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Machado VA, Santisteban ARN, Martins CM, Damasceno NRT, Fonseca FA, Neto AMF, Izar MC. Effects of phytosterol supplementation on lipoprotein subfractions and LDL particle quality. Sci Rep 2024; 14:11108. [PMID: 38750162 PMCID: PMC11096344 DOI: 10.1038/s41598-024-61897-4] [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: 10/04/2023] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Phytosterols are natural components of plant-based foods used as supplements because of their known cholesterol-lowering effect. However, their effects on lipoprotein subfractions and the quality of the LDL particle have not been studied in greater detail. We aimed to evaluate the effects of phytosterols supplements on lipids, lipoproteins subfractions, and on the quality of LDL. A prospective, pilot-type, open label, cross-over study, randomized 23 males in primary prevention of hypercholesterolemia to receive diet or diet plus phytosterol (2.6 g in 2 doses, with meals) for 12 weeks, when treatments were switched for another 12 weeks. Lipoprotein subfractions were analyzed by electrophoresis in polyacrylamide gel (Lipoprint System®). The Sampson equation estimated the small and dense (sd) and large and buoyant (lb) LDL subfractions from the lipid profile. Quality of LDL particle was analyzed by Z-scan and UV-vis spectroscopy. Primary outcome was the comparison of diet vs. diet plus phytosterols. Secondary outcomes assessed differences between baseline, diet and diet plus phytosterol. Non-parametric statistics were performed with p < 0.05. There was a trend to reduction on HDL-7 (p = 0.05) in diet plus phytosterol arm, with no effects on the quality of LDL particles. Heatmap showed strong correlations (ρ > 0.7) between particle size by different methods with both interventions. Diet plus phytosterol reduced TC, increased HDL-c, and reduced IDL-B, whereas diet increased HDL7, and reduced IDL-B vs. baseline (p < 0.05, for all). Phytosterol supplementation demonstrated small beneficial effects on HDL-7 subfraction, compared with diet alone, without effects on the quality of LDL particles.This trial is registered in Clinical Trials (NCT06127732) and can be accessed at https://clinicaltrials.gov .
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Affiliation(s)
- Valeria Arruda Machado
- Cardiology Division, Department of Medicine, Federal University of Sao Paulo, 340 - Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Celma Muniz Martins
- Cardiology Division, Department of Medicine, Federal University of Sao Paulo, 340 - Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Francisco A Fonseca
- Cardiology Division, Department of Medicine, Federal University of Sao Paulo, 340 - Sao Paulo, Sao Paulo, SP, Brazil
- Institute of Physics, National Institute of Complex Fluids, University of São Paulo, São Paulo, SP, Brazil
| | - Antonio M Figueiredo Neto
- Institute of Physics, National Institute of Complex Fluids, University of São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Izar
- Cardiology Division, Department of Medicine, Federal University of Sao Paulo, 340 - Sao Paulo, Sao Paulo, SP, Brazil.
- Institute of Physics, National Institute of Complex Fluids, University of São Paulo, São Paulo, SP, Brazil.
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2
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Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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3
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Class II LitR serves as an effector of "short" LOV-type blue-light photoreceptor in Pseudomonas mendocina. Sci Rep 2022; 12:21765. [PMID: 36526696 PMCID: PMC9758184 DOI: 10.1038/s41598-022-26254-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
PmlR2, a class II LitR/CarH family transcriptional regulator, and PmSB-LOV, a "short" LOV-type blue light photoreceptor, are adjacently encoded in Pseudomonas mendocina NBRC 14162. An effector protein for the "short" LOV-type photoreceptor in Pseudomonas has not yet been identified. Here, we show that PmlR2 is an effector protein of PmSB-LOV. Transcriptional analyses revealed that the expression of genes located near pmlR2 and its homolog gene, pmlR1, was induced in response to illumination. In vitro DNA-protein binding analyses showed that recombinant PmlR2 directly binds to the promoter region of light-inducible genes. Furthermore PmSB-LOV exhibited a typical LOV-type light-induced spectral change. Gel-filtration chromatography demonstrated that the illuminated PmSB-LOV was directly associated with PmlR2, whereas non-illuminated proteins did not interact. The inhibition of PmlR2 function following PmSB-LOV binding was verified by surface plasmon resonance: the DNA-binding ability of PmlR2 was specifically inhibited in the presence of blue light-illuminated-PmSB-LOV. An In vitro transcription assay showed a dose-dependent reduction in PmlR2 repressor activity in the presence of illuminated PmSB-LOV. Overall, evidence suggests that the DNA-binding activity of PmlR2 is inhibited by its direct association with blue light-activated PmSB-LOV, enabling transcription of light-inducible promoters by RNA polymerase.
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Cobalamin Riboswitches Are Broadly Sensitive to Corrinoid Cofactors to Enable an Efficient Gene Regulatory Strategy. mBio 2022; 13:e0112122. [PMID: 35993747 PMCID: PMC9600662 DOI: 10.1128/mbio.01121-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In bacteria, many essential metabolic processes are controlled by riboswitches, gene regulatory RNAs that directly bind and detect metabolites. Highly specific effector binding enables riboswitches to respond to a single biologically relevant metabolite. Cobalamin riboswitches are a potential exception because over a dozen chemically similar but functionally distinct cobalamin variants (corrinoid cofactors) exist in nature. Here, we measured cobalamin riboswitch activity in vivo using a Bacillus subtilis fluorescent reporter system and found, among 38 tested riboswitches, a subset responded to corrinoids promiscuously, while others were semiselective. Analyses of chimeric riboswitches and structural models indicate, unlike other riboswitch classes, cobalamin riboswitches indirectly differentiate among corrinoids by sensing differences in their structural conformation. This regulatory strategy aligns riboswitch-corrinoid specificity with cellular corrinoid requirements in a B. subtilis model. Thus, bacteria can employ broadly sensitive riboswitches to cope with the chemical diversity of essential metabolites. IMPORTANCE Some bacterial mRNAs contain a region called a riboswitch which controls gene expression by binding to a metabolite in the cell. Typically, riboswitches sense and respond to a limited range of cellular metabolites, often just one type. In this work, we found the cobalamin (vitamin B12) riboswitch class is an exception, capable of sensing and responding to multiple variants of B12-collectively called corrinoids. We found cobalamin riboswitches vary in corrinoid specificity with some riboswitches responding to each of the corrinoids we tested, while others responding only to a subset of corrinoids. Our results suggest the latter class of riboswitches sense intrinsic conformational differences among corrinoids in order to support the corrinoid-specific needs of the cell. These findings provide insight into how bacteria sense and respond to an exceptionally diverse, often essential set of enzyme cofactors.
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5
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Pellizza L, Bialer MG, Sieira R, Aran M. MliR, a novel MerR-like regulator of iron homeostasis, impacts metabolism, membrane remodeling, and cell adhesion in the marine Bacteroidetes Bizionia argentinensis. Front Microbiol 2022; 13:987756. [PMID: 36118216 PMCID: PMC9478572 DOI: 10.3389/fmicb.2022.987756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The MerR family is a group of transcriptional activators with conserved N-terminal helix-turn-helix DNA binding domains and variable C-terminal effector binding regions. In most MerR proteins the effector binding domain (EBD) contains a cysteine center suited for metal binding and mediates the response to environmental stimuli, such as oxidative stress, heavy metals or antibiotics. We here present a novel transcriptional regulator classified in the MerR superfamily that lacks an EBD domain and has neither conserved metal binding sites nor cysteine residues. This regulator from the psychrotolerant bacteria Bizionia argentinensis JUB59 is involved in iron homeostasis and was named MliR (MerR-like iron responsive Regulator). In silico analysis revealed that homologs of the MliR protein are widely distributed among different bacterial species. Deletion of the mliR gene led to decreased cell growth, increased cell adhesion and filamentation. Genome-wide transcriptomic analysis showed that genes associated with iron homeostasis were downregulated in mliR-deletion mutant. Through nuclear magnetic resonance-based metabolomics, ICP-MS, fluorescence microscopy and biochemical analysis we evaluated metabolic and phenotypic changes associated with mliR deletion. This work provides the first evidence of a MerR-family regulator involved in iron homeostasis and contributes to expanding our current knowledge on relevant metabolic pathways and cell remodeling mechanisms underlying in the adaptive response to iron availability in bacteria.
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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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7
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Poddar H, Heyes DJ, Schirò G, Weik M, Leys D, Scrutton NS. A guide to time-resolved structural analysis of light-activated proteins. FEBS J 2021; 289:576-595. [PMID: 33864718 DOI: 10.1111/febs.15880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023]
Abstract
Dynamical changes in protein structures are essential for protein function and occur over femtoseconds to seconds timescales. X-ray free electron lasers have facilitated investigations of structural dynamics in proteins with unprecedented temporal and spatial resolution. Light-activated proteins are attractive targets for time-resolved structural studies, as the reaction chemistry and associated protein structural changes can be triggered by short laser pulses. Proteins with different light-absorbing centres have evolved to detect light and harness photon energy to bring about downstream chemical and biological output responses. Following light absorption, rapid chemical/small-scale structural changes are typically localised around the chromophore. These localised changes are followed by larger structural changes propagated throughout the photoreceptor/photocatalyst that enables the desired chemical and/or biological output response. Time-resolved serial femtosecond crystallography (SFX) and solution scattering techniques enable direct visualisation of early chemical change in light-activated proteins on timescales previously inaccessible, whereas scattering gives access to slower timescales associated with more global structural change. Here, we review how advances in time-resolved SFX and solution scattering techniques have uncovered mechanisms of photochemistry and its coupling to output responses. We also provide a prospective on how these time-resolved structural approaches might impact on other photoreceptors/photoenzymes that have not yet been studied by these methods.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
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8
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Baumschlager A, Khammash M. Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria. Adv Biol (Weinh) 2021; 5:e2000256. [PMID: 34028214 DOI: 10.1002/adbi.202000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Light has become established as a tool not only to visualize and investigate but also to steer biological systems. This review starts by discussing the unique features that make light such an effective control input in biology. It then gives an overview of how light-control came to progress, starting with photoactivatable compounds and leading up to current genetic implementations using optogenetic approaches. The review then zooms in on optogenetics, focusing on photosensitive proteins, which form the basis for optogenetic engineering using synthetic biological approaches. As the regulation of transcription provides a highly versatile means for steering diverse biological functions, the focus of this review then shifts to transcriptional light regulators, which are presented in the biotechnologically highly relevant model organism Escherichia coli.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
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9
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Determination and Dissection of DNA-Binding Specificity for the Thermus thermophilus HB8 Transcriptional Regulator TTHB099. Int J Mol Sci 2020; 21:ijms21217929. [PMID: 33114549 PMCID: PMC7662524 DOI: 10.3390/ijms21217929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 01/26/2023] Open
Abstract
Transcription factors (TFs) have been extensively researched in certain well-studied organisms, but far less so in others. Following the whole-genome sequencing of a new organism, TFs are typically identified through their homology with related proteins in other organisms. However, recent findings demonstrate that structurally similar TFs from distantly related bacteria are not usually evolutionary orthologs. Here we explore TTHB099, a cAMP receptor protein (CRP)-family TF from the extremophile Thermus thermophilus HB8. Using the in vitro iterative selection method Restriction Endonuclease Protection, Selection and Amplification (REPSA), we identified the preferred DNA-binding motif for TTHB099, 5′–TGT(A/g)NBSYRSVN(T/c)ACA–3′, and mapped potential binding sites and regulated genes within the T. thermophilus HB8 genome. Comparisons with expression profile data in TTHB099-deficient and wild type strains suggested that, unlike E. coli CRP (CRPEc), TTHB099 does not have a simple regulatory mechanism. However, we hypothesize that TTHB099 can be a dual-regulator similar to CRPEc.
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10
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Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog. J Bacteriol 2020; 202:JB.00146-20. [PMID: 32967908 DOI: 10.1128/jb.00146-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/19/2020] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas putida KT2440 retains three homologs (PplR1 to PplR3) of the LitR/CarH family, an adenosyl B12-dependent light-sensitive MerR family transcriptional regulator. Transcriptome analysis revealed the existence of a number of photoinducible genes, including pplR1, phrB (encoding DNA photolyase), ufaM (furan-containing fatty acid synthase), folE (GTP cyclohydrolase I), cryB (cryptochrome-like protein), and multiple genes without annotated/known function. Transcriptional analysis by quantitative reverse transcription-PCR with knockout mutants of pplR1 to pplR3 showed that a triple knockout completely abolished the light-inducible transcription in P. putida, which indicates the occurrence of ternary regulation of PplR proteins. A DNase I footprint assay showed that PplR1 protein specifically binds to the promoter regions of light-inducible genes, suggesting a consensus PplR1-binding direct repeat, 5'-T(G/A)TACAN12TGTA(C/T)A-3'. The disruption of B12 biosynthesis cluster did not affect the light-inducible transcription; however, disruption of ppSB1-LOV (where LOV indicates "light, oxygen, or voltage") and ppSB2-LOV, encoding blue light photoreceptors adjacently located to pplR3 and pplR2, respectively, led to the complete loss of light-inducible transcription. Overall, the results suggest that the three PplRs and two PpSB-LOVs cooperatively regulate the light-inducible gene expression. The wide distribution of the pplR/ppSB-LOV cognate pair homologs in Pseudomonas spp. and related bacteria suggests that the response and adaptation to light are similarly regulated in the group of nonphototrophic bacteria.IMPORTANCE The LitR/CarH family is a new group of photosensor homologous to MerR-type transcriptional regulators. Proteins of this family are distributed to various nonphototrophic bacteria and grouped into at least five classes (I to V). Pseudomonas putida retaining three class II LitR proteins exhibited a genome-wide response to light. All three paralogs were functional and mediated photodependent activation of promoters directing the transcription of light-induced genes or operons. Two LOV (light, oxygen, or voltage) domain proteins, adjacently encoded by two litR genes, were also essential for the photodependent transcriptional control. Despite the difference in light-sensing mechanisms, the DNA binding consensus of class II LitR [T(G/A)TA(C/T)A] was the same as that of class I. This is the first study showing the actual involvement of class II LitR in light-induced transcription.
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11
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Lotfollahi Z, Mello APDQ, Costa ES, Oliveira CLP, Damasceno NRT, Izar MC, Neto AMF. Green-banana biomass consumption by diabetic patients improves plasma low-density lipoprotein particle functionality. Sci Rep 2020; 10:12269. [PMID: 32704082 PMCID: PMC7378544 DOI: 10.1038/s41598-020-69288-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/09/2020] [Indexed: 01/15/2023] Open
Abstract
The aim of this study was to investigate the effects of 6-months consumption of green-banana biomass on the LDL particle functionality in subjects with type 2 diabetes. Subjects (n = 39, mean age 65 years old) of both sexes with diabetes (HbA1c ≥ 6·5%) were randomized to receive nutritional support plus green-banana biomass (40 g) (n = 21) or diet alone (n = 18) for 6-months. Non-linear optical responses of LDL solutions from these participants were studied by Z-scan technique. UV-visible spectrophotometer was used to measure the absorbance of the LDL samples. Small Angle X-ray Scattering and Dynamic Light Scattering experiments were used to look for any structural changes in LDL samples and to determine their size distribution. The Lipoprint test was used to determine the LDL sub-fractions in terms of distribution and size. Consumption of green-banana biomass, reduced total- (p = 0.010), non-HDL-cholesterol (p = 0.043), glucose (p = 0.028) and HbA1c (p = 0.0007), and also improved the protection of the LDL particle against oxidation, by the increase in carotenoids content in the particles (p = 0.007). This higher protection against modifications may decrease the risk of developing cardiovascular disease. These benefits of the green-banana biomass encourage the use of resistant starches with potential clinical applications in individuals with pre-diabetes and diabetes.
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Affiliation(s)
- Zahra Lotfollahi
- Complex Fluids Group, Instituto de Física, Universidade de São Paulo, Rua Do Matão, 1371, Butantã, São Paulo, SP, CEP: 05508-090, Brazil
| | | | - Edna S Costa
- Federal University of São Paulo, São Paulo, Brazil
| | - Cristiano L P Oliveira
- Complex Fluids Group, Instituto de Física, Universidade de São Paulo, Rua Do Matão, 1371, Butantã, São Paulo, SP, CEP: 05508-090, Brazil
| | | | | | - Antonio Martins Figueiredo Neto
- Complex Fluids Group, Instituto de Física, Universidade de São Paulo, Rua Do Matão, 1371, Butantã, São Paulo, SP, CEP: 05508-090, Brazil.
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12
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Zhang J, Gao C, Yu XM, Lun HY, Du ZJ. Chryseobacterium lacus sp. nov. Isolated From the Surface Water of Two Lakes With Light-Induced Carotenoid Production. Front Microbiol 2020; 11:251. [PMID: 32194523 PMCID: PMC7064467 DOI: 10.3389/fmicb.2020.00251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/03/2020] [Indexed: 01/01/2023] Open
Abstract
Two Gram-stain-negative, rod-shaped, gliding, catalase-positive, and facultative anaerobic strains, YLOS41T and XH07, were isolated from surface water of Yilong Lake and West Lake of Dali in Yunnan Province, respectively. Both strains were yellow-colored under light conditions and white-colored under dark conditions. The results of physiological and chemotaxonomic characterization, sequencing and phylogenetic analysis, and draft genome sequence comparison demonstrated that the two strains represented a single novel species within the genus Chryseobacterium, for which the name Chryseobacterium lacus sp. nov. is proposed. The type strain is YLOS41T (= KCTC 62352T = MCCC 1H00300T), and the second strain is XH07 (= KCTC 62993). During the cultivation process, we found that the colony color of the two strains changed from white to yellow with illumination. The study investigated the effects of light irradiation on the strain YLOS41T. Results showed that light irradiation did not affect the growth of cells but significantly increased carotenoid synthesis, which caused the change of colony color. In-depth metabolic analysis was conducted by transcriptome. The predominant changes were found for genes involved in carotenoid synthesis as protection from light damage. Based on the genome and transcriptome, we proved that strain YLOS41T possessed a complete synthetic pathway of carotenoid and speculated that the production was zeaxanthin. This was the first report of Chryseobacterium species with light-induced carotenoid synthesis. This study enhances our present knowledge on how Chryseobacterium species isolated from surface water responds to light damage.
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Affiliation(s)
- Jing Zhang
- Marine College, Shandong University, Weihai, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Cheng Gao
- Marine College, Shandong University, Weihai, China
| | - Xue-Mei Yu
- Marine College, Shandong University, Weihai, China
| | - He-Yuan Lun
- Marine College, Shandong University, Weihai, China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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13
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Sumi S, Suzuki Y, Matsuki T, Yamamoto T, Tsuruta Y, Mise K, Kawamura T, Ito Y, Shimada Y, Watanabe E, Watanabe S, Toriyabe M, Takano Shiratori H, Ueda K, Takano H. Light-inducible carotenoid production controlled by a MarR-type regulator in Corynebacterium glutamicum. Sci Rep 2019; 9:13136. [PMID: 31511549 PMCID: PMC6739363 DOI: 10.1038/s41598-019-49384-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/23/2019] [Indexed: 01/21/2023] Open
Abstract
Carotenoid production in some non-phototropic bacteria occurs in a light-dependent manner to protect cells from photo-oxidants. Knowledge regarding the transcriptional regulator involved in the light-dependent production of carotenoids of non-phototrophic bacteria has been mainly confined to coenzyme B12-based photo-sensitive regulator CarH/LitR family proteins belonging to a MerR family transcriptional regulator. In this study, we found that bacteria belonging to Micrococcales and Corynebacteriales exhibit light-dependent carotenoid-like pigment production including an amino acid-producer Corynebacterium glutamicum AJ1511. CrtR is a putative MarR family transcriptional regulator located in the divergent region of a carotenoid biosynthesis gene cluster in the genome of those bacteria. A null mutant for crtR of C. glutamicum AJ1511 exhibited constitutive production of carotenoids independent of light. A complemented strain of the crtR mutant produced carotenoids in a light-dependent manner. Transcriptional analysis revealed that the expression of carotenoid biosynthesis genes is regulated in a light-dependent manner in the wild type, while the transcription was upregulated in the crtR mutant irrespective of light. In vitro experiments demonstrated that a recombinant CrtR protein binds to the specific sequences within the intergenic region of crtR and crtE, which corresponds to −58 to −7 for crtE, and +26 to −28 for crtR with respect to the transcriptional start site, and serves as a repressor for crtE transcription directed by RNA polymerase containing SigA. Taken together, the results indicate that CrtR light-dependently controls the expression of the carotenoid gene cluster in C. glutamicum and probably closely related Actinobacteria.
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Affiliation(s)
- Satoru Sumi
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yuto Suzuki
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Tetsuro Matsuki
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Takahiro Yamamoto
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yudai Tsuruta
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Kou Mise
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Takuya Kawamura
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yusuke Ito
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Yuka Shimada
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Erika Watanabe
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Shoko Watanabe
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Minami Toriyabe
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Hatsumi Takano Shiratori
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan
| | - Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, 252-0880, Japan.
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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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15
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Li H. Selection-free markerless genome manipulations in the polyploid bacterium Thermus thermophilus. 3 Biotech 2019; 9:148. [PMID: 30944795 DOI: 10.1007/s13205-019-1682-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/14/2019] [Indexed: 12/17/2022] Open
Abstract
A genome manipulation approach based on double-crossover homologous recombination was developed in the polyploid model organism Thermus thermophilus HB27 without the use of any selectable marker. The method was established and optimized by targeting the megaplasmid-encoded β-glucosidase gene bgl. When linear and supercoiled forms of marker-free suicide vector were used for transformations, the frequencies of obtaining apparent Bgl- mutant were 10- 5 and 10- 3, respectively; while the frequency could reach 10- 2 when transformation with concatemer form of the same vector. All randomly selected Bgl- colonies from the transformations were found to be true bgl knockout mutants. Thus, markerless gene deletion mutants could be constructed in T. thermophilus by the direct selection-free method. The functionality of this approach was further demonstrated by deletion of one chromosomal locus (TTC_0340-0341) as well as by generation of a reporter strain for the phytoene synthase promoter (PcrtB), homozygous mutants of the both targets could also be detected with a frequency of approximately 10- 2. During the genome modification process, heterozygous cells carrying two different alleles at a same locus (e.g., bgl and pyrE) could also be generated. However, in the absence of selection pressure, these strains could rapidly convert to homozygous strains containing only one of the two alleles. This indicated that allele segregation could occur in the heterozygous T. thermophilus cells, which probably explained the ease of obtaining homozygous gene deletion mutants with high frequency (10- 2) in the polyploid genomic background, as after the mutant allele had been introduced to the target region, allele segregation would lead to homozygous mutant cells. This marker-free genome manipulation approach does not require phenotype-based screens, and is applicable in gene deletion and tagging applications.
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Affiliation(s)
- Haijuan Li
- College of Biological and Environmental Engineering, Xi'an University, No. 168 South Taibai Road, Xi'an, 710065 China
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Role and Function of Class III LitR, a Photosensor Homolog from Burkholderia multivorans. J Bacteriol 2018; 200:JB.00285-18. [PMID: 30249707 DOI: 10.1128/jb.00285-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/13/2018] [Indexed: 11/20/2022] Open
Abstract
The LitR/CarH protein family is an adenosyl B12 (AdoB12)-dependent photoreceptor family with DNA-binding activity, and its homologs are widely distributed in the genomes of diverse bacterial genera. In this investigation, we studied the role and functions of a LitR homolog from a Gram-negative soil bacterium, Burkholderia multivorans, which does not possess an AdoB12-binding domain. Transcriptome analysis indicated the existence of 19 light-induced genes, including folE2, cfaB, litS, photolyase gene phrB2, and cryB, located in the region flanking litR Disruption of litR caused constitutive expression of all the light-inducible genes, while mutation in the light-induced sigma factor gene, litS, abolished the transcription of the phrB2 operon and the cfa operon, indicating that LitR and LitS play a central role in light-inducible transcription. A gel shift assay showed that recombinant protein LitR specifically binds to the promoter regions of litR and the folE2 operon, and its binding was weakened by UV-A illumination. LitR absorbs light at maximally near 340 nm and exhibited a photocyclic response and light-dependent dissociation of multimer into tetramer. The litR mutant produced a 20-fold-higher intracellular level of folate than that of the wild-type strain. Thus, the evidence suggests that LitR light-dependently regulates the transcription of litR itself and the folE2 operon, resulting in the production of folate, and then the expressed RNA polymerase complex containing σLitS directs the transcription of the phrB2 operon and the cfa operon. These light-dependent characteristics suggest that class III LitR, in complex with a UV-A-absorbing molecule, follows a novel light-sensing mechanism.IMPORTANCE Members of the LitR/CarH family are adenosyl B12-based photosensory transcriptional regulator involved in light-inducible carotenoid production in nonphototrophic bacteria. Our study provides the first evidence of the involvement of a class III LitR, which lacks an adenosyl B12-binding domain in the light response of Burkholderia multivorans belonging to betaproteobacteria. Our biochemical analysis suggests that class III LitR protein exhibits features as a photosensor including absorption of light at the UV-A region (λmax = ca. 340 nm), photocyclic response, and light-dependent dissociation. This suggests that class III LitR associates with a UV-A-absorbing molecule, and it has a photosensing mechanism distinguishable from that of the B12-based type.
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Fernández-Zapata J, Pérez-Castaño R, Aranda J, Colizzi F, Polanco MC, Orozco M, Padmanabhan S, Elías-Arnanz M. Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B 12-based photoreceptor. J Biol Chem 2018; 293:17888-17905. [PMID: 30262667 DOI: 10.1074/jbc.ra118.004838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/20/2018] [Indexed: 11/06/2022] Open
Abstract
Newly discovered bacterial photoreceptors called CarH sense light by using 5'-deoxyadenosylcobalamin (AdoCbl). They repress their own expression and that of genes for carotenoid synthesis by binding in the dark to operator DNA as AdoCbl-bound tetramers, whose light-induced disassembly relieves repression. High-resolution structures of Thermus thermophilus CarHTt have provided snapshots of the dark and light states and have revealed a unique DNA-binding mode whereby only three of four DNA-binding domains contact an operator comprising three tandem direct repeats. To gain further insights into CarH photoreceptors and employing biochemical, spectroscopic, mutational, and computational analyses, here we investigated CarHBm from Bacillus megaterium We found that apoCarHBm, unlike monomeric apoCarHTt, is an oligomeric molten globule that forms DNA-binding tetramers in the dark only upon AdoCbl binding, which requires a conserved W-X 9-EH motif. Light relieved DNA binding by disrupting CarHBm tetramers to dimers, rather than to monomers as with CarHTt CarHBm operators resembled that of CarHTt, but were larger by one repeat and overlapped with the -35 or -10 promoter elements. This design persisted in a six-repeat, multipartite operator we discovered upstream of a gene encoding an Spx global redox-response regulator whose photoregulated expression links photooxidative and general redox responses in B. megaterium Interestingly, CarHBm recognized the smaller CarHTt operator, revealing an adaptability possibly related to the linker bridging the DNA- and AdoCbl-binding domains. Our findings highlight a remarkable plasticity in the mode of action of B12-based CarH photoreceptors, important for their biological functions and development as optogenetic tools.
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Affiliation(s)
- Jesús Fernández-Zapata
- From the Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, 28006 Madrid
| | - Ricardo Pérez-Castaño
- 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, Murcia 30100
| | - Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona; Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona
| | - Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona; Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona
| | - María Carmen Polanco
- 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, Murcia 30100
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona; Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona; Department of Biochemistry and Biomedicine, University of Barcelona, 08028 Barcelona, Spain
| | - S Padmanabhan
- From the Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, 28006 Madrid.
| | - 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, Murcia 30100.
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18
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Hagi T, Kobayashi M, Nomura M. Whole-transcriptome analysis of oxidative stress response genes in carotenoid-producing Enterococcus gilvus. Biosci Biotechnol Biochem 2017; 82:1053-1057. [PMID: 29161967 DOI: 10.1080/09168451.2017.1399790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Whole-transcriptome analysis of aerobic stress response gene in Enterococcus gilvus was performed using RNA-sequencing to identify carotenoid-based stress response genes in lactic acid bacteria. The expression of gene responsible for pyruvate dehydrogenase complex synthesis was highly upregulated after aerobic treatment. In addition, the expression of transcriptional regulator spx and genes encoding UvrABC system protein was also upregulated.
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Affiliation(s)
- Tatsuro Hagi
- a Animal Products Research Division, Institute of Livestock and Grassland Science , National Agriculture and Food Research Organization (NARO) , Ibaraki , Japan
| | - Miho Kobayashi
- a Animal Products Research Division, Institute of Livestock and Grassland Science , National Agriculture and Food Research Organization (NARO) , Ibaraki , Japan
| | - Masaru Nomura
- a Animal Products Research Division, Institute of Livestock and Grassland Science , National Agriculture and Food Research Organization (NARO) , Ibaraki , Japan
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19
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Koepff J, Morschett H, Busche T, Winkler A, Kalinowski J, Wiechert W, Oldiges M. Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans. Biotechnol Prog 2017; 34:287-292. [DOI: 10.1002/btpr.2566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/25/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Joachim Koepff
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
| | - Holger Morschett
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
| | - Tobias Busche
- Bielefeld University, Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld Germany
| | - Anika Winkler
- Bielefeld University, Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld Germany
| | - Jörn Kalinowski
- Bielefeld University, Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld Germany
| | - Wolfgang Wiechert
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
- RWTH Aachen University, Computational Systems Biotechnology, Aachener Verfahrenstechnik; Aachen Germany
| | - Marco Oldiges
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
- RWTH Aachen University, Inst. of Biotechnology; Aachen Germany
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20
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Lee M, Um H, Van Dyke MW. Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus transcriptional regulator FadR. PLoS One 2017; 12:e0184796. [PMID: 28902898 PMCID: PMC5597230 DOI: 10.1371/journal.pone.0184796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/31/2017] [Indexed: 11/18/2022] Open
Abstract
One of the primary transcriptional regulators of fatty acid homeostasis in many prokaryotes is the protein FadR. To better understand its biological function in the extreme thermophile Thermus thermophilus HB8, we sought to first determine its preferred DNA-binding sequences in vitro using the combinatorial selection method Restriction Endonuclease Protection, Selection, and Amplification (REPSA) and then use this information to bioinformatically identify potential regulated genes. REPSA determined a consensus FadR-binding sequence 5´-TTRNACYNRGTNYAA-3´, which was further characterized using quantitative electrophoretic mobility shift assays. With this information, a search of the T. thermophilus HB8 genome found multiple operons potentially regulated by FadR. Several of these were identified as encoding proteins involved in fatty acid biosynthesis and degradation; however, others were novel and not previously identified as targets of FadR. The role of FadR in regulating these genes was validated by physical and functional methods, as well as comparative genomic approaches to further characterize regulons in related organisms. Taken together, our study demonstrates that a systematic approach involving REPSA, biophysical characterization of protein-DNA binding, and bioinformatics can be used to postulate biological roles for potential transcriptional regulators.
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Affiliation(s)
- Minwoo Lee
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Hyejin Um
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Michael W. Van Dyke
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
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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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22
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Mandelli F, Couger MB, Paixão DAA, Machado CB, Carnielli CM, Aricetti JA, Polikarpov I, Prade R, Caldana C, Paes Leme AF, Mercadante AZ, Riaño-Pachón DM, Squina FM. Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis. Extremophiles 2017; 21:775-788. [DOI: 10.1007/s00792-017-0942-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/29/2017] [Indexed: 12/25/2022]
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23
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Elucidation of roles for vitamin B 12 in regulation of folate, ubiquinone, and methionine metabolism. Proc Natl Acad Sci U S A 2017; 114:E1205-E1214. [PMID: 28137868 DOI: 10.1073/pnas.1612360114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Only a small fraction of vitamin B12-requiring organisms are able to synthesize B12 de novo, making it a common commodity in microbial communities. Initially recognized as an enzyme cofactor of a few enzymes, recent studies have revealed additional B12-binding enzymes and regulatory roles for B12 Here we report the development and use of a B12-based chemical probe to identify B12-binding proteins in a nonphototrophic B12-producing bacterium. Two unexpected discoveries resulted from this study. First, we identified a light-sensing B12-binding transcriptional regulator and demonstrated that it controls folate and ubiquinone biosynthesis. Second, our probe captured proteins involved in folate, methionine, and ubiquinone metabolism, suggesting that it may play a role as an allosteric effector of these processes. These metabolic processes produce precursors for synthesis of DNA, RNA, and protein. Thereby, B12 likely modulates growth, and by limiting its availability to auxotrophs, B12-producing organisms may facilitate coordination of community metabolism.
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24
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Van Dyke MW, Beyer MD, Clay E, Hiam KJ, McMurry JL, Xie Y. Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PLoS One 2016; 11:e0159408. [PMID: 27428627 PMCID: PMC4948773 DOI: 10.1371/journal.pone.0159408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/02/2016] [Indexed: 01/04/2023] Open
Abstract
One of the first steps towards elucidating the biological function of a putative transcriptional regulator is to ascertain its preferred DNA-binding sequences. This may be rapidly and effectively achieved through the application of a combinatorial approach, one involving very large numbers of randomized oligonucleotides and reiterative selection and amplification steps to enrich for high-affinity nucleic acid-binding sequences. Previously, we had developed the novel combinatorial approach Restriction Endonuclease Protection, Selection and Amplification (REPSA), which relies not on the physical separation of ligand-nucleic acid complexes but instead selects on the basis of ligand-dependent inhibition of enzymatic template inactivation, specifically cleavage by type IIS restriction endonucleases. Thus, no prior knowledge of the ligand is required for REPSA, making it more amenable for discovery purposes. Here we describe using REPSA, massively parallel sequencing, and bioinformatics to identify the preferred DNA-binding sites for the transcriptional regulator SbtR, encoded by the TTHA0167 gene from the model extreme thermophile Thermus thermophilus HB8. From the resulting position weight matrix, we can identify multiple operons potentially regulated by SbtR and postulate a biological role for this protein in regulating extracellular transport processes. Our study provides a proof-of-concept for the application of REPSA for the identification of preferred DNA-binding sites for orphan transcriptional regulators and a first step towards determining their possible biological roles.
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Affiliation(s)
- Michael W. Van Dyke
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
| | - Matthew D. Beyer
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Emily Clay
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Kamir J. Hiam
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Jonathan L. McMurry
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Ying Xie
- Department of Computer Science, Kennesaw State University, Kennesaw, Georgia, United States of America
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25
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Feng Y, Zhang Y, Ebright RH. Structural basis of transcription activation. Science 2016; 352:1330-3. [PMID: 27284196 DOI: 10.1126/science.aaf4417] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/09/2016] [Indexed: 01/25/2023]
Abstract
Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)-promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, we report a 4.4 angstrom crystal structure of an intact bacterial class II transcription activation complex. The structure comprises Thermus thermophilus transcription activator protein TTHB099 (TAP) [homolog of Escherichia coli catabolite activator protein (CAP)], T. thermophilus RNAP σ(A) holoenzyme, a class II TAP-dependent promoter, and a ribotetranucleotide primer. The structure reveals the interactions between RNAP holoenzyme and DNA responsible for transcription initiation and reveals the interactions between TAP and RNAP holoenzyme responsible for transcription activation. The structure indicates that TAP stimulates isomerization through simple, adhesive, stabilizing protein-protein interactions with RNAP holoenzyme.
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Affiliation(s)
- Yu Feng
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yu Zhang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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26
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Takano H, Mise K, Maruyama T, Hagiwara K, Ueda K. Role of the semi-conserved histidine residue in the light-sensing domain of LitR, a MerR-type photosensory transcriptional regulator. MICROBIOLOGY-SGM 2016; 162:1500-1509. [PMID: 27283316 DOI: 10.1099/mic.0.000321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The LitR/CarH protein family transcriptional regulator is a new type of photoreceptor based on the function of adenosyl B12 (AdoB12) as a light-sensitive ligand. Here, we studied a semi-conserved histidine residue (His132) in the light-sensing (AdoB12-binding) domain at the C-terminus of LitR from a thermophilic Gram-negative bacterium, Thermus thermophilus HB27. The in vivo mutation of His132 within LitR caused a reduction in the rate of carotenoid production in response to illumination. BIAcore analysis revealed that the illuminated-LitRH132A possesses high DNA-binding activity compared to the wild-type protein. The subunit structure analysis showed that LitRH132A performed an incomplete subunit dissociation. The ability of LitRH132A to associate with AdoB12 was reduced compared with that of the wild-type protein in an equilibration dialysis experiment. Overall, these results suggest that His132 of LitR is involved in the association with AdoB12 as well as the light-sensitive DNA-binding activity based on oligomer dissociation.
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Affiliation(s)
- Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Kou Mise
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Takafumi Maruyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Kenta Hagiwara
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
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27
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Takano H. The regulatory mechanism underlying light-inducible production of carotenoids in nonphototrophic bacteria. Biosci Biotechnol Biochem 2016; 80:1264-73. [PMID: 26967471 DOI: 10.1080/09168451.2016.1156478] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Light is a ubiquitous environmental factor serving as an energy source and external stimulus. Here, I review the conserved molecular mechanism of light-inducible production of carotenoids in three nonphototrophic bacteria: Streptomyces coelicolor A3(2), Thermus thermophilus HB27, and Bacillus megaterium QM B1551. A MerR family transcriptional regulator, LitR, commonly plays a central role in their light-inducible carotenoid production. Genetic and biochemical studies on LitR proteins revealed a conserved function: LitR in complex with adenosyl B12 (AdoB12) has a light-sensitive DNA-binding activity and thus suppresses the expression of the Crt biosynthesis gene cluster. The in vitro DNA-binding and transcription assays showed that the LitR-AdoB12 complex serves as a repressor allowing transcription initiation by RNA polymerase in response to illumination. The existence of novel light-inducible genes and the unique role of the megaplasmid were revealed by the transcriptomic analysis of T. thermophilus. The findings suggest that LitR is a general regulator responsible for the light-inducible carotenoid production in the phylogenetically divergent nonphototrophic bacteria, and that LitR performs diverse physiological functions in bacteria.
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Affiliation(s)
- Hideaki Takano
- a Applied Biological Science and Life Science Research Center, College of Bioresource Sciences , Nihon University , Fujisawa , Japan
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Jost M, Fernández-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PYT, Kang G, Padmanabhan S, Elías-Arnanz M, Drennan CL. Structural basis for gene regulation by a B12-dependent photoreceptor. Nature 2015; 526:536-41. [PMID: 26416754 PMCID: PMC4634937 DOI: 10.1038/nature14950] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/14/2015] [Indexed: 12/29/2022]
Abstract
Photoreceptor proteins enable organisms to sense and respond to light. The newly discovered CarH-type photoreceptors use a vitamin B12 derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. Here, we present crystal structures of Thermus thermophilus CarH in all three relevant states: in the dark, both free and bound to operator DNA, and after light exposure. These structures provide a visualization of how adenosylcobalamin mediates CarH tetramer formation in the dark, how this tetramer binds to the promoter −35 element to repress transcription, and how light exposure leads to a large-scale conformational change that activates transcription. In addition to the remarkable functional repurposing of adenosylcobalamin from an enzyme cofactor to a light sensor, we find that nature also repurposed two independent protein modules in assembling CarH. These results expand the biological role of vitamin B12 and provide fundamental insight into a new mode of light-dependent gene regulation.
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Affiliation(s)
- Marco Jost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Jésus Fernández-Zapata
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - María Carmen Polanco
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Juan Manuel Ortiz-Guerrero
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Montserrat Elías-Arnanz
- Department of Genetics and Microbiology, Area of Genetics (Unidad Asociada al Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas), Faculty of Biology, Universidad de Murcia, Murcia 30100, Spain
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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Fernandez-López R, Ruiz R, de la Cruz F, Moncalián G. Transcription factor-based biosensors enlightened by the analyte. Front Microbiol 2015; 6:648. [PMID: 26191047 PMCID: PMC4486848 DOI: 10.3389/fmicb.2015.00648] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/15/2015] [Indexed: 01/17/2023] Open
Abstract
Whole cell biosensors (WCBs) have multiple applications for environmental monitoring, detecting a wide range of pollutants. WCBs depend critically on the sensitivity and specificity of the transcription factor (TF) used to detect the analyte. We describe the mechanism of regulation and the structural and biochemical properties of TF families that are used, or could be used, for the development of environmental WCBs. Focusing on the chemical nature of the analyte, we review TFs that respond to aromatic compounds (XylS-AraC, XylR-NtrC, and LysR), metal ions (MerR, ArsR, DtxR, Fur, and NikR) or antibiotics (TetR and MarR). Analyzing the structural domains involved in DNA recognition, we highlight the similitudes in the DNA binding domains (DBDs) of these TF families. Opposite to DBDs, the wide range of analytes detected by TFs results in a diversity of structures at the effector binding domain. The modular architecture of TFs opens the possibility of engineering TFs with hybrid DNA and effector specificities. Yet, the lack of a crisp correlation between structural domains and specific functions makes this a challenging task.
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Affiliation(s)
| | | | | | - Gabriel Moncalián
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria – Consejo Superior de Investigaciones CientíficasSantander, Spain
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Jost M, Simpson JH, Drennan CL. The Transcription Factor CarH Safeguards Use of Adenosylcobalamin as a Light Sensor by Altering the Photolysis Products. Biochemistry 2015; 54:3231-4. [PMID: 25966286 PMCID: PMC4455981 DOI: 10.1021/acs.biochem.5b00416] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The newly discovered light-dependent
transcription factor CarH
uses adenosylcobalamin as a light sensor to regulate expression of
protective genes in bacteria upon exposure to sunlight. This use of
adenosylcobalamin is a clever adaptation of a classic enzyme cofactor,
taking advantage of its photolabile Co–C bond. However, it
is also puzzling in that photolysis of adenosylcobalamin generates
the 5′-deoxyadenosyl radical that could damage DNA. Here, using
liquid chromatography and spectroscopic techniques, we demonstrate
that CarH suppresses release of the 5′-deoxyadenosyl radical
and instead effects conversion to a nonreactive 4′,5′-anhydroadenosine.
In this manner, CarH safeguards use of adenosylcobalamin in light-dependent
gene regulation.
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Affiliation(s)
- Marco Jost
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeffrey H Simpson
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Catherine L Drennan
- †Department of Chemistry and ‡Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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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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Fundamental role of cobalamin biosynthesis in the developmental growth of Streptomyces coelicolor A3 (2). Appl Microbiol Biotechnol 2014; 99:2329-37. [DOI: 10.1007/s00253-014-6325-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/15/2014] [Accepted: 12/02/2014] [Indexed: 12/21/2022]
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Takano H, Agari Y, Hagiwara K, Watanabe R, Yamazaki R, Beppu T, Shinkai A, Ueda K. LdrP, a cAMP receptor protein/FNR family transcriptional regulator, serves as a positive regulator for the light-inducible gene cluster in the megaplasmid of Thermus thermophilus. Microbiology (Reading) 2014; 160:2650-2660. [DOI: 10.1099/mic.0.082263-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
LdrP (TT_P0055) (LitR-dependent regulatory protein) is one of the four cAMP receptor protein (CRP)/FNR family transcriptional regulators retained by the extremely thermophilic bacterium Thermus thermophilus. Previously, we reported that LdrP served as a positive regulator for the light-induced transcription of crtB, a carotenoid biosynthesis gene encoded on the megaplasmid of this organism. Here, we showed that LdrP also functions as an activator of the expression of genes clustered around the crtB gene under the control of LitR, an adenosyl B12-bound light-sensitive regulator. Transcriptome analysis revealed the existence of 19 LitR-dependent genes on the megaplasmid. S1 nuclease protection assay confirmed that the promoters preceding TT_P0044 (P44), TT_P0049 (P49) and TT_P0070 (P70) were activated upon illumination in the WT strain. An ldrP mutant lost the ability to activate P44, P49 and P70, whilst disruption of litR resulted in constitutive transcription from these promoters irrespective of illumination, indicating that these genes were photo-dependently regulated by LdrP and LitR. An in vitro transcription experiment demonstrated that LdrP directly activated mRNA synthesis from P44 and P70 by the Thermus RNA polymerase holocomplex. The present evidence indicated that LdrP was the positive regulator essential for the transcription of the T. thermophilus light-inducible cluster encoded on the megaplasmid.
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Affiliation(s)
- Hideaki Takano
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Yoshihiro Agari
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Kenta Hagiwara
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Ren Watanabe
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Ryuta Yamazaki
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Teruhiko Beppu
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Akeo Shinkai
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
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Hagi T, Kobayashi M, Nomura M. Aerobic condition increases carotenoid production associated with oxidative stress tolerance in Enterococcus gilvus. FEMS Microbiol Lett 2013; 350:223-30. [PMID: 24325446 DOI: 10.1111/1574-6968.12341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 01/10/2023] Open
Abstract
Although it is known that a part of lactic acid bacteria can produce carotenoid, little is known about the regulation of carotenoid production. The objective of this study was to determine whether aerobic growth condition influences carotenoid production in carotenoid-producing Enterococcus gilvus. Enterococcus gilvus was grown under aerobic and anaerobic conditions. Its growth was slower under aerobic than under anaerobic conditions. The decrease in pH levels and production of lactic acid were also lower under aerobic than under anaerobic conditions. In contrast, the amount of carotenoid pigments produced by E. gilvus was significantly higher under aerobic than under anaerobic conditions. Further, real-time quantitative reverse transcription PCR revealed that the expression level of carotenoid biosynthesis genes crtN and crtM when E. gilvus was grown under aerobic conditions was 2.55-5.86-fold higher than when it was grown under anaerobic conditions. Moreover, after exposure to 16- and 32-mM H2O2, the survival rate of E. gilvus grown under aerobic conditions was 61.5- and 72.5-fold higher, respectively, than when it was grown under anaerobic conditions. Aerobic growth conditions significantly induced carotenoid production and the expression of carotenoid biosynthesis genes in E. gilvus, resulting in increased oxidative stress tolerance.
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Affiliation(s)
- Tatsuro Hagi
- Animal Products Research Division, NARO Institute of Livestock and Grassland Science, Ibaraki, Japan
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Fujita A, Misumi Y, Honda S, Sato T, Koyama Y. Construction of new cloning vectors that employ the phytoene synthase encoding gene for color screening of cloned DNA inserts in Thermus thermophilus. Gene 2013; 527:655-62. [PMID: 23845779 DOI: 10.1016/j.gene.2013.06.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 01/15/2023]
Abstract
Strains of Thermus thermophilus produce unique carotenoids called thermozeaxanthins and their colonies are light-yellow pigmented. Here, we developed a new cloning system allowing for the rapid and convenient detection of recombinants by color screening based on carotenoid production in T. thermophilus. We constructed two cloning vectors that overexpress the crtB gene encoding a phytoene synthase under the strong promoter of the slpA gene. Phytoene synthase is one of essential enzymes for the production of carotenoids. We also isolated a carotenoid-overproducing mutant that formed orange colonies. Because disruption of crtB in the carotenoid-overproducing mutant resulted in white colonies, we used the disruptant as a host strain. Whereas transformants carrying a new cloning vector, pTRK1-PRslpA-crtBcas, grew into unusual red-pigmented colonies probably because of the extreme accumulation of thermozeaxanthins, those carrying the vector with a foreign DNA inserts formed white colonies. Thus, recombinants can be detected easily by color screening (red/white screening) in T. thermophilus. This cloning system requires no additional chromogenic substrate in the medium. We also constructed a promoter-probe vector, pTRK1-crtBmcs-PP, employing the open reading frame of crtB with multiple cloning sites. Using this vector, a series of colony-color phenotypes is observed probably depending on promoter activities of foreign DNA inserts, which enables the rapid probing of promoters. These vectors are useful to simplify cloning procedures and to identify the promoters of different strengths in T. thermophilus.
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Affiliation(s)
- Atsushi Fujita
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Midorigaoka, Ikeda, Osaka 563-8577, Japan.
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36
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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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37
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Agari Y, Kuramitsu S, Shinkai A. X-ray crystal structure of TTHB099, a CRP/FNR superfamily transcriptional regulator from Thermus thermophilus HB8, reveals a DNA-binding protein with no required allosteric effector molecule. Proteins 2012; 80:1490-4. [PMID: 22383301 DOI: 10.1002/prot.24049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 01/18/2012] [Accepted: 01/25/2012] [Indexed: 11/07/2022]
Affiliation(s)
- Yoshihiro Agari
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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