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Zhou B, Guo Y, Xue Y, Ji X, Huang Y. Comprehensive insights into the mechanism of keratin degradation and exploitation of keratinase to enhance the bioaccessibility of soybean protein. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:177. [PMID: 37978558 PMCID: PMC10655438 DOI: 10.1186/s13068-023-02426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Keratin is a recalcitrant protein and can be decomposed in nature. However, the mechanism of keratin degradation is still not well understood. In this study, Bacillus sp. 8A6 can completely degrade the feather in 20 h, which is an efficient keratin degrader reported so far. Comprehensive transcriptome analysis continuously tracks the metabolism of Bacillus sp. 8A6 throughout its growth in feather medium. It reveals for the first time how the strain can acquire nutrients and energy in an oligotrophic feather medium for proliferation in the early stage. Then, the degradation of the outer lipid layer of feather can expose the internal keratin structure for disulfide bonds reduction by sulfite from the newly identified sulfite metabolic pathway, disulfide reductases and iron uptake. The resulting weakened keratin has been further proposedly de-assembled by the S9 protease and hydrolyzed by synergistic effects of the endo, exo and oligo-proteases from S1, S8, M3, M14, M20, M24, M42, M84 and T3 families. Finally, bioaccessible peptides and amino acids are generated and transported for strain growth. The keratinase has been applied for soybean hydrolysis, which generates 2234 peptides and 559.93 mg/L17 amino acids. Therefore, the keratinases, inducing from the poultry waste, have great potential to be further applied for producing bioaccessible peptides and amino acids for feed industry.
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Affiliation(s)
- Beiya Zhou
- College of Mathematical Sciences, Bohai University, Jinzhou, 121013, Liaoning, China
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Huizhou Institute of Green Energy and Advanced Materials, Huizhou, 516000, Guangdong, China
| | - Yandong Guo
- College of Mathematical Sciences, Bohai University, Jinzhou, 121013, Liaoning, China.
| | - Yaju Xue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiuling Ji
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yuhong Huang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
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Qiu J, Barrett K, Wilkens C, Meyer AS. Bioinformatics based discovery of new keratinases in protease family M36. N Biotechnol 2022; 68:19-27. [PMID: 35032710 DOI: 10.1016/j.nbt.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 10/19/2022]
Abstract
Keratinases are proteases that can catalyze the degradation of insoluble keratinous biomass. Keratinases in protease family M36 (MEROPS database) are endo-acting proteases. In total, 687 proteases are classified in family M36. In the present study, new keratinolytic enzymes were identified in protease family M36 using the bioinformatics tool Conserved Unique Peptide Patterns (CUPP). Via CUPP, M36 family members were classified into 11 groups, with CUPP group 1 containing the three currently known and sequenced family M36 keratinases (derived from the fungi Fusarium oxysporum, Microsporum canis and Onygena corvina) as well as an additional 71 uncharacterized M36 proteases. In order to assess the relevance of CUPP group 1 categorization to keratinolytic function, four uncharacterized M36 proteases and the known keratinase from F. oxysporum (in CUPP group 1) were selected for recombinant expression and keratinolytic activity assessment. The four hitherto unknown M36 proteases were from Phaeosphaeria nodorum, Aspergillus clavatus, Pseudogymnoascus pannorum and Nectria haematococca, and represent four different fungal taxonomical classes. The genes encoding the selected M36 proteases were individually expressed in Pichia pastoris and all proteases displayed keratinase activity on keratin azure. Additionally, the activity on different keratinase substrates, optimal reaction conditions and thermal stability were determined for the two most active new keratinases. The results validate the applicability of CUPP for function-based discovery of non-characterized keratinases and present new robust keratinases for potential use in keratin upgrading.
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Affiliation(s)
- Jingwen Qiu
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kristian Barrett
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Casper Wilkens
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Anne S Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, DTU Bioengineering, Building 221, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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Koutsoumanis K, Allende A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Bottari B, Cummins E, Ylivainio K, Muñoz Guajardo I, Ortiz‐Pelaez A, Alvarez‐Ordóñez A. Inactivation of indicator microorganisms and biological hazards by standard and/or alternative processing methods in Category 2 and 3 animal by-products and derived products to be used as organic fertilisers and/or soil improvers. EFSA J 2021; 19:e06932. [PMID: 34900004 PMCID: PMC8638561 DOI: 10.2903/j.efsa.2021.6932] [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] [Indexed: 11/18/2022] Open
Abstract
The European Commission requested EFSA to assess if different thermal processes achieve a 5 log10 reduction in Enterococcus faecalis or Salmonella Senftenberg (775W) and (if relevant) a 3 log10 reduction in thermoresistant viruses (e.g. Parvovirus) as well as if different chemical processes achieve a 3 log10 reduction of eggs of Ascaris sp., in eight groups of Category 2 and 3 derived products and animal by-products (ABP). These included (1) ash derived from incineration, co-incineration and combustion; (2) glycerine derived from the production of biodiesel and renewable fuels; (3) other materials derived from the production of biodiesel and renewable fuels; (4) hides and skins; (5) wool and hair; (6) feathers and down; (7) pig bristles; and (8) horns, horn products, hooves and hoof products. Data on the presence of viral hazards and on thermal and chemical inactivation of the targeted indicator microorganisms and biological hazards under relevant processing conditions were extracted via extensive literature searches. The evidence was assessed via expert knowledge elicitation. The certainty that the required log10 reductions in the most resistant indicator microorganisms or biological hazards will be achieved for each of the eight groups of materials mentioned above by the thermal and/or chemical processes was (1) 99-100% for the two processes assessed; (2) 98-100% in Category 2 ABP, at least 90-99% in Category 3 ABP; (3) 90-99% in Category 2 ABP; at least 66-90% in Category 3 ABP; (4) 10-66% and 33-66%; (5) 1-33% and 10-50%; (6) 66-90%; (7) 33-66% and 50-95%; (8) 66-95%, respectively. Data generation on the occurrence and reduction of biological hazards by thermal and/or chemical methods in these materials and on the characterisation of the usage pathways of ABP as organic fertilisers/soil improvers is recommended.
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Espersen R, Huang Y, Falco FC, Hägglund P, Gernaey KV, Lange L, Svensson B. Exceptionally rich keratinolytic enzyme profile found in the rare actinomycetes Amycolatopsis keratiniphila D2 T. Appl Microbiol Biotechnol 2021; 105:8129-8138. [PMID: 34605969 DOI: 10.1007/s00253-021-11579-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/25/2022]
Abstract
The non-spore forming Gram-positive actinomycetes Amycolatopsis keratiniphila subsp. keratiniphila D2T (DSM 44,409) has a high potential for keratin valorization as demonstrated by a novel biotechnological microbial conversion process consisting of a bacterial growth phase and a keratinolytic phase, respectively. Compared to the most gifted keratinolytic Bacillus species, a very large number of 621 putative proteases are encoded by the genome of Amycolatopsis keratiniphila subsp. keratiniphila D2T, as predicted by using Peptide Pattern Recognition (PPR) analysis. Proteome analysis by using LC-MS/MS on aliquots of the supernatant of A. keratiniphila subsp. keratiniphila D2T culture on slaughterhouse pig bristle meal, removed at 24, 48, 96 and 120 h of growth, identified 43 proteases. This was supplemented by proteome analysis of specific fractions after enrichment of the supernatant by anion exchange chromatography leading to identification of 50 proteases. Overall 57 different proteases were identified corresponding to 30% of the 186 proteins identified from the culture supernatant and distributed as 17 metalloproteases from 11 families, including an M36 protease, 38 serine proteases from 4 families, and 13 proteolytic enzymes from other families. Notably, M36 keratinolytic proteases are prominent in fungi, but seem not to have been discovered in bacteria previously. Two S01 family peptidases, named T- and C-like proteases, prominent in the culture supernatant, were purified and shown to possess a high azo-keratin/azo-casein hydrolytic activity ratio. The C-like protease revealed excellent thermostability, giving promise for successful applications in biorefinery processes. Notably, the bacterium seems not to secrete enzymes for cleavage of disulfides in the keratinous substrates. KEY POINTS: • A. keratiniphila subsp. keratiniphila D2T is predicted to encode 621 proteases. • This actinomycete efficiently converts bristle meal to a protein hydrolysate. • Proteome analysis identified 57 proteases in its secretome.
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Affiliation(s)
- Roall Espersen
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 224, DK 2800 Kgs., Lyngby, Denmark
- Center for Vaccine Research, Statens Serum Institut, Artillerivej 5 Building 81, DK 2300, Copenhagen S, Denmark
| | - Yuhong Huang
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 227, DK 2800 Kgs., Lyngby, Denmark
- Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, People's Republic of China
| | - Francesco C Falco
- Process and Systems Engineering Center, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 228 A, DK 2800 Kgs., Lyngby, Denmark
| | - Per Hägglund
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 224, DK 2800 Kgs., Lyngby, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, DK 2200, Copenhagen N, Denmark
| | - Krist V Gernaey
- Process and Systems Engineering Center, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 228 A, DK 2800 Kgs., Lyngby, Denmark
| | - Lene Lange
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 227, DK 2800 Kgs., Lyngby, Denmark
- Bioeconomy, Research & Advisory, Karensgade 5, DK 2500, Valby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 224, DK 2800 Kgs., Lyngby, Denmark.
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Gonzalo M, Espersen R, Al‐Soud WA, Cristiano Falco F, Hägglund P, Sørensen SJ, Svensson B, Jacquiod S. Azo dying of α-keratin material improves microbial keratinase screening and standardization. Microb Biotechnol 2020; 13:984-996. [PMID: 32110845 PMCID: PMC7264887 DOI: 10.1111/1751-7915.13541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 11/30/2022] Open
Abstract
Microbial conversion through enzymatic reactions has received a lot of attention as a cost-effective and environmentally friendly way to recover amino acids and short peptides from keratin materials. However, accurate assessment of microbial keratinase activity is not straightforward, and current available methods lack sensitivity and standardization. Here, we suggest an optimized Azokeratin assay, with substrate generated directly from azo-dyed raw keratin material. We introduced supernatant filtration in the protocol for optimal stopping of keratinase reactions instead of the widely used trichloroacetic acid (TCA), as it generated biases and impacted the sensitivity. We furthermore suggest a method for standardization of keratinase activity signals using proteinase K, a well-known keratinase, as a reference enabling reproducibility between studies. Lastly, we evaluated our developed method with several bacterial isolates through benchmarking against a commercial assay (Keratin Azure). Under different setups, the Azokeratin method was more sensitive than commonly used Keratin Azure-based assays (3-fold). We argue that this method could be applied with any type of keratin substrate, enabling more robust and sensitive results which can be used for further comparison with other studies, thus representing an important progress within the field of microbial keratin degradation.
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Affiliation(s)
- Milena Gonzalo
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
- Present address:
Interactions Arbres/Micro‐organismesINRA/Univ. de LorraineChampenouxFrance
| | - Roall Espersen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkDK‐2800LyngbyDenmark
| | - Waleed A. Al‐Soud
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Francesco Cristiano Falco
- Department of Chemical and Biochemical EngineeringTechnical University of DenmarkDK‐2800LyngbyDenmark
| | - Per Hägglund
- Department of Biotechnology and BiomedicineTechnical University of DenmarkDK‐2800LyngbyDenmark
- Present address:
Department of Biomedical SciencesPanum Institute 12.6University of CopenhagenCopenhagenDenmark
| | - Søren J. Sørensen
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
| | - Birte Svensson
- Department of Biotechnology and BiomedicineTechnical University of DenmarkDK‐2800LyngbyDenmark
| | - Samuel Jacquiod
- Section of MicrobiologyUniversity of CopenhagenDK‐2100CopenhagenDenmark
- Present address:
AgroécologieAgroSup DijonINRAEUniv. BourgogneUniv. Bourgogne Franche‐ComtéF‐21000DijonFrance
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