Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation
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 investm...
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MDPI AG
2023-12-01
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| Series: | Microorganisms |
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| author | Daniel Mawuena Afordoanyi Yaw Abayie Akosah Lidiya Shnakhova Keremli Saparmyradov Roderic Gilles Claret Diabankana Shamil Validov |
| author_facet | Daniel Mawuena Afordoanyi Yaw Abayie Akosah Lidiya Shnakhova Keremli Saparmyradov Roderic Gilles Claret Diabankana Shamil Validov |
| author_sort | Daniel Mawuena Afordoanyi |
| collection | DOAJ |
| description | 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 <i>Rhodococcus</i> 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 <i>Rhodococcus erythropolis</i> 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 (<i>vanW</i>, <i>vanY</i>, <i>RbpA</i>, <i>iri</i>, and <i>folC</i>) 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 (<i>ACR3</i>, <i>arsC</i>, <i>corA</i>, <i>DsbA</i>, <i>modA</i>, and <i>recG</i>) 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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| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
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| publishDate | 2023-12-01 |
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| spelling | doaj.art-df0550108fce4df285e63d75527055432024-01-29T14:06:10ZengMDPI AGMicroorganisms2076-26072023-12-011218810.3390/microorganisms12010088Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth StimulationDaniel Mawuena Afordoanyi0Yaw Abayie Akosah1Lidiya Shnakhova2Keremli Saparmyradov3Roderic Gilles Claret Diabankana4Shamil Validov5Laboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, RussiaDepartment of Molecular Pathobiology, College of Dentistry, New York University, New York, NY 10010, USADermatology Department, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, RussiaLaboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, RussiaLaboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, RussiaLaboratory of Molecular Genetics and Microbiology Methods, Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, RussiaAnthropogenic 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 <i>Rhodococcus</i> 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 <i>Rhodococcus erythropolis</i> 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 (<i>vanW</i>, <i>vanY</i>, <i>RbpA</i>, <i>iri</i>, and <i>folC</i>) 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 (<i>ACR3</i>, <i>arsC</i>, <i>corA</i>, <i>DsbA</i>, <i>modA</i>, and <i>recG</i>) 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.https://www.mdpi.com/2076-2607/12/1/88antiSMASH<i>Rhodococcus erythropolis</i>full genomesecondary metabolitesresistant genespan-genome |
| spellingShingle | Daniel Mawuena Afordoanyi Yaw Abayie Akosah Lidiya Shnakhova Keremli Saparmyradov Roderic Gilles Claret Diabankana Shamil Validov Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation Microorganisms antiSMASH <i>Rhodococcus erythropolis</i> full genome secondary metabolites resistant genes pan-genome |
| title | Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation |
| title_full | Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation |
| title_fullStr | Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation |
| title_full_unstemmed | Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation |
| title_short | Biotechnological Key Genes of the <i>Rhodococcus erythropolis</i> MGMM8 Genome: Genes for Bioremediation, Antibiotics, Plant Protection, and Growth Stimulation |
| title_sort | biotechnological key genes of the i rhodococcus erythropolis i mgmm8 genome genes for bioremediation antibiotics plant protection and growth stimulation |
| topic | antiSMASH <i>Rhodococcus erythropolis</i> full genome secondary metabolites resistant genes pan-genome |
| url | https://www.mdpi.com/2076-2607/12/1/88 |
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