1
|
Castrillo ML, Bich GÁ, Amerio NS, Barengo MP, Zapata PD, Saparrat MCN, Villalba LL. Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma. Front Microbiol 2023; 14:1141087. [PMID: 37383640 PMCID: PMC10294050 DOI: 10.3389/fmicb.2023.1141087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/24/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. Methods The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. Results T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. Discussion The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.
Collapse
Affiliation(s)
- María Lorena Castrillo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gustavo Ángel Bich
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia Soledad Amerio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcela Paola Barengo
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mario Carlos Nazareno Saparrat
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Agrarias y Forestales, Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Instituto de Botánica Carlos Spegazzini, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- Cátedra de Microbiología Agrícola, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones “Dra. María Ebe Reca”-InBioMis, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| |
Collapse
|
2
|
Bankefa OE, Samuel-Osamoka FC, Oladeji SJ. Improved enzyme production on corncob hydrolysate by a xylose-evolved Pichia pastoris cell factory. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:1280-1287. [PMID: 35250053 PMCID: PMC8882561 DOI: 10.1007/s13197-021-05135-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
The global shift from the usage of crude oil in bio-production is receiving much attention owing to environmental concern associated with fossil fuel. Lignocellulosic biomass (LB) is a good carbon candidate for bio-production because it is environmental-friendly. Corncob being one of such LB is rich in glucose and xylose, which can be utilized for bio-production. We co-utilize these sugars for the production of enzymes from Pichia pastoris GS115 (Wild Type: WT). Glucose utilization was efficient from synthetic and real hydrolysate but xylose utilization was very low, hence, the need for optimization. Mutants were selected upon Adaptive Laboratory Evolution to efficiently utilize xylose. As expected, all the mutants examined showed improved xylose utilization but surprisingly, there was only 1.8 g/l residual xylose in the 50th generation (GS50). The 30th evolutionary generation (GS30) compared well with the WT by completely utilizing the glucose and also accumulated 48 OD600 cell biomass, which is the highest among all the strains evaluated. More importantly, GS30 secreted 72.6 U/ml and 45.1 U/ml β-galactosidase and β-mannanase on hydrolysate respectively, which are higher than the titre for the WT. Conclusively, this study demonstrated the efficacy of corn corncob hydrolysate in biomanufacturing and gives insight for the optimization study.
Collapse
Affiliation(s)
- Olufemi Emmanuel Bankefa
- Department of Microbiology, Federal University Oye-Ekiti, P.M.B. 373, Ekiti, Nigeria.,Biosolution Technologies, Akure, Ondo Nigeria
| | | | - Seye Julius Oladeji
- Department of Microbiology, Federal University Oye-Ekiti, P.M.B. 373, Ekiti, Nigeria.,School of Food Science and Engineering, South China University of Technology, Tianhe District, Wushan Road, Guangzhou, 381, 510641 Guangdong China
| |
Collapse
|
3
|
Hernandez-Patlan D, Solis-Cruz B, Latorre JD, Merino-Guzman R, Morales Rodríguez M, Ausland C, Hernandez-Velasco X, Ortiz Holguin O, Delgado R, Hargis BM, Singh P, Tellez-Isaias G. Whole-Genome Sequence and Interaction Analysis in the Production of Six Enzymes From the Three Bacillus Strains Present in a Commercial Direct-Fed Microbial (Norum™) Using a Bliss Independence Test. Front Vet Sci 2022; 9:784387. [PMID: 35274019 PMCID: PMC8902298 DOI: 10.3389/fvets.2022.784387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
The three Bacillus strains present in Norum™ were initially selected by their excellent to good relative enzyme activity (REA) production score for amylase, protease, lipase, phytase, cellulase, β-glucanase, and xylanase. Further studies confirmed that the three isolates also showed an antibacterial activity, Gram-positive and Gram-negative poultry pathogens. Norum™ (Eco-Bio/Euxxis Bioscience LLC) is a Bacillus spore direct-fed microbial (DFM). The Bacillus isolates were screened and selected based on in vitro enzyme production profiles. Moreover, in chickens fed high non-starch polysaccharides, this DFM demonstrated to reduce digesta viscosity, bacterial translocation, increase performance, bone mineralization, and balance the intestinal microbiota. In the present study, we present the whole-genome sequence of each of the three isolates in Norum™, as well as the synergistic, additive, or antagonistic effects on the enzyme production behavior of the three Bacillus strains and their combinations when grown together vs. when grown individually. The whole-genome sequence identified isolate AM1002 as Bacillus subtilis (isolate 1), isolate AM0938 as Bacillus amyloliquefaciens (isolate 2), and isolate JD17 as Bacillus licheniformis (isolate 3). The three Bacillus isolates used in the present study produce different enzymes (xylanase, cellulase, phytase, lipase, protease, and β-glucanase). However, this production was modified when two or more Bacillus strains were combined, suggesting possible synergistic, antagonistic, or additive interactions. The Bliss analysis suggested (p < 0.05) that the combination of Bacillus strains 1–2 and 1–2–3 had intermediate effects and predicted that the combination of Bacillus strains 2–3 could have better effects than the combination of all the three Bacillus strains. In summary, the current study demonstrated the need of selecting Bacillus strains based on quantitative enzyme determination and data analysis to assess the impacts of combinations to avoid antagonistic interactions that could limit treatment efficacy. These results suggest that using Bacillus strains 2–3 together could lead to a new generation of DFMs with effects superior to those already examined in Bacillus strains 1–2–3 and, therefore, a potential alternative to growth-promoting antibiotics. More research utilizing poultry models is being considered to confirm and expand the existing findings.
Collapse
Affiliation(s)
- Daniel Hernandez-Patlan
- Laboratorio 5: LEDEFAR, Unidad de Investigacion Multidisciplinaria, Facultad de Estudios Superiores (FES) Cuautitlan, Universidad Nacional Autonoma de Mexico, Cuautitlán Izcalli, Mexico
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de Mexico, Tultitlán, Mexico
| | - Bruno Solis-Cruz
- Laboratorio 5: LEDEFAR, Unidad de Investigacion Multidisciplinaria, Facultad de Estudios Superiores (FES) Cuautitlan, Universidad Nacional Autonoma de Mexico, Cuautitlán Izcalli, Mexico
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de Mexico, Tultitlán, Mexico
| | - Juan D. Latorre
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Ruben Merino-Guzman
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Miguel Morales Rodríguez
- Division de Ingeniería en Nanotecnología, Universidad Politécnica del Valle de Mexico, Tultitlán, Mexico
| | - Catie Ausland
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
| | - Xochitl Hernandez-Velasco
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | | | | | - Billy M. Hargis
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Pallavi Singh
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, United States
| | - Guillermo Tellez-Isaias
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
- *Correspondence: Guillermo Tellez-Isaias
| |
Collapse
|
4
|
Velázquez JE, Sadañoski MA, Zapata PD, Comelli NA, Villalba LL. Bioproduction of α-terpineol and R-(+)-limonene derivatives by terpene-tolerant ascomycete fungus as a potential contribution to the citrus value chain. J Appl Microbiol 2020; 130:76-89. [PMID: 32648320 DOI: 10.1111/jam.14777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/12/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022]
Abstract
AIMS The aims of this article were to select fungal species with high tolerance and high growth rate in mediums supplemented with limonene and citrus essential oils (CEOs), and to test the bioconversion capability of the chosen isolates for the bioproduction of aroma compounds. METHODS AND RESULTS Based on the use of predictive mycology, 21 of 29 isolates were selected after assaying R-(+)-limonene and CEO tolerance (10 g l-1 ). With a dendrogram divisive coefficient of 0·937, the subcluster two with isolates Aspergillus niger LBM 055, Penicillium sp. LBM 150, Penicillium sp. LBM 151 and Penicillium sp. LBM 154 gathered the highest tolerance and mycelia growth speed. Ultrastructural analysis indicated that culture media containing limonene had no visible toxic activity that could promote morphological changes in the fungal cell wall. The biomass of A. niger LBM055 was distinctive in liquid media supplemented with R-(+)-limonene (0·57 ± 0·07 g) and it was selected to prove bioconversion capacity, under static and agitated conditions, and converted up to 98% of limonene, yielding a wide variety of products that were quantified by GC-FID. It was obtained at molecular weights less than limonene (64-100%), between limonene and α-terpineol (12-72%) and greater than α-terpineol (2-48%). CONCLUSIONS Aspergillus niger LBM 055, Penicillium sp. LBM 150, Penicillium sp. LBM 151 and Penicillium sp. LBM 154 showed to the highest tolerance and growth rate in mediums supplemented with R-(+)-limonene and orange and lemon essential oils. Particularly, A. niger LBM055, showed limonene bioconversion capability and produced different molecular weights compounds such us α-terpineol. SIGNIFICANCE AND IMPACT OF THE STUDY Different bioproducts can be obtained by changing operative condition with the same fungus, and this bioprocess aspect is a significant approach to be adopted on industrial scale leading to the creation of new natural flavours and fragrance compositions.
Collapse
Affiliation(s)
- J E Velázquez
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca", CONICET, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - M A Sadañoski
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca", CONICET, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - P D Zapata
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca", CONICET, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - N A Comelli
- Departamento de Ciencias Básicas, Área Química, Facultad de Ingeniería y Ciencias Agropecuarias, Universidad Nacional de San Luis - Instituto de Investigación en Tecnología Química (INTEQUI - CONICET), San Luis, Argentina
| | - L L Villalba
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Exactas, Químicas y Naturales, Instituto de Biotecnología Misiones "Dra. María Ebe Reca", CONICET, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| |
Collapse
|