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Rath G, Nivedita S, Behera SS, Behera HT, Gouda SK, Raina V, Achary KG, Behera SK, Ray L. l-Asparaginase producing novel Streptomyces sp. HB2AG: optimization of process parameters and whole genome sequence analysis. 3 Biotech 2023; 13:201. [PMID: 37215374 PMCID: PMC10195970 DOI: 10.1007/s13205-023-03620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
l-asparaginase (ASNase) is a key enzyme widely used as an anti-cancer drug and is also used in the pharmaceutical and food processing industries. This enzyme's applications are determined by its source and nature. The production of the enzyme through the fermentation process is also crucial for economic feasibility. Searching for a new potent microbial strain is necessary for increased ASNase synthesis. In this work, a potent strain was isolated from the sediment of Chilika Lake and selected for its high ASNase production potential. It was recognized following Bergey's manual of determinative and phylogenetic analysis was carried out by 16S rDNA sequencing. The isolated organism was Streptomyces sp. HB2AG. Additionally, a genome-wide analysis of HB2AG was performed. The result showed that the HB2AG genome possesses a chromosome with 6,099,956 bp and GC content of 74.0%. The whole genome analysis of the strain HB2AG revealed the presence of ASNase (ansA, ansB) and Asparagine synthase (asnB) in the HB2AG genome. Optimization of media composition is crucial for microbial growth and obtaining the desired end product. The current effort focuses on the Taguchi orthogonal design to determine optimum factor combinations that would allow the strain to produce maximum ASNase enzyme. Results showed that compared to unoptimized media, approximately 1.76-fold higher ASNase production was observed in Sea Water Luria Bertani (SWLB) media, pH-5, 0.5% (w/v) of lactose, 0.5% (w/v) of casein, 2.5% (w/v) NaCl, 1 mM Ca2+ and 0.1% Tween 80. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03620-0.
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Affiliation(s)
- Gupteswar Rath
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha India
| | - Suchismita Nivedita
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha India
| | | | | | - Sudhansu Kumar Gouda
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha India
| | - Vishakha Raina
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha India
| | | | | | - Lopamudra Ray
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha India
- School of Law, KIIT Deemed to be University, Bhubaneswar, Odisha India
- School of Biotechnology and School of Law, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha India
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Thakur Z, Vaid RK, Anand T, Tripathi BN. Comparative Genome Analysis of 19 Trueperella pyogenes Strains Originating from Different Animal Species Reveal a Genetically Diverse Open Pan-Genome. Antibiotics (Basel) 2022; 12:antibiotics12010024. [PMID: 36671226 PMCID: PMC9854608 DOI: 10.3390/antibiotics12010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Trueperella pyogenes is a Gram-positive opportunistic pathogen that causes severe cases of mastitis, metritis, and pneumonia in a wide range of animals, resulting in significant economic losses. Although little is known about the virulence factors involved in the disease pathogenesis, a comprehensive comparative genome analysis of T. pyogenes genomes has not been performed till date. Hence, present investigation was carried out to characterize and compare 19 T. pyogenes genomes originating in different geographical origins including the draftgenome of the first Indian origin strain T. pyogenes Bu5. Additionally, candidate virulence determinants that could be crucial for their pathogenesis were also detected and analyzed by using various bioinformatics tools. The pan-genome calculations revealed an open pan-genome of T. pyogenes. In addition, an inventory of virulence related genes, 190 genomic islands, 31 prophage sequences, and 40 antibiotic resistance genes that could play a significant role in organism's pathogenicity were detected. The core-genome based phylogeny of T. pyogenes demonstrates a polyphyletic, host-associated group with a high degree of genomic diversity. The identified core-genome can be further used for screening of drug and vaccine targets. The investigation has provided unique insights into pan-genome, virulome, mobiliome, and resistome of T. pyogenes genomes and laid the foundation for future investigations.
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Affiliation(s)
- Zoozeal Thakur
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Rajesh Kumar Vaid
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar 125001, India
- Correspondence:
| | - Taruna Anand
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar 125001, India
| | - Bhupendra Nath Tripathi
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar 125001, India
- Division of Animal Science, Krishi Bhavan, New Delhi 110001, India
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Ma L, Yang W, Huang S, Liu R, Li H, Huang X, Xiong J, Liu X. Integrative Assessments on Molecular Taxonomy of Acidiferrobacter thiooxydans ZJ and Its Environmental Adaptation Based on Mobile Genetic Elements. Front Microbiol 2022; 13:826829. [PMID: 35250944 PMCID: PMC8889020 DOI: 10.3389/fmicb.2022.826829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Acidiferrobacter spp. are facultatively anaerobic acidophiles that belong to a distinctive Acidiferrobacteraceae family, which are similar to Ectothiorhodospiraceae phylogenetically, and are closely related to Acidithiobacillia class/subdivision physiologically. The limited genome information has kept them from being studied on molecular taxonomy and environmental adaptation in depth. Herein, Af. thiooxydans ZJ was isolated from acid mine drainage (AMD), and the complete genome sequence was reported to scan its genetic constitution for taxonomic and adaptative feature exploration. The genome has a single chromosome of 3,302,271 base pairs (bp), with a GC content of 63.61%. The phylogenetic tree based on OrthoANI highlighted the unique position of Af. thiooxydans ZJ, which harbored more unique genes among the strains from Ectothiorhodospiraceae and Acidithiobacillaceae by pan-genome analysis. The diverse mobile genetic elements (MGEs), such as insertion sequence (IS), clustered regularly interspaced short palindromic repeat (CRISPR), prophage, and genomic island (GI), have been identified and characterized in Af. thiooxydans ZJ. The results showed that Af. thiooxydans ZJ may effectively resist the infection of foreign viruses and gain functional gene fragments or clusters to shape its own genome advantageously. This study will offer more evidence of the genomic plasticity and improve our understanding of evolutionary adaptation mechanisms to extreme AMD environment, which could expand the potential utilization of Af. thiooxydans ZJ as an iron and sulfur oxidizer in industrial bioleaching.
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Affiliation(s)
- Liyuan Ma
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Weiyi Yang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Shanshan Huang
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Rui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Huiying Li
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xinping Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Junming Xiong
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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da Silva Filho AC, Marchaukoski JN, Raittz RT, De Pierri CR, de Jesus Soares Machado D, Fadel-Picheth CMT, Picheth G. Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila. Front Microbiol 2021; 12:769380. [PMID: 34912316 PMCID: PMC8667584 DOI: 10.3389/fmicb.2021.769380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Aeromonas are Gram-negative rods widely distributed in the environment. They can cause severe infections in fish related to financial losses in the fish industry, and are considered opportunistic pathogens of humans causing infections ranging from diarrhea to septicemia. The objective of this study was to determine in silico the contribution of genomic islands to A. hydrophila. The complete genomes of 17 A. hydrophila isolates, which were separated into two phylogenetic groups, were analyzed using a genomic island (GI) predictor. The number of predicted GIs and their characteristics varied among strains. Strains from group 1, which contains mainly fish pathogens, generally have a higher number of predicted GIs, and with larger size, than strains from group 2 constituted by strains recovered from distinct sources. Only a few predicted GIs were shared among them and contained mostly genes from the core genome. Features related to virulence, metabolism, and resistance were found in the predicted GIs, but strains varied in relation to their gene content. In strains from group 1, O Ag biosynthesis clusters OX1 and OX6 were identified, while strains from group 2 each had unique clusters. Metabolic pathways for myo-inositol, L-fucose, sialic acid, and a cluster encoding QueDEC, tgtA5, and proteins related to DNA metabolism were identified in strains of group 1, which share a high number of predicted GIs. No distinctive features of group 2 strains were identified in their predicted GIs, which are more diverse and possibly better represent GIs in this species. However, some strains have several resistance attributes encoded by their predicted GIs. Several predicted GIs encode hypothetical proteins and phage proteins whose functions have not been identified but may contribute to Aeromonas fitness. In summary, features with functions identified on predicted GIs may confer advantages to host colonization and competitiveness in the environment.
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Affiliation(s)
| | - Jeroniza Nunes Marchaukoski
- Department of Bioinformatics, Professional and Technical Education Sector, Federal University of Parana, Curitiba, Brazil
| | - Roberto Tadeu Raittz
- Department of Bioinformatics, Professional and Technical Education Sector, Federal University of Parana, Curitiba, Brazil
| | | | - Diogo de Jesus Soares Machado
- Department of Bioinformatics, Professional and Technical Education Sector, Federal University of Parana, Curitiba, Brazil
| | | | - Geraldo Picheth
- Department of Clinical Analysis, Federal University of Parana, Curitiba, Brazil
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