Innovations in CAZyme Gene Diversity and Its Modification for Biorefinery Applications

Overview

Journal Biotechnol Rep (Amst)

Specialty Biotechnology

Date 2020 Sep 23

PMID 32963975

Citations 17

Authors

Dixita Chettri

Ashwani Kumar Verma

Anil Kumar Verma

Affiliations

Soon will be listed here.

Abstract

For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.

Citing Articles

Comparative Genomic Analyses of Pathotypes with Different Virulence Levels and Lifestyles.

Morelos-Martinez M, Cano-Camacho H, Diaz-Tapia K, Simpson J, Lopez-Romero E, Zavala-Paramo M J Fungi (Basel). 2024; 10(9).

PMID: 39330411 PMC: 11432805. DOI: 10.3390/jof10090651.

Characterization of a GDS(L)-like hydrolase from Pleurotus sapidus with an unusual SGNH motif.

Fingerhut M, Henrich L, Lauber C, Broel N, Ghezellou P, Karrer D AMB Express. 2024; 14(1):98.

PMID: 39225819 PMC: 11372007. DOI: 10.1186/s13568-024-01752-x.

Elucidating the biotechnological potential of the genera Parageobacillus and Saccharococcus through comparative genomic and pan-genome analysis.

Mol M, De Maayer P BMC Genomics. 2024; 25(1):723.

PMID: 39054411 PMC: 11270796. DOI: 10.1186/s12864-024-10635-1.

Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes.

Klimek D, Herold M, Calusinska M BMC Genomics. 2024; 25(1):523.

PMID: 38802741 PMC: 11131199. DOI: 10.1186/s12864-024-10413-z.

Current models in bacterial hemicellulase-encoding gene regulation.

Novak J, Gardner J Appl Microbiol Biotechnol. 2024; 108(1):39.

PMID: 38175245 PMC: 10766802. DOI: 10.1007/s00253-023-12977-4.

References

Zappe H, Jones D, Woods D . Cloning and expression of Clostridium acetobutylicum endoglucanase, cellobiase and amino acid biosynthesis genes in Escherichia coli. J Gen Microbiol. 1986; 132(5):1367-72. DOI: 10.1099/00221287-132-5-1367. View

Hagen L, Brooke C, Shaw C, Norbeck A, Piao H, Arntzen M . Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISME J. 2020; 15(2):421-434. PMC: 8026616. DOI: 10.1038/s41396-020-00769-x. View

Chuankhayan P, Hsieh C, Huang Y, Hsieh Y, Guan H, Hsieh Y . Crystal structures of Aspergillus japonicus fructosyltransferase complex with donor/acceptor substrates reveal complete subsites in the active site for catalysis. J Biol Chem. 2010; 285(30):23251-64. PMC: 2906318. DOI: 10.1074/jbc.M110.113027. View

Bredon M, Dittmer J, Noel C, Moumen B, Bouchon D . Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate. Microbiome. 2018; 6(1):162. PMC: 6142342. DOI: 10.1186/s40168-018-0536-y. View

Geiser E, Reindl M, Blank L, Feldbrugge M, Wierckx N, Schipper K . Activating Intrinsic Carbohydrate-Active Enzymes of the Smut Fungus Ustilago maydis for the Degradation of Plant Cell Wall Components. Appl Environ Microbiol. 2016; 82(17):5174-85. PMC: 4988183. DOI: 10.1128/AEM.00713-16. View

Munir R, Schellenberg J, Henrissat B, Verbeke T, Sparling R, Levin D . Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability. PLoS One. 2014; 9(8):e104260. PMC: 4125193. DOI: 10.1371/journal.pone.0104260. View

Mo X, Chen C, Pang H, Feng Y, Feng J . Identification and characterization of a novel xylanase derived from a rice straw degrading enrichment culture. Appl Microbiol Biotechnol. 2010; 87(6):2137-46. DOI: 10.1007/s00253-010-2712-2. View

Proba K, Worn A, Honegger A, Pluckthun A . Antibody scFv fragments without disulfide bonds made by molecular evolution. J Mol Biol. 1998; 275(2):245-53. DOI: 10.1006/jmbi.1997.1457. View

Mhetras N, Liddell S, Gokhale D . Purification and characterization of an extracellular β-xylosidase from Pseudozyma hubeiensis NCIM 3574 (PhXyl), an unexplored yeast. AMB Express. 2016; 6(1):73. PMC: 5023640. DOI: 10.1186/s13568-016-0243-7. View

10.

Lyu Q, Zhang K, Zhu Q, Li Z, Liu Y, Fitzek E . Structural and biochemical characterization of a multidomain alginate lyase reveals a novel role of CBM32 in CAZymes. Biochim Biophys Acta Gen Subj. 2018; 1862(9):1862-1869. DOI: 10.1016/j.bbagen.2018.05.024. View

11.

Linger J, Adney W, Darzins A . Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl Environ Microbiol. 2010; 76(19):6360-9. PMC: 2950452. DOI: 10.1128/AEM.00230-10. View

12.

Gilbert J, Dupont C . Microbial metagenomics: beyond the genome. Ann Rev Mar Sci. 2011; 3:347-71. DOI: 10.1146/annurev-marine-120709-142811. View

13.

Rosnow J, Anderson L, Nair R, Baker E, Wright A . Profiling microbial lignocellulose degradation and utilization by emergent omics technologies. Crit Rev Biotechnol. 2016; 37(5):626-640. DOI: 10.1080/07388551.2016.1209158. View

14.

Mattanovich D, Branduardi P, Dato L, Gasser B, Sauer M, Porro D . Recombinant protein production in yeasts. Methods Mol Biol. 2011; 824:329-58. DOI: 10.1007/978-1-61779-433-9_17. View

15.

Pauly M, Keegstra K . Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J. 2008; 54(4):559-68. DOI: 10.1111/j.1365-313X.2008.03463.x. View

16.

Stark L, Giersch T, Wunschiers R . Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics. Anaerobe. 2013; 29:85-90. DOI: 10.1016/j.anaerobe.2013.09.007. View

17.

Gomez-Flores M, Nakhla G, Hafez H . Microbial kinetics of Clostridium termitidis on cellobiose and glucose for biohydrogen production. Biotechnol Lett. 2015; 37(10):1965-71. DOI: 10.1007/s10529-015-1891-4. View

18.

Shao Z, Zhao H, Giver L, Arnold F . Random-priming in vitro recombination: an effective tool for directed evolution. Nucleic Acids Res. 1998; 26(2):681-3. PMC: 147287. DOI: 10.1093/nar/26.2.681. View

19.

van Zyl P, Moodley V, Rose S, Roth R, van Zyl W . Production of the Aspergillus aculeatus endo-1,4-beta-mannanase in A. niger. J Ind Microbiol Biotechnol. 2009; 36(4):611-7. DOI: 10.1007/s10295-009-0551-x. View

20.

Sun X, Liu Z, Qu Y, Li X . The effects of wheat bran composition on the production of biomass-hydrolyzing enzymes by Penicillium decumbens. Appl Biochem Biotechnol. 2008; 146(1-3):119-28. DOI: 10.1007/s12010-007-8049-3. View