of protein localization and gene expression in Clostridium difficile. Appl Environ Microbiol 2015; 81:1652-60. [PMID: 25527559 PMCID: PMC4325159 DOI: 10.1128/aem.03446-14] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/17/2014] [Indexed: 01/05/2023] Open
Abstract
Fluorescent proteins are powerful reporters in biology, but most require O2 for chromophore maturation, making them inherently difficult to use in anaerobic bacteria. Clostridium difficile, a strict anaerobe with a genomic GC content of only 29%, is the leading cause of hospital-acquired diarrhea in developed countries, and new methods for studying this pathogen are sorely needed. We recently demonstrated that a cyan fluorescent protein called CFPopt that has been codon optimized for production in low-GC bacteria can be used to study protein localization in C. difficile provided the cells are fixed prior to exposure to air. We describe here a codon-optimized variant of mCherry (mCherryOpt) that exhibits faster acquisition of fluorescence and a better signal-to-noise ratio than CFPopt. We utilized mCherryOpt to construct plasmids for studying protein localization (pRAN473) and gene expression (pDSW1728) in C. difficile. Plasmid pRAN473 is an mCherryOpt fusion vector with a tetracycline-inducible promoter. To document its biological utility, we demonstrated septal localization of two cell division proteins, MldA and ZapA. Plasmid pDSW1728 is designed for cloning a promoter of interest upstream of mCherryOpt. As proof of principle, we studied the expression of the pdaV operon, which is required for lysozyme resistance. In confirmation and extension of previous reports, we found that expression of the pdaV operon requires the alternative sigma factor σ(v) and that induction by lysozyme is dose dependent and uniform across the population of lysozyme-treated cells.
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Affiliation(s)
- Eric M Ransom
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
| | | | - David S Weiss
- Department of Microbiology, University of Iowa, Iowa City, Iowa, USA
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20
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Mukherjee A, Schroeder CM. Flavin-based fluorescent proteins: emerging paradigms in biological imaging. Curr Opin Biotechnol 2015; 31:16-23. [DOI: 10.1016/j.copbio.2014.07.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 02/07/2023]
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21
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Line L, Alhede M, Kolpen M, Kühl M, Ciofu O, Bjarnsholt T, Moser C, Toyofuku M, Nomura N, Høiby N, Jensen PØ. Physiological levels of nitrate support anoxic growth by denitrification of Pseudomonas aeruginosa at growth rates reported in cystic fibrosis lungs and sputum. Front Microbiol 2014; 5:554. [PMID: 25386171 PMCID: PMC4208399 DOI: 10.3389/fmicb.2014.00554] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022] Open
Abstract
Chronic Pseudomonas aeruginosa lung infection is the most severe complication in patients with cystic fibrosis (CF). The infection is characterized by the formation of biofilm surrounded by numerous polymorphonuclear leukocytes (PMNs) and strong O2 depletion in the endobronchial mucus. We have reported that O2 is mainly consumed by the activated PMNs, while O2 consumption by aerobic respiration is diminutive and nitrous oxide (N2O) is produced in infected CF sputum. This suggests that the reported growth rates of P. aeruginosa in lungs and sputum may result from anaerobic respiration using denitrification. The growth rate of P. aeruginosa achieved by denitrification at physiological levels (~400 μM) of nitrate (NO(-) 3) is however, not known. Therefore, we have measured growth rates of anoxic cultures of PAO1 and clinical isolates (n = 12) in LB media supplemented with NO(-) 3 and found a significant increase of growth when supplementing PAO1 and clinical isolates with ≥150 μM NO(-) 3 and 100 μM NO(-) 3, respectively. An essential contribution to growth by denitrification was demonstrated by the inability to establish a significantly increased growth rate by a denitrification deficient ΔnirS-N mutant at <1 mM of NO(-) 3. Activation of denitrification could be achieved by supplementation with as little as 62.5 μM of NO(-) 3 according to the significant production of N2O by the nitrous oxide reductase deficient ΔnosZ mutant. Studies of the promoter activity, gene transcripts, and enzyme activity of the four N-oxide reductases in PAO1 (Nar, Nir, Nor, Nos) further verified the engagement of denitrification, showing a transient increase in activation and expression and rapid consumption of NO(-) 3 followed by a transient increase of NO(-) 2. Growth rates obtained by denitrification in this study were comparable to our reported growth rates in the majority of P. aeruginosa cells in CF lungs and sputum. Thus, we have demonstrated that denitrification is required for P. aeruginosa growth in infected endobronchial CF mucus.
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Affiliation(s)
- Laura Line
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Morten Alhede
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen Copenhagen, Denmark ; Plant Functional Biology and Climate Change Cluster, University of Technology Sydney Sydney, NSW, Australia ; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University Singapore, Singapore
| | - Oana Ciofu
- Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Claus Moser
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark
| | - Masanori Toyofuku
- Graduate School of Life and Environmental Sciences, University of Tsukuba Tsukuba, Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba Tsukuba, Japan
| | - Niels Høiby
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark ; Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Peter Ø Jensen
- Department of Clinical Microbiology Rigshospitalet, Copenhagen, Denmark
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22
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Toyofuku M, Zhou S, Sawada I, Takaya N, Uchiyama H, Nomura N. Membrane vesicle formation is associated with pyocin production under denitrifying conditions inPseudomonas aeruginosa PAO1. Environ Microbiol 2013; 16:2927-38. [DOI: 10.1111/1462-2920.12260] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Masanori Toyofuku
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Shengmin Zhou
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Isao Sawada
- Department of Material and Environmental Chemistry; Graduate School of Engineering; Utsunomiya University; Utsunomiya Tochigi Japan
| | - Naoki Takaya
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Hiroo Uchiyama
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki 305-8572 Japan
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23
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Bacterial community morphogenesis is intimately linked to the intracellular redox state. J Bacteriol 2013; 195:1371-80. [PMID: 23292774 DOI: 10.1128/jb.02273-12] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Many microbial species form multicellular structures comprising elaborate wrinkles and concentric rings, yet the rules governing their architecture are poorly understood. The opportunistic pathogen Pseudomonas aeruginosa produces phenazines, small molecules that act as alternate electron acceptors to oxygen and nitrate to oxidize the intracellular redox state and that influence biofilm morphogenesis. Here, we show that the depth occupied by cells within colony biofilms correlates well with electron acceptor availability. Perturbations in the environmental provision, endogenous production, and utilization of electron acceptors affect colony development in a manner consistent with redox control. Intracellular NADH levels peak before the induction of colony wrinkling. These results suggest that redox imbalance is a major factor driving the morphogenesis of P. aeruginosa biofilms and that wrinkling itself is an adaptation that maximizes oxygen accessibility and thereby supports metabolic homeostasis. This type of redox-driven morphological change is reminiscent of developmental processes that occur in metazoans.
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Mukherjee A, Weyant KB, Walker J, Schroeder CM. Directed evolution of bright mutants of an oxygen-independent flavin-binding fluorescent protein from Pseudomonas putida. J Biol Eng 2012; 6:20. [PMID: 23095243 PMCID: PMC3488000 DOI: 10.1186/1754-1611-6-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/19/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fluorescent reporter proteins have revolutionized our understanding of cellular bioprocesses by enabling live cell imaging with exquisite spatio-temporal resolution. Existing fluorescent proteins are predominantly based on the green fluorescent protein (GFP) and related analogs. However, GFP-family proteins strictly require molecular oxygen for maturation of fluorescence, which precludes their application for investigating biological processes in low-oxygen environments. A new class of oxygen-independent fluorescent reporter proteins was recently reported based on flavin-binding photosensors from Bacillus subtilis and Pseudomonas putida. However, flavin-binding fluorescent proteins show very limited brightness, which restricts their utility as biological imaging probes. RESULTS In this work, we report the discovery of bright mutants of a flavin-binding fluorescent protein from P. putida using directed evolution by site saturation mutagenesis. We discovered two mutations at a chromophore-proximal amino acid (F37S and F37T) that confer a twofold enhancement in brightness relative to the wild type fluorescent protein through improvements in quantum yield and holoprotein fraction. In addition, we observed that substitution with other aromatic amino acids at this residue (F37Y and F37W) severely diminishes fluorescence emission. Therefore, we identify F37 as a key amino acid residue in determining fluorescence. CONCLUSIONS To increase the scope and utility of flavin-binding fluorescent proteins as practical fluorescent reporters, there is a strong need for improved variants of the wild type protein. Our work reports on the application of site saturation mutagenesis to isolate brighter variants of a flavin-binding fluorescent protein, which is a first-of-its-kind approach. Overall, we anticipate that the improved variants will find pervasive use as fluorescent reporters for biological studies in low-oxygen environments.
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Affiliation(s)
- Arnab Mukherjee
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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25
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Rittmann S, Herwig C. A comprehensive and quantitative review of dark fermentative biohydrogen production. Microb Cell Fact 2012; 11:115. [PMID: 22925149 PMCID: PMC3443015 DOI: 10.1186/1475-2859-11-115] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/03/2012] [Indexed: 01/25/2023] Open
Abstract
Biohydrogen production (BHP) can be achieved by direct or indirect biophotolysis, photo-fermentation and dark fermentation, whereof only the latter does not require the input of light energy. Our motivation to compile this review was to quantify and comprehensively report strains and process performance of dark fermentative BHP. This review summarizes the work done on pure and defined co-culture dark fermentative BHP since the year 1901. Qualitative growth characteristics and quantitative normalized results of H2 production for more than 2000 conditions are presented in a normalized and therefore comparable format to the scientific community.Statistically based evidence shows that thermophilic strains comprise high substrate conversion efficiency, but mesophilic strains achieve high volumetric productivity. Moreover, microbes of Thermoanaerobacterales (Family III) have to be preferred when aiming to achieve high substrate conversion efficiency in comparison to the families Clostridiaceae and Enterobacteriaceae. The limited number of results available on dark fermentative BHP from fed-batch cultivations indicates the yet underestimated potential of this bioprocessing application. A Design of Experiments strategy should be preferred for efficient bioprocess development and optimization of BHP aiming at improving medium, cultivation conditions and revealing inhibitory effects. This will enable comparing and optimizing strains and processes independent of initial conditions and scale.
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Affiliation(s)
- Simon Rittmann
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
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26
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Fluorescent proteins in microbial biotechnology—new proteins and new applications. Biotechnol Lett 2011; 34:175-86. [DOI: 10.1007/s10529-011-0767-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
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27
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Zhang C, Lv FX, Xing XH. Bioengineering of the Enterobacter aerogenes strain for biohydrogen production. BIORESOURCE TECHNOLOGY 2011; 102:8344-8349. [PMID: 21764301 DOI: 10.1016/j.biortech.2011.06.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 06/03/2011] [Accepted: 06/04/2011] [Indexed: 05/31/2023]
Abstract
Enterobacter aerogenes is one of the most widely-studied model strains for fermentative hydrogen production. To improve the hydrogen yield of E. aerogenes, the bioengineering on a biomolecular level and metabolic network level is of importance. In this review, the fermentative technology of E. aerogenes for hydrogen production will be first briefly summarized. And then the bioengineering of E. aerogenes for the improvement of hydrogen yield will be thoroughly reviewed, including the anaerobic metabolic networks for hydrogen evolution in E. aerogenes, metabolic engineering for improving hydrogen production in E. aerogenes and mixed culture of E. aerogenes with other hydrogen-producing bacteria to enhance the overall yield in anaerobic cultivation. Finally, a perspective on E. aerogenes as a hydrogen producer including systems bioengineering approach for improving the hydrogen yield and application of the engineered E. aerogenes in mixed culture will be presented.
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Affiliation(s)
- Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China
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28
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Lu Y, Wang L, Ma K, Li G, Zhang C, Zhao H, Lai Q, Li HP, Xing XH. Characteristics of hydrogen production of an Enterobacter aerogenes mutant generated by a new atmospheric and room temperature plasma (ARTP). Biochem Eng J 2011. [DOI: 10.1016/j.bej.2011.02.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Han B, Gopalan V, Ezeji TC. Acetone production in solventogenic Clostridium species: new insights from non-enzymatic decarboxylation of acetoacetate. Appl Microbiol Biotechnol 2011; 91:565-76. [DOI: 10.1007/s00253-011-3276-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/24/2011] [Accepted: 03/25/2011] [Indexed: 10/18/2022]
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30
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Improved hydrogen production under microaerophilic conditions by overexpression of polyphosphate kinase in Enterobacter aerogenes. Enzyme Microb Technol 2011; 48:187-92. [DOI: 10.1016/j.enzmictec.2010.09.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 09/23/2010] [Accepted: 09/28/2010] [Indexed: 11/22/2022]
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31
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Mudhoo A, Forster-Carneiro T, Sánchez A. Biohydrogen production and bioprocess enhancement: A review. Crit Rev Biotechnol 2010; 31:250-63. [DOI: 10.3109/07388551.2010.525497] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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32
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Fluorescent Proteins as a Visible Molecular Signal for Rapid Quantification of Bioprocesses: Potential and Challenges. Chin J Chem Eng 2010. [DOI: 10.1016/s1004-9541(09)60140-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Tracy BP, Gaida SM, Papoutsakis ET. Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr Opin Biotechnol 2010; 21:85-99. [DOI: 10.1016/j.copbio.2010.02.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 01/29/2010] [Accepted: 02/02/2010] [Indexed: 02/01/2023]
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34
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Shin JH, Yoon JH, Lee SH, Park TH. Hydrogen production from formic acid in pH-stat fed-batch operation for direct supply to fuel cell. BIORESOURCE TECHNOLOGY 2010; 101 Suppl 1:S53-S58. [PMID: 19364642 DOI: 10.1016/j.biortech.2009.03.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Revised: 02/03/2009] [Accepted: 03/12/2009] [Indexed: 05/27/2023]
Abstract
Enterobacter asburiae SNU-1 harvested after cultivation was used as a whole cell biocatalyst, for the production of hydrogen. Formic acid was efficiently converted to hydrogen using the harvested cells with an initial hydrogen production rate and total hydrogen production of 491 ml/l/h and 6668 ml/l, respectively, when 1 g/l of whole cell enzyme was used. Moreover, new pH-stat fed-batch operation was conducted, and total hydrogen production was 1.4 times higher than that of batch operation. For practical application, bio-hydrogen produced from formic acid using harvested cells was directly applied to PEMFC for power generation.
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Affiliation(s)
- Jong-Hwan Shin
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
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35
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Lu Y, Zhao H, Zhang C, Lai Q, Wu X, Xing XH. Alteration of hydrogen metabolism of ldh-deleted Enterobacter aerogenes by overexpression of NAD+-dependent formate dehydrogenase. Appl Microbiol Biotechnol 2009; 86:255-62. [PMID: 19830418 DOI: 10.1007/s00253-009-2274-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 09/07/2009] [Accepted: 09/23/2009] [Indexed: 11/24/2022]
Abstract
The NAD+-dependent formate dehydrogenase FDH1 gene (fdh1), cloned from Candida boidinii, was expressed in the ldh-deleted mutant of Enterobacter aerogenes IAM1183 strain. The plasmid of pCom10 driven by the PalkB promoter was used to construct the fdh1 expression system and thus introduce a new dihydronicotinamide adenine dinucleotide (NADH) regeneration pathway from formate in the ldh-deleted mutant. The knockout of NADH-consuming lactate pathway affected the whole cellular metabolism, and the hydrogen yield increased by 11.4% compared with the wild strain. Expression of fdh1 in the ldh-deleted mutant caused lower final cell concentration and final pH after 16 h cultivation, and finally resulted in 86.8% of increase in hydrogen yield per mole consumed glucose. The analysis of cellular metabolites and estimated redox state balance in the fdhl-expressed strain showed that more excess of reducing power was formed by the rewired NADH regeneration pathway, changing the metabolic distribution and promoting the hydrogen production.
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Affiliation(s)
- Yuan Lu
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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36
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Correcting for the inner filter effect in measurements of fluorescent proteins in high-cell-density cultures. Anal Biochem 2009; 390:197-202. [DOI: 10.1016/j.ab.2009.04.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 04/08/2009] [Accepted: 04/18/2009] [Indexed: 11/24/2022]
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37
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Lu Y, Zhao H, Zhang C, Lai Q, Wu X, Xing XH. Expression of NAD+-dependent formate dehydrogenase in Enterobacter aerogenes and its involvement in anaerobic metabolism and H2 production. Biotechnol Lett 2009; 31:1525-30. [PMID: 19533026 DOI: 10.1007/s10529-009-0036-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 11/26/2022]
Abstract
An expression system for NAD(+)-dependent formate dehydrogenase gene (fdh1), from Candida boidinii, was constructed and cloned into Enterobacter aerogenes IAM1183. With the fdh1 expression, the total H(2) yield was attributed to a decrease in activity of the lactate pathway and an increase of the formate pathway flux due to the NADH regeneration. Analysis of the redox state balance and ethanol-to-acetate ratio in the fdhl-expressed strain showed that increased reducing power arose from the reconstruction of NADH regeneration pathway from formate thereby contributing to the improved H(2) production.
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Affiliation(s)
- Yuan Lu
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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38
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Lu Y, Lai Q, Zhang C, Zhao H, Ma K, Zhao X, Chen H, Liu D, Xing XH. Characteristics of hydrogen and methane production from cornstalks by an augmented two- or three-stage anaerobic fermentation process. BIORESOURCE TECHNOLOGY 2009; 100:2889-2895. [PMID: 19231169 DOI: 10.1016/j.biortech.2009.01.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Revised: 01/08/2009] [Accepted: 01/09/2009] [Indexed: 05/27/2023]
Abstract
This paper presents the co-production of hydrogen and methane from cornstalks by a two- or three-stage anaerobic fermentation process augmented with effective artificial microbial community. Two-stage fermentation by using the anaerobic sludge and DGGE analysis showed that effective and stable strains should be introduced into the system. We introduced Enterobacter aerogens or Clostridium paraputrificum into the hydrogen stage, and C. paraputrificum was proven to be more effective. In the three-stage process consisting of the improved hydrolysis, hydrogen and methane production stages, the highest soluble sugars (0.482 kg/kg cornstalks) were obtained after the introduction of Clostridium thermocellum in the hydrolysis stage, under the thermophilic (55 degrees C) and acidic (pH 5.0) conditions. Hydrolysates from 1 kg of cornstalks could produce 2.61 mol (63.7 l) hydrogen by augmentation with C. paraputrificum and 4.69 mol (114.6 l) methane by anaerobic granular sludge, corresponding to 54.1% energy recovery.
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Affiliation(s)
- Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Tsinghua Yuan, Beijing 100084, China
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39
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Temperature influence on fluorescence intensity and enzyme activity of the fusion protein of GFP and hyperthermophilic xylanase. Appl Microbiol Biotechnol 2009; 84:511-7. [DOI: 10.1007/s00253-009-2006-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 03/23/2009] [Accepted: 04/07/2009] [Indexed: 11/25/2022]
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40
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Clong and knochout of formate hydrogenlyase and H2-uptake hydrogenase genes in Enterobacter aerogenes for enhanced hydrogen production. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Expression of green fluorescent protein fused to magnetosome proteins in microaerophilic magnetotactic bacteria. Appl Environ Microbiol 2008; 74:4944-53. [PMID: 18539817 DOI: 10.1128/aem.00231-08] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The magnetosomes of magnetotactic bacteria are prokaryotic organelles consisting of a magnetite crystal bounded by a phospholipid bilayer that contains a distinct set of proteins with various functions. Because of their unique magnetic and crystalline properties, magnetosome particles are potentially useful as magnetic nanoparticles in a number of applications, which in many cases requires the coupling of functional moieties to the magnetosome membrane. In this work, we studied the use of green fluorescent protein (GFP) as a reporter for the magnetosomal localization and expression of fusion proteins in the microaerophilic Magnetospirillum gryphiswaldense by flow cytometry, fluorescence microscopy, and biochemical analysis. Although optimum conditions for high fluorescence and magnetite synthesis were mutually exclusive, we established oxygen-limited growth conditions, which supported growth, magnetite biomineralization, and GFP fluorophore formation at reasonable rates. Under these optimized conditions, we studied the subcellular localization and expression of the GFP-tagged magnetosome proteins MamC, MamF, and MamG by fluorescence microscopy and immunoblotting. While all fusions specifically localized at the magnetosome membrane, MamC-GFP displayed the strongest expression and fluorescence. MamC-GFP-tagged magnetosomes purified from cells displayed strong fluorescence, which was sensitive to detergents but stable under a wide range of temperature and salt concentrations. In summary, our data demonstrate the use of GFP as a reporter for protein localization under magnetite-forming conditions and the utility of MamC as an anchor for magnetosome-specific display of heterologous gene fusions.
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42
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Zhang C, Xing XH. Quantification of a specific bacterial strain in an anaerobic mixed culture for biohydrogen production by the aerobic fluorescence recovery (AFR) technique. Biochem Eng J 2008. [DOI: 10.1016/j.bej.2007.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Drepper T, Eggert T, Circolone F, Heck A, Krauss U, Guterl JK, Wendorff M, Losi A, Gärtner W, Jaeger KE. Reporter proteins for in vivo fluorescence without oxygen. Nat Biotechnol 2007; 25:443-5. [PMID: 17351616 DOI: 10.1038/nbt1293] [Citation(s) in RCA: 285] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 02/06/2007] [Indexed: 11/09/2022]
Abstract
Fluorescent reporter proteins such as green fluorescent protein are valuable noninvasive molecular tools for in vivo real-time imaging of living specimens. However, their use is generally restricted to aerobic systems, as the formation of their chromophores strictly requires oxygen. Starting with blue-light photoreceptors from Bacillus subtilis and Pseudomonas putida that contain light-oxygen-voltage-sensing domains, we engineered flavin mononucleotide-based fluorescent proteins that can be used as fluorescent reporters in both aerobic and anaerobic biological systems.
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Affiliation(s)
- Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Research Center Juelich, Stetternicher Forst, D-52426 Juelich, Germany
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Abstract
The recent explosion in the diversity of available fluorescent proteins (FPs) promises a wide variety of new tools for biological imaging. With no unified standard for assessing these tools, however, a researcher is faced with difficult questions. Which FPs are best for general use? Which are the brightest? What additional factors determine which are best for a given experiment? Although in many cases, a trial-and-error approach may still be necessary in determining the answers to these questions, a unified characterization of the best available FPs provides a useful guide in narrowing down the options.
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Affiliation(s)
- Nathan C Shaner
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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