Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region
Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of th...
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.973324/full |
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| author | Marianela Cobos Marianela Cobos Marianela Cobos Ruth C. Condori Miguel A. Grandez Segundo L. Estela Marjorie T. Del Aguila Marjorie T. Del Aguila Carlos G. Castro Carlos G. Castro Hicler N. Rodríguez Jhon A. Vargas Jhon A. Vargas Alvaro B. Tresierra Luis A. Barriga Jorge L. Marapara Jorge L. Marapara Pedro M. Adrianzén Pedro M. Adrianzén Roger Ruiz Juan C. Castro Juan C. Castro |
| author_facet | Marianela Cobos Marianela Cobos Marianela Cobos Ruth C. Condori Miguel A. Grandez Segundo L. Estela Marjorie T. Del Aguila Marjorie T. Del Aguila Carlos G. Castro Carlos G. Castro Hicler N. Rodríguez Jhon A. Vargas Jhon A. Vargas Alvaro B. Tresierra Luis A. Barriga Jorge L. Marapara Jorge L. Marapara Pedro M. Adrianzén Pedro M. Adrianzén Roger Ruiz Juan C. Castro Juan C. Castro |
| author_sort | Marianela Cobos |
| collection | DOAJ |
| description | Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications. |
| first_indexed | 2024-04-12T10:43:14Z |
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| id | doaj.art-1c4ed4f5d8794dff9cd465dc46642fd2 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-12T10:43:14Z |
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| series | Frontiers in Genetics |
| spelling | doaj.art-1c4ed4f5d8794dff9cd465dc46642fd22022-12-22T03:36:31ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-11-011310.3389/fgene.2022.973324973324Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin regionMarianela Cobos0Marianela Cobos1Marianela Cobos2Ruth C. Condori3Miguel A. Grandez4Segundo L. Estela5Marjorie T. Del Aguila6Marjorie T. Del Aguila7Carlos G. Castro8Carlos G. Castro9Hicler N. Rodríguez10Jhon A. Vargas11Jhon A. Vargas12Alvaro B. Tresierra13Luis A. Barriga14Jorge L. Marapara15Jorge L. Marapara16Pedro M. Adrianzén17Pedro M. Adrianzén18Roger Ruiz19Juan C. Castro20Juan C. Castro21Laboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúDepartamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria de Zungarococha, Iquitos, PerúLaboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúLaboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúLaboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúLaboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúLaboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúInstituto de Física de São Carlos, Universidade de São Paulo, São Carlos, BrazilLaboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúLaboratorio de Biotecnología y Bioenergética (LBB), Universidad Científica del Perú (UCP), Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúDepartamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria de Zungarococha, Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúDepartamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria de Zungarococha, Iquitos, PerúFacultad de Industrias Alimentarias, Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria de Zungarococha Iquitos, Iquitos, PerúUnidad Especializada de Biotecnología, Centro de Investigación de Recursos Naturales de la UNAP (CIRNA), Universidad Nacional de la Amazonia Peruana (UNAP), Iquitos, PerúDepartamento Académico de Ciencias Biomédicas y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional de la Amazonia Peruana (UNAP), Ciudad Universitaria de Zungarococha, Iquitos, PerúCyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications.https://www.frontiersin.org/articles/10.3389/fgene.2022.973324/fullbiotechnological exploitationcyanobacteriagenome analysismicrobial biodiversitynutraceuticalsbiochemical analysis |
| spellingShingle | Marianela Cobos Marianela Cobos Marianela Cobos Ruth C. Condori Miguel A. Grandez Segundo L. Estela Marjorie T. Del Aguila Marjorie T. Del Aguila Carlos G. Castro Carlos G. Castro Hicler N. Rodríguez Jhon A. Vargas Jhon A. Vargas Alvaro B. Tresierra Luis A. Barriga Jorge L. Marapara Jorge L. Marapara Pedro M. Adrianzén Pedro M. Adrianzén Roger Ruiz Juan C. Castro Juan C. Castro Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region Frontiers in Genetics biotechnological exploitation cyanobacteria genome analysis microbial biodiversity nutraceuticals biochemical analysis |
| title | Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region |
| title_full | Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region |
| title_fullStr | Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region |
| title_full_unstemmed | Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region |
| title_short | Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region |
| title_sort | genomic analysis and biochemical profiling of an unaxenic strain of synechococcus sp isolated from the peruvian amazon basin region |
| topic | biotechnological exploitation cyanobacteria genome analysis microbial biodiversity nutraceuticals biochemical analysis |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.973324/full |
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