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Sosa-Fajardo A, Díaz-Muñoz C, Van der Veken D, Pradal I, Verce M, Weckx S, Leroy F. Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites. BMC Genomics 2024; 25:575. [PMID: 38849728 PMCID: PMC11161930 DOI: 10.1186/s12864-024-10490-0] [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: 09/01/2023] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated. RESULTS The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms. CONCLUSIONS Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.
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Affiliation(s)
- Ana Sosa-Fajardo
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - David Van der Veken
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Inés Pradal
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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Múnera-Jaramillo J, López GD, Suesca E, Carazzone C, Leidy C, Manrique-Moreno M. The role of staphyloxanthin in the regulation of membrane biophysical properties in Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184288. [PMID: 38286247 DOI: 10.1016/j.bbamem.2024.184288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/14/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
Staphylococcus aureus is an opportunistic pathogen that is considered a global health threat. This microorganism can adapt to hostile conditions by regulating membrane lipid composition in response to external stress factors such as changes in pH and ionic strength. S. aureus synthesizes and incorporates in its membrane staphyloxanthin, a carotenoid providing protection against oxidative damage and antimicrobial agents. Staphyloxanthin is known to modulate the physical properties of the bacterial membranes due to the rigid diaponeurosporenoic group it contains. In this work, preparative thin layer chromatography and liquid chromatography mass spectrometry were used to purify staphyloxanthin from S. aureus and characterize its structure, identifying C15, C17 and C19 as the main fatty acids in this carotenoid. Changes in the biophysical properties of models of S. aureus membranes containing phosphatidylglycerol, cardiolipin, and staphyloxanthin were evaluated. Infrared spectroscopy shows that staphyloxanthin reduces the liquid-crystalline to gel phase transition temperature in the evaluated model systems. Interestingly, these shifts are not accompanied by strong changes in trans/gauche isomerization, indicating that chain conformation in the liquid-crystalline phase is not altered by staphyloxanthin. In contrast, headgroup spacing, measured by Laurdan GP fluorescence spectroscopy, and lipid core dynamics, measured by DPH fluorescence anisotropy, show significant shifts in the presence of staphyloxanthin. The combined results show that staphyloxanthin reduces lipid core dynamics and headgroup spacing without altering acyl chain conformations, therefore decoupling these normally correlated effects. We propose that the rigid diaponeurosporenoic group in staphyloxanthin and its positioning in the membrane is likely responsible for the results observed.
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Affiliation(s)
- Jessica Múnera-Jaramillo
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, Medellin, Colombia
| | - Gerson-Dirceu López
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, Bogotá, Colombia; PhysCheMath Research Group, Chemistry Department, Universidad de América, Bogotá D.C., Colombia
| | - Elizabeth Suesca
- Biophysics Group, Department of Physics, Universidad de los Andes, Bogotá, Colombia
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, Bogotá, Colombia
| | - Chad Leidy
- Biophysics Group, Department of Physics, Universidad de los Andes, Bogotá, Colombia.
| | - Marcela Manrique-Moreno
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, Medellin, Colombia.
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Hwang CY, Seo SM, Cho ES, Nam YD, Park SL, Lim SI, Seo MJ. A Novel Carotenoid-Producing Bacterium, Paenibacillus aurantius sp. nov., Isolated from Korean Marine Environment. Microorganisms 2023; 11:2719. [PMID: 38004730 PMCID: PMC10673419 DOI: 10.3390/microorganisms11112719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/24/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
The novel bacterial strain MBLB1776T was isolated from marine mud in Uljin, the Republic of Korea. Cells were Gram-positive, spore-forming, non-motile, and non-flagellated rods. Growth was observed at a temperature range of 10-45 °C, pH range of 6.0-8.0, and NaCl concentrations of 0-4% (w/v). Phylogenetic analysis of the 16S rRNA gene sequence revealed that MBLB1776T belonged to the genus Paenibacillus and was closely related to Paenibacillus cavernae C4-5T (94.83% similarity). Anteiso-C15:0, iso-C16:0, C16:0, and iso-C15:0 were the predominant fatty acids. Menaquinone 7 was identified as the major isoprenoid quinone. The major polar lipids included diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Its whole genome was 6.3 Mb in size, with a G+C content of 55.8 mol%. Average nucleotide identity and in silico DNA-DNA hybridization values were below the species delineation threshold. Gene function analysis revealed the presence of a complete C30 carotenoid biosynthetic pathway. Intriguingly, MBLB1776T harbored carotenoid pigments, imparting an orange color to whole cells. Based on this comprehensive polyphasic taxonomy, the MBLB1776T strain represents a novel species within the genus Paenibacillus, for which the name Paenibacillus aurantius sp. nov is proposed. The type strain was MBLB1776T (=KCTC 43279T = JCM 34220T). This is the first report of a carotenoid-producing Paenibacillus sp.
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Affiliation(s)
- Chi Young Hwang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon 22012, Republic of Korea; (C.Y.H.); (E.-S.C.)
| | - Sung Man Seo
- Advanced Geo-Materials Research Department, Pohang Branch, Korea Institute of Geoscience and Mineral Resources, Pohang 37559, Republic of Korea;
| | - Eui-Sang Cho
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon 22012, Republic of Korea; (C.Y.H.); (E.-S.C.)
| | - Young-Do Nam
- Personalized Diet Research Group, Korea Food Research Institute, Wanju 55365, Republic of Korea; (Y.-D.N.); (S.-L.P.)
| | - So-Lim Park
- Personalized Diet Research Group, Korea Food Research Institute, Wanju 55365, Republic of Korea; (Y.-D.N.); (S.-L.P.)
| | - Seong-Il Lim
- Personalized Diet Research Group, Korea Food Research Institute, Wanju 55365, Republic of Korea; (Y.-D.N.); (S.-L.P.)
| | - Myung-Ji Seo
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon 22012, Republic of Korea; (C.Y.H.); (E.-S.C.)
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
- Research Center for Bio Materials & Process Development, Incheon National University, Incheon 22012, Republic of Korea
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4
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Zamudio-Chávez L, Suesca E, López GD, Carazzone C, Manrique-Moreno M, Leidy C. Staphylococcus aureus Modulates Carotenoid and Phospholipid Content in Response to Oxygen-Restricted Growth Conditions, Triggering Changes in Membrane Biophysical Properties. Int J Mol Sci 2023; 24:14906. [PMID: 37834354 PMCID: PMC10573160 DOI: 10.3390/ijms241914906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
Staphylococcus aureus membranes contain carotenoids formed during the biosynthesis of staphyloxanthin. These carotenoids are considered virulence factors due to their activity as scavengers of reactive oxygen species and as inhibitors of antimicrobial peptides. Here, we show that the growth of S. aureus under oxygen-restricting conditions downregulates carotenoid biosynthesis and modifies phospholipid content in biofilms and planktonic cells analyzed using LC-MS. At oxygen-restrictive levels, the staphyloxanthin precursor 4,4-diapophytofluene accumulates, indicating that the dehydrogenation reaction catalyzed by 4,4'-diapophytoene desaturases (CrtN) is inhibited. An increase in lysyl-phosphatidylglycerol is observed under oxygen-restrictive conditions in planktonic cells, and high levels of cardiolipin are detected in biofilms compared to planktonic cells. Under oxygen-restriction conditions, the biophysical parameters of S. aureus membranes show an increase in lipid headgroup spacing, as measured with Laurdan GP, and decreased bilayer core order, as measured with DPH anisotropy. An increase in the liquid-crystalline to gel phase melting temperature, as measured with FTIR, is also observed. S. aureus membranes are therefore less condensed under oxygen-restriction conditions at 37 °C. However, the lack of carotenoids leads to a highly ordered gel phase at low temperatures, around 15 °C. Carotenoids are therefore likely to be low in S. aureus found in tissues with low oxygen levels, such as abscesses, leading to altered membrane biophysical properties.
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Affiliation(s)
- Laura Zamudio-Chávez
- Biophysics Group, Physics Department, Universidad de los Andes, Bogotá 111211, Colombia; (L.Z.-C.); (E.S.)
| | - Elizabeth Suesca
- Biophysics Group, Physics Department, Universidad de los Andes, Bogotá 111211, Colombia; (L.Z.-C.); (E.S.)
| | - Gerson-Dirceu López
- PhysCheMath Research Group, Chemistry Department, Universidad de América, Bogotá 111211, Colombia;
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, Bogotá 111211, Colombia;
| | - Marcela Manrique-Moreno
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, Medellin 050010, Colombia;
| | - Chad Leidy
- Biophysics Group, Physics Department, Universidad de los Andes, Bogotá 111211, Colombia; (L.Z.-C.); (E.S.)
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5
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Mo XH, Sun YM, Bi YX, Zhao Y, Yu GH, Tan LL, Yang S. Characterization of C 30 carotenoid and identification of its biosynthetic gene cluster in Methylobacterium extorquens AM1. Synth Syst Biotechnol 2023; 8:527-535. [PMID: 37637201 PMCID: PMC10448405 DOI: 10.1016/j.synbio.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Methylobacterium species, the representative bacteria distributed in phyllosphere region of plants, often synthesize carotenoids to resist harmful UV radiations. Methylobacterium extorquens is known to produce a carotenoid pigment and recent research revealed that this carotenoid has a C30 backbone. However, its exact structure remains unknown. In the present study, the carotenoid produced by M. extorquens AM1 was isolated and its structure was determined as 4-[2-O-11Z-octadecenoyl-β-glucopyranosyl]-4,4'-diapolycopenedioc acid (1), a glycosylated C30 carotenoid. Furthermore, the genes related to the C30 carotenoid synthesis were investigated. Squalene, the precursor of the C30 carotenoid, is synthesized by the co-occurrence of META1p1815, META1p1816 and META1p1817. Further overexpression of the genes related to squalene synthesis improved the titer of carotenoid 1. By using gene deletion and gene complementation experiments, the glycosyltransferase META1p3663 and acyltransferase META1p3664 were firstly confirmed to catalyze the tailoring steps from 4,4'-diapolycopene-4,4'-dioic acid to carotenoid 1. In conclusion, the structure and biosynthetic genes of carotenoid 1 produced by M. extorquens AM1 were firstly characterized in this work, which shed lights on engineering M. extorquens AM1 for producing carotenoid 1 in high yield.
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Affiliation(s)
- Xu-Hua Mo
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yu-Man Sun
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yu-Xing Bi
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yan Zhao
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Gui-Hong Yu
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Ling-ling Tan
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, Shandong, 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
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6
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Kim M, Cha IT, Lee KE, Li M, Park SJ. Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium. Microbiol Spectr 2023; 11:e0100323. [PMID: 37594286 PMCID: PMC10655711 DOI: 10.1128/spectrum.01003-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments. Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium. Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, Jeju, South Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju, South Korea
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Rontani JF, Bonin P. Cellular Damage of Bacteria Attached to Senescent Phytoplankton Cells as a Result of the Transfer of Photochemically Produced Singlet Oxygen: A Review. Microorganisms 2023; 11:1565. [PMID: 37375067 PMCID: PMC10303659 DOI: 10.3390/microorganisms11061565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent phytoplankton cells to the bacteria attached to them in response to irradiation by sunlight. This paper summarizes and reviews the key findings of these studies, i.e., the demonstration of the process at work and the effect of different parameters (intensity of solar irradiance, presence of bacterial carotenoids, and presence of polar matrices such as silica, carbonate, and exopolymeric substances around phytoplankton cells) on this transfer. A large part of this review looks at how this type of alteration of bacteria can affect the preservation of algal material in the marine environment, especially in polar regions where conditions drive increased transfer of singlet oxygen from sympagic algae to bacteria.
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Affiliation(s)
- Jean-François Rontani
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France;
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Salamzade R, Cheong JA, Sandstrom S, Swaney MH, Stubbendieck RM, Starr NL, Currie CR, Singh AM, Kalan LR. Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC. Microb Genom 2023; 9:mgen000988. [PMID: 37115189 PMCID: PMC10210951 DOI: 10.1099/mgen.0.000988] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/20/2023] [Indexed: 04/29/2023] Open
Abstract
Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed l ineage s pecific a nalysis of BGCs (lsa BGC; https://github.com/Kalan-Lab/lsaBGC ) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsa BGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsa BGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsa BGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | - J.Z. Alex Cheong
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Mary Hannah Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, WI, USA
| | | | - Nicole Lane Starr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Anne Marie Singh
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
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9
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Linden M, Flegler A, Feuereisen MM, Weber F, Lipski A, Schieber A. Effects of flavonoids on membrane adaptation of food-associated bacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184137. [PMID: 36746312 DOI: 10.1016/j.bbamem.2023.184137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/07/2023]
Abstract
The effects of naringenin and the biflavonoids amentoflavone and tetrahydroamentoflavone on select bacterial lipids (carotenoids, fatty acids, and menaquinones) and membrane fluidity based on Laurdan generalized polarization were investigated. For this purpose, the pigment-forming food-associated microorganisms Staphylococcus xylosus (DSM 20266T and J70), Staphylococcus carnosus DSM 20501T, and Micrococcus luteus (ATCC 9341 and J3) were studied. The results suggest an envelope stress response by microorganisms due to flavonoids and an employment of adaptive mechanisms using carotenoids, fatty acids, and menaquinones. The flavonoid monomer naringenin impacted carotenoids, fatty acids, menaquinones, and membrane fluidity. Naringenin significantly influenced the carotenoid profile, particularly by an increase in the relative proportion of 4,4'-diaponeurosporenoic acid in Staphylococcus xylosus. Amentoflavone caused changes mainly in the membrane of Micrococcus luteus and decreased the menaquinone content. Tetrahydroamentoflavone mainly affected the carotenoids in the investigated strains. The noticeably different CCS value of tetrahydroamentoflavone compared to naringenin and amentoflavone revealed further insights into the structure-dependent effects of flavonoids. This study provides valuable insights into the response of pigment-forming food-associated microorganisms to naringenin, amentoflavone, and tetrahydroamentoflavone, which is important for the targeted and safe application of the latter as natural preservatives and useful for further research on the mechanisms of action.
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Affiliation(s)
- Maria Linden
- Institute of Nutritional and Food Sciences, Molecular Food Technology, University of Bonn, Friedrich-Hirzebruch-Allee 7, D-53115 Bonn, Germany
| | - Alexander Flegler
- Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, D-53115 Bonn, Germany
| | - Michelle M Feuereisen
- Institute of Nutritional and Food Sciences, Molecular Food Technology, University of Bonn, Friedrich-Hirzebruch-Allee 7, D-53115 Bonn, Germany
| | - Fabian Weber
- Institute of Nutritional and Food Sciences, Molecular Food Technology, University of Bonn, Friedrich-Hirzebruch-Allee 7, D-53115 Bonn, Germany
| | - André Lipski
- Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, D-53115 Bonn, Germany
| | - Andreas Schieber
- Institute of Nutritional and Food Sciences, Molecular Food Technology, University of Bonn, Friedrich-Hirzebruch-Allee 7, D-53115 Bonn, Germany.
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10
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Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity. Int J Mol Sci 2023; 24:ijms24044158. [PMID: 36835570 PMCID: PMC9966250 DOI: 10.3390/ijms24044158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4'-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.
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11
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Kwiatkowski P, Kurzawski M, Kukula-Koch W, Pruss A, Sienkiewicz M, Płaziński W, Dołęgowska B, Wojciechowska-Koszko I. Staphyloxanthin inhibitory potential of trans-anethole: A preliminary study. Biomed Pharmacother 2023; 158:114153. [PMID: 36566523 DOI: 10.1016/j.biopha.2022.114153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The reduction of staphyloxanthin (STX) production in Staphylococcus aureus under trans-anethole (TA) influence was proven in former studies. However, no tests concerning the impact of TA on a biosynthetic pathway of this carotenoid pigment have been published so far. Thus, for the first time, the present preliminary study evaluated the influence of TA on the expression level of genes (crtOPQMN operon and aldH) encoding STX pathway enzymes. Additional attention was paid to the identification of STX and its intermediates. Gene expression and identification of extracted compounds were conducted using quantitative real-time PCR and HPLC-MS techniques, respectively. The analyzes showed no difference in crtM, crtN, crtO, crtP, crtQ, and aldH gene expression between bacterial samples isolated from the non-stimulated (control) medium and the stimulated one with TA. Compared to the control group that showed the presence of all metabolic intermediates and STX, the TA-treated bacteria were characterized by a lack or a significant reduction of the majority of compounds, except 4,4'-diaponeurosporenoate, the content of which was elevated in the TA-treated sample. Moreover, in silico molecular docking analysis revealed that TA is capable to create relatively strong interactions with both 4,4'-diapophytoene synthase and 4,4'-diapophytoene desaturase. The preliminary findings indicate that the previously observed TA effect reducing the number of S. aureus colonies pigmentation is probably not associated with the expression levels of genes encoding STX pathway enzymes. It has been proven that adding TA to the medium can interfere with the formation of STX at different levels of its biosynthetic pathway.
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Affiliation(s)
- Paweł Kwiatkowski
- Department of Diagnostic Immunology, Pomeranian Medical University in Szczecin, Poland.
| | - Mateusz Kurzawski
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University in Szczecin, Poland
| | - Wirginia Kukula-Koch
- Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Lublin, Poland
| | - Agata Pruss
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, Poland
| | - Monika Sienkiewicz
- Department of Pharmaceutical Microbiology and Microbiological Diagnostic, Medical University of Lodz, Poland
| | - Wojciech Płaziński
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland; Department of Biopharmacy, Medical University of Lublin, Poland
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, Poland
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12
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Kim M, Jung DH, Hwang CY, Siziya IN, Park YS, Seo MJ. 4,4'-Diaponeurosporene Production as C 30 Carotenoid with Antioxidant Activity in Recombinant Escherichia coli. Appl Biochem Biotechnol 2023; 195:135-151. [PMID: 36066805 DOI: 10.1007/s12010-022-04147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 01/13/2023]
Abstract
Carotenoids, a group of isoprenoid pigments, are naturally synthesized by various microorganisms and plants, and are industrially used as ingredients in food, cosmetic, and pharmaceutical product formulations. Although several types of carotenoids and diverse microbial carotenoid producers have been reported, studies on lactic acid bacteria (LAB)-derived carotenoids are relatively insufficient. There is a notable lack of research focusing on C30 carotenoids, the functional characterizations of their biosynthetic genes and their mass production by genetically engineered microorganisms. In this study, the biosynthesis of 4,4'-diaponeurosporene in Escherichia coli harboring the core biosynthetic genes, dehydrosqualene synthase (crtM) and dehydrosqualene desaturase (crtN), from Lactiplantibacillus plantarum subsp. plantarum KCCP11226 was constructed to evaluate and enhance 4,4'-diaponeurosporene production and antioxidant activity. The production of 4,4'-diapophytoene, a substrate of 4,4'-diaponeurosporene, was confirmed in E. coli expressing only the crtM gene. In addition, recombinant E. coli carrying both C30 carotenoid biosynthesis genes (crtM and crtN) was confirmed to biosynthesize 4,4'-diaponeurosporene and exhibited a 6.1-fold increase in carotenoid production compared to the wild type and had a significantly higher antioxidant activity compared to synthetic antioxidant, butylated hydroxytoluene. This study presents the discovery of an important novel E. coli platform in consideration of the industrial applicability of carotenoids.
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Affiliation(s)
- Mibang Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Gyeongbuk, Korea.,Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Dong-Hyun Jung
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Chi Young Hwang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Inonge Noni Siziya
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea.,Research Center for Bio Material & Process Development, Incheon National University, Incheon, 22012, Republic of Korea
| | - Young-Seo Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 13120, Republic of Korea
| | - Myung-Ji Seo
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea. .,Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea. .,Research Center for Bio Material & Process Development, Incheon National University, Incheon, 22012, Republic of Korea.
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13
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The squalene route to C30 carotenoid biosynthesis and the origins of carotenoid biosynthetic pathways. Proc Natl Acad Sci U S A 2022; 119:e2210081119. [PMID: 36534808 PMCID: PMC9907078 DOI: 10.1073/pnas.2210081119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Carotenoids are isoprenoid lipids found across the tree of life with important implications in oxidative stress adaptations, photosynthetic metabolisms, as well as in membrane dynamics. The canonical view is that C40 carotenoids are synthesized from phytoene and C30 carotenoids from diapophytoene. Squalene is mostly associated with the biosynthesis of polycyclic triterpenes, although there have been suggestions that it could also be involved in the biosynthesis of C30 carotenoids. However, demonstration of the existence of this pathway in nature is lacking. Here, we demonstrate that C30 carotenoids are synthesized from squalene in the Planctomycetes bacteria and that this squalene route to C30 carotenoids is the most widespread in prokaryotes. Using the evolutionary history of carotenoid and squalene amino oxidases, we propose an evolutionary scenario to explain the origin and diversification of the different carotenoid and squalene-related pathways. We show that carotenoid biosynthetic pathways have been constantly transferred and neofunctionalized during prokaryotic evolution. One possible origin of the squalene pathway connects it with the one of C40 carotenoid synthesis of Cyanobacteria. The widespread occurrence of the squalene route to C30 carotenoids in Bacteria increases the functional repertoire of squalene, establishing it as a general hub of carotenoids and polycyclic triterpenes synthesis.
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14
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Rao L, Xu Y, Shen L, Wang X, Zhao H, Wang B, Zhang J, Xiao Y, Guo Y, Sheng Y, Cheng L, Song Z, Yu F. Small-molecule compound SYG-180-2-2 attenuates Staphylococcus aureus virulence by inhibiting hemolysin and staphyloxanthin production. Front Cell Infect Microbiol 2022; 12:1008289. [PMID: 36310881 PMCID: PMC9606476 DOI: 10.3389/fcimb.2022.1008289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022] Open
Abstract
Multi-drug resistant Staphylococcus aureus infection is still a serious threat to global health. Therefore, there is an urgent need to develop new antibacterial agents based on virulence factor therapy to overcome drug resistance. Previously, we synthesized SYG-180-2-2 (C21H16N2OSe), an effective small molecule compound against biofilm. The aim of this study was to investigate the anti-virulence efficacy of SYG-180-2-2 against Staphylococcus aureus. MIC results demonstrated no apparent antibacterial activity of the SYG-180-2-2. The growth curve assay showed that SYG-180-2-2 had nonlethal effect on S. aureus. Besides, SYG-180-2-2 strongly inhibited the hemolytic activity and staphyloxanthin synthesis in S. aureus. Inhibition of staphyloxanthin by SYG-180-2-2 enhanced the sensitivity of S. aureus to oxidants and human whole blood. In addition, SYG-180-2-2 significantly decreased the expression of saeR-mediated hemolytic gene hlb and staphyloxanthin-related crtM, crtN and sigB genes by quantitative polymerase chain reaction (qPCR). Meanwhile, the expression of oxidative stress-related genes sodA, sodM and katA also decreased. Galleria Mellonella assay revealed that SYG-180-2-2 was not toxic to larvae. Further, the larvae infection model showed that the virulence of bacteria was significantly reduced after 4 μg/mL SYG-180-2-2 treatment. SYG-180-2-2 also reduced skin abscess formation in mice by reducing bacterial burden and subcutaneous inflammation. In conclusion, SYG-180-2-2 might be a promising agent to attenuate the virulence of S. aureus by targeting genes associated with hemolytic activity and staphyloxanthin synthesis.
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Affiliation(s)
- Lulin Rao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanlei Xu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li Shen
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinyi Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huilin Zhao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bingjie Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jiao Zhang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanghua Xiao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yaoguang Sheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lixia Cheng
- Integrated Traditional Chinese and Western Medicine Hospital, Hangzhou, China
| | - Zengqiang Song
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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15
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Moyo AC, Dufossé L, Giuffrida D, van Zyl LJ, Trindade M. Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa. Microb Cell Fact 2022; 21:43. [PMID: 35305628 PMCID: PMC8933910 DOI: 10.1186/s12934-022-01752-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The genus Planococcus is comprised of halophilic bacteria generally reported for the production of carotenoid pigments and biosurfactants. In previous work, we showed that the culturing of the orange-pigmented Planococcus sp. CP5-4 isolate increased the evaporation rate of industrial wastewater brine effluent, which we attributed to the orange pigment. This demonstrated the potential application of this bacterium for industrial brine effluent management in evaporation ponds for inland desalination plants. Here we identified a C30-carotenoid biosynthetic gene cluster responsible for pigment biosynthesis in Planococcus sp. CP5-4 through isolation of mutants and genome sequencing. We further compare the core genes of the carotenoid biosynthetic gene clusters identified from different Planococcus species' genomes which grouped into gene cluster families containing BGCs linked to different carotenoid product chemotypes. Lastly, LC-MS analysis of saponified and unsaponified pigment extracts obtained from cultures of Planococcus sp. CP5-4, revealed the structure of the main (predominant) glucosylated C30-carotenoid fatty acid ester produced by Planococcus sp. CP5-4. RESULTS Genome sequence comparisons of isolated mutant strains of Planococcus sp. CP5-4 showed deletions of 146 Kb and 3 Kb for the non-pigmented and "yellow" mutants respectively. Eight candidate genes, likely responsible for C30-carotenoid biosynthesis, were identified on the wild-type genome region corresponding to the deleted segment in the non-pigmented mutant. Six of the eight candidate genes formed a biosynthetic gene cluster. A truncation of crtP was responsible for the "yellow" mutant phenotype. Genome annotation revealed that the genes encoded 4,4'-diapolycopene oxygenase (CrtNb), 4,4'- diapolycopen-4-al dehydrogenase (CrtNc), 4,4'-diapophytoene desaturase (CrtN), 4,4'- diaponeurosporene oxygenase (CrtP), glycerol acyltransferase (Agpat), family 2 glucosyl transferase 2 (Gtf2), phytoene/squalene synthase (CrtM), and cytochrome P450 hydroxylase enzymes. Carotenoid analysis showed that a glucosylated C30-carotenoid fatty acid ester, methyl 5-(6-C17:3)-glucosyl-5, 6'-dihydro-apo-4, 4'-lycopenoate was the main carotenoid compound produced by Planococcus sp. CP5-4. CONCLUSION We identified and characterized the carotenoid biosynthetic gene cluster and the C30-carotenoid compound produced by Planococcus sp. CP5-4. Mass-spectrometry guided analysis of the saponified and unsaponified pigment extracts showed that methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate esterified to heptadecatrienoic acid (C17:3). Furthermore, through phylogenetic analysis of the core carotenoid BGCs of Planococcus species we show that various C30-carotenoid product chemotypes, apart from methyl 5-glucosyl-5, 6-dihydro-apo-4, 4'-lycopenoate and 5-glucosyl-4, 4-diaponeurosporen-4'-ol-4-oic acid, may be produced that could offer opportunities for a variety of applications.
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Affiliation(s)
- Anesu Conrad Moyo
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa
- BioCiTi Laboratory, 4th Floor Block B, Bandwidth Barn, Woodstock Exchange Building, 66-68 Albert Road, Woodstock, Cape Town, 7925, South Africa
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, ESIROI Agroalimentaire, Université de La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 9, F-97744, Saint-Denis, France
| | - Daniele Giuffrida
- Università Degli Studi Di Messina, Dip. B.I.O.M.O.R.F, Polo Annunziata, 98168, Messina, ME, Italy
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, 7535, South Africa.
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16
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Tang H, Qu X, Zhang W, Chen X, Zhang S, Xu Y, Yang H, Wang Y, Yang J, Yuan WE, Yue B. Photosensitizer Nanodot Eliciting Immunogenicity for Photo-Immunologic Therapy of Postoperative Methicillin-Resistant Staphylococcus aureus Infection and Secondary Recurrence. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107300. [PMID: 34865257 DOI: 10.1002/adma.202107300] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/11/2021] [Indexed: 06/13/2023]
Abstract
The treatment of postoperative infection caused by multidrug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), has become an intractable clinical challenge owing to its low therapeutic efficacy and high risk of recurrence. Apart from imperfect antibacterial therapies, induction of insufficient immunogenicity, required for the successful clearance of a pathogen, may also contribute to the problem. Herein, an ultra-micro photosensitizer, AgB nanodots, using photothermal therapy, photodynamic therapy, and Ag+ ion sterilization, are utilized to efficiently clear invading MRSA both in vitro and in vivo. AgB nanodots are also found to upregulate host immunogenicity in a murine model and establish immunological memory by promoting the upregulated expression of danger signals that are commonly induced by stress-related responses, including sudden temperature spikes or excess reactive oxygen production. These stimulations boost the antibacterial effects of macrophages, dendritic cells, T cells, or even memory B cells, which is usually defined as infection-related immunogenic cell death. Hence, the proposed AgB nanodot strategy may offer a novel platform for the effective treatment of postoperative infection while providing a systematic immunotherapeutic strategy to combat persistent infections, thereby markedly reducing the incidence of recurrence following recovery from primary infections.
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Affiliation(s)
- Haozheng Tang
- Department of Bone and Joint Surgery, Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong Middle Road, Shanghai, 200001, P. R. China
| | - Xinhua Qu
- Department of Bone and Joint Surgery, Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong Middle Road, Shanghai, 200001, P. R. China
| | - Wenkai Zhang
- Pharm-X Center, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xuan Chen
- Pharm-X Center, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Shutao Zhang
- Department of Bone and Joint Surgery, Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong Middle Road, Shanghai, 200001, P. R. China
| | - Yang Xu
- Pharm-X Center, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Hongtao Yang
- Department of Plastic and Reconstructive Surgery, The Ohio State University, Columbus, OH, 43210, USA
- School of Medical Science and Engineering, Beihang University, Beijing, 100191, P. R. China
| | - You Wang
- Department of Bone and Joint Surgery, Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong Middle Road, Shanghai, 200001, P. R. China
| | - Jianping Yang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai, 201620, P. R. China
| | - Wei-En Yuan
- Pharm-X Center, Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Bing Yue
- Department of Bone and Joint Surgery, Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shandong Middle Road, Shanghai, 200001, P. R. China
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17
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López GD, Álvarez-Rivera G, Carazzone C, Ibáñez E, Leidy C, Cifuentes A. Bacterial Carotenoids: Extraction, Characterization, and Applications. Crit Rev Anal Chem 2021; 53:1239-1262. [PMID: 34915787 DOI: 10.1080/10408347.2021.2016366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Natural carotenoids are secondary metabolites that exhibit antioxidant, anti-inflammatory, and anti-cancer properties. These types of compounds are highly demanded by pharmaceutical, cosmetic, nutraceutical, and food industries, leading to the search for new natural sources of carotenoids. In recent years, the production of carotenoids from bacteria has become of great interest for industrial applications. In addition to carotenoids with C40-skeletons, some bacteria have the ability to synthesize characteristic carotenoids with C30-skeletons. In this regard, a great variety of methodologies for the extraction and identification of bacterial carotenoids has been reported and this is the first review that condenses most of this information. To understand the diversity of carotenoids from bacteria, we present their biosynthetic origin in order to focus on the methodologies employed in their extraction and characterization. Special emphasis has been made on high-performance liquid chromatography-mass spectrometry (HPLC-MS) for the analysis and identification of bacterial carotenoids. We end up this review showing their potential commercial use. This review is proposed as a guide for the identification of these metabolites, which are frequently reported in new bacteria strains.
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Affiliation(s)
- Gerson-Dirceu López
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | | | - Chiara Carazzone
- Chemistry Department, Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Universidad de los Andes, Bogotá, Colombia
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
| | - Chad Leidy
- Physics Department, Laboratory of Biophysics, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research (CIAL), CSIC, Madrid, Spain
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18
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Lin Y, Huang L, Zhang X, Yang J, Chen X, Li F, Liu J, Huang R. Multi-Omics Analysis Reveals Anti- Staphylococcus aureus Activity of Actinomycin D Originating from Streptomyces parvulus. Int J Mol Sci 2021; 22:ijms222212231. [PMID: 34830114 PMCID: PMC8621895 DOI: 10.3390/ijms222212231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus (S. aureus) is a common pathogen that causes various serious diseases, including chronic infections. Discovering new antibacterial agents is an important aspect of the pharmaceutical field because of the lack of effective antibacterial drugs. In our research, we found that one anti-S. aureus substance is actinomycin D, originating from Streptomyces parvulus (S. parvulus); then, we further focused on the anti-S. aureus ability and the omics profile of S. aureus in response to actinomycin D. The results revealed that actinomycin D had a significant inhibitory activity on S. aureus with a minimum inhibitory concentration (MIC) of 2 μg/mL and a minimum bactericidal concentration (MBC) of 64 μg/mL. Bacterial reactive oxygen species (ROS) increased 3.5-fold upon treatment with actinomycin D, as was measured with the oxidation-sensitive fluorescent probe DCFH-DA, and H2O2 increased 3.5 times with treatment by actinomycin D. Proteomics and metabolomics, respectively, identified differentially expressed proteins in control and treatment groups, and the co-mapped correlation network of proteomics and metabolomics annotated five major pathways that were potentially related to disrupting the energy metabolism and oxidative stress of S. aureus. All findings contributed to providing new insight into the mechanisms of the anti-S. aureus effects of actinomycin D originating from S. parvulus.
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Affiliation(s)
- Yuqi Lin
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (L.H.); (J.Y.); (X.C.); (F.L.)
| | - Li Huang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (L.H.); (J.Y.); (X.C.); (F.L.)
| | - Xiaoyong Zhang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China;
| | - Jiajia Yang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (L.H.); (J.Y.); (X.C.); (F.L.)
| | - Xiaodan Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (L.H.); (J.Y.); (X.C.); (F.L.)
| | - Fengming Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (L.H.); (J.Y.); (X.C.); (F.L.)
| | - Jun Liu
- Laboratory of Pathogenic Biology, The Marine Biomedical Research Institute, Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Medical University, Zhanjiang 524023, China
- Correspondence: (J.L.); (R.H.)
| | - Riming Huang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (L.H.); (J.Y.); (X.C.); (F.L.)
- Correspondence: (J.L.); (R.H.)
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Takemura M, Takagi C, Aikawa M, Araki K, Choi SK, Itaya M, Shindo K, Misawa N. Heterologous production of novel and rare C 30-carotenoids using Planococcus carotenoid biosynthesis genes. Microb Cell Fact 2021; 20:194. [PMID: 34627253 PMCID: PMC8502411 DOI: 10.1186/s12934-021-01683-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus maritimus strain iso-3 was isolated from an intertidal sediment that looked industrially polluted, from the Clyde estuary in the UK. This bacterium was found to produce a yellow acyclic carotenoid with a basic carbon 30 (C30) structure, which was determined to be methyl 5-glucosyl-5,6-dihydro-4,4′-diapolycopenoate. In the present study, we tried to isolate and identify genes involved in carotenoid biosynthesis from this marine bacterium, and to produce novel or rare C30-carotenoids with anti-oxidative activity in Escherichia coli by combinations of the isolated genes. Results A carotenoid biosynthesis gene cluster was found out through sequence analysis of the P. maritimus genomic DNA. This cluster consisted of seven carotenoid biosynthesis candidate genes (orf1–7). Then, we isolated the individual genes and analyzed the functions of these genes by expressing them in E. coli. The results indicated that orf2 and orf1 encoded 4,4′-diapophytoene synthase (CrtM) and 4,4′-diapophytoene desaturase (CrtNa), respectively. Furthermore, orf4 and orf5 were revealed to code for hydroxydiaponeurosporene desaturase (CrtNb) and glucosyltransferase (GT), respectively. By utilizing these carotenoid biosynthesis genes, we produced five intermediate C30-carotenoids. Their structural determination showed that two of them were novel compounds, 5-hydroxy-5,6-dihydro-4,4′-diaponeurosporene and 5-glucosyl-5,6-dihydro-4,4′-diapolycopene, and that one rare carotenoid 5-hydroxy-5,6-dihydro-4,4′-diapolycopene is included there. Moderate singlet oxygen-quenching activities were observed in the five C30-carotenoids including the two novel and one rare compounds. Conclusions The carotenoid biosynthesis genes from P. maritimus strain iso-3, were isolated and functionally identified. Furthermore, we were able to produce two novel and one rare C30-carotenoids in E. coli, followed by positive evaluations of their singlet oxygen-quenching activities. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01683-3.
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Affiliation(s)
- Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
| | - Chiharu Takagi
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Mayuri Aikawa
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Kanaho Araki
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Seon-Kang Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Mitsuhiro Itaya
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano, 380-8553, Japan
| | - Kazutoshi Shindo
- Department of Food and Nutrition, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
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Rizk S, Henke P, Santana-Molina C, Martens G, Gnädig M, Nguyen NA, Devos DP, Neumann-Schaal M, Saenz JP. Functional diversity of isoprenoid lipids in Methylobacterium extorquens PA1. Mol Microbiol 2021; 116:1064-1078. [PMID: 34387371 DOI: 10.1111/mmi.14794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/29/2021] [Accepted: 08/10/2021] [Indexed: 11/29/2022]
Abstract
Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE, and crtB we disrupted the production of squalene, and phytoene in Methylobacterium extorquens PA1, which are the presumed precursors for hopanoids and carotenoids, respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C30 backbone, rather than the previously predicted canonical C40 phytoene-derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C30 pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1.
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Affiliation(s)
- Sandra Rizk
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Petra Henke
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Carlos Santana-Molina
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Gesa Martens
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Marén Gnädig
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | | | - Damien P Devos
- Centro Andaluz de Biologıa del Desarrollo (CABD)-CSIC, Junta de Andalucıa, Universidad Pablo de Olavide, Seville, Spain
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - James P Saenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
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21
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López GD, Suesca E, Álvarez-Rivera G, Rosato AE, Ibáñez E, Cifuentes A, Leidy C, Carazzone C. Carotenogenesis of Staphylococcus aureus: New insights and impact on membrane biophysical properties. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158941. [PMID: 33862238 DOI: 10.1016/j.bbalip.2021.158941] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
Staphyloxanthin (STX) is a saccharolipid derived from a carotenoid in Staphylococcus aureus involved in oxidative-stress tolerance and antimicrobial peptide resistance. STX influences the biophysical properties of the bacterial membrane and has been associated to the formation of lipid domains in the regulation of methicillin-resistance. In this work, a targeted metabolomics and biophysical characterization study was carried out to investigate the biosynthetic pathways of carotenoids, and their impact on the membrane biophysical properties. Five different S. aureus strains were investigated, including three wild-type strains containing the crtM gene related to STX biosynthesis, a crtM-deletion mutant, and a crtMN plasmid-complemented variant. LC-DAD-MS/MS analysis of extracts allowed the identification of 34 metabolites related to carotenogenesis in S. aureus at different growth phases (8, 24 and 48 h), showing the progression of these metabolites as the bacteria advances into the stationary phase. For the first time, 22 members of a large family of carotenoids were identified, including STX and STX-homologues, as well as Dehydro-STX and Dehydro-STX-homologues. Moreover, thermotropic behavior of the CH2 stretch of lipid acyl chains in live cells by FTIR, show that the presence of STX increases acyl chain order at the bacterial growth temperature. Indeed, the cooperative melting event of the bacterial membrane, which occurs around 15 °C in the native strains, shifts with increased carotenoid content. These results show the diversity biosynthetic of carotenoids in S. aureus, and their influence on membrane biophysical properties.
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Affiliation(s)
- Gerson-Dirceu López
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, Bogotá D.C., Colombia; Laboratory of Biophysics, Physics Department, Universidad de los Andes, Bogotá D.C., Colombia; Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Madrid, Spain
| | - Elizabeth Suesca
- Laboratory of Biophysics, Physics Department, Universidad de los Andes, Bogotá D.C., Colombia
| | | | - Adriana E Rosato
- Molecular Microbiology Diagnostics-Research, Riverside University Health System, Professor Loma Linda University, Moreno Valley, CA, USA
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Madrid, Spain
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC, Madrid, Spain
| | - Chad Leidy
- Laboratory of Biophysics, Physics Department, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, Bogotá D.C., Colombia.
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Han M, Lee PC. Microbial Production of Bioactive Retinoic Acid Using Metabolically Engineered Escherichia coli. Microorganisms 2021; 9:microorganisms9071520. [PMID: 34361955 PMCID: PMC8305374 DOI: 10.3390/microorganisms9071520] [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: 06/12/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial production of bioactive retinoids, including retinol and retinyl esters, has been successfully reported. Previously, there are no reports on the microbial biosynthesis of retinoic acid. Two genes (blhSR and raldhHS) encoding retinoic acid biosynthesis enzymes [β-carotene 15,15′-oxygenase (Blh) and retinaldehyde dehydrogenase2 (RALDH2)] were synthetically redesigned for modular expression. Co-expression of the blhSR and raldhHS genes on the plasmid system in an engineered β-carotene-producing Escherichia coli strain produced 0.59 ± 0.06 mg/L of retinoic acid after flask cultivation. Deletion of the ybbO gene encoding a promiscuous aldehyde reductase induced a 2.4-fold increase in retinoic acid production to 1.43 ± 0.06 mg/L. Engineering of the 5’-UTR sequence of the blhSR and raldhHS genes enhanced retinoic acid production to 3.46 ± 0.16 mg/L. A batch culture operated at 37 °C, pH 7.0, and 50% DO produced up to 8.20 ± 0.05 mg/L retinoic acid in a bioreactor. As the construction and culture of retinoic acid–producing bacterial strains are still at an early stage in the development, further optimization of the expression level of the retinoic acid pathway genes, protein engineering of Blh and RALDH2, and culture optimization should synergistically increase the current titer of retinoic acid in E. coli.
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23
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Pinto OHB, Costa FS, Rodrigues GR, da Costa RA, da Rocha Fernandes G, Júnior ORP, Barreto CC. Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids. MICROBIAL ECOLOGY 2021; 81:169-179. [PMID: 32617619 DOI: 10.1007/s00248-020-01548-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.
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Affiliation(s)
- Otávio Henrique Bezerra Pinto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Laboratory of Enzymology, Institute of Biological Sciences, Department of Cell Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Flávio Silva Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Gisele Regina Rodrigues
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Rosiane Andrade da Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil
| | - Gabriel da Rocha Fernandes
- Research Center René Rachou, Oswaldo Cruz Foundation (Fiocruz), Avenida Augusto de Lima 1715, Barro Preto, Belo Horizonte, 30190-002, Brazil
| | - Osmindo Rodrigues Pires Júnior
- Department of Physiological Sciences, Institute of Biological Sciences, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Cristine Chaves Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, SGAN 916 Módulo B Avenida W5 - Asa Norte, Brasília, 70790-160, Brazil.
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24
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Genome Mining Reveals Two Missing CrtP and AldH Enzymes in the C30 Carotenoid Biosynthesis Pathway in Planococcus faecalis AJ003 T. Molecules 2020; 25:molecules25245892. [PMID: 33322786 PMCID: PMC7764019 DOI: 10.3390/molecules25245892] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
Planococcus faecalis AJ003T produces glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid as its main carotenoid. Five carotenoid pathway genes were presumed to be present in the genome of P. faecalis AJ003T; however, 4,4-diaponeurosporene oxidase (CrtP) was non-functional, and a gene encoding aldehyde dehydrogenase (AldH) was not identified. In the present study, a genome mining approach identified two missing enzymes, CrtP2 and AldH2454, in the glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid biosynthetic pathway. Moreover, CrtP2 and AldH enzymes were functional in heterologous Escherichia coli and generated two carotenoid aldehydes (4,4′-diapolycopene-dial and 4,4′-diaponeurosporene-4-al) and two carotenoid carboxylic acids (4,4′-diaponeurosporenoic acid and 4,4′-diapolycopenoic acid). Furthermore, the genes encoding CrtP2 and AldH2454 were located at a distance the carotenoid gene cluster of P. faecalis.
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25
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Rossi BF, Bonsaglia ÉCR, Castilho IG, Dantas STA, Langoni H, Pantoja JCF, Júnior AF, Gonçalves JL, Santos MV, Mota RA, Rall VLM. First investigation of Staphylococcus argenteus in a Brazilian collections of S. aureus isolated from bovine mastitis. BMC Vet Res 2020; 16:252. [PMID: 32690007 PMCID: PMC7372812 DOI: 10.1186/s12917-020-02472-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/13/2020] [Indexed: 02/04/2023] Open
Abstract
Background Staphylococcus argenteus is a new specie positive coagulase staphylococci. We investigate the presence of S. argenteus in isolates previously classified as S. aureus, obtained from the milk of cows with mastitis in Brazil. Results Among 856 S. aureus tested in chocolate agar, tryptone soya agar and salt egg yolk agar, white or colorless colonies were observed in 185 (21.6%) isolates. Regarding the ctrOPQMN operon, 111 (60%) presented the complete cluster. Despite some missing genes in this cluster, the remaining strains (74) were confirmed as S. aureus using the nrps gene. Conclusions As far as we know, this is the first review of S. aureus collection in Brazil and S. argenteus does not appear to be a significant problem in Brazilian herds.
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Affiliation(s)
- Bruna F Rossi
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Post Office Box 510, Botucatu, Sao Paulo, 18618-970, Brazil
| | - Érika C R Bonsaglia
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Post Office Box 510, Botucatu, Sao Paulo, 18618-970, Brazil.
| | - Ivana G Castilho
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Post Office Box 510, Botucatu, Sao Paulo, 18618-970, Brazil
| | - Stéfani T A Dantas
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Post Office Box 510, Botucatu, Sao Paulo, 18618-970, Brazil
| | - Hélio Langoni
- Department of Hygiene Veterinary and Public Health, Sao Paulo State University, Botucatu, SP, Brazil
| | - José C F Pantoja
- Department of Hygiene Veterinary and Public Health, Sao Paulo State University, Botucatu, SP, Brazil
| | - Ary Fernandes Júnior
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Post Office Box 510, Botucatu, Sao Paulo, 18618-970, Brazil
| | - Juliano L Gonçalves
- Department of Animal Science, School of Veterinary Medicine and Animal Science (USP), Pirassununga, SP, Brazil
| | - Marcos V Santos
- Department of Animal Science, School of Veterinary Medicine and Animal Science (USP), Pirassununga, SP, Brazil
| | - Rinaldo A Mota
- Departament of Veterinary Medicine, Federal Rural University of Pernambuco, Recife, PE, Brazil
| | - Vera L M Rall
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University - UNESP, Post Office Box 510, Botucatu, Sao Paulo, 18618-970, Brazil
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26
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Seel W, Baust D, Sons D, Albers M, Etzbach L, Fuss J, Lipski A. Carotenoids are used as regulators for membrane fluidity by Staphylococcus xylosus. Sci Rep 2020; 10:330. [PMID: 31941915 PMCID: PMC6962212 DOI: 10.1038/s41598-019-57006-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/19/2019] [Indexed: 01/10/2023] Open
Abstract
Carotenoids are associated with several important biological functions as antenna pigments in photosynthesis or protectives against oxidative stress. Occasionally they were also discussed as part of the cold adaptation mechanism of bacteria. For two Staphylococcus xylosus strains we demonstrated an increased content of staphyloxanthin and other carotenoids after growth at 10 °C but no detectable carotenoids after grow at 30 °C. By in vivo measurements of generalized polarization and anisotropy with two different probes Laurdan and TMA-DPH we detected a strong increase in membrane order with a simultaneous increase in membrane fluidity at low temperatures accompanied by a broadening of the phase transition. Increased carotenoid concentration was also correlated with an increased resistance of the cells against freeze-thaw stress. In addition, the fatty acid profile showed a moderate adaptation to low temperature by increasing the portion of anteiso-branched fatty acids. The suppression of carotenoid synthesis abolished the effects observed and thus confirmed the causative function of the carotenoids in the modulation of membrane parameters. A differential transcriptome analysis demonstrated the upregulation of genes involved in carotenoid syntheses under low temperature growth conditions. The presented data suggests that upregulated synthesis of carotenoids is a constitutive component in the cold adaptation strategy of Staphylococcus xylosus and combined with modifications of the fatty acid profile constitute the adaptation to grow under low temperature conditions.
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Affiliation(s)
- Waldemar Seel
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutritional and Food Science, Food Microbiology and Hygiene, 53115, Bonn, Germany
| | - Denise Baust
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutritional and Food Science, Food Microbiology and Hygiene, 53115, Bonn, Germany
| | - Dominik Sons
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutritional and Food Science, Food Microbiology and Hygiene, 53115, Bonn, Germany
| | - Maren Albers
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutritional and Food Science, Food Microbiology and Hygiene, 53115, Bonn, Germany
| | - Lara Etzbach
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutritional and Food Science, Molecular Food Technology, 53115, Bonn, Germany
| | - Janina Fuss
- Max Planck-Genome-Centre Cologne, 50829, Cologne, Germany
- Institute of Clinical Molecular Biology, Kiel University (CAU)/University Hospital Schleswig Holstein, 24105, Kiel, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutritional and Food Science, Food Microbiology and Hygiene, 53115, Bonn, Germany.
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27
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Redesign and reconstruction of a mevalonate pathway and its application in terpene production in Escherichia coli. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.100291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Characterization and engineering of a carotenoid biosynthesis operon from Bacillus megaterium. Metab Eng 2018; 49:47-58. [DOI: 10.1016/j.ymben.2018.07.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/11/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022]
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29
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Cueno ME, Imai K. Network analytics approach towards identifying potential antivirulence drug targets within the Staphylococcus aureus staphyloxanthin biosynthetic network. Arch Biochem Biophys 2018; 645:81-86. [PMID: 29551420 DOI: 10.1016/j.abb.2018.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/23/2018] [Accepted: 03/11/2018] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus is associated with several clinically significant infections among humans and infections associated with antibiotic-resistant strains are growing in frequency. Antivirulence strategies shift the target of drugs from bacterial growth to the infection process resulting to milder evolutionary pressure for the development of bacterial resistant strains. Staphyloxanthin (STX) is a yellowish-orange carotenoid pigment synthesized by S. aureus and this carotenoid functions as an important virulence factor for the bacteria. In this study, we elucidated whether network analytics can be used as a viable tool to identify significant components in the STX biosynthetic network which in-turn could serve as possible antivirulence drug targets. For confirmation, we correlated our results to known drugs that were able to inhibit STX biosynthesis. Throughout this study, we established that crtN(1) activity and 4,4'-diaponeurosporene amounts are significant components in the STX biosynthetic network and, moreover, network analytics can aid in identifying antivirulence drug targets within the STX biosynthetic network. Similarly, we found that network analytics is capable of identifying multiple potential targets simultaneously. Taken together, we propose that an effective antivirulence drug against S. aureus STX biosynthesis would involve targeting crtN(1) activity, 4,4'-diaponeurosporene levels, or both components.
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Affiliation(s)
- Marni E Cueno
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, 101-8310, Japan.
| | - Kenichi Imai
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, 101-8310, Japan
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30
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Choi JY, Kim JH, Lee PC. Flavobacterium kingsejongi sp. nov., a carotenoid-producing species isolated from Antarctic penguin faeces. Int J Syst Evol Microbiol 2018; 68:911-916. [DOI: 10.1099/ijsem.0.002610] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jun Young Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Jin Ho Kim
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 16499, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 16499, Republic of Korea
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31
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Complete genome sequence of Planococcus faecalis AJ003 T, the type species of the genus Planococcus and a microbial C30 carotenoid producer. J Biotechnol 2018; 266:72-76. [PMID: 29237561 DOI: 10.1016/j.jbiotec.2017.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 11/23/2022]
Abstract
A novel type strain, Planococcus faecalis AJ003T, isolated from the feces of Antarctic penguins, synthesizes a rare C30 carotenoid, glycosyl-4,4'-diaponeurosporen-4'-ol-4-oic acid. The complete genome of P. faecalis AJ003T comprises a single circular chromosome (3,495,892 bp; 40.9% G + C content). Annotation analysis has revealed 3511 coding DNA sequences and 99 RNAs; seven genes associated with the MEP pathway and five genes involved in the carotenoid pathway have been identified. The functionality and complementation of 4,4'-diapophytoene synthase (CrtM) and two copies of heterologous 4,4'-diapophytoene desaturase (CrtN) involved in carotenoid biosynthesis were analyzed in Escherichia coli.
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Christo-Foroux E, Vallaeys T, Loux V, Dassa E, Deutscher J, Wandersman C, Livernois A, Hot C, Criscuolo A, Dauga C, Clermont D, Chesneau O. Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group. Syst Appl Microbiol 2017; 40:401-410. [PMID: 28890241 DOI: 10.1016/j.syapm.2017.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depict the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.
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Affiliation(s)
- Eugene Christo-Foroux
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Tatiana Vallaeys
- Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France.
| | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France.
| | - Elie Dassa
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Josef Deutscher
- CNRS, UMR 8261 Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Université Paris Diderot, Sorbonne-Paris-Cité, 13 rue Pierre et Marie Curie, Paris, France.
| | - Cécile Wandersman
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Aurélien Livernois
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France
| | - Chloe Hot
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Alexis Criscuolo
- Hub, Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Catherine Dauga
- International Group of Data Analysis (IGDA), Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Dominique Clermont
- Collection de l'Institut Pasteur (CIP), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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The Staphylococcus aureus AirSR Two-Component System Mediates Reactive Oxygen Species Resistance via Transcriptional Regulation of Staphyloxanthin Production. Infect Immun 2017; 85:IAI.00838-16. [PMID: 27872240 DOI: 10.1128/iai.00838-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/18/2016] [Indexed: 01/22/2023] Open
Abstract
Staphylococcus aureus is an important opportunistic pathogen and is the etiological agent of many hospital- and community-acquired infections. The golden pigment, staphyloxanthin, of S. aureus colonies distinguishes it from other staphylococci and related Gram-positive cocci. Staphyloxanthin is the product of a series of biosynthetic steps that produce a unique membrane-embedded C30 golden carotenoid and is an important antioxidant. We observed that a strain with an inducible airR overexpression cassette had noticeably increased staphyloxanthin production compared to the wild-type strain under aerobic culturing conditions. Further analysis revealed that depletion or overproduction of the AirR response regulator resulted in a corresponding decrease or increase in staphyloxanthin production and susceptibility to killing by hydrogen peroxide, respectively. Furthermore, the genetic elimination of staphyloxanthin during AirR overproduction abolished the protective phenotype of increased staphyloxanthin production in a whole-blood survival assay. Promoter reporter and gel shift assays determined that the AirR response regulator is a direct positive regulator of the staphyloxanthin-biosynthetic operon, crtOPQMN, but is epistatic to alternative sigma factor B. Taken together, these data indicate that AirSR positively regulates the staphyloxanthin-biosynthetic operon crtOPQMN, promoting survival of S. aureus in the presence of oxidants.
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Zhang DF, Xu X, Song Q, Bai Y, Zhang Y, Song M, Shi C, Shi X. Identification of Staphylococcus argenteus in Eastern China based on a nonribosomal peptide synthetase (NRPS) gene. Future Microbiol 2016; 11:1113-21. [PMID: 27561462 DOI: 10.2217/fmb-2016-0017] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate whether the Staphylococcus argenteus is present in Eastern China and to verify the utility of a new screening process. MATERIALS & METHODS Phenotype observation, PCR assay targeting a hypothetical nonribosomal peptide synthetase (NRPS) gene, phylogenetic analysis of rpoB and multilocus sequence typing were used to screen and identify strains of S. argenteus from 839 presumptive S. aureus isolates. RESULTS Eighty-nine (89/839, 10.6%) of the presumptive S. aureus isolates produced white colonies on tryptone soya agar plates. Of the white-colony isolates, six (6/89, 7%) were S. argenteus, 75 (75/89, 84%) were S. aureus and eight (8/89, 9%) were other bacteria. CONCLUSION The PCR-based method targeting the NRPS gene can simultaneously identify and distinguish S. argenteus and S. aureus. All representative sequences of rpoB generated in this study were deposited in GenBank under accession numbers SJTU F20002, KT767581; SJTU F20269, KT767582; SJTU F20419, KT767583; SJTU F20420, KT767584; SJTU F20124, KT767585; SJTU F21164, KT767586; SJTU F21285, KT767587; SJTU F21224, KT767588; SJTU F21155, KT767589; SJTU F21294, KT767590; SJTU F20030, KT767591; SJTU F20044, KT767592; SJTU F20135, KT767593; SJTU F20123, KT767594; SJTU F21319, KT767595, respectively. All the new sequence types (STs) were submitted to a multilocus sequence typing database and the assigned ST numbers are ST3261 (151-469-20-101-145-150-131), ST3262 (12-3-1-1-4-4-410) and ST3267 (2-471-2-2-6-3-2).
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Affiliation(s)
- Dao-Feng Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xuebin Xu
- Department of Microbiological Lab, Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Qifa Song
- Department of Microbiology, Ningbo Municipal Center for Disease Control & Prevention, Ningbo, Zhejiang, China
| | - Yalong Bai
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Minghui Song
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Kim SH, Kim MS, Lee BY, Lee PC. Generation of structurally novel short carotenoids and study of their biological activity. Sci Rep 2016; 6:21987. [PMID: 26902326 PMCID: PMC4763220 DOI: 10.1038/srep21987] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/04/2016] [Indexed: 12/19/2022] Open
Abstract
Recent research interest in phytochemicals has consistently driven the efforts in the metabolic engineering field toward microbial production of various carotenoids. In spite of systematic studies, the possibility of using C30 carotenoids as biologically functional compounds has not been explored thus far. Here, we generated 13 novel structures of C30 carotenoids and one C35 carotenoid, including acyclic, monocyclic, and bicyclic structures, through directed evolution and combinatorial biosynthesis, in Escherichia coli. Measurement of radical scavenging activity of various C30 carotenoid structures revealed that acyclic C30 carotenoids showed higher radical scavenging activity than did DL-α-tocopherol. We could assume high potential biological activity of the novel structures of C30 carotenoids as well, based on the neuronal differentiation activity observed for the monocyclic C30 carotenoid 4,4′-diapotorulene on rat bone marrow mesenchymal stem cells. Our results demonstrate that a series of structurally novel carotenoids possessing biologically beneficial properties can be synthesized in E. coli.
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Affiliation(s)
- Se H Kim
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark
| | - Moon S Kim
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, South Korea
| | - Bun Y Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, South Korea
| | - Pyung C Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, South Korea
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36
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Vermassen A, Dordet-Frisoni E, de La Foye A, Micheau P, Laroute V, Leroy S, Talon R. Adaptation of Staphylococcus xylosus to Nutrients and Osmotic Stress in a Salted Meat Model. Front Microbiol 2016; 7:87. [PMID: 26903967 PMCID: PMC4742526 DOI: 10.3389/fmicb.2016.00087] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/18/2016] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus xylosus is commonly used as starter culture for meat fermentation. Its technological properties are mainly characterized in vitro, but the molecular mechanisms for its adaptation to meat remain unknown. A global transcriptomic approach was used to determine these mechanisms. S. xylosus modulated the expression of about 40-50% of the total genes during its growth and survival in the meat model. The expression of many genes involved in DNA machinery and cell division, but also in cell lysis, was up-regulated. Considering that the S. xylosus population remained almost stable between 24 and 72 h of incubation, our results suggest a balance between cell division and cell lysis in the meat model. The expression of many genes encoding enzymes involved in glucose and lactate catabolism was up-regulated and revealed that glucose and lactate were used simultaneously. S. xylosus seemed to adapt to anaerobic conditions as revealed by the overexpression of two regulatory systems and several genes encoding cofactors required for respiration. In parallel, genes encoding transport of peptides and peptidases that could furnish amino acids were up-regulated and thus concomitantly a lot of genes involved in amino acid synthesis were down-regulated. Several genes involved in glutamate homeostasis were up-regulated. Finally, S. xylosus responded to the osmotic stress generated by salt added to the meat model by overexpressing genes involved in transport and synthesis of osmoprotectants, and Na(+) and H(+) extrusion.
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Affiliation(s)
| | | | - Anne de La Foye
- INRA, Plateforme d'Exploration du MétabolismeSaint-Genès Champanelle, France
| | - Pierre Micheau
- INRA, UR454 MicrobiologieSaint-Genès Champanelle, France
| | - Valérie Laroute
- Université de Toulouse, INSA, UPS, INP, LISBPToulouse, France
| | - Sabine Leroy
- INRA, UR454 MicrobiologieSaint-Genès Champanelle, France
| | - Régine Talon
- INRA, UR454 MicrobiologieSaint-Genès Champanelle, France
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37
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Chen F, Di H, Wang Y, Cao Q, Xu B, Zhang X, Yang N, Liu G, Yang CG, Xu Y, Jiang H, Lian F, Zhang N, Li J, Lan L. Small-molecule targeting of a diapophytoene desaturase inhibits S. aureus virulence. Nat Chem Biol 2016; 12:174-9. [PMID: 26780405 DOI: 10.1038/nchembio.2003] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/13/2015] [Indexed: 02/07/2023]
Abstract
The surge of antibiotic resistance in Staphylococcus aureus has created a dire need for innovative anti-infective agents that attack new targets, to overcome resistance. In S. aureus, carotenoid pigment is an important virulence factor because it shields the bacterium from host oxidant killing. Here we show that naftifine, a US Food and Drug Administration (FDA)-approved antifungal drug, blocks biosynthesis of carotenoid pigment at nanomolar concentrations. This effect is mediated by competitive inhibition of S. aureus diapophytoene desaturase (CrtN), an essential enzyme for carotenoid pigment synthesis. We found that naftifine attenuated the virulence of a variety of clinical S. aureus isolates, including methicillin-resistant S. aureus (MRSA) strains, in mouse infection models. Specifically, we determined that naftifine is a lead compound for potent CrtN inhibitors. In sum, these findings reveal that naftifine could serve as a chemical probe to manipulate CrtN activity, providing proof of concept that CrtN is a druggable target against S. aureus infections.
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Affiliation(s)
- Feifei Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hongxia Di
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Youxin Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiao Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bin Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xue Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Nana Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Guijie Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yong Xu
- Humanwell Healthcare (Group) Co. Ltd., Wuhan, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fulin Lian
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Naixia Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jian Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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Kim JH, Kang HJ, Yu BJ, Kim SC, Lee PC. Planococcus faecalis sp. nov., a carotenoid-producing species isolated from stools of Antarctic penguins. Int J Syst Evol Microbiol 2015; 65:3373-3378. [DOI: 10.1099/ijsem.0.000423] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taxonomic studies were performed on a novel carotenoid-producing strain, designated AJ003T, isolated from faeces of Antarctic penguins. Cells of strain AJ003T were aerobic, Gram-stain-positive, cocci-shaped and orange. Strain AJ003T was capable of growing in a broad temperature range, including sub-zero growth (below − 20 to 30 °C). 16S rRNA gene sequence analysis revealed that strain AJ003T was closely related to Planococcus halocryophilus Or1T (97.4 % similarity), Planococcus antarcticus DSM 14505T (97.3 %), Planococcus kocurii NCIMB 629T (97.3 %), and Planococcus donghaensis JH1T (97.1 %). The predominant cellular fatty acids were anteiso-C15 : 0, and iso-C16 : 0.MK-7 and MK-8 were the quinones identified, and the major pigment was glycosyl-4,4′-diaponeurosporen-4′-ol-4-oic acid. The major polar lipid was phosphatidylglycerol. DNA–DNA relatedness of strain AJ003T with respect to its closest phylogenetic neighbours was 38.2 ± 0.5 % for Planococcus halocryophilus DSM 24743T, 32.2 ± 0.2 % for Planococcus antarcticus DSM 14505T, 21.0 ± 0.3 % for Planococcus kocurii DSM 20747T and 18.6 ± 1.4 % for Planococcus donghaensis KCTC 13050T. The DNA G+C content of strain AJ003T was 40.0 ± 0.6 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain AJ003T is concluded to represent a novel species of the genus Planococcus, for which the name Planococcus faecalis sp. nov. is proposed. The type strain is AJ003T ( = KCTC 33580T = CECT 8759T).
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Affiliation(s)
- Jin Ho Kim
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Korea
| | - Hyung Jun Kang
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Korea
| | - Byung Jo Yu
- IT Convergence Materials R&BD Group, Chungcheong Regional Division, Korea Institute of Industrial Technology (KITECH), Cheonan, Chungnam 330-825, South Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Gwanhangno, Yusong-gu, Taejon 305-701, Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Korea
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39
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Kim JH, Kim SH, Kim KH, Lee PC. Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond. Int J Syst Evol Microbiol 2015; 65:2824-2830. [DOI: 10.1099/ijs.0.000337] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taxonomic studies were performed on an astaxanthin-dideoxyglycoside-producing strain, designated PB304T, isolated from soil near a pond in Daejeon city, South Korea. Cells of strain PB304T were Gram-staining-negative, strictly aerobic, orange-coloured and motile, and occurred as single or paired short chains. PB304T did not contain bacteriochlorophyll a. 16S rRNA gene sequence analysis revealed that strain PB304T was closely related to ‘Sphingomonas humi’ KCTC 12341 (98.7 %), Sphingomonas kaistensis KCTC 12344T (97.9 %), Sphingomonas astaxanthinifaciens DSM 22298T (97.6 %) and Sphingomonas ginsengisoli KCTC 12630T (97.5 %). Analysis of pufLM gene sequences revealed strain PB304T to be closely related to ‘S. humi’ KCTC 12341 (88.1 %). The major cellular fatty acids were C16 : 0, summed feature 4 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c), and summed feature 7 (comprising C18 : 1ω7c/ω9t/ω12t). Ubiquinone 10 (Q-10) was the sole quinone identified, and the major pigment was astaxanthin dideoxyglycoside. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The polyamine was spermidine. The DNA–DNA relatedness values of strain PB304T with respect to its closest phylogenetic neighbours were 57.1 % for ‘S. humi’ KCTC 12341, 51.2 % for Sphingomonas kaistensis KCTC 12334T, 50.6 % for Sphingomonas astaxanthinifaciens DSM 22298T and 50.2 % for Sphingomonas ginsengisoli KCTC 12630T. The DNA G+C content of strain PB304T was 66.6 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain PB304T is concluded to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lacus is proposed. The type strain is PB304T ( = KCTC 32458T = CECT 8383T).
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Affiliation(s)
- Jin Ho Kim
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Republic of Korea
| | - Se Hyeuk Kim
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Republic of Korea
| | - Kyong Ho Kim
- Department of Microbiology, Pukyong National University, Busan 608-737, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Republic of Korea
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40
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Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6. Enzyme Microb Technol 2015; 77:29-37. [PMID: 26138397 DOI: 10.1016/j.enzmictec.2015.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 11/22/2022]
Abstract
The γ-carotenoids, such as myxol and saproxanthin, have a high potential to be utilized in nutraceutical and pharmaceutical industries for their neuro-protective and antioxidant effects. CrtD is involved in the production of γ-carotenoids by desaturating the C3'-C4' position of 1'-OH-γ-carotenoid. We determined the crystal structure of CrtD from Nonlabens dokdonensis DSW-6 (NdCrtD), the first structure of CrtD family enzymes. The NdCrtD structure was composed of two distinct domains, an FAD-binding domain and a substrate-binding domain, and the substrate-binding domain can be divided into two subdomains, a Rossmann fold-like subdomain and a lid subdomain. Although the FAD-binding domain showed a structure similar to canonical FAD-containing enzymes, the substrate-binding domain exhibited a novel structure to constitute a long and hydrophobic tunnel with a length of ∼40 Å. The molecular docking-simulation reveals that the tunnel provides an appropriate substrate-binding site for the carotenoid such as 1'-OH-γ-carotene with a length of ∼35 Å. We could predict residues related to recognize the 1'-hydroxyl group and to stabilize the hydrophobic end without hydroxyl group. Moreover, we suggest that the flexible entrance loop may undergo an open-closed formational change during the binding of the substrate.
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41
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Steiger S, Perez-Fons L, Cutting SM, Fraser PD, Sandmann G. Annotation and functional assignment of the genes for the C30 carotenoid pathways from the genomes of two bacteria: Bacillus indicus and Bacillus firmus. Microbiology (Reading) 2015; 161:194-202. [DOI: 10.1099/mic.0.083519-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sabine Steiger
- Biosynthesis Group, Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Simon M. Cutting
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Paul D. Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Gerhard Sandmann
- Biosynthesis Group, Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
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42
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Kim SH, Kim JH, Lee BY, Lee PC. The astaxanthin dideoxyglycoside biosynthesis pathway in Sphingomonas sp. PB304. Appl Microbiol Biotechnol 2014; 98:9993-10003. [DOI: 10.1007/s00253-014-6050-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 08/10/2014] [Accepted: 08/18/2014] [Indexed: 01/18/2023]
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43
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Kim JH, Choi BH, Jo M, Kim SC, Lee PC. Flavobacterium faecale sp. nov., an agarase-producing species isolated from stools of Antarctic penguins. Int J Syst Evol Microbiol 2014; 64:2884-2890. [DOI: 10.1099/ijs.0.059618-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taxonomic studies were performed on an agarase-producing strain, designated WV33T, isolated from faeces of Antarctic penguins. Cells of strain WV33T were Gram-staining-negative, strictly aerobic, orange and rod-shaped. Strain WV33T displayed agarase activity and was able to utilize galactose as a sole carbon source. 16S rRNA gene sequence analysis revealed that strain WV33T was closely related to
Flavobacterium algicola
TC2T (98.0 % similarity),
F. frigidarium
ATCC 700810T (96.9 %) and
F. frigoris
LMG 21922T (96.1 %). The predominant cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0, C15 : 0, C16 : 0 and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone 6 (MK-6) was the sole quinone identified, and the major pigment was zeaxanthin. The major polar lipid was phosphatidylethanolamine. DNA–DNA relatedness of strain WV33T with respect to its closest phylogenetic neighbours was 25 % for
F. algicola
NBRC 102673T, 23 % for
F. frigidarium
DSM 17623T and 21 % for
F. frigoris
DSM 15719T. The DNA G+C content of strain WV33T was 37±0.6 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain WV33T is concluded to represent a novel species of the genus
Flavobacterium
, for which the name Flavobacterium faecale sp. nov. is proposed. The type strain is WV33T ( = KCTC 32457T = CECT 8384T).
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Affiliation(s)
- Jin Ho Kim
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Republic of Korea
| | - Bo Hyun Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Republic of Korea
| | - Minho Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 500-185, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Gwanhangno, Yusong-gu, Taejon 305-701, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Republic of Korea
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15'-monooxygenase. PLoS One 2014; 9:e103318. [PMID: 25058308 PMCID: PMC4110020 DOI: 10.1371/journal.pone.0103318] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/29/2014] [Indexed: 12/30/2022] Open
Abstract
The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Roy D. Sleator
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
- * E-mail: (CH); (RDS); (JRM)
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Department of Hepatology and Gastroenterology, Imperial College London, London, United Kingdom
- * E-mail: (CH); (RDS); (JRM)
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (CH); (RDS); (JRM)
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Kim JH, Kim SH, Yoon JH, Lee PC. Carotenoid production from n-alkanes with a broad range of chain lengths by the novel species Gordonia ajoucoccus A2T. Appl Microbiol Biotechnol 2014; 98:3759-68. [DOI: 10.1007/s00253-014-5516-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/30/2022]
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Heo J, Kim SH, Lee PC. New insight into the cleavage reaction of Nostoc sp. strain PCC 7120 carotenoid cleavage dioxygenase in natural and nonnatural carotenoids. Appl Environ Microbiol 2013; 79:3336-45. [PMID: 23524669 PMCID: PMC3648047 DOI: 10.1128/aem.00071-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/15/2013] [Indexed: 01/13/2023] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. In this study, we investigated the activity and substrate preferences of NSC3, a CCD of Nostoc sp. strain PCC 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. NSC3 cleaved β-apo-8'-carotenal at 3 positions, C-13 C-14, C-15 C-15', and C-13' C-14', revealing a unique cleavage pattern. NSC3 cleaves the natural structure of carotenoids 4,4'-diaponeurosporene, 4,4'-diaponeurosporen-4'-al, 4,4'-diaponeurosporen-4'-oic acid, 4,4'-diapotorulene, and 4,4'-diapotorulen-4'-al to generate novel cleavage products (apo-14'-diaponeurosporenal, apo-13'-diaponeurosporenal, apo-10'-diaponeurosporenal, apo-14'-diapotorulenal, and apo-10'-diapotorulenal, respectively). The study of carotenoids with natural or nonnatural structures produced by using synthetic modules could provide information valuable for understanding the cleavage reactions or substrate preferences of other CCDs in vivo and in vitro.
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Affiliation(s)
- Jinsol Heo
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-Dong, Yeongtong-gu, Suwon, South Korea
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Kim JR, Kim SH, Lee SY, Lee PC. Construction of homologous and heterologous synthetic sucrose utilizing modules and their application for carotenoid production in recombinant Escherichia coli. BIORESOURCE TECHNOLOGY 2013; 130:288-295. [PMID: 23313673 DOI: 10.1016/j.biortech.2012.11.148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
Sucrose is one of the most promising carbon sources for industrial fermentation. We expressed synthetic modules expressing genes of the PEP-PTS and non-PTS pathways in Escherichia coli K12 for comparison. We selected PEP-PTS pathway genes of Lactobacillus plantarum and Staphylococcus xylosus and non-PTS pathway genes of sucrose-utilizing (Scr(+)) E. coli EC3132. Switchable Scr(+) modules expressing E. coli EC3132 non-PTS genes conferred better sucrose-utilizing ability on Scr(-)E. coli K12 than E. coli EC3132. Scr(+) modules expressing S. xylosus PEP-PTS genes conferred a sucrose-utilizing ability on E. coli K12. Among L. plantarum PEP-PTS genes, SacA(LP) and SacK(LP) were functional in E. coli K12. CscA(EC)-CscB(EC)-CscK(EC) (non-PEP-PTS module) or ScrA(SX)-SacA(LP)-SacK(LP) (PEP-PTS module) was introduced to a diapolycopene-producing E. coli strain. In both Scr(+)E. coli K12, the sucrose-utilizing ability of the modules was not affected by diapolycopene formation, indicating that the modular Scr(+) systems could be employed for developing sustainable bioprocesses using sucrose.
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Affiliation(s)
- Jong Rae Kim
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon 443-749, Republic of Korea
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48
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Heterologous carotenoid-biosynthetic enzymes: functional complementation and effects on carotenoid profiles in Escherichia coli. Appl Environ Microbiol 2012; 79:610-8. [PMID: 23144136 DOI: 10.1128/aem.02556-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A limited number of carotenoid pathway genes from microbial sources have been studied for analyzing the pathway complementation in the heterologous host Escherichia coli. In order to systematically investigate the functionality of carotenoid pathway enzymes in E. coli, the pathway genes of carotenogenic microorganisms (Brevibacterium linens, Corynebacterium glutamicum, Rhodobacter sphaeroides, Rhodobacter capsulatus, Rhodopirellula baltica, and Pantoea ananatis) were modified to form synthetic expression modules and then were complemented with Pantoea agglomerans pathway enzymes (CrtE, CrtB, CrtI, CrtY, and CrtZ). The carotenogenic pathway enzymes in the synthetic modules showed unusual activities when complemented with E. coli. For example, the expression of heterologous CrtEs of B. linens, C. glutamicum, and R. baltica influenced P. agglomerans CrtI to convert its substrate phytoene into a rare product-3,4,3',4'-tetradehydrolycopene-along with lycopene, which was an expected product, indicating that CrtE, the first enzyme in the carotenoid biosynthesis pathway, can influence carotenoid profiles. In addition, CrtIs of R. sphaeroides and R. capsulatus converted phytoene into an unusual lycopene as well as into neurosporene. Thus, this study shows that the functional complementation of pathway enzymes from different sources is a useful methodology for diversifying biosynthesis as nature does.
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