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Kojima T, Masuda S. Construction of the Rhodobacter sphaeroides strain overproducing 5-aminolevulinic acid by insertion of endogenous promoter. J GEN APPL MICROBIOL 2024; 69:270-277. [PMID: 37482422 DOI: 10.2323/jgam.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
5-Aminolevulinic acid (ALA) is a precursor of heme and a natural amino acid synthesized in the cells of most living organisms. Currently, ALA is used as an ingredient in pharmaceuticals, supplements, cosmetics, feed, fertilizers, and other products. ALA is mainly produced by industrial fermentation by the photosynthetic bacterium Rhodobacter sphaeroides. In this study, we tried to improve the ALA productivity by R. sphaeroides using a genetic strategy to highly express ALA synthase (ALAS) genes. We inserted a constitutive promoter (PrrnB or Prsp_7571) upstream of genes encoding ALAS (hemA and/or hemT) to construct strains that constitutively express ALAS. The highest transcript levels of hemA were observed in the strain where PrrnB was inserted into the hemA promoter region and were 3.5-fold higher than those in the wild-type. The highest transcript levels of hemT were observed in the strain where PrrnB was inserted into the hemT promoter region and were 46-fold higher than those in the wild-type. The maximum ALAS activity was observed in crude cell extracts of the strain where PrrnB was inserted into the hemT promoter region under optimized growth conditions that was 2.7-fold higher than that in the wild type. This strain showed 12-fold accumulation of ALA compared to the wild-type. Thus, we improved ALA productivity without using exogenous DNA sequences. In the future, further improvement in ALA productivity may be expected by applying this approach to current industrial ALA-producing bacteria.
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Affiliation(s)
- Takuma Kojima
- Fermentation Research Center, Neopharma Japan Co., Ltd
- Department of Life Science and Technology, Tokyo Institute of Technology
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology
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2
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Kretz J, Israel V, McIntosh M. Design-Build-Test of Synthetic Promoters for Inducible Gene Regulation in Alphaproteobacteria. ACS Synth Biol 2023; 12:2663-2675. [PMID: 37561940 DOI: 10.1021/acssynbio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Inducible gene expression is useful for biotechnological applications and for studying gene regulation and function in bacteria. Many inducible systems that perform in model organisms such as the Gammaproteobacterium Escherichia coli do not perform well in other bacteria that are of biotechnological interest. Typical problems include weak or leaky expression. Here, we describe an invention named ACIT (Alphaproteobacteria chromosomally integrating transcription-control cassette) that is carried on a suicide plasmid to enable insertion into the chromosome of the host. ACIT consists of multiple DNA fragments specifically arranged in a cassette that allows tight transcription control over any gene or gene cluster of interest following homologous recombination. At the heart of the invention is the ability to modify or exchange parts, e.g., promoters, to suit particular bacteria and growth conditions, allowing for customized gene expression control. Furthermore, ACIT provides a basis for a design-build-test approach for controlling gene expression in less studied bacteria. We describe examples of its control over pigment and exopolysaccharide production, growth, cell form, and social behavior in various Alphaproteobacteria.
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Affiliation(s)
- Jonas Kretz
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Vera Israel
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
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3
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Grützner J, Börner J, Jäger A, Klug G. The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides. Int J Mol Sci 2023; 24:ijms24119515. [PMID: 37298460 DOI: 10.3390/ijms24119515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In natural habitats, bacteria frequently need to adapt to changing environmental conditions. Regulation of transcription plays an important role in this process. However, riboregulation also contributes substantially to adaptation. Riboregulation often acts at the level of mRNA stability, which is determined by sRNAs, RNases, and RNA-binding proteins. We previously identified the small RNA-binding protein CcaF1, which is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides. Rhodobacter is a facultative phototroph that can perform aerobic and anaerobic respiration, fermentation, and anoxygenic photosynthesis. Oxygen concentration and light conditions decide the pathway for ATP production. Here, we show that CcaF1 promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins. Levels of mRNAs for transcriptional regulators of photosynthesis genes are not affected by CcaF1. RIP-Seq analysis compares the binding of CcaF1 to RNAs during microaerobic and photosynthetic growth. The stability of the pufBA mRNA for proteins of the light-harvesting I complex is increased by CcaF1 during phototrophic growth but decreased during microaerobic growth. This research underlines the importance of RNA-binding proteins in adaptation to different environments and demonstrates that an RNA-binding protein can differentially affect its binding partners in dependence upon growth conditions.
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Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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Diversity of Cytochrome c Oxidase Assembly Proteins in Bacteria. Microorganisms 2022; 10:microorganisms10050926. [PMID: 35630371 PMCID: PMC9145763 DOI: 10.3390/microorganisms10050926] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/10/2022] Open
Abstract
Cytochrome c oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form water in a reaction coupled to energy conservation. The three-subunit core of the enzyme is conserved, whereas several proteins identified to function in the biosynthesis of the common family A1 cytochrome c oxidase show diversity in bacteria. Using the model organisms Bacillus subtilis, Corynebacterium glutamicum, Paracoccus denitrificans, and Rhodobacter sphaeroides, the present review focuses on proteins for assembly of the heme a, heme a3, CuB, and CuA metal centers. The known biosynthesis proteins are, in most cases, discovered through the analysis of mutants. All proteins directly involved in cytochrome c oxidase assembly have likely not been identified in any organism. Limitations in the use of mutants to identify and functionally analyze biosynthesis proteins are discussed in the review. Comparative biochemistry helps to determine the role of assembly factors. This information can, for example, explain the cause of some human mitochondrion-based diseases and be used to find targets for new antimicrobial drugs. It also provides information regarding the evolution of aerobic bacteria.
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Le NTM, Le VV, Shin D, Park SM. Growth-promoting Effect of Alginate Oligosaccharides on Rhodobacter sphaeroides. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-021-0246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Chacón L, Arias-Andres M, Mena F, Rivera L, Hernández L, Achi R, Garcia F, Rojas-Jimenez K. Short-term exposure to benzalkonium chloride in bacteria from activated sludge alters the community diversity and the antibiotic resistance profile. JOURNAL OF WATER AND HEALTH 2021; 19:895-906. [PMID: 34874898 DOI: 10.2166/wh.2021.171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The continuous introduction of cleaning products containing benzalkonium chloride (BAC) from household discharges can mold the microbial communities in wastewater treatment plants (WWTPs) in a way still poorly understood. In this study, we performed an in vitro exposure of activated sludge from a WWTP in Costa Rica to BAC, quantified the changes in intI1, sul2, and qacE/qacEΔ1 gene profiles, and determined alterations in the bacterial community composition. The analysis of the qPCR data revealed elevated charges of antibiotic resistance genes in the microbial community; after BAC's exposure, a significant increase in the qacE/qacEΔ1 gene, which is related to ammonium quaternary resistance, was observed. The 16S rRNA gene sequences' analysis showed pronounced variations in the structure of the bacterial communities, including reduction of the alpha diversity values and an increase of the relative abundance of Alphaproteobacteria, particularly of Rhodospseudomonas and Rhodobacter. We confirmed that the microbial communities presented high resilience to BAC at the mg/mL concentration, probably due to constant exposure to this pollutant. They also presented antibiotic resistance-related genes with similar mechanisms to tolerate this substance. These mechanisms should be explored more thoroughly, especially in the context of high use of disinfectant.
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Affiliation(s)
- Luz Chacón
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, P.O. Box: 11501-20160, San José, Costa Rica E-mail:
| | - Maria Arias-Andres
- Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Universidad Nacional, Campus Omar Dengo, P.O. Box 86-3000, Heredia, Costa Rica
| | - Freylan Mena
- Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Universidad Nacional, Campus Omar Dengo, P.O. Box 86-3000, Heredia, Costa Rica
| | - Luis Rivera
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, P.O. Box: 11501-20160, San José, Costa Rica E-mail:
| | - Lorena Hernández
- Centro de Investigación en Productos Naturales (CIPRONA), Universidad de Costa Rica, P.O. Box: 11501-20160, San José, Costa Rica
| | - Rosario Achi
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, P.O. Box: 11501-20160, San José, Costa Rica E-mail:
| | - Fernando Garcia
- Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, P.O. Box: 11501-20160, San José, Costa Rica
| | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, P.O. Box: 11501-20160, San José, Costa Rica
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Du Z, Behrens SF. Tracking de novo protein synthesis in the activated sludge microbiome using BONCAT-FACS. WATER RESEARCH 2021; 205:117696. [PMID: 34601360 DOI: 10.1016/j.watres.2021.117696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/31/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
In order to ensure stable performance of engineered biotechnologies that rely on mixed microbial community systems, it is important to identify process-specific microbial traits and study their in-situ activity and responses to changing environmental conditions and system operational parameters. We used BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT) in combination with Fluorescence-Activated Cell Sorting (FACS) and 16S rRNA gene amplicon sequencing to identify translationally active cells in activated sludge. We found that only a subset of the activated sludge microbiome is translationally active during the aerobic treatment phase of a full-scale sequencing batch reactor designed to enhance biological phosphorus removal from municipal wastewater. Relative abundance of amplicon sequence variants was not a reliable predictor of species activity. BONCAT-positive and -negative cells revealed a broad range of population-wide and taxa-specific translational heterogeneity. BONCAT-FACS in combination with amplicon sequencing can provide new insights into the ecophysiology of highly dynamic microbiomes in activated sludge systems.
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Affiliation(s)
- Zhe Du
- The BioTechnology Institute, University of Minnesota Twin Cities, St. Paul, MN, 55108, USA
| | - Sebastian F Behrens
- The BioTechnology Institute, University of Minnesota Twin Cities, St. Paul, MN, 55108, USA; Department of Civil, Environmental, and Geo-Engineering, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA.
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8
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Adnan F, Jalil A, Ahmed T, Rahman A, Dawood N, Haider G, Siddiqui MF, Rostock L, Guenther S, Schaufler K. TRAP transporter TakP: a key player in the resistance against selenite-induced oxidative stress in Rhodobacter sphaeroides. Microbiol Res 2021; 252:126828. [PMID: 34543948 DOI: 10.1016/j.micres.2021.126828] [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: 06/25/2020] [Revised: 03/28/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022]
Abstract
Almost one-third of all proteins require metal ions as an essential component in key biological processes and approximately half of all enzymes are associated with one or more metal ions. The naturally occurring selenium is very toxic at higher levels, but few bacteria can reduce it into the less toxic insoluble elemental selenium. Selenium is required for the synthesis of selenocysteine, an essential residue involved in the active sites of various enzymes. The purple non-sulphur bacteria, Rhodobacter sphaeroidesis demonstrated for its selenite reduction capacity. The exact mechanism of selenite toxicity is unknown but it reacts with glutathione to form selenodiglutathione, producing the highly toxic compounds namely, H2O2and O2-. A R. sphaeroidesstrain with mutated takP gene, a member of the TRAP (tripartite ATP-independent periplasmic) family of transporter, was reported to be showing more resistance towards selenite in the growth medium but the reason for the resistance is unknown. TRAP transporters are the best-studied family of substrate-binding protein and in our previous study it was confirmed that the gene takP in R. sphaeroides is down-regulated by a small non-coding RNA SorY, providing more resistance to the bacterium against the oxidative stress. By comparative growth analysis and sensitivity assays in the presence of 2 mM selenite, it was observed that the SorY knockout strain is more sensitive to selenite while overexpression of the sRNA conferred more resistance to the bacterium like the takP mutant strain. TakP is involved in the import of malate into the cell, which under oxidative stress needs to be down-regulated to limit malate flux into the cell. Limited malate flux leads to metabolic rearrangements in the cell to avoid excessive generation of prooxidant NADH and facilitate constant generation of antioxidant NADPH. In the presence and absence of selenite, a drastic increase in the NADPH and decrease in the NADH levels are reported respectively. Accumulation of metallic selenium in the cytoplasm was detected via atomic absorption spectrophotometer and our analysis clearly demonstrated the presence of more selenium in the electron micrographs of the SorY knockout strain compared to the takP mutant grown under dark semi-aerobic growth conditions in the presence of selenite. Hence based on our analysis, it is confirmed that lack of TakP transporter led to reduced selenite influx into the cytoplasm, relieving cells with limited generation of ROS, eventually exhibiting more resistance against selenite-induced oxidative stress.
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Affiliation(s)
- Fazal Adnan
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Amna Jalil
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Tahir Ahmed
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Afra Rahman
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Nawal Dawood
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Ghulam Haider
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | | | - Leon Rostock
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Germany.
| | - Sebastian Guenther
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Germany.
| | - Katharina Schaufler
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Germany; Institute of infection medicine, Kiel University, Germany.
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Schmid F, Novion Ducassou J, Couté Y, Gescher J. Developing Rhodobacter sphaeroides for cathodic biopolymer production. BIORESOURCE TECHNOLOGY 2021; 336:125340. [PMID: 34090098 DOI: 10.1016/j.biortech.2021.125340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
In this work, Rhodobacter sphaeroides was identified as a potential cathodic production strain for photoautotrophic production processes. First, a stable cultivation in a bioelectrochemical system (BES) was established under conditions in which hydrogen produced by a poised cathode served as an electron donor. It was shown that both the introduction of a plasmid vector and exposure to the corresponding antibiotic selection pressure caused a strong improvement in both cathodic biofilm formation and electrochemical properties. A quantitative proteomic analysis identified key players in the molecular adaptation to biofilm growth on the cathodic surface. Furthermore, biofilm formation kinetics were quantified by optical coherence tomography measurements, which showed a strong tendency for biofilm formation together with a robust biofilm architecture. A media switch to N2-limited conditions resulted in increased cathodic poly(3-hydroxybutyrate) (PHB) accumulation, suggesting R. sphaeroides as a potential strain for photoautotrophic PHB production in future industrial applications.
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Affiliation(s)
- Ferdinand Schmid
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe Germany
| | - Julia Novion Ducassou
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048 38000, Grenoble France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048 38000, Grenoble France
| | - Johannes Gescher
- Institute for Applied Biosciences, Department of Applied Biology, Karlsruhe Institute of Technology, Karlsruhe Germany.
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Wang H, Sha X, Li R, Li Y, Khaleque HN, Zhang Y, Bohu T, Bai Z, Zhuang X. Comparative Genome Analysis Provides Molecular Evidence for Reclassification of the Photosynthetic Bacterium Rhodobacter sphaeroides EBL0706 as a Strain of Luteovulum azotoformans. Microorganisms 2021; 9:microorganisms9081754. [PMID: 34442833 PMCID: PMC8398827 DOI: 10.3390/microorganisms9081754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/04/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we conducted a genome-wide comparative analysis of a former Rhodobacter sphaeroides strain EBL0706, which is now recorded as Luteovulum sphaeroides EBL0706. The genome of EBL0706 was compared with that of Luteovulum azotoformans ATCC 17025, Luteovulum azotoformans KA25, and Luteovulum sphaeroides 2.4.1. The average nucleotide identity (ANI), tetra nucleotide signatures (Tetra), digital DNA–DNA hybridization (dDDH) values, comparative genome, and phylogenetic analysis proposed that EBL0706 is a strain of Luteovulum azotoformans. Functional annotations identified a total of 4034 protein-coding genes in the genome of EBL0706, including a complete photosynthetic gene cluster. This study provides genomic molecular verification for the strain EBL0706 to be reclassified to Luteovulum azotoformans.
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Affiliation(s)
- Haoyu Wang
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, China;
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
| | - Xiaoling Sha
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Huachen Jiguang Technology, Co. Ltd., Beijing 101407, China
| | - Yijing Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yuxiu Zhang
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, China;
- Correspondence: (Y.Z.); (T.B.); Tel.: +86-10-6233-1792 (Y.Z.); +853-6855-7877 (T.B.)
| | - Tsing Bohu
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa 999078, Macao
- CSIRO Mineral Resources, Australian Resources and Research Centre, Kensington, WA 6151, Australia
- Correspondence: (Y.Z.); (T.B.); Tel.: +86-10-6233-1792 (Y.Z.); +853-6855-7877 (T.B.)
| | - Zhihui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (X.S.); (R.L.); (Y.L.); (Z.B.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Fedotovskaya O, Albertsson I, Nordlund G, Hong S, Gennis RB, Brzezinski P, Ädelroth P. Identification of a cytochrome bc 1-aa 3 supercomplex in Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148433. [PMID: 33932366 DOI: 10.1016/j.bbabio.2021.148433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Respiration is carried out by a series of membrane-bound complexes in the inner mitochondrial membrane or in the cytoplasmic membrane of bacteria. Increasing evidence shows that these complexes organize into larger supercomplexes. In this work, we identified a supercomplex composed of cytochrome (cyt.) bc1 and aa3-type cyt. c oxidase in Rhodobacter sphaeroides. We purified the supercomplex using a His-tag on either of these complexes. The results from activity assays, native and denaturing PAGE, size exclusion chromatography, electron microscopy, optical absorption spectroscopy and kinetic studies on the purified samples support the formation and coupled quinol oxidation:O2 reduction activity of the cyt. bc1-aa3 supercomplex. The potential role of the membrane-anchored cyt. cy as a component in supercomplexes was also investigated.
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Affiliation(s)
- Olga Fedotovskaya
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ingrid Albertsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Gustav Nordlund
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sangjin Hong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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12
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Grützner J, Billenkamp F, Spanka DT, Rick T, Monzon V, Förstner KU, Klug G. The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover. Nucleic Acids Res 2021; 49:3003-3019. [PMID: 33706375 PMCID: PMC8034643 DOI: 10.1093/nar/gkab146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 02/10/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Many different protein domains are conserved among numerous species, but their function remains obscure. Proteins with DUF1127 domains number >17 000 in current databases, but a biological function has not yet been assigned to any of them. They are mostly found in alpha- and gammaproteobacteria, some of them plant and animal pathogens, symbionts or species used in industrial applications. Bioinformatic analyses revealed similarity of the DUF1127 domain of bacterial proteins to the RNA binding domain of eukaryotic Smaug proteins that are involved in RNA turnover and have a role in development from Drosophila to mammals. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in maturation of the CcsR sRNAs that are processed from the 3' UTR of the ccaF mRNA and have a role in the oxidative stress defense. CcaF1 binds to many cellular RNAs of different type, several mRNAs with a function in cysteine / methionine / sulfur metabolism. It affects the stability of the CcsR RNAs and other non-coding RNAs and mRNAs. Thus, the widely distributed DUF1127 domain can mediate RNA-binding, affect stability of its binding partners and consequently modulate the bacterial transcriptome, thereby influencing different physiological processes.
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Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | - Fabian Billenkamp
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
- Institute of Animal Nutrition, Friedrich Loeffler Institute, Bundesalle 37, D-38116 Braunschweig, Germany
| | - Daniel-Timon Spanka
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | - Tim Rick
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | | | - Konrad U Förstner
- ZB MED-Information Center of Life Science, Germany
- Institute of Information Science, TH Köln, University of Applied Science, Gustav-Heinemann-Ufer 54, D-50968 Köln, Cologne, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
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13
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Henry KK, Ross W, Myers KS, Lemmer KC, Vera JM, Landick R, Donohue TJ, Gourse RL. A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation. Proc Natl Acad Sci U S A 2020; 117:29658-29668. [PMID: 33168725 PMCID: PMC7703639 DOI: 10.1073/pnas.2010087117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacterium Rhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription from R. sphaeroides rRNA promoters was unexpectedly weak, correlating with absence of -7T, the very highly conserved thymine found at the last position in -10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position -7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating that R. sphaeroides RNAP can utilize -7T when present. rRNA promoters were activated by purified R. sphaeroides CarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 native R. sphaeroides promoters tested in vitro that lacked -7T, whereas it had no effect on three of the four native promoters that contained -7T. Genome-wide bioinformatic analysis of promoters from R. sphaeroides and two other α-proteobacterial species indicated that 30 to 43% contained -7T, whereas 90 to 99% of promoters from non-α-proteobacteria contained -7T. Thus, promoters lacking -7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction in R. sphaeroides CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.
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Affiliation(s)
- Kemardo K Henry
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706;
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Kimberly C Lemmer
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Jessica M Vera
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Robert Landick
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706;
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14
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Orsi E, Beekwilder J, Eggink G, Kengen SWM, Weusthuis RA. The transition of Rhodobacter sphaeroides into a microbial cell factory. Biotechnol Bioeng 2020; 118:531-541. [PMID: 33038009 PMCID: PMC7894463 DOI: 10.1002/bit.27593] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/29/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022]
Abstract
Microbial cell factories are the workhorses of industrial biotechnology and improving their performances can significantly optimize industrial bioprocesses. Microbial strain engineering is often employed for increasing the competitiveness of bio‐based product synthesis over more classical petroleum‐based synthesis. Recently, efforts for strain optimization have been standardized within the iterative concept of “design‐build‐test‐learn” (DBTL). This approach has been successfully employed for the improvement of traditional cell factories like Escherichia coli and Saccharomyces cerevisiae. Within the past decade, several new‐to‐industry microorganisms have been investigated as novel cell factories, including the versatile α‐proteobacterium Rhodobacter sphaeroides. Despite its history as a laboratory strain for fundamental studies, there is a growing interest in this bacterium for its ability to synthesize relevant compounds for the bioeconomy, such as isoprenoids, poly‐β‐hydroxybutyrate, and hydrogen. In this study, we reflect on the reasons for establishing R. sphaeroides as a cell factory from the perspective of the DBTL concept. Moreover, we discuss current and future opportunities for extending the use of this microorganism for the bio‐based economy. We believe that applying the DBTL pipeline for R. sphaeroides will further strengthen its relevance as a microbial cell factory. Moreover, the proposed use of strain engineering via the DBTL approach may be extended to other microorganisms that have not been critically investigated yet for industrial applications.
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Affiliation(s)
- Enrico Orsi
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Gerrit Eggink
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands.,Wageningen Food and Biobased Research, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University, Wageningen, The Netherlands
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15
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Genome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria, Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444. Microbiol Resour Announc 2020; 9:9/36/e00880-20. [PMID: 32883797 PMCID: PMC7471390 DOI: 10.1128/mra.00880-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Here, we report the genome-wide identification of transcription start sites (TSSs) from two Alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, Alphaproteobacteria. Here, we report the genome-wide identification of transcription start sites (TSSs) from two Alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, Alphaproteobacteria.
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16
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Nolorbe-Payahua CD, de Freitas AS, Roesch LFW, Zanette J. Environmental contamination alters the intestinal microbial community of the livebearer killifish Phalloceros caudimaculatus. Heliyon 2020; 6:e04190. [PMID: 32613104 PMCID: PMC7322053 DOI: 10.1016/j.heliyon.2020.e04190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 05/22/2020] [Accepted: 06/08/2020] [Indexed: 10/26/2022] Open
Abstract
Intestinal microbiota perform important functions for the health of fishes. Knowing the microbial composition and evaluating the possible effects caused by anthropogenic pollution in the intestinal microbiota of fish populations might represent an important step in defining microbial biomarkers for water pollution. This study evaluated the impact of environmental contamination on the gut microbiota of the livebearer killifish Phalloceros caudimaculatus. The 16S survey using the V4 region of the 16S rRNA gene was used to characterize and compare the microbiota of two P. caudimaculatus populations from streams with different levels of environmental contamination in Rio Grande, RS, Brazil. Twelve bacterial operational taxonomic units (OTUs) (around one-third of the total) were shared between both fish populations. They represent the core microbiota of the gut in this species. The dominant phyla were Protebacteria and Firmicutes, with more than 80% of relative abundance. The dominant genus was Burkholderia with more than 35% of the relative abundance irrespective of the environmental condition. We detected a lower microbial diversity (Shannon index and observed OTUs) in fish from the polluted stream compared to the reference stream. The PERMANOVA analysis showed that the intestinal microbial communities from fish living in the polluted stream were distinct from those found in the reference stream (p < 0.05). Finally, we identified Luteolibacter, Methylocaldum and Rhodobacter genera, which correlated strongly with the polluted stream. These taxa might represent potential microbial biomarkers of exposure to environmental contaminants in the guts of fish. Confirmation of these findings in other polluted environments might allow the development of a microbiota-based screening approach for environmental evaluation in ecotoxicological studies in aquatic ecosystems.
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Affiliation(s)
- Christian Deyvis Nolorbe-Payahua
- Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas - ICB, Campus Carreiros, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, 96203-900, Brazil
| | - Anderson Santos de Freitas
- Centro Interdisciplinar de Pesquisas em Biotecnologia - CIP-Biotec, Campus São Gabriel, Universidade Federal do Pampa, São Gabriel, RS, 97300-162, Brazil
| | - Luiz Fernando Wurdig Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia - CIP-Biotec, Campus São Gabriel, Universidade Federal do Pampa, São Gabriel, RS, 97300-162, Brazil
| | - Juliano Zanette
- Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas - ICB, Campus Carreiros, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, 96203-900, Brazil
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17
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Metabolic flux ratio analysis by parallel 13C labeling of isoprenoid biosynthesis in Rhodobacter sphaeroides. Metab Eng 2019; 57:228-238. [PMID: 31843486 DOI: 10.1016/j.ymben.2019.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/02/2019] [Accepted: 12/12/2019] [Indexed: 11/21/2022]
Abstract
Metabolic engineering for increased isoprenoid production often benefits from the simultaneous expression of the two naturally available isoprenoid metabolic routes, namely the 2-methyl-D-erythritol 4-phosphate (MEP) pathway and the mevalonate (MVA) pathway. Quantification of the contribution of these pathways to the overall isoprenoid production can help to obtain a better understanding of the metabolism within a microbial cell factory. Such type of investigation can benefit from 13C metabolic flux ratio studies. Here, we designed a method based on parallel labeling experiments (PLEs), using [1-13C]- and [4-13C]glucose as tracers to quantify the metabolic flux ratios in the glycolytic and isoprenoid pathways. By just analyzing a reporter isoprenoid molecule and employing only four equations, we could describe the metabolism involved from substrate catabolism to product formation. These equations infer 13C atom incorporation into the universal isoprenoid building blocks, isopentenyl-pyrophosphate (IPP) and dimethylallyl-pyrophosphate (DMAPP). Therefore, this renders the method applicable to the study of any of isoprenoid of interest. As proof of principle, we applied it to study amorpha-4,11-diene biosynthesis in the bacterium Rhodobacter sphaeroides. We confirmed that in this species the Entner-Doudoroff pathway is the major pathway for glucose catabolism, while the Embden-Meyerhof-Parnas pathway contributes to a lesser extent. Additionally, we demonstrated that co-expression of the MEP and MVA pathways caused a mutual enhancement of their metabolic flux capacity. Surprisingly, we also observed that the isoprenoid flux ratio remains constant under exponential growth conditions, independently from the expression level of the MVA pathway. Apart from proposing and applying a tool for studying isoprenoid biosynthesis within a microbial cell factory, our work reveals important insights from the co-expression of MEP and MVA pathways, including the existence of a yet unclear interaction between them.
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18
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Thomas PJ, Boller AJ, Satagopan S, Tabita FR, Cavanaugh CM, Scott KM. Isotope discrimination by form IC RubisCO from
Ralstonia eutropha
and
Rhodobacter sphaeroides
, metabolically versatile members of ‘
Proteobacteria
’ from aquatic and soil habitats. Environ Microbiol 2018; 21:72-80. [DOI: 10.1111/1462-2920.14423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/18/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Phaedra J. Thomas
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Amanda J. Boller
- Department of Integrative Biology University of South Florida Tampa FL USA
| | - Sriram Satagopan
- Department of Microbiology The Ohio State University Columbus OH USA
| | - F. Robert Tabita
- Department of Microbiology The Ohio State University Columbus OH USA
| | - Colleen M. Cavanaugh
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Kathleen M. Scott
- Department of Integrative Biology University of South Florida Tampa FL USA
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19
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Zhang L, Zhang S, Lv X, Qiu Z, Zhang Z, Yan L. Dissolved organic matter release in overlying water and bacterial community shifts in biofilm during the decomposition of Myriophyllum verticillatum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:929-937. [PMID: 29758915 DOI: 10.1016/j.scitotenv.2018.03.275] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/13/2018] [Accepted: 03/22/2018] [Indexed: 05/16/2023]
Abstract
This study investigated the alterations in biomass, nutrients and dissolved organic matter concentration in overlying water and determined the bacterial 16S rRNA gene in biofilms attached to plant residual during the decomposition of Myriophyllum verticillatum. The 55-day decomposition experimental results show that plant decay process can be well described by the exponential model, with the average decomposition rate of 0.037d-1. Total organic carbon, total nitrogen, and organic nitrogen concentrations increased significantly in overlying water during decomposition compared to control within 35d. Results from excitation emission matrix-parallel factor analysis showed humic acid-like and tyrosine acid-like substances might originate from plant degradation processes. Tyrosine acid-like substances had an obvious correlation to organic nitrogen and total nitrogen (p<0.01). Decomposition rates were positively related to pH, total organic carbon, oxidation-reduction potential and dissolved oxygen but negatively related to temperature in overlying water. Microbe densities attached to plant residues increased with decomposition process. The most dominant phylum was Bacteroidetes (>46%) at 7d, Chlorobi (20%-44%) or Proteobacteria (25%-34%) at 21d and Chlorobi (>40%) at 55d. In microbes attached to plant residues, sugar- and polysaccharides-degrading genus including Bacteroides, Blvii28, Fibrobacter, and Treponema dominated at 7d while Chlorobaculum, Rhodobacter, Methanobacterium, Thiobaca, Methanospirillum and Methanosarcina at 21d and 55d. These results gain the insight into the dissolved organic matter release and bacterial community shifts during submerged macrophytes decomposition.
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Affiliation(s)
- Lisha Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Xiaoyang Lv
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Zheng Qiu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Ziqiu Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Liying Yan
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
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20
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Schempp FM, Drummond L, Buchhaupt M, Schrader J. Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2247-2258. [PMID: 28418659 DOI: 10.1021/acs.jafc.7b00473] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terpenoid flavor and fragrance compounds are of high interest to the aroma industry. Microbial production offers an alternative sustainable access to the desired terpenoids independent of natural sources. Genetically engineered microorganisms can be used to synthesize terpenoids from cheap and renewable resources. Due to its modular architecture, terpenoid biosynthesis is especially well suited for the microbial cell factory concept: a platform host engineered for a high flux toward the central C5 prenyl diphosphate precursors enables the production of a broad range of target terpenoids just by varying the pathway modules converting the C5 intermediates to the product of interest. In this review typical terpenoid flavor and fragrance compounds marketed or under development by biotech and aroma companies are given, and the specificities of the aroma market are discussed. The main part of this work focuses on key strategies and recent advances to engineer microbes to become efficient terpenoid producers.
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Affiliation(s)
- Florence M Schempp
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Laura Drummond
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Markus Buchhaupt
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Jens Schrader
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
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21
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Chidgey JW, Jackson PJ, Dickman MJ, Hunter CN. PufQ regulates porphyrin flux at the haem/bacteriochlorophyll branchpoint of tetrapyrrole biosynthesis via interactions with ferrochelatase. Mol Microbiol 2017; 106:961-975. [PMID: 29030914 PMCID: PMC5725709 DOI: 10.1111/mmi.13861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 11/29/2022]
Abstract
Facultative phototrophs such as Rhodobacter sphaeroides can switch between heterotrophic and photosynthetic growth. This transition is governed by oxygen tension and involves the large-scale production of bacteriochlorophyll, which shares a biosynthetic pathway with haem up to protoporphyrin IX. Here, the pathways diverge with the insertion of Fe2+ or Mg2+ into protoporphyrin by ferrochelatase or magnesium chelatase, respectively. Tight regulation of this branchpoint is essential, but the mechanisms for switching between respiratory and photosynthetic growth are poorly understood. We show that PufQ governs the haem/bacteriochlorophyll switch; pufQ is found within the oxygen-regulated pufQBALMX operon encoding the reaction centre-light-harvesting photosystem complex. A pufQ deletion strain synthesises low levels of bacteriochlorophyll and accumulates the biosynthetic precursor coproporphyrinogen III; a suppressor mutant of this strain harbours a mutation in the hemH gene encoding ferrochelatase, substantially reducing ferrochelatase activity and increasing cellular bacteriochlorophyll levels. FLAG-immunoprecipitation experiments retrieve a ferrochelatase-PufQ-carotenoid complex, proposed to regulate the haem/bacteriochlorophyll branchpoint by directing porphyrin flux toward bacteriochlorophyll production under oxygen-limiting conditions. The co-location of pufQ and the photosystem genes in the same operon ensures that switching of tetrapyrrole metabolism toward bacteriochlorophyll is coordinated with the production of reaction centre and light-harvesting polypeptides.
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Affiliation(s)
- Jack W. Chidgey
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
| | - Philip J. Jackson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
- ChELSI Institute, Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield S1 3JDUK
| | - Mark J. Dickman
- ChELSI Institute, Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield S1 3JDUK
| | - C. Neil Hunter
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffield S10 2TNUK
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22
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Unveiling the compositional variety of cardiolipins in Rhodobacter sphaeroides by liquid chromatography with electrospray ionization and multistage collision-induced dissociation mass spectrometry. Anal Bioanal Chem 2017. [DOI: 10.1007/s00216-017-0444-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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23
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Tang G, Wang S, Lu D, Huang L, Li N, Luo L. Two-component regulatory system ActS/ActR is required for Sinorhizobium meliloti adaptation to oxidative stress. Microbiol Res 2017; 198:1-7. [DOI: 10.1016/j.micres.2017.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/14/2017] [Accepted: 01/17/2017] [Indexed: 11/16/2022]
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24
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Schwieterman EW, Cockell CS, Meadows VS. Nonphotosynthetic pigments as potential biosignatures. ASTROBIOLOGY 2015; 15:341-61. [PMID: 25941875 PMCID: PMC4442567 DOI: 10.1089/ast.2014.1178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Previous work on possible surface reflectance biosignatures for Earth-like planets has typically focused on analogues to spectral features produced by photosynthetic organisms on Earth, such as the vegetation red edge. Although oxygenic photosynthesis, facilitated by pigments evolved to capture photons, is the dominant metabolism on our planet, pigmentation has evolved for multiple purposes to adapt organisms to their environment. We present an interdisciplinary study of the diversity and detectability of nonphotosynthetic pigments as biosignatures, which includes a description of environments that host nonphotosynthetic biologically pigmented surfaces, and a lab-based experimental analysis of the spectral and broadband color diversity of pigmented organisms on Earth. We test the utility of broadband color to distinguish between Earth-like planets with significant coverage of nonphotosynthetic pigments and those with photosynthetic or nonbiological surfaces, using both 1-D and 3-D spectral models. We demonstrate that, given sufficient surface coverage, nonphotosynthetic pigments could significantly impact the disk-averaged spectrum of a planet. However, we find that due to the possible diversity of organisms and environments, and the confounding effects of the atmosphere and clouds, determination of substantial coverage by biologically produced pigments would be difficult with broadband colors alone and would likely require spectrally resolved data.
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Affiliation(s)
- Edward W. Schwieterman
- University of Washington Astronomy Department, Seattle, Washington, USA
- NAI Virtual Planetary Laboratory, Seattle, Washington, USA
- University of Washington Astrobiology Program, Seattle, Washington, USA
| | - Charles S. Cockell
- University of Edinburgh School of Physics and Astronomy, Edinburgh, UK
- UK Centre for Astrobiology, Edinburgh, UK
| | - Victoria S. Meadows
- University of Washington Astronomy Department, Seattle, Washington, USA
- NAI Virtual Planetary Laboratory, Seattle, Washington, USA
- University of Washington Astrobiology Program, Seattle, Washington, USA
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25
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An integrated approach to reconstructing genome-scale transcriptional regulatory networks. PLoS Comput Biol 2015; 11:e1004103. [PMID: 25723545 PMCID: PMC4344238 DOI: 10.1371/journal.pcbi.1004103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 12/23/2014] [Indexed: 11/24/2022] Open
Abstract
Transcriptional regulatory networks (TRNs) program cells to dynamically alter their gene expression in response to changing internal or environmental conditions. In this study, we develop a novel workflow for generating large-scale TRN models that integrates comparative genomics data, global gene expression analyses, and intrinsic properties of transcription factors (TFs). An assessment of this workflow using benchmark datasets for the well-studied γ-proteobacterium Escherichia coli showed that it outperforms expression-based inference approaches, having a significantly larger area under the precision-recall curve. Further analysis indicated that this integrated workflow captures different aspects of the E. coli TRN than expression-based approaches, potentially making them highly complementary. We leveraged this new workflow and observations to build a large-scale TRN model for the α-Proteobacterium Rhodobacter sphaeroides that comprises 120 gene clusters, 1211 genes (including 93 TFs), 1858 predicted protein-DNA interactions and 76 DNA binding motifs. We found that ~67% of the predicted gene clusters in this TRN are enriched for functions ranging from photosynthesis or central carbon metabolism to environmental stress responses. We also found that members of many of the predicted gene clusters were consistent with prior knowledge in R. sphaeroides and/or other bacteria. Experimental validation of predictions from this R. sphaeroides TRN model showed that high precision and recall was also obtained for TFs involved in photosynthesis (PpsR), carbon metabolism (RSP_0489) and iron homeostasis (RSP_3341). In addition, this integrative approach enabled generation of TRNs with increased information content relative to R. sphaeroides TRN models built via other approaches. We also show how this approach can be used to simultaneously produce TRN models for each related organism used in the comparative genomics analysis. Our results highlight the advantages of integrating comparative genomics of closely related organisms with gene expression data to assemble large-scale TRN models with high-quality predictions. The ever growing amount of genomic data enables the assembly of large-scale network models that can provide important new insights into living systems. However, assembly and validation of such large-scale models can be challenging, since we often lack sufficient information to make accurate predictions. This work describes a new approach for constructing large-scale transcriptional regulatory networks of individual cells. We show that the reconstructed network captures a significantly larger fraction of cellular regulatory processes than networks generated by other existing approaches. We predict this approach, with appropriate refinements, will allow reconstruction of large-scale transcriptional network models for a variety of other organisms. As we work towards modeling the function of cells or complex ecosystems, individually reconstructed network models of signaling, information transfer and metabolism, can be integrated to provide high information predictions and insights not otherwise obtainable.
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26
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Abstract
UNLABELLED Many pathways of carbon and energy metabolism are conserved across the phylogeny, but the networks that regulate their expression or activity often vary considerably among organisms. In this work, we show that two previously uncharacterized transcription factors (TFs) are direct regulators of genes encoding enzymes of central carbon and energy metabolism in the alphaproteobacterium Rhodobacter sphaeroides. The LacI family member CceR (RSP_1663) directly represses genes encoding enzymes in the Entner-Doudoroff pathway, while activating those encoding the F1F0 ATPase and enzymes of the tricarboxylic acid (TCA) cycle and gluconeogenesis, providing a direct transcriptional network connection between carbon and energy metabolism. We identified bases that are important for CceR DNA binding and showed that DNA binding by this TF is inhibited by 6-phosphogluconate. We also showed that the GntR family TF AkgR (RSP_0981) directly activates genes encoding several TCA cycle enzymes, and we identified conditions where its activity is increased. The properties of single and double ΔCceR and ΔAkgR mutants illustrate that these 2 TFs cooperatively regulate carbon and energy metabolism. Comparative genomic analysis indicates that CceR and AkgR orthologs are found in other alphaproteobacteria, where they are predicted to have a conserved function in regulating central carbon metabolism. Our characterization of CceR and AkgR has provided important new insight into the networks that control central carbon and energy metabolism in alphaproteobacteria that can be exploited to modify or engineer new traits in these widespread and versatile bacteria. IMPORTANCE To extract and conserve energy from nutrients, cells coordinate a set of metabolic pathways into integrated networks. Many pathways that conserve energy or interconvert metabolites are conserved across cells, but the networks regulating these processes are often highly variable. In this study, we characterize two previously unknown transcriptional regulators of carbon and energy metabolism that are conserved in alphaproteobacteria, a group of abundant, environmentally and biotechnologically important organisms. We identify the genes they regulate, the DNA sequences they recognize, the metabolite that controls the activity of one of the regulators, and conditions where they are required for growth. We provide important new insight into conserved cellular networks that can also be used to improve a variety of hosts for converting feedstock into valuable products.
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27
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Imam S, Fitzgerald CM, Cook EM, Donohue TJ, Noguera DR. Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides. PHOTOSYNTHESIS RESEARCH 2015; 123:167-182. [PMID: 25428581 DOI: 10.1007/s11120-014-0061-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
Obtaining a better understanding of the physiology and bioenergetics of photosynthetic microbes is an important step toward optimizing these systems for light energy capture or production of valuable commodities. In this work, we analyzed the effect of light intensity on bioproduction, biomass formation, and maintenance energy during photoheterotrophic growth of Rhodobacter sphaeroides. Using data obtained from steady-state bioreactors operated at varying dilution rates and light intensities, we found that irradiance had a significant impact on biomass yield and composition, with significant changes in photopigment, phospholipid, and biopolymer storage contents. We also observed a linear relationship between incident light intensity and H2 production rate between 3 and 10 W m(-2), with saturation observed at 100 W m(-2). The light conversion efficiency to H2 was also higher at lower light intensities. Photosynthetic maintenance energy requirements were also significantly affected by light intensity, with links to differences in biomass composition and the need to maintain redox homeostasis. Inclusion of the measured condition-dependent biomass and maintenance energy parameters and the measured photon uptake rate into a genome-scale metabolic model for R. sphaeroides (iRsp1140) significantly improved its predictive performance. We discuss how our analyses provide new insights into the light-dependent changes in bioenergetic requirements and physiology during photosynthetic growth of R. sphaeroides and potentially other photosynthetic organisms.
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Affiliation(s)
- Saheed Imam
- Program in Cellular and Molecular Biology, University of Wisconsin, Madison, WI, USA
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Imam S, Noguera DR, Donohue TJ. Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet 2014; 10:e1004837. [PMID: 25503406 PMCID: PMC4263372 DOI: 10.1371/journal.pgen.1004837] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 10/20/2014] [Indexed: 12/18/2022] Open
Abstract
Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis. Photosynthetic organisms are among the most abundant life forms on earth. Their unique ability to harvest solar energy and use it to fix atmospheric carbon dioxide is at the foundation of the global food chain. This paper reports the first comprehensive analysis of networks that control expression of photosynthesis genes using Rhodobacter sphaeroides, a microbe that has been studied for decades as a model of solar energy capture and other aspects of the photosynthetic lifestyle. We find a previously unappreciated complexity in the level of control of photosynthetic genes, while identifying new links between photosynthesis and central processes like iron availability. This organism is an ancestor of modern day plants, so our data can inform studies in other photosynthetic organisms and improve our ability to harness solar energy for food and industrial processes.
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Affiliation(s)
- Saheed Imam
- Program in Cellular and Molecular Biology, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin – Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Civil and Environmental Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Timothy J. Donohue
- Department of Bacteriology, University of Wisconsin – Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Peña-Castillo L, Mercer RG, Gurinovich A, Callister SJ, Wright AT, Westbye AB, Beatty JT, Lang AS. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. BMC Genomics 2014; 15:730. [PMID: 25164283 PMCID: PMC4158056 DOI: 10.1186/1471-2164-15-730] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 08/21/2014] [Indexed: 01/05/2023] Open
Abstract
Background The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-730) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St, John's, NL A1B 3X5, Canada.
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Kaluzhnaya OV, Itskovich VB. Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414060052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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A Rhodobacter sphaeroides protein mechanistically similar to Escherichia coli DksA regulates photosynthetic growth. mBio 2014; 5:e01105-14. [PMID: 24781745 PMCID: PMC4010833 DOI: 10.1128/mbio.01105-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
ABSTRACT DksA is a global regulatory protein that, together with the alarmone ppGpp, is required for the "stringent response" to nutrient starvation in the gammaproteobacterium Escherichia coli and for more moderate shifts between growth conditions. DksA modulates the expression of hundreds of genes, directly or indirectly. Mutants lacking a DksA homolog exhibit pleiotropic phenotypes in other gammaproteobacteria as well. Here we analyzed the DksA homolog RSP2654 in the more distantly related Rhodobacter sphaeroides, an alphaproteobacterium. RSP2654 is 42% identical and similar in length to E. coli DksA but lacks the Zn finger motif of the E. coli DksA globular domain. Deletion of the RSP2654 gene results in defects in photosynthetic growth, impaired utilization of amino acids, and an increase in fatty acid content. RSP2654 complements the growth and regulatory defects of an E. coli strain lacking the dksA gene and modulates transcription in vitro with E. coli RNA polymerase (RNAP) similarly to E. coli DksA. RSP2654 reduces RNAP-promoter complex stability in vitro with RNAPs from E. coli or R. sphaeroides, alone and synergistically with ppGpp, suggesting that even though it has limited sequence identity to E. coli DksA (DksAEc), it functions in a mechanistically similar manner. We therefore designate the RSP2654 protein DksARsp. Our work suggests that DksARsp has distinct and important physiological roles in alphaproteobacteria and will be useful for understanding structure-function relationships in DksA and the mechanism of synergy between DksA and ppGpp. IMPORTANCE The role of DksA has been analyzed primarily in the gammaproteobacteria, in which it is best understood for its role in control of the synthesis of the translation apparatus and amino acid biosynthesis. Our work suggests that DksA plays distinct and important physiological roles in alphaproteobacteria, including the control of photosynthesis in Rhodobacter sphaeroides. The study of DksARsp, should be useful for understanding structure-function relationships in the protein, including those that play a role in the little-understood synergy between DksA and ppGpp.
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Tikh IB, Quin MB, Schmidt-Dannert C. A tale of two reductases: extending the bacteriochlorophyll biosynthetic pathway in E. coli. PLoS One 2014; 9:e89734. [PMID: 24586995 PMCID: PMC3931815 DOI: 10.1371/journal.pone.0089734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/23/2014] [Indexed: 12/23/2022] Open
Abstract
The creation of a synthetic microbe that can harvest energy from sunlight to drive its metabolic processes is an attractive approach to the economically viable biosynthetic production of target compounds. Our aim is to design and engineer a genetically tractable non-photosynthetic microbe to produce light-harvesting molecules. Previously we created a modular, multienzyme system for the heterologous production of intermediates of the bacteriochlorophyll (BChl) pathway in E. coli. In this report we extend this pathway to include a substrate promiscuous 8-vinyl reductase that can accept multiple intermediates of BChl biosynthesis. We present an informative comparative analysis of homologues of 8-vinyl reductase from the model photosynthetic organisms Rhodobacter sphaeroides and Chlorobaculum tepidum. The first purification of the enzymes leads to their detailed biochemical and biophysical characterization. The data obtained reveal that the two 8-vinyl reductases are substrate promiscuous, capable of reducing the C8-vinyl group of Mg protoporphyrin IX, Mg protoporphyrin IX methylester, and divinyl protochlorophyllide. However, activity is dependent upon the presence of chelated Mg2+ in the porphyrin ring, with no activity against non-Mg2+ chelated intermediates observed. Additionally, CD analyses reveal that the two 8-vinyl reductases appear to bind the same substrate in a different fashion. Furthermore, we discover that the different rates of reaction of the two 8-vinyl reductases both in vitro, and in vivo as part of our engineered system, results in the suitability of only one of the homologues for our BChl pathway in E. coli. Our results offer the first insights into the different functionalities of homologous 8-vinyl reductases. This study also takes us one step closer to the creation of a nonphotosynthetic microbe that is capable of harvesting energy from sunlight for the biosynthesis of molecules of choice.
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Affiliation(s)
- Ilya B. Tikh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Maureen B. Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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Kim TG, Jeong SY, Cho KS. Functional rigidity of a methane biofilter during the temporal microbial succession. Appl Microbiol Biotechnol 2013; 98:3275-86. [DOI: 10.1007/s00253-013-5371-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 11/29/2022]
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Daub ME, Herrero S, Chung KR. Reactive oxygen species in plant pathogenesis: the role of perylenequinone photosensitizers. Antioxid Redox Signal 2013; 19:970-89. [PMID: 23259634 DOI: 10.1089/ars.2012.5080] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
SIGNIFICANCE Reactive oxygen species (ROS) play multiple roles in interactions between plants and microbes, both as host defense mechanisms and as mediators of pathogenic and symbiotic associations. One source of ROS in these interactions are photoactivated, ROS-generating perylenequinone pigments produced via polyketide metabolic pathways in plant-associated fungi. These natural products, including cercosporin, elsinochromes, hypocrellins, and calphostin C, are being utilized as medicinal agents, enzyme inhibitors, and in tumor therapy, but in nature, they play a role in the establishment of pathogenic associations between fungi and their plant hosts. RECENT ADVANCES Photoactivated perylenequinones are photosensitizers that use light energy to form singlet oxygen (¹O₂) and free radical oxygen species which damage cellular components based on localization of the perylenequinone molecule. Production of perylenequinones during infection commonly results in lipid peroxidation and membrane damage, leading to leakage of nutrients from cells into the intercellular spaces colonized by the pathogen. Perylenequinones show almost universal toxicity against organisms, including plants, mice, bacteria, and most fungi. The producing fungi are resistant, however, and serve as models for understanding resistance mechanisms. CRITICAL ISSUES Studies of resistance mechanisms by perylenequinone-producing fungi such as Cercospora species are leading to an understanding of cellular resistance to ¹O₂ and oxidative stress. Recent studies show commonalities between resistance mechanisms in these fungi with extensive studies of ¹O₂ and oxidative stress responses in photosynthetic organisms. FUTURE DIRECTIONS Such studies hold promise both for improved medical use and for engineering crop plants for disease resistance.
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Affiliation(s)
- Margaret E Daub
- Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USA.
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Imam S, Noguera DR, Donohue TJ. Global insights into energetic and metabolic networks in Rhodobacter sphaeroides. BMC SYSTEMS BIOLOGY 2013; 7:89. [PMID: 24034347 PMCID: PMC3849096 DOI: 10.1186/1752-0509-7-89] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/10/2013] [Indexed: 11/29/2022]
Abstract
Background Improving our understanding of processes at the core of cellular lifestyles can be aided by combining information from genetic analyses, high-throughput experiments and computational predictions. Results We combined data and predictions derived from phenotypic, physiological, genetic and computational analyses to dissect the metabolic and energetic networks of the facultative photosynthetic bacterium Rhodobacter sphaeroides. We focused our analysis on pathways crucial to the production and recycling of pyridine nucleotides during aerobic respiratory and anaerobic photosynthetic growth in the presence of an organic electron donor. In particular, we assessed the requirement for NADH/NADPH transhydrogenase enzyme, PntAB during respiratory and photosynthetic growth. Using high-throughput phenotype microarrays (PMs), we found that PntAB is essential for photosynthetic growth in the presence of many organic electron donors, particularly those predicted to require its activity to produce NADPH. Utilizing the genome-scale metabolic model iRsp1095, we predicted alternative routes of NADPH synthesis and used gene expression analyses to show that transcripts from a subset of the corresponding genes were conditionally increased in a ΔpntAB mutant. We then used a combination of metabolic flux predictions and mutational analysis to identify flux redistribution patterns utilized in the ΔpntAB mutant to compensate for the loss of this enzyme. Data generated from metabolic and phenotypic analyses of wild type and mutant cells were used to develop iRsp1140, an expanded genome-scale metabolic reconstruction for R. sphaeroides with improved ability to analyze and predict pathways associated with photosynthesis and other metabolic processes. Conclusions These analyses increased our understanding of key aspects of the photosynthetic lifestyle, highlighting the added importance of NADPH production under these conditions. It also led to a significant improvement in the predictive capabilities of a metabolic model for the different energetic lifestyles of a facultative organism.
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Affiliation(s)
- Saheed Imam
- Department of Bacteriology, University of Wisconsin, Madison, Suite 5166, Wisconsin Energy Institute, 1552 University Avenue, Madison, WI 53726-4084, USA.
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Chiu SW, Roberts MAJ, Leake MC, Armitage JP. Positioning of chemosensory proteins and FtsZ through the Rhodobacter sphaeroides cell cycle. Mol Microbiol 2013; 90:322-37. [PMID: 23944351 DOI: 10.1111/mmi.12366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2013] [Indexed: 12/28/2022]
Abstract
Bacterial chemotaxis depends on signalling through large protein complexes. Each cell must inherit a complex on division, suggesting some co-ordination with cell division. In Escherichia coli the membrane-spanning chemosensory complexes are polar and new static complexes form at pre-cytokinetic sites, ensuring positioning at the new pole after division and suggesting a role for the bacterial cytoskeleton. Rhodobacter sphaeroides has both membrane-associated and cytoplasmic, chromosome-associated chemosensory complexes. We followed the relative positions of the two chemosensory complexes, FtsZ and MreB in aerobic and in photoheterotrophic R. sphaeroides cells using fluorescence microscopy. FtsZ forms polar spots after cytokinesis, which redistribute to the midcell forming nodes from which FtsZ extends circumferentially to form the Z-ring. Membrane-associated chemosensory proteins form a number of dynamic unit-clusters with mature clusters containing about 1000 CheW(3) proteins. Individual clusters diffuse randomly within the membrane, accumulating at new poles after division but not colocalizing with either FtsZ or MreB. The cytoplasmic complex colocalizes with FtsZ at midcells in new-born cells. Before cytokinesis one complex moves to a daughter cell, followed by the second moving to the other cell. These data indicate that two homologous complexes use different mechanisms to ensure partitioning, and neither complex utilizes FtsZ or MreB for positioning.
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Affiliation(s)
- Sheng-Wen Chiu
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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Satoh S, Mimuro M, Tanaka A. Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences. PLoS One 2013; 8:e70290. [PMID: 23922968 PMCID: PMC3724816 DOI: 10.1371/journal.pone.0070290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 06/18/2013] [Indexed: 12/03/2022] Open
Abstract
Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.
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Affiliation(s)
- Soichirou Satoh
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Mamoru Mimuro
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
- CREST, Japan Science and Technology Agency, Sapporo, Japan
- * E-mail:
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Kim TG, Yun J, Hong SH, Cho KS. Effects of water temperature and backwashing on bacterial population and community in a biological activated carbon process at a water treatment plant. Appl Microbiol Biotechnol 2013; 98:1417-27. [DOI: 10.1007/s00253-013-5057-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 12/17/2022]
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Kojadinovic M, Armitage JP, Tindall MJ, Wadhams GH. Response kinetics in the complex chemotaxis signalling pathway of Rhodobacter sphaeroides. J R Soc Interface 2013; 10:20121001. [PMID: 23365194 DOI: 10.1098/rsif.2012.1001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chemotaxis is one of the best-characterized signalling systems in biology. It is the mechanism by which bacteria move towards optimal environments and is implicated in biofilm formation, pathogenesis and symbiosis. The properties of the bacterial chemosensory response have been described in detail for the single chemosensory pathway of Escherichia coli. We have characterized the properties of the chemosensory response of Rhodobacter sphaeroides, an α-proteobacterium with multiple chemotaxis pathways, under two growth conditions allowing the effects of protein expression levels and cell architecture to be investigated. Using tethered cell assays, we measured the responses of the system to step changes in concentration of the attractant propionate and show that, independently of the growth conditions, R. sphaeroides is chemotactic over at least five orders of magnitude and has a sensing profile following Weber's Law. Mathematical modelling also shows that, as E. coli, R. sphaeroides is capable of showing fold-change detection (FCD). Our results indicate that general features of bacterial chemotaxis such as the range and sensitivity of detection, adaptation times, adherence to Weber's Law and the presence of FCD may be integral features of chemotaxis systems in general, regardless of network complexity, protein expression levels and cellular architecture across different species.
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Affiliation(s)
- Mila Kojadinovic
- Department of Biochemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Network identification and flux quantification of glucose metabolism in Rhodobacter sphaeroides under photoheterotrophic H(2)-producing conditions. J Bacteriol 2011; 194:274-83. [PMID: 22056932 DOI: 10.1128/jb.05624-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nonsulfur purple bacteria that exhibit unusual metabolic versatility can produce hydrogen gas (H(2)) using the electrons derived from metabolism of organic compounds during photoheterotrophic growth. Here, based on (13)C tracer experiments, we identified the network of glucose metabolism and quantified intracellular carbon fluxes in Rhodobacter sphaeroides KD131 grown under H(2)-producing conditions. Moreover, we investigated how the intracellular fluxes in R. sphaeroides responded to knockout mutations in hydrogenase and poly-β-hydroxybutyrate synthase genes, which led to increased H(2) yield. The relative contribution of the Entner-Doudoroff pathway and Calvin-Benson-Bassham cycle to glucose metabolism differed significantly in hydrogenase-deficient mutants, and this flux change contributed to the increased formation of the redox equivalent NADH. Disruption of hydrogenase and poly-β-hydroxybutyrate synthase resulted in a significantly increased flux through the phosphoenolpyruvate carboxykinase and a reduced flux through the malic enzyme. A remarkable increase in the flux through the tricarboxylic acid cycle, a major NADH producer, was observed for the mutant strains. The in vivo regulation of the tricarboxylic acid cycle flux in photoheterotrophic R. sphaeroides was discussed based on the measurements of in vitro enzyme activities and intracellular concentrations of NADH and NAD(+). Overall, our results provide quantitative insights into how photoheterotrophic cells manipulate the metabolic network and redistribute intracellular fluxes to generate more electrons for increased H(2) production.
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Abstract
Aerobic respiration in bacteria, Archaea, and mitochondria is performed by oxygen reductase members of the heme-copper oxidoreductase superfamily. These enzymes are redox-driven proton pumps which conserve part of the free energy released from oxygen reduction to generate a proton motive force. The oxygen reductases can be divided into three main families based on evolutionary and structural analyses (A-, B- and C-families), with the B- and C-families evolving after the A-family. The A-family utilizes two proton input channels to transfer protons for pumping and chemistry, whereas the B- and C-families require only one. Generally, the B- and C-families also have higher apparent oxygen affinities than the A-family. Here we use whole cell proton pumping measurements to demonstrate differential proton pumping efficiencies between representatives of the A-, B-, and C-oxygen reductase families. The A-family has a coupling stoichiometry of 1 H(+)/e(-), whereas the B- and C-families have coupling stoichiometries of 0.5 H(+)/e(-). The differential proton pumping stoichiometries, along with differences in the structures of the proton-conducting channels, place critical constraints on models of the mechanism of proton pumping. Most significantly, it is proposed that the adaptation of aerobic respiration to low oxygen environments resulted in a concomitant reduction in energy conservation efficiency, with important physiological and ecological consequences.
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iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC SYSTEMS BIOLOGY 2011; 5:116. [PMID: 21777427 PMCID: PMC3152904 DOI: 10.1186/1752-0509-5-116] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Accepted: 07/21/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Rhodobacter sphaeroides is one of the best studied purple non-sulfur photosynthetic bacteria and serves as an excellent model for the study of photosynthesis and the metabolic capabilities of this and related facultative organisms. The ability of R. sphaeroides to produce hydrogen (H₂), polyhydroxybutyrate (PHB) or other hydrocarbons, as well as its ability to utilize atmospheric carbon dioxide (CO₂) as a carbon source under defined conditions, make it an excellent candidate for use in a wide variety of biotechnological applications. A genome-level understanding of its metabolic capabilities should help realize this biotechnological potential. RESULTS Here we present a genome-scale metabolic network model for R. sphaeroides strain 2.4.1, designated iRsp1095, consisting of 1,095 genes, 796 metabolites and 1158 reactions, including R. sphaeroides-specific biomass reactions developed in this study. Constraint-based analysis showed that iRsp1095 agreed well with experimental observations when modeling growth under respiratory and phototrophic conditions. Genes essential for phototrophic growth were predicted by single gene deletion analysis. During pathway-level analyses of R. sphaeroides metabolism, an alternative route for CO₂ assimilation was identified. Evaluation of photoheterotrophic H2 production using iRsp1095 indicated that maximal yield would be obtained from growing cells, with this predicted maximum ~50% higher than that observed experimentally from wild type cells. Competing pathways that might prevent the achievement of this theoretical maximum were identified to guide future genetic studies. CONCLUSIONS iRsp1095 provides a robust framework for future metabolic engineering efforts to optimize the solar- and nutrient-powered production of biofuels and other valuable products by R. sphaeroides and closely related organisms.
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New motion analysis system for characterization of the chemosensory response kinetics of Rhodobacter sphaeroides under different growth conditions. Appl Environ Microbiol 2011; 77:4082-8. [PMID: 21515726 DOI: 10.1128/aem.00341-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We developed a new set of software tools that enable the speed and response kinetics of large numbers of tethered bacterial cells to be rapidly measured and analyzed. The software provides precision, accuracy, and a good signal-to-noise ratio combined with ease of data handling and processing. The software was tested on the single-cell chemosensory response kinetics of large numbers of Rhodobacter sphaeroides cells grown under either aerobic or photoheterotrophic conditions and either in chemostats or in batch cultures, allowing the effects of growth conditions on responses to be accurately measured. Aerobically and photoheterotrophically grown R. sphaeroides exhibited significantly different chemosensory response kinetics and cell-to-cell variability in their responses to 100 μM propionate. A greater proportion of the population of aerobically grown cells responded to a 100 μM step decrease in propionate; they adapted faster and showed less cell-to-cell variability than photosynthetic populations. Growth in chemostats did not significantly reduce the measured cell to cell variability but did change the adaptation kinetics for photoheterotrophically grown cells.
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Kniggendorf AK, Gaul TW, Meinhardt-Wollweber M. Effects of ethanol, formaldehyde, and gentle heat fixation in confocal resonance Raman microscopy of purple nonsulfur bacteria. Microsc Res Tech 2011; 74:177-83. [DOI: 10.1002/jemt.20889] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Moskvin OV, Bolotin D, Wang A, Ivanov PS, Gomelsky M. Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacterium. Biosystems 2010; 103:125-31. [PMID: 21070832 DOI: 10.1016/j.biosystems.2010.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 10/29/2010] [Accepted: 10/31/2010] [Indexed: 01/10/2023]
Abstract
We present Rhodobase, a web-based meta-analytical tool for analysis of transcriptional regulation in a model anoxygenic photosynthetic bacterium, Rhodobacter sphaeroides. The gene association meta-analysis is based on the pooled data from 100 of R. sphaeroides whole-genome DNA microarrays. Gene-centric regulatory networks were visualized using the StarNet approach (Jupiter, D.C., VanBuren, V., 2008. A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PLoS ONE 3, e1717) with several modifications. We developed a means to identify and visualize operons and superoperons. We designed a framework for the cross-genome search for transcription factor binding sites that takes into account high GC-content and oligonucleotide usage profile characteristic of the R. sphaeroides genome. To facilitate reconstruction of directional relationships between co-regulated genes, we screened upstream sequences (-400 to +20bp from start codons) of all genes for putative binding sites of bacterial transcription factors using a self-optimizing search method developed here. To test performance of the meta-analysis tools and transcription factor site predictions, we reconstructed selected nodes of the R. sphaeroides transcription factor-centric regulatory matrix. The test revealed regulatory relationships that correlate well with the experimentally derived data. The database of transcriptional profile correlations, the network visualization engine and the optimized search engine for transcription factor binding sites analysis are available at http://rhodobase.org.
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Affiliation(s)
- Oleg V Moskvin
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.
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Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight. ISME JOURNAL 2009; 3:1402-19. [DOI: 10.1038/ismej.2009.74] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Chapalain A, Chevalier S, Orange N, Murillo L, Papadopoulos V, Feuilloley MGJ. Bacterial ortholog of mammalian translocator protein (TSPO) with virulence regulating activity. PLoS One 2009; 4:e6096. [PMID: 19564920 PMCID: PMC2699550 DOI: 10.1371/journal.pone.0006096] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 05/21/2009] [Indexed: 11/18/2022] Open
Abstract
The translocator protein (TSPO), previously designated as peripheral-type benzodiazepine receptor, is a protein mainly located in the outer mitochondrial membrane of eukaryotic cells. TSPO is implicated in major physiological functions and functionally associated with other proteins such as the voltage-dependent anionic channel, also designated as mitochondrial porin. Surprisingly, a TSPO-related protein was identified in the photosynthetic bacterium Rhodobacter sphaeroides but it was initially considered as a relict of evolution. In the present study we cloned a tspO gene in Pseudomonas fluorescens MF37, a non-photosynthetic eubacterium and we used bioinformatics tools to identify TSPO in the genome of 97 other bacteria. P. fluorescens TSPO was recognized by antibodies against mouse protein and by PK 11195, an artificial ligand of mitochondrial TSPO. As in eukaryotes, bacterial TSPO appears functionally organized as a dimer and the apparent Kd for PK 11195 is in the same range than for its eukaryotic counterpart. When P. fluorescens MF37 was treated with PK 11195 (10(-5) M) adhesion to living or artificial surfaces and biofilm formation activity were increased. Conversely, the apoptotic potential of bacteria on eukaryotic cells was significantly reduced. This effect of PK11195 was abolished in a mutant of P. fluorescens MF37 deficient for its major outer membrane porin, OprF. The present results demonstrate the existence of a bacterial TSPO that shares common structural and functional characteristics with its mammalian counterpart. This protein, apparently involved in adhesion and virulence, reveals the existence of a possible new inter kingdom signalling system and suggests that the human microbiome should be involuntarily exposed to the evolutionary pressure of benzodiazepines and related molecules. This discovery also represents a promising opportunity for the development of alternative antibacterial strategies.
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Affiliation(s)
- Annelise Chapalain
- Laboratory of Cold Microbiology UPRES EA4312, University of Rouen, Evreux, France
- ADIPpharm, Evreux, France
| | - Sylvie Chevalier
- Laboratory of Cold Microbiology UPRES EA4312, University of Rouen, Evreux, France
| | - Nicole Orange
- Laboratory of Cold Microbiology UPRES EA4312, University of Rouen, Evreux, France
- ADIPpharm, Evreux, France
| | - Laurence Murillo
- Laboratory of Cold Microbiology UPRES EA4312, University of Rouen, Evreux, France
| | - Vassilios Papadopoulos
- The Research Institute of the McGill University Health Centre & Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Marc G. J. Feuilloley
- Laboratory of Cold Microbiology UPRES EA4312, University of Rouen, Evreux, France
- ADIPpharm, Evreux, France
- * E-mail:
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Regulation of gene expression by PrrA in Rhodobacter sphaeroides 2.4.1: role of polyamines and DNA topology. J Bacteriol 2009; 191:4341-52. [PMID: 19411327 DOI: 10.1128/jb.00243-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the present study, we show in vitro binding of PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, to the PrrA site 2, within the RSP3361 locus. Specific binding, as shown by competition experiments, requires the phosphorylation of PrrA. The binding affinity of PrrA for site 2 was found to increase 4- to 10-fold when spermidine was added to the binding reaction. The presence of extracellular concentrations of spermidine in growing cultures of R. sphaeroides gave rise to a twofold increase in the expression of the photosynthesis genes pucB and pufB, as well as the RSP3361 gene, under aerobic growth conditions, as shown by the use of lacZ transcriptional fusions, and led to the production of light-harvesting spectral complexes. In addition, we show that negative supercoiling positively regulates the expression of the RSP3361 gene, as well as pucB. We show the importance of supercoiling through an evaluation of the regulation of gene expression in situ by supercoiling, in the case of the former gene, as well as using the DNA gyrase inhibitor novobiocin. We propose that polyamines and DNA supercoiling act synergistically to regulate expression of the RSP3361 gene, partly by affecting the affinity of PrrA binding to the PrrA site 2 within the RSP3361 gene.
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Half-Site DNA sequence and spacing length contributions to PrrA binding to PrrA site 2 of RSP3361 in Rhodobacter sphaeroides 2.4.1. J Bacteriol 2009; 191:4353-64. [PMID: 19411326 DOI: 10.1128/jb.00244-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The consensus DNA binding sequence for PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, is poorly defined. We have performed mutational analysis of PrrA site 2, of the RSP3361 gene, to which PrrA binds in vitro (J. M. Eraso and S. Kaplan, J. Bacteriol. 191:4341-4352, 2009), to further define the consensus sequence for DNA binding. Two half-sites of equal length, containing 6 nucleotides each, were required for PrrA binding to this DNA sequence. Systematic nucleotide substitutions in both inverted half-sites led to a decrease in binding affinity of phosphorylated PrrA in vitro, the level of which was dependent on the substitution. The reduced binding affinities were confirmed by competition experiments and led to proportional decreases in the expression of lacZ transcriptional fusions to the RSP3361 gene in vivo. The 5-nucleotide spacer region between the half-sites was found to be optimal for PrrA binding to the wild-type half-sites, as shown by decreased PrrA DNA binding affinities to synthetic DNA sequences without spacer regions or with spacer regions ranging from 1 to 10 nucleotides. The synthetic spacer region alleles also showed decreased gene expression in vivo when analyzed using lacZ transcriptional fusions. We have studied three additional DNA sequences to which PrrA binds in vitro. They are located in the regulatory regions of genes positively regulated by PrrA and contain spacer regions with 5 or 8 nucleotides. We demonstrate that PrrA can bind in vitro to DNA sequences with different lengths in the spacer regions between the half-sites.
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