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Silva FCO, Malaisamy A, Cahú TB, de Araújo MIF, Soares PAG, Vieira AT, Dos Santos Correia MT. Polysaccharides from exudate gums of plants and interactions with the intestinal microbiota: A review of vegetal biopolymers and prediction of their prebiotic potential. Int J Biol Macromol 2024; 254:127715. [PMID: 37918599 DOI: 10.1016/j.ijbiomac.2023.127715] [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: 08/01/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Polysaccharides in plant-exuded gums are complex biopolymers consisting of a wide range of structural variability (linkages, monosaccharide composition, substituents, conformation, chain length and branching). The structural features of polysaccharides confer the ability to be exploited in different industrial sectors and applications involving biological systems. Moreover, these characteristics are attributed to a direct relationship in the process of polysaccharide enzymatic degradation by the fermentative action in the gut microbiota, through intrinsic interactions connecting bacterial metabolism and the production of various metabolites that are associated with regulatory effects on the host homeostasis system. Molecular docking analysis between bacterial target proteins and arabinogalactan-type polysaccharide obtained from gum arabic allowed the identification of intermolecular interactions provided bacterial enzymatic mechanism for the degradation of several arabinogalactan monosaccharide chains, as a model for the study and prediction of potential fermentable polysaccharide. This review discusses the main structural characteristics of polysaccharides from exudate gums of plants and their interactions with the intestinal microbiota.
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Affiliation(s)
- Francisca Crislândia Oliveira Silva
- Department of Biochemistry, Biotechnology Laboratory (LaBioTec), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - University City, CEP 50.670-901 Recife, PE, Brazil
| | - Arunkumar Malaisamy
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Thiago Barbosa Cahú
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro (UFRJ), University City, CEP 21941-913 Rio de Janeiro, RJ, Brazil
| | - Maria Isabela Ferreira de Araújo
- Department of Biochemistry, Biotechnology Laboratory (LaBioTec), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - University City, CEP 50.670-901 Recife, PE, Brazil
| | - Paulo Antônio Galindo Soares
- Department of Biochemistry, Biotechnology Laboratory (LaBioTec), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - University City, CEP 50.670-901 Recife, PE, Brazil
| | - Angélica Thomaz Vieira
- Department of Biochemistry and Immunology, Laboratory of Microbiota and Immunomodulation (LMI), Federal University of Minas Gerais (UFMG), Antonio Carlos, 6627 - Pampulha, CEP 30.161-970 Belo Horizonte, MG, Brazil
| | - Maria Tereza Dos Santos Correia
- Department of Biochemistry, Glycoprotein Laboratory (BIOPROT), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - University City, CEP 50.670-901 Recife, PE, Brazil.
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Lakra U, Lincoln Singh Munda V, Nigam VK, Sharma SR. Optimisation, characterization, and biological evaluation of novel exopolysaccharide from Bacillus licheniformis (BITSL006). Nat Prod Res 2023:1-10. [PMID: 37812180 DOI: 10.1080/14786419.2023.2265041] [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: 06/17/2023] [Accepted: 09/23/2023] [Indexed: 10/10/2023]
Abstract
The study investigated production, characterisation, and biological properties of exopolysaccharide (EPS) from a thermophilic bacterium, Bacillus licheniformis using sucrose as a main carbon source at a temperature of 75 °C, resulting in a yield of 2.87 g/L. The surface topology of EPS was determined using FESEM indicating its porous nature. Subsequently, FTIR was employed to examine EPS and identified the presence of carboxyl and hydroxyl groups, which are believed to be associated with water-holding capacity (WHC). Comparing the FTIR spectrum of various exopolysaccharides, it was inferred that the exopolysaccharide derived from Ramkund closely resembles dextran. EDX and ICP-MS analysis revealed the presence of Sulphur and Selenium which might be involved in the anticancer properties of EPS. This is the first report on bacterial EPS from a hot spring (Ram kund) with antioxidant property, WHC, and high solubility. These properties offer beneficial resources for exploration in the pharmaceutical and agriculture industries.
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Affiliation(s)
- Usha Lakra
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | | | - Vinod Kumar Nigam
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Shubha Rani Sharma
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
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Chettri D, Verma AK. Biological significance of carbohydrate active enzymes and searching their inhibitors for therapeutic applications. Carbohydr Res 2023; 529:108853. [PMID: 37235954 DOI: 10.1016/j.carres.2023.108853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/01/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Glycans are the most abundant and diverse group of biomolecules with a crucial role in all the biological processes. Their structural and functional diversity is not genetically encoded, but depends on Carbohydrate Active Enzymes (CAZymes) which carry out all catalytic activities in terms of synthesis, modification, and degradation. CAZymes comprise large families of enzymes with specific functions and are widely used for various commercial applications ranging from biofuel production to textile and food industries with impact on biorefineries. To understand the structure and functional mechanism of these CAZymes for their modification for industrial use, together with knowledge of therapeutic aspects of their dysfunction associated with various diseases, CAZyme inhibitors can be used as a valuable tool. In search for new inhibitors, the screening of various secondary metabolites using high-throughput techniques and rational design techniques have been explored. The inhibitors can thus help tune CAZymes and are emerging as a potential research interest.
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Affiliation(s)
- Dixita Chettri
- Department of Microbiology, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Anil Kumar Verma
- Department of Microbiology, Sikkim University, Gangtok, 737102, Sikkim, India.
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Vaish S, Parveen R, Singh N, Gupta D, Basantani MK. Computational insights into diverse aspects of glutathione S-transferase gene family in Papaver somniferum. JOURNAL OF PLANT RESEARCH 2022; 135:823-852. [PMID: 36066757 DOI: 10.1007/s10265-022-01408-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Plant glutathione S-transferases are an ancient protein superfamily having antioxidant activity. These proteins are primarily involved in diverse plant functions such as plant growth and development, secondary metabolism, signaling pathways and defense against biotic and abiotic stresses. The current study aimed to comprehensively identify and characterize the GST gene family in the medicinally important crop Papaver somniferum. A total of 93 GST proteins were identified belonging to eight GST classes and found to be majorly localized in the cytoplasm. All GST genes were found on eleven opium chromosomes. Gene duplication analysis showed segmental duplication as a key factor for opium GST gene family expansion under strong purifying selection. Phylogenetic analysis with gymnosperm, angiosperm and bryophyte revealed the evolution of GSTs earlier than their division into separate groups and also prior to the divergence of monocot and dicot. The secondary structure prediction showed the dominance of α-helices indicative of PsomGSTs as structurally stable and elastic proteins. Gene architecture showed the conservation of number of exons across the classes. MEME analysis revealed only a few class specific and many across class conserved motifs. Ser was found to be the active site residue of tau, phi, theta and zeta class and Cys was catalytic residue of DHAR, lambda and GHR class. Promoter analyses identified many cis-acting regulatory elements related to hormonal, cellular, stress and light response functions. Ser was the key phosphorylation site. Only three glycosylation sites were found across the 93 PsomGSTs. 3D structure prediction was also performed and was validated. Interactome analyses revealed the correlation of PsomGSTs with glutathione metabolizing proteins. Gene enrichment analysis and KEGG pathway analyzed the involvement of PsomGSTs in three major pathways i.e. glutathione metabolism, tyrosine metabolism and ascorbate metabolism. The outcome revealed high model quality of PsomGSTs. The results of the current study will be of potential significance to understand the functional and structural importance of the GST gene family in opium, a medicinally important crop.
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Affiliation(s)
- Swati Vaish
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh, 225003, India
| | - Reshma Parveen
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh, 225003, India
| | - Nootan Singh
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh, 225003, India
| | - Divya Gupta
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh, 225003, India
| | - Mahesh Kumar Basantani
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow Deva Road, Barabanki, Uttar Pradesh, 225003, India.
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Vaish S, Parveen R, Gupta D, Basantani MK. Genome-wide identification and characterization of glutathione S-transferase gene family in Musa acuminata L. AAA group and gaining an insight to their role in banana fruit development. J Appl Genet 2022; 63:609-631. [PMID: 35689012 DOI: 10.1007/s13353-022-00707-x] [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: 02/09/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 10/18/2022]
Abstract
Glutathione S-transferases are a multifunctional protein superfamily that is involved in diverse plant functions such as defense mechanisms, signaling, stress response, secondary metabolism, and plant growth and development. Although the banana whole-genome sequence is available, the distribution of GST genes on banana chromosomes, their subcellular localization, gene structure, their evolutionary relation with each other, conserved motifs, and their roles in banana are still unknown. A total of 62 full-length GST genes with the canonical thioredoxin fold have been identified belonging to nine GST classes, namely tau, phi, theta, zeta, lambda, DHAR, EF1G, GHR, and TCHQD. The 62 GST genes were distributed into 11 banana chromosomes. All the MaGSTs were majorly localized in the cytoplasm. Gene architecture showed the conservation of exon numbers in individual GST classes. Multiple Em for Motif Elicitation analyses revealed few class-specific motifs and many motifs were found in all the GST classes. Multiple sequence alignment of banana GST amino acid sequences with rice, Arabidopsis, and soybean sequences revealed the Ser and Cys as conserved catalytic residues. Gene duplication analyses showed the tandem duplication as a driving force for GST gene family expansion in banana. Cis-regulatory element analysis showed the dominance of light-responsive element followed by stress- and hormone-responsive elements. Expression profiling analyses were also done by RNA-seq data. It was observed that MaGSTs are involved in various stages of fruit development. MaGSTU1 was highly upregulated. The comprehensive and organized studies of MaGST gene family provide groundwork for further functional analysis of MaGST genes in banana at molecular level and further for plant breeding approaches.
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Affiliation(s)
- Swati Vaish
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Reshma Parveen
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Divya Gupta
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India
| | - Mahesh Kumar Basantani
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow-Deva Road, Barabanki, 225003, Uttar Pradesh, India.
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Performance of Novel Antimicrobial Protein Bg_9562 and In Silico Predictions on Its Properties with Reference to Its Antimicrobial Efficiency against Rhizoctonia solani. Antibiotics (Basel) 2022; 11:antibiotics11030363. [PMID: 35326826 PMCID: PMC8944631 DOI: 10.3390/antibiotics11030363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023] Open
Abstract
Bg_9562 is a potential broad-spectrum antifungal effector protein derived from the bacteria Burkholderia gladioli strain NGJ1 and is effective against Rhizoctonia solani, the causal agent of sheath blight in rice. In the present study, in vitro antifungal assays showed that Bg_9562 was efficient at 35 °C and 45 °C and ineffective either at high acidic pH (3.0) or alkaline pH (9.5) conditions. Compatibility studies between the native bioagents Trichoderma asperellum TAIK1 and Bacillus subtilis BIK3 indicated that Bg_9562 was compatible with the bioagents. A field study using foliar spray of the Bg_9562 protein indicated the need of formulating the protein before its application. In silico analysis predicted that Bg_9562 possess 111 amino acid residues (46 hydrophobic residues, 12 positive and 8 negative residues) with the high aliphatic index of 89.92, attributing to its thermostability with a half-life of 30 h. Bg_9562 (C491H813N137O166S5) possessed a protein binding potential of 1.27 kcal/mol with a better possibility of interacting and perturbing the membrane, the main target for antimicrobial proteins. The secondary structure revealed the predominance of random coils in its structure, and the best 3D model of Bg_9562 was predicted using an ab initio method with Robetta and AlphaFold 2. The predicted binding ligands were nucleic acids and zinc with confidence scores of 0.07 and 0.05, respectively. The N-terminal region (1–14 residues) and C-terminal region (101 to 111) of Bg_9562 residues were predicted to be disordered regions. Stability and binding properties of the protein from the above studies would help to encapsulate Bg_9562 using a suitable carrier to maintain efficiency and improve delivery against Rhizoctonia solani in the most challenging rice ecosphere.
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Stress Dependent Biofilm Formation and Bioactive Melanin Pigment Production by a Thermophilic Bacillus Species from Chilean Hot Spring. Polymers (Basel) 2022; 14:polym14040680. [PMID: 35215592 PMCID: PMC8880475 DOI: 10.3390/polym14040680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic bacteria able to survive extreme temperature stress are of great biotechnological interest due to their extracellular production of bioactive molecules as a part of a survival strategy, or by intracellular modifications. In the present study, thermophilic Bacillus haynesii CamB6, isolated from a Chilean hot spring, was studied for the formation of different stress response molecules. The polymeric pigment produced by the bacterial strain was characterized by different physicochemical techniques. On exposure to ranges of temperature (50–60 °C), pH (5.0–7.0), and sources of nitrogen and carbon (1–5 g·L−1), the bacteria responded with a biofilm network formation in a hydrophobic polystyrene surface. Biofilm formation under fed-batch conditions was also statistically validated. The bacteria showed a planktonic pellicle network formation in the presence of induced hypoxia and salinity stress (19.45 g·L−1) under static conditions. Salinity stress also resulted in the intracellular response of brown pigment production. The pigment was structurally and functionally characterized by UV-Vis absorbance and the presence of different characteristic peaks via FTIR analysis (bacterial pyomelanin fingerprints) were assessed. A high thermal stability and TGA profile indicated the brown pigment was a probable pyomelanin candidate. Micropyrolysis (Py-GC/MS) showed that isoprene, pyrrole, benzene, pyridine, and their derivatives were the major components detected. In addition, acetic acid, indole, phenol, and its derivatives were observed. The absence of sulfocompounds in the pyrolyzed products agreed with those reported in the literature for pyomelanin. The pigment surface morphology was analyzed via SEM, and the elemental composition via EDS also demonstrated the similarity of the brown pigment to that of the melanin family. The pyomelanin pigment was observed to be bioactive with promising antioxidant capacity (H2O2, Fe2+) compared to the standard antioxidant molecules. In conclusion, B. haynesii CamB6 demonstrated the formation of several biomolecules as a stress response mechanism that is bioactive, showing its probable biotechnological applications in future.
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Banerjee A, Sarkar S, Govil T, González-Faune P, Cabrera-Barjas G, Bandopadhyay R, Salem DR, Sani RK. Extremophilic Exopolysaccharides: Biotechnologies and Wastewater Remediation. Front Microbiol 2021; 12:721365. [PMID: 34489911 PMCID: PMC8417407 DOI: 10.3389/fmicb.2021.721365] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/26/2021] [Indexed: 01/18/2023] Open
Abstract
Various microorganisms thrive under extreme environments, like hot springs, hydrothermal vents, deep marine ecosystems, hyperacid lakes, acid mine drainage, high UV exposure, and more. To survive against the deleterious effect of these extreme circumstances, they form a network of biofilm where exopolysaccharides (EPSs) comprise a substantial part. The EPSs are often polyanionic due to different functional groups in their structural backbone, including uronic acids, sulfated units, and phosphate groups. Altogether, these chemical groups provide EPSs with a negative charge allowing them to (a) act as ligands toward dissolved cations as well as trace, and toxic metals; (b) be tolerant to the presence of salts, surfactants, and alpha-hydroxyl acids; and (c) interface the solubilization of hydrocarbons. Owing to their unique structural and functional characteristics, EPSs are anticipated to be utilized industrially to remediation of metals, crude oil, and hydrocarbons from contaminated wastewaters, mines, and oil spills. The biotechnological advantages of extremophilic EPSs are more diverse than traditional biopolymers. The present review aims at discussing the mechanisms and strategies for using EPSs from extremophiles in industries and environment bioremediation. Additionally, the potential of EPSs as fascinating biomaterials to mediate biogenic nanoparticles synthesis and treat multicomponent water contaminants is discussed.
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Affiliation(s)
- Aparna Banerjee
- Centro de investigación en Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación Y Posgrado, Universidad Católica del Maule, Talca, Chile
- Centro de Biotecnología de los Recursos Naturales (CENBio), Facultad de Ciencias Agrarias Y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Shrabana Sarkar
- Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Burdwan, India
| | - Tanvi Govil
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
- Composite and Nanocomposite Advanced Manufacturing – Biomaterials Center, Rapid City, SD, United States
| | - Patricio González-Faune
- Escuela Ingeniería en Biotecnología, Facultad de Ciencias Agrarias Y Forestales, Universidad Católica del Maule, Talca, Chile
| | | | - Rajib Bandopadhyay
- Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Burdwan, India
| | - David R. Salem
- Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Burdwan, India
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
- Department of Materials and Metallurgical Engineering, South Dakota Mines, Rapid City, SD, United States
| | - Rajesh K. Sani
- Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Burdwan, India
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
- BuGReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States
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