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Ashy RA. Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum. Saudi J Biol Sci 2023; 30:103789. [PMID: 37680975 PMCID: PMC10480775 DOI: 10.1016/j.sjbs.2023.103789] [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: 08/02/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.
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Affiliation(s)
- Ruba Abdulrahman Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
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Akram F, Haq IU, Shah FI, Aqeel A, Ahmed Z, Mir AS, Qureshi SS, Raja SI. Genus Thermotoga: A valuable home of multifunctional glycoside hydrolases (GHs) for industrial sustainability. Bioorg Chem 2022; 127:105942. [PMID: 35709577 DOI: 10.1016/j.bioorg.2022.105942] [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: 12/31/2021] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Nature is a dexterous and prolific chemist for cataloging a number of hostile niches that are the ideal residence of various thermophiles. Apart from having other species, these subsurface environments are considered a throne of bacterial genus Thermotoga. The genome sequence of Thermotogales encodes complex and incongruent clusters of glycoside hydrolases (GHs), which are superior to their mesophilic counterparts and play a prominent role in various applications due to their extreme intrinsic stability. They have a tremendous capacity to use a wide variety of simple and multifaceted carbohydrates through GHs, formulate fermentative hydrogen and bioethanol at extraordinary yield, and catalyze high-temperature reactions for various biotechnological applications. Nevertheless, no stringent rules exist for the thermo-stabilization of biocatalysts present in the genus Thermotoga. These enzymes endure immense attraction in fundamental aspects of how these polypeptides attain and stabilize their distinctive three-dimensional (3D) structures to accomplish their physiological roles. Moreover, numerous genome sequences from Thermotoga species have revealed a significant fraction of genes most closely related to those of archaeal species, thus firming a staunch belief of lateral gene transfer mechanism. However, the question of its magnitude is still in its infancy. In addition to GHs, this genus is a paragon of encapsulins which carry pharmacological and industrial significance in the field of life sciences. This review highlights an intricate balance between the genomic organizations, factors inducing the thermostability, and pharmacological and industrial applications of GHs isolated from genus Thermotoga.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan.
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan; Pakistan Academy of Science, Islamabad, Pakistan
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Zeeshan Ahmed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Azka Shahzad Mir
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Sumbal Sajid Qureshi
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Saleha Ibadat Raja
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
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Synergistic action of thermophilic pectinases for pectin bioconversion into D-galacturonic acid. Enzyme Microb Technol 2022; 160:110071. [DOI: 10.1016/j.enzmictec.2022.110071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 11/19/2022]
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Recent advances in the production strategies of microbial pectinases—A review. Int J Biol Macromol 2019; 122:1017-1026. [DOI: 10.1016/j.ijbiomac.2018.09.048] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/20/2018] [Accepted: 09/10/2018] [Indexed: 02/01/2023]
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Evangelista DE, de Araújo EA, Neto MO, Kadowaki MAS, Polikarpov I. Biochemical characterization and low-resolution SAXS structure of an exo-polygalacturonase from Bacillus licheniformis. N Biotechnol 2018; 40:268-274. [DOI: 10.1016/j.nbt.2017.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 09/07/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
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Stoller JR, Wagschal K, Lee CC, Jordan DB. A general correction to catalytic rates determined for nonprocessive exo-depolymerases acting on both substrate and product in the initial-rate measurement. Anal Biochem 2017; 523:46-49. [DOI: 10.1016/j.ab.2017.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 02/09/2017] [Indexed: 11/16/2022]
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Expression and Characterization of Hyperthermostable Exo-polygalacturonase TtGH28 from Thermotoga thermophilus. Mol Biotechnol 2016; 58:509-19. [DOI: 10.1007/s12033-016-9948-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Gomes E, de Souza AR, Orjuela GL, Da Silva R, de Oliveira TB, Rodrigues A. Applications and Benefits of Thermophilic Microorganisms and Their Enzymes for Industrial Biotechnology. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_21] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Biochemical characterization of three distinct polygalacturonases from Neosartorya fischeri P1. Food Chem 2015; 188:569-75. [DOI: 10.1016/j.foodchem.2015.05.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 04/17/2015] [Accepted: 05/05/2015] [Indexed: 11/19/2022]
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Cloning, expression and characterization of a novel thermophilic polygalacturonase from Caldicellulosiruptor bescii DSM 6725. Int J Mol Sci 2014; 15:5717-29. [PMID: 24705464 PMCID: PMC4013591 DOI: 10.3390/ijms15045717] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/04/2022] Open
Abstract
We cloned the gene ACM61449 from anaerobic, thermophilic Caldicellulosiruptor bescii, and expressed it in Escherichia coli origami (DE3). After purification through thermal treatment and Ni-NTA agarose column extraction, we characterized the properties of the recombinant protein (CbPelA). The optimal temperature and pH of the protein were 72 °C and 5.2, respectively. CbPelA demonstrated high thermal-stability, with a half-life of 14 h at 70 °C. CbPelA also showed very high activity for polygalacturonic acid (PGA), and released monogalacturonic acid as its sole product. The Vmax and Km of CbPelA were 384.6 U·mg−1 and 0.31 mg·mL−1, respectively. CbPelA was also able to hydrolyze methylated pectin (48% and 10% relative activity on 20%–34% and 85% methylated pectin, respectively). The high thermo-activity and methylated pectin hydrolization activity of CbPelA suggest that it has potential applications in the food and textile industry.
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Yuan P, Meng K, Wang Y, Luo H, Shi P, Huang H, Bai Y, Yang P, Yao B. A protease-resistant exo-polygalacturonase from Klebsiella sp. Y1 with good activity and stability over a wide pH range in the digestive tract. BIORESOURCE TECHNOLOGY 2012; 123:171-176. [PMID: 22940315 DOI: 10.1016/j.biortech.2012.07.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/02/2012] [Accepted: 07/13/2012] [Indexed: 06/01/2023]
Abstract
Polygalacturonases are important feed and food additives. In the present study an exo-polygalacturonase gene (pgu B) was cloned from Klebsiella sp. Y1 CGMCC 4433 and expressed in Escherichia coli BL21 (DE3). pgu B encodes a 658-amino acid polypeptide belonging to Glycoside Hydrolase Family 28. The optimal pH and temperature of exo-PGU B activity were 6.0 and 40-50°C, respectively. The enzyme exhibited >35% of maximum activity within the pH range of 2.0-12.0. Exo-PGU B or an exo-PGU B/ endo-polygalacturonase mixture reduced the viscosity of polygalacturonic acid (1.0%, w/v) by 15.6 and 39.4%, respectively. Under simulated alimentary tract conditions, exo-PGU B was very stable (>25% activity from pH 1.5 to 6.8) and active, releasing 53.7 and 109.6μg of galacturonic acid from 400 to 800μg of polygalacturonic acid, respectively. These properties make exo-PGU B a potentially valuable additive for applications in feed and food.
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Affiliation(s)
- Peng Yuan
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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Purification and characterization of a pectin lyase produced by Geobacillus stearothermophilus Ah22 and its application in fruit juice production. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0217-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Purification and characterization of an exo-polygalacturonase from Pycnoporus sanguineus. ACTA ACUST UNITED AC 2009; 113:1404-10. [DOI: 10.1016/j.mycres.2009.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 08/25/2009] [Accepted: 09/18/2009] [Indexed: 11/20/2022]
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Pijning T, van Pouderoyen G, Kluskens L, van der Oost J, Dijkstra BW. The crystal structure of a hyperthermoactive exopolygalacturonase fromThermotoga maritimareveals a unique tetramer. FEBS Lett 2009; 583:3665-70. [DOI: 10.1016/j.febslet.2009.10.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 10/15/2009] [Accepted: 10/15/2009] [Indexed: 12/15/2022]
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VanFossen AL, Lewis DL, Nichols JD, Kelly RM. Polysaccharide Degradation and Synthesis by Extremely Thermophilic Anaerobes. Ann N Y Acad Sci 2008; 1125:322-37. [DOI: 10.1196/annals.1419.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Drone J, Dion M, Tellier C, Rabiller C. In vivo selection for the enhancement of Thermotoga maritima exopolygalacturonase activity at neutral pH and low temperature. Protein Eng Des Sel 2007; 20:7-14. [PMID: 17218336 DOI: 10.1093/protein/gzl048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The aim of this study was to develop an Escherichia coli-based metabolic selection system for the uncovering of new oligogalacturonate-active enzymes. Based on the expression of the specific permease TogMNAB, this system enabled the entry of oligogalacturonates into the cytoplasm of E. coli thus providing a modified strain usable for this purpose. This tool was used for the metabolic selection of Thermotoga maritima exopolygalacturonase (TmGalU) mutants enabling the uptake of sodium trigalacturonate as the sole carbon source by the bacterium. In only one round of error-prone PCR and selection, mutants of TmGalU with a 4-fold increased turnover at pH 7.0 and 2-fold more active at 37 degrees C than wild-type enzyme were isolated. These results show the versatility of this strain for the evolution of oligogalacturonate-active enzymes.
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Affiliation(s)
- Jullien Drone
- Université de Nantes, Nantes Atlantique Universités, UMR CNRS 6204, Biotechnologie, Biocatalyse, Biorégulation, 2, rue de la Houssinière, BP 92208, F-44322 Nantes, France
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Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. FEMS Microbiol Rev 2006; 30:872-905. [PMID: 17064285 DOI: 10.1111/j.1574-6976.2006.00039.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
High-throughput sequencing of microbial genomes has allowed the application of functional genomics methods to species lacking well-developed genetic systems. For the model hyperthermophile Thermotoga maritima, microarrays have been used in comparative genomic hybridization studies to investigate diversity among Thermotoga species. Transcriptional data have assisted in prediction of pathways for carbohydrate utilization, iron-sulfur cluster synthesis and repair, expolysaccharide formation, and quorum sensing. Structural genomics efforts aimed at the T. maritima proteome have yielded hundreds of high-resolution datasets and predicted functions for uncharacterized proteins. The information gained from genomics studies will be particularly useful for developing new biotechnology applications for T. maritima enzymes.
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Affiliation(s)
- Shannon B Conners
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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Celestino SMC, Maria de Freitas S, Javier Medrano F, Valle de Sousa M, Filho EXF. Purification and characterization of a novel pectinase from Acrophialophora nainiana with emphasis on its physicochemical properties. J Biotechnol 2006; 123:33-42. [PMID: 16337707 DOI: 10.1016/j.jbiotec.2005.10.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 09/28/2005] [Accepted: 10/24/2005] [Indexed: 11/19/2022]
Abstract
An extracellular pectinase (PECI) was purified to apparent homogeneity from liquid state cultures of the thermophilic fungus Acrophialophora nainiana by ultrafiltration and a combination of gel filtration and ion-exchange chromatographic procedures. The molecular masses of PECI were 35,500 and 30,749 Da, as determined by SDS-PAGE and mass spectrometry, respectively. It was more active at 60 degrees C and pH 8.0 and showed high stability at 50 degrees C with half-life of 7 days. However at 60 and 70 degrees C, PECI was much less stable with half lives of approximately 20 and 3 min, respectively. The thermostability of purified PECI was also investigated by fluorescence and circular dichroism spectroscopy. Fluorescence revealed that the unfolding transition region was observed between 45 and 70 degrees C. A major decrease in the stability was found at 70 degrees C. Circular dichroism measurements at pH between 5.0 and 9.0 showed a transition temperature (T(m)) range of 50-55 degrees . The thermodynamic analysis of these results showed that EPGI is thermal stable protein exhibiting maximum stability (DeltaG(25)) of 22.65 and 19.19 kcal/mol at pH 8.0 and 9.0, respectively. The apparent K(m) value on pectin from citrus fruits was 4.22 mgml(-1). PECI exhibited no detectable activity of pectin methylesterase, endo-polygalacturonase, mannanase, xylanase and cellulase. However, it showed exo-polygalacturonase and pectin lyase activities. The presence of carbohydrate was detected in the pure PECI. It was activated by l-tryptophan, DEPC, DTT, DTNB, DTP, l-cystein and beta-mercaptoethanol and inhibited by NBS, Fe(2+), Cu(2+), Zn(2+), Mn(2+), Al(3+) and Ca(2+). The enzyme showed homology with a pectin lyases from Xanthomonas campestris and Bacillus licheniformis.
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Affiliation(s)
- S Maria C Celestino
- Laboratório de Enzimologia, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, CEP 70910-900, Brazil
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