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Ma Y, Sun Z, Yang H, Xie W, Song M, Zhang B, Sui L. The biosynthesis mechanism of bacterioruberin in halophilic archaea revealed by genome and transcriptome analysis. Appl Environ Microbiol 2024:e0054024. [PMID: 38829054 DOI: 10.1128/aem.00540-24] [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: 03/24/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024] Open
Abstract
Halophilic archaea are promising microbial cell factories for bacterioruberin (BR) production. BR is a natural product with multi-bioactivities, allowing potential application in many fields. In the previous work, a haloarchaeon Halorubrum sp. HRM-150 with a high proportion of BR (about 85%) was isolated, but the low yield impeded its large-scale production. This work figured out BR synthesis characteristics and mechanisms, and proposed strategies for yield improvement. First, glucose (10 g/L) and tryptone (15 g/L) were tested to be better sources for BR production. Besides, the combination of glucose and starch achieved the diauxic growth, and the biomass and BR productivity increased by 85% and 54% than using glucose. Additionally, this work first proposed the BR synthesis pattern, which differs from that of other carotenoids. As a structural component of cell membranes, the BR synthesis is highly coupled with growth, which was most active in the logarithm phase. Meanwhile, the osmotic down shock at the logarithm phase could increase the BR productivity without sacrificing the biomass. Moreover, the de-novo pathway for BR synthesis with a key gene of lyeJ, and its competitive pathways (notably tetraether lipids and retinal) were revealed through genome, transcriptome, and osmotic down shock. Therefore, the BR yield is expected to be improved through mutant construction, such as the overexpression of key gene lyeJ and the knockout of competitive genes, which need to be further explored. The findings will contribute to a better understanding of the metabolism mechanism in haloarchaea and the development of haloarchaea as microbial cell factories. IMPORTANCE Recent studies have revealed that halophilic microorganism is a promising microbial factory for the next-generation industrialization. Among them, halophilic archaea are advantageous as microbial factories due to their low contamination risk and low freshwater consumption. The halophilic archaea usually accumulate long chain C50 carotenoids, which are barely found in other organisms. Bacterioruberin (BR), the major C50 carotenoid, has multi-bioactivities, allowing potential application in food, cosmetic, and biomedical industries. However, the low yield impedes its large-scale application. This work figured out the BR synthesis characteristics and mechanism, and proposed several strategies for BR yield improvement, encouraging halophilic archaea to function as microbial factories for BR production. Meanwhile, the archaea have special evolutionary status and unique characteristics in taxonomy, the revelation of BR biosynthesis mechanism is beneficial for a better understanding of archaea.
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Affiliation(s)
- Yingchao Ma
- Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory of Early Durability Evaluation of Innovative Drugs, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Zhongshi Sun
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Huan Yang
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Wei Xie
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Mengyu Song
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| | - Bo Zhang
- Tianjin Key Laboratory of Early Durability Evaluation of Innovative Drugs, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Liying Sui
- Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin University of Science and Technology, Tianjin, China
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
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Giani M, Pire C, Martínez-Espinosa RM. Bacterioruberin: Biosynthesis, Antioxidant Activity, and Therapeutic Applications in Cancer and Immune Pathologies. Mar Drugs 2024; 22:167. [PMID: 38667784 PMCID: PMC11051356 DOI: 10.3390/md22040167] [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: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Halophilic archaea, also termed haloarchaea, are a group of moderate and extreme halophilic microorganisms that constitute the major microbial populations in hypersaline environments. In these ecosystems, mainly aquatic, haloarchaea are constantly exposed to ionic and oxidative stress due to saturated salt concentrations and high incidences of UV radiation (mainly in summer). To survive under these harsh conditions, haloarchaea have developed molecular adaptations including hyperpigmentation. Regarding pigmentation, haloarchaeal species mainly synthesise the rare C50 carotenoid called bacterioruberin (BR) and its derivatives, monoanhydrobacterioruberin and bisanhydrobacterioruberin. Due to their colours and extraordinary antioxidant properties, BR and its derivatives have been the aim of research in several research groups all over the world during the last decade. This review aims to summarise the most relevant characteristics of BR and its derivatives as well as describe their reported antitumoral, immunomodulatory, and antioxidant biological activities. Based on their biological activities, these carotenoids can be considered promising natural biomolecules that could be used as tools to design new strategies and/or pharmaceutical formulas to fight against cancer, promote immunomodulation, or preserve skin health, among other potential uses.
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Affiliation(s)
- Micaela Giani
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
| | - Carmen Pire
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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Zhu P, Hou J, Xiong Y, Xie R, Wang Y, Wang F. Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis. Microorganisms 2024; 12:707. [PMID: 38674651 PMCID: PMC11052028 DOI: 10.3390/microorganisms12040707] [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: 03/05/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.
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Affiliation(s)
- Pengfei Zhu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Jialin Hou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Yixuan Xiong
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Fengping Wang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Southern Marine Science and Engineering, Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
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Rao A, Driessen AJM. Unraveling the multiplicity of geranylgeranyl reductases in Archaea: potential roles in saturation of terpenoids. Extremophiles 2024; 28:14. [PMID: 38280122 PMCID: PMC10821996 DOI: 10.1007/s00792-023-01330-2] [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: 07/17/2023] [Accepted: 12/15/2023] [Indexed: 01/29/2024]
Abstract
The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes, such as carotenoids, respiratory quinones, and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for saturation of the isoprene chains of phospholipids, have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs.
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Affiliation(s)
- Alka Rao
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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Serino I, Squillaci G, Errichiello S, Carbone V, Baraldi L, La Cara F, Morana A. Antioxidant Capacity of Carotenoid Extracts from the Haloarchaeon Halorhabdus utahensis. Antioxidants (Basel) 2023; 12:1840. [PMID: 37891919 PMCID: PMC10603985 DOI: 10.3390/antiox12101840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Herein, we report on the production, characterization, and antioxidant power assessment of carotenoids from the haloarchaeon Halorhabdus utahensis. It was grown at 37 °C and 180 rpm agitation in halobacteria medium supplemented with glucose, fructose, and xylose, each at concentrations of 0.2%, 1%, and 2%, and the carotenoid yield and composition were investigated. The microorganism produced the carotenoids under all the conditions tested, and their amount followed the order glucose < xylose < fructose. The highest yield was achieved in 2% fructose growth medium with 550.60 ± 7.91 μg/g dry cell and 2428.15 ± 49.33 μg/L. Separation and identification of the carotenoids were performed by RP-HPLC and HPLC/APCI-ITMSn. Bacterioruberin was the main carotenoid detected and accounted for 60.6%, 56.4%, and 58.9% in 2% glucose, 1% xylose, and 2% fructose extracts, respectively. Several geometric isomers of bacterioruberin were distinguished, and representatives of monoanhydrobacterioruberin, and bisanhydrobacterioruberin were also detected. The assignment to cis-isomers was attempted through analysis of the UV/Vis spectra, intensity of cis peaks, and spectral fine structures. The extracts exhibited superoxide scavenging activity higher than butylhydroxytoluene, ascorbic acid, and Trolox, selected as antioxidant references. The anti-hyaluronidase capacity was investigated, and the 2% fructose extract showed the highest activity reaching 90% enzyme inhibition with 1.5 μg. The overall data confirm that Hrd. utahensis can be regarded as an interesting source of antioxidants that can find applications in the food and cosmetic sectors.
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Affiliation(s)
- Ismene Serino
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Via Costantinopoli 16, 80138 Naples, Italy;
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy (CNR), Via Pietro Castellino 111, 80131 Naples, Italy; (G.S.); (S.E.); (F.L.C.)
| | - Giuseppe Squillaci
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy (CNR), Via Pietro Castellino 111, 80131 Naples, Italy; (G.S.); (S.E.); (F.L.C.)
| | - Sara Errichiello
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy (CNR), Via Pietro Castellino 111, 80131 Naples, Italy; (G.S.); (S.E.); (F.L.C.)
| | - Virginia Carbone
- Institute of Food Sciences, National Research Council of Italy (CNR), Via Roma 64, 83100 Avellino, Italy;
| | - Lidia Baraldi
- Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore”, National Research Council of Italy (CNR), Via S. Pansini 5, 80131 Naples, Italy;
| | - Francesco La Cara
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy (CNR), Via Pietro Castellino 111, 80131 Naples, Italy; (G.S.); (S.E.); (F.L.C.)
| | - Alessandra Morana
- Research Institute on Terrestrial Ecosystems, National Research Council of Italy (CNR), Via Pietro Castellino 111, 80131 Naples, Italy; (G.S.); (S.E.); (F.L.C.)
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Delgado-Garcia M, Gómez-Secundino O, Rodríguez JA, Mateos-Díaz JC, Muller-Santos M, Aguilar CN, Camacho-Ruiz RM. Identification, Antioxidant Capacity, and Matrix Metallopeptidase 9 (MMP-9) In Silico Inhibition of Haloarchaeal Carotenoids from Natronococcus sp. and Halorubrum tebenquichense. Microorganisms 2023; 11:2344. [PMID: 37764188 PMCID: PMC10537243 DOI: 10.3390/microorganisms11092344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Natural pigments from haloarchaea are of great interest; bacterioruberin is the major pigment, it shows higher antioxidant power when compared with β-carotene. However, characterization of bacterioruberin and its isomers along with its antioxidant and the matrix metallopeptidase 9 (MMP-9) inhibition activities in extracts from Natronoccoccus sp. TC6 and Halorubrum tebenquichense SU10 was not previously described, being the aim of this work. The carotenoids profile was performed by UV-Vis spectrophotometry, thin-layer chromatography, nuclear magnetic resonance spectroscopy, and high-resolution mass spectrometry (UPLC-ESI-MS/MS). Antioxidant capacity was determined for DPPH, ABTS, and FRAP. In addition, MMP-9 inhibition was studied using docking simulations. The carotenoid profile of studied strains was composed of bacterioruberin, some derivatives like mono, bis, and tris anhydrobacterioruberin, and also some bacterioruberin cis isomers. The carotenoid pools showed antioxidant capacity for DPPH > ABTS > FRAP; Natronococcus sp. TC6 carotenoid pool was better for ABTS and DPPH, while Halorubrum tebenquichense SU10 carotenoid pool was better for FRAP. Additionally, docking and molecular dynamics suggest that bacterioruberin inhibits MMP-9 through hydrophobic interactions near the catalytic site. Bacterioruberin shows the higher binding energy of -8.3 (kcal/mol). The carotenoids profile of both strains was elucidated, their antioxidant activity and singular participation of each carotenoid on MMP-9 in silico inhibition were evaluated.
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Affiliation(s)
- Mariana Delgado-Garcia
- Bioengineering Department, Instituto Tecnológico de Estudios Superiores de Monterrey, Campus Guadalajara, Zapopan 45201, Jalisco, Mexico;
| | - Osvaldo Gómez-Secundino
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan 44270, Jalisco, Mexico; (O.G.-S.); (J.A.R.); (J.C.M.-D.)
| | - Jorge A. Rodríguez
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan 44270, Jalisco, Mexico; (O.G.-S.); (J.A.R.); (J.C.M.-D.)
| | - Juan Carlos Mateos-Díaz
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan 44270, Jalisco, Mexico; (O.G.-S.); (J.A.R.); (J.C.M.-D.)
| | - Marcelo Muller-Santos
- Biochemistry and Molecular Biology Department, Universidade Federal do Paraná, Curitiba 81530-900, Brazil;
| | - Cristobal N. Aguilar
- Food Research Department, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico;
| | - Rosa Maria Camacho-Ruiz
- Industrial Biotechnology, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan 44270, Jalisco, Mexico; (O.G.-S.); (J.A.R.); (J.C.M.-D.)
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Arumugam S, Ramessh C, Kaliappan GK, Govindhan R, Prakasam SB, Murugan S, Pandian S, Asgar E, Ravi P. Lycopersene: A review on extraction, identification and purification and applications. Chem Biol Drug Des 2023; 101:158-174. [PMID: 36377692 DOI: 10.1111/cbdd.14158] [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: 06/03/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Lycopersene is a stable and safe triterpenoid. Lycopersen had utilized as an antioxidant, antimutagenic, antiproliferative, cytotoxicity, antibacterial and pesticide. Obtaining pure Lycopersene from natural sources is very important for fundamental research and the above applications. The present overview provides an up-to-date and comprehensive summary of the various methods used for extraction, isolation and purification of Lycopersene from natural sources with its applications in food, cosmetics and pharmaceutical fields. Many different extraction methods ranging from conventional techniques (e.g. Soxhlet extraction, Maceration and Rotary evaporator) and other advanced extraction technologies (e.g. Solid-phase microextraction, steam distillation with Clevenger, Clevenger apparatus, Chromatography on SiO2 column, centrifuge, sonication) had been used to obtain Lycopersene from flora and fauna. Purification techniques, alone or in combination, have been investigated for isolation and purification of Lycopersene from crude extracts in various natural sources. The review of Lycopersene identified cap areas like purity and application in various fields.
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Affiliation(s)
| | - Chelvi Ramessh
- Department of Agronomy, Agriculture and Research Institute, Madurai, India
| | | | - Rajiv Govindhan
- Department of Crop Management, Kumaraguru Institute of Agriculture, Erode, India
| | | | | | - Sureshkumar Pandian
- CAS in Marine Biology, Faculty of Marine Sciences, Annamalai University, Cuddalore, India
| | - Ebadollahi Asgar
- Department of Plant Sciences, Moghan College of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabili, Iran
| | - Prasanth Ravi
- CAS in Marine Biology, Faculty of Marine Sciences, Annamalai University, Cuddalore, India
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Hwang CY, Cho ES, Rhee WJ, Kim E, Seo MJ. Genomic and physiological analysis of C50 carotenoid-producing novel Halorubrum ruber sp. nov. J Microbiol 2022; 60:1007-1020. [DOI: 10.1007/s12275-022-2173-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/20/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
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Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes. Appl Environ Microbiol 2022; 88:e0244921. [PMID: 35477253 PMCID: PMC9128505 DOI: 10.1128/aem.02449-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recently, methanogenic archaea belonging to the genus Methanothrix were reported to have a fundamental role in maintaining stable ecosystem functioning in anaerobic bioreactors under different configurations/conditions. In this study, we reconstructed three Methanothrix metagenome-assembled genomes (MAGs) from granular sludge collected from saline upflow anaerobic sludge blanket (UASB) reactors, where Methanothrix harundinacea was previously implicated with the formation of compact and stable granules under elevated salinity levels (up to 20 g/L Na+). Genome annotation and pathway analysis of the Methanothrix MAGs revealed a genetic repertoire supporting their growth under high salinity. Specifically, the most dominant Methanothrix (MAG_279), classified as a subspecies of Methanothrix_A harundinacea_D, had the potential to augment its salinity resistance through the production of different glycoconjugates via the N-glycosylation process, and via the production of compatible solutes as Nε-acetyl-β-lysine and ectoine. The stabilization and reinforcement of the cell membrane via the production of isoprenoids was identified as an additional stress-related pathway in this microorganism. The improved understanding of the salinity stress-related mechanisms of M. harundinacea highlights its ecological niche in extreme conditions, opening new perspectives for high-efficiency methanisation of organic waste at high salinities, as well as the possible persistence of this methanogen in highly-saline natural anaerobic environments. IMPORTANCE Using genome-centric metagenomics, we discovered a new Methanothrix harundinacea subspecies that appears to be a halotolerant acetoclastic methanogen with the flexibility for adaptation in the anaerobic digestion process both at low (5 g/L Na+) and high salinity conditions (20 g/L Na+). Annotation of the recovered M. harundinacea genome revealed salinity stress-related functions, including the modification of EPS glycoconjugates and the production of compatible solutes. This is the first study reporting these genomic features within a Methanothrix sp., a milestone further supporting previous studies that identified M. harundinacea as a key-driver in anaerobic granulation under high salinity stress.
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Martínez GM, Pire C, Martínez-Espinosa RM. Hypersaline environments as natural sources of microbes with potential applications in biotechnology: the case of solar evaporation systems to produce salt in Alicante County (Spain). CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100136. [PMID: 35909606 PMCID: PMC9325878 DOI: 10.1016/j.crmicr.2022.100136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/14/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guillermo Martínez Martínez
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Corresponding author.
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Serrano S, Mendo S, Caetano T. Haloarchaea have a high genomic diversity for the biosynthesis of carotenoids of biotechnological interest. Res Microbiol 2021; 173:103919. [PMID: 34942349 DOI: 10.1016/j.resmic.2021.103919] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/27/2022]
Abstract
Haloarchaea are mostly components of the microbial biomass of saline aquatic environments, where they can be a dietary source of heterotrophic metazoans or contribute to flamingo's plumage coloration. The diversity of secondary metabolites (SMs) produced by haloarchaea, which might play multiple ecological roles and have diverse biotechnological applications has been largely understudied. Herein, 67 haloarchaeal complete genomes were analyzed and 182 SMs biosynthetic gene clusters (BGCs) identified that encode the production of terpenes (including carotenoids), RiPPs and siderophores. Terpene BGCs were further analysed and it was concluded that all haloarchaea might produce squalene and bacterioruberin, which one a strong antioxidant. Most of them have other carotenoid BGCs that include a putative β-carotene ketolase that was not characterized so far in haloarchaea, but may be involved with canthaxanthin's biosynthesis. The production of bacterioruberin by Haloferax mediterranei ATCC 33500 was found to be not related to its antimicrobial activity.
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Affiliation(s)
- Susana Serrano
- CESAM and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Aveiro, Portugal.
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12
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Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India. Mar Drugs 2021; 19:md19080442. [PMID: 34436281 PMCID: PMC8400781 DOI: 10.3390/md19080442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/14/2022] Open
Abstract
This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.
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Bernabeu E, Miralles-Robledillo JM, Giani M, Valdés E, Martínez-Espinosa RM, Pire C. In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification. Biomolecules 2021; 11:biom11071043. [PMID: 34356667 PMCID: PMC8301774 DOI: 10.3390/biom11071043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Affiliation(s)
- Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Elena Valdés
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
- Correspondence: ; Tel.: +34-965903400 (ext. 2064)
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Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
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Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico. Microorganisms 2021; 9:microorganisms9051096. [PMID: 34065163 PMCID: PMC8160830 DOI: 10.3390/microorganisms9051096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022] Open
Abstract
The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3′-sn-glycerol-1′-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.
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Kasirajan L, Maupin-Furlow JA. Halophilic archaea and their potential to generate renewable fuels and chemicals. Biotechnol Bioeng 2020; 118:1066-1090. [PMID: 33241850 DOI: 10.1002/bit.27639] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.
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Affiliation(s)
- Lakshmi Kasirajan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Coimbatore, India
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Genetics Institute, University of Florida, Gainesville, Florida, USA
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Carotenoids as a Protection Mechanism against Oxidative Stress in Haloferax mediterranei. Antioxidants (Basel) 2020; 9:antiox9111060. [PMID: 33137984 PMCID: PMC7694103 DOI: 10.3390/antiox9111060] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Haloarchaea are extremophilic microorganisms that in their natural ecosystem encounter several sources of oxidative stress. They have developed different strategies to cope with these harsh environmental conditions, among which bacterioruberin production is a very notable strategy. Bacterioruberin (BR) is a C50 carotenoid synthesized in response to different types of stress. Previous works demonstrated that it shows interesting antioxidant properties with potential applications in biotechnology. In this study, Haloferax mediterranei strain R-4 was exposed to different concentrations of the oxidant compound H2O2 to evaluate the effect on carotenoid production focusing the attention on the synthesis of bacterioruberin. Hfx. mediterranei was able to grow in the presence of H2O2 from 1 mM to 25 mM. Cells produced between 16% and 78% (w/v) more carotenoids under the induced oxidative stress compared to control cultures. HPLC-MS analysis detected BR as the major identified carotenoid and confirmed the gradual increase of BR content as higher concentrations of hydrogen peroxide were added to the medium. These results shed some light on the biological role of bacterioruberin in haloarchaea, provide interesting information about the increase of the cellular pigmentation under oxidative stress conditions and will allow the optimization of the production of this pigment at large scale using these microbes as biofactories.
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