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Hui TKL, Lo ICN, Wong KKW, Tsang CTT, Tsang LM. Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs. BMC Microbiol 2024; 24:57. [PMID: 38350856 PMCID: PMC10863281 DOI: 10.1186/s12866-024-03209-4] [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: 10/07/2023] [Accepted: 01/28/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Sesarmid crabs dominate mangrove habitats as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory are not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove ecosystems. Although endogenous cellulase expressions were reported in crabs, it remains unknown if endogenous enzymes alone can complete the whole lignocellulolytic pathway, or if they also depend on the contribution from the intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach. RESULTS Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs with different dietary preferences revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab gut microbiomes have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. Herbivorous and detritivorous crabs showed highly similar CAZyme composition despite dissimilarities in taxonomic profiles observed in both groups, suggesting a stronger selection force on gut microbiota by functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of gut microbiota in supplementing nitrogen that is deficient in plant diet. CONCLUSIONS Endosymbiotic microbes play an important role in lignocellulose degradation in most crab species. Their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity in digesting mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in the crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrates.
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Affiliation(s)
- Tom Kwok Lun Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Irene Ching Nam Lo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Karen Ka Wing Wong
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chandler Tsz To Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Lee ZJ, Xie C, Ng K, Suleria HAR. Unraveling the bioactive interplay: seaweed polysaccharide, polyphenol and their gut modulation effect. Crit Rev Food Sci Nutr 2023:1-24. [PMID: 37991467 DOI: 10.1080/10408398.2023.2274453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Seaweed is rich in many unique bioactive compounds such as polyphenols and sulfated polysaccharides that are not found in terrestrial plant. The discovery of numerous biological activities from seaweed has made seaweed an attractive functional food source with the potential to be exploited for human health benefits. During food processing and digestion, cell wall polysaccharide and polyphenols commonly interact, and this may influence the nutritional properties of food. Interactions between cell wall polysaccharide and polyphenols in plant-based system has been extensively studied. However, similar interactions in seaweed have received little attention despite the vast disparity between the structural and chemical composition of plant and seaweed cell wall. This poses a challenge in extracting seaweed bioactive compounds with intact biological properties. This review aims to summarize the cell wall polysaccharide and polyphenols present in brown, red and green seaweed, and current knowledge on their potential interactions. Moreover, this review gives an overview of the gut modulation effect of seaweed polysaccharide and polyphenol.
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Affiliation(s)
- Zu Jia Lee
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Cundong Xie
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Ken Ng
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Hafiz A R Suleria
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
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Wang J, Zhao K, Li M, Fan H, Wang M, Xia S, Chen Y, Bai X, Liu Z, Ni J, Sun W, Jia X, Lai S. A Preliminary Study of the Potential Molecular Mechanisms of Individual Growth and Rumen Development in Calves with Different Feeding Patterns. Microorganisms 2023; 11:2423. [PMID: 37894081 PMCID: PMC10609084 DOI: 10.3390/microorganisms11102423] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
At present, it is common to feed calves with "Concentrate", "Concentrate + hay" and TMR "Total Mixed Rations" feeding patterns in China, which achieved well feeding efficiency, but the three feeding patterns molecular regulation mechanism in actual production is still unclear. The study aimed to explore the most suitable feeding pattern for Chinese Holstein calves to improve the rumen fermentation function and growth performance of calves. In this regard, the interactions between rumen microorganisms and host metabolism were investigated. The rumen volume and weight of calves in the GF group were significantly higher than those in the GFF and TMR groups (p < 0.05), and the rumen pH of calves in the GF group was 6.47~6.79. Metagenomics analysis revealed that the rumen microbiome of GF and GFF calves had higher relative abundances of Methanobrevibacter, Methanosphaera, and Methanolacinia (p < 0.05). Prevotella multisaccharivorax was significantly more abundant in the rumen of GF calves (p < 0.05), indicating that GF group calves had a stronger ability to ferment sugars. Notably, in the pyruvate metabolic pathway, phosphoenolpyruvate carboxylase was significantly up-regulated in GF calves compared with the TMR group, and pyruvate-phosphate dikinase was significantly down-regulated. Metabolomic results showed that Ursodeoxycholic acid was significantly up-regulated in GF calves, and most of the differential metabolites were enriched in Bile secretion pathways. The association analysis study found that the microorganisms of Prevotella and Ruminococcaceae might cooperate with the host, which was helpful for the digestion and absorption of lipids and made the calves have better growth. The three feeding modes had similar effects, but the 'GF' feeding pattern was more beneficial to the individual growth and ruminal development regarding ruminal morphology, contents physiology and microorganisms. Furthermore, the synergistic effect of rumen microorganisms and the host could more effectively hydrolyze lipid substances and promote the absorption of lipids, which was of great significance to the growth of calves.
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Affiliation(s)
- Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.W.); (W.S.); (X.J.)
| | - Kaisen Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Mianying Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Huimei Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Meigui Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Siqi Xia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Yang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Xue Bai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Zheliang Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Jiale Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (K.Z.); (M.L.); (H.F.); (S.X.)
| | - Wenqiang Sun
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.W.); (W.S.); (X.J.)
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.W.); (W.S.); (X.J.)
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.W.); (W.S.); (X.J.)
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Guo R, Zhang W, Shen W, Zhang G, Xie T, Li L, Jinmei J, Liu Y, Kong F, Guo B, Li B, Sun Y, Liu S. Analysis of gut microbiota in chinese donkey in different regions using metagenomic sequencing. BMC Genomics 2023; 24:524. [PMID: 37670231 PMCID: PMC10478257 DOI: 10.1186/s12864-023-09575-z] [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: 03/23/2023] [Accepted: 08/11/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited. RESULTS In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose. CONCLUSION According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.
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Affiliation(s)
- Rong Guo
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wei Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wei Shen
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Guoliang Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China
| | - Taifeng Xie
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ling Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jiacuo Jinmei
- Tibet Autonomous Region Animal husbandry Station, Tibet, China
| | - Yiduan Liu
- Yunnan Provincial Animal Husbandry Station, Yunnan, China
| | - Fanyong Kong
- Honghe state animal husbandry technology extension station, Honghe, Yunnan, China
| | - Baozhu Guo
- Zhangjiakou City animal husbandry technology extension station, Zhangjiakou, Hebei, China
| | - Benke Li
- Binzhou City Agricultural Technology Extension Center, Binzhou, Shandong, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China.
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China.
- Vocational College of Dongying, Dongying, Shandong, China.
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China.
- Gene Bank of Equine Genetic Resources, Qingdao, Shandong, China.
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5
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Isolation of a new strain of Aspergillus and molecular structure elucidation of unknown metabolite produced from castor oil. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2022.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Honarmandrad Z, Kucharska K, Gębicki J. Processing of Biomass Prior to Hydrogen Fermentation and Post-Fermentative Broth Management. Molecules 2022; 27:7658. [PMID: 36364485 PMCID: PMC9658980 DOI: 10.3390/molecules27217658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 09/10/2023] Open
Abstract
Using bioconversion and simultaneous value-added product generation requires purification of the gaseous and the liquid streams before, during, and after the bioconversion process. The effect of diversified process parameters on the efficiency of biohydrogen generation via biological processes is a broad object of research. Biomass-based raw materials are often applied in investigations regarding biohydrogen generation using dark fermentation and photo fermentation microorganisms. The literature lacks information regarding model mixtures of lignocellulose and starch-based biomass, while the research is carried out based on a single type of raw material. The utilization of lignocellulosic and starch biomasses as the substrates for bioconversion processes requires the decomposition of lignocellulosic polymers into hexoses and pentoses. Among the components of lignocelluloses, mainly lignin is responsible for biomass recalcitrance. The natural carbohydrate-lignin shields must be disrupted to enable lignin removal before biomass hydrolysis and fermentation. The matrix of chemical compounds resulting from this kind of pretreatment may significantly affect the efficiency of biotransformation processes. Therefore, the actual state of knowledge on the factors affecting the culture of dark fermentation and photo fermentation microorganisms and their adaptation to fermentation of hydrolysates obtained from biomass requires to be monitored and a state of the art regarding this topic shall become a contribution to the field of bioconversion processes and the management of liquid streams after fermentation. The future research direction should be recognized as striving to simplification of the procedure, applying the assumptions of the circular economy and the responsible generation of liquid and gas streams that can be used and purified without large energy expenditure. The optimization of pre-treatment steps is crucial for the latter stages of the procedure.
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Affiliation(s)
| | - Karolina Kucharska
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdansk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233 Gdansk, Poland
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Influence of hemicellulose content and cellulose crystal change on cellulose nanofibers properties. Int J Biol Macromol 2022; 213:780-790. [PMID: 35690158 DOI: 10.1016/j.ijbiomac.2022.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/25/2022] [Accepted: 06/05/2022] [Indexed: 01/09/2023]
Abstract
This study aimed to evaluate the properties of cellulose nanofibers (CNFs) with different hemicellulose contents and cellulose II polymorphs. A link was found between these polysaccharides and the properties of CNFs. A decrease in crystallinity (from 69 to 63%) and changes in the crystalline structure of cellulose subjected to an alkaline environment were observed, promoting the partial conversion of cellulose I to cellulose II (from 2 to 42%) and preventing CNFs production at NaOH concentrations higher than 5%. Most treatments showed pseudoplastic fluid behavior, except for the 10% NaOH treatment over 2 h, which showed Newtonian fluid behavior. The quality index of the reference CNFs (TEMPO-oxidized) was the highest (80 ± 3), followed by that of the 5% NaOH-treated (68 ± 3 and 22% energy savings compared to the untreated sample), and the untreated (63 ± 3) samples; and the 10% NaOH treatments had quality indices of 51 ± 3 and 32 ± 1, respectively.
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8
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Application of Enzyme-Assisted Extraction for the Recovery of Natural Bioactive Compounds for Nutraceutical and Pharmaceutical Applications. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Enzyme-assisted extraction (EAE) involves the use of hydrolytic enzymes for the degradation of the cell wall or other cell components. This supports the diffusion of the solvent into the plant or fungal material, leading to easier elution of its metabolites. This technique has been gaining increasing attention, as it is considered an eco-friendly and cost-effective improvement on classical or modern extraction methods. Its promising application in improving the recovery of different classes of bioactive metabolites (e.g., polyphenols, carotenoids, polysaccharides, proteins, components of essential oil, and terpenes) has been reported by many scientific papers. This review summarises information on the theoretical aspects of EAE (e.g., the components of the cell walls and the types of enzymes used) and the most recent discoveries in the effective involvement of enzyme-assisted extraction of natural products (plants, mushrooms, and animals) for nutraceutical and pharmaceutical applications.
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Wang S, Liang H, Wang H, Li L, Xu Y, Liu Y, Liu M, Wei J, Ma T, Le C, Yang J, He C, Liu J, Zhao J, Zhao Y, Lisby M, Sahu SK, Liu H. The chromosome-scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:538-553. [PMID: 34687252 PMCID: PMC8882806 DOI: 10.1111/pbi.13735] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 05/30/2023]
Abstract
Dipterocarpaceae are typical tropical plants (dipterocarp forests) that are famous for their high economic value because of their production of fragrant oleoresins, top-quality timber and usage in traditional Chinese medicine. Currently, the lack of Dipterocarpaceae genomes has been a limiting factor to decipher the fragrant oleoresin biosynthesis and gain evolutionary insights into high-quality wood formation in Dipterocarpaceae. We generated chromosome-level genome assemblies for two representative Dipterocarpaceae species viz. Dipterocarpus turbinatus Gaertn. f. and Hopea hainanensis Merr. et Chun. Our whole-genome duplication (WGD) analysis revealed that Dipterocarpaceae underwent a shared WGD event, which showed significant impacts on increased copy numbers of genes related to the biosynthesis of terpene, BAHD acyltransferases, fatty acid and benzenoid/phenylpropanoid, which probably confer to the formation of their characteristic fragrant oleoresin. Additionally, compared with common soft wood plants, the expansion of gene families was also found to be associated with wood formation, such as in CESA (cellulose synthase), CSLE (cellulose synthase-like protein E), laccase and peroxidase in Dipterocarpaceae genomes, which might also contribute to the formation of harder, stronger and high-density timbers. Finally, an integrative analysis on a combination of genomic, transcriptomic and metabolic data from different tissues provided further insights into the molecular basis of fragrant oleoresins biosynthesis and high-quality wood formation of Dipterocarpaceae. Our study contributes the first two representative genomes for Dipterocarpaceae, which are valuable genetic resources for further researches on the fragrant oleoresins and superior-quality timber, genome-assisted breeding and improvement, and conservation biology of this family.
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Affiliation(s)
- Sibo Wang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Hongping Liang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Hongli Wang
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Linzhou Li
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Yan Xu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Yang Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Min Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Jinpu Wei
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Tao Ma
- Key Laboratory of Bio‐resource and Eco‐Environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengduChina
| | - Cheng Le
- BGI‐Yunnan, BGI‐ShenzhenYunnanChina
| | - Jinlong Yang
- BGI‐Yunnan, BGI‐ShenzhenYunnanChina
- College of Forensic ScienceXi'an Jiaotong UniversityXi'anChina
| | | | - Jie Liu
- Forestry Bureau of RuiliYunnan Dehong, RuiliChina
| | | | | | - Michael Lisby
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Huan Liu
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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Klaus T, Ninck S, Albersmeier A, Busche T, Wibberg D, Jiang J, Elcheninov AG, Zayulina KS, Kaschani F, Bräsen C, Overkleeft HS, Kalinowski J, Kublanov IV, Kaiser M, Siebers B. Activity-Based Protein Profiling for the Identification of Novel Carbohydrate-Active Enzymes Involved in Xylan Degradation in the Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1E. Front Microbiol 2022; 12:734039. [PMID: 35095781 PMCID: PMC8790579 DOI: 10.3389/fmicb.2021.734039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/22/2021] [Indexed: 12/02/2022] Open
Abstract
Activity-based protein profiling (ABPP) has so far scarcely been applied in Archaea in general and, especially, in extremophilic organisms. We herein isolated a novel Thermococcus strain designated sp. strain 2319x1E derived from the same enrichment culture as the recently reported Thermococcus sp. strain 2319x1. Both strains are able to grow with xylan as the sole carbon and energy source, and for Thermococcus sp. strain 2319x1E (optimal growth at 85°C, pH 6–7), the induction of xylanolytic activity in the presence of xylan was demonstrated. Since the solely sequence-based identification of xylanolytic enzymes is hardly possible, we established a complementary approach by conducting comparative full proteome analysis in combination with ABPP using α- or β-glycosidase selective probes and subsequent mass spectrometry (MS)-based analysis. This complementary proteomics approach in combination with recombinant protein expression and classical enzyme characterization enabled the identification of a novel bifunctional maltose-forming α-amylase and deacetylase (EGDIFPOO_00674) belonging to the GH57 family and a promiscuous β-glycosidase (EGIDFPOO_00532) with β-xylosidase activity. We thereby further substantiated the general applicability of ABPP in archaea and expanded the ABPP repertoire for the identification of glycoside hydrolases in hyperthermophiles.
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Affiliation(s)
- Thomas Klaus
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sabrina Ninck
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jianbing Jiang
- Section of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Kseniya S Zayulina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Farnusch Kaschani
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Herman S Overkleeft
- Section of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Markus Kaiser
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
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11
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Narváez-Barragán DA, Tovar-Herrera OE, Guevara-García A, Serrano M, Martinez-Anaya C. Mechanisms of plant cell wall surveillance in response to pathogens, cell wall-derived ligands and the effect of expansins to infection resistance or susceptibility. FRONTIERS IN PLANT SCIENCE 2022; 13:969343. [PMID: 36082287 PMCID: PMC9445675 DOI: 10.3389/fpls.2022.969343] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 05/13/2023]
Abstract
Cell wall integrity is tightly regulated and maintained given that non-physiological modification of cell walls could render plants vulnerable to biotic and/or abiotic stresses. Expansins are plant cell wall-modifying proteins active during many developmental and physiological processes, but they can also be produced by bacteria and fungi during interaction with plant hosts. Cell wall alteration brought about by ectopic expression, overexpression, or exogenous addition of expansins from either eukaryote or prokaryote origin can in some instances provide resistance to pathogens, while in other cases plants become more susceptible to infection. In these circumstances altered cell wall mechanical properties might be directly responsible for pathogen resistance or susceptibility outcomes. Simultaneously, through membrane receptors for enzymatically released cell wall fragments or by sensing modified cell wall barrier properties, plants trigger intracellular signaling cascades inducing defense responses and reinforcement of the cell wall, contributing to various infection phenotypes, in which expansins might also be involved. Here, we review the plant immune response activated by cell wall surveillance mechanisms, cell wall fragments identified as responsible for immune responses, and expansin's roles in resistance and susceptibility of plants to pathogen attack.
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Affiliation(s)
| | | | | | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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12
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Motto M, Sahay S. Energy plants (crops): potential natural and future designer plants. HANDBOOK OF BIOFUELS 2022:73-114. [DOI: 10.1016/b978-0-12-822810-4.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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13
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Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics. Microorganisms 2021; 10:microorganisms10010071. [PMID: 35056520 PMCID: PMC8777777 DOI: 10.3390/microorganisms10010071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.
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14
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Lenz RR, Louie KB, Søndreli KL, Galanie SS, Chen JG, Muchero W, Bowen BP, Northen TR, LeBoldus JM. Metabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours Postinoculation. PHYTOPATHOLOGY 2021; 111:2052-2066. [PMID: 33881913 DOI: 10.1094/phyto-02-21-0053-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sphaerulina musiva is an economically and ecologically important fungal pathogen that causes Septoria stem canker and leaf spot disease of Populus species. To bridge the gap between genetic markers and structural barriers previously found to be linked to Septoria canker disease resistance in poplar, we used hydrophilic interaction liquid chromatography and tandem mass spectrometry to identify and quantify metabolites involved with signaling and cell wall remodeling. Fluctuations in signaling molecules, organic acids, amino acids, sterols, phenolics, and saccharides in resistant and susceptible P. trichocarpa inoculated with S. musiva were observed. The patterns of 222 metabolites in the resistant host implicate systemic acquired resistance (SAR), cell wall apposition, and lignin deposition as modes of resistance to this hemibiotrophic pathogen. This pattern is consistent with the expected response to the biotrophic phase of S. musiva colonization during the first 24 h postinoculation. The fungal pathogen metabolized key regulatory signals of SAR, other phenolics, and precursors of lignin biosynthesis that were depleted in the susceptible host. This is the first study to characterize metabolites associated with the response to initial colonization by S. musiva between resistant and susceptible hosts.
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Affiliation(s)
- Ryan R Lenz
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Katherine B Louie
- Metabolomics Technology, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Kelsey L Søndreli
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Benjamin P Bowen
- Metabolomics Technology, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Trent R Northen
- Metabolomics Technology, DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Jared M LeBoldus
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
- Forest Resources, Engineering, and Management Department, Oregon State University, Corvallis, OR 97331
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15
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Roy S, Dikshit PK, Sherpa KC, Singh A, Jacob S, Chandra Rajak R. Recent nanobiotechnological advancements in lignocellulosic biomass valorization: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 297:113422. [PMID: 34351298 DOI: 10.1016/j.jenvman.2021.113422] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 05/22/2023]
Abstract
Increase in human population, rapid industrialization, excessive utilization of fossil fuel utilization and anthropogenic activities have caused serious threats to the environment in terms of greenhouse gas emissions (GHGs), global warming, air pollution, acid rain, etc. This destruction in sustainability can be averted by a paradigm shift in the fuel production from fossil resources to bioenergy. Amongst different forms of bioenergy, lignocellulosic biomass can be utilized as an attractive substrate for the production of several high-value products owing to its renewability, easy availability, and abundance. Additionally, utilization of these waste biomasses reduces the environmental hazards associated with its disposal. Impedance of lignin and crystalline nature of cellulose pose major bottlenecks in biomass based energy. Though, several physio-chemicals processes are recommended as mitigation route but none of them seems to be promising for large scale application. In recent years, a right fusion of biological treatment combined with nanotechnology for efficient pretreatment and subsequent hydrolysis of biomass by ubiquitous enzymes seems to be promising alternative. In addition, to overcome these difficulties, nanotechnology-based methods have been recently adopted in catalytic valorization of lignocellulosic biomass. The present review has critically discussed the application of nano-biotechnology in lignocellulosic biomass valorization in terms of pretreatment and hydrolysis. A detailed discussion on the application of various nanoparticles in these processes, enzyme immobilization and end-production utilization is presented in this review. Finally, the review emphasizes the major challenges of this process along with different routes and recommendations to address the issues.
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Affiliation(s)
- Sharmili Roy
- Division of Oncology, School of Medicine, Stanford University, CA, 94305, USA
| | - Pritam Kumar Dikshit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, 201310, India
| | - Knawang Chhunji Sherpa
- Advanced Technology Development Centre, Indian Institute of Technology, Kharagpur, 721302, India
| | - Anshu Singh
- Agricultural and Food Engineering Department, Indian Institute of Technology, Kharagpur, 721302, India
| | - Samuel Jacob
- Department of Biotechnology, School of Engineering, SRM Institute of Science and Technology, Kattankulathur, India
| | - Rajiv Chandra Rajak
- Department of Botany, Marwari College, Ranchi University, Ranchi, 834008, India.
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Siemińska-Kuczer A, Szymańska-Chargot M, Zdunek A. Recent advances in interactions between polyphenols and plant cell wall polysaccharides as studied using an adsorption technique. Food Chem 2021; 373:131487. [PMID: 34741970 DOI: 10.1016/j.foodchem.2021.131487] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023]
Abstract
Polyphenols include flavonoids, phenolic acids, tannins and lignans which are known to have antioxidant, UV protection and antimicrobial properties. Among them the most commonly investigated are flavonoids and phenolic acids, which, due to their plant origin, may interact with the plant cell wall (PCW) components, specifically with its polysaccharides. Knowledge concerning the nature of the interactions between these components may be used in the production of functional food or in the development of food packaging materials with additional properties. The content of polyphenols in such products is responsible for their colour and taste, and may also act as a natural preservative. On the other hand, the PCW components may have protective role of polyphenols which has impact on their release in the human digestive system. Therefore, this review is an attempt to summarize the current state of knowledge that emerged after 2017 concerning the interaction of PCW components with polyphenols, with a particular focus on hemicellulose and pectin.
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Affiliation(s)
- Anna Siemińska-Kuczer
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
| | | | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
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17
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Villa-Rivera MG, Cano-Camacho H, López-Romero E, Zavala-Páramo MG. The Role of Arabinogalactan Type II Degradation in Plant-Microbe Interactions. Front Microbiol 2021; 12:730543. [PMID: 34512607 PMCID: PMC8424115 DOI: 10.3389/fmicb.2021.730543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Arabinogalactans (AGs) are structural polysaccharides of the plant cell wall. A small proportion of the AGs are associated with hemicellulose and pectin. Furthermore, AGs are associated with proteins forming the so-called arabinogalactan proteins (AGPs), which can be found in the plant cell wall or attached through a glycosylphosphatidylinositol (GPI) anchor to the plasma membrane. AGPs are a family of highly glycosylated proteins grouped with cell wall proteins rich in hydroxyproline. These glycoproteins have important and diverse functions in plants, such as growth, cellular differentiation, signaling, and microbe-plant interactions, and several reports suggest that carbohydrate components are crucial for AGP functions. In beneficial plant-microbe interactions, AGPs attract symbiotic species of fungi or bacteria, promote the development of infectious structures and the colonization of root tips, and furthermore, these interactions can activate plant defense mechanisms. On the other hand, plants secrete and accumulate AGPs at infection sites, creating cross-links with pectin. As part of the plant cell wall degradation machinery, beneficial and pathogenic fungi and bacteria can produce the enzymes necessary for the complete depolymerization of AGs including endo-β-(1,3), β-(1,4) and β-(1,6)-galactanases, β-(1,3/1,6) galactanases, α-L-arabinofuranosidases, β-L-arabinopyranosidases, and β-D-glucuronidases. These hydrolytic enzymes are secreted during plant-pathogen interactions and could have implications for the function of AGPs. It has been proposed that AGPs could prevent infection by pathogenic microorganisms because their degradation products generated by hydrolytic enzymes of pathogens function as damage-associated molecular patterns (DAMPs) eliciting the plant defense response. In this review, we describe the structure and function of AGs and AGPs as components of the plant cell wall. Additionally, we describe the set of enzymes secreted by microorganisms to degrade AGs from AGPs and its possible implication for plant-microbe interactions.
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Affiliation(s)
- Maria Guadalupe Villa-Rivera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
| | - Everardo López-Romero
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
| | - María Guadalupe Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
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Qiao Y, Qiao S, Yu X, Min Q, Pi C, Qiu J, Ma H, Yi J, Zhan Q, Xu X. Plant tissue imaging with bipyramidal upconversion nanocrystals by introducing Tm 3+ ions as energy trapping centers. NANOSCALE 2021; 13:8181-8187. [PMID: 33884383 DOI: 10.1039/d0nr07399g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plant cell imaging is critical for agricultural production and plant pathology study. Advanced upconversion nanoparticles (UCNPs) are being developed as fluorescent probes for imaging cells and tissues in vivo and in vitro. Unfortunately, the thick cellulosic walls as barriers together with hemicelluloses and pectin hinder the entrance of macromolecules into the epidermal plant cell. Hence, realizing satisfactory temporal and spatial resolution with UCNPs remains an arduous task. Here, bipyramidal LiErF4:1%Tm3+@LiYF4 core-shell UCNPs with a super-bright red emission upon 980 nm laser excitation are explored, where the introduction of Tm3+ ions permits alleviation of the energy loss at defective sites and a significant improvement of the upconversion output. The as-obtained bipyramidal UCNPs could readily puncture plant cell walls and further penetrate into cell membranes, facilitating improved tissue imaging of cellular internalization, as demonstrated with the luminescence images obtained by multiphoton laser-scanning microscopy. Hence our work opens up a new avenue for exploring effective upconversion nanoparticles for achieving high resolution imaging of plant tissues.
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Affiliation(s)
- Yufang Qiao
- Faculty of Materials Science and Engineering, Kunming University of Science and Technology, Kunming, 650093, China.
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Lopes DCB, Carraro CB, Silva RN, de Paula RG. Molecular Characterization of Xyloglucanase cel74a from Trichoderma reesei. Int J Mol Sci 2021; 22:ijms22094545. [PMID: 33925273 PMCID: PMC8123685 DOI: 10.3390/ijms22094545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei is used on an industrial scale to produce enzymes of biotechnological interest. This fungus has a complex cellulolytic system involved in the degradation of lignocellulosic biomass. However, several aspects related to the regulation of the expression of holocellulolytic genes and the production of cellulases by this fungus are still understood. METHODS Here, we constructed a null mutant strain for the xyloglucanase cel74a gene and performed the characterization of the Δcel74a strain to evaluate the genetic regulation of the holocellulases during sugarcane bagasse (SCB) cultivation. RESULTS Our results demonstrate that the deletion of xyloglucanase cel74a may impact the regulation of holocellulase expression during SCB cultivation. The expression of cellulases cel7a, cel7b, and cel6a was reduced in Δcel74a strain, while the hemicellulases xyn1 and xyn2 were increased in the presence of SCB. The cel74a mutation also affected the xyloglucan hydrolysis patterns. In addition, CEL74A activity was modulated in the presence of calcium, suggesting that this ion may be required for efficient degradation of xyloglucan. CONCLUSIONS CEL74A affects the regulation of holocellulolytic genes and the efficient degradation of SCB in T. reesei. This data makes a significant contribution to our understanding of the carbon utilization of fungal strains as a whole.
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Affiliation(s)
- Douglas Christian Borges Lopes
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
| | - Cláudia Batista Carraro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
| | - Roberto Nascimento Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
- Correspondence:
| | - Renato Graciano de Paula
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria 29047-105, ES, Brazil
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Mota TR, Oliveira DM, Simister R, Whitehead C, Lanot A, Dos Santos WD, Rezende CA, McQueen-Mason SJ, Gomez LD. Design of experiments driven optimization of alkaline pretreatment and saccharification for sugarcane bagasse. BIORESOURCE TECHNOLOGY 2021; 321:124499. [PMID: 33310387 DOI: 10.1016/j.biortech.2020.124499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
To maximize the sugar release from sugarcane bagasse, a high-resolution Fractional Factorial Design (FFD) was combined with a Central Composite Orthogonal (CCO) design to simultaneously evaluate a wide range of variables for alkaline pretreatment (NaOH: 0.1-1 mol/L, temperature: 100-220 °C, and time: 20-80 min) and enzymatic saccharification (enzyme loading: 2.5-17.5%, and reaction volume: 550-850 µL). A total of 46 experimental conditions were evaluated and the maximum sugar yield (423 mg/g) was obtained after 18 h enzymatic hydrolysis under optimized conditions (0.25 mol/L NaOH at 202 °C for 40 min, with 12.5% of enzyme loading). Biomass compositional analyses showed that the pretreatments strongly removed lignin (up to 70%), silica (up to 80%) and promoted cellulose enrichment (25-110%). This robust design of experiments resulted in maximizing enzymatic hydrolysis efficiency of sugarcane bagasse and further indicated that this combined approach is versatile for other lignocellulosic biomasses.
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Affiliation(s)
- Thatiane R Mota
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná, 87020-900, Brazil
| | - Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná, 87020-900, Brazil
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Caragh Whitehead
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Alexandra Lanot
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom
| | - Wanderley D Dos Santos
- Department of Biochemistry, State University of Maringá, UEM, Maringá, Paraná, 87020-900, Brazil
| | - Camila A Rezende
- Institute of Chemistry, University of Campinas, UNICAMP, Campinas, São Paulo 13083‑970, Brazil
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom.
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, CNAP, University of York, York YO10 5DD, United Kingdom.
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Oliveira DM, Mota TR, Salatta FV, de Almeida GHG, Olher VGA, Oliveira MAS, Marchiosi R, Ferrarese-Filho O, Dos Santos WD. Feruloyl esterase activity and its role in regulating the feruloylation of maize cell walls. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:49-54. [PMID: 32906021 DOI: 10.1016/j.plaphy.2020.08.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/30/2020] [Indexed: 06/11/2023]
Abstract
Cell walls of grasses have ferulic acid (FA) ester-linked to the arabinosyl substitutions of arabinoxylan (AX). Feruloyl esterases (FAE) are carboxylic acid esterases that release FA from cell walls and synthetic substrates. Despite the importance of FA for cell wall recalcitrance and in response to biotic and abiotic stresses, the physiological function of plant FAEs remains unclear. Here, we developed a simple method for the determination of FAE activity (ZmFAE) in maize using the total protein extract and investigated its role in regulating the feruloylation of cell wall. The method includes a single protein extraction and enzymatic reaction with protein concentration as low as 65 μg at 35 °C for 30 min, using methyl ferulate as the substrate. The methodology allowed the determination of the apparent Km (392.82 μM) and Vmax (79.15 pkat mg-1 protein). We also found that ZmFAE activity was correlated (r = 0.829) with the levels of FA in seedling roots, plant roots and leaves of maize. Furthermore, the exposure to osmotic stress resulted in a 50% increase in ZmFAE activity in seedling roots. These data suggest that FAE-catalyzed reaction is important for cell wall feruloylation during plant development and in response to abiotic stress. We conclude proposing a model for the feruloylation and deferuloylation of AX, which explains the role of FAE in regulating the levels of ester-linked FA. Our model might orient further studies investigating the role of plant FAEs and assist strategies for genetic engineering of grasses to obtain plants with reduced biomass recalcitrance.
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Affiliation(s)
- Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, PR, Brazil.
| | - Thatiane R Mota
- Department of Biochemistry, State University of Maringá, Maringá, PR, Brazil
| | - Fábio V Salatta
- Department of Biochemistry, State University of Maringá, Maringá, PR, Brazil
| | | | | | - Marco A S Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, PR, Brazil
| | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Maringá, PR, Brazil
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Bertella S, Luterbacher JS. Lignin Functionalization for the Production of Novel Materials. TRENDS IN CHEMISTRY 2020. [DOI: 10.1016/j.trechm.2020.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Zoghlami A, Paës G. Lignocellulosic Biomass: Understanding Recalcitrance and Predicting Hydrolysis. Front Chem 2019; 7:874. [PMID: 31921787 PMCID: PMC6930145 DOI: 10.3389/fchem.2019.00874] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Lignocellulosic biomass (LB) is an abundant and renewable resource from plants mainly composed of polysaccharides (cellulose and hemicelluloses) and an aromatic polymer (lignin). LB has a high potential as an alternative to fossil resources to produce second-generation biofuels and biosourced chemicals and materials without compromising global food security. One of the major limitations to LB valorisation is its recalcitrance to enzymatic hydrolysis caused by the heterogeneous multi-scale structure of plant cell walls. Factors affecting LB recalcitrance are strongly interconnected and difficult to dissociate. They can be divided into structural factors (cellulose specific surface area, cellulose crystallinity, degree of polymerization, pore size and volume) and chemical factors (composition and content in lignin, hemicelluloses, acetyl groups). Goal of this review is to propose an up-to-date survey of the relative impact of chemical and structural factors on biomass recalcitrance and of the most advanced techniques to evaluate these factors. Also, recent spectral and water-related measurements accurately predicting hydrolysis are presented. Overall, combination of relevant factors and specific measurements gathering simultaneously structural and chemical information should help to develop robust and efficient LB conversion processes into bioproducts.
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Affiliation(s)
- Aya Zoghlami
- FARE Laboratory, INRAE, University of Reims Champagne-Ardenne, Reims, France
| | - Gabriel Paës
- FARE Laboratory, INRAE, University of Reims Champagne-Ardenne, Reims, France
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Kozaki R, Miyake H. Enzymatic and molecular characterization of an endoglucanase E from Clostridium cellulovorans 743B. J Biosci Bioeng 2019; 128:398-404. [DOI: 10.1016/j.jbiosc.2019.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/08/2019] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
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Mosina NL, Schubert WD, Cowan DA. Characterization and homology modelling of a novel multi-modular and multi-functional Paenibacillus mucilaginosus glycoside hydrolase. Extremophiles 2019; 23:681-686. [PMID: 31372752 DOI: 10.1007/s00792-019-01121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/21/2019] [Indexed: 10/26/2022]
Abstract
Glycoside hydrolases, particularly cellulases, xylanases and mannanases, are essential for the depolymerisation of lignocellulosic substrates in various industrial bio-processes. In the present study, a novel glycoside hydrolase from Paenibacillus mucilaginosus (PmGH) was expressed in E. coli, purified and characterised. Functional analysis indicated that PmGH is a 130 kDa thermophilic multi-modular and multi-functional enzyme, comprising a GH5, a GH6 and two CBM3 domains and exhibiting cellulase, mannanase and xylanase activities. The enzyme displayed optimum hydrolytic activities at pH 6 and 60 °C and moderate thermostability. Homology modelling of the full-length protein highlighted the structural and functional novelty of native PmGH, with no close structural homologs identified. However, homology modelling of the individual GH5, GH6 and the two CBM3 domains yielded excellent models based on related structures from the Protein Data Bank. The catalytic GH5 and GH6 domains displayed a (β/α)8 and a distorted seven stranded (β/α) fold, respectively. The distinct homology at the domain level but low homology of the full-length protein suggests that this protein evolved by exogenous gene acquisition and recombination.
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Affiliation(s)
- Ntsoaki Leticia Mosina
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Wolf-Dieter Schubert
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa
| | - Don A Cowan
- Department Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Lynnwood Road, Hatfield, Pretoria, 0002, South Africa.
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Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach. Arch Microbiol 2019; 201:1385-1397. [PMID: 31338542 DOI: 10.1007/s00203-019-01706-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 12/30/2022]
Abstract
Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.
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Oliveira DM, Mota TR, Oliva B, Segato F, Marchiosi R, Ferrarese-Filho O, Faulds CB, Dos Santos WD. Feruloyl esterases: Biocatalysts to overcome biomass recalcitrance and for the production of bioactive compounds. BIORESOURCE TECHNOLOGY 2019; 278:408-423. [PMID: 30704902 DOI: 10.1016/j.biortech.2019.01.064] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 05/25/2023]
Abstract
Ferulic acid and its hydroxycinnamate derivatives represent one of the most abundant forms of low molecular weight phenolic compounds in plant biomass. Feruloyl esterases are part of a microorganism's plant cell wall-degrading enzymatic arsenal responsible for cleaving insoluble wall-bound hydroxycinnamates and soluble cytosolic conjugates. Stimulated by industrial requirements, accelerating scientific discoveries and knowledge transfer, continuous improvement efforts have been made to identify, create and repurposed biocatalysts dedicated to plant biomass conversion and biosynthesis of high-added value molecules. Here we review the basic knowledge and recent advances in biotechnological characteristics and the gene content encoding for feruloyl esterases. Information about several enzymes is systematically organized according to their function, biochemical properties, substrate specificity, and biotechnological applications. This review contributes to further structural, functional, and biotechnological R&D both for obtaining hydroxycinnamates from agricultural by-products as well as for lignocellulose biomass treatments aiming for production of bioethanol and other derivatives of industrial interest.
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Affiliation(s)
- Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil.
| | - Thatiane R Mota
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Fernando Segato
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, São Paulo, Brazil
| | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Maringá, Paraná, Brazil
| | | | - Craig B Faulds
- Aix-Marseille Université, INRA UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009 Marseille, France
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