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Poddar H, Rios-Santacruz R, Heyes DJ, Shanmugam M, Brookfield A, Johannissen LO, Levy CW, Jeffreys LN, Zhang S, Sakuma M, Colletier JP, Hay S, Schirò G, Weik M, Scrutton NS, Leys D. Redox driven B 12-ligand switch drives CarH photoresponse. Nat Commun 2023; 14:5082. [PMID: 37604813 PMCID: PMC10442372 DOI: 10.1038/s41467-023-40817-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/09/2023] [Indexed: 08/23/2023] Open
Abstract
CarH is a coenzyme B12-dependent photoreceptor involved in regulating carotenoid biosynthesis. How light-triggered cleavage of the B12 Co-C bond culminates in CarH tetramer dissociation to initiate transcription remains unclear. Here, a series of crystal structures of the CarH B12-binding domain after illumination suggest formation of unforeseen intermediate states prior to tetramer dissociation. Unexpectedly, in the absence of oxygen, Co-C bond cleavage is followed by reorientation of the corrin ring and a switch from a lower to upper histidine-Co ligation, corresponding to a pentacoordinate state. Under aerobic conditions, rapid flash-cooling of crystals prior to deterioration upon illumination confirm a similar B12-ligand switch occurs. Removal of the upper His-ligating residue prevents monomer formation upon illumination. Combined with detailed solution spectroscopy and computational studies, these data demonstrate the CarH photoresponse integrates B12 photo- and redox-chemistry to drive large-scale conformational changes through stepwise Co-ligation changes.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - Ronald Rios-Santacruz
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - Muralidharan Shanmugam
- Photon Science Institute, Department of Chemistry, University of Manchester, Manchester, UK
| | - Adam Brookfield
- Photon Science Institute, Department of Chemistry, University of Manchester, Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - Colin W Levy
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - Laura N Jeffreys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | | | - Sam Hay
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK.
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK.
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Poddar H, Heyes DJ, Zhang S, Hardman SJ, Sakuma M, Scrutton NS. An unusual light-sensing function for coenzyme B 12 in bacterial transcription regulator CarH. Methods Enzymol 2022; 668:349-372. [PMID: 35589201 DOI: 10.1016/bs.mie.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coenzyme B12 is one of the most complex cofactors found in nature and synthesized de novo by certain groups of bacteria. Although its use in various enzymatic reactions is well characterized, only recently an unusual light-sensing function has been ascribed to coenzyme B12. It has been reported that the coenzyme B12 binding protein CarH, found in the carotenoid biosynthesis pathway of several thermostable bacteria, binds to the promoter region of DNA and suppresses transcription. To overcome the harmful effects of light-induced damage in the cells, CarH releases DNA in the presence of light and promotes transcription and synthesis of carotenoids, thereby working as a photoreceptor. CarH is able to achieve this by exploiting the photosensitive nature of the CoC bond between the adenosyl moiety and the cobalt atom in the coenzyme B12 molecule. Extensive structural and spectroscopy studies provided a mechanistic understanding of the molecular basis of this unique light-sensitive reaction. Most studies on CarH have used the ortholog from the thermostable bacterium Thermus thermophilus, due to the ease with which it can be expressed and purified in high quantities. In this chapter we give an overview of this intriguing class of photoreceptors and report a step-by-step protocol for expression, purification and spectroscopy experiments (both static and time-resolved techniques) employed in our laboratory to study CarH from T. thermophilus. We hope the contents of this chapter will be of interest to the wider coenzyme B12 community and apprise them of the potential and possibilities of using coenzyme B12 as a light-sensing probe in a protein scaffold.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Samantha J Hardman
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Michiyo Sakuma
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, United Kingdom.
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3
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Padmanabhan S, Pérez-Castaño R, Osete-Alcaraz L, Polanco MC, Elías-Arnanz M. Vitamin B 12 photoreceptors. VITAMINS AND HORMONES 2022; 119:149-184. [PMID: 35337618 DOI: 10.1016/bs.vh.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Photoreceptor proteins enable living organisms to sense light and transduce this signal into biochemical outputs to elicit appropriate cellular responses. Their light sensing is typically mediated by covalently or noncovalently bound molecules called chromophores, which absorb light of specific wavelengths and modulate protein structure and biological activity. Known photoreceptors have been classified into about ten families based on the chromophore and its associated photosensory domain in the protein. One widespread photoreceptor family uses coenzyme B12 or 5'-deoxyadenosylcobalamin, a biological form of vitamin B12, to sense ultraviolet, blue, or green light, and its discovery revealed both a new type of photoreceptor and a novel functional facet of this vitamin, best known as an enzyme cofactor. Large strides have been made in our understanding of how these B12-based photoreceptors function, high-resolution structural descriptions of their functional states are available, as are details of their unusual photochemistry. Additionally, they have inspired notable applications in optogenetics/optobiochemistry and synthetic biology. Here, we provide an overview of what is currently known about these B12-based photoreceptors, their discovery, distribution, molecular mechanism of action, and the structural and photochemical basis of how they orchestrate signal transduction and gene regulation, and how they have been used to engineer optogenetic control of protein activities in living cells.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Lucía Osete-Alcaraz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - María Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain.
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Ahearne A, Albataineh H, Dowd SE, Stevens DC. Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery. Microorganisms 2021; 9:microorganisms9071376. [PMID: 34202719 PMCID: PMC8307915 DOI: 10.3390/microorganisms9071376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Discoveries of novel myxobacteria have started to unveil the potentially vast phylogenetic diversity within the family Myxococcaceae and have brought about an updated approach to myxobacterial classification. While traditional approaches focused on morphology, 16S gene sequences, and biochemistry, modern methods including comparative genomics have provided a more thorough assessment of myxobacterial taxonomy. Herein, we utilize long-read genome sequencing for two myxobacteria previously classified as Archangium primigenium and Chondrococcus macrosporus, as well as four environmental myxobacteria newly isolated for this study. Average nucleotide identity and digital DNA-DNA hybridization scores from comparative genomics suggest previously classified as A. primigenium to instead be a novel member of the genus Melittangium, C. macrosporus to be a potentially novel member of the genus Corallococcus with high similarity to Corallococcus exercitus, and the four isolated myxobacteria to include another novel Corallococcus species, a novel Pyxidicoccus species, a strain of Corallococcus exiguus, and a potentially novel Myxococcus species with high similarity to Myxococcus stipitatus. We assess the biosynthetic potential of each sequenced myxobacterium and suggest that genus-level conservation of biosynthetic pathways support our preliminary taxonomic assignment. Altogether, we suggest that long-read genome sequencing benefits the classification of myxobacteria and improves determination of biosynthetic potential for prioritization of natural product discovery.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Hanan Albataineh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA;
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
- Correspondence: ; Tel.: +1-662-915-5730
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5
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Light-Triggered Carotenogenesis in Myxococcus xanthus: New Paradigms in Photosensory Signaling, Transduction and Gene Regulation. Microorganisms 2021; 9:microorganisms9051067. [PMID: 34063365 PMCID: PMC8156234 DOI: 10.3390/microorganisms9051067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Myxobacteria are Gram-negative δ-proteobacteria found predominantly in terrestrial habitats and often brightly colored due to the biosynthesis of carotenoids. Carotenoids are lipophilic isoprenoid pigments that protect cells from damage and death by quenching highly reactive and toxic oxidative species, like singlet oxygen, generated upon growth under light. The model myxobacterium Myxococcus xanthus turns from yellow in the dark to red upon exposure to light because of the photoinduction of carotenoid biosynthesis. How light is sensed and transduced to bring about regulated carotenogenesis in order to combat photooxidative stress has been extensively investigated in M. xanthus using genetic, biochemical and high-resolution structural methods. These studies have unearthed new paradigms in bacterial light sensing, signal transduction and gene regulation, and have led to the discovery of prototypical members of widely distributed protein families with novel functions. Major advances have been made over the last decade in elucidating the molecular mechanisms underlying the light-dependent signaling and regulation of the transcriptional response leading to carotenogenesis in M. xanthus. This review aims to provide an up-to-date overview of these findings and their significance.
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6
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2-Hydroxysorangiadenosine: Structure and Biosynthesis of a Myxobacterial Sesquiterpene-Nucleoside. Molecules 2020; 25:molecules25112676. [PMID: 32527018 PMCID: PMC7321100 DOI: 10.3390/molecules25112676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/02/2022] Open
Abstract
Myxobacteria represent an under-investigated source for biologically active natural products featuring intriguing structural moieties with potential applications, e.g., in the pharmaceutical industry. Sorangiadenosine and the here-discovered 2-hydroxysorangiadenosine are myxobacterial sesquiterpene–nucleosides with an unusual structural moiety, a bicyclic eudesmane-type sesquiterpene. As the biosynthesis of these rare terpene–nucleoside hybrid natural products remains elusive, we investigated secondary metabolomes and genomes of several 2-hydroxysorangiadenosine-producing myxobacteria. We report the isolation and full structure elucidation of 2-hydroxysorangiadenosine and its cytotoxic and antibiotic activities and propose a biosynthetic pathway in the myxobacterium Vitiosangium cumulatum MCy10943T.
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7
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Pérez J, Muñoz-Dorado J, Moraleda-Muñoz A. The complex global response to copper in the multicellular bacterium Myxococcus xanthus. Metallomics 2019; 10:876-886. [PMID: 29961779 DOI: 10.1039/c8mt00121a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The complex copper response of the multicellular proteobacterium M. xanthus includes structural genes similar to those described in other bacteria, such as P1B-type ATPases, multicopper oxidases, and heavy metal efflux systems. However, the two time-dependent expression profiles of the different copper systems are unique. There are a number of genes responsible for an immediate response, whose expression increases after the addition of copper, but rapidly decreases thereafter to basal levels. The regulatory element that controls this early response is CorE, a novel extracytoplasmic function σ factor that is activated by Cu2+ and inactivated by Cu+. Other genes are part of a maintenance response. These genes show a profile that slows up after the copper addition and reaches a plateau at 24-48 h incubation. Most of the genes involved in this response are encoded by the operon curA, which is regulated by the two-component system CorSR. Moreover, other genes involved in the maintenance response are regulated by different regulatory elements that remain unknown. Additionally, copper activates the transcription of the structural genes for carotenoid synthesis through a mechanism that requires the activation of the σ factor CarQ. Bearing in mind that M. xanthus is not very resistant to copper, it is speculated that the complexity of its copper response might be related to its complex life cycle.
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Affiliation(s)
- Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, E-18071 Granada, Spain.
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8
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Padmanabhan S, Pérez-Castaño R, Elías-Arnanz M. B12-based photoreceptors: from structure and function to applications in optogenetics and synthetic biology. Curr Opin Struct Biol 2019; 57:47-55. [DOI: 10.1016/j.sbi.2019.01.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
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9
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Gregory K, Salvador LA, Akbar S, Adaikpoh BI, Stevens DC. Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. Microorganisms 2019; 7:E181. [PMID: 31238501 PMCID: PMC6616573 DOI: 10.3390/microorganisms7060181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023] Open
Abstract
Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.
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Affiliation(s)
- Katherine Gregory
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Laura A Salvador
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Shukria Akbar
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Barbara I Adaikpoh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - D Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
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10
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Keyfi F, Abbaszadegan MR, Sankian M, Rolfs A, Orolicki S, Pournasrollah M, Alijanpour M, Varasteh A. Mutation analysis of genes related to methylmalonic acidemia: identification of eight novel mutations. Mol Biol Rep 2019; 46:271-285. [PMID: 30712249 DOI: 10.1007/s11033-018-4469-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 11/02/2018] [Indexed: 11/28/2022]
Abstract
Methylmalonic acidemia (MMA), an inherited metabolic disease, results from genetic defects in methylmalonyl-CoA mutase or any of the proteins involved in adenosylcobalamin synthesis. This enzyme is classified into several complementation groups and genotypic classes. In this work we explain the biochemical, structural and genetic analysis of 25 MMA patients, from Iran. The diagnosis was established by the measurement of propionylcarnitine in blood using tandem mass spectrometry and confirmed using a gas chromatography-flame ionization detector. Using clinical, biochemical, structural and molecular analyses we identified 15 mut MMA, three cblA, one cblB, and four cblC-deficient patients. Among mutations identified in the MUT gene (MUT) only one, the c.1874A>C (p.D625A) variant, is likely a mut- mutation. The remaining mutations are probably mut0. Here, we present the first molecular analysis of MMA in Iranian patients and have identified eight novel mutations. Four novel mutations (p.D625A, p.R326G, p.V157F, p.F379L) were seen exclusively in patients from northern Iran. One novel splice site mutation (c.2125-3C>G) in MUT and two novel mutation (p.N225M and p.A99P) in the MMAA gene were associated with patients from eastern Iran. The rs184829210 SNP was recognized only in patients with the novel c.958G>A (p.A320T) mutation. This study confirms pathogenesis of deficient enzyme activity in MUT, MMAA, MMAB, and MMACHC as previous observations. These results could act as a basis for the performance of pharmacological therapies for increasing the activity of proteins derived from these mutations.
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Affiliation(s)
- Fatemeh Keyfi
- Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences, Mashhad, Iran.,Division of Metabolic disorders, Pardis Clinical and Genetic Laboratory, Mashhad, Iran.,Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad R Abbaszadegan
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arndt Rolfs
- Albrecht Kossel Institute for Neuroregeneration, University of Rostock, Rostock, Germany.,Chief Medical Director, Centogene AG, Rostock, Germany
| | | | - Mohammad Pournasrollah
- Non-contagious pediatric disease Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Morteza Alijanpour
- Non-contagious pediatric disease Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Abdolreza Varasteh
- Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences, Mashhad, Iran. .,Division of Metabolic disorders, Pardis Clinical and Genetic Laboratory, Mashhad, Iran. .,Allergy Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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11
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Padmanabhan S, Jost M, Drennan CL, Elías-Arnanz M. A New Facet of Vitamin B 12: Gene Regulation by Cobalamin-Based Photoreceptors. Annu Rev Biochem 2017; 86:485-514. [PMID: 28654327 PMCID: PMC7153952 DOI: 10.1146/annurev-biochem-061516-044500] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Living organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5'-deoxyadenosylcobalamin, a form of vitamin B12 that is best known as an enzyme cofactor, has expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5'-deoxyadenosylcobalamin and light. This review surveys current knowledge about these B12-dependent photoreceptors, their distribution and mode of action, and the structural and photochemical basis of how they orchestrate signal transduction and control gene expression.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain;
| | - Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158-2140;
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética, Unidad Asociada al Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain;
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12
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Abstract
This Perspective provides the first detailed overview of the photoresponse of vitamin B12 and its derivatives, from the early, photophysical events to the burgeoning area of B12-dependent photobiology.
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Affiliation(s)
- Alex R. Jones
- School of Chemistry
- Photon Science Institute and Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
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13
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The photochemical mechanism of a B12-dependent photoreceptor protein. Nat Commun 2015; 6:7907. [PMID: 26264192 PMCID: PMC4557120 DOI: 10.1038/ncomms8907] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023] Open
Abstract
The coenzyme B12-dependent photoreceptor protein, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. On binding of coenzyme B12 the monomeric apoprotein forms tetramers in the dark, which bind operator DNA thus blocking transcription. Under illumination the CarH tetramer dissociates, weakening its affinity for DNA and allowing transcription. The mechanism by which this occurs is unknown. Here we describe the photochemistry in CarH that ultimately triggers tetramer dissociation; it proceeds via a cob(III)alamin intermediate, which then forms a stable adduct with the protein. This pathway is without precedent and our data suggest it is independent of the radical chemistry common to both coenzyme B12 enzymology and its known photochemistry. It provides a mechanistic foundation for the emerging field of B12 photobiology and will serve to inform the development of a new class of optogenetic tool for the control of gene expression. Coenzyme B12 traditionally acts as cofactor to light-independent metabolic enzymes in bacteria and humans. Here, Kutta et al. present a time-resolved photochemical description of a B12-dependent photoreceptor protein, which represents a mechanistic foundation for B12 photobiology.
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Role and Function of LitR, an Adenosyl B12-Bound Light-Sensitive Regulator of Bacillus megaterium QM B1551, in Regulation of Carotenoid Production. J Bacteriol 2015; 197:2301-15. [PMID: 25917914 DOI: 10.1128/jb.02528-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/23/2015] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED The LitR/CarH family of proteins is a light-sensitive MerR family of transcriptional regulators that contain an adenosyl B12 (coenzyme B12 or AdoB12)-binding domain at the C terminus. The genes encoding these proteins are found in phylogenetically diverse bacterial genera; however, the biochemical properties of these proteins from Gram-positive bacteria remain poorly understood. We performed genetic and biochemical analyses of a homolog of the LitR protein from Bacillus megaterium QM B1551, a Gram-positive endospore-forming soil bacterium. Carotenoid production was induced by illumination in this bacterium. In vivo analysis demonstrated that LitR plays a central role in light-inducible carotenoid production and serves as a negative regulator of the light-inducible transcription of crt and litR itself. Biochemical evidence showed that LitR in complex with AdoB12 binds to the promoter regions of litR and the crt operon in a light-sensitive manner. In vitro transcription experiments demonstrated that AdoB12-LitR inhibited the specific transcription of the crt promoter generated by a σ(A)-containing RNA polymerase holoenzyme under dark conditions. Collectively, these data indicate that the AdoB12-LitR complex serves as a photoreceptor with DNA-binding activity in B. megaterium QM B1551 and that its function as a transcriptional repressor is fundamental to the light-induced carotenoid production. IMPORTANCE Members of the LitR/CarH family are AdoB12-based photosensors involved in light-inducible carotenoid production in nonphototrophic Gram-negative bacteria. Our study revealed that Bacillus LitR in complex with AdoB12 also serves as a transcriptional regulator with a photosensory function, which indicates that the LitR/CarH family is generally involved in the light-inducible carotenoid production of nonphototrophic bacteria.
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15
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Takano H, Beppu T, Ueda K. The CarA/LitR-Family Transcriptional Regulator: Its Possible Role as a Photosensor and Wide Distribution in Non-Phototrophic Bacteria. Biosci Biotechnol Biochem 2014; 70:2320-4. [PMID: 16960358 DOI: 10.1271/bbb.60230] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
LitR is a MerR-family regulator that controls light-induced carotenogenesis in Streptomyces coelicolor. The introduction of litR conferred photo-dependent transcription activities on Streptomyces griseus, which does not perform photo-responsive carotenogenesis. LitR discovers homologs encoded at illumination-related loci of various non-phototrophic bacterial genomes. Probably, LitR acts not only as a transcriptional regulator but also a photosensor.
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Affiliation(s)
- Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
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Analytical ultracentrifugation studies of oligomerization and DNA-binding of TtCarH, a Thermus thermophilus coenzyme B12-based photosensory regulator. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:463-76. [PMID: 23512413 DOI: 10.1007/s00249-013-0897-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 12/23/2022]
Abstract
Thermus thermophilus transcriptional factor TtCarH belongs to a newly discovered class of photoreceptors that use 5'-deoxyadenosylcobalamin (AdoB12) as the light-sensing chromophore. Photoregulation relies on the repressor activity of AdoB12-bound oligomers in the dark, which light counteracts by oligomer disruption due to AdoB12 photolysis. In this study, we investigated TtCarH self-association and binding to DNA in the dark and in the light using analytical ultracentrifugation (AUC) methods, both sedimentation velocity (SV) as well as equilibrium (SE). From a methodological point of view, this study shows that AUC can provide hydrodynamic insights in cases where light is a crucial determinant of solution properties. For the light-sensitive TtCarH, absorbance as well as interference AUC data yielded comparable results. Sedimentation coefficients and whole-body hydrodynamic analysis from SV experiments indicate that in solution apo-TtCarH and light-exposed AdoB12-TtCarH are predominantly aspherical, ellipsoidal monomers, in accord with SE data. By comparison, AdoB12-TtCarH exists as a more compact tetramer in the dark, with smaller forms such as dimers or monomers remaining undetected and low levels of larger oligomers appearing at higher protein concentrations. AUC analyses indicate that in the dark AdoB12-TtCarH associates as a tetramer with DNA but forms smaller complexes in the apo form or if exposed to light. The self-association and DNA-binding properties of TtCarH deduced from AUC are consistent with data from size-exclusion and DNA-binding gel-shift assays. AUC analyses together with hydrodynamic modeling provide insights into the AdoB12- and light-dependent self-association and DNA-binding of TtCarH.
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17
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Light-dependent gene regulation by a coenzyme B12-based photoreceptor. Proc Natl Acad Sci U S A 2011; 108:7565-70. [PMID: 21502508 DOI: 10.1073/pnas.1018972108] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Cobalamin (B(12)) typically functions as an enzyme cofactor but can also regulate gene expression via RNA-based riboswitches. B(12)-directed gene regulatory mechanisms via protein factors have, however, remained elusive. Recently, we reported down-regulation of a light-inducible promoter in the bacterium Myxococcus xanthus by two paralogous transcriptional repressors, of which one, CarH, but not the other, CarA, absolutely requires B(12) for activity even though both have a canonical B(12)-binding motif. Unanswered were what underlies this striking difference, what is the specific cobalamin used, and how it acts. Here, we show that coenzyme B(12) (5'-deoxyadenosylcobalamin, AdoB(12)), specifically dictates CarH function in the dark and on exposure to light. In the dark, AdoB(12)-binding to the autonomous domain containing the B(12)-binding motif foments repressor oligomerization, enhances operator binding, and blocks transcription. Light, at various wavelengths at which AdoB(12) absorbs, dismantles active repressor oligomers by photolysing the bound AdoB(12) and weakens repressor-operator binding to allow transcription. By contrast, AdoB(12) alters neither CarA oligomerization nor operator binding, thus accounting for its B(12)-independent activity. Our findings unveil a functional facet of AdoB(12) whereby it serves as the chromophore of a unique photoreceptor protein class acting in light-dependent gene regulation. The prevalence of similar proteins of unknown function in microbial genomes suggests that this distinct B(12)-based molecular mechanism for photoregulation may be widespread in bacteria.
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18
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Elías-Arnanz M, Padmanabhan S, Murillo FJ. The regulatory action of the myxobacterial CarD/CarG complex: a bacterial enhanceosome? FEMS Microbiol Rev 2010; 34:764-78. [PMID: 20561058 DOI: 10.1111/j.1574-6976.2010.00235.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A global regulatory complex made up of two unconventional transcriptional factors, CarD and CarG, is implicated in the control of various processes in Myxococcus xanthus, a Gram-negative bacterium that serves as a prokaryotic model system for multicellular development and the response to blue light. CarD has a unique two-domain architecture composed of: (1) a C-terminal DNA-binding domain that resembles eukaryotic high mobility group A (HMGA) proteins, which are relatively abundant, nonhistone components of chromatin that remodel DNA and prime it for the assembly of multiprotein-DNA complexes essential for various DNA transactions, and (2) an N-terminal domain involved in interactions with CarG and RNA polymerase, which is also the founding member of the large CarD_TRCF family of bacterial proteins. CarG, which does not bind DNA directly, has a zinc-binding motif of the type found in the archaemetzincin class of metalloproteases that, in CarG, appears to play a purely structural role. This review aims to provide an overview of the known molecular details and insights emerging from the study of the singular CarD-CarG prokaryotic regulatory complex and its parallels with enhanceosomes, the higher order, nucleoprotein transcription complexes in eukaryotes.
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Affiliation(s)
- Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Area de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
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19
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Galbis-Martínez L, Galbis-Martínez M, Murillo FJ, Fontes M. An anti-antisigma factor in the response of the bacterium Myxococcus xanthus to blue light. MICROBIOLOGY-SGM 2008; 154:895-904. [PMID: 18310035 DOI: 10.1099/mic.0.2007/013359-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cells of the Gram-negative bacterium Myxococcus xanthus respond to blue light by producing carotenoids, pigments that play a protective role against the oxidative effects of light. Blue light triggers a network of regulatory actions that lead to the transcriptional activation of the structural genes for carotenoid synthesis. The product of carF, similar to a family of proteins of unknown function called Kua, is an early regulator of this process. Previous genetic data indicate that CarF participates in the light-dependent inactivation of the antisigma factor CarR. In the dark, CarR sequesters the ECF-sigma factor CarQ to the membrane, thereby preventing the activation of the structural genes for carotenoid synthesis. Using a bacterial two-hybrid system, we show here that both CarF and CarQ physically interact with CarR. These results, together with the finding that CarF is located at the membrane, support the hypothesis that CarF acts as an anti-antisigma factor. Comparison of CarF with other Kua proteins shows a remarkable conservation of a number of histidine residues. The effects on CarF function of several histidine to alanine substitutions and of the truncation of specific CarF domains are also reported here.
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Affiliation(s)
- Lilian Galbis-Martínez
- Departamento de Genética y Microbiología (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Marisa Galbis-Martínez
- Departamento de Genética y Microbiología (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Francisco J Murillo
- Departamento de Genética y Microbiología (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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20
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Pérez-Marín MC, Padmanabhan S, Polanco MC, Murillo FJ, Elías-Arnanz M. Vitamin B12 partners the CarH repressor to downregulate a photoinducible promoter in Myxococcus xanthus. Mol Microbiol 2008; 67:804-19. [PMID: 18315685 DOI: 10.1111/j.1365-2958.2007.06086.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A light-inducible promoter, P(B), drives expression of the carB operon in Myxococcus xanthus. Repressed by CarA in the dark, P(B) is activated when CarS, produced in the light, sequesters CarA to prevent operator-CarA binding. The MerR-type, N-terminal domain of CarA, which mediates interactions with both operator and CarS, is linked to a C-terminal oligomerization module with a predicted cobalamin-binding motif. Here, we show that although CarA does bind vitamin B12, mutating the motif involved has no effect on its ability to repress P(B). Intriguingly, P(B) could be repressed in the dark even with no CarA, so long as B12 and an intact CarA operator were present. We have discovered that this effect of B12 depends on the gene immediately downstream of carA. Its product, CarH, also consists of a MerR-type, N-terminal domain that specifically recognizes the CarA operator and CarS, linked to a predicted B12-binding C-terminal oligomerization module. The B12-mediated repression of P(B) in the dark is relieved by deleting carH, by mutating the DNA- or B12-binding residues of CarH, or by illumination. Our findings unveil parallel regulatory circuits that control a light-inducible promoter using a transcriptional factor repertoire that includes a paralogous gene pair and vitamin B12.
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Affiliation(s)
- Mari Cruz Pérez-Marín
- Departamento de Genética y Microbiología, Area de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
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21
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Navarro-Avilés G, Jiménez MA, Pérez-Marín MC, González C, Rico M, Murillo FJ, Elías-Arnanz M, Padmanabhan S. Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor. Mol Microbiol 2007; 63:980-94. [PMID: 17233828 DOI: 10.1111/j.1365-2958.2006.05567.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Blue light induces carotenogenesis in Myxococcus xanthus. The carB operon encodes all but one of the structural genes involved, and its expression is regulated by the CarA-CarS repressor-antirepressor pair. In the dark, CarA-operator binding represses carB. CarS, produced on illumination, interacts physically with CarA to dismantle the CarA-operator complex and activate carB. Both operator and CarS bind to the autonomously folded N-terminal domain of CarA, CarA(Nter), which in excess represses carB. Here, we report the NMR structure of CarA(Nter), and map residues that interact with operator and CarS by NMR chemical shift perturbations, and in vivo and in vitro analyses of site-directed mutants. We show CarA(Nter) adopts the winged-helix topology of MerR-family DNA-binding domains, and conserves the majority of the helix-turn-helix and wing contacts with DNA. Tellingly, helix alpha2 in CarA, a key element in operator DNA recognition, is also critical for interaction with CarS, implying that the CarA-CarS protein-protein and the CarA-operator protein-DNA interfaces overlap. Thus, binding of CarA to operator and to antirepressor are mutually exclusive, and CarA may discern structural features in the acidic CarS protein that resemble operator DNA. Repressor inactivation by occluding the DNA-binding region may be a recurrent mechanism of action for acidic antirepressors.
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Affiliation(s)
- Gloria Navarro-Avilés
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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22
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Takano H, Asker D, Beppu T, Ueda K. Genetic control for light-induced carotenoid production in non-phototrophic bacteria. J Ind Microbiol Biotechnol 2005; 33:88-93. [PMID: 16091943 DOI: 10.1007/s10295-005-0005-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 06/16/2005] [Indexed: 10/25/2022]
Abstract
Carotenoids are naturally occurring yellow or orange pigments that serve as a protectant against photo-oxidative damages. Among the wide variety of producers, the prokaryotes generate a broad spectrum of carotenoids with diverse chemical structures that are expected to have a high potential in biotechnological applications. Bacterial carotenogenesis occurs in a constitutive or light-induced manner, which suggests the diversity of the regulatory mechanism. The mechanism for light-induced carotenoid production in non-phototrophic bacteria has been studied in detail in Myxococcus xanthus, a Gram-negative gliding bacterium. The complicated mechanism involves the activation of an extracytoplasmic function (ECF) sigma factor (CarQ), which leads to the sequestration of a MerR family transcriptional regulator (CarA) that represses the expression of the carotenoid biosynthesis genes in the dark. Recently, we identified another regulatory mechanism for light-induced carotenogenesis in Streptomyces coelicolor A3(2), a Gram-positive soil bacterium. In this organism, the transcription of the carotenoid biosynthesis gene cluster is specified by LitS, a photo-inducible ECF sigma factor. The evidence indicates that the photo-dependent transcription of litS is mediated by LitR, a MerR family transcriptional regulator. In addition, it is suggested that the conformational alteration of LitR upon receiving the illumination signal determines its binding to DNA. The carboxy-terminal domain of LitR contains a possible binding site for Vitamin B12, which may serve as a capturing apparatus for the illumination signal.
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Affiliation(s)
- Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252-8510, Japan
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23
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Oltean S, Banerjee R. A B12-responsive internal ribosome entry site (IRES) element in human methionine synthase. J Biol Chem 2005; 280:32662-8. [PMID: 16051610 DOI: 10.1074/jbc.m501964200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Regulation of homocysteine, a sulfur-containing amino acid that is a risk factor for cardiovascular diseases, is poorly understood. Methionine synthase (MS) is a key enzyme that clears intracellular homocysteine, and its activity is induced by its cofactor, vitamin B12, at a translational level. In this study, we demonstrate that translation of MS, which has a long and highly structured 5'-untranslated region, is initiated from an internal ribosome entry site (IRES), which is modulated by B12. The minimal IRES element spans 71 bases immediately upstream of the initiation codon. Electrophoretic mobility shift analysis reveals the presence of a B12 -dependent protein-RNA complex and suggests the possibility that B12-dependent increase of IRES efficiency is mediated via a protein. Modulation of the IRES-dependent translation of an essential gene by the cofactor of the encoded enzyme represents a novel example of a gene-nutrient interaction.
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Affiliation(s)
- Sebastian Oltean
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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24
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O'Mahony R, Doran J, Coffey L, Cahill OJ, Black GW, O'Reilly C. Characterisation of the nitrile hydratase gene clusters of Rhodococcus erythropolis strains AJ270 and AJ300 and Microbacterium sp. AJ115 indicates horizontal gene transfer and reveals an insertion of IS1166. Antonie van Leeuwenhoek 2005; 87:221-32. [PMID: 15803388 DOI: 10.1007/s10482-004-3721-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 09/23/2004] [Indexed: 10/25/2022]
Abstract
The nitrile metabolising strains AJ270, AJ300 and AJ115 were isolated from the same location. The strains have very similar nitrile metabolising profiles. Sequencing of the 16S rRNA gene indicates that strains AJ270 and AJ300 are novel strains of Rhodococcus erythropolis while strain AJ115 is a novel Microbacterium strain very closely related to Microbacterium oxydans and Microbacterium liquefaciens. Analysis of the structure of the nitrile hydratase/amidase gene clusters in the three strains indicates that this region is identical in these strains and that this structure is different to other nitrile hydratase/amidase gene clusters. The major difference seen is the insertion of a complete copy of the insertion sequence IS1166 in the nhr2 gene. This copy of IS1166 generates a 10 bp direct duplication at the point of insertion and has one ORF encoding a protein of 434 amino acids, with 98% homology to the transposase of IS666 from Mycobacterium avium. A gene oxd, encoding aldoxime dehydratase is found upstream of the nitrile hydratase gene cluster and an open reading frame encoding a protein with homology to GlnQ type ABC transporters is found downstream of the nitrile hydratase/amidase genes. The identity of the nitrile hydratase/amidase gene clusters in the three strains suggests horizontal gene transfer of this region. Analysis of the strains for both linear and circular plasmids indicates that both are present in the strains but hybridisation studies indicate that the nitrile hydratase/amidase gene cluster is chromosomally located. The nitrile hydratase/amidase enzymes of strain AJ270 are inducible with acetonitrile or acetamide. Interestingly although a number of Fe-type nitrile hydratases have been shown to be photosensitive, the enzyme from strain AJ270 is not.
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Affiliation(s)
- Rebecca O'Mahony
- Department of Chemical and Life Sciences, Waterford Institute of Technology, Cork Road, Waterford, Ireland
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25
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Moraleda-Muñoz A, Pérez J, Fontes M, Murillo FJ, Muñoz-Dorado J. Copper induction of carotenoid synthesis in the bacterium Myxococcus xanthus. Mol Microbiol 2005; 56:1159-68. [PMID: 15882411 DOI: 10.1111/j.1365-2958.2005.04613.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Copper induces a red pigmentation in cells of the bacterium Myxococcus xanthus when they are incubated in the dark, at suboptimal growth conditions. The colouration results from the accumulation of carotenoids, as demonstrated by chemical analysis, and by the lack of a copper effect on M. xanthus mutants affected in known structural genes for carotenoid synthesis. None of several other metals or oxidative agents can mimic the copper effect on carotenoid synthesis. Until now, blue light was the only environmental agent known to induce carotenogenesis in M. xanthus. As happens for the blue light, copper activates the transcription of the structural genes for carotenoid synthesis through the transcriptional activation of the carQRS operon. This encodes the ECF sigma factor CarQ, directly or indirectly responsible for the activation of the structural genes, and the anti-sigma factor CarR, which physically interacts with CarQ to blocks its action in the absence of external stimuli. All but one of the other regulatory elements known to participate in the induction of carotenoid synthesis by blue light are required for the response to copper. The exception is CarF, a protein required for the light-mediated dismantling of the CarR-CarQ complex. In addition to carotenogenesis, copper induces other unknown cellular mechanisms that confer tolerance to the metal.
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Affiliation(s)
- Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Avda, Fuentenueva s/n, E-18071 Granada, Spain
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26
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Pérez-Marín MC, López-Rubio JJ, Murillo FJ, Elías-Arnanz M, Padmanabhan S. The N terminus of Myxococcus xanthus CarA repressor is an autonomously folding domain that mediates physical and functional interactions with both operator DNA and antirepressor protein. J Biol Chem 2004; 279:33093-103. [PMID: 15163666 DOI: 10.1074/jbc.m405225200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the Myxococcus xanthus carB operon, which encodes the majority of the enzymes involved in light-induced carotenogenesis, is down-regulated in the dark by the CarA repressor binding to its bipartite operator. CarS, produced on illumination, relieves repression of carB by physically interacting with CarA to dis-mantle CarA-DNA complexes. Here, we demonstrate that the N- and C-terminal portions of CarA are organized as distinct structural and functional domains. Specifically, we show that the 78 N-terminal residues of CarA, CarA(Nter), form a monomeric, highly helical, autonomously folding unit with significant structural stability. Significantly, CarA(Nter) houses both the operator and CarS binding specificity determinants of CarA. CarA(Nter) binds operator with a lower affinity than whole CarA, and the CarA(Nter)-CarS complex has a 1:1 stoichiometry. In vitro, sufficiently high concentrations of CarA(Nter) block M. xanthus RNA polymerase-promoter binding, and this is relieved by CarS. In vivo, substitution of the gene carA by that for CarA(Nter) results in constitutive expression of carB just as in a carA-deleted background. However, re-engineering the latter strain to overexpress CarA(Nter) restores repression of carB. Thus, the 78-residue N-terminal portion of CarA is an autonomously folded, dual function domain that orchestrates specific DNA-protein and protein-protein interactions and, when overexpressed, can be functionally competent in vivo.
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Affiliation(s)
- Mari Cruz Pérez-Marín
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia 30071, Spain
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27
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Abstract
The MerR family is a group of transcriptional activators with similar N-terminal helix-turn-helix DNA binding regions and C-terminal effector binding regions that are specific to the effector recognised. The signature of the family is amino acid similarity in the first 100 amino acids, including a helix-turn-helix motif followed by a coiled-coil region. With increasing recognition of members of this class over the last decade, particularly with the advent of rapid bacterial genome sequencing, MerR-like regulators have been found in a wide range of bacterial genera, but not yet in archaea or eukaryotes. The few MerR-like regulators that have been studied experimentally have been shown to activate suboptimal sigma(70)-dependent promoters, in which the spacing between the -35 and -10 elements recognised by the sigma factor is greater than the optimal 17+/-1 bp. Activation of transcription is through protein-dependent DNA distortion. The majority of regulators in the family respond to environmental stimuli, such as oxidative stress, heavy metals or antibiotics. A subgroup of the family activates transcription in response to metal ions. This subgroup shows sequence similarity in the C-terminal effector binding region as well as in the N-terminal region, but it is not yet clear how metal discrimination occurs. This subgroup of MerR family regulators includes MerR itself and may have evolved to generate a variety of specific metal-responsive regulators by fine-tuning the sites of metal recognition.
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Affiliation(s)
- Nigel L Brown
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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28
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Browning DF, Whitworth DE, Hodgson DA. Light-induced carotenogenesis in Myxococcus xanthus: functional characterization of the ECF sigma factor CarQ and antisigma factor CarR. Mol Microbiol 2003; 48:237-51. [PMID: 12657058 DOI: 10.1046/j.1365-2958.2003.03431.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Illumination of dark-grown Myxococcus xanthus with blue light leads to the induction of carotenoid synthesis. Central to this response is the activation of the light-inducible promoter, PcarQRS, and the transcription of three downstream genes, carQ, carR and carS. Sequence analysis predicted that CarQ is a member of the ECF (extracytoplasmic function) subfamily of RNA polymerase sigma factors, and that CarR is an inner membrane protein. Genetic analysis strongly implied that CarR is an antisigma factor that sequesters CarQ in a transcriptionally inactive complex. Using in vitro transcription run-off assays, we present biochemical evidence that CarQ functions as a bacterial sigma factor and is responsible for transcription initiation at PcarQRS. Similar experiments using the crtI promoter failed to implicate CarQ in direct transcription of the crtI gene. Experiments using the yeast two-hybrid system demonstrated a protein-protein interaction between CarQ and CarR, providing evidence of a CarQ-CarR complex. The yeast two-hybrid system data also indicated that CarR is capable of oligomerization. Fractionation of M. xanthus membranes with the detergent sarkosyl showed that CarR was associated with the inner membrane. Furthermore, CarR was found to be unstable in illuminated stationary phase cells, providing a possible mechanism by which the CarR-CarQ complex is disrupted.
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Affiliation(s)
- Douglas F Browning
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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29
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Gomelsky L, Sram J, Moskvin OV, Horne IM, Dodd HN, Pemberton JM, McEwan AG, Kaplan S, Gomelsky M. Identification and in vivo characterization of PpaA, a regulator of photosystem formation in Rhodobacter sphaeroides. MICROBIOLOGY (READING, ENGLAND) 2003; 149:377-388. [PMID: 12624200 DOI: 10.1099/mic.0.25972-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A regulatory protein, PpaA, involved in photosystem formation in the anoxygenic phototrophic proteobacterium Rhodobacter sphaeroides has been identified and characterized in vivo. Based on the phenotypes of cells expressing the ppaA gene in extra copy and on the phenotype of the ppaA null mutant, it was concluded that PpaA activates photopigment production and puc operon expression under aerobic conditions. This is in contrast to the function of the PpaA homologue from Rhodobacter capsulatus, AerR, which acts as a repressor under aerobic conditions [Dong, C., Elsen, S., Swem, L. R. & Bauer, C. E. (2002). J Bacteriol 184, 2805-2814]. The expression of the ppaA gene increases several-fold in response to a decrease in oxygen tension, suggesting that the PpaA protein is active under conditions of low or no oxygen. However, no discernible phenotype of a ppaA null mutant was observed under anaerobic conditions tested thus far. The photosystem gene repressor PpsR mediates repression of ppaA gene expression under aerobic conditions. Sequence analysis of PpaA homologues from several anoxygenic phototrophic bacteria revealed a putative corrinoid-binding domain. It is suggested that PpaA binds a corrinoid cofactor and the availability or structure of this cofactor affects PpaA activity.
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Affiliation(s)
- Larissa Gomelsky
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071-3944, USA
| | - Jakub Sram
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071-3944, USA
| | - Oleg V Moskvin
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071-3944, USA
| | - Irene M Horne
- Department of Microbiology and Parasitology, University of Queensland, Brisbane 4072, Australia
| | - Helen N Dodd
- Department of Microbiology and Parasitology, University of Queensland, Brisbane 4072, Australia
| | - John M Pemberton
- Department of Microbiology and Parasitology, University of Queensland, Brisbane 4072, Australia
| | - Alastair G McEwan
- Department of Microbiology and Parasitology, University of Queensland, Brisbane 4072, Australia
| | - Samuel Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030, USA
| | - Mark Gomelsky
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071-3944, USA
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30
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Fontes M, Galbis-Martínez L, Murillo FJ. A novel regulatory gene for light-induced carotenoid synthesis in the bacterium Myxococcus xanthus. Mol Microbiol 2003; 47:561-71. [PMID: 12519205 DOI: 10.1046/j.1365-2958.2003.03319.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Myxococcus xanthus cells respond to blue light by producing carotenoids. Light triggers a network of regulatory actions that lead to the transcriptional activation of the carotenoid genes. By screening the colour phenotype of a collection of Tn5-lac insertion mutants, we have isolated a new mutant devoid of carotenoid synthesis. We map the transposon insertion, which co-segregates with the mutant phenotype, to a previously unknown gene designated here as carF. An in frame deletion within carF causes the same phenotype as the Tn5-lac insertion. The carF deletion prevents the activation of the normally light-inducible genes, without affecting the expression of any of the regulatory genes known to be expressed in a light-independent manner. Until now, the switch that sets off the regulatory cascade had been identified with light-driven inactivation of protein CarR, an antisigma factor. The exact mechanism of this inactivation has remained elusive. We show by epistatic analysis that the carF gene product participates in the light-dependent inactivation of CarR. The predicted CarF amino acid sequence reveals no known prokaryotic homologues. On the other hand, CarF is remarkably similar to Kua, a family of proteins of unknown function that is widely distributed among eukaryotes.
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Affiliation(s)
- Marta Fontes
- Departamento de Genética y Microbiología, Facultad de Biologie, Universidad de Murcia, Spain
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