Skip to main content
SpringerLink
Log in

Evaluation of thermostable endoglucanase in Paenibacillus lautus strain BHU3 for yield enhancement

  • Original Article
  • Published:
Systems Microbiology and Biomanufacturing Aims and scope Submit manuscript

Abstract

In the present study, Paenibacillus lautus strain BHU3 isolated from landfill soil was evaluated for the presence of potential endoglucanases which are the first candidate of cellulase enzyme system to act on cellulose. In-silico analysis revealed high potential thermostable endoglucanases which can efficiently interact with cellulose. The most potent and thermostable endoglucanase (locus tag id. CPZ30_18280) belonged to glycosyl family-5 and had interaction energy of − 12.981 kcal/mol for the best docked cluster containing three out of ten docking conformations, and Tm value of 73.3 °C. MD simulation of 100 ns proved highly stable binding interactions of CPZ30_18280 endoglucanase with cellulose with root mean square deviation (RMSD) values ranging from 0.15 to 0.30 nm. Consistent interactions with characteristic active site residues (tyrosine, tryptophan and aspartate) of glycosyl family-5 endoglucanases were found. Further, to enhance the production of endoglucanases, the fermentation conditions were optimized employing approaches like one factor at a time (OFAT) and response surface methodology (RSM). Maximum activity of endoglucanase was determined at 60 °C. The optimized conditions for enhanced production of endoglucanase (10.15 U/mL) were pH 6.63, yeast extract conc. 3.44 g/L, wheat bran 3.59%, and inoculum size 2.65%. Hence, P. lautus strain BHU3 has enormous potential to synthesize highly efficient thermostable endoglucanases under optimized regime using agro-wastes. Thus, it could find immense industrial applications including large scale cellulose conversion to bioethanol.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Availability of data and materials

All data generated during this study have been incorporated in this communication either as main data or as a supplementary electronic file.

Code availability

Not applicable.

References

  1. Sadhu S, Maiti TK. Cellulase production by bacteria: a review. Microbiol Res J. 2013;3:235–58.

    Google Scholar 

  2. Gastelum-Arellanez A, Paredes-López O, Olalde-Portugal V. Extracellular endoglucanase activity from Paenibacillus polymyxa BEb-40: production, optimization and enzymatic characterization. World J Microbiol Biotechnol. 2014;30:2953–65.

    Article  CAS  PubMed  Google Scholar 

  3. Pandey A. Biofuels: alternative feedstocks and conversion processes. Cambridge: Academic Press; 2011.

    Google Scholar 

  4. Maki M, Leung KT, Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int J Biol Sci. 2009;5(5):500–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Zhang XZ, Zhang YHP. Cellulases: characteristics, sources, production, and applications, Bioprocessing technologies in biorefinery for sustainable production of fuels, chemicals, and polymers. Hoboken: Wiley; 2013. p. 131–46.

    Google Scholar 

  6. Balan V. Current challenges in commercially producing biofuels from lignocellulosic biomass. Int Sch Res Not. 2014;1:31.

    Google Scholar 

  7. Zhao C, Deng L, Fang H. Mixed culture of recombinant Trichoderma reesei and Aspergillus niger for cellulase production to increase the cellulose degrading capability. Biomass Bioenerg. 2018;112:93–8.

    Article  CAS  Google Scholar 

  8. Ariffin H, Abdullah N, Kalsom MU, Shirai Y, Hassan M. Production and characterization of cellulase by Bacillus pumilus EB3. Int J Eng Technol. 2006;3(1):47–53.

    Google Scholar 

  9. Rastogi G, Bhalla A, Adhikari A, Bischoff KM, Hughes SR, Christopher LP, Sani RK. Characterization of thermostable cellulases produced by Bacillus and Geobacillus strains. Bioresour Technol. 2010;101(22):8798–806.

    Article  CAS  PubMed  Google Scholar 

  10. Patel MA, Ou MS, Ingram LO, Shanmugam K. Simultaneous saccharification and co-fermentation of crystalline cellulose and sugar cane bagasse hemicellulose hydrolysate to lactate by a thermotolerant acidophilic Bacillus sp. Biotechnol Prog. 2005;21(5):1453–60.

    Article  CAS  PubMed  Google Scholar 

  11. Zhuang J, Marchant MA, Nokes SE, Strobel HJ. Economic analysis of cellulase production methods for bio-ethanol. Appl Eng Agric. 2007;23(5):679–87.

    Article  Google Scholar 

  12. Chellapandi P, Jani HM. Production of endoglucanase by the native strains of Streptomyces isolates in submerged fermentation. Braz J Microbiol. 2008;39(1):122–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Annamalai N, Rajeswari MV, Balasubramanian T. Enzymatic saccharification of pretreated rice straw by cellulase produced from Bacillus carboniphilus CAS 3 utilizing lignocellulosic wastes through statistical optimization. Biomass Bioenerg. 2014;68:151–60.

    Article  CAS  Google Scholar 

  14. Deka D, Bhargavi P, Sharma A, Goyal D, Jawed M, Goyal A. Enhancement of cellulase activity from a new strain of Bacillus subtilis by medium optimization and analysis with various cellulosic substrates. Enzyme Res. 2011;2011:1–8.

    Article  CAS  Google Scholar 

  15. Ma L, Lu Y, Yan H, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Screening of cellulolytic bacteria from rotten wood of Qinling (China) for biomass degradation and cloning of cellulases from Bacillus methylotrophicus. BMC Biotechnol. 2020;20:1.

    Article  Google Scholar 

  16. Cho KM, Hong SY, Lee SM, Kim YH, Kahng GG, Kim H, Yun HD. A cel44C-man26A gene of endophytic Paenibacillus polymyxa GS01 has multi-glycosyl hydrolases in two catalytic domains. Appl Microbiol Biotechnol. 2006;73(3):618–30.

    Article  CAS  PubMed  Google Scholar 

  17. Mormeneo M, Pastor FJ, Zueco J. Efficient expression of a Paenibacillus barcinonensis endoglucanase in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol. 2012;39(1):115–23.

    Article  CAS  PubMed  Google Scholar 

  18. Akaracharanya A, Taprig T, Sitdhipol J, Tanasupawat S. Characterization of cellulase producing Bacillus and Paenibacillus strains from Thai soils. J Appl Pharm Sci. 2014;4(5):6.

    Google Scholar 

  19. Liang YL, Zhang Z, Wu M, Wu Y, Feng JX. Isolation, screening, and identification of cellulolytic bacteria from natural reserves in the subtropical region of China and optimization of cellulase production by Paenibacillus terrae ME27-1. Biomed Res Int. 2014;2014:1.

    Google Scholar 

  20. Madhaiyan M, Poonguzhali S, Saravanan VS, Duraipandiyan V, Al-Dhabi NA, Kwon SW, Whitman WB. Paenibacillus polysaccharolyticus sp. nov., a xylanolytic and cellulolytic bacteria isolated from leaves of Bamboo Phyllostachys aureosulcata. Int J Syst Evol Microbiol. 2017;67(7):2127–33.

    Article  CAS  PubMed  Google Scholar 

  21. Almuharef I, Rahman MS, Qin W. High production of cellulase by a newly isolated strain Paenibacillus sp. IM7. J Waste Biomass Valori. 2019;2019:1–10.

    Google Scholar 

  22. Yang L, Peplowski L, Shen Y, Yang H, Chen X, Shen W, Xia Y. Enhancing thermostability and activity of sucrose phosphorylase for high-level production of 2-O-α-D-glucosylglycerol. Syst Microbiol and Biomanuf. 2022. https://doi.org/10.1007/s43393-022-00090-y.

    Article  Google Scholar 

  23. Zhou H, Zheng P, Chen P, Yu X, Wu D. Enhanced thermostability and catalytic efficiency of glucose oxidase in Pichia Pastoris. Syst Microbiol and Biomanuf. 2022;2:296–304.

    Article  CAS  Google Scholar 

  24. Schaechter M. Encyclopedia of microbiology. Cambridge: Academic Press; 2009.

    Google Scholar 

  25. Nigam P, Singh D. Solid-state (substrate) fermentation systems and their applications in biotechnology. J Basic Microbiol. 1994;34(6):405–23.

    Article  CAS  Google Scholar 

  26. Reczey K, Szengyel Z, Eklund R, Zacchi G. Cellulase production by T. reesei. Bioresour Technol. 1996;57(1):25–30.

    Article  CAS  Google Scholar 

  27. Balusu R, Paduru RM, Seenayya G, Reddy G. Production of ethanol from cellulosic biomass by Clostridium thermocellum SS19 in submerged fermentation: screening of nutrients using Plackett-Burman design. Appl Biochem Biotechnol. 2004;117(3):133–41.

    Article  CAS  PubMed  Google Scholar 

  28. Stevenson L, Phillips F, O’Sullivan K, Walton J. Wheat bran: its composition and benefits to health, a European perspective. Int J Food Sci Nutr. 2012;63(8):1001–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Vasudeo Z, Lew C. Optimization of culture conditions for production of cellulase by a thermophilic Bacillus strain. J Chem Chemical Eng. 2011;5(6):521–7.

    CAS  Google Scholar 

  30. Li Y, Cui F, Liu Z, Xu Y, Zhao H. Improvement of xylanase production by Penicillium oxalicum ZH-30 using response surface methodology. Enzyme Microb Technol. 2007;40(5):1381–8.

    Article  CAS  Google Scholar 

  31. Ferreira S, Duarte AP, Ribeiro MH, Queiroz JA, Domingues FC. Response surface optimization of enzymatic hydrolysis of Cistus ladanifer and Cytisus striatus for bioethanol production. Biochem Eng J. 2009;45(3):192–200.

    Article  CAS  Google Scholar 

  32. Xu R, Ma S, Wang Y, Liu L, Li P. Screening, identification and statistic optimization of a novel exopolysaccharide producing Lactobacillus paracasei HCT. Afr J Microbiol Res. 2010;4:783–95.

    CAS  Google Scholar 

  33. Özer A, Gürbüz G, Çalimli A, Körbahti BK. Biosorption of copper (II) ions on Enteromorpha prolifera: application of response surface methodology (RSM). Chem Eng Technol. 2009;146(3):377–87.

    Article  CAS  Google Scholar 

  34. Sreena CP, Sebastian D. Augmented cellulase production by Bacillus subtilis strain MU S1 using different statistical experimental designs. J Genet Eng Biotechnol. 2018;16(1):9–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Yadav S, Dubey SK. Cellulose degradation potential of Paenibacillus lautus strain BHU3 and its whole genome sequence. Bioresour Technol. 2018;262:124–31.

    Article  CAS  PubMed  Google Scholar 

  36. Yadav S, Pandey AK, Dubey SK. Molecular modeling, docking and simulation dynamics of β-glucosidase reveals high-efficiency, thermo-stable, glucose tolerant enzyme in Paenibacillus lautus BHU3 strain. Int J Biol Macromol. 2020;168:371–82.

    Article  PubMed  CAS  Google Scholar 

  37. Pucci F, Kwasigroch JM, Rooman M. SCooP: an accurate and fast predictor of protein stability curves as a function of temperature. J Bioinformatics. 2017;33(21):3415–22.

    Article  CAS  Google Scholar 

  38. Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596(7873):583–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8. Proteins Struct Funct Bioinform. 2009;77(S9):114–22.

    Article  CAS  Google Scholar 

  40. Schüttelkopf AW, Van Aalten DM. PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr D Biol Crystallogr. 2004;60(8):1355–63.

    Article  PubMed  CAS  Google Scholar 

  41. Teather RM, Wood PJ. Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol. 1982;43(4):777–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ghose T. Measurement of cellulase activities. Pure Appl Chem. 1987;59(2):257–68.

    Article  CAS  Google Scholar 

  43. López-Mondéjar R, Zühlke D, Becher D, Riedel K, Baldrian P. Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems. Sci Rep. 2016;6:25279.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Lee YJ, Kim BK, Lee BH, Jo KI, Lee NK, Chung CH, Lee YC, Lee JW. Purification and characterization of cellulase produced by Bacillus amyoliquefaciens DL-3 utilizing rice hull. Bioresour Technol. 2008;99(2):378–86.

    Article  CAS  PubMed  Google Scholar 

  45. Vasic K, Knez Z, Leitgeb M. Bioethanol production by enzymatic hydrolysis from different lignocellulosic sources. Molecules. 2021;26:1–23.

    Article  CAS  Google Scholar 

  46. Ejaz U, Sohail M, Ghanemi A. Cellulases: from bioactivity to a variety of industrial applications. Biomimetics (Basel, Switzerl). 2021;6:1–11.

    Google Scholar 

  47. Lemos LN, Pereira RV, Quaggio RB, Martins LF, Moura L, da Silva AR, Antunes LP, da Silva AM, Setubal JC. Genome-centric analysis of a thermophilic and cellulolytic bacterial consortium derived from composting. Front Microbiol. 2017;8:644.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Wang W, Archbold T, Lam JJ. A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota. Sci Rep. 2019;9:1–13.

    CAS  Google Scholar 

  49. Petersen L, Ardèvol A, Rovira C, Reilly PJ. Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: a QM/MM metadynamics study. J Phys Chem. 2009;113(20):7331–9.

    Article  CAS  Google Scholar 

  50. Abdel-Mawgoud AM, Aboulwafa MM, Hassouna NAH. Optimization of surfactin production by Bacillus subtilis Isolate BS5. Appl Biochem Biotechnol. 2008;150(3):305–25.

    Article  CAS  PubMed  Google Scholar 

  51. Reddy L, Wee YJ, Yun JS, Ryu HW. Optimization of alkaline protease production by batch culture of Bacillus sp. RKY3 through Plackett-Burman and response surface methodological approaches. Bioresour Technol. 2008;99(7):2242–9.

    Article  CAS  PubMed  Google Scholar 

  52. Sukumaran RK, Singhania RR, Pandey A. Microbial cellulases-production, applications and challenges. 2005.

  53. Yin LJ, Huang PS, Lin HH. Isolation of cellulase-producing bacteria and characterization of the cellulase from the isolated bacterium Cellulomonas sp. YJ5. J Agric Food Chem. 2010;58(17):9833–7.

    Article  CAS  PubMed  Google Scholar 

  54. Swathy R, Rambabu K, Banat F, Ho SH, Chu DT, Show PL. Production and optimization of high grade cellulase from waste date seeds by Cellulomonas uda NCIM 2353 for biohydrogen production. Int J Hydrogen Energ. 2020;45(42):22260–70.

    Article  CAS  Google Scholar 

  55. Waeonukul R, Kyu KL, Sakka K, Ratanakhanokchai K. Isolation and characterization of a multienzyme complex (cellulosome) of the Paenibacillus curdlanolyticus B-6 grown on Avicel under aerobic conditions. J Biosci Bioeng. 2009;107(6):610–4.

    Article  CAS  PubMed  Google Scholar 

  56. Asha BM, Revathi M, Yadav A, Sakthivel N. Purification and characterization of a thermophilic cellulase from a novel cellulolytic strain, Paenibacillus barcinonensis. J Microbiol Biotechnol. 2012;22(11):1501–9.

    Article  CAS  PubMed  Google Scholar 

  57. Paudel YP, Qin W. Characterization of novel cellulase-producing bacteria isolated from rotting wood samples. Appl Biochem Biotechnol. 2015;177(5):1186–98.

    Article  CAS  PubMed  Google Scholar 

  58. Tangüler H, Erten H. The effect of different temperatures on autolysis of baker’s yeast for the production of yeast extract. Turk J Agric For. 2009;33(2):149–54.

    Google Scholar 

  59. Mihajlovski KR, Davidović SZ, Carević MB, Radovanović NR, Šiler-Marinković SS, Rajilić-Stojanović MD, Dimitrijević-Branković SI. Carboxymethyl cellulase production from a Paenibacillus sp. Hemijska Industrija. 2016;70(3):329–38.

    Article  Google Scholar 

  60. Almuharef I, Rahman MS, Qin W. High production of cellulase by a newly isolated strain Paenibacillus sp. IM7. J Waste Biomass Valoriz. 2019;11:1–10.

    Google Scholar 

  61. Sun S, Zhang Y, Liu K, Chen X, Jiang C, Huang M, Zang H, Li C. Insight into biodegradation of cellulose by psychrotrophic bacterium Pseudomonas sp. LKR-1 from the cold region of China: optimization of cold-active cellulase production and the associated degradation pathways. Cellulose. 2020;27(1):315–33.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Authors are gratefully acknowledged to Coordinator, Centre of Advanced Study, Botany, for providing essential facilities related to this study.

Funding

This research work was financially assisted by University Grants Commission, Government of India, New Delhi, in the form of Junior and Senior Research Fellowship to Suman (Grant No. 09/013 (0617)/2016-EMR-I).

Author information

Author notes

  1. Suman Yadav and Anand Kumar Pandey have equal contribution.

Authors and Affiliations

  1. Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India

    Suman Yadav & Suresh Kumar Dubey

  2. Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, 284128, India

    Anand Kumar Pandey

Authors
  1. Suman Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anand Kumar Pandey
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Suresh Kumar Dubey
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SKD: conceptualization, supervised the research work. SY: performed the research and analyzed the wet lab data. AKP: ran the MD simulations and analyzed the data. SY, AKP, SKD: writing and review the ms.

Corresponding author

Correspondence to Suresh Kumar Dubey.

Ethics declarations

Conflict of interest

The authors that declare there is no conflict of interest for the present manuscript.

Compliance with ethics requirements

This article does not contain any studies with human or any animals participants.

Consent to participate

Not applicable.

Consent for publication

Not applicable.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 894 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yadav, S., Pandey, A.K. & Dubey, S.K. Evaluation of thermostable endoglucanase in Paenibacillus lautus strain BHU3 for yield enhancement. Syst Microbiol and Biomanuf 2, 607–622 (2022). https://doi.org/10.1007/s43393-022-00105-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s43393-022-00105-8

Keywords

Search

Navigation