1
|
Sourice M, Oriol C, Aubert C, Mandin P, Py B. Genetic dissection of the bacterial Fe-S protein biogenesis machineries. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119746. [PMID: 38719030 DOI: 10.1016/j.bbamcr.2024.119746] [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: 01/25/2024] [Revised: 04/12/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
Iron‑sulfur (Fe-S) clusters are one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters are essential cofactors for the activity of a large variety of metalloproteins that play crucial physiological roles. Fe-S protein biogenesis is a complex process that starts with the acquisition of the elements (iron and sulfur atoms) and their assembly into an Fe-S cluster that is subsequently inserted into the target proteins. The Fe-S protein biogenesis is ensured by multiproteic systems conserved across all domains of life. Here, we provide an overview on how bacterial genetics approaches have permitted to reveal and dissect the Fe-S protein biogenesis process in vivo.
Collapse
Affiliation(s)
- Mathieu Sourice
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Charlotte Oriol
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Pierre Mandin
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies et Biotechnologie, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France.
| |
Collapse
|
2
|
Abstract
Building iron-sulfur (Fe-S) clusters and assembling Fe-S proteins are essential actions for life on Earth. The three processes that sustain life, photosynthesis, nitrogen fixation, and respiration, require Fe-S proteins. Genes coding for Fe-S proteins can be found in nearly every sequenced genome. Fe-S proteins have a wide variety of functions, and therefore, defective assembly of Fe-S proteins results in cell death or global metabolic defects. Compared to alternative essential cellular processes, there is less known about Fe-S cluster synthesis and Fe-S protein maturation. Moreover, new factors involved in Fe-S protein assembly continue to be discovered. These facts highlight the growing need to develop a deeper biological understanding of Fe-S cluster synthesis, holo-protein maturation, and Fe-S cluster repair. Here, we outline bacterial strategies used to assemble Fe-S proteins and the genetic regulation of these processes. We focus on recent and relevant findings and discuss future directions, including the proposal of using Fe-S protein assembly as an antipathogen target.
Collapse
|
3
|
Das M, Dewan A, Shee S, Singh A. The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis. Antioxidants (Basel) 2021; 10:antiox10070997. [PMID: 34201508 PMCID: PMC8300815 DOI: 10.3390/antiox10070997] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 12/02/2022] Open
Abstract
Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2−). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.
Collapse
|
4
|
Nie X, Jäger A, Börner J, Klug G. Interplay between formation of photosynthetic complexes and expression of genes for iron-sulfur cluster assembly in Rhodobacter sphaeroides? PHOTOSYNTHESIS RESEARCH 2021; 147:39-48. [PMID: 33064275 PMCID: PMC7728643 DOI: 10.1007/s11120-020-00789-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Formation of photosynthetic complexes leads to a higher demand for Fe-S clusters. We hypothesized that in the facultative phototrophic alpha-proteobacterium Rhodobacter sphaeroides expression of the isc-suf operon for Fe-S cluster formation may be increased under conditions that promote formation of photosynthetic complexes and that, vice versa, lack of the IscR regulator may also affect photosynthesis gene expression. To test this hypothesis, we monitored the activities of the isc-suf sense and anti-sense promoters under different growth conditions and in mutants which are impaired in formation of photosynthetic complexes. We also tested expression of photosynthesis genes in a mutant lacking the IscR regulator. Our results are not in agreement with a co-regulation of the Isc-Suf system and the photosynthetic apparatus at level of transcription. We provide evidence that, coordination of the systems occurs at post-transcriptional levels. Increased levels of isc-suf mRNAs under conditions promoting formation of photosynthetic complexes are due to higher RNA stability.
Collapse
Affiliation(s)
- Xin Nie
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, 610500, China
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany.
| |
Collapse
|
5
|
SufR, a [4Fe-4S] Cluster-Containing Transcription Factor, Represses the sufRBDCSU Operon in Streptomyces avermitilis Iron-Sulfur Cluster Assembly. Appl Environ Microbiol 2020; 86:AEM.01523-20. [PMID: 32680866 DOI: 10.1128/aem.01523-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/14/2020] [Indexed: 01/21/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous and versatile inorganic cofactors that are crucial for many fundamental bioprocesses in nearly all organisms. How cells maintain Fe-S cluster homeostasis is not well understood in Gram-positive bacteria. Genomic analysis showed that the Suf system, which is encoded by the sufRBDCSU operon, is the sole Fe-S cluster assembly system in the genus Streptomyces Streptomyces avermitilis is the industrial producer of avermectins, which are widely used as agricultural pesticides and antiparasitic agents. sufR (SAV6324) encodes a putative ArsR-family transcriptional regulator, which was characterized as a repressor of the sufRBDCSU operon in this investigation. Spectroscopy and mass spectrometry demonstrated that anaerobically isolated SufR contained an oxidation-sensitive [4Fe-4S] cluster and existed as a homodimer. Electrophoretic mobility shift assays (EMSAs) and DNase I footprinting analyses revealed that [4Fe-4S]-SufR bound specifically and tightly to a 14-bp palindromic sequence (CAAC-N6-GTTG) in the promoter region of the sufR operon, repressing expression of the sufRBDCSU operon. The presence of the [4Fe-4S] cluster is critical for the DNA-binding activity of SufR. Cys182, Cys195, and Cys223 in the C-terminal region of SufR are essential for [4Fe-4S] cluster coordination, but Cys178 is not. The fourth non-Cys ligand in coordination of the [4Fe-4S] cluster for SufR remains to be identified. The findings clarify the transcriptional control of the suf operon by [4Fe-4S] SufR to satisfy the various Fe-S cluster demands. SufR senses the intracellular Fe-S cluster status and modulates the expression of the sole Fe-S cluster assembly system via its Fe-S cluster occupancy.IMPORTANCE Fe-S clusters function as cofactors of proteins controlling diverse biological processes, such as respiration, photosynthesis, nitrogen fixation, DNA replication, and gene regulation. The mechanism of how Actinobacteria regulate the expression of the sole Fe-S cluster assembly system in response to the various Fe-S cluster demands remains to be elucidated. In this study, we showed that SufR functions as a transcriptional repressor of the sole Fe-S cluster assembly system in the avermectin producer S. avermitilis [4Fe-4S]-SufR binds to the promoter region of the suf operon and represses its expression. When Fe-S cluster levels are insufficient, SufR loses its [4Fe-4S] cluster and DNA-binding activity. Apo-SufR dissociates from the promoter region of suf operon, and the expression of the suf system is strongly increased by derepression to promote the synthesis of Fe-S clusters. The study clarifies how Streptomyces maintains its Fe-S cluster homeostasis through the activity of SufR to modulate the various Fe-S cluster demands.
Collapse
|
6
|
FurA-Dependent Microcystin Synthesis under Copper Stress in Microcystis aeruginosa. Microorganisms 2020; 8:microorganisms8060832. [PMID: 32492911 PMCID: PMC7356878 DOI: 10.3390/microorganisms8060832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 11/17/2022] Open
Abstract
Massive blooms of cyanobacteria frequently occur with microcystin (MC) production. Cyanobacteria are exposed to copper stresses such as copper algaecides which are often used to remove cyanobacterial blooms. However, copper increased the MC production of cyanobacteria, and the underlying mechanism remains unclear. The present study investigated the relationship between copper exposure (0.5 and 3 µM) and MC synthesis in Microcystis aeruginosa PCC 7806. The study concluded that the content of intracellular MCs increased by nearly two times both in 0.5 and 3 µM copper. High-throughput RNA sequencing (RNA-seq) provided evidence that copper mainly attacked Fe-S clusters, with evidence of changes in iron, sulfur, iron uptake regulators (fur), glutaredoxins and dehydratase genes. The transcription of numbers of genes implicated in iron uptake, MC synthesis and furA was also evaluated with quantitative real-time PCR (qRT-PCR). In these three Cu treatment groups, the amount of MCs increased as copper elevated. As the expression of mcyD gene was directly regulated by FurA and copper ions affected the expression of the FurA-related genes, we believed that MC synthesis genes were controlled by copper. This study has made a further understanding of the mechanism of the increase in MC synthesis of M. aeruginosa PCC 7806 treated with copper-based algaecides. We aimed to understand the mechanism of copper ion influencing the synthesis of MCs.
Collapse
|
7
|
Baussier C, Fakroun S, Aubert C, Dubrac S, Mandin P, Py B, Barras F. Making iron-sulfur cluster: structure, regulation and evolution of the bacterial ISC system. Adv Microb Physiol 2020; 76:1-39. [PMID: 32408945 DOI: 10.1016/bs.ampbs.2020.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron sulfur (Fe-S) clusters rank among the most ancient and conserved prosthetic groups. Fe-S clusters containing proteins are present in most, if not all, organisms. Fe-S clusters containing proteins are involved in a wide range of cellular processes, from gene regulation to central metabolism, via gene expression, RNA modification or bioenergetics. Fe-S clusters are built by biogenesis machineries conserved throughout both prokaryotes and eukaryotes. We focus mostly on bacterial ISC machinery, but not exclusively, as we refer to eukaryotic ISC system when it brings significant complementary information. Besides covering the structural and regulatory aspects of Fe-S biogenesis, this review aims to highlight Fe-S biogenesis facets remaining matters of discussion, such as the role of frataxin, or the link between fatty acid metabolism and Fe-S homeostasis. Last, we discuss recent advances on strategies used by different species to make and use Fe-S clusters in changing redox environmental conditions.
Collapse
Affiliation(s)
- Corentin Baussier
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Soufyan Fakroun
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Corinne Aubert
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Sarah Dubrac
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
| | - Pierre Mandin
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, CNRS-Aix Marseille Université, UMR 7283, Institut de Microbiologie de la Méditerranée, Institut de Microbiologie, Bioénergies et Biotechnologies, Marseille, France
| | - Frédéric Barras
- Stress Adaptation and Metabolism Unit, Department of Microbiology, Institut Pasteur, Paris, France; ERL CNRS 6002, CNRS, Paris, France
| |
Collapse
|
8
|
Gao F. Iron-Sulfur Cluster Biogenesis and Iron Homeostasis in Cyanobacteria. Front Microbiol 2020; 11:165. [PMID: 32184761 PMCID: PMC7058544 DOI: 10.3389/fmicb.2020.00165] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/23/2020] [Indexed: 01/23/2023] Open
Abstract
Iron–sulfur (Fe–S) clusters are ancient and ubiquitous cofactors and are involved in many important biological processes. Unlike the non-photosynthetic bacteria, cyanobacteria have developed the sulfur utilization factor (SUF) mechanism as their main assembly pathway for Fe–S clusters, supplemented by the iron–sulfur cluster and nitrogen-fixing mechanisms. The SUF system consists of cysteine desulfurase SufS, SufE that can enhance SufS activity, SufBC2D scaffold complex, carrier protein SufA, and regulatory repressor SufR. The S source for the Fe–S cluster assembly mainly originates from L-cysteine, but the Fe donor remains elusive. This minireview mainly focuses on the biogenesis pathway of the Fe–S clusters in cyanobacteria and its relationship with iron homeostasis. Future challenges of studying Fe–S clusters in cyanobacteria are also discussed.
Collapse
Affiliation(s)
- Fudan Gao
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| |
Collapse
|
9
|
Bai Y, Chen T, Happe T, Lu Y, Sawyer A. Iron-sulphur cluster biogenesis via the SUF pathway. Metallomics 2019; 10:1038-1052. [PMID: 30019043 DOI: 10.1039/c8mt00150b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Iron-sulphur (Fe-S) clusters are versatile cofactors, which are essential for key metabolic processes in cells, such as respiration and photosynthesis, and which may have also played a crucial role in establishing life on Earth. They can be found in almost all living organisms, from unicellular prokaryotes and archaea to multicellular animals and plants, and exist in diverse forms. This review focuses on the most ancient Fe-S cluster assembly system, the sulphur utilization factor (SUF) mechanism, which is crucial in bacteria for cell survival under stress conditions such as oxidation and iron starvation, and which is also present in the chloroplasts of green microalgae and plants, where it is responsible for plastidial Fe-S protein maturation. We explain the SUF Fe-S cluster assembly process, the proteins involved, their regulation and provide evolutionary insights. We specifically focus on examples from Fe-S cluster synthesis in the model organisms Escherichia coli and Arabidopsis thaliana and discuss in an in vivo context the assembly of the [FeFe]-hydrogenase H-cluster from Chlamydomonas reinhardtii.
Collapse
Affiliation(s)
- Y Bai
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | | | | | | | | |
Collapse
|
10
|
Blanco-Ameijeiras S, Cabanes DJE, Hassler CS. Towards the development of a new generation of whole-cell bioreporters to sense iron bioavailability in oceanic systems-learning from the case of Synechococcus sp. PCC7002 iron bioreporter. J Appl Microbiol 2019; 127:1291-1304. [PMID: 30970168 DOI: 10.1111/jam.14277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/17/2019] [Accepted: 04/04/2019] [Indexed: 12/24/2022]
Abstract
Whole-cell bioreporters are genetically modified micro-organisms designed to sense bioavailable forms of nutrients or toxic compounds in aquatic systems. As they represent the most promising cost-efficient tools available for such purpose, engineering and use of bioreporters is rapidly growing in association with wide applicability. Bioreporters are urgently needed to determine phytoplankton iron (Fe) limitation, which has been reported in up to 30% of the ocean, with consequences affecting Earth's global carbon cycle and climate. This study presents a critical evaluation and optimization of the only Cyanobacteria bioreporter available to sense Fe limitation in marine systems (Synechococcus sp. PCC7002). The nonmonotonic biphasic dose-response curve between the bioreporters' signal and Fe bioavailability impairs an appropriate data interpretation, highlighting the need for new carefully designed bioreporters. Here, limitations under low Fe concentrations were related to cellular energy stress, nonlinear expression of the targeted promoter and siderophore expression. Furthermore, we provide critical standard criteria for the development of new Fe bioreporters. Finally, based on gene expression data under a range of marine Fe concentrations, we propose novel sensor genes for the development of new Cyanobacteria Fe bioreporters for distinct marine regions.
Collapse
Affiliation(s)
- S Blanco-Ameijeiras
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - D J E Cabanes
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - C S Hassler
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| |
Collapse
|
11
|
Carrier MC, Bourassa JS, Massé E. Cellular Homeostasis: A Small RNA at the Crossroads of Iron and Photosynthesis. Curr Biol 2019; 27:R380-R383. [PMID: 28535387 DOI: 10.1016/j.cub.2017.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cyanobacterium Synechocystis relies on iron to perform oxygenic photosynthesis. This makes Synechocystis particularly sensitive to iron starvation. A new study shows that the small RNA IsaR1 is a major effector of the iron-stress response, remodeling the photosynthetic apparatus.
Collapse
Affiliation(s)
- Marie-Claude Carrier
- University of Sherbrooke, CRCHUS, Faculty of Medicine and Health Sciences, Department of Biochemistry, Sherbrooke, Quebec, Canada
| | - Jean-Sébastien Bourassa
- University of Sherbrooke, CRCHUS, Faculty of Medicine and Health Sciences, Department of Biochemistry, Sherbrooke, Quebec, Canada
| | - Eric Massé
- University of Sherbrooke, CRCHUS, Faculty of Medicine and Health Sciences, Department of Biochemistry, Sherbrooke, Quebec, Canada.
| |
Collapse
|
12
|
Gordon GC, Pfleger BF. Regulatory Tools for Controlling Gene Expression in Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1080:281-315. [PMID: 30091100 PMCID: PMC6662922 DOI: 10.1007/978-981-13-0854-3_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are attractive hosts for converting carbon dioxide and sunlight into desirable chemical products. To engineer these organisms and manipulate their metabolic pathways, the biotechnology community has developed genetic tools to control gene expression. Many native cyanobacterial promoters and related sequence elements have been used to regulate genes of interest, and heterologous tools that use non-native small molecules to induce gene expression have been demonstrated. Overall, IPTG-based induction systems seem to be leaky and initially demonstrate small dynamic ranges in cyanobacteria. Consequently, a variety of other induction systems have been optimized to enable tighter control of gene expression. Tools require significant optimization because they function quite differently in cyanobacteria when compared to analogous use in model heterotrophs. We hypothesize that these differences are due to fundamental differences in physiology between organisms. This review is not intended to summarize all known products made in cyanobacteria nor the performance (titer, rate, yield) of individual strains, but instead will focus on the genetic tools and the inherent aspects of cellular physiology that influence gene expression in cyanobacteria.
Collapse
Affiliation(s)
- Gina C Gordon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
13
|
Pandey M, Talwar S, Bose S, Pandey AK. Iron homeostasis in Mycobacterium tuberculosis is essential for persistence. Sci Rep 2018; 8:17359. [PMID: 30478257 PMCID: PMC6255865 DOI: 10.1038/s41598-018-35012-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 10/09/2018] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis, caused by the obligate intracellular pathogen Mycobacterium tuberculosis (Mtb), is responsible for 2-3 million deaths annually worldwide. Intracellular adaptability, which is critical for long-term persistence, requires the pathogen to neutralize host-mediated insults. The iron-sulphur (Fe-S) cofactor is essential for many enzymes critical for such 'adaptation'. The Mtb genome harbors only one putative iron-sulphur cluster (ISC) operon (rv1460-66) predicted to be involved in the generation of the Fe-S cofactor. Except for rv1460, all other genes in this operon are anticipated to be essential. The current study investigated the role of rv1460, an sufR homologue of Mtb (sufRTB), in maintaining intracellular Fe homeostasis and its implications on mycobacterial pathogenesis. We found that Mtb ISC locus (rv1461-66) was transcribed as a single multigene transcript. We successfully generated the sufRTB null mutant strain (ΔsufRTB) of Mtb, suggesting nonessentiality of the gene under normal growth conditions. The mutant strain demonstrated enhanced biofilm generation and failed to grow under a low-Fe condition. Growth characterization studies indicated that SufRTB-mediated intracellular Fe homeostasis is essential for Mtb to persist in the host. Targeting mycobacterial persistence by inhibiting SufRTB protein activity may be a novel intervention strategy in tuberculosis treatment.
Collapse
Affiliation(s)
- Manitosh Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, Haryana, India
| | - Sakshi Talwar
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, Haryana, India
| | - Sutapa Bose
- Earth and Environmental Science Research Laboratory, Dept. of Earth Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, Nadia, West Bengal, India
| | - Amit Kumar Pandey
- Mycobacterial Pathogenesis Laboratory, Translational Health Science and Technology Institute (THSTI), Faridabad, 121001, Haryana, India.
| |
Collapse
|
14
|
Pala ZR, Saxena V, Saggu GS, Garg S. Recent Advances in the [Fe-S] Cluster Biogenesis (SUF) Pathway Functional in the Apicoplast of Plasmodium. Trends Parasitol 2018; 34:800-809. [PMID: 30064903 DOI: 10.1016/j.pt.2018.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/26/2018] [Accepted: 05/31/2018] [Indexed: 10/28/2022]
Abstract
Iron-sulfur [Fe-S] clusters are one of the most ancient, ubiquitous, structurally and functionally versatile natural biosynthetic prosthetic groups required by various proteins involved in important metabolic processes. Genome mining and localization studies in Plasmodium have shown two evolutionarily distinct biogenesis pathways: the ISC pathway in mitochondria and the SUF pathway in the apicoplast. In recent years, the myriad efforts made to elucidate the SUF pathway have deciphered the role of various proteins involved in the pathway and their importance for the parasite life cycle in both asexual and sexual stages. This review aims to discuss recent research in the apicoplast [Fe-S] biogenesis pathway from Plasmodium to enhance our current understanding of parasite biology with an overall aim to identify gaps to strengthen our fight against malaria.
Collapse
Affiliation(s)
- Zarna Rajeshkumar Pala
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan, India
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan, India
| | - Gagandeep Singh Saggu
- Laboratory of Malaria and Vector Research, National Institute of Allergic and Infectious Diseases, National Institute of Health, Rockville, MD, USA
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Pilani Campus, Rajasthan, India.
| |
Collapse
|
15
|
Willemse D, Weber B, Masino L, Warren RM, Adinolfi S, Pastore A, Williams MJ. Rv1460, a SufR homologue, is a repressor of the suf operon in Mycobacterium tuberculosis. PLoS One 2018; 13:e0200145. [PMID: 29979728 PMCID: PMC6034842 DOI: 10.1371/journal.pone.0200145] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022] Open
Abstract
Iron–sulphur (Fe-S) clusters are ubiquitous co-factors which require multi-protein systems for their synthesis. In Mycobacterium tuberculosis, the Rv1460-Rv1461-Rv1462-Rv1463-csd-Rv1465-Rv1466 operon (suf operon) encodes the primary Fe-S cluster biogenesis system. The first gene in this operon, Rv1460, shares homology with the cyanobacterial SufR, which functions as a transcriptional repressor of the sufBCDS operon. Rv1460’s function in M. tuberculosis has however not been determined. In this study, we demonstrate that M. tuberculosis mutants lacking a functional Rv1460 protein are impaired for growth under standard culture conditions. Elevated expression of Rv1460 and Rv1461 was observed in the mutant, implicating Rv1460 in the regulation of the suf operon. Binding of an Fe-S cluster to purified recombinant Rv1460 was confirmed by UV-visible spectroscopy and circular dichroism. Furthermore, three conserved cysteine residues, C203, C216 and C244, proposed to provide ligands for the coordination of an Fe-S cluster, were shown to be required for the function of Rv1460 in M. tuberculosis. Rv1460 therefore seems to be functionally analogous to cyanobacterial SufR.
Collapse
Affiliation(s)
- Danicke Willemse
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Brandon Weber
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Laura Masino
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Robin M. Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Salvatore Adinolfi
- Pharmaceutical Science and Technology, University of Turin, Turin, Italy
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London, London, United Kingdom
| | - Monique J. Williams
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
- * E-mail:
| |
Collapse
|
16
|
Kreula SM, Kaewphan S, Ginter F, Jones PR. Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining. PeerJ 2018; 6:e4806. [PMID: 29844966 PMCID: PMC5970561 DOI: 10.7717/peerj.4806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/30/2018] [Indexed: 01/17/2023] Open
Abstract
The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from ‘reading the literature’. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already ‘known’, and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to (i) discover novel candidate associations between different genes or proteins in the network, and (ii) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource.
Collapse
Affiliation(s)
- Sanna M Kreula
- Department of Biochemistry, University of Turku, Turku, Finland.,University of Turku Graduate School, University of Turku, Turku, Finland
| | - Suwisa Kaewphan
- University of Turku Graduate School, University of Turku, Turku, Finland.,Turku Centre for Computer Science (TUCS), Turku, Finland.,Department of Future Technologies, University of Turku, Turku, Finland
| | - Filip Ginter
- Department of Future Technologies, University of Turku, Turku, Finland
| | - Patrik R Jones
- Department of Life Sciences, Imperial College London, London, United Kingdom
| |
Collapse
|
17
|
Ma Q, Lei HL, Yan R, Zhou M. Enhanced Expression of an Iron–Sulfur Protein Slr0351 of Synechocystis sp. PCC 6803 in E. coli by Truncating the Transmembrane Region. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018020073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
18
|
Pérez AA, Ferlez BH, Applegate AM, Walters K, He Z, Shen G, Golbeck JH, Bryant DA. Presence of a [3Fe-4S] cluster in a PsaC variant as a functional component of the photosystem I electron transfer chain in Synechococcus sp. PCC 7002. PHOTOSYNTHESIS RESEARCH 2018; 136:31-48. [PMID: 28916964 DOI: 10.1007/s11120-017-0437-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/23/2017] [Indexed: 06/07/2023]
Abstract
A site-directed C14G mutation was introduced into the stromal PsaC subunit of Synechococcus sp. strain PCC 7002 in vivo in order to introduce an exchangeable coordination site into the terminal FB [4Fe-4S] cluster of Photosystem I (PSI). Using an engineered PSI-less strain (psaAB deletion), psaC was deleted and replaced with recombinant versions controlled by a strong promoter, and the psaAB deletion was complemented. Modified PSI accumulated at lower levels in this strain and supported slower photoautotrophic growth than wild type. As-isolated PSI complexes containing PsaCC14G showed resonances with g values of 2.038 and 2.007 characteristic of a [3Fe-4S]1+ cluster. When the PSI complexes were illuminated at 15 K, these resonances partially disappeared and two new sets of resonances appeared. The majority set had g values of 2.05, 1.95, and 1.85, characteristic of FA-, and the minority set had g values of 2.11, 1.90, and 1.88 from FB' in the modified site. The S = 1/2 spin state of the latter implied the presence of a thiolate as the terminal ligand. The [3Fe-4S] clusters could be partially reconstituted with iron, producing a larger population of [4Fe-4S] clusters. Rates of flavodoxin reduction were identical in PSI complexes isolated from wild type and the PsaCC14G variant strain; this implied equivalent capacity for forward electron transfer in PSI complexes that contained [3Fe-4S] and [4Fe-4S] clusters. The development of this cyanobacterial strain is a first step toward translation of in vitro PSI-based biosolar molecular wire systems in vivo and provides new insights into the formation of Fe/S clusters.
Collapse
Affiliation(s)
- Adam A Pérez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
| | - Bryan H Ferlez
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 28824, USA
| | - Amanda M Applegate
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
- Musculoskeletal Transplant Foundation, Jessup, PA, 18434, USA
| | - Karim Walters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Zhihui He
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
| |
Collapse
|
19
|
Molecular basis of function and the unusual antioxidant activity of a cyanobacterial cysteine desulfurase. Biochem J 2017; 474:2435-2447. [PMID: 28592683 DOI: 10.1042/bcj20170290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 11/17/2022]
Abstract
Cysteine desulfurases, which supply sulfur for iron-sulfur cluster biogenesis, are broadly distributed in all phyla including cyanobacteria, the progenitors of plant chloroplasts. The SUF (sulfur utilization factor) system is responsible for Fe-S cluster biosynthesis under stress. The suf operon from cyanobacterium Anabaena PCC 7120 showed the presence of a cysteine desulfurase, sufS (alr2495), but not the accessory sulfur-accepting protein (SufE). However, an open reading frame (alr3513) encoding a SufE-like protein (termed AsaE, Anabaena sulfur acceptor E) was found at a location distinct from the suf operon. The purified SufS protein existed as a pyridoxal 5' phosphate (PLP)-containing dimer with a relatively low desulfurase activity. Interestingly, in the presence of the AsaE protein, the catalytic efficiency of this reaction increased 10-fold. In particular, for sulfur mobilization, the AsaE protein partnered only SufS and not other cysteine desulfurases from Anabaena. The SufS protein was found to physically interact with the AsaE protein, demonstrating that AsaE was indeed the missing partner of Anabaena SufS. The conserved cysteine of the SufS or the AsaE protein was essential for activity but not for their physical association. Curiously, overexpression of the SufS protein in Anabaena caused reduced formation of reactive oxygen species on exposure to hydrogen peroxide (H2O2), resulting in superior oxidative stress tolerance to the oxidizing agent when compared with the wild-type strain. Overall, the results highlight the functional interaction between the two proteins that mediate sulfur mobilization, in the cyanobacterial SUF pathway, and further reveal that overexpression of SufS can protect cyanobacteria from oxidative stress.
Collapse
|
20
|
Georg J, Kostova G, Vuorijoki L, Schön V, Kadowaki T, Huokko T, Baumgartner D, Müller M, Klähn S, Allahverdiyeva Y, Hihara Y, Futschik ME, Aro EM, Hess WR. Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1. Curr Biol 2017; 27:1425-1436.e7. [PMID: 28479323 DOI: 10.1016/j.cub.2017.04.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 01/01/2023]
Abstract
Oxygenic photosynthesis crucially depends on proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Here, we show that the small regulatory RNA (sRNA) IsaR1 (Iron-Stress-Activated RNA 1) plays a pivotal role in acclimation to low-iron conditions. The IsaR1 regulon consists of more than 15 direct targets, including Fe2+-containing proteins involved in photosynthetic electron transfer, detoxification of anion radicals, citrate cycle, and tetrapyrrole biogenesis. IsaR1 is essential for maintaining physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (1) directly, via posttranscriptional repression of gene expression; (2) indirectly, via suppression of pigment; and (3) Fe/S cluster biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a critically important riboregulator. These findings provide a new perspective for understanding the regulation of iron homeostasis in photosynthetic organisms.
Collapse
Affiliation(s)
- Jens Georg
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Gergana Kostova
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Linda Vuorijoki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Verena Schön
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Tuomas Huokko
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Desirée Baumgartner
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Maximilian Müller
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Stephan Klähn
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Matthias E Futschik
- CCMAR - Center of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, Devon PL4 8AA, UK
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
| |
Collapse
|
21
|
Vuorijoki L, Tiwari A, Kallio P, Aro EM. Inactivation of iron-sulfur cluster biogenesis regulator SufR in Synechocystis sp. PCC 6803 induces unique iron-dependent protein-level responses. Biochim Biophys Acta Gen Subj 2017; 1861:1085-1098. [PMID: 28216046 DOI: 10.1016/j.bbagen.2017.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/31/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Iron-sulfur (Fe-S) clusters are protein-bound cofactors associated with cellular electron transport and redox sensing, with multiple specific functions in oxygen-evolving photosynthetic cyanobacteria. The aim here was to elucidate protein-level effects of the transcriptional repressor SufR involved in the regulation of Fe-S cluster biogenesis in the cyanobacterium Synechocystis sp. PCC 6803. METHODS The approach was to quantitate 94 pre-selected target proteins associated with various metabolic functions using SRM in Synechocystis. The evaluation was conducted in response to sufR deletion under different iron conditions, and complemented with EPR analysis on the functionality of the photosystems I and II as well as with RT-qPCR to verify the effects of SufR also on transcript level. RESULTS The results on both protein and transcript levels show that SufR acts not only as a repressor of the suf operon when iron is available but also has other direct and indirect functions in the cell, including maintenance of the expression of pyruvate:ferredoxin oxidoreductase NifJ and other Fe-S cluster proteins under iron sufficient conditions. Furthermore, the results imply that in the absence of iron the suf operon is repressed by some additional regulatory mechanism independent of SufR. CONCLUSIONS The study demonstrates that Fe-S cluster metabolism in Synechocystis is stringently regulated, and has complex interactions with multiple primary functions in the cell, including photosynthesis and central carbon metabolism. GENERAL SIGNIFICANCE The study provides new insight into the regulation of Fe-S cluster biogenesis via suf operon, and the associated wide-ranging protein-level changes in photosynthetic cyanobacteria.
Collapse
Affiliation(s)
- Linda Vuorijoki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Arjun Tiwari
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Pauli Kallio
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| |
Collapse
|
22
|
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S. Finding approximate gene clusters with Gecko 3. Nucleic Acids Res 2016; 44:9600-9610. [PMID: 27679480 PMCID: PMC5175365 DOI: 10.1093/nar/gkw843] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 12/15/2022] Open
Abstract
Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min.
Collapse
Affiliation(s)
- Sascha Winter
- Chair for Bioinformatics, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Katharina Jahn
- Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Computational Biology Group, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Stefanie Wehner
- RNA Bioinformatics and High Throughput Analysis, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9LA, Scotland, UK
| | - Leon Kuchenbecker
- Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High Throughput Analysis, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jens Stoye
- Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
| |
Collapse
|
23
|
Abstract
Iron-sulfur (Fe-S) clusters are fundamental to numerous biological processes in most organisms, but these protein cofactors can be prone to damage by various oxidants (e.g., O2, reactive oxygen species, and reactive nitrogen species) and toxic levels of certain metals (e.g., cobalt and copper). Furthermore, their synthesis can also be directly influenced by the level of available iron in the environment. Consequently, the cellular need for Fe-S cluster biogenesis varies with fluctuating growth conditions. To accommodate changes in Fe-S demand, microorganisms employ diverse regulatory strategies to tailor Fe-S cluster biogenesis according to their surroundings. Here, we review the mechanisms that regulate Fe-S cluster formation in bacteria, primarily focusing on control of the Isc and Suf Fe-S cluster biogenesis systems in the model bacterium Escherichia coli.
Collapse
Affiliation(s)
- Erin L Mettert
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, ,
| | - Patricia J Kiley
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, ,
| |
Collapse
|
24
|
UpCoT: an integrated pipeline tool for clustering upstream DNA sequences of orthologous genes in prokaryotic genomes. 3 Biotech 2016; 6:74. [PMID: 28330144 PMCID: PMC4755962 DOI: 10.1007/s13205-016-0363-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/08/2016] [Indexed: 11/30/2022] Open
Abstract
UpCoT is a pipeline tool developed by automating the series of steps involved in prediction of cis-regulatory elements. UpCoT generates orthologs for each gene in target genome using bi-directional best blast hit against the reference genomes, then identifies potential orthologous transcriptional units using intergenic distance. Finally it generates the FASTA files containing upstream sequences of orthologous transcriptional units of each gene in target genome. The inputs of UpCoT are protein sequence files (*.faa), genome sequence files (*.fna) and gene co-ordinate files (*.ptt) for target and reference genomes. The clustered-upstream DNA sequences can be used by motif prediction tool, such as MEME, Bio-prospector, Gibbs motif sampler, MDscan for prediction of conserved DNA elements. We tested the performance of UpCoT by selecting the genome of Synechocystis sp PCC 6803 as the target and 13 different cyanobacterial genomes as reference. The clustered upstream sequences generated by UpCoT of groES, ycf24 and nirA were used for cis-regulatory element prediction. The results were consistent with the experimentally identified cis-regulatory elements. Therefore, UpCoT is a reliable and automated pipeline package for prediction of orthologs, orthologous transcriptional units, and orthologous upstream sequences of a selected prokaryotic genome. UpCoT can be downloaded from http://jssplab.uohyd.ac.in/upcot/.
Collapse
|
25
|
Mettert EL, Kiley PJ. Fe-S proteins that regulate gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1284-93. [PMID: 25450978 DOI: 10.1016/j.bbamcr.2014.11.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/24/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023]
Abstract
Iron-sulfur (Fe-S) cluster containing proteins that regulate gene expression are present in most organisms. The innate chemistry of their Fe-S cofactors makes these regulatory proteins ideal for sensing environmental signals, such as gases (e.g. O2 and NO), levels of Fe and Fe-S clusters, reactive oxygen species, and redox cycling compounds, to subsequently mediate an adaptive response. Here we review the recent findings that have provided invaluable insight into the mechanism and function of these highly significant Fe-S regulatory proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
Collapse
Affiliation(s)
- Erin L Mettert
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
| | - Patricia J Kiley
- University of Wisconsin-Madison, Department of Biomolecular Chemistry, 440 Henry Mall, Biochemical Sciences Building, Room 4204C, Madison, WI 53706, USA.
| |
Collapse
|
26
|
Outten FW. Recent advances in the Suf Fe-S cluster biogenesis pathway: Beyond the Proteobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1464-9. [PMID: 25447545 DOI: 10.1016/j.bbamcr.2014.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 01/21/2023]
Abstract
Fe-S clusters play critical roles in cellular function throughout all three kingdoms of life. Consequently, Fe-S cluster biogenesis systems are present in most organisms. The Suf (sulfur formation) system is the most ancient of the three characterized Fe-S cluster biogenesis pathways, which also include the Isc and Nif systems. Much of the first work on the Suf system took place in Gram-negative Proteobacteria used as model organisms. These early studies led to a wealth of biochemical, genetic, and physiological information on Suf function. From those studies we have learned that SufB functions as an Fe-S scaffold in conjunction with SufC (and in some cases SufD). SufS and SufE together mobilize sulfur for cluster assembly and SufA traffics the complete Fe-S cluster from SufB to target apo-proteins. However, recent progress on the Suf system in other organisms has opened up new avenues of research and new hypotheses about Suf function. This review focuses primarily on the most recent discoveries about the Suf pathway and where those new models may lead the field. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
Collapse
Affiliation(s)
- F Wayne Outten
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC 29208, USA.
| |
Collapse
|
27
|
Giner-Lamia J, López-Maury L, Florencio FJ. Global transcriptional profiles of the copper responses in the cyanobacterium Synechocystis sp. PCC 6803. PLoS One 2014; 9:e108912. [PMID: 25268225 PMCID: PMC4182526 DOI: 10.1371/journal.pone.0108912] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/27/2014] [Indexed: 12/22/2022] Open
Abstract
Copper is an essential element involved in fundamental processes like respiration and photosynthesis. However, it becomes toxic at high concentration, which has forced organisms to control its cellular concentration. We have recently described a copper resistance system in the cyanobacterium Synechocystis sp. PCC 6803, which is mediated by the two-component system, CopRS, a RND metal transport system, CopBAC and a protein of unknown function, CopM. Here, we report the transcriptional responses to copper additions at non-toxic (0.3 µM) and toxic concentrations (3 µM) in the wild type and in the copper sensitive copR mutant strain. While 0.3 µM copper slightly stimulated metabolism and promoted the exchange between cytochrome c6 and plastocyanin as soluble electron carriers, the addition of 3 µM copper catalyzed the formation of ROS, led to a general stress response and induced expression of Fe-S cluster biogenesis genes. According to this, a double mutant strain copRsufR, which expresses constitutively the sufBCDS operon, tolerated higher copper concentration than the copR mutant strain, suggesting that Fe-S clusters are direct targets of copper toxicity in Synechocystis. In addition we have also demonstrated that InrS, a nickel binding transcriptional repressor that belong to the CsoR family of transcriptional factor, was involved in heavy metal homeostasis, including copper, in Synechocystis. Finally, global gene expression analysis of the copR mutant strain suggested that CopRS only controls the expression of copMRS and copBAC operons in response to copper.
Collapse
Affiliation(s)
- Joaquin Giner-Lamia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Sevilla, Spain
| | - Luis López-Maury
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Sevilla, Spain
- * E-mail: (LLM); (FJF)
| | - Francisco J. Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Sevilla, Spain
- * E-mail: (LLM); (FJF)
| |
Collapse
|
28
|
The unique regulation of iron-sulfur cluster biogenesis in a Gram-positive bacterium. Proc Natl Acad Sci U S A 2014; 111:E2251-60. [PMID: 24847070 DOI: 10.1073/pnas.1322728111] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Iron-sulfur clusters function as cofactors of a wide range of proteins, with diverse molecular roles in both prokaryotic and eukaryotic cells. Dedicated machineries assemble the clusters and deliver them to the final acceptor molecules in a tightly regulated process. In the prototypical Gram-negative bacterium Escherichia coli, the two existing iron-sulfur cluster assembly systems, iron-sulfur cluster (ISC) and sulfur assimilation (SUF) pathways, are closely interconnected. The ISC pathway regulator, IscR, is a transcription factor of the helix-turn-helix type that can coordinate a [2Fe-2S] cluster. Redox conditions and iron or sulfur availability modulate the ligation status of the labile IscR cluster, which in turn determines a switch in DNA sequence specificity of the regulator: cluster-containing IscR can bind to a family of gene promoters (type-1) whereas the clusterless form recognizes only a second group of sequences (type-2). However, iron-sulfur cluster biogenesis in Gram-positive bacteria is not so well characterized, and most organisms of this group display only one of the iron-sulfur cluster assembly systems. A notable exception is the unique Gram-positive dissimilatory metal reducing bacterium Thermincola potens, where genes from both systems could be identified, albeit with a diverging organization from that of Gram-negative bacteria. We demonstrated that one of these genes encodes a functional IscR homolog and is likely involved in the regulation of iron-sulfur cluster biogenesis in T. potens. Structural and biochemical characterization of T. potens and E. coli IscR revealed a strikingly similar architecture and unveiled an unforeseen conservation of the unique mechanism of sequence discrimination characteristic of this distinctive group of transcription regulators.
Collapse
|
29
|
Ludwig M, Pandelia ME, Chew CY, Zhang B, Golbeck JH, Krebs C, Bryant DA. ChlR protein of Synechococcus sp. PCC 7002 is a transcription activator that uses an oxygen-sensitive [4Fe-4S] cluster to control genes involved in pigment biosynthesis. J Biol Chem 2014; 289:16624-39. [PMID: 24782315 DOI: 10.1074/jbc.m114.561233] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Synechococcus sp. PCC 7002 and many other cyanobacteria have two genes that encode key enzymes involved in chlorophyll a, biliverdin, and heme biosynthesis: acsFI/acsFII, ho1/ho2, and hemF/hemN. Under atmospheric O2 levels, AcsFI synthesizes 3,8-divinyl protochlorophyllide from Mg-protoporphyrin IX monomethyl ester, Ho1 oxidatively cleaves heme to form biliverdin, and HemF oxidizes coproporphyrinogen III to protoporphyrinogen IX. Under microoxic conditions, another set of genes directs the synthesis of alternative enzymes AcsFII, Ho2, and HemN. In Synechococcus sp. PCC 7002, open reading frame SynPCC7002_A1993 encodes a MarR family transcriptional regulator, which is located immediately upstream from the operon comprising acsFII, ho2, hemN, and desF (the latter encodes a putative fatty acid desaturase). Deletion and complementation analyses showed that this gene, denoted chlR, is a transcriptional activator that is essential for transcription of the acsFII-ho2-hemN-desF operon under microoxic conditions. Global transcriptome analyses showed that ChlR controls the expression of only these four genes. Co-expression of chlR with a yfp reporter gene under the control of the acsFII promoter from Synechocystis sp. PCC 6803 in Escherichia coli demonstrated that no other cyanobacterium-specific components are required for proper functioning of this regulatory circuit. A combination of analytical methods and Mössbauer and EPR spectroscopies showed that reconstituted, recombinant ChlR forms homodimers that harbor one oxygen-sensitive [4Fe-4S] cluster. We conclude that ChlR is a transcriptional activator that uses a [4Fe-4S] cluster to sense O2 levels and thereby control the expression of the acsFII-ho2-hemN-desF operon.
Collapse
Affiliation(s)
- Marcus Ludwig
- From the Departments of Biochemistry and Molecular Biology and
| | - Maria-Eirini Pandelia
- Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - Chyue Yie Chew
- From the Departments of Biochemistry and Molecular Biology and
| | - Bo Zhang
- Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - John H Golbeck
- From the Departments of Biochemistry and Molecular Biology and Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - Carsten Krebs
- From the Departments of Biochemistry and Molecular Biology and Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - Donald A Bryant
- From the Departments of Biochemistry and Molecular Biology and the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| |
Collapse
|
30
|
Nagarajan S, Srivastava S, Sherman LA. Essential role of the plasmid hik31 operon in regulating central metabolism in the dark in Synechocystis sp. PCC 6803. Mol Microbiol 2013; 91:79-97. [PMID: 24237382 DOI: 10.1111/mmi.12442] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2013] [Indexed: 12/13/2022]
Abstract
The plasmid hik31 operon (P3, slr6039-slr6041) is located on the pSYSX plasmid in Synechocystis sp. PCC 6803. A P3 mutant (ΔP3) had a growth defect in the dark and a pigment defect that was worsened by the addition of glucose. The glucose defect was from incomplete metabolism of the substrate, was pH dependent, and completely overcome by the addition of bicarbonate. Addition of organic carbon and nitrogen sources partly alleviated the defects of the mutant in the dark. Electron micrographs of the mutant revealed larger cells with division defects, glycogen limitation, lack of carboxysomes, deteriorated thylakoids and accumulation of polyhydroxybutyrate and cyanophycin. A microarray experiment over two days of growth in light-dark plus glucose revealed downregulation of several photosynthesis, amino acid biosynthesis, energy metabolism genes; and an upregulation of cell envelope and transport and binding genes in the mutant. ΔP3 had an imbalance in carbon and nitrogen levels and many sugar catabolic and cell division genes were negatively affected after the first dark period. The mutant suffered from oxidative and osmotic stress, macronutrient limitation, and an energy deficit. Therefore, the P3 operon is an important regulator of central metabolism and cell division in the dark.
Collapse
Affiliation(s)
- Sowmya Nagarajan
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | | | | |
Collapse
|
31
|
Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME JOURNAL 2013; 7:2178-91. [PMID: 23739051 PMCID: PMC3806265 DOI: 10.1038/ismej.2013.83] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/21/2013] [Indexed: 12/22/2022]
Abstract
Biological soil crusts (BSCs) cover extensive portions of the earth's deserts. In order to survive desiccation cycles and utilize short periods of activity during infrequent precipitation, crust microorganisms must rely on the unique capabilities of vegetative cells to enter a dormant state and be poised for rapid resuscitation upon wetting. To elucidate the key events involved in the exit from dormancy, we performed a wetting experiment of a BSC and followed the response of the dominant cyanobacterium, Microcoleus vaginatus, in situ using a whole-genome transcriptional time course that included two diel cycles. Immediate, but transient, induction of DNA repair and regulatory genes signaled the hydration event. Recovery of photosynthesis occurred within 1 h, accompanied by upregulation of anabolic pathways. Onset of desiccation was characterized by the induction of genes for oxidative and photo-oxidative stress responses, osmotic stress response and the synthesis of C and N storage polymers. Early expression of genes for the production of exopolysaccharides, additional storage molecules and genes for membrane unsaturation occurred before drying and hints at preparedness for desiccation. We also observed signatures of preparation for future precipitation, notably the expression of genes for anaplerotic reactions in drying crusts, and the stable maintenance of mRNA through dormancy. These data shed light on possible synchronization between this cyanobacterium and its environment, and provides key mechanistic insights into its metabolism in situ that may be used to predict its response to climate, and or, land-use driven perturbations.
Collapse
Affiliation(s)
- Lara Rajeev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Reprint of: Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:923-37. [PMID: 23660107 DOI: 10.1016/j.bbabio.2013.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
Collapse
|
33
|
Roche B, Aussel L, Ezraty B, Mandin P, Py B, Barras F. Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:455-69. [PMID: 23298813 DOI: 10.1016/j.bbabio.2012.12.010] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/21/2012] [Accepted: 12/27/2012] [Indexed: 12/17/2022]
Abstract
Iron/sulfur centers are key cofactors of proteins intervening in multiple conserved cellular processes, such as gene expression, DNA repair, RNA modification, central metabolism and respiration. Mechanisms allowing Fe/S centers to be assembled, and inserted into polypeptides have attracted much attention in the last decade, both in eukaryotes and prokaryotes. Basic principles and recent advances in our understanding of the prokaryotic Fe/S biogenesis ISC and SUF systems are reviewed in the present communication. Most studies covered stem from investigations in Escherichia coli and Azotobacter vinelandii. Remarkable insights were brought about by complementary structural, spectroscopic, biochemical and genetic studies. Highlights of the recent years include scaffold mediated assembly of Fe/S cluster, A-type carriers mediated delivery of clusters and regulatory control of Fe/S homeostasis via a set of interconnected genetic regulatory circuits. Also, the importance of Fe/S biosynthesis systems in mediating soft metal toxicity was documented. A brief account of the Fe/S biosynthesis systems diversity as present in current databases is given here. Moreover, Fe/S biosynthesis factors have themselves been the object of molecular tailoring during evolution and some examples are discussed here. An effort was made to provide, based on the E. coli system, a general classification associating a given domain with a given function such as to help next search and annotation of genomes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
Collapse
Affiliation(s)
- Béatrice Roche
- Institut de Microbiologie de la Méditerranée, Marseille, France
| | | | | | | | | | | |
Collapse
|
34
|
Couturier J, Touraine B, Briat JF, Gaymard F, Rouhier N. The iron-sulfur cluster assembly machineries in plants: current knowledge and open questions. FRONTIERS IN PLANT SCIENCE 2013; 4:259. [PMID: 23898337 PMCID: PMC3721309 DOI: 10.3389/fpls.2013.00259] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/25/2013] [Indexed: 05/18/2023]
Abstract
Many metabolic pathways and cellular processes occurring in most sub-cellular compartments depend on the functioning of iron-sulfur (Fe-S) proteins, whose cofactors are assembled through dedicated protein machineries. Recent advances have been made in the knowledge of the functions of individual components through a combination of genetic, biochemical and structural approaches, primarily in prokaryotes and non-plant eukaryotes. Whereas most of the components of these machineries are conserved between kingdoms, their complexity is likely increased in plants owing to the presence of additional assembly proteins and to the existence of expanded families for several assembly proteins. This review focuses on the new actors discovered in the past few years, such as glutaredoxin, BOLA and NEET proteins as well as MIP18, MMS19, TAH18, DRE2 for the cytosolic machinery, which are integrated into a model for the plant Fe-S cluster biogenesis systems. It also discusses a few issues currently subjected to an intense debate such as the role of the mitochondrial frataxin and of glutaredoxins, the functional separation between scaffold, carrier and iron-delivery proteins and the crosstalk existing between different organelles.
Collapse
Affiliation(s)
- Jérémy Couturier
- Interactions Arbres/Micro-organismes, Faculté des Sciences, UMR1136 Université de Lorraine-INRAVandoeuvre, France
| | - Brigitte Touraine
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Jean-François Briat
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Frédéric Gaymard
- Biochimie et Physiologie Moléculaire des Plantes, Centre National de la Recherche Scientifique-INRA-Université Montpellier 2Montpellier, France
| | - Nicolas Rouhier
- Interactions Arbres/Micro-organismes, Faculté des Sciences, UMR1136 Université de Lorraine-INRAVandoeuvre, France
- *Correspondence: Nicolas Rouhier, Université de Lorraine, UMR1136 Université de Lorraine-INRA, Interactions Arbres/Micro-organismes, Faculté des Sciences, Bd des aiguillettes, BP 239,54506 Vandoeuvre, France e-mail:
| |
Collapse
|
35
|
Crack JC, Green J, Hutchings MI, Thomson AJ, Le Brun NE. Bacterial iron-sulfur regulatory proteins as biological sensor-switches. Antioxid Redox Signal 2012; 17:1215-31. [PMID: 22239203 PMCID: PMC3430481 DOI: 10.1089/ars.2012.4511] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE In recent years, bacterial iron-sulfur cluster proteins that function as regulators of gene transcription have emerged as a major new group. In all cases, the cluster acts as a sensor of the environment and enables the organism to adapt to the prevailing conditions. This can range from mounting a response to oxidative or nitrosative stress to switching between anaerobic and aerobic respiratory pathways. The sensitivity of these ancient cofactors to small molecule reactive oxygen and nitrogen species, in particular, makes them ideally suited to function as sensors. RECENT ADVANCES An important challenge is to obtain mechanistic and structural information about how these regulators function and, in particular, how the chemistry occurring at the cluster drives the subsequent regulatory response. For several regulators, including FNR, SoxR, NsrR, IscR, and Wbl proteins, major advances in understanding have been gained recently and these are reviewed here. CRITICAL ISSUES A common theme emerging from these studies is that the sensitivity and specificity of the cluster of each regulatory protein must be exquisitely controlled by the protein environment of the cluster. FUTURE DIRECTIONS A major future challenge is to determine, for a range of regulators, the key factors for achieving control of sensitivity/specificity. Such information will lead, eventually, to a system understanding of stress response, which often involves more than one regulator.
Collapse
Affiliation(s)
- Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | | | | | | | | |
Collapse
|
36
|
Verkhovsky M, Bloch DA, Verkhovskaya M. Tightly-bound ubiquinone in the Escherichia coli respiratory Complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1550-6. [DOI: 10.1016/j.bbabio.2012.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/23/2012] [Accepted: 04/25/2012] [Indexed: 12/12/2022]
|
37
|
Barzantny H, Schröder J, Strotmeier J, Fredrich E, Brune I, Tauch A. The transcriptional regulatory network of Corynebacterium jeikeium K411 and its interaction with metabolic routes contributing to human body odor formation. J Biotechnol 2012; 159:235-48. [DOI: 10.1016/j.jbiotec.2012.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/12/2012] [Accepted: 01/17/2012] [Indexed: 01/08/2023]
|
38
|
Midorikawa T, Narikawa R, Ikeuchi M. A deletion mutation in the spacing within the psaA core promoter enhances transcription in a cyanobacterium Synechocystis sp. PCC 6803. PLANT & CELL PHYSIOLOGY 2012; 53:164-172. [PMID: 22102696 DOI: 10.1093/pcp/pcr159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Transcriptional regulation of PSI reaction center psaA is one of the important physiological responses to changing environments. We previously reported that the Rrf2-type transcriptional regulator Slr0846 activates transcription of psaA in Synechocystis sp. PCC 6803. In the Δslr0846 mutant, transcripts from two promoters, P1 and P2, were downshifted and, as a result, a lower Chl content and slower growth were observed. Here, we report spontaneous suppressors which recovered Chl accumulation and photoautotrophic growth. Sequencing of the whole promoter region revealed in some suppressors the same single nucleotide deletion in a 9 bp G stretch (-21 to -29 from the transcriptional start point of P1), which is located between the -35 and -10 elements of the P1 core promoter (hereafter the -G mutation). The transcripts from P1 were higher in abundance in this pseudorevertant than in the Δslr0846 mutant. When the promoter was fused to a reporter gene, the -G mutation conferred ~4 times higher expression than the wild-type promoter. It has been shown that the P1 promoter activity of psaA is regulated by a high light regulatory element 1 just upstream of -35. The -G mutated P1 promoter still retained the high light response. Thus, the -G mutation enhanced the expression level of psaA without a loss of the response to the high light conditions. This is the first study of the spontaneous mutation of a spacer length of a promoter for expression in cyanobacteria.
Collapse
Affiliation(s)
- Takafumi Midorikawa
- Department of Biological Science, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan
| | | | | |
Collapse
|
39
|
Xu XM, Møller SG. Iron-sulfur clusters: biogenesis, molecular mechanisms, and their functional significance. Antioxid Redox Signal 2011; 15:271-307. [PMID: 20812788 DOI: 10.1089/ars.2010.3259] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Iron-sulfur clusters [Fe-S] are small, ubiquitous inorganic cofactors representing one of the earliest catalysts during biomolecule evolution and are involved in fundamental biological reactions, including regulation of enzyme activity, mitochondrial respiration, ribosome biogenesis, cofactor biogenesis, gene expression regulation, and nucleotide metabolism. Although simple in structure, [Fe-S] biogenesis requires complex protein machineries and pathways for assembly. [Fe-S] are assembled from cysteine-derived sulfur and iron onto scaffold proteins followed by transfer to recipient apoproteins. Several predominant iron-sulfur biogenesis systems have been identified, including nitrogen fixation (NIF), sulfur utilization factor (SUF), iron-sulfur cluster (ISC), and cytosolic iron-sulfur protein assembly (CIA), and many protein components have been identified and characterized. In eukaryotes ISC is mainly localized to mitochondria, cytosolic iron-sulfur protein assembly to the cytosol, whereas plant sulfur utilization factor is localized mainly to plastids. Because of this spatial separation, evidence suggests cross-talk mediated by organelle export machineries and dual targeting mechanisms. Although research efforts in understanding iron-sulfur biogenesis has been centered on bacteria, yeast, and plants, recent efforts have implicated inappropriate [Fe-S] biogenesis to underlie many human diseases. In this review we detail our current understanding of [Fe-S] biogenesis across species boundaries highlighting evolutionary conservation and divergence and assembling our knowledge into a cellular context.
Collapse
Affiliation(s)
- Xiang Ming Xu
- Centre for Organelle Research CORE, University of Stavanger, Norway
| | | |
Collapse
|
40
|
Kumar M, Khan FG, Sharma S, Kumar R, Faujdar J, Sharma R, Chauhan DS, Singh R, Magotra SK, Khan IA. Identification of Mycobacterium tuberculosis genes preferentially expressed during human infection. Microb Pathog 2010; 50:31-8. [PMID: 21035536 DOI: 10.1016/j.micpath.2010.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 10/19/2010] [Accepted: 10/21/2010] [Indexed: 10/18/2022]
Abstract
The identification of Mycobacterium tuberculosis genes, specifically expressed during infection is a key step in understanding molecular mechanism of mycobacterial pathogenesis. Such genes likely encode proteins required for mycobacterium's survival and progressive infection within the host. In this study, we applied in-vivo-induced antigen technology (IVIAT) to M. tuberculosis and identified 11 putative in-vivo induced genes encoding for immunogenic proteins of diverse functions; these included transcriptional regulators (Rv1460 and Rv2565), biosynthesis and macromolecule metabolism (leuD, guaB1, plcC, hupB and glyS), polyketide synthases (pks6 and pks9), cell processes (ctpA) and one with unknown function (Rv3701c). Quantitative real time-PCR analysis of these genes in the specimens obtained from TB patients demonstrated induced expression of eight genes as compared with bacteria grown in-vitro. In addition, distribution of these genes in different strains of M. tuberculosis was analyzed using PCR and their nucleotide sequence alignments and they were found to be widely distributed among M. tuberculosis isolates including multiple-drug resistant (MDR) and extensively-drug resistant (XDR). This study identified several antigenic determinants of M. tuberculosis expressed during infection, which might help pathogens adapt to or counter hostile environments and suggesting their role during disease process.
Collapse
Affiliation(s)
- Manoj Kumar
- Clinical Microbiology Division, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu Tawi 180001, India
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Summerfield TC, Nagarajan S, Sherman LA. Gene expression under low-oxygen conditions in the cyanobacterium Synechocystis sp. PCC 6803 demonstrates Hik31-dependent and -independent responses. MICROBIOLOGY-SGM 2010; 157:301-312. [PMID: 20929957 DOI: 10.1099/mic.0.041053-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have investigated the response of the cyanobacterium Synechocystis sp. PCC 6803 during growth at very low O2 concentration (bubbled with 99.9 % N(2)/0.1 % CO2). Significant transcriptional changes upon low-O2 incubation included upregulation of a cluster of genes that contained psbA1 and an operon that includes a gene encoding the two-component regulatory histidine kinase, Hik31. This regulatory cluster is of particular interest, since there are virtually identical copies on both the chromosome and plasmid pSYSX. We used a knockout mutant lacking the chromosomal copy of hik31 and studied differential transcription during the aerobic-low-O2 transition in this ΔHik31 strain and the wild-type. We observed two distinct responses to this transition, one Hik31 dependent, the other Hik31 independent. The Hik31-independent responses included the psbA1 induction and genes involved in chlorophyll biosynthesis. In addition, there were changes in a number of genes that may be involved in assembling or stabilizing photosystem (PS)II, and the hox operon and the LexA-like protein (Sll1626) were upregulated during low-O2 growth. This family of responses mostly focused on PSII and overall redox control. There was also a large set of genes that responded differently in the absence of the chromosomal Hik31. In the vast majority of these cases, Hik31 functioned as a repressor and transcription was enhanced when Hik31 was deleted. Genes in this category encoded both core and peripheral proteins for PSI and PSII, the main phycobilisome proteins, chaperones, the ATP synthase cluster and virtually all of the ribosomal proteins. These findings, coupled with the fact that ΔHik31 grew better than the wild-type under low-O2 conditions, suggested that Hik31 helps to regulate growth and overall cellular homeostasis. We detected changes in the transcription of other regulatory genes that may compensate for the loss of Hik31. We conclude that Hik31 regulates an important series of genes that relate to energy production and growth and that help to determine how Synechocystis responds to changes in O2 conditions.
Collapse
Affiliation(s)
- Tina C Summerfield
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Sowmya Nagarajan
- Purdue University, Department of Biological Sciences, 201 S. University St, Hansen Hall, West Lafayette, IN 47907, USA
| | - Louis A Sherman
- Purdue University, Department of Biological Sciences, 201 S. University St, Hansen Hall, West Lafayette, IN 47907, USA
| |
Collapse
|
42
|
Los DA, Zorina A, Sinetova M, Kryazhov S, Mironov K, Zinchenko VV. Stress sensors and signal transducers in cyanobacteria. SENSORS (BASEL, SWITZERLAND) 2010; 10:2386-415. [PMID: 22294932 PMCID: PMC3264485 DOI: 10.3390/s100302386] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 02/15/2010] [Accepted: 03/03/2010] [Indexed: 11/17/2022]
Abstract
In living cells, the perception of environmental stress and the subsequent transduction of stress signals are primary events in the acclimation to changes in the environment. Some molecular sensors and transducers of environmental stress cannot be identified by traditional and conventional methods. Based on genomic information, a systematic approach has been applied to the solution of this problem in cyanobacteria, involving mutagenesis of potential sensors and signal transducers in combination with DNA microarray analyses for the genome-wide expression of genes. Forty-five genes for the histidine kinases (Hiks), 12 genes for serine-threonine protein kinases (Spks), 42 genes for response regulators (Rres), seven genes for RNA polymerase sigma factors, and nearly 70 genes for transcription factors have been successfully inactivated by targeted mutagenesis in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Screening of mutant libraries by genome-wide DNA microarray analysis under various stress and non-stress conditions has allowed identification of proteins that perceive and transduce signals of environmental stress. Here we summarize recent progress in the identification of sensory and regulatory systems, including Hiks, Rres, Spks, sigma factors, transcription factors, and the role of genomic DNA supercoiling in the regulation of the responses of cyanobacterial cells to various types of stress.
Collapse
Affiliation(s)
- Dmitry A. Los
- Laboratory of Intracellular Regulation, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, 127276, Moscow, Russia; E-Mails: (A.Z.); (M.S.); (K.M.)
| | - Anna Zorina
- Laboratory of Intracellular Regulation, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, 127276, Moscow, Russia; E-Mails: (A.Z.); (M.S.); (K.M.)
| | - Maria Sinetova
- Laboratory of Intracellular Regulation, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, 127276, Moscow, Russia; E-Mails: (A.Z.); (M.S.); (K.M.)
| | - Sergey Kryazhov
- Department of Genetics, Faculty of Biology, Moscow State University, Moscow, Russia; E-Mails: (S.K.); (V.V.Z.)
| | - Kirill Mironov
- Laboratory of Intracellular Regulation, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, 127276, Moscow, Russia; E-Mails: (A.Z.); (M.S.); (K.M.)
| | - Vladislav V. Zinchenko
- Department of Genetics, Faculty of Biology, Moscow State University, Moscow, Russia; E-Mails: (S.K.); (V.V.Z.)
| |
Collapse
|
43
|
Zhang LF, Yang HM, Cui SX, Hu J, Wang J, Kuang TY, Norling B, Huang F. Proteomic analysis of plasma membranes of cyanobacterium Synechocystis sp. Strain PCC 6803 in response to high pH stress. J Proteome Res 2009; 8:2892-902. [PMID: 19351138 DOI: 10.1021/pr900024w] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are unique prokaryotes possessing plasma-, outer- and thylakoid membranes. The plasma membrane of a cyanobacterial cell serves as a crucial barrier against its environment and is essential for biogenesis of cyanobacterial photosystems. Previously, we have identified 79 different proteins in the plasma membrane of Synechocystis sp. Strain PCC 6803 based on 2D- and 1D- gels and MALDI-TOF MS. In this work, we have performed a proteomic study screening for high-pH-stress proteins in Synechocystis. 2-D gel profiles of plasma membranes isolated from both control and high pH-treated cells were constructed and compared quantitatively based on different protein staining methods including DIGE analysis. A total of 55 differentially expressed protein spots were identified using MALDI-TOF MS and MALDI-TOF/TOF MS, corresponding to 39 gene products. Twenty-five proteins were enhanced/induced and 14 reduced by high pH. One-third of the enhanced/induced proteins were transport and binding proteins of ABC transporters including 3 phosphate transport proteins. Other proteins include MinD involved in cell division, Cya2 in signaling and proteins involved in photosynthesis and respiration. Furthermore, among these proteins regulated by high pH, eight were found to be hypothetical proteins. Functional significance of the high-pH-stress proteins is discussed integrating current knowledge on cyanobacterial cell physiology.
Collapse
Affiliation(s)
- Li-Fang Zhang
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Shcolnick S, Summerfield TC, Reytman L, Sherman LA, Keren N. The mechanism of iron homeostasis in the unicellular cyanobacterium synechocystis sp. PCC 6803 and its relationship to oxidative stress. PLANT PHYSIOLOGY 2009; 150:2045-56. [PMID: 19561120 PMCID: PMC2719147 DOI: 10.1104/pp.109.141853] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 06/17/2009] [Indexed: 05/21/2023]
Abstract
In this article, we demonstrate the connection between intracellular iron storage and oxidative stress response in cyanobacteria. Iron is essential for the survival of all organisms. However, the redox properties that make iron a valuable cofactor also lead to oxidative interactions, resulting in the formation of harmful radicals. Therefore, iron accumulation in cells should be tightly regulated, a process in which ferritin family proteins play an important role. Synechocystis sp. PCC 6803 contains two ferritin-type storage complexes, bacterioferritin and MrgA. Previous studies demonstrated the role of bacterioferritin and MrgA in iron storage. In addition, MrgA was found to play a key role in oxidative stress response. Here, we examined the dual role of the ferritin family proteins using physiological and transcriptomic approaches. Microarray analysis of iron-limited wild-type and DeltamrgA cultures revealed a substantial up-regulation of oxidative stress-related genes in mutant cells. The PerR regulator was found to play an important role in that process. Furthermore, we were able to demonstrate the connection between internal iron quota, the presence of the two storage complexes, and the sensitivity to externally applied oxidative stress. These data suggest a pivotal role for the ferritin-type proteins of Synechocystis sp. PCC 6803 in coordinating iron homeostasis and in oxidative stress response. The combined action of the two complexes allows for the safe accumulation and release of iron from storage by minimizing damage resulting from interactions between reduced iron and the oxygen radicals that are produced in abundance by the photosynthetic apparatus.
Collapse
Affiliation(s)
- Sigal Shcolnick
- Alexander Silberman Institute of Life Sciences, Department of Plant and Environmental Sciences, Hebrew University of Jerusalem, Edmond Safra Campus-Givat Ram, Jerusalem 91904, Israel
| | | | | | | | | |
Collapse
|
45
|
Transcriptional regulation and structural modeling of the FutC subunit of an ABC-type iron transporter in Synechocystis sp. strain PCC 6803. Arch Microbiol 2009; 191:561-70. [DOI: 10.1007/s00203-009-0482-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Revised: 03/23/2009] [Accepted: 04/21/2009] [Indexed: 10/20/2022]
|
46
|
The glutathione/glutaredoxin system is essential for arsenate reduction in Synechocystis sp. strain PCC 6803. J Bacteriol 2009; 191:3534-43. [PMID: 19304854 DOI: 10.1128/jb.01798-08] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Arsenic resistance in Synechocystis sp. strain PCC 6803 is mediated by an operon of three genes in which arsC codes for an arsenate reductase with unique characteristics. Here we describe the identification of two additional and nearly identical genes coding for arsenate reductases in Synechocystis sp. strain PCC 6803, which we have designed arsI1 and arsI2, and the biochemical characterization of both ArsC (arsenate reductase) and ArsI. Functional analysis of single, double, and triple mutants shows that both ArsI enzymes are active arsenate reductases but that their roles in arsenate resistance are essential only in the absence of ArsC. Based on its biochemical properties, ArsC belongs to a family that, though related to thioredoxin-dependent arsenate reductases, uses the glutathione/glutaredoxin system for reduction, whereas ArsI belongs to the previously known glutaredoxin-dependent family. We have also analyzed the role in arsenate resistance of the three glutaredoxins present in Synechocystis sp. strain PCC 6803 both in vitro and in vivo. Only the dithiolic glutaredoxins, GrxA (glutaredoxin A) and GrxB (glutaredoxin B), are able to donate electrons to both types of reductases in vitro, while GrxC (glutaredoxin C), a monothiolic glutaredoxin, is unable to donate electrons to either type. Analysis of glutaredoxin mutant strains revealed that only those lacking the grxA gene have impaired arsenic resistance.
Collapse
|
47
|
Jin Z, Heinnickel M, Krebs C, Shen G, Golbeck JH, Bryant DA. Biogenesis of iron-sulfur clusters in photosystem I: holo-NfuA from the cyanobacterium Synechococcus sp. PCC 7002 rapidly and efficiently transfers [4Fe-4S] clusters to apo-PsaC in vitro. J Biol Chem 2008; 283:28426-35. [PMID: 18694929 DOI: 10.1074/jbc.m803395200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The NfuA protein has been postulated to act as a scaffolding protein in the biogenesis of photosystem (PS) I and other iron-sulfur (Fe/S) proteins in cyanobacteria and chloroplasts. To determine the properties of NfuA, recombinant NfuA from Synechococcus sp. PCC 7002 was overproduced and purified. In vitro reconstituted NfuA contained oxygen- and EDTA-labile Fe/S cluster(s), which had EPR properties consistent with [4Fe-4S] clusters. After reconstitution with 57Fe2+, Mössbauer studies of NfuA showed a broad quadrupole doublet that confirmed the presence of [4Fe-4S]2+ clusters. Native gel electrophoresis under anoxic conditions and chemical cross-linking showed that holo-NfuA forms dimers and tetramers harboring Fe/S cluster(s). Combined with iron and sulfide analyses, the results indicated that one [4Fe-4S] cluster was bound per NfuA dimer. Fe/S cluster transfer from holo-NfuA to apo-PsaC of PS I was studied by reconstitution of PS I complexes using P700-F(X) core complexes, PsaD, apo-PsaC, and holo-NfuA. Electron transfer measurements by time-resolved optical spectroscopy showed that holo-NfuA rapidly and efficiently transferred [4Fe-4S] clusters to PsaC in a reaction that required contact between the two proteins. The NfuA-reconstituted PS I complexes had typical charge recombination kinetics from [F(A)/F(B)](-) to P700+ and light-induced low-temperature EPR spectra. These results establish that cyanobacterial NfuA can act as a scaffolding protein for the insertion of [4Fe-4S] clusters into PsaC of PS I in vitro.
Collapse
Affiliation(s)
- Zhao Jin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | | | | | | | | |
Collapse
|
48
|
Nodop A, Pietsch D, Höcker R, Becker A, Pistorius EK, Forchhammer K, Michel KP. Transcript profiling reveals new insights into the acclimation of the mesophilic fresh-water cyanobacterium Synechococcus elongatus PCC 7942 to iron starvation. PLANT PHYSIOLOGY 2008; 147:747-63. [PMID: 18424627 PMCID: PMC2409038 DOI: 10.1104/pp.107.114058] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 04/17/2008] [Indexed: 05/05/2023]
Abstract
The regulatory network for acclimation of the obligate photoautotrophic fresh water cyanobacterium Synechococcus elongatus PCC 7942 to iron (Fe) limitation was studied by transcript profiling with an oligonucleotide whole genome DNA microarray. Six regions on the chromosome with several Fe-regulated genes each were identified. The irpAB and fut region encode putative Fe uptake systems, the suf region participates in [Fe-sulfur] cluster assembly under oxidative stress and Fe limitation, the isiAB region encodes CP43' and flavodoxin, the idiCB region encodes the NuoE-like electron transport associated protein IdiC and the transcriptional activator IdiB, and the ackA/pgam region encodes an acetate kinase and a phosphoglycerate mutase. We also investigated the response of two S. elongatus PCC 7942 mutants to Fe starvation. These were mutant K10, lacking IdiB but containing IdiC, and mutant MuD, representing a idiC-merodiploid mutant with a strongly reduced amount of IdiC as well as IdiB. The absence of IdiB in mutant K10 or the strongly reduced amount of IdiB in mutant MuD allowed for the identification of additional members of the Fe-responsive IdiB regulon. Besides idiA and the irpAB operon somB(1), somA(2), ftr1, ackA, pgam, and nat also seem to be regulated by IdiB. In addition to the reduced amount of IdiB in MuD, the low concentration of IdiC may be responsible for a number of additional changes in the abundance of mainly photosynthesis-related transcripts as compared to the wild type and mutant K10. This fact may explain why it has been impossible to obtain a fully segregated IdiC-free mutant, whereas it was possible to obtain a fully segregated IdiB-free mutant.
Collapse
Affiliation(s)
- Anke Nodop
- Lehrstuhl für Molekulare Zellphysiologie , Universität Bielefeld, D-33615 Bielefeld, Germany
| | | | | | | | | | | | | |
Collapse
|
49
|
Abstract
Iron-sulfur (Fe-S) clusters are required for critical biochemical pathways, including respiration, photosynthesis, and nitrogen fixation. Assembly of these iron cofactors is a carefully controlled process in cells to avoid toxicity from free iron and sulfide. Multiple Fe-S cluster assembly pathways are present in bacteria to carry out basal cluster assembly, stress-responsive cluster assembly, and enzyme-specific cluster assembly. Although biochemical and genetic characterization is providing a partial picture of in vivo Fe-S cluster assembly, a number of mechanistic questions remain unanswered. Furthermore, new factors involved in Fe-S cluster assembly and repair have recently been identified and are expanding the complexity of current models. Here we attempt to summarize recent advances and to highlight new avenues of research in the field of Fe-S cluster assembly.
Collapse
|
50
|
Vignais PM, Billoud B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview. Chem Rev 2007; 107:4206-72. [PMID: 17927159 DOI: 10.1021/cr050196r] [Citation(s) in RCA: 1026] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paulette M. Vignais
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
| | - Bernard Billoud
- CEA Grenoble, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF 5092, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 rue des Martyrs, 38054 Grenoble cedex 9, France, and Atelier de BioInformatique Université Pierre et Marie Curie (Paris 6), 12 rue Cuvier, 75005 Paris, France
| |
Collapse
|