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Embarcadero-Jiménez S, Araujo-Palomares CL, Moreno-Perlín T, Ramírez-Álvarez N, Quezada-Hernández C, Batista-García RA, Sanchez-Flores A, Calcáneo-Hernández G, Silva-Jiménez H. Physiology and comparative genomics of the haloalkalitolerant and hydrocarbonoclastic marine strain Rhodococcus ruber MSA14. Arch Microbiol 2024; 206:328. [PMID: 38935150 DOI: 10.1007/s00203-024-04050-z] [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: 04/05/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Marine hydrocarbonoclastic bacteria can use polycyclic aromatic hydrocarbons as carbon and energy sources, that makes these bacteria highly attractive for bioremediation in oil-polluted waters. However, genomic and metabolic differences between species are still the subject of study to understand the evolution and strategies to degrade PAHs. This study presents Rhodococcus ruber MSA14, an isolated bacterium from marine sediments in Baja California, Mexico, which exhibits adaptability to saline environments, a high level of intrinsic pyrene tolerance (> 5 g L- 1), and efficient degradation of pyrene (0.2 g L- 1) by 30% in 27 days. Additionally, this strain demonstrates versatility by using naphthalene and phenanthrene as individual carbon sources. The genome sequencing of R. ruber MSA14 revealed a genome spanning 5.45 Mbp, a plasmid of 72 kbp, and three putative megaplasmids, lengths between 110 and 470 Kbp. The bioinformatics analysis of the R. ruber MSA14 genome revealed 56 genes that encode enzymes involved in the peripheral and central pathways of aromatic hydrocarbon catabolism, alkane, alkene, and polymer degradation. Within its genome, R. ruber MSA14 possesses genes responsible for salt tolerance and siderophore production. In addition, the genomic analysis of R. ruber MSA14 against 13 reference genomes revealed that all compared strains have at least one gene involved in the alkanes and catechol degradation pathway. Overall, physiological assays and genomic analysis suggest that R. ruber MSA14 is a new haloalkalitolerant and hydrocarbonoclastic strain toward a wide range of hydrocarbons, making it a promising candidate for in-depth characterization studies and bioremediation processes as part of a synthetic microbial consortium, as well as having a better understanding of the catabolic potential and functional diversity among the Rhodococci group.
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Affiliation(s)
- Salvador Embarcadero-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Cynthia Lizzeth Araujo-Palomares
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Tonatiuh Moreno-Perlín
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, C.P. 62209, México
| | - Nancy Ramírez-Álvarez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Cristina Quezada-Hernández
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, C.P. 62209, México
- Departamento de Biología Animal, Biología Vegetal y Ecología, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas s/n, Jaén, 23071, España
| | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Unidad Universitaria de Secuenciación Masiva y Bioinformática, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, C.P. 62210, México
| | - Gabriela Calcáneo-Hernández
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, C.P. 04510, México
| | - Hortencia Silva-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada, No. 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, México.
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Afordoanyi DM, Akosah YA, Shnakhova L, Saparmyradov K, Diabankana RGC, Validov S. Biotechnological Key Genes of the Rhodococcus erythropolis MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation. Microorganisms 2023; 12:88. [PMID: 38257915 PMCID: PMC10819586 DOI: 10.3390/microorganisms12010088] [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: 11/03/2023] [Revised: 12/07/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Anthropogenic pollution, including residues from the green revolution initially aimed at addressing food security and healthcare, has paradoxically exacerbated environmental challenges. The transition towards comprehensive green biotechnology and bioremediation, achieved with lower financial investment, hinges on microbial biotechnology, with the Rhodococcus genus emerging as a promising contender. The significance of fully annotating genome sequences lies in comprehending strain constituents, devising experimental protocols, and strategically deploying these strains to address pertinent issues using pivotal genes. This study revolves around Rhodococcus erythropolis MGMM8, an associate of winter wheat plants in the rhizosphere. Through the annotation of its chromosomal genome and subsequent comparison with other strains, its potential applications were explored. Using the antiSMASH server, 19 gene clusters were predicted, encompassing genes responsible for antibiotics and siderophores. Antibiotic resistance evaluation via the Comprehensive Antibiotic Resistance Database (CARD) identified five genes (vanW, vanY, RbpA, iri, and folC) that were parallel to strain CCM2595. Leveraging the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) for biodegradation, heavy metal resistance, and remediation genes, the presence of chlorimuron-ethyl, formaldehyde, benzene-desulfurization degradation genes, and heavy metal-related genes (ACR3, arsC, corA, DsbA, modA, and recG) in MGMM8 was confirmed. Furthermore, quorum-quenching signal genes, critical for curbing biofilm formation and virulence elicited by quorum-sensing in pathogens, were also discerned within MGMM8's genome. In light of these predictions, the novel isolate MGMM8 warrants phenotypic assessment to gauge its potential in biocontrol and bioremediation. This evaluation extends to isolating active compounds for potential antimicrobial activities against pathogenic microorganisms. The comprehensive genome annotation process has facilitated the genetic characterization of MGMM8 and has solidified its potential as a biotechnological strain to address global anthropogenic predicaments.
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Affiliation(s)
- Daniel Mawuena Afordoanyi
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia (R.G.C.D.)
- Tatar Scientific Research Institute of Agricultural Chemistry and Soil Science, FRC Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia
| | - Yaw Abayie Akosah
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY 10010, USA
| | - Lidiya Shnakhova
- Dermatology Department, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Keremli Saparmyradov
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia (R.G.C.D.)
| | - Roderic Gilles Claret Diabankana
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia (R.G.C.D.)
| | - Shamil Validov
- Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia (R.G.C.D.)
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Peng M, Siebert DL, Engqvist MKM, Niemeyer CM, Rabe KS. Modeling-Assisted Design of Thermostable Benzaldehyde Lyases from Rhodococcus erythropolis for Continuous Production of α-Hydroxy Ketones. Chembiochem 2022; 23:e202100468. [PMID: 34558792 PMCID: PMC9293332 DOI: 10.1002/cbic.202100468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/23/2021] [Indexed: 12/18/2022]
Abstract
Enantiopure α-hydroxy ketones are important building blocks of active pharmaceutical ingredients (APIs), which can be produced by thiamine-diphosphate-dependent lyases, such as benzaldehyde lyase. Here we report the discovery of a novel thermostable benzaldehyde lyase from Rhodococcus erythropolis R138 (ReBAL). While the overall sequence identity to the only experimentally confirmed benzaldehyde lyase from Pseudomonas fluorescens Biovar I (PfBAL) was only 65 %, comparison of a structural model of ReBAL with the crystal structure of PfBAL revealed only four divergent amino acids in the substrate binding cavity. Based on rational design, we generated two ReBAL variants, which were characterized along with the wild-type enzyme in terms of their substrate spectrum, thermostability and biocatalytic performance in the presence of different co-solvents. We found that the new enzyme variants have a significantly higher thermostability (up to 22 °C increase in T50 ) and a different co-solvent-dependent activity. Using the most stable variant immobilized in packed-bed reactors via the SpyCatcher/SpyTag system, (R)-benzoin was synthesized from benzaldehyde over a period of seven days with a stable space-time-yield of 9.3 mmol ⋅ L-1 ⋅ d-1 . Our work expands the important class of benzaldehyde lyases and therefore contributes to the development of continuous biocatalytic processes for the production of α-hydroxy ketones and APIs.
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Affiliation(s)
- Martin Peng
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Dominik L. Siebert
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Martin K. M. Engqvist
- Chalmers University of TechnologyDepartment of Biology and Biological EngineeringDivision of Systems and Synthetic BiologyKemivägen 10412 96GothenburgSweden
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Kersten S. Rabe
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG 1)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
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Frederick J, Hennessy F, Horn U, de la Torre Cortés P, van den Broek M, Strych U, Willson R, Hefer CA, Daran JMG, Sewell T, Otten LG, Brady D. The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870. BMC Genomics 2020; 21:3. [PMID: 31898479 PMCID: PMC6941271 DOI: 10.1186/s12864-019-6405-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. RESULTS The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. CONCLUSIONS The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.
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Affiliation(s)
- Joni Frederick
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
- Present Address: LadHyx, UMR CNRS 7646, École Polytechnique, 91128 Palaiseau, France
| | - Fritha Hennessy
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
| | - Uli Horn
- Meraka, CSIR, Meiring Naude Road, Brummeria, 0091 South Africa
| | - Pilar de la Torre Cortés
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marcel van den Broek
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ulrich Strych
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Present Address: Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue, Houston, TX 77030 USA
| | - Richard Willson
- Biology and Biochemistry, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
- Chemical and Biomolecular Engineering, University of Houston, 4800 Calhoun Road, Houston, TX 77204 USA
| | - Charles A. Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002 South Africa
- Present Address: AgResearch Limited, Lincoln Research Centre, Private Bag 4749, Christchurch, 8140 New Zealand
| | - Jean-Marc G. Daran
- Industrial Microbiology, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Trevor Sewell
- Electron Microscope Unit, University of Cape Town, Rondebosch, 7701 South Africa
| | - Linda G. Otten
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dean Brady
- Protein Technologies, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, South Africa
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO, Wits, 2050 South Africa
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Chan KG. Whole-genome sequencing in the prediction of antimicrobial resistance. Expert Rev Anti Infect Ther 2016; 14:617-9. [PMID: 27215476 DOI: 10.1080/14787210.2016.1193005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Kok-Gan Chan
- a Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science , University of Malaya , Kuala Lumpur , Malaysia
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Faure D, Joly D. Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences. Genetica 2015; 143:129-32. [PMID: 25736916 DOI: 10.1007/s10709-015-9831-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 02/23/2015] [Indexed: 01/27/2023]
Abstract
Next-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.
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Affiliation(s)
- Denis Faure
- GDR3692 Génomique Environnementale, CNRS, Université Paris-Sud, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France,
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