Microbial Enzymes E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Fachliteratur
• Sprache: Englisch

Seitenzahl: 1558

Veröffentlichungsjahr: 2024

Beschreibung

Comprehensive discussion of production and purification strategies for microbial enzymes important to various industries, from food and beverages to pharmaceuticals

Microbial Enzymes provides expert insight into diverse aspects of microbial enzymes, highlighting strategies for their production, purification, and manipulation, elucidating eco-friendly industrial applications, and discussing several production processes, such as the production of cellulose and non-synthetic indigo dye. This book emphasizes recent technological interventions in microbial enzyme technology like metagenomics, system biology, molecular biology, genomics, directed evolution, and bioinformatics.

The important microbial enzymes highlighted in this book include xylanases, ureases, methane monooxygenase, polyhydroxyalkanoates, pectinases, peroxidases, α-L-rhamnosidase, alkane hydroxylases, laccases, proteases, gallic acid decarboxylase, chitinases, beta-glucosidase, lipases, inulinases, tannase, mycozyme, ACC deaminase, ligninolytic enzymes, and many more.

Novel treatment methods involving strains of microorganisms with desirable properties applicable in the process of bioremediation through mitigating climate concern, increasing green production technology, improving agriculture productivity, and providing a means of earning a livelihood are discussed. Readers will also gain state-of-the-art background knowledge on existing technologies and their current challenges and future prospects.

Contributed to by leading experts in the field and edited by four highly qualified academics, Microbial Enzymes explores important topics including:

• Strategies for the discovery and enhancement of enzyme function, and potentials of system biology to better understand the kinetics of industrially important enzymes
• Production and therapeutic applications of monoclonal antibodies in cancer and other diseases, and characterization of tannase as a virulence factor
• Opportunities to produce enzymes through food waste and byproducts, and recent developments in computational tools
• Use of Omics tools in the discovery of fungal enzymes and secondary metabolites

Microbial Enzymes is a thorough and highly practical reference on the subject for students, scientists, biotechnologists, microbiologists, and policymakers working in environmental microbiology, biotechnology, and environmental sciences.

Leseprobe

Table of Contents

Cover

Table of Contents

Title Page

Copyright

Volume 1

About the Editors

Preface

1 Xylanases: Sources, Production, and Purification Strategies

1.1 Introduction

1.2 Sources, Production, and Purification Strategies

1.3 Structure

1.4 Xylanases as Biocatalyst

1.5 Genomics Studies on Xylanases

1.6 Xylanases as a Promising Enzyme for Industrial Applications

1.7 Industrial Food Applications

1.8 Future Trends

1.9 Conclusions

Acknowledgments

References

2 Exploration of the Microbial Urease and Their Industrial Applications

2.1 Urease Enzyme and Its History

2.2 Urea Hydrolysis

2.3 Sources and Molecular Attributes of Urease Enzyme

2.4 Urease Purification

2.5 Applications of Urease Enzyme

2.6 Conclusion and Future Aspects

References

3 Methane Monooxygenase Production and Its Limitations

3.1 Introduction

3.2 Classes of MMO

3.3 Structure and Active Site of MMO

3.4 Mechanism of Action

3.5 Regulation of MMO

3.6 Sources of MMO

3.7 Genetic Engineering of MMOs

3.8 MMO Production

3.9 Applications of MMO and Methanotrophs

3.10 Limitations in MMO Production

3.11 Conclusion

References

4 Polyhydroxyalkanoates: An Eco-sustainable Development Toward a Green World

4.1 Introduction

4.2 Structure, Classification, and Properties of PHAs

4.3 Production and Synthesis of PHAs

4.4 Applications of PHAs in the Health Sector

4.5 Tissue Engineering

4.6 Bio-implantation Patches

4.7 Drug Delivery

4.8 Surgical Applications

4.9 Orthopedic Applications

4.10 Industrial Applications of PHAs

4.11 Agricultural Applications

4.12 Conclusion and Future Prospective

Acknowledgments

References

5 An Insight into Production Strategies for Microbial Pectinases: An Overview

5.1 Introduction

5.2 Microbial Pectinases

5.3 Microbial Pectinases: Mode of Action and Classifications

5.4 Sources of Microbial Pectinases

5.5 Production of Microbial Pectinases

5.6 Bioreactors-based Production of Microbial Pectinases

5.7 Response Surface Methodology for Enhancing Production of Microbial Pectinases

5.8 Purification of Microbial Pectinases

5.9 Immobilization of Microbial Pectinases

5.10 Future Prospects and Conclusion

References

6 Hydrocarbon-degrading Enzymes from Mangrove-associated Fungi and Their Applications

6.1 Introduction

6.2 Hydrocarbon Pollution

6.3 Mangrove Environments

6.4 Mangrove-associated Fungi as Hydrocarbon Degraders

6.5 Ligninolytic Enzymes from Mangrove-associated Fungi

6.6 Applications and Future Prospects

6.7 Conclusion

References

7 Industrially Important Microbial Enzymes Production and Their Applications

7.1 Introduction

7.2 Sources of Industrially Important Microbial Enzymes

7.3 Application of Microbial Enzymes in Industries

7.4 Challenges and Future Trends of Microbial Enzymes

7.5 Conclusion

Authors’ Contributions

Acknowledgments

References

8 Peroxidases: Role in Bioremediation

8.1 Introduction

8.2 Classification of Peroxidases

8.3 Applications of Different Peroxidases for Environmental Pollution Management

8.4 Conclusion

Acknowledgment

References

9 Microbial α-L-Rhamnosidase and Its Significance in Therapeutics

9.1 Introduction

9.2 Sources

9.3 Substrate Specificity and Optimality

9.4 Isolation of Microbial Strains for Producing α-L

-Rhamnosidase Enzyme

9.5 Assay Method

9.6 Purification Method

9.7 Biochemical Properties and Application of α-L

-Rhamnosidase

9.8 Summary

References

10 The Use of Microbial Enzymes in the Food Industries: A Global Perspective

10.1 Introduction

10.2 Global Perspective and Demand for Microbial Enzymes in the Food Industry

10.3 Production of Industrial Enzymes

10.4 Approach to Boost Properties of Microbial Enzymes

10.5 Microbial Enzymes in Food Industries

10.6 Conclusion and Future Perspectives

References

11 Alkane Hydroxylases: Sources and Applications

11.1 Introduction

11.2 Sources of Alkane Hydroxylases

11.3 Production, Purification, and Characterization of Alkane Hydroxylases

11.4 Applications of Alkane Hydroxylases

11.5 Future Prospects

11.6 Conclusion

References

12 An Overview of Production of Bacterial and Fungal Laccases and Their Industrial Applications

12.1 Introduction

12.2 Structure of Laccase

12.3 Mode of Action

12.4 Sources of Laccase

12.5 Substrates, Mediators, and Screening of Laccases

12.6 Production of Bacterial Laccases

12.7 Production of Fungal Laccases

12.8 Applications of Laccases

12.9 Conclusion and Future Scope

References

13 Magic of Microbial Enzymes: Earthworm’s Gut as a Bioreactor

13.1 Introduction

13.2 Classification of Enzymes

13.3 Earthworms: Intestines of the Earth

13.4 Earthworms and Their Relation with Microbes and Enzymes

13.5 Importance of Enzymes Related to Earthworms and the Associated Microorganisms

13.6 Conclusions and Future Perspectives

References

14 Proteases from Thermophilic Bacteria: Their Significant Characteristics and Recombinant Production

14.1 Introduction

14.2 Thermophilic Bacteria

14.3 Thermophilic Proteases

14.4 Stability of Thermophilic Proteases and Underlying Mechanisms

14.5 Significance of Thermophilic Proteases

14.6 Recombinant Thermophilic Protease Production Strategies and Related Challenges

14.7 Enzyme Engineering Strategies

14.8 Applications

14.9 Conclusion and Future Perspectives

References

15 Mining and Redesigning of Microbial Enzymes for the Degradation of Organophosphorus Pesticides

15.1 Introduction

15.2 Selection of the Starting Gene

15.3 DNA Level Processes for the Creation of Gene Library

15.4 Screening of the Gene Library

15.5 Characterization of Designed Enzymes

15.6 Conclusion and Future Perspectives

References

16 Use of Omics Tools Toward the Discovery of Fungal Enzymes and Secondary Metabolites

16.1 Introduction

16.2 Biotechnological Applications of Key Fungal Enzymes

16.3 Biotechnological Potential of Fungal Metabolites

16.4

In Silico

Tools for Fungal Enzymes and Secondary Metabolites Prediction

16.5 Use of

In Silico

Tools for the Prediction of Fungal Enzymes and Secondary Metabolites

16.6 Implications and Limitations of the

In Silico

Studies in Fungal Biology

16.7 Conclusions and Prospects

References

17 Bioprospecting of Microbial Enzymes with Application in Environmental Biotechnology: An Omic Approach

17.1 Introduction

17.2 Environmental Biotechnology Areas

17.3 Microbial Enzymes Applied in Environmental Recovery

17.4 Microbial Enzymes for Bioproduct Manufacturing

17.5 Omics Approaches for Bioprospecting Enzymes

17.6 Conclusion and Perspectives

References

18 Recent Trends in Computational Tools for Industrially Important Enzymes

18.1 Introduction

18.2 Strategies for Discovering Enzymes

18.3 Computational Methods for Enzyme Function Prediction

18.4 Conclusion

Acknowledgments

References

19 Microbial Gallic Acid Decarboxylase: An Overview and Advancement in Application Potential Study Through Bioinformatics

19.1 Introduction

19.2 Isolation and Selection of Gallic Acid Decarboxylase Producing Microbes

19.3 Purification of GAD Enzyme and Biomolecular Properties

19.4 Gallic Acid Decarboxylase Assay

19.5 Molecular Biological Aspects of Gallic Acid Decarboxylase with Special Reference to Human Gut Lactic Acid Bacteria

19.6

In Silico

Aspects of Gallic Acid Decarboxylase

19.7 Discussion

19.8 Conclusions

References

20 Microbial Chitinases: Potential Applications in Agriculture

20.1 Introduction

20.2 Chitin Structure and Its Degradation by Chitinases

20.3 Microbial Sources of Chitinase

20.4 Chitinolytic Microorganisms as Potential Biological Control Agents or Biopesticides

20.5 Metagenomic Approaches as a Tool to Unravel New Microbial Chitinases

20.6 Conclusion and Future Perspectives

References

Volume 2

21 β-Glucosidase Production and Its Applications

21.1 Introduction

21.2 Structure and Specificity of β-Glucosidase

21.3 Classes of β-Glucosidase Enzyme

21.4 Mechanism of Reaction Catalysis of β-Glucosidase

21.5 Source of β-Glucosidase

21.6 β-Glucosidase Production

21.7 Methods of Bacterial β-Glucosidase Production

21.8 Methods of Fungal β-Glucosidase Production

21.9 Genetic Engineering of β-Glucosidase

21.10 Applications

21.11 Conclusion

References

22 Mining of Enzyme with Novel Activity Through Combination of Genomic Information and Traditional Biochemical Approach

22.1 Introduction

22.2 Experimental Identification of UDP-

N

-acetylglucosamine Biosynthetic Pathway in

S. tokodaii

22.3 Experimental Identification of UDP-

N

-acetylgalactosamine Biosynthetic Pathway in

S. tokodaii

22.4 Conclusion and Future Perspectives

References

23 Strategies for Discovery and Enhancement of Enzyme Function: Current Developments and Opportunities

23.1 Introduction

23.2 Bioprospecting of Novel Microbial Extremozymes

23.3 Computational Tools in Protein Engineering for Improved Enzymes

23.4 Conclusion and Future Prospects

References

24 Promises of Systems Biology to Better Understand the Kinetics of Industrially Important Enzymes

24.1 Introduction

24.2 System Biology: An Integration of Interdisciplinary Approaches

24.3 Data Integration and Model Construction in System Biology

24.4 Methods of System Biology

24.5 Challenges and Limitation

24.6 Conclusion

Acknowledgment

References

25 Metagenomics: New Insight in Microbial Diagnosis

25.1 Introduction

25.2 Classification

25.3 Methods and Protocols

25.4 Sequencing Platforms

25.5 Milestones in Metagenomics

25.6 Conclusions and Future Perspectives

References

26 Production and Therapeutic Applications of Monoclonal Antibodies in Cancer and Other Diseases

26.1 Introduction

26.2 Background of Monoclonal Antibodies

26.3 Nomenclature of Monoclonal Antibodies

26.4 Structure of Monoclonal Antibodies

26.5 Monoclonal Antibody Production

26.6 Therapeutic Applications of Monoclonal Antibody

26.7 Challenges and Future Prospects

Acknowledgments

References

27 Microbial Alkaline Protease: Production, Purification, and Applications

27.1 Introduction

27.2 Alkaline Protease Production

27.3 Purification of Alkaline Proteases

27.4 Applications of Alkaline Protease in Different Industries

27.5 Future Prospects of Using Microbial Alkaline Proteases

27.6 Conclusions

References

28 Microbial Lipases in Modern Detergency: Sources, Production, and Application

28.1 Introduction

28.2 Detergent Features

28.3 Enzymes in Detergents

28.4 Lipases and Their Characteristics

28.5 Microbial Lipases: Sources, Production, and Purification

28.6 Diverse Industrial Applications of Microbial Lipases

28.7 Conclusion and Future Perspectives

References

29 Production of Inulin Oligosaccharides from Microbial Inulinases and Their Applications

29.1 Introduction

29.2 Substrate: Inulin

29.3 Inulin Oligosaccharides

29.4 Strategies to Enhance Production of Inulin Oligosaccharides

29.5 Applications of Inulin Oligosaccharides (IOS)

29.6 Commercial Statistics of Inulin Oligosaccharide Production with Future Perspectives

29.7 Conclusion

References

30 Characterization of Phytopathogen’s Tannase as a Virulence Factor

30.1 Introduction

30.2 Material and Methods

30.3 Results and Discussion

30.4 Correlation Between Inhibition of Tannase Activity and Pathogenicity

30.5 Conclusion

References

31 Mycozyme-based Functional Oligosaccharides

31.1 Introduction

31.2 Functional Oligosaccharides

31.3 Conclusion

References

32 Microbial Laccases: Structure, Function, and Applications

32.1 Introduction

32.2 Structure, Classification, and Mode of Action of Laccases

32.3 Mode of Action of Laccases

32.4 The Biological Function of Laccase Enzymes Based on Their Source

32.5 Industrial Application of Laccases

32.6 Sensors and Biofuel Cells

32.7 Plastics and Biopolymers

32.8 Paints and Coatings

32.9 Nanobiotechnology

32.10 Ethanol Production

32.11 Conclusions

References

33 Microbial ACC Deaminase: Stress Modulators in Plants

33.1 Introduction

33.2 Ethylene Synthesis and Response in Plants

33.3 Biochemistry of ACC Deaminase

33.4 Genetic Regulation and Enzymology of ACC Deaminase

33.5 Role of ACC Deaminase from PGPR in Biotic and Abiotic Stresses

33.6 Conclusions and Future Viewpoints

Acknowledgments

References

34 Ligninolytic Enzyme: Microbial Sources, Production, Purification, and Biotechnological Applications

34.1 Introduction

34.2 Source of Microbial Ligninolytic Enzymes

34.3 Intein-mediated Affinity-fusion Purification of Ligninolytic Enzyme

34.4 Structural View of Microbial Ligninolytic Enzyme

34.5 Catalytic Cycle of Ligninolytic Enzymes

34.6 Industrial Application of Microbial Ligninolytic Enzymes

34.7 Conclusion

Acknowledgment

References

35 Bioinformatic-driven Research in Microbial Enzymes: An Overview

35.1 Introduction

35.2 Enzyme Mining

35.3 Computational Insight for Enzyme Modeling

35.4 Conclusion

Acknowledgments

References

36 Food Waste and By-products: An Opportunity to Produce Enzymes for Industrial Applications

36.1 Introduction

36.2 Types of Agro-industrial Food Waste

36.3 Food Processing By-products from the Different Industries

36.4 Economic Impact of Food Waste

36.5 Challenges in Enzyme Production

36.6 Production of Enzymes from the Fermentation Process

36.7 Fermentation Strategies and Enzyme Industries

36.8 New Trends and Challenges in Enzyme Production Using By-products

36.9 Industrial Important Enzymes Production

36.10 Enzyme Immobilization Strategies

36.11 Fermentation Processes and Control of Process

36.12 Conclusions

References

Index

End User License Agreement

List of Tables

Chapter 1

Table 1.1 Thermophilic and hyper-thermophilic microorganisms producing therm...

Chapter 2

Table 2.1 Urease-producing microbial sources and their habitat.

Chapter 4

Table 4.1 Types of PHAs.

Table 4.2 List of microorganisms producing PHAs.

Table 4.3 List of PHAs producing microorganisms having clinical importance....

Chapter 5

Table 5.1 The sources of microbial pectinases.

Table 5.2 Bioreactor based production of microbial pectinases.

Table 5.3 RSM-based enhancement of production of microbial pectinases.

Table 5.4 Purification studies of microbial pectinases.

Table 5.5 Immobilization studies of microbial pectinase over different polym...

Chapter 6

Table 6.1 Fungi associated with mangrove ecosystems and their reported hydro...

Table 6.2 Mangrove-associated fungi with ligninolytic enzymes used for hydro...

Chapter 7

Table 7.1 Production of microbial enzymes, sources, and their applications i...

Chapter 8

Table 8.1 Examples of oxidoreductases being used for the remediation of real...

Table 8.2 Decolorization and detoxification of synthetic, textile dyes, and ...

Chapter 9

Table 9.1 Source organisms of α-

L

-rhamnosidase enzyme among different class....

Table 9.2 Biochemical and kinetic properties of α-

L

-rhamnosidase from differ...

Chapter 10

Table 10.1 List of companies manufacturing industrial enzymes.

Table 10.2 Industrial microbial enzyme, enzyme classes, types of reaction, a...

Chapter 11

Table 11.1 Different sources of alkane hydroxylases.

Chapter 12

Table 12.1 Sources, production conditions, and properties of bacterial lacca...

Chapter 14

Table 14.1 Recombinant proteases from thermophilic bacteria and their applic...

Chapter 16

Table 16.1 List of commercially important fungal enzymes.

Table 16.2 Secondary metabolites from fungi and their biological activities....

Table 16.3 List of the bioinformatic resources that can be applied for funga...

Chapter 17

Table 17.1 Main factors affecting biological processes.

Table 17.2 Commercial kits used to extract DNA from environmental.

Chapter 18

Table 18.1 Genome mining tools for BGC identification.

Chapter 19

Table 19.1 Microbial sources of gallic acid decarboxylase (GAD).

Table 19.2 Biochemical properties of some microbial gallic acid decarboxylas...

Table 19.3 Sequence properties like isoelectric point (pI), length, instabil...

Table 19.4 Isolated and network aromatic–aromatic interactions in gallic aci...

Table 19.5 Isolated and network salt bridges in gallic acid decarboxylase (6...

Chapter 20

Table 20.1 Recent reports on the application of some microbial chitinases as...

Chapter 21

Table 21.1 Some bacterial and fungal sources of β-glucosidase.

Table 21.2 β-glucosidase production improvement through genetic engineering ...

Chapter 22

Table 22.1 Distribution of three genes in each microorganism.

Chapter 23

Table 23.1 Microbial enzymes obtained from various extreme environments.

Chapter 24

Table 24.1 Representation and description of pathways, software, and tools i...

Chapter 26

Table 26.1 Classical nomenclature of monoclonal antibody based on Internatio...

Table 26.2 Updated International Nonproprietary Name (INN) nomenclature for ...

Table 26.3 FDA-approved monoclonal antibodies (mAbs) for cancer treatment.

Table 26.4 FDA-approved monoclonal antibodies (mAbs) for microbial diseases....

Table 26.5 FDA approved monoclonal antibodies (mAbs) for other diseases.

Chapter 27

Table 27.1 Alkaline protease from bacteria by solid-state fermentation.

Table 27.2 Alkaline protease from bacteria by submerged fermentation.

Table 27.3 Optimum T

0

and pH for different bacterial spp.

Table 27.4 Alkaline protease from Actinomycetes species.

Table 27.5 Alkaline protease from fungi.

Chapter 28

Table 28.1 The enzymes in detergent and their specific actions according to ...

Chapter 29

Table 29.1 Inulin-rich feedstocks [14, 15].

Table 29.2 Reaction conditions for activity of different endo inulinases for...

Table 29.3 Types offeedstocks, fermentation type, and action of inulinases....

Chapter 30

Table 30.1 Tannic acid agar medium composition (100 ml).

Table 30.2 Tannic acid broth medium composition (100 ml).

Table 30.3 Morphological characteristics of the bacterial isolates from vari...

Table 30.4 Growth of Isolates.

Table 30.5 Comparison of tannase activity with or without inhibitor.

Chapter 31

Table 31.1 Mycozyme producing functional oligosaccharides.

Table 31.2 Production strategy of functional oligosaccharides.

Chapter 32

Table 32.1 Laccase-producing organisms, their biochemical characterization, ...

Table 32.2 Recent advances for improving industrial applicability of laccase...

Chapter 33

Table 33.1 List of the PGPR ACC deaminase and their role in different crops ...

Chapter 34

Table 34.1 Source of ligninolytic enzyme, with optimum pH and temperature.

Chapter 35

Table 35.1 Software for metagenomics analysis.

Table 35.2 Different microbial enzymes mined using metagenomics approach.

Table 35.3 Extremophilic enzymes and their sources.

Table 35.4

In silico

tool used for enzyme mining and characterization.

Chapter 36

Table 36.1 Utility of some common enzymes in the food industries [31, 32].

List of Illustrations

Chapter 1

Figure 1.1 3D structure representation of Xys1 from

Streptomyces halstedii

. ...

Figure 1.2 3D structure representation of xylanase from

Thermomyces lanugino

...

Chapter 2

Figure 2.1 General scheme for urease enzyme purification.

Figure 2.2 Schematic representations of some applications of urease.

Chapter 3

Figure 3.1 Different metabolic pathways employed by methanotrophs (organisms...

Figure 3.2 Structural arrangement of the operon responsible for encoding sol...

Figure 3.3 The operons responsible for encoding pMMO (particulate methane mo...

Figure 3.4 sMMO (soluble methane monooxygenase) of

Methylococcus capsulatus

...

Figure 3.5 The representation of

Methylococcus capsulatus

(Bath) pMMO (PDB a...

Figure 3.6 Catalytic process of soluble methane monooxygenase (sMMO), depict...

Figure 3.7 Catalytic cycle of pMMO in the presence of DQH

2

; PT, proton trans...

Figure 3.8 Regulation of the MMO genes in

Methylosinus trichosporium

OB3b by...

Figure 3.9 Distribution of sMMO and pMMO among different types of methane-ut...

Chapter 4

Figure 4.1 Structure of PHAs. (a) Structure of PHAs and accumulation of PHAs...

Figure 4.2 Graphical representation of the diverse applications of PHAs in v...

Chapter 5

Figure 5.1 Pectin and microbial pectinases.

Figure 5.2 Flowchart of bioprocessing of pectinases.

Chapter 6

Figure 6.1 Classification of hydrocarbons.

Figure 6.2 Quantity (tonnes) of oil spilled globally from 1970 to 2020s.

Figure 6.3 A mangrove forest in Malaysia during high tide (a) and low tide (...

Figure 6.4 Pneumatophores (exposed breathing roots) of the mangrove

Avicenni

...

Figure 6.5 Percentage of mangrove coverage per country.

Figure 6.6 Illustrative distribution of associated fungal communities in a m...

Figure 6.7 Percentage of reported mangrove-associated fungi per fungal group...

Chapter 7

Figure 7.1 Different sources of microbial enzymes.

Figure 7.2 Microbial enzymes in different industrial applications [14, 46]....

Figure 7.3 Performance evaluation of the purified amylases Amy586 on bread p...

Figure 7.4 Schematic illustration of lignocellulosic substrates in related f...

Figure 7.5 Starch hydrolysis process in the presence of amylase.

Figure 7.6 Systematic illustration of the production of methanol from biomas...

Chapter 8

Figure 8.1 Peroxidases and their types.

Chapter 9

Figure 9.1 Hydrolysis of naringin into prunin and

L

-rhamnose.

Figure 9.2 Citrus fruits and grapes are great sources of naringin and hesper...

Figure 9.3 (a) Naringin, (b) rutin, (c) quercitrin, (d) hesperidin, (e) neoh...

Figure 9.4 Hydrolysis of

p

-nitrophenyl-α-

L

-rhamnopyranoside by α-

L

-rhamnosid...

Chapter 10

Figure 10.1 A schematic diagram of microbial enzyme production.

Figure 10.2 A schematic diagram illustrating the protein engineering process...

Chapter 11

Figure 11.1 Schematic representation of the catalytic process of alkane hydr...

Figure 11.2 Schematic representation of extraction and purification of alkan...

Figure 11.3 Alkane hydroxylase mediated degradation pathway of

n

-alkane.

Figure 11.4 Proposed DNA repair mechanism by AlkB with methyladenine as subs...

Chapter 12

Figure 12.1 Phylogenetic tree depicting some of the different sources of lac...

Figure 12.2 The active site of laccase. The orientation of copper atoms and ...

Figure 12.3 Different sources of laccase and its various applications.

Chapter 13

Figure 13.1 The classification of enzymes based on the reaction catalyzed. W...

Figure 13.2 Physical, chemical, and biological effects of earthworms on soil...

Figure 13.3 Schematic representation showing the complex interrelationship b...

Chapter 14

Figure 14.1 Thermophiles and their significance.

Chapter 15

Figure 15.1 An overview of protein engineering. Different strategies may be ...

Figure 15.2 Schematic representation of random mutagenesis by error-prone PC...

Figure 15.3 DNA shuffling. This mutagenesis method allows the recombination ...

Figure 15.4 Different methods of high-throughput screening. Colorimetric scr...

Figure 15.5 High-throughput screening by double emulsion method using whole ...

Chapter 16

Figure 16.1 Graphical abstract of the applications of the fungal enzymes/sec...

Chapter 17

Figure 17.1 Main mechanisms of detoxification of xenobiotics.

Figure 17.2 Degradation process or enzymes immobilized in layers of ionic re...

Figure 17.3 Mechanisms of action of hydrolytic enzymes.

Figure 17.4 Biodiesel biosynthesis process.

Figure 17.5 Biosynthesis of bioproducts from industrial waste.

Figure 17.6 PHA biosynthetic metabolic pathway.

PhaA

, β-ketothiolase;

PhaB

, ...

Figure 17.7 Workflow for obtaining the functionality of overexpressed genes ...

Figure 17.8 Overview of new approaches used to improve environmental biotech...

Chapter 18

Figure 18.1 Schematic representation of approaches for mining novel enzymes ...

Chapter 19

Figure 19.1 Decarboxylation of gallic acid by gallic acid decarboxylase into...

Figure 19.2 Amino acid conservations with variations in different sequences ...

Figure 19.3 The crystal structure of gallic acid decarboxylase (homotrimer) ...

Figure 19.4 Secondary structure of gallic acid decarboxylase (PDB ID:7KD9) f...

Figure 19.5 (a) Tunnels, (b) cavities, and (c) voids in structure of gallic ...

Chapter 20

Figure 20.1 Some of the major sources of chitin.

Figure 20.2 Classification of chitinases.

Figure 20.3 Chitinases belong to different glycosyl hydrolase families.

Figure 20.4 Different sources for the isolation of chitinolytic microorganis...

Figure 20.5 A schematic overview of applications of chitinase.

Chapter 21

Figure 21.1 Summary of the cellulose degradation by cellulase enzyme complex...

Figure 21.2 Classification of cellulase enzyme.

Figure 21.3 Crystal structure of TIM (β/α)

8

barrel (PDB code 6YQY): (a) Side...

Figure 21.4 Structure of the active site of β-glucosidase (TsBGL) from

Therm

...

Figure 21.5 Structure β-glucosidase enzymes from various glucosyl hydrolase ...

Figure 21.6 Diagrammatic depiction of the retaining and inverting catalytic ...

Chapter 22

Figure 22.1 The previously identified UDP-

N

-acetylglucosamine biosynthetic p...

Figure 22.2 HPLC elution profile of the nucleotide sugar. HPLC elution profi...

Figure 22.3 SDS-PAGE separation patterns of the purified recombinant ST2186 ...

Figure 22.4 UPLC elution profile of glutamine and the products produced by t...

Figure 22.5 Sequence alignment of the N-terminal regions of the ST2186 prote...

Figure 22.6 HPLC elution profile of the product by the ST0242 protein. HPLC ...

Figure 22.7 Outline of the confirmed UDP-

N

-acetylglucosamine and UDP-

N

-acety...

Figure 22.8 Elution profiles of standards and the phosphorylated amino-sugar...

Figure 22.9 SDS-PAGE separation patterns of the purified fraction and the re...

Figure 22.10 Elution profiles of the substrate and the phosphorylated amino-...

Chapter 23

Figure 23.1 Flowchart showing the possible steps used for the enhancement of...

Chapter 24

Figure 24.1 Overview of different sections of system biology.

Figure 24.2 Schematic representation of top-down and bottom-up approaches of...

Figure 24.3 Different sectors of the Flux Balance Analysis software model.

Chapter 25

Figure 25.1 An overview presentation of mNGS procedure using Illumina Miseq ...

Figure 25.2 mNGS data analysis platform.

Chapter 26

Figure 26.1 Structure of a monoclonal antibody (mAb). The mAb molecule posse...

Figure 26.2 Production of monoclonal antibody using hybridoma technology. Th...

Figure 26.3 Schematic representation of phage display technique to produce m...

Figure 26.4 Therapeutics application of monoclonal antibody (mAb). The mAbs ...

Chapter 27

Figure 27.1 Alkalophilic sites of alkaline proteases.

Figure 27.2 Applications of alkaline protease in different industries.

Chapter 28

Figure 28.1 (a) Enzymatic action of lipases on triglyceride. (b) Industrial ...

Figure 28.2 The combinatorial effects of both enzymes.

Chapter 29

Figure 29.1 Overview of inulin oligosaccharide production.

Figure 29.2 Applications of inulin oligosaccharides (IOS).

Chapter 31

Figure 31.1 Functional properties of prebiotic oligosaccharides.

Chapter 32

Figure 32.1 Structure of laccases in

M. albomyces

.

Figure 32.2 Catalytic cycle of laccase showing the mechanism of reduction an...

Figure 32.3 Biological function of laccases from different sources and its a...

Chapter 33

Figure 33.1 Overall effect of various abiotic and biotic and PGPR strains mi...

Chapter 34

Figure 34.1 (a,b) Active site of copper and iron metal containing ligninolyt...

Figure 34.2 Catalytic cycle of Laccase [7, 16].

Figure 34.3 Catalytic cycle of MnP [7, 19].

Figure 34.4 Catalytic cycle of LiP.

Chapter 35

Figure 35.1 Overview of bioinformatics intervention in microbial enzyme for ...

Figure 35.2 Molecular docking of enzyme (PNL) and substrate (digalacturonic ...

Chapter 36

Figure 36.1 Agro-industrial food waste in the production of different biopro...

Figure 36.2 Classification of different types of agro-industrial food waste....

Guide

Cover

Table of Contents

Title Page

Title Page

Copyright

Copyright

About the Editors

Preface

Begin Reading

Index

End User License Agreement

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Microbial Enzymes

Production, Purification, and Industrial Applications

Volume 1

Edited by Dinesh Yadav, Pankaj Chowdhary, Gautam Anand, and Rajarshi Kumar Gaur

Microbial Enzymes

Production, Purification, and Industrial Applications

Volume 2

Edited by Dinesh Yadav, Pankaj Chowdhary, Gautam Anand, and Rajarshi Kumar Gaur

Editors

Dr. Dinesh YadavDeen Dayal Upadhyaya Gorakhpur UniversityDepartment of Biotechnology Civil LinesGorakhpur, Uttar Pradesh 273009India

Dr. Pankaj ChowdharySociety for Green EnvironmentNew Delhi 110067India

Dr. Gautam AnandAgricultural Research OrganizationVolcani InstituteDepartment of Plant Pathology and Weed ResearchRishon LeZion 7505101Israel

Dr. Rajarshi Kumar GaurDeen Dayal Upadhyaya Gorakhpur UniversityDepartment of BiotechnologyGorakhpur, Uttar Pradesh 273009India

Cover Image: © Christoph Burgstedt/Shutterstock

All books published by WILEY-VCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche Nationalbibliothek The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.

© 2025 WILEY-VCH GmbH, Boschstraße 12, 69469 Weinheim, Germany

All rights reserved, including rights for text and data mining and training of artificial technologies or similar technologies (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

Print ISBN: 978-3-527-35291-3ePDF ISBN: 978-3-527-84435-7ePub ISBN: 978-3-527-84436-4oBook ISBN: 978-3-527-84434-0

Editors

Dr. Dinesh YadavDeen Dayal Upadhyaya Gorakhpur UniversityDepartment of Biotechnology Civil LinesGorakhpur, Uttar Pradesh 273009India

Dr. Pankaj ChowdharySociety for Green EnvironmentNew Delhi 110067India

Dr. Gautam AnandAgricultural Research OrganizationVolcani InstituteDepartment of Plant Pathology and Weed ResearchRishon LeZion 7505101Israel

Dr. Rajarshi Kumar GaurDeen Dayal Upadhyaya Gorakhpur UniversityDepartment of BiotechnologyGorakhpur, Uttar Pradesh 273009India

Cover Image: © Christoph Burgstedt/Shutterstock

All books published by WILEY-VCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche Nationalbibliothek The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.

© 2025 WILEY-VCH GmbH, Boschstraße 12, 69469 Weinheim, Germany

All rights reserved, including rights for text and data mining and training of artificial technologies or similar technologies (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

Print ISBN: 978-3-527-35292-0ePDF ISBN: 978-3-527-84435-7ePub ISBN: 978-3-527-84436-4oBook ISBN: 978-3-527-84434-0

About the Editors

Dr. Dinesh Yadav  is Professor of the Department of Biotechnology and currently the Director of the Research and Development Cell at DDU Gorakhpur University. He has served as the Dean of the Faculty of Rural Sciences, Head of the Department of Biotechnology, Nodal Officer of the IPR Cell and Coordinator of Centre for Genomics and Bioinformatics at D.D.U. Gorakhpur University. He has also served as Associate Professor of the Department of Molecular Biology and Genetic Engineering at G.B. Pant University of Agriculture and Technology, Pantnagar, from 2006 to 2009. He completed his master’s degree in biotechnology from Devi Ahilya University, Indore, in 1996 and PhD from G.B. Pant University of Agriculture and Technology, Pantnagar, in 2002. He has more than 23 years of teaching and research experience.

He has availed the DST-BOYSCAST Fellowship at the Australian Centre for Plant Functional Genomics (ACPFG), University of Adelaide, South Australia, from 3 May 2012 to 12 April 2013. He was awarded for Excellence in Teaching and Research in Higher Education by the University on Teacher’s Day, 5 September 2021. He received Dr. Pushpendra Kumar Gupta Vishisht Krishi Vaigyanik Puraskar (2015) in the field of agricultural sciences by Uttar Pradesh Academy of Agricultural Sciences (UPAAS), Lucknow, and the Young Scientist Award (2008) by the Uttarakhand State Council of Science & Technology in the discipline of biotechnology, biochemistry, and microbiology.

His areas of specialization include molecular biology, bioinformatics, plant biotechnology, and enzyme technology. He has published more than 150 research papers, including reviews, books, book chapters, and conference proceedings, and has more than 300 GenBank accession numbers. A total of 48 indigenously isolated microbial strains (fungal and bacterial) have been deposited in several culture collection centers in India. He has carried out nine projects with support from funding agencies such as DBT, UGC, UP Council of Agricultural Research, Lucknow, and DST as PI/Co-PI and Mentor. Presently, he is involved in three projects funded by CST (UP) and UPCAR (Lucknow).

He has guided 12 students to PhD in biotechnology, and four students have submitted PhD thesis. He has also supervised more than 114 students for MSc dissertations and short project works in biotechnology. He has been a mentor for five postdoctoral fellowships, namely UGC-Dr. D.S. Kothari (twice), DST-Women Scientist-A, DST-Women Scientist-B, and SERB National PDF.

He is a life member of various scientific societies such as BRSI, Trivandrum; SBC(I), Bangalore; Indian Science Congress Association, Calcutta; Society of Plant Biochemistry and Biotechnology, IARI, New Delhi, Association of Microbiologists of India (AMI), New Delhi; and UPAAS, Lucknow.

He has delivered more than 100 invited talks and lectures at conferences and symposiums and served as Mentor for the DST-INSPIRE Science Internship Camp and Inspire Awards. Currently, he is working on plant-specific transcription factor-DOF (DNA binding with one finger) and nuclear factor-Y (NF-Y) for developing biotic and abiotic stress tolerance crops and pectinases group of enzymes with potential applications in different industries.

His research works have been published in journals of national and international repute, including Journal of Experimental Botany, Cellulose, World Journal of Microbiology and Biotechnology, Environmental Science and Pollution Research, Theoretical and Applied Genetics, Cellulose, Frontiers in Microbiology, Planta, World Journal of Microbiology and Biotechnology, Process Biochemistry, Molecular Biology Reports, Plant Systematics and Evolution, Molecular Biotechnology, Applied Biochemistry and Biotechnology, Annals of Microbiology, Journal of Basic Microbiology, 3 Biotech, Biologia, Journal of Cereal Sciences, Physiology and Molecular Biology of Plants, Biochemistry (Moscow), Current Proteomics, Interdisciplinary Sciences: Computational Life Sciences, Biocatalysis and Agricultural Biotechnology, Cell Biochemistry and Biophysics, Online Journal of Bioinformatics, Chemistry and Ecology, African Journal of Biotechnology, Applied Biochemistry and Microbiology, Sugar Tech, and Enzyme Research.

Dr. Pankaj Chowdhary  is President of the Society for Green Environment (SGE), New Delhi, India. He completed his PhD in 2018 in the area of microbiology from the Department of Environmental Microbiology at Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India. His doctorate work was mainly focused on the role of ligninolytic-enzyme-producing bacterial strains in the decolorization and degradation of coloring compounds from distillery wastewater. His main research areas include microbial biotechnology, biodegradation and bioremediation of environmental contaminants in industrial wastewaters, metagenomics, and lignocellulosic waste valorization. He has edited eight international books and authored two books. He has published more than 60 research and review papers in national and international peer-reviewed journals with a high impact factor, published by Springer, Elsevier, Royal Society of Chemistry (RSC), Taylor & Francis Group, and Frontiers. He has also published many national and international book chapters and magazine articles on the biodegradation and bioremediation of environmental pollutants. He has presented many posters and papers relevant to research areas in national and international conferences. He has actively worked as a potential reviewer for various SCI journals published by reputed international publishers (Springer, Elsevier, RSC, Taylor & Francis Group, Wiley, and Frontiers). He is a life member of the Association of Microbiologists of India (AMI) and the Indian Science Congress Association (ISCA), Kolkata, India”.

Dr. Gautam Anand  is a postdoctoral fellow at the Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO) – Volcani Institute, Israel. He obtained his MSc and PhD degrees in biotechnology from Deen Dayal Upadhyaya Gorakhpur University, India. During his PhD, he worked on an industrially important microbial enzyme of the pectinases group, namely polygalacturonase. He was selected for the Agricultural Research Organization – Postdoctoral Fellowship, Israel, for the year 2020–2021 and the Valazzy Pikovsky Fellowship for postdoctoral research at the Hebrew University of Jerusalem, Israel, for the year 2018–2019. He has also worked as a postdoctoral fellow at the Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel. He has worked extensively on plant–fungus interactions. His main area of research is characterizing the importance of trafficking pathways in fungal virulence using deletion mutagenesis and cell biology techniques. Dr. Anand has also worked on fungal pectinases, particularly polygalacturonases and pectin lyases. He has published more than 30 papers in reputable international journals and 14 book chapters.

Dr. Rajarshi Kumar Gaur  earned his PhD in 2005. Currently, he is Professor at the Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India. His PhD focused on the molecular characterization of sugarcane viruses, namely, mosaic, streak mosaic, and yellow luteovirus. He received the MA SHAV Fellowship from the Israel government for his postdoctoral studies and joined the Volcani Centre, Israel, and Ben-Gurion University, Negev, Israel. In 2007, he received a Visiting Scientist Fellowship from the Swedish Institute Fellowship, Sweden, to work at Umeå University, Umeå, Sweden. He received a Postdoctoral Fellowship from ICGEB, Italy, in 2008. He has made significant contributions to the study on sugarcane viruses and has published 135 national and international papers, authored 27 edited books, and presented about 50 papers in national and international conferences. He is an honored Fellow of Linnean Society, Royal Society of Biology, Society of Plant Research, Society of Applied Biology (FSAB), International Society of Biotechnology (FISBT), and Indian Virological Society (FIVS). He has received awards such as Prof. B.M. Johri Memorial Award, Society of Plant Research (SPR); Excellent Teaching Award by Astha Foundation, Meerut; UGC-Research Teacher Award; Young Scientist Award-2012 in Biotechnology by Society of Plant Research (SPR), Meerut; and Scientific & Applied Research Centre Gold Medal Award (2011) for outstanding contribution in the field of biotechnology. He has visited several laboratories in the United States, Canada, New Zealand, the United Kingdom, Thailand, Sweden, and Italy. Currently, he is handling national and international grants and international collaborative projects on plant viruses and disease management.

Preface

The book Microbial Enzymes: Production, Purification, and Industrial Applications provides an insight into diverse aspects of microbial enzymes, highlighting strategies for their production, purification, manipulation, and elucidating multifarious industrial applications. Microbial enzymes have played a pivotal role in several industries, and over the years, substantial efforts have been made to reveal the hidden potential of untapped microbial diversity in search of a repertoire of enzymes. A plethora of microbial enzymes have been reported so far, and efforts have been made to incorporate many of these enzymes in this book authored by experts. An emphasis has also been placed on discussing the recent technological interventions in microbial enzyme technology, such as metagenomics, system biology, molecular biology, genomics, directed evolution, and bioinformatics, in this book. The important microbial enzymes highlighted in this book include xylanases, ureases, methane monooxygenase, polyhydroxyalkanoates, pectinases, peroxidases, α-L-rhamnosidase, alkane hydroxylases, laccases, proteases, gallic acid decarboxylase, chitinases, beta-glucosidase, lipases, inulinases, tannase, mycozyme, ACC deaminase, and ligninolytic enzymes, among others. Few chapters are exclusively focused on microbial enzyme intervention as an eco-friendly approach in diverse industrial applications.

From an environmental point of view, all the recent and classic microbial treatment technologies should be amplified to make them more viable and feasible. Contaminate mitigation or removal using enzyme technology has become an attractive and potential alternative in recent days. Further, recent developments in the fields of biotechnology, molecular biology, ecology, and microbiology have been applied to develop different novel treatment methods involving novel strains of microorganisms with desirable properties that would be applicable in the process of bioremediation. Various types of beneficial microbes are present in the ecosystem, and they can play a key role in mitigating climate concern, improving green production technology, enhancing agriculture productivity, and providing a means of earning a livelihood. A few chapters have highlighted the omics-driven research in microbial enzyme technology.

This book is a good collection of chapters reflecting multidimensional aspects of microbial enzyme technology, and it will be of immense importance for students, scientists, biotechnologists, microbiologists, and policymakers working in environmental microbiology, biotechnology, and environmental sciences with the basics and advanced enzyme technology. Moreover, readers can also get state-ofthe- art or background information on existing technologies, their challenges, and future prospects.

The editors express sincere thanks to the contributors for submitting their work in a timely and proper manner. The editors are also thankful to national and international reviewers for their evaluation and valuable suggestions and comments to heighten the book’s quality for readers. Further, editors also acknowledge the cooperation received from the Wiley team for their guidance in finalizing this book.

2024, Gorakhpur        

Dinesh Yadav, PhD

Deen Dayal Upadhyaya Gorakhpur UniversityDepartment of Biotechnology, Civil LinesGorakhpur, Uttar Pradesh 273009, India

Pankaj Chowdhary, PhD

Society for Green EnvironmentNew Delhi 110067, India

Gautam Anand, PhD

Agricultural Research OrganizationVolcani InstituteDepartment of Plant Pathology and Weed ResearchRishon LeZion 7505101, Israel

Rajarshi Kumar Gaur, PhD

Deen Dayal Upadhyaya Gorakhpur UniversityDepartment of BiotechnologyGorakhpur, Uttar Pradesh 273009, India

1Xylanases: Sources, Production, and Purification Strategies

Mariana Delgado-Garcia1, Lizeth G. Campos-Muzquiz2, Rocio G. Castillo-Godina2, Sendar D. Nery-Flores2, Lissethe Palomo-Ligas2, Adriana C. Flores-Gallegos2, Beatriz del C. Cutiño-Laguna2, and Raul Rodriguez-Herrera2

1Technological Institute of Superior Studies of Monterrey, Campus Guadalajara, School of Engineering and Sciences, Av. General Ramón Corona 2514, Nuevo México, Zapopan, 45138 Jalisco, México

2Universidad Autónoma de Coahuila, School of Chemistry, Blvd. V. Carranza y Jose Cárdenas s/n, Col. Republica, Saltillo, Coahuila 25280, México

1.1 Introduction

The cell wall of the plant is composed of different lignocellulosic compounds, being the xylan the main compound of hemicellulose. This structure consists of xylose united by β-1,4-glycosidic bonds and different branches of α-D-glucuronide, arabinose, galactose, acetate, methyl glucuronic acid, and other simple sugars [1, 2]. Xylanase is a group of hydrolytic enzymes involved in the hydrolysis of xylan to convert it into monosaccharides and xylooligosaccharides. The xylanase system is constituted by glycosyl hydrolases (endo-xylanases, exo-xylanases, β-D-xylosidases, α-glucuronidase, and α-L-arabinofuranosidases) and esterases [3].

The heterogeneous composition of hemicellulose hampers the complete depolymerization by a single enzyme, requiring the action of both glycosyl hydrolases and esterases [4]. Each enzyme of the xylanase group contributes to xylan degradation in a specific way: endo-xylanase randomly cleaves the xylan; exo and endo xylanases acting on the xylan backbone and producing short-chain oligomers; β-D-xylosidases cleaves xylose monomers, α-L-arabinofuranosidases removes the side groups, α-D-glucuronidases, and acetylxylan esterases remove acetyl and phenolic side branches and act synergistically on the complex polymer [4, 5]. The most common natural sources of xylanases are produced by different biological systems such as bacteria, protozoans, fungi, plants, and mollusks. Actually, it has been reported that xylanases have been identified from lignocellulose-degrading microbiota from cow rumen and, the termite hindgut. There are two strategies applied to date for microbial xylanase production, either using native microorganisms or genetic engineering modified microorganisms [3, 4].

Xylanase production from nonmodified fungi and bacteria must use proper microorganisms, which should produce acceptable yields and should not produce toxins or any other unsought products [6]. Xylanases can be produced by hydrolysis of xylan by the microorganisms that express the enzyme gene. Nonetheless, due to the xylan complexity, the production of this enzyme from different microorganisms on a large-scale is hard because one of the main problems is the presence of other enzymes. This problem is also present during the purification steps, increasing costs. Hence, one alternative is the use of modified strains for large-scale xylanase production [7, 8].

In the case of bacteria, the alkaline-thermostable xylanase-producing trait is useful in most industrial applications since it reduces the steps due to the higher pH level required for the optimal growth and activity of the microorganism [9]. Xylanases require N-glycosylation as one of the most important posttranslational modifications; therefore, not all bacterial expression hosts are suitable, such as Escherichia coli, which lacks the pgl gene, to produce this modification. Because of this, other alternative expression hosts are Bacillus subtilis and Lactobacillus sp. [10, 11].

Filamentous fungi are an important option to produce high amounts of xylanases in comparison to yeast and bacteria [12]. A problem associated with fungal xylanases is cellulase excretion; therefore, an operational process to obtain xylanolytic systems free of cellulases is very important in this case [13]. Another major problem associated with fungi is the reduced xylanase yield in fermenter studies, principally for the agitation that promotes fungal disruption, leading to low productivity [14].

Some examples of xylanases-producing fungus used in industry are Penicillium canescens, Streptomyces sp. P12–137, Thermomyces lanuginosus SD-21, Penicillium fellutanum, Penicillium sclerotiorum, Acremonium furcatum, Aspergillus niger PPI, Neocallimastix sp. Strain L2, Cochliobolus sativus Cs6, Bacillus circulans D1, Streptomyces sp. strain Ib 24D, and Paecilomyces themophila J18. The substrate used by these microorganisms for fermentation is derived from cereals as soya, wheat, corn, and oat [15–25]. On the other hand, yeasts are good expression hosts due to their ability to perform eukaryotic posttranslational modifications, high cell density growth, and secretion of proteins into fermentation media [26, 27]. Some yeasts used for xylanase production are Saccharomyces cerevisiae and Pichia pastoris [28, 29]

Plants are also used for xylanases production, using bio-farming. The requirements for this objective are (i) high-level expression, (ii) stability and functionality of enzymes to be expressed, and (iii) easy purification. In planta expression of lignocellulose-digesting enzymes from mesophilic bacteria and fungi can compromise plant biomass production because of autohydrolysis of cell walls and others such as growth, yield, germination, fertility and susceptibility of the host to disease [30]. There are enzymes that can be used during the lignocellulose pretreatment without losing their enzymatic activity for their hypo-thermophilic capacity [31].

Recently, there has been much industrial interest on xylanases, from native microorganisms and recombinant hosts for different applications. For example, in the baking industry, endo-1,4-β-xylanase from Aspergillus oryzae, B. subtilis, and Trichoderma longibrachiatum is used for bread making, the production of maize starch and alcohol through fermentation. Particularly, in the bread industry, the uses of xylanase are intended for flexibility and stabilization of dough (breaking down polysaccharides) and improve gluten strength. This impacts the sensory perception of bread [32].

In the animal nutrition industry, xylanases from Acidothermus cellulolyticus and Neocallimastix patriciarum are used to reduce feed conversion rate and enhance the digestibility of cereal feeds in poultry and ruminant [33, 34]. Lactobacillus xylanases depolymerize hemicellulose, making silage more stable and digestible by cattle [35]. The most common uses of xylanases have been used in the paper and pulp industry for the benefits of the quality of the products as purity, bright, and more permeability of fiber surface and diffusion during the bleaching processes [36–38]. Due to the current crisis of energy, the utilization of lignocellulosic agents is considered as sustainable biomass to produce nonfossil fuels. These biomasses should be hydrolyzed for bioethanol production from agricultural waste such as corncob, chili residue, rice straw, banana peel, apple pomace, and others [3, 39–42].

Xylanases have an important role in hydrolyzing the xylan and generate value-added products, such as xylitol. Xylitol is a sweetener used in soft drinks, candies, ice cream, chewing gum, and various pharmaceutical products as a natural sweetener in toothpaste [43]. Other uses have been explored, e.g., extracellular xylanase from a culture of Aspergillus carneus M34 and used to treat xylooligosaccharide. Feruloyl xylooligosaccharides showed antioxidative capacity in a cell model of ultraviolet B (UVB)-induced oxidative damage, demonstrating the potential of xylanases use in photo-protectant preparation [44].

1.2 Sources, Production, and Purification Strategies

Xylanases can be obtained in a large number of biologic systems such as fungi, bacteria (Bacillus pumilus, B. subtilis, Bacillus amyloliquefaciens, Bacillus cereus, B. circulans, Bacillus megatorium, Bacillotherus licheniformis, Bacillotherus sp., Streptomyces roseiscleroticus, Streptomyces cuspidosporus, Streptomyces actuosus, Pseudonomas sp., Clostridium absonum, and Thermoactinomyces thalophilus), yeasts, and seaweed [45]. Some other organisms such as mycorrhizae, actinomycetes, protozoa, insects, crustaceans, snails, and some plant seeds during the germination phase have been identified as xylanase sources [46]. Filamentous fungi being the main producers of xylanolytic enzymes, compared to other microorganisms [47]. In this way, xylanases have different applications, according to the source of production and some studies have focused on optimizing enzyme production, mainly from more powerful fungal and bacterial strains or through mutant strains for higher enzyme production [26, 48–50].

Fungal strains are important producers of xylanases due to their high yield and extracellular release of enzymes. They also show greater xylanase activity than yeast and bacteria. However, they present some characteristics that make them little available for use in industry. Fungal xylanases cannot be used in the pulp and paper industry because they need an alkaline pH and a temperature higher than 60 °C [45]. These xylanases are efficient at temperatures below 50 °C and a pH range of 4–6. The fungal sources of xylanases are A. niger, Aspergillus fetidus, Aspergillus brasiliensis, Aspergillus flavus, Aspergillus nidulans, Aspergillus terreus Penicillium sp., Trichoderma reesei, T. longibrachiatum, Trichoderma harzianum, Trichoderma viride, Trichoderma atroviride, Fusarium oxysporum, T. lanuginosus, Alternaria sp., Talaromyces emersonii, Schizophyllum commune, and Piromyces sp. [47]. Although many of the reports focus on studies of xylanolytic systems from filamentous fungi mainly, and by bacteria, there are some reports on obtaining xylanases from yeasts [51, 52]. Two Cryptococcus yeast strains had been identified as producers of xylanases with a thermostable behavior [52]. Other reports are on the identification of yeast strains able to produce cellulase-free xylanases to solve the most common problem during the search of biologic systems for xylanase production [53].

From the great variety of xylanase-producing microorganisms, some thermophilic microorganisms have been isolated, which grow at an optimal temperature between 50 and 80 °C, and extremophiles or hyperthermophiles, which grow at temperatures above 80 °C [54]. Thermophilic microorganisms are sources of enzymes with greater activity at high temperatures [55]; these sources are important because xylanolytic enzymes are required to be able to withstand aggressive working conditions, such as acidic or alkaline environments and high temperatures, this due to its various industrial applications. For this reason, xylanases have been isolated from extremophilic bacteria and fungi. According to the analyses of genomic and transcriptomic profiles of xylanase-producing extremophilic fungi, it is argued that the discovery of new sources of thermostable xylanases, using molecular tools such as directed evolution, can satisfy the growing demand for thermostable xylanases. Table 1.1 shows a list of xylanases that come from thermophilic and hyperthermophilic microorganisms [61, 62].

Table 1.1 Thermophilic and hyper-thermophilic microorganisms producing thermostable xylanases.

Source

Specie

GH family

References

Bacteria

Caldicellulosiruptor

sp.

10

[56]

Bacteria

Caldicoprobacter algeriensis

11

[56]

Bacteria

Dictyoglomus thermophilum

11

[57]

Bacteria

Microcella alkaliphila

10

[58]

Hongo

Aspergillus niger

11

[59]

Hongo

Malbranchea cinnamomea

11

[44]

Hongo

Thermomyces lanuginosus

11

[60]

Recent studies have focused on xylanase production optimization, for which they have used new strains of endophytic fungi, which were good producers of xylanases when solid-state fermentation (SSF) is used [63]. In the past, about 80–90% of commercial xylanases have been produced by submerged fermentation (SmF); however, SSF has a great option, such as less space requirement, low cost, and the application of circular economy for the use of agricultural waste as a substrate for enzyme production. Therefore the xylanase production process has been optimized by Fusarium solani, using SSF. This fungal strain produces xylanases with low cellulolytic activity [64].