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Sinetova MA, Kupriyanova EV, Los DA. Spirulina/Arthrospira/Limnospira-Three Names of the Single Organism. Foods 2024; 13:2762. [PMID: 39272527 PMCID: PMC11395459 DOI: 10.3390/foods13172762] [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: 07/16/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024] Open
Abstract
Recent advances in research techniques have enabled rapid progress in the study of spirulina, an ancient edible cyanobacteria. Nowadays, spirulina species are classified into three genera: Spirulina, Arthrospira, and Limnospira. The latter now refers to industrially manufactured spirulina strains. Whole-genome sequencing revealed gene clusters involved in metabolite production, and the physiology of spirulina. Omics technologies demonstrated the absence of hazardous compounds in spirulina cells, confirming the safety of this biomass as a food product. Spirulina is a good source of different chemicals used in food manufacturing, food supplements, and pharmaceuticals. Spirulina's enrichment with inherent biologically active substances makes it a potential supplier of natural products for dietary and pharmaceutical applications. Spirulina is also a prospective component of both terrestrial and space-based life support systems. Here, we review current breakthroughs in spirulina research and clarify fallacies that can be found in both professional literature and public media.
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Affiliation(s)
- Maria A Sinetova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Elena V Kupriyanova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Dmitry A Los
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
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2
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Hu X, He B, Liu Y, Ma S, Yu C. Genomic characterization of a novel ureolytic bacteria, Lysinibacillus capsici TSBLM, and its application to the remediation of acidic heavy metal-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172170. [PMID: 38575034 DOI: 10.1016/j.scitotenv.2024.172170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/06/2024]
Abstract
Soil heavy metal contamination is an essential challenge in ecological and environmental management, especially for acidic soils. Microbially induced carbonate precipitation (MICP) is an effective and environmentally friendly remediation technology for heavy metal contaminated sites, and one of the key factors for its realization lies in the microorganisms. In this study, Lysinibacillus capsici TSBLM was isolated from heavy metal contaminated soil around a gold mine, and inferred to be a novel ureolytic bacteria after phylogenomic inference and genome characterization. The urease of L. capsici TSBLM was analyzed by genetic analysis and molecular docking, and further applied this bacteria to the remediation of Cu and Pb in solution and acidic soils to investigate its biomineralization mechanism and practical application. The results revealed L. capsici TSBLM possessed a comprehensive urease gene cluster ureABCEFGD, and the encoded urease docked with urea at the lowest binding energy site (ΔG = -3.43 kcal/mol) connected to three amino acids threonine, aspartic, and alanine. The urease of L. capsici TSBLM is synthesized intracellularly but mainly functions extracellularly. L. capsici TSBLM removes Cu/Pb from the solution by generating heavy metal carbonates or co-precipitating with CaCO3 vaterite. For acidic heavy metal-contaminated soil, the carbonate-bound states of Cu and Pb increased significantly from 7 % to 16 % and from 23 % to 35 % after 30 days by L. capsici TSBLM. Soil pH improved additionally. L. capsici TSBLM maintained the dominant status in the remediated soil after 30 days, demonstrating good environmental adaptability and curing persistence. The results provided new strain resources and practical application references for the remediation of acidic heavy metal contaminated soil based on MICP.
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Affiliation(s)
- Xuesong Hu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Banghua He
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Yingchao Liu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Suya Ma
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Caihong Yu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China.
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3
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Castillo M, Guevara G, Baldanta S, Rodríguez PS, Agudo L, Nogales J, Carrasco AD, Arribas-Aguilar F, Pérez-Pérez J, García JL, Galán B, Navarro Llorens JM. Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems. Microbiol Res 2024; 279:127572. [PMID: 38101163 DOI: 10.1016/j.micres.2023.127572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The filamentous cyanobacterium Limnospira platensis, formerly known as Arthrospira platensis or spirulina, is one of the most commercially important species of microalgae. Due to its high nutritional value, pharmacological and industrial applications it is extensively cultivated on a large commercial scale. Despite its widespread use, its precise manipulation is still under development due to the lack of effective genetic protocols. Genetic transformation of Limnospira has been attempted but the methods reported have not been generally reproducible in other laboratories. Knowledge of the transformation defense mechanisms is essential for understanding its physiology and for broadening their applications. With the aim to understand more about the genetic defenses of L. platensis, in this work we have identified the restriction-modification and CRISPR-Cas systems and we have cloned and characterized thirteen methylases. In parallel, we have also characterized the methylome and orphan methyltransferases using genome-wide analysis of DNA methylation patterns and RNA-seq. The identification and characterization of these enzymes will be a valuable resource to know how this strain avoids being genetically manipulated and for further genomics studies.
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Affiliation(s)
- María Castillo
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Govinda Guevara
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Sara Baldanta
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Patricia Suárez Rodríguez
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Lucía Agudo
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Asunción Díaz Carrasco
- DNA Sequencing facility, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Fernando Arribas-Aguilar
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Julián Pérez-Pérez
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - José Luis García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Beatriz Galán
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
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Dreher TW, Matthews R, Davis EW, Mueller RS. Woronichinia naegeliana: A common nontoxigenic component of temperate freshwater cyanobacterial blooms with 30% of its genome in transposons. HARMFUL ALGAE 2023; 125:102433. [PMID: 37220973 DOI: 10.1016/j.hal.2023.102433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 05/25/2023]
Abstract
Monitoring in the U.S. state of Washington across the period 2007-2019 showed that Woronichinia has been present in many lakes state-wide. This cyanobacterium was commonly dominant or sub-dominant in cyanobacterial blooms in the wet temperate region west of the Cascade Mountains. In these lakes, Woronichinia often co-existed with Microcystis, Dolichospermum and Aphanizomenon flos-aquae and the cyanotoxin microcystin has often been present in those blooms, although it has not been known whether Woronichinia is a toxin producer. We report the first complete genome of Woronichinia naegeliana WA131, assembled from the metagenome of a sample collected from Wiser Lake, Washington, in 2018. The genome contains no genes for cyanotoxin biosynthesis or taste-and-odor compounds, but there are biosynthetic gene clusters for other bioactive peptides, including anabaenopeptins, cyanopeptolins, microginins and ribosomally produced, post-translationally modified peptides. Genes for photosynthesis, nutrient acquisition, vitamin synthesis and buoyancy that are typical of bloom-forming cyanobacteria are present, although nitrate and nitrite reductase genes are conspicuously absent. However, the 7.9 Mbp genome is 3-4 Mbp larger than those of the above-mentioned frequently co-existing cyanobacteria. The increased genome size is largely due to an extraordinary number of insertion sequence elements (transposons), which account for 30.3% of the genome and many of which are present in multiple copies. The genome contains a relatively large number of pseudogenes, 97% of which are transposase genes. W. naegeliana WA131 thus seems to be able to limit the potentially deleterious effects of high rates of recombination and transposition to the mobilome fraction of its genome.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA.
| | - Robin Matthews
- Department of Environmental Sciences, Western Washington University, Bellingham, WA 98225, USA.
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA
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Tabakh H, Jester BW, Zhao H, Kuestner R, Khuong N, Shanitta C, Takeuchi R, Roberts J. Protocol for the transformation and engineering of edible algae Arthrospira platensis to generate heterologous protein-expressing strains. STAR Protoc 2023; 4:102087. [PMID: 36853691 PMCID: PMC9929480 DOI: 10.1016/j.xpro.2023.102087] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/01/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Here, we present a protocol for harnessing the natural transformability of the edible algae Arthrospira platensis (common name: spirulina) to generate strains that express heterologous proteins. We describe the preparation of plasmids and the steps to grow A. platensis. We then detail the transformation and passage of the strains, followed by genomic DNA extraction and genotyping to assess integration of the gene of interest. This simple transformation protocol can be applied to genome manipulation of edible algae. For complete details on the use and execution of this protocol, please refer to Jester et al. (2022).1.
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Affiliation(s)
| | | | - Hui Zhao
- Lumen Bioscience, Seattle, WA 98103, USA
| | | | - Nhi Khuong
- Lumen Bioscience, Seattle, WA 98103, USA
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Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:455. [PMID: 36838420 PMCID: PMC9964548 DOI: 10.3390/microorganisms11020455] [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: 12/12/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Department of Biology, University of Padua, 35100 Padua, Italy
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Natha, QLD 4111, Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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Thi Nguyen LT, Thi Le NH, Thi Ta HK, Dang Nguyen K. Isolation of DNA from Arthrospira platensis and whole blood using magnetic nanoparticles (Fe3O4@OA and Fe3O4@OA@SiO2). J Anal Sci Technol 2022. [DOI: 10.1186/s40543-022-00337-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractMagnetic nanoparticles (MNPs) provide a fast, cost-effective, and organic-free method for DNA isolation. In this paper, we synthesized MNP coated with oleic acid (Fe3O4@OA) and silica nanoparticles (Fe3O4@OA@SiO2), characterized the properties of MNP using TEM, VSM, and FTIR, and investigated their efficiency in DNA isolation from cyanobacteria. The yield and quality of isolated DNA were evaluated and compared with those from animal blood and those obtained by the silica column or organic solvents. The results showed the successful preparations of Fe3O4@OA and Fe3O4@OA@SiO2 with superparamagnetic behaviors and a mean diameter of 7 nm and 106 nm, respectively. The FTIR spectra of Fe3O4@OA confirmed the bonding of OA to the surface of iron oxide, while those of Fe3O4@OA@SiO2 showed the exposed silanol groups. Although MNPs yielded a lower quantity of DNA compared with phenol/chloroform extraction, they showed the potential protection of the integrity of DNA against centrifugal and shear forces. Fe3O4@OA@SiO2 favored more nucleic acid absorption than Fe3O4@OA, producing a 1.2 and 1.6 times greater amount of DNA from Arthrospira platensis and animal blood respectively. The purity of DNA isolated from Arthrospira platensis was also higher than that of animal blood. These findings indicate a new and simple approach for the isolation of DNA from Arthrospira genus.
Graphical Abstract
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Cao S, Brandis G, Huseby DL, Hughes D. Positive selection during niche adaptation results in large-scale and irreversible rearrangement of chromosomal gene order in bacteria. Mol Biol Evol 2022; 39:6554941. [PMID: 35348727 PMCID: PMC9016547 DOI: 10.1093/molbev/msac069] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Analysis of bacterial genomes shows that, whereas diverse species share many genes in common, their linear order on the chromosome is often not conserved. Whereas rearrangements in gene order could occur by genetic drift, an alternative hypothesis is rearrangement driven by positive selection during niche adaptation (SNAP). Here, we provide the first experimental support for the SNAP hypothesis. We evolved Salmonella to adapt to growth on malate as the sole carbon source and followed the evolutionary trajectories. The initial adaptation to growth in the new environment involved the duplication of 1.66 Mb, corresponding to one-third of the Salmonella chromosome. This duplication is selected to increase the copy number of a single gene, dctA, involved in the uptake of malate. Continuing selection led to the rapid loss or mutation of duplicate genes from either copy of the duplicated region. After 2000 generations, only 31% of the originally duplicated genes remained intact and the gene order within the Salmonella chromosome has been significantly and irreversibly altered. These results experientially validate predictions made by the SNAP hypothesis and show that SNAP can be a strong driving force for rearrangements in chromosomal gene order.
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Affiliation(s)
- Sha Cao
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,These authors contributed equally: Sha Cao, Gerrit Brandis
| | - Gerrit Brandis
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.,These authors contributed equally: Sha Cao, Gerrit Brandis
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Miura MC, Nagata S, Tamaki S, Tomita M, Kanai A. Distinct Expansion of Group II Introns During Evolution of Prokaryotes and Possible Factors Involved in Its Regulation. Front Microbiol 2022; 13:849080. [PMID: 35295308 PMCID: PMC8919778 DOI: 10.3389/fmicb.2022.849080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/07/2022] [Indexed: 11/23/2022] Open
Abstract
Group II introns (G2Is) are ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are suggested to have been an important evolutionary factor in the prokaryote-to-eukaryote transition, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative genomes had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative genomes had an average of 3.0 G2Is. The greatest number of G2Is per genome was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1-U3) to the previous classification. This analysis suggested that about 30% of all IEPs are non-canonical IEPs. The number of G2Is per genome was defined almost at the phylum level, and at least in the following two phyla, Firmicutes, and Cyanobacteriota, the type of IEP was largely associated as a factor in the G2I increase, i.e., there was an explosive increase in G2Is with bacterial C-type IEPs, mainly in the phylum Firmicutes, and in G2Is with CL-type IEPs, mainly in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.
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Affiliation(s)
- Masahiro C. Miura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Shohei Nagata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Satoshi Tamaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
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Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. Microbiol Spectr 2022; 10:e0259121. [PMID: 35107332 PMCID: PMC8809349 DOI: 10.1128/spectrum.02591-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rhodanobacter species dominate in the Oak Ridge Reservation (ORR) subsurface environments contaminated with acids, nitrate, metal radionuclides, and other heavy metals. To uncover the genomic features underlying adaptations to these mixed-waste environments and to guide genetic tool development, we sequenced the whole genomes of eight Rhodanobacter strains isolated from the ORR site. The genome sizes ranged from 3.9 to 4.2 Mb harboring 3,695 to 4,035 protein-coding genes and GC contents approximately 67%. Seven strains were classified as R. denitrificans and one strain, FW510-R12, as R. thiooxydans based on full length 16S rRNA sequences. According to gene annotation, the top two Cluster of Orthologous Groups (COGs) with high pan-genome expansion rates (Pan/Core gene ratio) were “replication, recombination and repair” and “defense mechanisms.” The denitrifying genes had high DNA homologies except the predicted protein structure variances in NosZ. In contrast, heavy metal resistance genes were diverse with between 7 to 34% of them were located in genomic islands, and these results suggested origins from horizontal gene transfer. Analysis of the methylation patterns in four strains revealed the unique 5mC methylation motifs. Most orthologs (78%) had ratios of nonsynonymous to synonymous substitutions (dN/dS) less than one when compared to the type strain 2APBS1, suggesting the prevalence of negative selection. Overall, the results provide evidence for the important roles of horizontal gene transfer and negative selection in genomic adaptation at the contaminated field site. The complex restriction-modification system genes and the unique methylation motifs in Rhodanobacter strains suggest the potential recalcitrance to genetic manipulation. IMPORTANCE Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties. Using Illumina, PacBio, and Oxford Nanopore sequencing platforms, we obtained the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the heterogeneity of methylation patterns in strains isolated from the same well. Although all strains contained a complete set of denitrifying genes, the predicted tertiary structures of NosZ differed. The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation. In addition, these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.
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Comparative Genomics and Physiological Investigation of a New Arthrospira/Limnospira Strain O9.13F Isolated from an Alkaline, Winter Freezing, Siberian Lake. Cells 2021; 10:cells10123411. [PMID: 34943919 PMCID: PMC8700078 DOI: 10.3390/cells10123411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 11/24/2022] Open
Abstract
Cyanobacteria from the genus Arthrospira/Limnospira are considered haloalkalotolerant organisms with optimal growth temperatures around 35 °C. They are most abundant in soda lakes in tropical and subtropical regions. Here, we report the comprehensive genome-based characterisation and physiological investigation of the new strain O9.13F that was isolated in a temperate climate zone from the winter freezing Solenoye Lake in Western Siberia. Based on genomic analyses, the Siberian strain belongs to the Arthrospira/Limnospira genus. The described strain O9.13F showed the highest relative growth index upon cultivation at 20 °C, lower than the temperature 35 °C reported as optimal for the Arthrospira/Limnospira strains. We assessed the composition of fatty acids, proteins and photosynthetic pigments in the biomass of strain O9.13F grown at different temperatures, showing its potential suitability for cultivation in a temperate climate zone. We observed a decrease of gamma-linolenic acid favouring palmitic acid in the case of strain O9.13F compared to tropical strains. Comparative genomics showed no unique genes had been found for the Siberian strain related to its tolerance to low temperatures. In addition, this strain does not possess a different set of genes associated with the salinity stress response from those typically found in tropical strains. We confirmed the absence of plasmids and functional prophage sequences. The genome consists of a 4.94 Mbp with a GC% of 44.47% and 5355 encoded proteins. The Arthrospira/Limnospira strain O9.13F presented in this work is the first representative of a new clade III based on the 16S rRNA gene, for which a genomic sequence is available in public databases (PKGD00000000).
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Krüger-Genge A, Jung CGH, Braune S, Harb K, Westphal S, Klöpzig S, Küpper JH, Jung F. Effect of Arthrospira powders from different producers on the formation of endothelial cell monolayers. Clin Hemorheol Microcirc 2021; 79:193-203. [PMID: 34487037 DOI: 10.3233/ch-219200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Arthrospira platensis (AP) and some of its derived products have well-established biological activities as antioxidants or as agents to reduce cardiovascular disease risk factors. Furthermore, AP products have gained increasing importance as potential anti-cancer agents. However, the ingredients of the available products vary greatly with the origin, the type of production and processing, which could have significant consequences for their biological effects. Therefore, the composition and biological influence of five distinct AP powders, which were acquired commercially or produced at a public biotechnology institute, were investigated in regard to their endothelialization capacity using a cell impedance- (CI) based measurement method. The study revealed that the AP composition and especially the influence on HUVEC proliferation differed significantly between the five AP powders up to 109%.Thus, it could be shown that the method used allows the reliable detection of quantitative differences in biological effects of different AP preparations.
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Affiliation(s)
- A Krüger-Genge
- Fraunhofer Institute for Applied Polymer Research (IAP), Department of Biomaterials, Healthcare and Cosmeceuticals, Potsdam-Golm, Germany
| | - C G H Jung
- Institute of Biotechnology, Molecular Cell Biology, Brandenburg University of Technology, Senftenberg, Germany
| | - S Braune
- Institute of Biotechnology, Molecular Cell Biology, Brandenburg University of Technology, Senftenberg, Germany
| | - K Harb
- Fraunhofer Institute for Applied Polymer Research (IAP), Department of Biomaterials, Healthcare and Cosmeceuticals, Potsdam-Golm, Germany
| | - S Westphal
- Fraunhofer Institute for Applied Polymer Research (IAP), Department of Biomaterials, Healthcare and Cosmeceuticals, Potsdam-Golm, Germany
| | - S Klöpzig
- Fraunhofer Institute for Applied Polymer Research (IAP), Department of Biomaterials, Healthcare and Cosmeceuticals, Potsdam-Golm, Germany
| | - J-H Küpper
- Institute of Biotechnology, Molecular Cell Biology, Brandenburg University of Technology, Senftenberg, Germany
| | - F Jung
- Institute of Biotechnology, Molecular Cell Biology, Brandenburg University of Technology, Senftenberg, Germany
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Subermaniam K, Teoh SL, Yow YY, Tang YQ, Lim LW, Wong KH. Marine algae as emerging therapeutic alternatives for depression: A review. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:997-1013. [PMID: 34804417 PMCID: PMC8591755 DOI: 10.22038/ijbms.2021.54800.12291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022]
Abstract
Depression is a complex heterogeneous brain disorder characterized by a range of symptoms, resulting in psychomotor and cognitive disabilities and suicidal thoughts. Its prevalence has reached an alarming level affecting millions of people globally. Despite advances in current pharmacological treatments, the heterogenicity of clinical response and incidences of adverse effects have shifted research focus to identification of new natural substances with minimal or no adverse effects as therapeutic alternatives. Marine algae-derived extracts and their constituents are considered potential sources of secondary metabolites with diverse beneficial effects. Marine algae with enormous health benefits are emerging as a natural source for discovering new alternative antidepressants. Its medicinal properties exhibited shielding efficacy against neuroinflammation, oxidative stress, and mitochondrial dysfunction, which are indicated to underlie the pathogenesis of many neurological disorders. Marine algae have been found to ameliorate depressive-like symptoms and behaviors in preclinical and clinical studies by restoring monoaminergic neurotransmission, hypothalamic-pituitary-adrenal axis function, neuroplasticity, and continuous neurogenesis in the dentate gyrus of the hippocampus via modulating brain-derived neurotrophic factors and antineuroinflammatory activity. Although antidepressant effects of marine algae have not been validated in comparison with currently available synthetic antidepressants, they have been reported to have effects on the pathophysiology of depression, thus suggesting their potential as novel antidepressants. In this review, we analyzed the currently available research on the potential benefits of marine algae on depression, including their effects on the pathophysiology of depression, potential clinical relevance of their antidepressant effects in preclinical and clinical studies, and the underlying mechanisms of these effects.
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Affiliation(s)
- Kogilavani Subermaniam
- Department of Anatomy, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia,Training Management Division, Ministry of Health Malaysia, 62675 Putrajaya, Malaysia
| | - Seong Lin Teoh
- Department of Anatomy, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center, Jalan Yaacob Latif, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Yoon-Yen Yow
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Yin Quan Tang
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor’s University Lakeside Campus, 47500 Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Lee Wei Lim
- Neuromodulation Laboratory, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kah Hui Wong
- Department of Anatomy, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia,Corresponding author: K.H. Wong, Department of Anatomy, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia. Tel: +60379674729; Fax: +60379674724;
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14
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Hicks M, Tran-Dao TK, Mulroney L, Bernick DL. De-novo Assembly of Limnospira fusiformis Using Ultra-Long Reads. Front Microbiol 2021; 12:657995. [PMID: 33936015 PMCID: PMC8085491 DOI: 10.3389/fmicb.2021.657995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/26/2021] [Indexed: 11/13/2022] Open
Abstract
The Limnospira genus is a recently established clade that is economically important due to its worldwide use in biotechnology and agriculture. This genus includes organisms that were reclassified from Arthrospira, which are commercially marketed as "Spirulina." Limnospira are photoautotrophic organisms that are widely used for research in nutrition, medicine, bioremediation, and biomanufacturing. Despite its widespread use, there is no closed genome for the Limnospira genus, and no reference genome for the type strain, Limnospira fusiformis. In this work, the L. fusiformis genome was sequenced using Oxford Nanopore Technologies MinION and assembled using only ultra-long reads (>35 kb). This assembly was polished with Illumina MiSeq reads sourced from an axenic L. fusiformis culture; axenicity was verified via microscopy and rDNA analysis. Ultra-long read sequencing resulted in a 6.42 Mb closed genome assembled as a single contig with no plasmid. Phylogenetic analysis placed L. fusiformis in the Limnospira clade; some Arthrospira were also placed in this clade, suggesting a misclassification of these strains. This work provides a fully closed and accurate reference genome for the economically important type strain, L. fusiformis. We also present a rapid axenicity method to isolate L. fusiformis. These contributions enable future biotechnological development of L. fusiformis by way of genetic engineering.
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Affiliation(s)
- McKenna Hicks
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA United States
| | - Thuy-Khanh Tran-Dao
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA United States
| | - Logan Mulroney
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA United States
| | - David L. Bernick
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA United States
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15
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Maghembe R, Damian D, Makaranga A, Nyandoro SS, Lyantagaye SL, Kusari S, Hatti-Kaul R. Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae. Antibiotics (Basel) 2020; 9:antibiotics9050229. [PMID: 32375367 PMCID: PMC7277505 DOI: 10.3390/antibiotics9050229] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/10/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
"Omics" represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and 'blind'-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism's inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.
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Affiliation(s)
- Reuben Maghembe
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
| | - Donath Damian
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
| | - Abdalah Makaranga
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- International Center for Genetic Engineering and Biotechnology (ICGEB), Omics of Algae Group, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Stephen Samwel Nyandoro
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania;
| | - Sylvester Leonard Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biochemistry, Mbeya College of Health and Allied Sciences, University of Dar es Salaam, P.O. Box 608, Mbeya, Tanzania
| | - Souvik Kusari
- Institute of Environmental Research (INFU), Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
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16
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Dagnino-Leone J, Figueroa M, Uribe E, Hinrichs MV, Ortiz-López D, Martínez-Oyanedel J, Bunster M. Biosynthesis and characterization of a recombinant eukaryotic allophycocyanin using prokaryotic accessory enzymes. Microbiologyopen 2020; 9:e989. [PMID: 31970933 PMCID: PMC7066465 DOI: 10.1002/mbo3.989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Phycobiliproteins (PBPs) are colored fluorescent proteins present in cyanobacteria, red alga, and cryptophyta. These proteins have many potential uses in biotechnology going from food colorants to medical applications. Allophycocyanin, the simplest PBP, is a heterodimer of αβ subunits that oligomerizes as a trimer (αβ)3. Each subunit contains a phycocyanobilin, bound to a cysteine residue, which is responsible for its spectroscopic properties. In this article, we are reporting the expression of recombinant allophycocyanin (rAPC) from the eukaryotic red algae Agarophyton chilensis in Escherichia coli, using prokaryotic accessory enzymes to obtain a fully functional rAPC. Three duet vectors were used to include coding sequences of α and β subunits from A. chilensis and accessorial enzymes (heterodimeric lyase cpc S/U, heme oxygenase 1, phycocyanobilin oxidoreductase) from cyanobacteria Arthrospira maxima. rAPC was purified using several chromatographic steps. The characterization of the pure rAPC indicates very similar spectroscopic properties, λmaxAbs, λmaxEm, fluorescence lifetime, and chromophorylation degree, with native allophycocyanin (nAPC) from A. chilensis. This method, to produce high‐quality recombinant allophycocyanin, can be used to express and characterize other macroalga phycobiliproteins, to be used for biotechnological or biomedical purposes.
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Affiliation(s)
- Jorge Dagnino-Leone
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Maximiliano Figueroa
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Elena Uribe
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - María Victoria Hinrichs
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Diego Ortiz-López
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - José Martínez-Oyanedel
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
| | - Marta Bunster
- Departamento de Bioquímica y Biología Molecular, Universidad de Concepción, Concepción, Chile
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17
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Jung F, Jung CG, Krüger-Genge A, Waldeck P, Küpper JH. Factors influencing the growth of Spirulina platensis in closed photobioreactors under CO2 – O2 conversion. ACTA ACUST UNITED AC 2019. [DOI: 10.3233/jcb-199004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friedrich Jung
- Institute of Biotechnology, Brandenburgische Technische Universität Cottbus-Senftenberg, Senftenberg, Germany
| | - Conrad G.H. Jung
- Carbon Biotech, Social Enterprise Stiftungs AG, Senftenberg, Germany
| | - Anne Krüger-Genge
- Fraunhofer Institute Applied Polymer Research (IAP), Division of Life Science and Bioprocesses, Department of Biomaterials and Healthcare, Potsdam-Golm, Germany
| | - Peter Waldeck
- Institute of Biotechnology, Brandenburgische Technische Universität Cottbus-Senftenberg, Senftenberg, Germany
| | - Jan-Heiner Küpper
- Institute of Biotechnology, Brandenburgische Technische Universität Cottbus-Senftenberg, Senftenberg, Germany
- Carbon Biotech, Social Enterprise Stiftungs AG, Senftenberg, Germany
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18
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Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution. Int J Genomics 2019; 2019:8987436. [PMID: 31950028 PMCID: PMC6948317 DOI: 10.1155/2019/8987436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/24/2019] [Accepted: 08/11/2019] [Indexed: 12/03/2022] Open
Abstract
Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.
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19
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Yan H, Zhu K, Teng M, Li X. A newly identified photolyase from Arthrospira platensis possesses a unique methenyltetrahydrofolate chromophore-binding pattern. FEBS Lett 2019; 594:740-750. [PMID: 31675429 DOI: 10.1002/1873-3468.13657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 01/03/2023]
Abstract
Cyclobutane pyrimidine dimers (CPD), as a common DNA damage caused by UV radiation, often lead to skin cancer. Here, we identified a photolyase from the alga Arthrospira platensis (designated as Ap-phr), which has been regarded as a safe organism for humans for centuries, that can efficiently repair CPD lesions in ssDNA and dsDNA in vitro. The 1.6 Å resolution crystal structure of Ap-phr revealed that it possesses a unique methenyltetrahydrofolate chromophore-binding pattern with high energy transfer efficiency. Our study of Ap-phr highlights its potential use in cosmetic, industrial and aesthetic medicine applications.
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Affiliation(s)
- Hui Yan
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Kongfu Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, National Synchrotron Radiation Laboratory, School of Life Sciences, University of Science and Technology of China, Hefei, China
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20
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Suzuki S, Yamaguchi H, Kawachi M. The Draft Genome of a Hydrogen-producing Cyanobacterium, Arthrospira platensis NIES-46. J Genomics 2019; 7:56-59. [PMID: 31588248 PMCID: PMC6775862 DOI: 10.7150/jgen.38149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/05/2019] [Indexed: 11/05/2022] Open
Abstract
Arthrospira is an economically important cyanobacterium that contains many useful products, including proteins, vitamins, lipids, and pigments, and it is distributed in several alkaline soda lakes. Arthrospira platensis NIES-46 produces large amounts of hydrogen. In this study, we sequenced the NIES-46 draft genome and performed comparative analyses among Arthrospira species to elucidate the genomic background of this strain. The genome consists of 5.7 Mbp with a GC% of 44.5% and encodes 5,008 proteins. Our phylogenetic analysis using multiple orthologous proteins shows that Arthrospira is divided into two clades and that NIES-46 is closely related to A. platensis NIES-39. The genome structure and protein functions are highly conserved between A. platensis NIES-39 and NIES-46, suggesting that these two strains have recently diverged. Genes involved in hydrogen production are well-conserved among Arthrospira species, indicating conserved abilities to produce hydrogen.
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Affiliation(s)
- Shigekatsu Suzuki
- Center for Biology and Environmental Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan
| | - Haruyo Yamaguchi
- Center for Biology and Environmental Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan
| | - Masanobu Kawachi
- Center for Biology and Environmental Studies, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, Japan
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21
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Wu X, Wu X, Shen L, Li J, Yu R, Liu Y, Qiu G, Zeng W. Whole Genome Sequencing and Comparative Genomics Analyses of Pandoraea sp. XY-2, a New Species Capable of Biodegrade Tetracycline. Front Microbiol 2019; 10:33. [PMID: 30761094 PMCID: PMC6361800 DOI: 10.3389/fmicb.2019.00033] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Few bacteria are resistant to tetracycline and can even biodegrade tetracycline in the environment. In this study, we isolated a bacterium Pandoraea sp. XY-2, which could biodegrade 74% tetracycline at pH 7.0 and 30°C within 6 days. Thereafter, we determined the whole genome sequence of Pandoraea sp. XY-2 genome is a single circular chromosome of 5.06 Mb in size. Genomic annotation showed that two AA6 family members-encoding genes and nine glutathione S-transferase (GSTs)-encoding genes could be relevant to tetracycline biodegradation. In addition, the average nucleotide identities (ANI) analysis between the genomes of Pandoraea sp. XY-2 and other Pandoraea spp. revealed that Pandoraea sp. XY-2 belongs to a new species. Moreover, comparative genome analysis of 36 Pandoraea strains identified the pan and specific genes, numerous single nucleotide polymorphisms (SNPs), insertions, and deletion variations (InDels) and different syntenial relationships in the genome of Pandoraea sp. XY-2. Finally, the evolution and the origin analysis of genes related to tetracycline resistance revealed that the six tetA(48) genes and two specificgenes tetG and tetR in Pandoraea sp. XY-2 were acquired by horizontal gene transfer (HGT) events from sources related to Paraburkholderia, Burkholderia, Caballeronia, Salmonella, Vibrio, Proteobacteria, Pseudomonas, Acinetobacter, Flavimaricola, and some unidentified sources. As a new species, Pandoraea sp. XY-2 will be an excellent resource for the bioremediation of tetracycline-contaminated environment.
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Affiliation(s)
- Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xiaoyan Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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22
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Chen L, Wang L, Song D, Xu Z. Reduced graphene oxide aerogel with packaged TiO 2
nanoparticles as a promising adsorbent for the separation of DNA from human whole blood. SEPARATION SCIENCE PLUS 2018. [DOI: 10.1002/sscp.201700044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Lei Chen
- Research Center for Analytical Sciences; Northeastern University; Shenyang China
| | - Lei Wang
- Research Center for Analytical Sciences; Northeastern University; Shenyang China
| | - Dan Song
- Research Center for Analytical Sciences; Northeastern University; Shenyang China
| | - Zhangrun Xu
- Research Center for Analytical Sciences; Northeastern University; Shenyang China
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23
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Teng JLL, Yeung ML, Chan E, Jia L, Lin CH, Huang Y, Tse H, Wong SSY, Sham PC, Lau SKP, Woo PCY. PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome. Front Microbiol 2017; 8:1448. [PMID: 28824579 PMCID: PMC5539568 DOI: 10.3389/fmicb.2017.01448] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/17/2017] [Indexed: 12/19/2022] Open
Abstract
Although PacBio third-generation sequencers have improved the read lengths of genome sequencing which facilitates the assembly of complete genomes, no study has reported success in using PacBio data alone to completely sequence a two-chromosome bacterial genome from a single library in a single run. Previous studies using earlier versions of sequencing chemistries have at most been able to finish bacterial genomes containing only one chromosome with de novo assembly. In this study, we compared the robustness of PacBio RS II, using one SMRT cell and the latest P6-C4 chemistry, with Illumina HiSeq 1500 in sequencing the genome of Burkholderia pseudomallei, a bacterium which contains two large circular chromosomes, very high G+C content of 68–69%, highly repetitive regions and substantial genomic diversity, and represents one of the largest and most complex bacterial genomes sequenced, using a reference genome generated by hybrid assembly using PacBio and Illumina datasets with subsequent manual validation. Results showed that PacBio data with de novo assembly, but not Illumina, was able to completely sequence the B. pseudomallei genome without any gaps or mis-assemblies. The two large contigs of the PacBio assembly aligned unambiguously to the reference genome, sharing >99.9% nucleotide identities. Conversely, Illumina data assembled using three different assemblers resulted in fragmented assemblies (201–366 contigs), sharing only 92.2–100% and 92.0–100% nucleotide identities to chromosomes I and II reference sequences, respectively, with no indication that the B. pseudomallei genome consisted of two chromosomes with four copies of ribosomal operons. Among all assemblies, the PacBio assembly recovered the highest number of core and virulence proteins, and housekeeping genes based on whole-genome multilocus sequence typing (wgMLST). Most notably, assembly solely based on PacBio outperformed even hybrid assembly using both PacBio and Illumina datasets. Hybrid approach generated only 74 contigs, while the PacBio data alone with de novo assembly achieved complete closure of the two-chromosome B. pseudomallei genome without additional costly bench work and further sequencing. PacBio RS II using P6-C4 chemistry is highly robust and cost-effective and should be the platform of choice in sequencing bacterial genomes, particularly for those that are well-known to be difficult-to-sequence.
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Affiliation(s)
- Jade L L Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Elaine Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Lilong Jia
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Chi Ho Lin
- Centre for Genomic Sciences, The University of Hong KongHong Kong, Hong Kong
| | - Yi Huang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Herman Tse
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Samson S Y Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Pak Chung Sham
- Centre for Genomic Sciences, The University of Hong KongHong Kong, Hong Kong.,Department of Psychiatry, The University of Hong KongHong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, Hong Kong
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, Hong Kong
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Sugiyama K, Ebisawa M, Yamada M, Nagashima Y, Suzuki H, Maoka T, Takaichi S. Functional Lycopene Cyclase (CruA) in Cyanobacterium, Arthrospira platensis NIES-39, and its Role in Carotenoid Synthesis. PLANT & CELL PHYSIOLOGY 2017; 58:831-838. [PMID: 28371918 DOI: 10.1093/pcp/pcx015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 01/23/2017] [Indexed: 05/15/2023]
Abstract
The genus Arthrospira is filamentous, non-nitrogen-fixing cyanobacteria that is commercially important. We identified the molecular structures of carotenoids in Arthrospira platensis NIES-39. The major carotenoid identified was β-carotene. In addition, the hydroxyl derivatives of β-cryptoxanthin and (3R,3'R)-zeaxanthin were also found to be present. The carotenoid glycosides were identified as (3R,2'S)-myxol 2'-methylpentoside and oscillol 2,2'-dimethylpentoside. The methylpentoside moiety was a mixture of fucoside and chinovoside in an approximate ratio of 1 : 4. Trace amounts of the ketocarotenoid 3'-hydroxyechinenone were also found. Three types of lycopene cyclases have been functionally confirmed in carotenogenesis organisms. In cyanobacteria, the functional lycopene cyclases (CrtL, CruA and CruP) have only been found in four species. In this study, we found that CruA exhibited lycopene cyclase activity in transformed Escherichia coli, which contains lycopene, but CruP exhibited no lycopene cyclase activity and crtL was absent. This is the third cyanobacterial species in which CruA activity has been confirmed. Neurosporene was not a substrate of CruA in E. coli, whereas lycopene cyclases of CrtY (bacteria), CrtL (plants) and CrtYB (fungi) have been reported to convert neurosporene to 7,8-dihydro-β-carotene. β-Carotene hydroxylase (CrtR) was found to convert β-carotene to zeaxanthin in transformed E. coli, which contains β-carotene. Among the β-carotene hydroxylases, bacterial CrtZ and eukaryotic CrtR and BCH have similarities, whereas cyanobacterial CrtR appears to belong to another clade. Based on the identification of the carotenoids and the completion of the entire nucleotide sequence of the A. platensis NIES-39 genome, we propose a biosynthetic pathway for the carotenoids as well as the corresponding genes and enzymes.
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Affiliation(s)
- Kenjiro Sugiyama
- Department of Applied Chemistry, Kogakuin University, Hachioji, Japan
| | - Masashi Ebisawa
- Department of Applied Chemistry, Kogakuin University, Hachioji, Japan
| | - Masaharu Yamada
- Department of Applied Chemistry, Kogakuin University, Hachioji, Japan
| | | | | | - Takashi Maoka
- Research Institute for Production Development, Sakyoku, Kyoto, Japan
| | - Shinichi Takaichi
- Department of Biology, Nippon Medical School, Musashino, Tokyo, Japan
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