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Malik PK, Trivedi S, Mohapatra A, Kolte AP, Mech A, Victor T, Ahasic E, Bhatta R. Oat Brewery Waste Decreased Methane Production and Alters Rumen Fermentation, Microbiota Composition, and CAZymes Profiles. Microorganisms 2024; 12:1475. [PMID: 39065243 PMCID: PMC11279122 DOI: 10.3390/microorganisms12071475] [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: 06/13/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The transformation of oat brewery waste (OBW) into livestock feed could be a potential replacement for the expensive concentrate and one of the effective approaches for avoiding health hazards due to the accumulation of oat brewery waste in the environment. To explore the potential of OBW as a methane (CH4) mitigating agent, an in vitro study was undertaken to investigate the effect of graded replacement of concentrate with OBW on CH4 production, microbiota, feed fermentation, and CAZymes. A total of five treatments with variable proportions of OBW were formulated. The results indicated a linear decrease in the total gas production and a 38-52% decrease in CH4 production with a 60 and 100% replacement of concentrate with OBW. The inclusion of OBW also affected the abundance of microbes such as Firmicutes, Euryarchaeota, Methanobrevibacter, and protozoa numbers. This study demonstrated that OBW can partially replace the concentrate and effectively mitigate CH4 production; however, the concurrent decrease in fermentation cautioned for the partial replacement of concentrate with OBW at an appropriate level at which the fermentation remains unaffected while decreasing CH4 production. Therefore, waste from oat breweries can contribute to curtailing the accumulation of greenhouse gases (GHGs) in the atmosphere.
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Affiliation(s)
- Pradeep Kumar Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (S.T.); (A.M.); (A.P.K.); (A.M.)
| | - Shraddha Trivedi
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (S.T.); (A.M.); (A.P.K.); (A.M.)
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (S.T.); (A.M.); (A.P.K.); (A.M.)
| | - Atul Purshottam Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (S.T.); (A.M.); (A.P.K.); (A.M.)
| | - Anjumoni Mech
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (S.T.); (A.M.); (A.P.K.); (A.M.)
| | - Tsuma Victor
- International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, A-1400 Vienna, Austria; (T.V.); (E.A.)
| | - Elena Ahasic
- International Atomic Energy Agency, Vienna International Centre, P.O. Box 100, A-1400 Vienna, Austria; (T.V.); (E.A.)
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Windels A, Franceus J, Pleiss J, Desmet T. CANDy: Automated analysis of domain architectures in carbohydrate-active enzymes. PLoS One 2024; 19:e0306410. [PMID: 38990885 PMCID: PMC11238990 DOI: 10.1371/journal.pone.0306410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) can be found in all domains of life and play a crucial role in metabolic and physiological processes. CAZymes often possess a modular structure, comprising not only catalytic domains but also associated domains such as carbohydrate-binding modules (CBMs) and linker domains. By exploring the modular diversity of CAZy families, catalysts with novel properties can be discovered and further insight in their biological functions and evolutionary relationships can be obtained. Here we present the carbohydrate-active enzyme domain analysis tool (CANDy), an assembly of several novel scripts, tools and databases that allows users to analyze the domain architecture of all protein sequences in a given CAZy family. CANDy's usability is shown on glycoside hydrolase family 48, a small yet underexplored family containing multi-domain enzymes. Our analysis reveals the existence of 35 distinct domain assemblies, including eight known architectures, with the remaining assemblies awaiting characterization. Moreover, we substantiate the occurrence of horizontal gene transfer from prokaryotes to insect orthologs and provide evidence for the subsequent removal of auxiliary domains, likely through a gene fission event. CANDy is available at https://github.com/PyEED/CANDy.
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Affiliation(s)
- Alex Windels
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Jorick Franceus
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Tom Desmet
- Department of Biotechnology, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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Truong NH, Le TTH, Nguyen HD, Nguyen HT, Dao TK, Tran TMN, Tran HL, Nguyen DT, Nguyen TQ, Phan THT, Do TH, Phan NH, Ngo TCN, Vu VV. Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam. PeerJ 2024; 12:e17553. [PMID: 38938609 PMCID: PMC11210479 DOI: 10.7717/peerj.17553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/20/2024] [Indexed: 06/29/2024] Open
Abstract
Background White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.
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Affiliation(s)
- Nam-Hai Truong
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Thu-Hong Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Hong-Duong Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | | | - Trong-Khoa Dao
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Minh-Nguyet Tran
- The Key Laboratory of Enzyme and Protein Technology (KLEPT), VNU University of Science, Hanoi, Vietnam
| | - Huyen-Linh Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Dinh-Trong Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Quy Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Hong-Thao Phan
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Huyen Do
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Ngoc-Han Phan
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | - Thi-Cam-Nhung Ngo
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | - Van-Van Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
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St John FJ, Bynum L, Tauscheck DA, Crooks C. Use of xylosidase 3C from Segatella baroniae to discriminate xylan non-reducing terminus substitution characteristics. BMC Res Notes 2024; 17:175. [PMID: 38915023 PMCID: PMC11197168 DOI: 10.1186/s13104-024-06835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
OBJECTIVE New characterized carbohydrate-active enzymes are needed for use as tools to discriminate complex carbohydrate structural features. Fungal glycoside hydrolase family 3 (GH3) β-xylosidases have been shown to be useful for the structural elucidation of glucuronic acid (GlcA) and arabinofuranose (Araf) substituted oligoxylosides. A homolog of these GH3 fungal enzymes from the bacterium Segatella baroniae (basonym Prevotella bryantii), Xyl3C, has been previously characterized, but those studies did not address important functional specificity features. In an interest to utilize this enzyme for laboratory methods intended to discriminate the structure of the non-reducing terminus of substituted xylooligosaccharides, we have further characterized this GH3 xylosidase. RESULTS In addition to verification of basic functional characteristics of this xylosidase we have determined its mode of action as it relates to non-reducing end xylose release from GlcA and Araf substituted oligoxylosides. Xyl3C cleaves xylose from the non-reducing terminus of β-1,4-xylan until occurrence of a penultimate substituted xylose. If this substitution is O2 linked, then Xyl3C removes the non-reducing xylose to leave the substituted xylose as the new non-reducing terminus. However, if the substitution is O3 linked, Xyl3C does not hydrolyze, thus leaving the substitution one-xylose (penultimate) from the non-reducing terminus. Hence, Xyl3C enables discrimination between O2 and O3 linked substitutions on the xylose penultimate to the non-reducing end. These findings are contrasted using a homologous enzyme also from S. baroniae, Xyl3B, which is found to yield a penultimate substituted nonreducing terminus regardless of which GlcA or Araf substitution exists.
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Affiliation(s)
- Franz J St John
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA.
| | - Loreen Bynum
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA
| | - Dante A Tauscheck
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA
| | - Casey Crooks
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Dr, Madison, WI, 53726, USA
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An H, Ching XH, Cheah WJ, Lim WL, Ee KY, Chong CS, Lam MQ. Genomic analysis of a halophilic bacterium Nesterenkonia sp. CL21 with ability to produce a diverse group of lignocellulolytic enzymes. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01178-9. [PMID: 38842626 DOI: 10.1007/s12223-024-01178-9] [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: 11/25/2023] [Accepted: 05/26/2024] [Indexed: 06/07/2024]
Abstract
Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.
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Affiliation(s)
- Hongxuan An
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Xin Huey Ching
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wai Jun Cheah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wei Lun Lim
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), 02600, Arau, Perlis, Malaysia
| | - Kah Yaw Ee
- Department of Agricultural and Food Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
- Centre for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Ming Quan Lam
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
- Centre for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
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Claushuis B, Cordfunke RA, de Ru AH, van Angeren J, Baumann U, van Veelen PA, Wuhrer M, Corver J, Drijfhout JW, Hensbergen PJ. Non-prime- and prime-side profiling of Pro-Pro endopeptidase specificity using synthetic combinatorial peptide libraries and mass spectrometry. FEBS J 2024. [PMID: 38767318 DOI: 10.1111/febs.17160] [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: 03/18/2024] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
A group of bacterial proteases, the Pro-Pro endopeptidases (PPEPs), possess the unique ability to hydrolyze proline-proline bonds in proteins. Since a protease's function is largely determined by its substrate specificity, methods that can extensively characterize substrate specificity are valuable tools for protease research. Previously, we achieved an in-depth characterization of PPEP prime-side specificity. However, PPEP specificity is also determined by the non-prime-side residues in the substrate. To gain a more complete insight into the determinants of PPEP specificity, we characterized the non-prime- and prime-side specificity of various PPEPs using a combination of synthetic combinatorial peptide libraries and mass spectrometry. With this approach, we deepened our understanding of the P3-P3' specificities of PPEP-1 and PPEP-2, while identifying the endogenous substrate of PPEP-2 as the most optimal substrate in our library data. Furthermore, by employing the library approach, we investigated the altered specificity of mutants of PPEP-1 and PPEP-2. Additionally, we characterized a novel PPEP from Anoxybacillus tepidamans, which we termed PPEP-4. Based on structural comparisons, we hypothesized that PPEP-4 displays a PPEP-1-like prime-side specificity, which was substantiated by the experimental data. Intriguingly, another putative PPEP from Clostridioides difficile, CD1597, did not display Pro-Pro endoproteolytic activity. Collectively, we characterized PPEP specificity in detail using our robust peptide library method and, together with additional structural information, provide more insight into the intricate mechanisms that govern protease specificity.
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Affiliation(s)
- Bart Claushuis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Robert A Cordfunke
- Department of Immunology, Leiden University Medical Center, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Jordy van Angeren
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Ulrich Baumann
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Germany
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
| | - Jeroen Corver
- Leiden University Center of Infectious Diseases, Leiden University Medical Center, The Netherlands
| | - Jan W Drijfhout
- Department of Immunology, Leiden University Medical Center, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, The Netherlands
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Biswas S, Bhattar AVK, Bhatta R, Rahman H. Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet. Microorganisms 2023; 12:47. [PMID: 38257874 PMCID: PMC10818812 DOI: 10.3390/microorganisms12010047] [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: 11/09/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
A study was undertaken to compare the rumen microbial community composition, methane yield, rumen fermentation, and CAZyme profiles between cattle and buffaloes. The primary aim of this study was to ascertain the impact of the host species on the above when diet and environmental factors are fixed. A total of 43 phyla, 200 orders, 458 families, and 1722 microbial genera were identified in the study. Bacteroidetes was the most prominent bacterial phylum and constituted >1/3rd of the ruminal microbiota; however, their abundances were comparable between cattle and buffaloes. Firmicutes were the second most abundant bacteria, found to be negatively correlated with the Bacteroidetes. The abundances of Firmicutes as well as the F/B ratio were not different between the two host species. In this study, archaea affiliated with the nine phyla were identified, with Euryarchaeota being the most prominent. Like bacterial phyla, the abundances of Euryarchaeota methanogens were also similar between the cattle and buffaloes. At the order level, Methanobacteriales dominated the archaea. Methanogens from the Methanosarcinales, Methanococcales, Methanomicrobiales, and Methanomassiliicoccales groups were also identified, but at a lower frequency. Methanobrevibacter was the most prevalent genus of methanogens, accounting for approximately three percent of the rumen metagenome. However, their distribution was not different between the two host species. CAZymes affiliated with five classes, namely CBM, CE, GH, GT, and PL, were identified in the metagenome, where the GH class was the most abundant and constituted ~70% of the total CAZymes. The protozoal numbers, including Entodiniomorphs and Holotrichs, were also comparable between the cattle and buffaloes. Results from the study did not reveal any significant difference in feed intake, nutrient digestibility, and rumen fermentation between cattle and buffaloes fed on the same diet. As methane yield due to the similar diet composition, feed ingredients, rumen fermentation, and microbiota composition did not vary, these results indicate that the microbiota community structure and methane emissions are under the direct influence of the diet and environment, and the host species may play only a minor role until the productivity does not vary. More studies are warranted to investigate the effect of different diets and environments on microbiota composition and methane yield. Further, the impact of variable productivity on both the cattle and buffaloes when the diet and environmental factors are fixed needs to be ascertained.
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Affiliation(s)
- Pradeep K. Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Shraddha Trivedi
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110012, India
| | - Atul P. Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Siddharth Biswas
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Ashwin V. K. Bhattar
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore 560030, India; (P.K.M.)
| | - Habibar Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi 110012, India
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Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER. The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proc Natl Acad Sci U S A 2023; 120:e2306160120. [PMID: 38109545 PMCID: PMC10756260 DOI: 10.1073/pnas.2306160120] [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: 04/16/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.
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Affiliation(s)
| | | | - Charles Pepe-Ranney
- Soil & Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY14853
| | - Wenbo Chen
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA94025
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Nathalie H. Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
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Malik PK, Trivedi S, Kolte AP, Mohapatra A, Biswas S, Bhattar AVK, Bhatta R, Rahman H. Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet. Front Microbiol 2023; 14:1266025. [PMID: 38029196 PMCID: PMC10666647 DOI: 10.3389/fmicb.2023.1266025] [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: 07/24/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.
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Affiliation(s)
- Pradeep K. Malik
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Shraddha Trivedi
- International Livestock Research Institute, South Asia Regional Office, New Delhi, India
| | - Atul P. Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Archit Mohapatra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Siddharth Biswas
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | | | - Raghavendra Bhatta
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Habibar Rahman
- International Livestock Research Institute, South Asia Regional Office, New Delhi, India
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Christopher M, Sreeja-Raju A, Abraham A, Gokhale DV, Pandey A, Sukumaran RK. Early cellular events and potential regulators of cellulase induction in Penicillium janthinellum NCIM 1366. Sci Rep 2023; 13:5057. [PMID: 36977777 PMCID: PMC10050438 DOI: 10.1038/s41598-023-32340-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/26/2023] [Indexed: 03/30/2023] Open
Abstract
Cellulase production by fungi is tightly regulated in response to environmental cues, and understanding this mechanism is a key pre-requisite in the efforts to improve cellulase secretion. Based on UniProt descriptions of secreted Carbohydrate Active enZymes (CAZymes), 13 proteins of the cellulase hyper-producer Penicillium janthinellum NCIM 1366 (PJ-1366) were annotated as cellulases- 4 cellobiohydrolases (CBH), 7 endoglucanases (EG) and 2 beta glucosidases (BGL). Cellulase, xylanase, BGL and peroxidase activities were higher for cultures grown on a combination of cellulose and wheat bran, while EG was stimulated by disaccharides. Docking studies indicated that the most abundant BGL- Bgl2- has different binding sites for the substrate cellobiose and the product glucose, which helps to alleviate feedback inhibition, probably accounting for the low level of glucose tolerance exhibited. Out of the 758 transcription factors (TFs) differentially expressed on cellulose induction, 13 TFs were identified whose binding site frequencies on the promoter regions of the cellulases positively correlated with their abundance in the secretome. Further, correlation analysis of the transcriptional response of these regulators and TF-binding sites on their promoters indicated that cellulase expression is possibly preceded by up-regulation of 12 TFs and down-regulation of 16 TFs, which cumulatively regulate transcription, translation, nutrient metabolism and stress response.
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Affiliation(s)
- Meera Christopher
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - AthiraRaj Sreeja-Raju
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Amith Abraham
- Department of Chemical Engineering, Hanyang University, Seoul, Republic of Korea
| | | | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, Uttar Pradesh, India
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, India
- Centre for Energy and Environmental Sustainability, Lucknow, 226 029, India
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram, Kerala, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
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11
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Lamote B, da Fonseca MJM, Vanderstraeten J, Meert K, Elias M, Briers Y. Current challenges in designer cellulosome engineering. Appl Microbiol Biotechnol 2023; 107:2755-2770. [PMID: 36941434 DOI: 10.1007/s00253-023-12474-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023]
Abstract
Designer cellulosomes (DCs) are engineered multi-enzyme complexes, comprising carbohydrate-active enzymes attached to a common backbone, the scaffoldin, via high-affinity cohesin-dockerin interactions. The use of DCs in the degradation of renewable biomass polymers is a promising approach for biorefineries. Indeed, DCs have shown significant hydrolytic activities due to the enhanced enzyme-substrate proximity and inter-enzyme synergies, but technical hurdles in DC engineering have hindered further progress towards industrial application. The challenge in DC engineering lies in the large diversity of possible building blocks and architectures, resulting in a multivariate and immense design space. Simultaneously, the precise DC composition affects many relevant parameters such as activity, stability, and manufacturability. Since protein engineers face a lack of high-throughput approaches to explore this vast design space, DC engineering may result in an unsatisfying outcome. This review provides a roadmap to guide researchers through the process of DC engineering. Each step, starting from concept to evaluation, is described and provided with its challenges, along with possible solutions, both for DCs that are assembled in vitro or are displayed on the yeast cell surface. KEY POINTS: • Construction of designer cellulosomes is a multi-step process. • Designer cellulosome research deals with multivariate construction challenges. • Boosting designer cellulosome efficiency requires exploring a vast design space.
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Affiliation(s)
- Babette Lamote
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | | | - Julie Vanderstraeten
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Kenan Meert
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Marte Elias
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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12
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Sun XB, Gao DY, Cao JW, Liu Y, Rong ZT, Wang JK, Wang Q. BsLPMO10A from Bacillus subtilis boosts the depolymerization of diverse polysaccharides linked via β-1,4-glycosidic bonds. Int J Biol Macromol 2023; 230:123133. [PMID: 36621733 DOI: 10.1016/j.ijbiomac.2023.123133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/24/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023]
Abstract
Lytic polysaccharide monooxygenase (LPMO) is known as an oxidatively cleaving enzyme in recalcitrant polysaccharide deconstruction. Herein, we report a novel AA10 LPMO derived from Bacillus subtilis (BsLPMO10A). A substrate specificity study revealed that the enzyme exhibited an extensive active-substrate spectrum, particularly for polysaccharides linked via β-1,4 glycosidic bonds, such as β-(Man1 → 4Man), β-(Glc1 → 4Glc) and β-(Xyl1 → 4Xyl). HPAEC-PAD and MALDI-TOF-MS analyses indicated that BsLPMO10A dominantly liberated native oligosaccharides with a degree of polymerization (DP) of 3-6 and C1-oxidized oligosaccharides ranging from DP3ox to DP6ox from mixed linkage glucans and beechwood xylan. Due to its synergistic action with a variety of glycoside hydrolases, including glucanase IDSGLUC5-38, xylanase TfXYN11-1, cellulase IDSGLUC5-11 and chitinase BtCHI18-1, BsLPMO10A dramatically accelerated glucan, xylan, cellulose and chitin saccharification. After co-reaction for 72 h, the reducing sugars in Icelandic moss lichenan, beechwood xylan, phosphoric acid swollen cellulose and chitin yielded 3176 ± 97, 7436 ± 165, 649 ± 44, and 2604 ± 130 μmol/L, which were 1.47-, 1.56-, 1.44- and 1.25-fold higher than those in the GHs alone groups, respectively (P < 0.001). In addition, the synergy of BsLPMO10A and GHs was further validated by the degradation of natural feedstuffs, the co-operation of BsLPMO10A and GHs released 3266 ± 182 and 1725 ± 107 μmol/L of reducing sugars from Oryza sativa L. and Arachis hypogaea L. straws, respectively, which were significantly higher than those produced by GHs alone (P < 0.001). Furthermore, BsLPMO10A also accelerated the liberation of reducing sugars from Celluclast® 1.5 L, a commercial cellulase cocktail, on filter paper, A. hypogaea L. and O. sativa L. straws by 49.58 % (P < 0.05), 72.19 % (P < 0.001) and 54.36 % (P < 0.05), respectively. This work has characterized BsLPMO10A with a broad active-substrate scope, providing a promising candidate for lignocellulosic biomass biorefinery.
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Affiliation(s)
- Xiao-Bao Sun
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - De-Ying Gao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jia-Wen Cao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhou-Ting Rong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Jia-Kun Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qian Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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13
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Nathawat R, Maku RV, Patel HK, Sankaranarayanan R, Sonti RV. Role of the FnIII domain associated with a cell wall-degrading enzyme cellobiosidase of Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT PATHOLOGY 2022; 23:1011-1021. [PMID: 35278018 PMCID: PMC9190976 DOI: 10.1111/mpp.13205] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Cellobiosidase (CbsA) is an important secreted virulence factor of Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight of rice. CbsA is one of several cell wall-degrading enzymes secreted by Xoo via the type II secretion system (T2SS). CbsA is considered a fundamental virulence factor for vascular pathogenesis. CbsA has an N-terminal glycosyl hydrolase domain and a C-terminal fibronectin type III (FnIII) domain. Interestingly, the secreted form of CbsA lacks the FnIII domain during in planta growth. Here we show that the presence of the FnIII domain inhibits the enzyme activity of CbsA on polysaccharide substrates like carboxymethylcellulose. The FnIII domain is required for the interaction of CbsA with SecB chaperone, and this interaction is crucial for the stability and efficient transport of CbsA across the inner membrane. Deletion of the FnIII domain reduced virulence similar to ΔcbsA Xoo, which corroborates the importance of the FnIII domain in CbsA. Our work elucidates a hitherto unknown function of the FnIII domain in enabling the virulence-promoting activity of CbsA.
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Affiliation(s)
| | - Roshan V. Maku
- CSIR – Centre for Cellular and Molecular BiologyHyderabadIndia
- Present address:
DBT – National Institute of Animal BiotechnologyHyderabadIndia
| | | | | | - Ramesh V. Sonti
- CSIR – Centre for Cellular and Molecular BiologyHyderabadIndia
- Present address:
Indian Institute of Science Education and Research TirupatiTirupatiIndia
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14
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De Novo Metagenomic Analysis of Microbial Community Contributing in Lignocellulose Degradation in Humus Samples Harvested from Cuc Phuong Tropical Forest in Vietnam. DIVERSITY 2022. [DOI: 10.3390/d14030220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We aimed to investigate the microbial diversity, mine lignocellulose-degrading enzymes/proteins, and analyze the domain structures of the mined enzymes/proteins in humus samples collected from the Cuc Phuong National Park, Vietnam. Using a high-throughput Illumina sequencer, 52 Gbs of microbial DNA were assembled in 2,611,883 contigs, from which 4,104,872 open reading frames (ORFs) were identified. Among the total microbiome analyzed, bacteria occupied 99.69%; the five ubiquitous bacterial phyla included Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Acidobacteria, which accounted for 92.59%. Proteobacteria (75.68%), the most dominant, was 5.77 folds higher than the second abundant phylum Bacteroidetes (13.11%). Considering the enzymes/proteins involved in lignocellulose degradation, 22,226 ORFs were obtained from the annotation analysis using a KEGG database. The estimated ratio of Proteobacteria/Bacteroidetes was approximately 1:1 for pretreatment and hemicellulases groups and 2.4:1 for cellulases. Furthermore, analysis of domain structures revealed their diversity in lignocellulose-degrading enzymes. CE and PL were two main families in pretreatment; GH1 and GH3-FN3 were the highest domains in the cellulase group, whereas GH2 and GH43 represented the hemicellulase group. These results validate that natural tropical forest soil could be considered as an important source to explore bacteria and novel enzymes/proteins for the degradation of lignocellulose.
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15
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Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, Armengaud J, Chapon V. Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. THE ISME JOURNAL 2022; 16:705-716. [PMID: 34556817 PMCID: PMC8857325 DOI: 10.1038/s41396-021-01113-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.
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Affiliation(s)
- Nicolas Gallois
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Béatrice Alpha-Bazin
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Nicolas Bremond
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Philippe Ortet
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Laurie Piette
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Abbas Mohamad Ali
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - David Lemaire
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Pierre Legrand
- grid.426328.9Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192 Gif-sur-Yvette, France
| | - Nicolas Theodorakopoulos
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France ,grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Magali Floriani
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Laureline Février
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Christophe Den Auwer
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
| | - Pascal Arnoux
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Catherine Berthomieu
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Jean Armengaud
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Virginie Chapon
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France.
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16
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Xing M, Wang Y, Zhao Y, Chi Z, Chi Z, Liu G. C-Terminal Bacterial Immunoglobulin-like Domain of κ-Carrageenase Serves as a Multifunctional Module to Promote κ-Carrageenan Hydrolysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1212-1222. [PMID: 35057622 DOI: 10.1021/acs.jafc.1c07233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
κ-Carrageenase is an important component for κ-carrageenan oligosaccharide production. Generally, noncatalytic domains are appended to carbohydrate-active domains and potentiate catalytic activity. However, studies devoted to κ-carrageenase are relatively few. Here, a C-terminal bacterial immunoglobulin-like domain (Big_2) was identified in κ-carrageenase (PpCgk) from Pseudoalteromonas porphyrae. Biochemical characterization of native PpCgk and its two truncations, PpCgkCD (catalytic domain) and PpBig_2 (Big_2 domain), revealed that the specific activity, catalytic efficiency (kcat/Km(app)), specific κ-carrageenan-binding capacity, and thermostability of PpCgk were significantly higher than those of PpCgkCD, suggesting that the noncatalytic PpBig_2 domain is a multifunctional module and essential for maintaining the activity and thermostability of PpCgk. Furthermore, it was found that the mode of action of PpCgk was more processive on both the dissolved and gelled substrates than that of PpCgkCD, indicating that PpBig_2 contributes to the processivity of PpCgk. Interestingly, PpBig_2 can be used as an independent module to enhance the hydrolysis of κ-carrageenan through its disruptive function. In addition, sequence analysis suggests that Big_2 domains are highly conserved in bacterial κ-carrageenases, implying the universality of their noncatalytic functions. These findings reveal the multifunctional role of the noncatalytic PpBig_2 and will guide future functional analyses and biotechnology applications of Big_2 domains.
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Affiliation(s)
- Mengdan Xing
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yan Wang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yujuan Zhao
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Zhe Chi
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Zhenming Chi
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Guanglei Liu
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
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17
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van Leeuwen HC, Roelofs D, Corver J, Hensbergen P. Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100024. [PMID: 34841315 PMCID: PMC8610288 DOI: 10.1016/j.crmicr.2021.100024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial Pro-Pro-endopeptidase (PPEP) is the latest member of the metalloendopeptidase class (E.C. 3.4.24.89). PPEP homologs are found in two firmicutes orders, clostridiales and bacillales spread over 9 genera and more than 130 species. Some PPEP homologs have acquired additional anchor domains that bind noncovalently to various elements of the bacterial peptidoglycan cell wall. Prototype family members, PPEP-1 and PPEP-2, target bacterial surface adhesion proteins, but homologs could target other extracellular proteins.
Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by Clostridioides difficile, a human pathogen, and Paenibacillus alvei, a bee secondary invader, respectively. Both proteases seem to be involved in mediating bacterial adhesion by cleaving cell surface anchor proteins on the bacterium itself. By using basic alignment and phylogenetic profiling analysis, this work shows that the complete family of proteins that contain a PPEP domain includes proteins from more than 130 species spread over 9 genera. These analyses also suggest that the PPEP domain spread through horizontal gene transfer events between species within the Firmicutes’ classes Bacilli and Clostridia. Bacterial species containing PPEP homologs are found in diverse habitats, varying from human pathogens and gut microbiota to free-living bacteria, which were isolated from various environments, including extreme conditions such as hot springs, desert soil and salt lakes. The phylogenetic tree reveals the relationships between family members and suggests that smaller subgroups could share cleavage specificity, substrates and functional similarity. Except for PPEP-1 and PPEP-2, no cleavage specificity, specific physiological target, or function has been assigned for any of the other PPEP-family members. Some PPEP proteins have acquired additional domains that recognize and bind noncovalently to various elements of the bacterial peptidoglycan cell-wall, anchoring these PPEPs. Secreted or anchored to the cell-wall surface PPEP proteins seem to perform various functions.
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Affiliation(s)
- Hans C van Leeuwen
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, the Netherlands
| | - Dick Roelofs
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands
| | - Jeroen Corver
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - Paul Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
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18
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Coexpression of a β-d-Xylosidase from Thermotoga maritima and a Family 10 Xylanase from Acidothermus cellulolyticus Significantly Improves the Xylan Degradation Activity of the Caldicellulosiruptor bescii Exoproteome. Appl Environ Microbiol 2021; 87:e0052421. [PMID: 33990300 DOI: 10.1128/aem.00524-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caldicellulosiruptor species are hyperthermophilic, Gram-positive anaerobes and the most thermophilic cellulolytic bacteria so far described. They have been engineered to convert switchgrass to ethanol without pretreatment and represent a promising platform for the production of fuels, chemicals, and materials from plant biomass. Xylooligomers, such as xylobiose and xylotriose, that result from the breakdown of plant biomass more strongly inhibit cellulase activity than do glucose or cellobiose. High concentrations of xylobiose and xylotriose are present in C. bescii fermentations after 90 h of incubation, and removal or breakdown of these types of xylooligomers is crucial to achieving high conversion of plant biomass to product. In previous studies, the addition of exogenous β-d-xylosidase substantially improved the performance of glucanases and xylanases in vitro. β-d-Xylosidases are, in fact, essential enzymes in commercial preparations for efficient deconstruction of plant biomass. In addition, the combination of xylanase and β-d-xylosidase is known to exhibit synergistic action on xylan degradation. In spite of its ability to grow efficiently on xylan substrates, no extracellular β-d-xylosidase was identified in the C. bescii genome. Here, we report that the coexpression of a thermal stable β-d-xylosidase from Thermotoga maritima and a xylanase from Acidothermus cellulolyticus in a C. bescii strain containing the A. cellulolyticus E1 endoglucanase significantly increased the activity of the exoproteome as well as growth on xylan substrates. The combination of these enzymes also resulted in increased growth on crystalline cellulose in the presence of exogenous xylan. IMPORTANCE Caldicellulosiruptor species are bacteria that grow at extremely high temperature, more than 75°C, and are the most thermophilic bacteria so far described that are capable of growth on plant biomass. This native ability allows the use of unpretreated biomass as a growth substrate, eliminating the prohibitive cost of preprocessing/pretreatment of the biomass. They only grow under strictly anaerobic conditions, and the combination of high temperature and the lack of oxygen reduces the cost of fermentation and contamination by other microbes. They have been genetically engineered to convert switchgrass to ethanol without pretreatment and represent a promising platform for the production of fuels, chemicals, and materials from plant biomass. In this study, we introduced genes from other cellulolytic bacteria and identified a combination of enzymes that improves growth on plant biomass. An important feature of this study is that it measures growth, validating predictions made from adding enzyme mixtures to biomass.
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Nguyen KHV, Dao TK, Nguyen HD, Nguyen KH, Nguyen TQ, Nguyen TT, Nguyen TMP, Truong NH, Do TH. Some characters of bacterial cellulases in goats' rumen elucidated by metagenomic DNA analysis and the role of fibronectin 3 module for endoglucanase function. Anim Biosci 2021; 34:867-879. [PMID: 32882773 PMCID: PMC8100471 DOI: 10.5713/ajas.20.0115] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/19/2020] [Indexed: 12/20/2022] Open
Abstract
Objective Fibronectin 3 (FN3) and immunoglobulin like modules (Ig) are usually collocated beside modular cellulase catalytic domains. However, very few researches have investigated the role of these modules. In a previous study, we have sequenced and analyzed bacterial metagenomic DNA in Vietnamese goats’ rumen and found that cellulase-producing bacteria and cellulase families were dominant. In this study, the properties of modular cellulases and the role of a FN3 in unique endoglucanase belonging to glycosyl hydorlase (GH) family 5 were determined. Methods Based on Pfam analysis, the cellulases sequences containing FN3, Ig modules were extracted from 297 complete open reading frames (ORFs). The alkaline, thermostability, tertiary structure of deduced enzymes were predicted by AcalPred, TBI software, Phyre2 and Swiss models. Then, whole and truncated forms of a selected gene were expressed in Escherichia coli and purified by His-tag affinity column for assessment of FN3 ability to enhance enzyme activity, solubility and conformation. Results From 297 complete ORFs coding for cellulases, 148 sequences containing FN3, Ig were identified. Mostly FN3 appeared in 90.9% beta-glucosidases belonging to glycosyl hydrolase family 3 (GH3) and situated downstream of catalytic domains. The Ig was found upstream of 100% endoglucanase GH9. Rarely FN3 was seen to be situated downstream of X domain and upstream of catalytic domain endoglucanase GH5. Whole enzyme (called XFN3GH5 based on modular structure) and truncate forms FN3, XFN3, FN3GH5, GH5 were cloned in pET22b (+) and pET22SUMO to be expressed in single and fusion forms with a small ubiquitin-related modifier partner (S). The FN3, SFN3 increased GH5 solubility in FN3GH5, SFN3GH5. The SFN3 partly served for GH5 conformation in SFN3GH5, increased modules interaction and enzyme-soluble substrate affinity to enhance SXFN3GH5, SFN3GH5 activities in mixtures. Both SFN3 and SXFN3 did not anchor enzyme on filter paper but exfoliate and separate cellulose chains on filter paper for enzyme hydrolysis. Conclusion Based on these findings, the presence of FN3 module in certain cellulases was confirmed and it assisted for enzyme conformation and activity in both soluble and insoluble substrate.
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Pineau C, Guschinskaya N, Gonçalves IR, Ruaudel F, Robert X, Gouet P, Ballut L, Shevchik VE. Structure-function analysis of pectate lyase Pel3 reveals essential facets of protein recognition by the bacterial type 2 secretion system. J Biol Chem 2021; 296:100305. [PMID: 33465378 PMCID: PMC7949064 DOI: 10.1016/j.jbc.2021.100305] [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: 11/10/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/02/2022] Open
Abstract
The type II secretion system (T2SS) transports fully folded proteins of various functions and structures through the outer membrane of Gram-negative bacteria. The molecular mechanisms of substrate recruitment by T2SS remain elusive but a prevailing view is that the secretion determinants could be of a structural nature. The phytopathogenic γ-proteobacteria, Pectobacterium carotovorum and Dickeya dadantii, secrete similar sets of homologous plant cell wall degrading enzymes, mainly pectinases, by similar T2SSs, called Out. However, the orthologous pectate lyases Pel3 and PelI from these bacteria, which share 67% of sequence identity, are not secreted by the counterpart T2SS of each bacterium, indicating a fine-tuned control of protein recruitment. To identify the related secretion determinants, we first performed a structural characterization and comparison of Pel3 with PelI using X-ray crystallography. Then, to assess the biological relevance of the observed structural variations, we conducted a loop-substitution analysis of Pel3 combined with secretion assays. We showed that there is not one element with a definite secondary structure but several distant and structurally flexible loop regions that are essential for the secretion of Pel3 and that these loop regions act together as a composite secretion signal. Interestingly, depending on the crystal contacts, one of these key secretion determinants undergoes disorder-to-order transitions that could reflect its transient structuration upon the contact with the appropriate T2SS components. We hypothesize that such T2SS-induced structuration of some intrinsically disordered zones of secretion substrates could be part of the recruitment mechanism used by T2SS.
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Affiliation(s)
- Camille Pineau
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France; Microbiologie Adaptation et Pathogénie, Univ Lyon, INSA Lyon, UMR5240, Villeurbanne, France
| | - Natalia Guschinskaya
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France; Microbiologie Adaptation et Pathogénie, Univ Lyon, INSA Lyon, UMR5240, Villeurbanne, France
| | - Isabelle R Gonçalves
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France
| | - Florence Ruaudel
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France
| | - Xavier Robert
- Molecular Microbiology and Structural Biochemistry, Univ Lyon, UMR5086 CNRS, Lyon, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry, Univ Lyon, UMR5086 CNRS, Lyon, France
| | - Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, Univ Lyon, UMR5086 CNRS, Lyon, France.
| | - Vladimir E Shevchik
- Microbiologie Adaptation et Pathogénie, Univ Lyon, Université de Lyon 1, UMR5240 CNRS, Villeurbanne, France; Microbiologie Adaptation et Pathogénie, Univ Lyon, INSA Lyon, UMR5240, Villeurbanne, France.
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21
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Souto BDM, de Araújo ACB, Hamann PRV, Bastos ADR, Cunha IDS, Peixoto J, Kruger RH, Noronha EF, Quirino BF. Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase. PLoS One 2021; 16:e0245118. [PMID: 33449963 PMCID: PMC7810302 DOI: 10.1371/journal.pone.0245118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022] Open
Abstract
Functional screening of metagenomic libraries is an effective approach for identification of novel enzymes. A Caatinga biome goat rumen metagenomic library was screened using esculin as a substrate, and a gene from an unknown bacterium encoding a novel GH3 enzyme, BGL11, was identified. None of the BGL11 closely related genes have been previously characterized. Recombinant BGL11 was obtained and kinetically characterized. Substrate specificity of the purified protein was assessed using seven synthetic aryl substrates. Activity towards nitrophenyl-β-D-glucopyranoside (pNPG), 4-nitrophenyl-β-D-xylopyranoside (pNPX) and 4-nitrophenyl-β-D-cellobioside (pNPC) suggested that BGL11 is a multifunctional enzyme with β-glucosidase, β-xylosidase, and cellobiohydrolase activities. However, further testing with five natural substrates revealed that, although BGL11 has multiple substrate specificity, it is most active towards xylobiose. Thus, in its native goat rumen environment, BGL11 most likely functions as an extracellular β-xylosidase acting on hemicellulose. Biochemical characterization of BGL11 showed an optimal pH of 5.6, and an optimal temperature of 50°C. Enzyme stability, an important parameter for industrial application, was also investigated. At 40°C purified BGL11 remained active for more than 15 hours without reduction in activity, and at 50°C, after 7 hours of incubation, BGL11 remained 60% active. The enzyme kinetic parameters of Km and Vmax using xylobiose were determined to be 3.88 mM and 38.53 μmol.min-1.mg-1, respectively, and the Kcat was 57.79 s-1. In contrast to BLG11, most β-xylosidases kinetically studied belong to the GH43 family and have been characterized only using synthetic substrates. In industry, β-xylosidases can be used for plant biomass deconstruction, and the released sugars can be fermented into valuable bio-products, ranging from the biofuel ethanol to the sugar substitute xylitol.
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Affiliation(s)
| | | | | | | | - Isabel de Souza Cunha
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Julianna Peixoto
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
| | - Ricardo Henrique Kruger
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
| | - Eliane Ferreira Noronha
- Department of Cellular Biology, Laboratory of Enzymology, Universidade de Brasília, Brasília, DF, Brazil
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Aymé L, Hébert A, Henrissat B, Lombard V, Franche N, Perret S, Jourdier E, Heiss-Blanquet S. Characterization of three bacterial glycoside hydrolase family 9 endoglucanases with different modular architectures isolated from a compost metagenome. Biochim Biophys Acta Gen Subj 2021; 1865:129848. [PMID: 33460770 DOI: 10.1016/j.bbagen.2021.129848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Environmental bacteria express a wide diversity of glycoside hydrolases (GH). Screening and characterization of GH from metagenomic sources provides an insight into biomass degradation strategies of non-cultivated prokaryotes. METHODS In the present report, we screened a compost metagenome for lignocellulolytic activities and identified six genes encoding enzymes belonging to family GH9 (GH9a-f). Three of these enzymes (GH9b, GH9d and GH9e) were successfully expressed and characterized. RESULTS A phylogenetic analysis of the catalytic domain of pro- and eukaryotic GH9 enzymes suggested the existence of two major subgroups. Bacterial GH9s displayed a wide variety of modular architectures and those harboring an N-terminal Ig-like domain, such as GH9b and GH9d, segregated from the remainder. We purified and characterized GH9 endoglucanases from both subgroups and examined their stabilities, substrate specificities and product profiles. GH9e exhibited an original hydrolysis pattern, liberating an elevated proportion of oligosaccharides longer than cellobiose. All of the enzymes exhibited processive behavior and a synergistic action on crystalline cellulose. Synergy was also evidenced between GH9d and a GH48 enzyme identified from the same metagenome. CONCLUSIONS The characterized GH9 enzymes displayed different modular architectures and distinct substrate and product profiles. The presence of a cellulose binding domain was shown to be necessary for binding and digestion of insoluble cellulosic substrates, but not for processivity. GENERAL SIGNIFICANCE The identification of six GH9 enzymes from a compost metagenome and the functional variety of three characterized members highlight the importance of this enzyme family in bacterial biomass deconstruction.
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Affiliation(s)
- Laure Aymé
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Agnès Hébert
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France
| | - Nathalie Franche
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Stéphanie Perret
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Etienne Jourdier
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France.
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Lima RAT, De Oliveira G, Souza AA, Lopes FAC, Santana RH, Istvan P, Quirino BF, Barbosa J, De Freitas S, Garay AV, Krüger RH. Functional and structural characterization of a novel GH3 β-glucosidase from the gut metagenome of the Brazilian Cerrado termite Syntermes wheeleri. Int J Biol Macromol 2020; 165:822-834. [PMID: 33011259 DOI: 10.1016/j.ijbiomac.2020.09.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022]
Abstract
In this study, a GH3 family β-glucosidase (Bgl7226) from metagenomic sequences of the Syntermes wheeleri gut, a Brazilian Cerrado termite, was expressed, purified and characterized. The enzyme showed two optimum pHs (pH 7 and pH 10), and a maximum optimum temperature of about 40 °C using 4-Nitrophenyl β-D-glucopyranoside (pNPG) as substrate. Bgl7226 showed higher enzymatic activity at basic pH, but higher affinity (Km) at neutral pH. However, at neutral pH the Bgl7226 enzyme showed higher catalytic efficiency (kcat/Km) for pNPG substrate. Predictive analysis about the enzyme structure-function relationship by sequence alignment suggested the presence of multi-domains and conserved catalytic sites. Circular dichroism results showed that the secondary structure composition of the enzyme is pH-dependent. Small conformational changes occurred close to the optimum temperature of 40 o C, and seem important for the highest activity of Bgl7226 observed at pH 7 and 10. In addition, the small transition in the unfolding curves close to 40 o C is typical of intermediates associated with proteins structured in several domains. Bgl7226 has significant β-glucosidase activity which could be attractive for biotechnological applications, such as plant roots detoxification; specifically, our group is interested in cassava roots (Manihot esculenta) detoxification.
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Affiliation(s)
| | - Gideane De Oliveira
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Amanda Araújo Souza
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | | | - Renata Henrique Santana
- Instituto Federal de Brasília, Planaltina Campus, Brasília, DF 70910-900, Brazil; Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil
| | - Paula Istvan
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil; Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben- Gurion University of the Negev, Department of Environmental Hydrology & Microbiology, Israel
| | - Betania Ferraz Quirino
- Embrapa Agroenergy, Parque Estação Biológica (PqEB), PqEB s/n°, Brasília, DF 70770-901, Brazil
| | - João Barbosa
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Sonia De Freitas
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Aisel Valle Garay
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Ricardo Henrique Krüger
- Department of Cell Biology, Darcy Ribeiro Campus, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
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Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology. Comput Struct Biotechnol J 2020; 18:2744-2756. [PMID: 33101612 PMCID: PMC7560691 DOI: 10.1016/j.csbj.2020.09.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 01/03/2023] Open
Abstract
Genome-wide characterization of GH families is conducted for Mollusca. GH9, GH10, GH18 and GH20 families are remarkably expanded in molluscs. The wide adoption of CBMs likely facilitates the hydrolysis of polysaccharides. Hepatopancreas is the main organ for the prominent expression of GH families. Functional divergence of GH families possibly contributes to their adaptive roles.
The hydrolysis of sugar-containing compounds by glycoside hydrolases (GHs) plays essential roles in many major biological processes, but to date our systematic understanding of the functional diversity and evolution of GH families remains largely limited to a few well-studied terrestrial animals. Molluscs represent the largest marine phylum in the animal kingdom, and many of them are herbivorous that utilize algae as a main nutritional source, making them good subjects for studying the functional diversity and adaptive evolution of GH families. In the present study, we conducted genome-wide identification and functional and evolutionary analysis of all GH families across major molluscan lineages. We revealed that the remarkable expansion of the GH9, GH10, GH18 and GH20 families and the wide adoption of carbohydrate-binding modules in molluscan expanded GH families likely contributed to the efficient hydrolysis of marine algal polysaccharides and were involved in the consolidation of molluscan algae-feeding habits. Gene expression and network analysis revealed the hepatopancreas as the main organ for the prominent expression of approximately half of the GH families (well corresponding to the digestive roles of the hepatopancreas) and key or hub GHs in the coexpression gene network with potentially diverse functionalities. We also revealed the evolutionary signs of differential expansion and functional divergence of the GH family, which possibly contributed to lineage-specific adaptation. Systematic analysis of GH families at both genomic and transcriptomic levels provides important clues for understanding the functional divergence and evolution of GH gene families in molluscs in relation to their algae-feeding biology.
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25
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Srivastava S, Dafale NA, Purohit HJ. Functional genomics assessment of lytic polysaccharide mono-oxygenase with glycoside hydrolases in Paenibacillus dendritiformis CRN18. Int J Biol Macromol 2020; 164:3729-3738. [PMID: 32835796 DOI: 10.1016/j.ijbiomac.2020.08.147] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 11/25/2022]
Abstract
Recently discovered Lytic Polysaccharide Mono-Oxygenase (LPMO) enhances the enzymatic deconstruction of complex polysaccharide by oxidation. The present study demonstrates the agricultural waste hydrolyzing capabilities of Paenibacillus dendritiformis CRN18, which exhibits the enzyme activity of exo-glucanase, β-glucosidase, β-glucuronidase, endo-1, 4 β-xylanases, arabinosidase, and α-galactosidase as 0.1U/ml, 0.3U/ml, 0.09U/ml, 0.1U/ml, 0.05U/ml, and 0.41U/ml, respectively. The genome analysis of strain reveals the presence of four LPMO genes, along with lignocellulolytic genes. The gene structure of LPMO and its phylogenetic analysis shows the evolutionary relatedness with the Bacillus LPMO gene. Gene position of LPMOs in the genome of strains shows the close association of two LPMOs with chitin active enzyme GH18, and the other two are associated with hemicellulases (GH39, GH23). Protein-protein interaction and gene networking of LPMO sheds light on the co-occurrence, neighborhood, and interaction of LPMOs with chitinase and xylanase enzymes. Structural prediction of LPMOs unravels the information of the LPMO's binding site. Although the LPMO has been explored for its oxidative mechanism, a little light has been shed on its gene structure. This study provides insights into the LPMO gene structure in P. dendritiformis CRN18 and its potential in lignocellulose hydrolysis.
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Affiliation(s)
- Shweta Srivastava
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440 020, India; AcSIR-Academy for Scientific and Innovative Research, Ghaziabad 201 002, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440 020, India; AcSIR-Academy for Scientific and Innovative Research, Ghaziabad 201 002, India.
| | - Hemant J Purohit
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur 440 020, India
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Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae. Sci Rep 2020; 10:13775. [PMID: 32792608 PMCID: PMC7426924 DOI: 10.1038/s41598-020-70749-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022] Open
Abstract
Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (β-N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism.
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27
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Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
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Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
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Limsakul P, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Poomputsa K, Kosugi A, Sakka M, Sakka K, Ratanakhanokchai K. A novel AA10 from Paenibacillus curdlanolyticus and its synergistic action on crystalline and complex polysaccharides. Appl Microbiol Biotechnol 2020; 104:7533-7550. [PMID: 32651597 DOI: 10.1007/s00253-020-10758-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/24/2020] [Indexed: 02/08/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) play an important role in the degradation of complex polysaccharides in lignocellulosic biomass. In the present study, we characterized a modular LPMO (PcAA10A), consisting of a family 10 auxiliary activity of LPMO (AA10) catalytic domain, and non-catalytic domains including a family 5 carbohydrate-binding module, two fibronectin type-3 domains, and a family 3 carbohydrate-binding module from Paenibacillus curdlanolyticus B-6, which was expressed in a recombinant Escherichia coli. Comparison of activities between full-length PcAA10A and the catalytic domain polypeptide (PcAA10A_CD) indicates that the non-catalytic domains are important for the deconstruction of crystalline cellulose and complex polysaccharides contained in untreated lignocellulosic biomass. Interestingly, PcAA10A_CD acted not only on cellulose and chitin, but also on xylan, mannan, and xylan and cellulose contained in lignocellulosic biomass, which has not been reported for the AA10 family. Mutation of the key residues, Trp51 located at subsite - 2 and Phe171 located at subsite +2, in the substrate-binding site of PcAA10A_CD revealed that these residues are substantially involved in broad substrate specificity toward cellulose, xylan, and mannan, albeit with a low effect toward chitin. Furthermore, PcAA10A had a boosting effect on untreated corn hull degradation by P. curdlanolyticus B-6 endo-xylanase Xyn10D and Clostridium thermocellum endo-glucanase Cel9A. These results suggest that PcAA10A is a unique LPMO capable of cleaving and enhancing lignocellulosic biomass degradation, making it a good candidate for biotechnological applications. KEY POINTS: • PcAA10A is a novel modular LPMO family 10 from Paenibacillus curdlanolyticus. • PcAA10A showed broad substrate specificity on β-1,4 glycosidic linkage substrates. • Non-catalytic domains are important for degrading complex polysaccharides. • PcAA10A is a unique LPMO capable of enhancing lignocellulosic biomass degradation.
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Affiliation(s)
- Puangpen Limsakul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Kanokwan Poomputsa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Makiko Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan.
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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29
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da Silva VM, Cabral AD, Sperança MA, Squina FM, Muniz JRC, Martin L, Nicolet Y, Garcia W. High-resolution structure of a modular hyperthermostable endo-β-1,4-mannanase from Thermotoga petrophila: The ancillary immunoglobulin-like module is a thermostabilizing domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140437. [PMID: 32325255 DOI: 10.1016/j.bbapap.2020.140437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/20/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022]
Abstract
The endo-β-1,4-mannanase from the hyperthermostable bacterium Thermotoga petrophila (TpMan) is an enzyme that catalyzes the hydrolysis of mannan and heteromannan polysaccharides. Of the three domains that comprise TpMan, the N-terminal GH5 catalytic domain and the C-terminal carbohydrate-binding domain are connected through a central ancillary domain of unknown structure and function. In this study, we report the partial crystal structure of the TpMan at 1.45 Å resolution, so far, the first modular hyperthermostable endo-β-1,4-mannanase structure determined. The structure exhibits two domains, a (β/α)8-barrel GH5 catalytic domain connected via a linker to the central domain with an immunoglobulin-like β-sandwich fold formed of seven β-strands. Functional analysis showed that whereas the immunoglobulin-like domain does not have the carbohydrate-binding function, it stacks on the GH5 catalytic domain acting as a thermostabilizing domain and allowing operation at hyperthermophilic conditions. The carbohydrate-binding domain is absent in the crystal structure most likely due to its high flexibility around the immunoglobulin-like domain which may act also as a pivot. These results represent new structural and functional information useful on biotechnological applications for biofuel and food industries.
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Affiliation(s)
- Viviam M da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil; Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Aline D Cabral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Marcia A Sperança
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - João Renato C Muniz
- São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil.
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30
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Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22. 3 Biotech 2020; 10:160. [PMID: 32206494 DOI: 10.1007/s13205-020-2148-z] [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: 12/02/2019] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, a bacterial strain CP22 with ability to produce cellulase, xylanase and mannanase was isolated from the oil palm compost. Based on the 16S rRNA gene analysis, the strain was affiliated to genus Micromonospora. To further investigate genes that are related to cellulose and hemicellulose degradation, the genome of strain CP22 was sequenced, annotated and analyzed. The de novo assembled genome of strain CP22 featured a size of 5,856,203 bp with G + C content of 70.84%. Detailed genome analysis on lignocellulose degradation revealed a total of 60 genes consisting of 47 glycoside hydrolase domains and 16 carbohydrate esterase domains predicted to be involved in cellulolytic and hemicellulolytic deconstruction. Particularly, 20 genes encode for cellulases (8 endoglucanases, 3 exoglucanases and 9 β-glucosidases) and 40 genes encode for hemicellulases (15 endo-1,4-β-xylanase, 3 β-xylosidase, 3 α-arabinofuranosidase, 10 acetyl xylan esterase, 6 polysaccharide deacetylase, 1 β-mannanase, 1 β-mannosidase and 1 α-galactosidase). Thirty-two genes encoding carbohydrate-binding modules (CBM) from six different families (CBM2, CBM4, CBM6, CBM9, CBM13 and CBM22) were present in the genome of strain CP22. These CBMs were found in 27 cellulolytic and hemicellulolytic genes, indicating their potential role in enhancing the substrate-binding capability of the enzymes. CBM2 and CBM13 are the major CBMs present in cellulases and hemicellulases (xylanases and mannanases), respectively. Moreover, a GH10 xylanase was found to contain 3 CBMs (1 CBM9 and 2 CBM22) and these CBMs were reported to bind specifically to xylan. This genome-based analysis could facilitate the exploration of this strain for lignocellulosic biomass degradation.
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31
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Chen ML, Becraft ED, Pachiadaki M, Brown JM, Jarett JK, Gasol JM, Ravin NV, Moser DP, Nunoura T, Herndl GJ, Woyke T, Stepanauskas R. Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Front Microbiol 2020; 11:376. [PMID: 32226422 PMCID: PMC7081726 DOI: 10.3389/fmicb.2020.00376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/20/2020] [Indexed: 12/31/2022] Open
Abstract
Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.
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Affiliation(s)
- Michael L Chen
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Williams College, Williamstown, MA, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, University of North Alabama, Florence, AL, United States
| | - Maria Pachiadaki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jessica K Jarett
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Josep M Gasol
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.,Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, United States
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, United States
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32
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A novel multifunctional GH9 enzyme from Paenibacillus curdlanolyticus B-6 exhibiting endo/exo functions of cellulase, mannanase and xylanase activities. Appl Microbiol Biotechnol 2020; 104:2079-2096. [DOI: 10.1007/s00253-020-10388-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022]
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33
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Zadeh Hosseingholi E, Zarrini G, Pashazadeh M, Gheibi Hayat SM, Molavi G. In Silico Identification of Probable Drug and Vaccine Candidates Against Antibiotic-Resistant Acinetobacter baumannii. Microb Drug Resist 2019; 26:456-467. [PMID: 31742478 DOI: 10.1089/mdr.2019.0236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii is known as a Gram-negative bacterium that has become one of the most important health problems due to antibiotic resistance. Today, numerous efforts are being made to find new antibiotics against this nosocomial pathogen. As an alternative solution, finding bacterial target(s), necessary for survival and spread of most resistant strains, can be a benefit exploited in drug and vaccine design. In this study, a list of extensive drug-resistant and carbapenem-resistant (multidrug resistant) A. bumannii strains with complete sequencing of genome were prepared and common hypothetical proteins (HPs) composed of more than 200 amino acids were selected. Then, a number of bioinformatics tools were combined for functional assignments of HPs using their sequence. Overall, among 18 in silico investigated proteins, the results showed that 7 proteins implicated in transcriptional regulation, pilus assembly, protein catabolism, fatty acid biosynthesis, adhesion, urea catalysis, and hydrolysis of phosphate monoesters have theoretical potential of involvement in successful survival and pathogenesis of A. baumannii. In addition, immunological analyses with prediction softwares indicated 4 HPs to be probable vaccine candidates. The outcome of this work will be helpful to find novel vaccine design candidates and therapeutic targets for A. baumannii through experimental investigations.
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Affiliation(s)
| | - Gholamreza Zarrini
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Marayam Pashazadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Seyed Mohammad Gheibi Hayat
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Science, Yazd, Iran
| | - Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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34
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Sharma A, Sharma D, Verma SK. Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190369. [PMID: 31598288 PMCID: PMC6774946 DOI: 10.1098/rsos.190369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/21/2019] [Indexed: 05/15/2023]
Abstract
Xanthomonas translucens pv. undulosa (Xtu) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant-pathogen interactions. In this study, we have employed a systematic in silico approach to study the Zn-binding proteins of Xtu. From the whole proteome of Xtu, we have identified approximately 7.9% of proteins having Zn-binding sequence and structural motifs. Further, 115 proteins were found homologous to plant-pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of Xtu which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.
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35
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Processivity and the Mechanisms of Processive Endoglucanases. Appl Biochem Biotechnol 2019; 190:448-463. [DOI: 10.1007/s12010-019-03096-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022]
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36
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Ellilä S, Bromann P, Nyyssönen M, Itävaara M, Koivula A, Paulin L, Kruus K. Cloning of novel bacterial xylanases from lignocellulose-enriched compost metagenomic libraries. AMB Express 2019; 9:124. [PMID: 31385056 PMCID: PMC6682842 DOI: 10.1186/s13568-019-0847-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/25/2019] [Indexed: 11/18/2022] Open
Abstract
Xylanases are in important class of industrial enzymes that are essential for the complete hydrolysis of lignocellulosic biomass into fermentable sugars. In the present study, we report the cloning of novel xylanases with interesting properties from compost metagenomics libraries. Controlled composting of lignocellulosic materials was used to enrich the microbial population in lignocellulolytic organisms. DNA extracted from the compost samples was used to construct metagenomics libraries, which were screened for xylanase activity. In total, 40 clones exhibiting xylanase activity were identified and the thermostability of the discovered xylanases was assayed directly from the library clones. Five genes, including one belonging to the more rare family GH8, were selected for subcloning and the enzymes were expressed in recombinant form in E. coli. Preliminary characterization of the metagenome-derived xylanases revealed interesting properties of the novel enzymes, such as high thermostability and specific activity, and differences in hydrolysis profiles. One enzyme was found to perform better than a standard Trichoderma reesei xylanase in the hydrolysis of lignocellulose at elevated temperatures.
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37
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Han Z, Shang-Guan F, Yang J. Molecular and Biochemical Characterization of a Bimodular Xylanase From Marinifilaceae Bacterium Strain SPP2. Front Microbiol 2019; 10:1507. [PMID: 31312196 PMCID: PMC6614494 DOI: 10.3389/fmicb.2019.01507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 06/17/2019] [Indexed: 01/31/2023] Open
Abstract
In this study, the first xylantic enzyme from the family Marinifilaceae, XynSPP2, was identified from Marinifilaceae bacterium strain SPP2. Amino acid sequence analysis revealed that XynSPP2 is a rare Fn3-fused xylanase, consisting of a signal peptide, a fibronectin type-III domain (Fn3), and a C-terminal catalytic domain belonging to glycoside hydrolase family 10 (GH10). The catalytic domain shared 17–46% identities to those of biochemically characterized GH10 xylanases. Structural analysis revealed that the conserved asparagine and glutamine at the glycone −2/−3 subsite of GH10 xylanases are substituted by a tryptophan and a serine, respectively, in XynSPP2. Full-length XynSPP2 and its Fn3-deleted variant (XynSPP2ΔFn3) were overexpressed in Escherichia coli and purified by Ni-affinity chromatography. The optimum temperature and pH for both recombinant enzymes were 50°C and 6, respectively. The enzymes were stable under alkaline condition and at temperature lower than 50°C. With beechwood xylan as the substrate, XynSPP2 showed 2.8 times the catalytic efficiency of XynSPP2ΔFn3, indicating that the Fn3 module promotes xylanase activity. XynSPP2 was active toward xylooligosaccharides (XOSs) longer than xylotriose. Such a substrate preference can be explained by the unique −2/−3 subsite composition in the enzyme which provides new insight into subsite interaction within the GH10 family. XynSPP2 hydrolyzed beechwood xylan into small XOSs (xylotriose and xylotetraose as major products). No monosaccharide was detected by thin-layer chromatography which may be ascribed to putative transxylosylation activity of XynSPP2. Preferring long XOS substrate and lack of monosaccharide production suggest its potential in probiotic XOS manufacture.
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Affiliation(s)
- Zhenggang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Fang Shang-Guan
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jiangke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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38
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Lam MQ, Oates NC, Thevarajoo S, Tokiman L, Goh KM, McQueen-Mason SJ, Bruce NC, Chong CS. Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter. Genomics 2019; 112:952-960. [PMID: 31201854 DOI: 10.1016/j.ygeno.2019.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/13/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
The genus Meridianimaribacter is one of the least-studied genera within Cytophaga-Flavobacteria. To date, no genomic analysis of Meridianimaribacter has been reported. In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information coupled with experimental studies confirmed the ability of strain CL38 to degrade lignocellulosic biomass. Therefore, Meridianimaribacter sp. strain CL38, with its halotolerance, could be useful for seawater based lignocellulosic biorefining.
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Affiliation(s)
- Ming Quan Lam
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, United Kingdom
| | - Suganthi Thevarajoo
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, 79575 Iskandar Puteri, Johor, Malaysia
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, United Kingdom.
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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39
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Andreou A, Giastas P, Arnaouteli S, Tzanodaskalaki M, Tzartos SJ, Bethanis K, Bouriotis V, Eliopoulos EE. The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination. Acta Crystallogr F Struct Biol Commun 2019; 75:312-320. [PMID: 30950833 PMCID: PMC6450525 DOI: 10.1107/s2053230x19001766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Ba0331 is a putative polysaccharide deacetylase from Bacillus anthracis, the etiological agent of the disease anthrax, that contributes to adaptation of the bacterium under extreme conditions and to maintenance of the cell shape. In the present study, the crystal structure of Ba0331 was determined at 2.6 Å resolution. The structure consists of two domains: a fibronectin type 3-like (Fn3-like) domain and a NodB catalytic domain. The latter is present in all carbohydrate esterase family 4 enzymes, while a comparative analysis of the Fn3-like domain revealed structural plasticity despite the retention of the conserved Fn3-like domain characteristics.
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Affiliation(s)
- Athena Andreou
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Petros Giastas
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Sofia Arnaouteli
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Mary Tzanodaskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas N. Plastira 100, 70013 Heraklion, Crete, Greece
| | - Socrates J. Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Kostas Bethanis
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Hellas N. Plastira 100, 70013 Heraklion, Crete, Greece
| | - Elias E. Eliopoulos
- Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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40
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Kim CC, Healey GR, Kelly WJ, Patchett ML, Jordens Z, Tannock GW, Sims IM, Bell TJ, Hedderley D, Henrissat B, Rosendale DI. Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon. ISME JOURNAL 2019; 13:1437-1456. [PMID: 30728469 PMCID: PMC6776006 DOI: 10.1038/s41396-019-0363-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 01/07/2019] [Accepted: 01/19/2019] [Indexed: 12/16/2022]
Abstract
Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.
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Affiliation(s)
- Caroline C Kim
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand. .,Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.
| | - Genelle R Healey
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand.,Massey Institute of Food Science and Technology, School of Food and Nutrition, Massey University, Palmerston North, New Zealand
| | | | - Mark L Patchett
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Zoe Jordens
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Gerald W Tannock
- Department of Microbiology and Immunology, Microbiome Otago, University of Otago, Dunedin, 9016, New Zealand
| | - Ian M Sims
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, Lower Hutt, 5040, New Zealand
| | - Tracey J Bell
- Ferrier Research Institute, Victoria University of Wellington, Gracefield Research Centre, Lower Hutt, 5040, New Zealand
| | - Duncan Hedderley
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, F-13288, France.,Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Douglas I Rosendale
- The New Zealand Institute for Plant and Food Research, Palmerston North, 4474, New Zealand.
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41
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Xu Q, Alahuhta M, Wei H, Knoshaug EP, Wang W, Baker JO, Vander Wall T, Himmel ME, Zhang M. Expression of an endoglucanase-cellobiohydrolase fusion protein in Saccharomyces cerevisiae, Yarrowia lipolytica, and Lipomyces starkeyi. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:322. [PMID: 30524504 PMCID: PMC6278004 DOI: 10.1186/s13068-018-1301-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 05/28/2023]
Abstract
The low secretion levels of cellobiohydrolase I (CBHI) in yeasts are one of the key barriers preventing yeast from directly degrading and utilizing lignocellulose. To overcome this obstacle, we have explored the approach of genetically linking an easily secreted protein to CBHI, with CBHI being the last to be folded. The Trichoderma reesei eg2 (TrEGII) gene was selected as the leading gene due to its previously demonstrated outstanding secretion in yeast. To comprehensively characterize the effects of this fusion protein, we tested this hypothesis in three industrially relevant yeasts: Saccharomyces cerevisiae, Yarrowia lipolytica, and Lipomyces starkeyi. Our initial assays with the L. starkeyi secretome expressing differing TrEGII domains fused to a chimeric Talaromyces emersonii-T. reesei CBHI (TeTrCBHI) showed that the complete TrEGII enzyme, including the glycoside hydrolase (GH) 5 domain is required for increased expression level of the fusion protein when linked to CBHI. We found that this new construct (TrEGII-TeTrCBHI, Fusion 3) had an increased secretion level of at least threefold in L. starkeyi compared to the expression level of the chimeric TeTrCBHI. However, the same improvements were not observed when Fusion 3 construct was expressed in S. cerevisiae and Y. lipolytica. Digestion of pretreated corn stover with the secretomes of Y. lipolytica and L. starkeyi showed that conversion was much better using Y. lipolytica secretomes (50% versus 29%, respectively). In Y. lipolytica, TeTrCBHI performed better than the fusion construct. Furthermore, S. cerevisiae expression of Fusion 3 construct was poor and only minimal activity was observed when acting on the substrate, pNP-cellobiose. No activity was observed for the pNP-lactose substrate. Clearly, this approach is not universally applicable to all yeasts, but works in specific cases. With purified protein and soluble substrates, the exoglucanase activity of the GH7 domain embedded in the Fusion 3 construct in L. starkeyi was significantly higher than that of the GH7 domain in TeTrCBHI expressed alone. It is probable that a higher fraction of fusion construct CBHI is in an active form in Fusion 3 compared to just TeTrCBHI. We conclude that the strategy of leading TeTrCBHI expression with a linked TrEGII module significantly improved the expression of active CBHI in L. starkeyi.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Eric P. Knoshaug
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - John O. Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
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Tayi L, Kumar S, Nathawat R, Haque AS, Maku RV, Patel HK, Sankaranarayanan R, Sonti RV. A mutation in an exoglucanase of Xanthomonas oryzae pv. oryzae, which confers an endo mode of activity, affects bacterial virulence, but not the induction of immune responses, in rice. MOLECULAR PLANT PATHOLOGY 2018; 19:1364-1376. [PMID: 28976110 PMCID: PMC6638110 DOI: 10.1111/mpp.12620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/16/2017] [Accepted: 09/29/2017] [Indexed: 05/08/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, a serious disease of rice. Xoo secretes a repertoire of cell wall-degrading enzymes, including cellulases, xylanases and pectinases, to degrade various polysaccharide components of the rice cell wall. A secreted Xoo cellulase, CbsA, is not only a key virulence factor of Xoo, but is also a potent inducer of innate immune responses of rice. In this study, we solved the crystal structure of the catalytic domain of the CbsA protein to a resolution of 1.86 Å. The core structure of CbsA shows a central distorted TIM barrel made up of eight β strands with N- and C-terminal loops enclosing the active site, which is a characteristic structural feature of an exoglucanase. The aspartic acid at the 131st position of CbsA was predicted to be important for catalysis and was therefore mutated to alanine to study its role in the catalysis and biological functions of CbsA. Intriguingly, the D131A CbsA mutant protein displayed the enzymatic activity of a typical endoglucanase. D131A CbsA was as proficient as wild-type (Wt) CbsA in inducing rice immune responses, but was deficient in virulence-promoting activity. This indicates that the specific exoglucanase activity of the Wt CbsA protein is required for this protein to promote the growth of Xoo in rice.
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Affiliation(s)
- Lavanya Tayi
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
- Present address:
Centre for Plant Molecular BiologyOsmania UniversityHyderabad 500007India
| | - Sushil Kumar
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
- Present address:
Institute of Life SciencesNalco SquareBhuvaneshwar 751023India
| | | | - Asfarul S. Haque
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
- Present address:
Department of BiochemistryMcGill UniversityMontréalQC H3G 0B1Canada
| | - Roshan V. Maku
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
| | | | | | - Ramesh V. Sonti
- CSIR‐Centre for Cellular and Molecular BiologyHyderabad 500007India
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43
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GH43 endo-arabinanase from Bacillus licheniformis: Structure, activity and unexpected synergistic effect on cellulose enzymatic hydrolysis. Int J Biol Macromol 2018; 117:7-16. [PMID: 29800670 DOI: 10.1016/j.ijbiomac.2018.05.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/19/2018] [Accepted: 05/22/2018] [Indexed: 01/30/2023]
Abstract
The hydrolysis of the plant biomass provides many interesting opportunities for the generation of building blocks for the green chemistry industrial applications. An important progress has been made for the hydrolysis of the cellulosic component of the biomass while, for the hemicellulosic components, the advances are less straightforward. Here, we describe the cloning, expression and biochemical and structural characterization of BlAbn1, a GH43 arabinanase from Bacillus licheniformis. This enzyme is selective for linear arabinan and efficiently hydrolyzes this substrate, with a specific activity of 127 U/mg. The enzyme has optimal conditions for activity at pH 8.0 and 45 °C and its activity is only partially dependent of a bound calcium ion since 70% of the maximal activity is preserved even when 1 mM EDTA is added to the reaction medium. BlAbn1 crystal structure revealed a typical GH43 fold and narrow active site, which explains the selectivity for linear substrates. Unexpectedly, the enzyme showed a synergic effect with the commercial cocktail Accellerase 1500 on cellulose hydrolysis. Scanning Electron Microscopy, Solid-State NMR and relaxometry data indicate that the enzyme weakens the interaction between cellulose fibers in filter paper, thus providing an increased access to the cellulases of the cocktail.
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44
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Structural and biochemical characterization of a GH3 β-glucosidase from the probiotic bacteria Bifidobacterium adolescentis. Biochimie 2018; 148:107-115. [DOI: 10.1016/j.biochi.2018.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/13/2018] [Indexed: 11/20/2022]
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45
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Do TH, Le NG, Dao TK, Nguyen TMP, Le TL, Luu HL, Nguyen KHV, Nguyen VL, Le LA, Phung TN, van Straalen NM, Roelofs D, Truong NH. Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats' rumen. J GEN APPL MICROBIOL 2018. [PMID: 29526926 DOI: 10.2323/jgam.2017.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats' rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes' modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.
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Affiliation(s)
- Thi Huyen Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology
| | - Ngoc Giang Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology.,Department of Ecological Science, Vrije Universiteit Amsterdam
| | - Trong Khoa Dao
- Institute of Biotechnology, Vietnam Academy of Science and Technology.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology
| | | | - Tung Lam Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology
| | - Han Ly Luu
- Institute of Biotechnology, Vietnam Academy of Science and Technology
| | - Khanh Hoang Viet Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology.,Institute of New Technology/Academy of Military Science and Technology
| | - Van Lam Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology
| | - Lan Anh Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology
| | - Thu Nguyet Phung
- Institute of Biotechnology, Vietnam Academy of Science and Technology
| | | | - Dick Roelofs
- Department of Ecological Science, Vrije Universiteit Amsterdam
| | - Nam Hai Truong
- Institute of Biotechnology, Vietnam Academy of Science and Technology.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology
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46
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Akram F, Haq IU, Mukhtar H. Gene cloning, characterization and thermodynamic analysis of a novel multidomain hyperthermophilic GH family 3 β-glucosidase (TnBglB) from Thermotoga naphthophila RKU-10T. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47
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Spertino S, Boatti L, Icardi S, Manfredi M, Cattaneo C, Marengo E, Cavaletto M. Cellulomonas fimi secretomes: In vivo and in silico approaches for the lignocellulose bioconversion. J Biotechnol 2018; 270:21-29. [PMID: 29409863 DOI: 10.1016/j.jbiotec.2018.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/30/2017] [Accepted: 01/26/2018] [Indexed: 12/17/2022]
Abstract
Lignocellulose degradation is a challenging step for value added products and biofuels production. Cellulomonas fimi secretes complex mixtures of carbohydrate active enzymes (CAZymes) which synergistically degrade cellulose and hemicelluloses. Their characterization may provide new insights for enzymatic cocktails implementation. Bioinformatic analysis highlighted 1127 secreted proteins, constituting the in silico secretome, graphically represented in a 2DE map. According to Blast2GO functional annotation, many of these are involved in carbohydrates metabolism. In vivo secretomes were obtained, growing C. fimi on glucose, CMC or wheat straw for 24 h. Zymography revealed degradative activity on carbohydrates and proteomic analysis identified some CAZymes, only in secretomes obtained with CMC and wheat straw. An interaction between cellobiohydrolases is proposed as a strategy adopted by soluble multimodular cellulases. Such approach can be crucial for a better characterization and industrial exploitation of the synergism among C. fimi enzymes.
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Affiliation(s)
- Stefano Spertino
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy.
| | - Lara Boatti
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Sara Icardi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Marcello Manfredi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy; ISALIT S.r.l., Novara, Italy
| | - Chiara Cattaneo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Maria Cavaletto
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
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48
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Juárez-Hernández EO, Casados-Vázquez LE, Bideshi DK, Salcedo-Hernández R, Barboza-Corona JE. Role of the C-terminal and chitin insertion domains on enzymatic activity of endochitinase ChiA74 of Bacillus thuringiensis. Int J Biol Macromol 2017; 102:52-59. [DOI: 10.1016/j.ijbiomac.2017.03.191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/30/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
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49
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Pimentel AC, Ematsu GC, Liberato MV, Paixão DA, Franco Cairo JPL, Mandelli F, Tramontina R, Gandin CA, de Oliveira Neto M, Squina FM, Alvarez TM. Biochemical and biophysical properties of a metagenome-derived GH5 endoglucanase displaying an unconventional domain architecture. Int J Biol Macromol 2017; 99:384-393. [DOI: 10.1016/j.ijbiomac.2017.02.075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 11/15/2022]
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50
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A bacterial GH6 cellobiohydrolase with a novel modular structure. Appl Microbiol Biotechnol 2017; 101:2943-2952. [PMID: 28120014 DOI: 10.1007/s00253-017-8129-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/19/2016] [Accepted: 12/28/2016] [Indexed: 02/01/2023]
Abstract
Cel6D from Paenibacillus barcinonensis is a modular cellobiohydrolase with a novel molecular architecture among glycosyl hydrolases of family 6. It contains an N-terminal catalytic domain (family 6 of glycosyl hydrolases (GH6)), followed by a fibronectin III-like domain repeat (Fn31,2) and a C-terminal family 3b cellulose-binding domain (CBM3b). The enzyme has been identified and purified showing catalytic activity on cellulosic substrates and cellodextrins, with a marked preference for phosphoric acid swollen cellulose (PASC). Analysis of mode of action of Cel6D shows that it releases cellobiose as the only hydrolysis product from cellulose. Kinetic parameters were determined on PASC showing a K m of 68.73 mg/ml and a V max of 1.73 U/mg. A series of truncated derivatives of Cel6D have been constructed and characterized. Deletion of CBM3b caused a notable reduction in hydrolytic activity, while deletion of the Fn3 domain abolished activity, as the isolated GH6 domain was not active on any of the substrates tested. Mutant enzymes Cel6D-D146A and Cel6D-D97A were constructed in the residues corresponding to the putative acid catalyst and to the network for the nucleophilic attack. The lack of activity of the mutant enzymes indicates the important role of these residues in catalysis. Analysis of cooperative activity of Cel6D with cellulases from the same producing P. barcinonensis strain reveals high synergistic activity with processive endoglucanase Cel9B on hydrolysis of crystalline substrates. The characterized cellobiohydrolase can be a good contribution for depolymerization of cellulosic substrates and for the deconstruction of native cellulose.
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