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Pérez-Castaño R, Bastida-Martínez E, Fernández Zapata J, Polanco MDC, Galbis-Martínez ML, Iniesta AA, Fontes M, Padmanabhan S, Elías-Arnanz M. Coenzyme B 12 -dependent and independent photoregulation of carotenogenesis across Myxococcales. Environ Microbiol 2022; 24:1865-1886. [PMID: 35005822 PMCID: PMC9304148 DOI: 10.1111/1462-2920.15895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/28/2022]
Abstract
Light-induced carotenogenesis in Myxococcus xanthus is controlled by the B12 -based CarH repressor and photoreceptor, and by a separate intricate pathway involving singlet oxygen, the B12 -independent CarH paralog CarA and various other proteins, some eukaryotic-like. Whether other myxobacteria conserve these pathways and undergo photoregulated carotenogenesis is unknown. Here, comparative analyses across 27 Myxococcales genomes identified carotenogenic genes, albeit arranged differently, with carH often in their genomic vicinity, in all three Myxococcales suborders. However, CarA and its associated factors were found exclusively in suborder Cystobacterineae, with carA-carH invariably in tandem in a syntenic carotenogenic operon, except for Cystobacter/Melittangium, which lack CarA but retain all other factors. We experimentally show B12 -mediated photoregulated carotenogenesis in representative myxobacteria, and a remarkably plastic CarH operator design and DNA binding across Myxococcales. Unlike the two characterized CarH from other phyla, which are tetrameric, Cystobacter CarH (the first myxobacterial homolog amenable to analysis in vitro) is a dimer that combines direct CarH-like B12 -based photoregulation with CarA-like DNA-binding and inhibition by an antirepressor. This study provides new molecular insights into B12 -dependent photoreceptors. It further establishes the B12 -dependent pathway for photoregulated carotenogenesis as broadly prevalent across myxobacteria and its evolution, exclusively in one suborder, into a parallel complex B12 -independent circuit. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Jesús Fernández Zapata
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - María Del Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - María Luisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
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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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Abellón-Ruiz J, Bernal-Bernal D, Abellán M, Fontes M, Padmanabhan S, Murillo FJ, Elías-Arnanz M. The CarD/CarG regulatory complex is required for the action of several members of the large set of Myxococcus xanthus extracytoplasmic function σ factors. Environ Microbiol 2014; 16:2475-90. [PMID: 24428729 DOI: 10.1111/1462-2920.12386] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 12/27/2013] [Indexed: 11/25/2022]
Abstract
Extracytoplasmic function (ECF) σ factors are critical players in signal transduction networks involved in bacterial response to environmental changes. The Myxococcus xanthus genome reveals ∼45 putative ECF-σ factors, but for the overwhelming majority, the specific signals or mechanisms for selective activation and regulation remain unknown. One well-studied ECF-σ, CarQ, binds to its anti-σ, CarR, and is inactive in the dark but drives its own expression from promoter P(QRS) on illumination. This requires the CarD/CarG complex, the integration host factor (IHF) and a specific CarD-binding site upstream of P(QRS). Here, we show that DdvS, a previously uncharacterized ECF-σ, activates its own expression in a CarD/CarG-dependent manner but is inhibited when specifically bound to the N-terminal zinc-binding anti-σ domain of its cognate anti-σ, DdvA. Interestingly, we find that the autoregulatory action of 11 other ECF-σ factors studied here depends totally or partially on CarD/CarG but not IHF. In silico analysis revealed possible CarD-binding sites that may be involved in direct regulation by CarD/CarG of target promoter activity. CarD/CarG-linked ECF-σ regulation likely recurs in other myxobacteria with CarD/CarG orthologous pairs and could underlie, at least in part, the global regulatory effect of the complex on M. xanthus gene expression.
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Affiliation(s)
- Javier Abellón-Ruiz
- 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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CarF mediates signaling by singlet oxygen, generated via photoexcited protoporphyrin IX, in Myxococcus xanthus light-induced carotenogenesis. J Bacteriol 2012; 194:1427-36. [PMID: 22267513 DOI: 10.1128/jb.06662-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Blue light triggers carotenogenesis in the nonphototrophic bacterium Myxococcus xanthus by inducing inactivation of an anti-σ factor, CarR, and the consequent liberation of the cognate extracytoplasmic function (ECF) σ factor, CarQ. CarF, the protein implicated earliest in the response to light, does not resemble any known photoreceptor. It interacts physically with CarR and is required for its light-driven inactivation, but the mechanism is unknown. Blue-light sensing in M. xanthus has been attributed to the heme precursor protoporphyrin IX (PPIX), which can generate the highly reactive singlet oxygen species ((1)O(2)) by energy transfer to oxygen. However, (1)O(2) involvement in M. xanthus light-induced carotenogenesis remains to be established. Here, we present genetic evidence of the involvement of PPIX as well as (1)O(2) in light-induced carotenogenesis in M. xanthus and of how these are linked to CarF in the signal transduction pathway. Response to light was examined in carF-bearing and carF-deficient M. xanthus strains lacking endogenous PPIX due to deletion of hemB or accumulating PPIX due to deletion of hemH (hemB and hemH are early- and late-acting heme biosynthesis genes, respectively). This demonstrated that light induction of the CarQ-dependent promoter, P(QRS), correlated directly with cellular PPIX levels. Furthermore, we show that P(QRS) activation is triggered by (1)O(2) and is inhibited by exogenously supplied hemin and that CarF is essential for the action of (1)O(2). Thus, our findings indicate that blue light interaction with PPIX generates (1)O(2), which must be transmitted via CarF to trigger the transcriptional response underlying light-induced carotenogenesis in M. xanthus.
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Elías-Arnanz M, Padmanabhan S, Murillo FJ. Light-dependent gene regulation in nonphototrophic bacteria. Curr Opin Microbiol 2011; 14:128-35. [DOI: 10.1016/j.mib.2010.12.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 11/24/2022]
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Combinatorial regulation by MrpC2 and FruA involves three sites in the fmgE promoter region during Myxococcus xanthus development. J Bacteriol 2011; 193:2756-66. [PMID: 21441502 DOI: 10.1128/jb.00205-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Starvation causes cells in a dense population of Myxococcus xanthus to change their gliding movements and construct mounds. Short-range C-signaling between rod-shaped cells within mounds induces gene expression that promotes differentiation into spherical spores. Several C-signal-dependent genes have been shown to be regulated by cooperative binding of two transcription factors to the promoter region. These FruA- and MrpC2-regulated genes (designated fmg) each exhibit a different arrangement of binding sites. Here, we describe fmgE, which appears to be regulated by three sites for cooperative binding of FruA and MrpC2. Chromatin immunoprecipitation analysis showed that association of MrpC2 and/or its longer form, MrpC with the fmgE promoter region, depends on FruA, consistent with cooperative binding of the two proteins in vivo. Electrophoretic mobility shift assays with purified His(10)-MrpC2 and FruA-His(6) indicated cooperative binding in vitro to three sites in the fmgE promoter region. The effects of mutations on binding in vitro and on expression of fmgE-lacZ fusions correlated site 1 (at about position -100 relative to the transcriptional start site) with negative regulation and site 2 (just upstream of the promoter) and site 3 (at about position +100) with positive regulation. Site 3 was bound by His(10)-MrpC2 alone, or the combination of His(10)-MrpC2 and FruA-His(6), with the highest affinity, followed by site 1 and then site 2, supporting a model in which site 3 recruits MrpC2 and FruA to the fmgE promoter region, site 1 competes with site 2 for transcription factor binding, and site 2 occupancy is required to activate the promoter but only occurs when C-signaling produces a high concentration of active FruA.
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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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García-Moreno D, Abellón-Ruiz J, García-Heras F, Murillo FJ, Padmanabhan S, Elías-Arnanz M. CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD. Nucleic Acids Res 2010; 38:4586-98. [PMID: 20371514 PMCID: PMC2919716 DOI: 10.1093/nar/gkq214] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CarD, a global transcriptional regulator in Myxococcus xanthus, interacts with CarG via CarDNter, its N-terminal domain, and with DNA via a eukaryotic HMGA-type C-terminal domain. Genomic analysis reveals a large number of standalone proteins resembling CarDNter. These constitute, together with the RNA polymerase (RNAP) interacting domain, RID, of transcription–repair coupling factors, the CarD_TRCF protein family. We show that one such CarDNter-like protein, M. xanthus CdnL, cannot functionally substitute CarDNter (or vice versa) nor interact with CarG. Unlike CarD, CdnL is vital for growth, and lethality due to its absence is not rescued by homologs from various other bacteria. In mycobacteria, with no endogenous DksA, the function of the CdnL homolog mirrors that of Escherichia coli DksA. Our finding that CdnL, like DksA, is indispensable in M. xanthus implies that they are not functionally redundant. Cells are normal on CdnL overexpression, but divide aberrantly on CdnL depletion. CdnL localizes to the nucleoid, suggesting piggyback recruitment by factors such as RNAP, which we show interacts with CdnL, CarDNter and RID. Our study highlights a complex network of interactions involving these factors and RNAP, and points to a vital role for M. xanthus CdnL in an essential DNA transaction that affects cell division.
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Affiliation(s)
- Diana García-Moreno
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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9
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Regulated intramembrane proteolysis in the control of extracytoplasmic function sigma factors. Res Microbiol 2009; 160:696-703. [DOI: 10.1016/j.resmic.2009.08.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 08/24/2009] [Accepted: 08/25/2009] [Indexed: 11/18/2022]
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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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Iniesta AA, Cervantes M, Murillo FJ. Cooperation of two carotene desaturases in the production of lycopene in Myxococcus xanthus. FEBS J 2007; 274:4306-14. [PMID: 17662111 DOI: 10.1111/j.1742-4658.2007.05960.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Myxococcus xanthus, all known carotenogenic genes are grouped together in the gene cluster carB-carA, except for one, crtIb (previously named carC). We show here that the first three genes of the carB operon, crtE, crtIa, and crtB, encode a geranygeranyl synthase, a phytoene desaturase, and a phytoene synthase, respectively. We demonstrate also that CrtIa possesses cis-to-trans isomerase activity, and is able to dehydrogenate phytoene, producing phytofluene and zeta-carotene. Unlike the majority of CrtI-type phytoene desaturases, CrtIa is unable to perform the four dehydrogenation events involved in converting phytoene to lycopene. CrtIb, on the other hand, is incapable of dehydrogenating phytoene and lacks cis-to-trans isomerase activity. However, the presence of both CrtIa and CrtIb allows the completion of the four desaturation steps that convert phytoene to lycopene. Therefore, we report a unique mechanism where two distinct CrtI-type desaturases cooperate to carry out the four desaturation steps required for lycopene formation. In addition, we show that there is a difference in substrate recognition between the two desaturases; CrtIa dehydrogenates carotenes in the cis conformation, whereas CrtIb dehydrogenates carotenes in the trans conformation.
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Affiliation(s)
- Antonio A Iniesta
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Spain.
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Viswanathan P, Ueki T, Inouye S, Kroos L. Combinatorial regulation of genes essential for Myxococcus xanthus development involves a response regulator and a LysR-type regulator. Proc Natl Acad Sci U S A 2007; 104:7969-74. [PMID: 17470804 PMCID: PMC1876556 DOI: 10.1073/pnas.0701569104] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Myxococcus xanthus is a bacterium that undergoes multicellular development. C-signaling influences gene expression and movement of cells into aggregates. Expression of the dev operon, which includes genes essential for efficient sporulation, depends in part on C-signaling and reaches its highest level in cells within aggregates, ensuring that spores form within fruiting bodies. Here, an upstream DNA element was found to be essential for dev promoter activity and was bound by FruA, a response regulator in the C-signaling pathway. A second positive regulatory element, located approximately 350 bp downstream of the dev transcriptional start site, was bound by LadA, a newly identified transcription factor in the LysR family. Typically, LysR-type transcription factors bind upstream of the promoter and activate transcription in response to a coinducer. LadA appears to activate transcription from an unusual location for a LysR family member and likely subjects dev transcription to a different cue than does FruA. A ladA mutant exhibited similar developmental defects as dev mutants, suggesting that LadA may be devoted to dev regulation, unlike FruA, which regulates many developmental genes. FruA and LadA act on a regulatory region spanning >400 bp to bring about proper temporal and spatial expression of the dev operon, resembling the regulation of developmental genes in multicellular eukaryotes.
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Affiliation(s)
- Poorna Viswanathan
- *Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824; and
| | - Toshiyuki Ueki
- Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854
| | - Sumiko Inouye
- Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854
| | - Lee Kroos
- *Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824; and
- To whom correspondence should be addressed. E-mail:
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Viswanathan P, Murphy K, Julien B, Garza AG, Kroos L. Regulation of dev, an operon that includes genes essential for Myxococcus xanthus development and CRISPR-associated genes and repeats. J Bacteriol 2007; 189:3738-50. [PMID: 17369305 PMCID: PMC1913320 DOI: 10.1128/jb.00187-07] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of dev genes is important for triggering spore differentiation inside Myxococcus xanthus fruiting bodies. DNA sequence analysis suggested that dev and cas (CRISPR-associated) genes are cotranscribed at the dev locus, which is adjacent to CRISPR (clustered regularly interspaced short palindromic repeats). Analysis of RNA from developing M. xanthus confirmed that dev and cas genes are cotranscribed with a short upstream gene and at least two repeats of the downstream CRISPR, forming the dev operon. The operon is subject to strong, negative autoregulation during development by DevS. The dev promoter was identified. Its -35 and -10 regions resemble those recognized by M. xanthus sigma(A) RNA polymerase, the homolog of Escherichia coli sigma(70), but the spacer may be too long (20 bp); there is very little expression during growth. Induction during development relies on at least two positive regulatory elements located in the coding region of the next gene upstream. At least two positive regulatory elements and one negative element lie downstream of the dev promoter, such that the region controlling dev expression spans more than 1 kb. The results of testing different fragments for dev promoter activity in wild-type and devS mutant backgrounds strongly suggest that upstream and downstream regulatory elements interact functionally. Strikingly, the 37-bp sequence between the two CRISPR repeats that, minimally, are cotranscribed with dev and cas genes exactly matches a sequence in the bacteriophage Mx8 intP gene, which encodes a form of the integrase needed for lysogenization of M. xanthus.
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Affiliation(s)
- Poorna Viswanathan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Peñalver-Mellado M, García-Heras F, Padmanabhan S, García-Moreno D, Murillo FJ, Elías-Arnanz M. Recruitment of a novel zinc-bound transcriptional factor by a bacterial HMGA-type protein is required for regulating multiple processes in Myxococcus xanthus. Mol Microbiol 2006; 61:910-26. [PMID: 16879646 DOI: 10.1111/j.1365-2958.2006.05289.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enhanceosome assembly in eukaryotes often requires high mobility group A (HMGA) proteins. In prokaryotes, the only known transcriptional regulator with HMGA-like physical, structural and DNA-binding properties is Myxococcus xanthus CarD. Here, we report that every CarD-regulated process analysed also requires the product of gene carG, located immediately downstream of and transcriptionally coupled to carD. CarG has the zinc-binding H/C-rich metallopeptidase motif found in archaemetzincins, but with Q replacing a catalytically essential E. CarG, a monomer, binds two zinc atoms, shows no apparent metallopeptidase activity, and its stability in vivo absolutely requires the cysteines. This indicates a strictly structural role for zinc-binding. In vivo CarG localizes to the nucleoid but only if CarD is also present. In vitro CarG shows no DNA-binding but physically interacts with CarD via its N-terminal and not HMGA domain. CarD and CarG thus work as a single, physically linked, transcriptional regulatory unit, and if one exists in a bacterium so does the other. Like zinc-associated eukaryotic transcriptional adaptors in enhanceosome assembly, CarG regulates by interacting not with DNA but with another transcriptional factor.
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Affiliation(s)
- Marcos Peñalver-Mellado
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
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Wilson MJ, Lamont IL. Mutational analysis of an extracytoplasmic-function sigma factor to investigate its interactions with RNA polymerase and DNA. J Bacteriol 2006; 188:1935-42. [PMID: 16484205 PMCID: PMC1426564 DOI: 10.1128/jb.188.5.1935-1942.2006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 12/13/2005] [Indexed: 01/23/2023] Open
Abstract
The extracytoplasmic-function (ECF) family of sigma factors comprises a large group of proteins required for synthesis of a wide variety of extracytoplasmic products by bacteria. Residues important for core RNA polymerase (RNAP) binding, DNA melting, and promoter recognition have been identified in conserved regions 2 and 4.2 of primary sigma factors. Seventeen residues in region 2 and eight residues in region 4.2 of an ECF sigma factor, PvdS from Pseudomonas aeruginosa, were selected for alanine-scanning mutagenesis on the basis of sequence alignments with other sigma factors. Fourteen of the mutations in region 2 had a significant effect on protein function in an in vivo assay. Four proteins with alterations in regions 2.1 and 2.2 were purified as His-tagged fusions, and all showed a reduced affinity for core RNAP in vitro, consistent with a role in core binding. Region 2.3 and 2.4 mutant proteins retained the ability to bind core RNAP, but four mutants had reduced or no ability to cause core RNA polymerase to bind promoter DNA in a band-shift assay, identifying residues important for DNA binding. All mutations in region 4.2 reduced the activity of PvdS in vivo. Two of the region 4.2 mutant proteins were purified, and each showed a reduced ability to cause core RNA polymerase to bind to promoter DNA. The results show that some residues in PvdS have functions equivalent to those of corresponding residues in primary sigma factors; however, they also show that several residues not shared with primary sigma factors contribute to protein function.
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Affiliation(s)
- Megan J Wilson
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
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16
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Viswanathan K, Viswanathan P, Kroos L. Mutational analysis of the Myxococcus xanthus Omega4406 promoter region reveals an upstream negative regulatory element that mediates C-signal dependence. J Bacteriol 2006; 188:515-24. [PMID: 16385042 PMCID: PMC1347317 DOI: 10.1128/jb.188.2.515-524.2006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
C signaling plays a key role in coordinating cell movement and differentiation during the multicellular developmental process of Myxococcus xanthus. C signaling regulates expression of genes induced after about 6 h into development, when cells are forming mounds. One gene whose expression depends absolutely on C signaling was identified by insertion of a transposable element at site Omega4406 which generated a transcriptional fusion between lacZ and an upstream promoter. We have investigated regulation of the Omega4406 promoter. A 5' deletion revealed a negative regulatory element located between bp -533 and -100 relative to the transcriptional start site. In the absence of this element, the promoter was still developmentally regulated but about fourfold more active. Also, the truncated promoter region retained normal dependence on two developmental regulators, FruA and DevS, but lost its dependence on the C-signaling protein CsgA. We infer that C signaling partially overcomes the negative effect of the upstream element on activity of the Omega4406 promoter. Deletion of downstream DNA between bp 50 and 140 caused a threefold loss in expression, suggesting that a positive regulatory element lies in this region. Additional positive and negative regulatory elements are present in the region from bp -69 to -49, based on the effects of multiple-base-pair mutations. Within this region, a 5-bp element and a C-box-like sequence resemble sequences found in other developmentally regulated M. xanthus promoter regions, but the effects of single-base-pair changes in these sequences suggest that each functions uniquely. We conclude that regulation of the Omega4406 promoter involves multiple positive and negative regulatory elements located upstream and downstream of the region typically bound by RNA polymerase.
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Affiliation(s)
- Kartik Viswanathan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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17
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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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18
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Galbis-Martínez M, Fontes M, Murillo FJ. The high-mobility group A-type protein CarD of the bacterium Myxococcus xanthus as a transcription factor for several distinct vegetative genes. Genetics 2005; 167:1585-95. [PMID: 15342500 PMCID: PMC1471020 DOI: 10.1534/genetics.104.029207] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CarD is the only reported prokaryotic protein showing structural and functional features typical of eukaryotic high-mobility group A transcription factors. In prokaryotes, proteins similar to CarD appear to be confined primarily to myxobacteria. In Myxococcus xanthus, CarD has been previously shown to act as a positive element in two different regulatory networks: one for light-induced synthesis of carotenoids and the other for starvation-induced fruiting body formation. We have now tested the effect of a loss-of-function mutation in the carD gene (carD1) on the expression of a random collection of lacZ-tagged genes, which are normally expressed in the dark during vegetative growth in rich medium. Our results indicate that CarD plays a significant role in the transcriptional regulation of various indicated genes. The carD1 mutation downregulates some genes and upregulates others. Also reported here is the isolation of several mutations that suppress the strong effect of carD1 on the expression of a particular vegetative gene. One of them (sud-2) also suppresses the effect of carD1 on other vegetative genes and on fruiting-body formation. Thus, CarD and the sud-2 gene product appear to participate in a single mechanism, which underlies various apparently diverse regulatory phenomena ascribed to CarD.
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Affiliation(s)
- Marisa Galbis-Martínez
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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Whitworth DE, Bryan SJ, Berry AE, McGowan SJ, Hodgson DA. Genetic dissection of the light-inducible carQRS promoter region of Myxococcus xanthus. J Bacteriol 2004; 186:7836-46. [PMID: 15547254 PMCID: PMC529085 DOI: 10.1128/jb.186.23.7836-7846.2004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Myxococcus xanthus photoprotective carotenoids are produced in response to illumination due to regulated expression of carotenoid biosynthesis genes at two loci. Induction of the carotenogenesis regulon is dependent on expression of the carQRS operon. The first gene product of the operon, CarQ, is a sigma factor belonging to the ECF family and is responsible for light-dependent initiation of transcription at the carQRS promoter. We defined the minimal carQRS promoter as a 145-bp fragment of DNA upstream of the carQRS transcriptional start site, which includes the promoter for a divergent gene, gufA. In order to elucidate regions with the promoter required for activity, point mutations were introduced into the carQRS promoter between positions -151 and 6. While most sequence changes abolished carQRS promoter activity, two changes enhanced promoter activity and two changes caused the mutant promoter to become constitutive and independent of CarQ. The promoter-null point mutations and 6-bp deletion mutations implied that the carQRS promoter requires a functional gufA promoter for transcriptional activity and vice versa. By mapping the extent of the promoter region, identifying sequences important for promoter activity, and highlighting potential topological effects, we provide a foundation for further analysis of the carQRS promoter.
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Affiliation(s)
- David E Whitworth
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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20
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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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21
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López-Rubio JJ, Padmanabhan S, Lázaro JM, Salas M, Murillo FJ, Elías-Arnanz M. Operator design and mechanism for CarA repressor-mediated down-regulation of the photoinducible carB operon in Myxococcus xanthus. J Biol Chem 2004; 279:28945-53. [PMID: 15123730 DOI: 10.1074/jbc.m403459200] [Citation(s) in RCA: 24] [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
The carB operon encodes all except one of the enzymes involved in light-induced carotenogenesis in Myxococcus xanthus. Expression of its promoter (P(B)) is repressed in the dark by sequence-specific DNA binding of CarA to a palindrome (pI) located between positions -47 and -64 relative to the transcription start site. This promotes subsequent binding of CarA to additional sites that remain to be defined. CarS, produced in the light, interacts physically with CarA, abrogates CarA-DNA binding, and thereby derepresses P(B). In this study, we delineate the operator design that exists for CarA by precisely mapping out the second operator element. For this, we examined how stepwise deletions and site-directed mutagenesis in the region between the palindrome and the transcription start site affect CarA binding around P(B) in vitro and expression of P(B) in vivo. These revealed the second operator element to be an imperfect interrupted palindrome (pII) spanning positions -26 to -40. In vitro assays using purified M. xanthus RNA polymerase showed that CarA abolishes P(B)-RNA polymerase binding and runoff transcription and that both were restored by CarS, thus rationalizing the observations in vivo. CarA binding to pII (after association with pI) effectively occludes RNA polymerase from P(B) and so provides the operative mechanism for the repression of the carB operon by CarA. The bipartite operator design, whereby transcription is blocked by the low affinity CarA-pII binding and is readily restored by CarS, may have evolved to match the needs for a rapid and an effective response to light.
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Affiliation(s)
- José Juan López-Rubio
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia 30071
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22
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Campoy S, Fontes M, Padmanabhan S, Cortés P, Llagostera M, Barbé J. LexA-independent DNA damage-mediated induction of gene expression in Myxococcus xanthus. Mol Microbiol 2003; 49:769-81. [PMID: 12864858 DOI: 10.1046/j.1365-2958.2003.03592.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Myxococcus xanthus, a member of the Proteobacteria delta-class, has two independent recA genes, recA1 and recA2, but only recA2 is DNA damage-inducible. The lexA gene has been isolated from M. xanthus by PCR amplification with oligonucleotides designed after sequence identification by tblastn analysis of its genome at the Cereon Microbial Sequence Database. The M. xanthus purified LexA protein is shown to bind specifically to the consensus sequence CTRHAMRYBYGTTCAGS present upstream of lexA and recA2. A degenerate copy of this motif but with important differences can be identified in the region upstream of the recA1 gene. A knock-out lexA(Def) mutant that has been generated does not differ significantly from wild type in morphology, growth rate, light-induced carotenogenesis or development. Using transcriptional lacZ fusions and quantitative RT-PCR analysis, it has been demonstrated that expression of both lexA and recA2 genes is constitutive in the lexA(Def) mutant, whereas the transcription of the DNA damage non-inducible recA1 gene is not affected in this strain. recN and ssb, whose expression in Escherichia coli are LexA-regulated, are induced by DNA damage in the M. xanthus lexA(Def) mutant. These data reveal the existence of different regulatory mechanisms for DNA damage-inducible genes in bacteria belonging to different phyla.
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Affiliation(s)
- Susana Campoy
- Departament de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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23
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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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24
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Enz S, Mahren S, Menzel C, Braun V. Analysis of the ferric citrate transport gene promoter of Escherichia coli. J Bacteriol 2003; 185:2387-91. [PMID: 12644513 PMCID: PMC151517 DOI: 10.1128/jb.185.7.2387-2391.2003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FecI, an extracytoplasmic-function sigma factor, is required for initiation of transcription of the ferric citrate transport genes. A mutational analysis of the fecA promoter revealed that the nonconserved -10 region and a downstream regulatory element are important for fecA promoter activity. However, nucleotide substitutions in the well-conserved -35 region also have an effect on the fecA promoter activity. Titration of FecI suggests that the FecI-RNA polymerase holoenzyme does not bind strongly to the downstream regulatory element, which is therefore probably involved in a subsequent step of transcription initiation.
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Affiliation(s)
- Sabine Enz
- Mikrobiologie/Membranphysiologie, Universität Tübingen, Germany
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25
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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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26
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Abstract
Bacterial sigma (sigma) factors are an essential component of RNA polymerase and determine promoter selectivity. The substitution of one sigma factor for another can redirect some or all of the RNA polymerase in a cell to activate the transcription of genes that would otherwise be silent. As a class, alternative sigma factors play key roles in coordinating gene transcription during various stress responses and during morphological development. The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. Many bacteria, particularly those with more complex genomes, contain multiple ECF sigma factors and these regulators often outnumber all other types of sigma factor combined. Examples include Bacillus subtilis (7 ECF sigma factors), Mycobacterium tuberculosis (10), Caulobacter crescentus (13), Pseudomonas aeruginosa (approximately 19), and Streptomyces coelicolor (approximately 50). The roles and mechanisms of regulation for these various ECF sigma factors are largely unknown, but significant progress has been made in selected systems. As a general trend, most ECF sigma factors are cotranscribed with one or more negative regulators. Often, these include a transmembrane protein functioning as an anti-sigma factor that binds, and inhibits, the cognate sigma factor. Upon receiving a stimulus from the environment, the sigma factor is released and can bind to RNA polymerase to stimulate transcription. In many ways, these anti-sigma:sigma pairs are analogous to the more familiar two-component regulatory systems consisting of a transmembrane histidine protein kinase and a DNA-binding response regulator. Both are mechanisms of coordinating a cytoplasmic transcriptional response to signals perceived by protein domains external to the cell membrane. Here, I review current knowledge of some of the better characterized ECF sigma factors, discuss the variety of experimental approaches that have proven productive in defining the roles of ECF sigma factors, and present some unifying themes that are beginning to emerge as more systems are studied.
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Affiliation(s)
- John D Helmann
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853-8101, USA
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27
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Visca P, Leoni L, Wilson MJ, Lamont IL. Iron transport and regulation, cell signalling and genomics: lessons from Escherichia coli and Pseudomonas. Mol Microbiol 2002; 45:1177-90. [PMID: 12207687 DOI: 10.1046/j.1365-2958.2002.03088.x] [Citation(s) in RCA: 190] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A variety of bacterial species secrete and take up chelating compounds that enable acquisition of iron (siderophores). It has become clear that a common feature in regulation of different iron acquisition systems is the involvement of alternative sigma factor proteins of the extracytoplasmic function (ECF) family. Two of these proteins, PvdS from Pseudomonas aeruginosa and FecI from Escherichia coli K-12, have been studied extensively. PvdS directs transcription of genes required for the biosynthesis of a siderophore, pyoverdine, and FecI causes expression of genes for uptake of ferric citrate. FecI forms part of a signalling system that responds to the presence of ferric citrate. Here, we review recent advances in understanding of PvdS and of the Fec signalling system. PvdS and FecI are part of a distinct subfamily of ECF sigma factors involved in iron acquisition and hence named the iron-starvation sigmas. Analysis of microbial genome sequences shows that Fec-like signalling systems are present in a wide range of species and many such systems may be present in a single species. The availability of tools for large-scale genome analysis is likely to lead to rapid advances in our understanding of this expanding family of proteins.
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Affiliation(s)
- Paolo Visca
- Molecular Microbiology Unit, National Institute for Infectious Diseases, Via Portuense 292, 00149 Rome, Italy
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28
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Cervantes M, Murillo FJ. Role for vitamin B(12) in light induction of gene expression in the bacterium Myxococcus xanthus. J Bacteriol 2002; 184:2215-24. [PMID: 11914353 PMCID: PMC134944 DOI: 10.1128/jb.184.8.2215-2224.2002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A light-inducible promoter (P(B)) drives the carB operon (carotenoid genes) of the bacterium Myxococcus xanthus. A gene encoding a regulator of carotenoid biosynthesis was identified by studying mutant strains carrying a transcriptional fusion to P(B) and deletions in three candidate genes. Our results prove that the identified gene, named carA, codes for a repressor of the P(B) promoter in the dark. They also show that the carA gene product does not participate in the light activation of two other promoters connected with carotenoid synthesis or its regulation in M. xanthus. CarA is a novel protein consisting of a DNA-binding domain of the family of MerR helix-turn-helix transcriptional regulators, directly joined to a cobalamin-binding domain. In support of this, we report here that the presence of vitamin B(12) or some other cobalamin derivatives is absolutely required for activation of the P(B) promoter by light.
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Affiliation(s)
- María Cervantes
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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29
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López-Rubio JJ, Elías-Arnanz M, Padmanabhan S, Murillo FJ. A repressor-antirepressor pair links two loci controlling light-induced carotenogenesis in Myxococcus xanthus. J Biol Chem 2002; 277:7262-70. [PMID: 11748235 DOI: 10.1074/jbc.m110351200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The light-inducible carB operon encodes all but one of the structural genes for carotenogenesis in Myxococcus xanthus. It is transcriptionally controlled by two proteins expressed from two unlinked genetic loci: CarS from the light-inducible carQRS operon, and CarA from the light-independent carA operon. CarA represses transcription from the carB promoter (P(B)) in the dark, and CarS counteracts this on illumination. The CarA sequence revealed a helix-turn-helix DNA-binding motif of the type found in bacterial MerR transcriptional factors, whereas CarS contains no known DNA-binding motif. Here, we examine the molecular interplay between CarA and CarS. We demonstrate the following. (i) Whereas CarS exhibits no DNA binding in vitro, CarA binds specifically to a region encompassing P(B) to form at least two distinct complexes. (ii) A palindrome located between positions -46 and -63 relative to the transcription start point is essential but not sufficient for the formation of the two CarA-DNA complexes observed. (iii) CarS abrogates the specific DNA binding of CarA. CarA is therefore a repressor and CarS an antirepressor. (iv) CarS physically interacts with CarA; thus, the functional interaction between them is mediated by protein-protein interactions.
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Affiliation(s)
- José Juan López-Rubio
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia 30071, Spain
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30
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Wilson MJ, McMorran BJ, Lamont IL. Analysis of promoters recognized by PvdS, an extracytoplasmic-function sigma factor protein from Pseudomonas aeruginosa. J Bacteriol 2001; 183:2151-5. [PMID: 11222621 PMCID: PMC95118 DOI: 10.1128/jb.183.6.2151-2155.2001] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The alternative sigma factor PvdS is required by Pseudomonas aeruginosa for initiation of transcription from pyoverdine (pvd) promoters. Two divergent PvdS-dependent promoters (pvdE and pvdF) were characterized by deletion analysis, and the minimal promoter region for each included a sequence element, the iron starvation (IS) box, that is present in other pvd promoters. Site-directed mutagenesis showed that the IS box elements were essential for promoter activity in vivo. Band shift assays and in vitro transcription experiments showed that a complex of PvdS and core RNA polymerase required the presence of an IS box in order to bind to and initiate transcription from pvd promoters. These results indicate that IS box elements participate in sequence-specific recognition by PvdS to enable initiation of transcription from pvd promoters and are likely to represent a -35 sequence element for this sigma factor.
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Affiliation(s)
- M J Wilson
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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31
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Moreno AJ, Fontes M, Murillo FJ. ihfA gene of the bacterium Myxococcus xanthus and its role in activation of carotenoid genes by blue light. J Bacteriol 2001; 183:557-69. [PMID: 11133949 PMCID: PMC94911 DOI: 10.1128/jb.183.2.557-569.2001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Myxococcus xanthus responds to blue light by producing carotenoids. Several regulatory genes are known that participate in the light action mechanism, which leads to the transcriptional activation of the carotenoid genes. We had already reported the isolation of a carotenoid-less, Tn5-induced strain (MR508), whose mutant site was unlinked to the indicated regulatory genes. Here, we show that OmegaMR508::Tn5 affects all known light-inducible promoters in different ways. It blocks the activation of two of them by light but makes the activity of a third one light independent. The OmegaMR508 locus has been cloned and sequenced. The mutation had occurred at the promoter of a gene we propose is the M. xanthus ortholog of ihfA. This encodes the alpha subunit of the histone-like integration host factor protein. An in-frame deletion within ihfA causes the same effects as the OmegaMR508::Tn5 insertion. Like other IhfA proteins, the deduced amino acid sequence of M. xanthus IhfA shows much similarity to HU, another histone-like protein. Sequence comparison data, however, and the finding that the M. xanthus gene is preceded by gene pheT, as happens in other gram-negative bacteria, strongly argue for the proposed orthology relationship. The M. xanthus ihfA gene shows some unusual features, both from structural and physiological points of view. In particular, the protein is predicted to have a unique, long acidic extension at the carboxyl terminus, and it appears to be necessary for normal cell growth and even vital for a certain wild-type strain of M. xanthus.
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Affiliation(s)
- A J Moreno
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, 30100 Murcia, Spain
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Yamazaki H, Ohnishi Y, Horinouchi S. An A-factor-dependent extracytoplasmic function sigma factor (sigma(AdsA)) that is essential for morphological development in Streptomyces griseus. J Bacteriol 2000; 182:4596-605. [PMID: 10913094 PMCID: PMC94632 DOI: 10.1128/jb.182.16.4596-4605.2000] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2000] [Accepted: 05/17/2000] [Indexed: 11/20/2022] Open
Abstract
A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) at an extremely low concentration triggers streptomycin production and aerial mycelium formation in Streptomyces griseus. A-factor induces the expression of an A-factor-dependent transcriptional activator, AdpA, essential for both morphological and physiological differentiation by binding to the A-factor receptor protein ArpA, which has bound and repressed the adpA promoter, and dissociating it from the promoter. Nine DNA fragments that were specifically recognized and bound by histidine-tagged AdpA were isolated by cycles of a gel mobility shift-PCR method. One of them was located in front of a gene encoding an extracytoplasmic function sigma factor belonging to a subgroup of the primary sigma(70) family. The cloned gene was named AdpA-dependent sigma factor gene (adsA), and the gene product was named sigma(AdsA). Transcription of adsA depended on A-factor and AdpA, since adsA was transcribed at a very low and constant level in an A-factor-deficient mutant strain or in an adpA-disrupted strain. Consistent with this, transcription of adsA was greatly enhanced at or near the timing of aerial hyphae formation, as determined by low-resolution S1 nuclease mapping. High-resolution S1 mapping determined the transcriptional start point 82 nucleotides upstream of the translational start codon. DNase I footprinting showed that AdpA bound both strands symmetrically between the transcriptional start point and the translational start codon; AdpA protected the antisense strand from positions +7 to +41 with respect to the transcriptional start point and the sense strand from positions +12 to +46. A weak palindrome was found in the AdpA-binding site. The unusual position bound by AdpA as a transcriptional activator, in relation to the promoter, suggested the presence of a mechanism by which AdpA activates transcription of adsA in some unknown way. Disruption of the chromosomal adsA gene resulted in loss of aerial hyphae formation but not streptomycin or yellow pigment production, indicating that sigma(AdsA) is involved only in morphological development and not in secondary metabolic function. The presence of a single copy in each of the Streptomyces species examined by Southern hybridization suggests a common role in morphogenesis in this genus.
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Affiliation(s)
- H Yamazaki
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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Grass G, Grosse C, Nies DH. Regulation of the cnr cobalt and nickel resistance determinant from Ralstonia sp. strain CH34. J Bacteriol 2000; 182:1390-8. [PMID: 10671463 PMCID: PMC94428 DOI: 10.1128/jb.182.5.1390-1398.2000] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ralstonia sp. strain CH34 is resistant to nickel and cobalt cations. Resistance is mediated by the cnr determinant located on plasmid pMOL28. The cnr genes are organized in two clusters, cnrYXH and cnrCBA. As revealed by reverse transcriptase PCR and primer extension, transcription from these operons is initiated from promoters located upstream of the cnrY and cnrC genes. These two promoters exhibit conserved sequences at the -10 (CCGTATA) and -35 (CRAGGGGRAG) regions. The CnrH gene product, which is required for expression of both operons, is a sigma factor belonging to the sigma L family, whose activity seems to be governed by the membrane-bound CnrY and CnrX gene products in response to Ni(2+). Half-maximal activation from the cnrCBA operon was determined by using appropriate lacZ gene fusions and was shown to occur at an Ni(2+) concentration of about 50 microM.
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Affiliation(s)
- G Grass
- Institut für Mikrobiologie, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle, Germany
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Abstract
In response to starvation, myxobacteria build multicellular fruiting bodies that contain many thousands of cells and that have particular species-specific shapes. To coordinate fruiting body development, the myxobacterial cells signal to each other. The timing of and cellular responses to these signals help to give form to the fruiting body. Following identification of several signal molecules, important transcriptional regulators and other signals have recently been identified. Steps on signal transduction pathways have also been defined.
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Affiliation(s)
- D Kaiser
- Department of Biochemistry, Beckman Center, B300, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
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