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Bai M, He J, Zheng F, Lv S, Wang Z, Hrynsphan D, Savitskaya T, Chen J. Gene cloning, expression and performance validation of nitric oxide dismutase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173455. [PMID: 38782282 DOI: 10.1016/j.scitotenv.2024.173455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Nitrous oxide (N2O) is a significant contributor to global warming and possesses an ozone-depleting impact nearly 298 times that of CO2. To reduce N2O emissions, the newly-discovered nod gene which can directly convert NO into N2 and O2 was successfully cloned from the anaerobic denitrification sludge. The recombinant plasmid containing the nod gene was built, and the expression of nod gene in Escherichia coli was determined, leading to the construction of recombinant engineering bacteria. Results showed that the recombinant engineering bacteria E. coli BL21 (DE3)-pET28a-nod could autonomously degrade NO, with a degradation rate of 72 % within 48 h, and could produce 2479.72 ppm of N2 and 75.12 mL of O2. The cumulative O2 production of the sludge sample and recombinant E. coli within 8 h was 1.75 mL and 8.45 mL, respectively. The cumulative O2 production of recombinant E. coli was at least 4.82 times higher than that of the sludge sample. The investigation proposed a new biodegradation pathway for nitrogen pollution.
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Affiliation(s)
- Mengwei Bai
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiamei He
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fengzhen Zheng
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Sini Lv
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zeyu Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Dzmitry Hrynsphan
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk 220030, Belarus
| | - Tatsiana Savitskaya
- Research Institute of Physical and Chemical Problems, Belarusian State University, Minsk 220030, Belarus
| | - Jun Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China.
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Miralles-Robledillo JM, Martínez-Espinosa RM, Pire C. Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis. Appl Environ Microbiol 2024; 90:e0057124. [PMID: 38814058 PMCID: PMC11218638 DOI: 10.1128/aem.00571-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell, such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin-like transcriptional activators, proteins harboring a domain of unknown function (DUF2249), and cyanoglobin. In addition, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.IMPORTANCEDenitrification, a fundamental process within the nitrogen cycle, has been subject to extensive investigation due to its close association with anthropogenic activities, and its contribution to the global warming issue, mainly through the release of N2O emissions. Although our comprehension of denitrification and its implications is generally well established, most studies have been conducted in non-extreme environments with mesophilic microorganisms. Consequently, there is a significant knowledge gap concerning extremophilic denitrifiers, particularly those inhabiting hypersaline environments. The significance of this research was to delve into the process of haloarchaeal denitrification, utilizing the complete denitrifier haloarchaeon Haloferax mediterranei as a model organism. This research led to the analysis of the metabolic state of this microorganism under denitrifying conditions and the identification of regulatory signals and genes encoding proteins potentially involved in this pathway, serving as a valuable resource for future molecular studies.
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Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
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3
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Schaeffer RD, Zhang J, Medvedev KE, Kinch LN, Cong Q, Grishin NV. ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. PLoS Comput Biol 2024; 20:e1011586. [PMID: 38416793 PMCID: PMC10927120 DOI: 10.1371/journal.pcbi.1011586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/11/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
Protein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development of biological insights. Using our Evolutionary Classification of Protein Domains (ECOD) from experimental structures as a basis for classification, we describe the detection and cataloging of domains from 48 whole proteomes deposited in the AlphaFold Database. On average, we can provide positive classification (either of domains or other identifiable non-domain regions) for 90% of residues in all proteomes. We classified 746,349 domains from 536,808 proteins comprised of over 226,424,000 amino acid residues. We examine the varying populations of homologous groups in both eukaryotes and bacteria. In addition to containing a higher fraction of disordered regions and unassigned domains, eukaryotes show a higher proportion of repeated proteins, both globular and small repeats. We enumerate those highly populated domains that are shared in both eukaryotes and bacteria, such as the Rossmann domains, TIM barrels, and P-loop domains. Additionally, we compare the sampling of homologous groups from this whole proteome set against our stable ECOD reference and discuss groups that have been enriched by structure predictions. Finally, we discuss the implication of these results for protein target selection for future classification strategies for very large protein sets.
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Affiliation(s)
- R. Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kirill E. Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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Smiley MK, Sekaran DC, Forouhar F, Wolin E, Jovanovic M, Price-Whelan A, Dietrich LEP. MpaR-driven expression of an orphan terminal oxidase subunit supports Pseudomonas aeruginosa biofilm respiration and development during cyanogenesis. mBio 2024; 15:e0292623. [PMID: 38112469 PMCID: PMC10790758 DOI: 10.1128/mbio.02926-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Cyanide is an inhibitor of heme-copper oxidases, which are required for aerobic respiration in all eukaryotes and many prokaryotes. This fast-acting poison can arise from diverse sources, but mechanisms by which bacteria sense it are poorly understood. We investigated the regulatory response to cyanide in the pathogenic bacterium Pseudomonas aeruginosa, which produces cyanide as a virulence factor. Although P. aeruginosa has the capacity to produce a cyanide-resistant oxidase, it relies primarily on heme-copper oxidases and even makes additional heme-copper oxidase proteins specifically under cyanide-producing conditions. We found that the protein MpaR controls expression of cyanide-inducible genes in P. aeruginosa and elucidated the molecular details of this regulation. MpaR contains a DNA-binding domain and a domain predicted to bind pyridoxal phosphate (vitamin B6), a compound that is known to react spontaneously with cyanide. These observations provide insight into the understudied phenomenon of cyanide-dependent regulation of gene expression in bacteria.
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Affiliation(s)
- Marina K. Smiley
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Doran C. Sekaran
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Farhad Forouhar
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Erica Wolin
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Lars E. P. Dietrich
- Department of Biological Sciences, Columbia University, New York, New York, USA
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Smiley MK, Sekaran DC, Price-Whelan A, Dietrich LE. Cyanide-dependent control of terminal oxidase hybridization by Pseudomonas aeruginosa MpaR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543164. [PMID: 37398129 PMCID: PMC10312525 DOI: 10.1101/2023.05.31.543164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Pseudomonas aeruginosa is a common, biofilm-forming pathogen that exhibits complex pathways of redox metabolism. It produces four different types of terminal oxidases for aerobic respiration, and for one of these-the cbb3-type terminal oxidases-it has the capacity to produce at least 16 isoforms encoded by partially redundant operons. It also produces small-molecule virulence factors that interact with the respiratory chain, including the poison cyanide. Previous studies had indicated a role for cyanide in activating expression of an "orphan" terminal oxidase subunit gene called ccoN4 and that the product contributes to P. aeruginosa cyanide resistance, fitness in biofilms, and virulence-but the mechanisms underlying this process had not been elucidated. Here, we show that the regulatory protein MpaR, which is predicted to be a pyridoxal phosphate-binding transcription factor and is encoded just upstream of ccoN4, controls ccoN4 expression in response to endogenous cyanide. Paradoxically, we find that cyanide production is required to support CcoN4's contribution to respiration in biofilms. We identify a palindromic motif required for cyanide- and MpaR-dependent expression of ccoN4 and co-expressed, adjacent loci. We also characterize the regulatory logic of this region of the chromosome. Finally, we identify residues in the putative cofactor-binding pocket of MpaR that are required for ccoN4 expression. Together, our findings illustrate a novel scenario in which the respiratory toxin cyanide acts as a signal to control gene expression in a bacterium that produces the compound endogenously.
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Affiliation(s)
- Marina K. Smiley
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Doran C. Sekaran
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10025
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10025
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6
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Glass JB, Elbon CE, Williams LD. Something old, something new, something borrowed, something blue: the anaerobic microbial ancestry of aerobic respiration. Trends Microbiol 2023; 31:135-141. [PMID: 36058785 DOI: 10.1016/j.tim.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
Aerobic respiration evolved by bricolage, with modules cobbled together as microbial biochemistry coevolved with Earth's geochemistry. The mitochondrial electron transport chain represents a patchwork of respiratory modules inherited from microbial methanogenesis, iron oxidation, anoxygenic photosynthesis, and denitrification pathways, and preserves a biochemical record of Earth's redox environment over its four-billion-year history. Imprints of the anoxic early Earth are recognizable in Complex I's numerous iron-sulfur cofactors and vestigial binding sites for ferredoxin, nickel-iron, and molybdopterin, whereas the more recent advent of oxygen as a terminal electron acceptor necessitated use of heme and copper cofactors by Complex IV. Bricolage of respiratory complexes resulted in supercomplexes for improved electron transfer efficiency in some bacteria and archaea, and in many eukaryotes. Accessory subunits evolved to wrap mitochondrial supercomplexes for improved assembly and stability. Environmental microbes with 'fossil' proteins that are similar to ancestral forms of the respiratory complexes deserve further scrutiny and may reveal new insights on the evolution of aerobic respiration.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Claire E Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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Blanquet P, Silva L, Catrice O, Bruand C, Carvalho H, Meilhoc E. Sinorhizobium meliloti Controls Nitric Oxide-Mediated Post-Translational Modification of a Medicago truncatula Nodule Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1353-63. [PMID: 26422404 DOI: 10.1094/mpmi-05-15-0118-r] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nitric oxide (NO) is involved in various plant-microbe interactions. In the symbiosis between soil bacterium Sinorhizobium meliloti and model legume Medicago truncatula, NO is required for an optimal establishment of the interaction but is also a signal for nodule senescence. Little is known about the molecular mechanisms responsible for NO effects in the legume-rhizobium interaction. Here, we investigate the contribution of the bacterial NO response to the modulation of a plant protein post-translational modification in nitrogen-fixing nodules. We made use of different bacterial mutants to finely modulate NO levels inside M. truncatula root nodules and to examine the consequence on tyrosine nitration of the plant glutamine synthetase, a protein responsible for assimilation of the ammonia released by nitrogen fixation. Our results reveal that S. meliloti possesses several proteins that limit inactivation of plant enzyme activity via NO-mediated post-translational modifications. This is the first demonstration that rhizobia can impact the course of nitrogen fixation by modulating the activity of a plant protein.
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Affiliation(s)
- Pauline Blanquet
- 1 Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes, UMR441, Castanet-Tolosan, France
- 2 Centre National de la Recherche Scientifique, Laboratoire des Interactions Plantes-Microorganismes, UMR2594, Castanet-Tolosan, France; and
| | - Liliana Silva
- 3 Laboratório de Biologia Molecular da Assimilação do Azoto, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Olivier Catrice
- 1 Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes, UMR441, Castanet-Tolosan, France
- 2 Centre National de la Recherche Scientifique, Laboratoire des Interactions Plantes-Microorganismes, UMR2594, Castanet-Tolosan, France; and
| | - Claude Bruand
- 1 Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes, UMR441, Castanet-Tolosan, France
- 2 Centre National de la Recherche Scientifique, Laboratoire des Interactions Plantes-Microorganismes, UMR2594, Castanet-Tolosan, France; and
| | - Helena Carvalho
- 3 Laboratório de Biologia Molecular da Assimilação do Azoto, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Eliane Meilhoc
- 1 Institut National de la Recherche Agronomique, Laboratoire des Interactions Plantes-Microorganismes, UMR441, Castanet-Tolosan, France
- 2 Centre National de la Recherche Scientifique, Laboratoire des Interactions Plantes-Microorganismes, UMR2594, Castanet-Tolosan, France; and
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Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Large-scale determination of previously unsolved protein structures using evolutionary information. eLife 2015; 4:e09248. [PMID: 26335199 PMCID: PMC4602095 DOI: 10.7554/elife.09248] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 08/30/2015] [Indexed: 12/18/2022] Open
Abstract
The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available. These models, which are posted online for public access, provide structural information for the over 400,000 proteins belonging to the 58 families and suggest hypotheses about mechanism for the subset for which the function is known, and hypotheses about function for the remainder.
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Affiliation(s)
- Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Lisa Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Yuxing Liao
- Department of Biophysics, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - David E Kim
- Department of Biochemistry, University of Washington, Seattle, United States
| | | | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Biophysics, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, United States
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Xu S, Andrews D, Hill BC. The affinity of yeast and bacterial SCO proteins for CU(I) and CU(II). A capture and release strategy for copper transfer. Biochem Biophys Rep 2015; 4:10-19. [PMID: 29124182 PMCID: PMC5668878 DOI: 10.1016/j.bbrep.2015.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/11/2015] [Accepted: 08/13/2015] [Indexed: 12/20/2022] Open
Abstract
SCO (Synthesis of Cytochrome c Oxidase) proteins are present in prokaryotic and eukaryotic cells, and are often required for efficient synthesis of the respiratory enzyme cytochrome c oxidase. The Bacillus subtilis version of SCO (i.e., BsSCO) has much greater affinity for Cu(II) than it does for Cu(I) (Davidson and Hill, 2009), and this has been contrasted to mitochondrial SCO proteins that are characterized as being specific for Cu(I) (Nittis, George and Winge, 2001). This differential affinity has been proposed to reflect the different physiological environments in which these two members of the SCO protein family reside. In this study the affinity of mitochondrial SCO1 from yeast is compared directly to that of BsSCO in vitro. We find that the yeast SCO1 protein has similar preference for Cu(II) over Cu(I), as does BsSCO. We propose a mechanism for SCO function which would involve high-affinity binding to capture Cu(II), and relatively weak binding of Cu(I) to facilitate copper transfer. Yeast SCO1 prefers Cu(II) over Cu(I) by many orders of magnitude. Yeast SCO1 has similar copper-species preference as a bacterial SCO protein. High affinity binding of Cu(II) by SCO may be initial step in copper transfer. Conversion of SCO-Cu(II) to SCO-Cu(I) is required for copper transfer. A second cysteine pair in yeast SCO1 may be involved in redox sensing.
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Affiliation(s)
- Shuai Xu
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L3N6 Canada
| | - Diann Andrews
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L3N6 Canada
| | - Bruce C. Hill
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L3N6 Canada
- Protein Function Discovery Research Group, Queen’s University, Kingston, ON K7L3N6 Canada
- Corresponding author at: Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L3N6 Canada.Department of Biomedical and Molecular Sciences, Queen’s UniversityKingstonON K7L3N6Canada
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