Microbial Extremozymes: Novel Sources and Industrial Applications

340 Pages·2021·44.237 MB·English

by  Mohammed Kuddus

Microbial Extremozymes
Novel Sources and Industrial Applications
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Microbial Extremozymes
Novel Sources and Industrial Applications
Edited by
Mohammed Kuddus
Department of Biochemistry, College of Medicine, University of Hail, Saudi Arabia
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Contents
Contributors xi Thermal and catalytic properties 16
Thermophilicity and structural features 16
1 Microbial screening for extremozymes pH adaptations and structural features 17
Halophilicity and structural features 17
Mohammed Kuddus, Roohi, and Naushin Bano
Piezophiles and structural features 17
Introduction 1 Radiophiles and structural stability 18
What are extremozymes? 1 Metallophiles 18
Classification of extremophiles 1 Xerophiles and structural stability 18
Thermophiles 1 In silico tools to study extremozyme 18
Hyperthermophiles 2 Biophysical techniques to characterize
Psychrophiles 2 extremozymes 19
Acidophiles and alkaliphiles 3 Biotechnological applications of
Barophiles 3 extremozymes 19
Halophiles 3 Thermophilic pectinases 19
Radiophiles 3 Thermophilic cellulases 19
Industrial relevance of extremozymes 3 Thermophilic xylanases 20
Screening for extremozymes 4 Thermophilic amylases 20
Screening of thermophiles 4 Thermophilic proteases 20
Screening of psychrophiles 4 Thermophilic lipases 21
Screening of alkaliphiles and acidophiles 5 Thermophilic laccases 21
Screening of barophiles 5 Thermophilic phytases 21
Screening of halophiles 5 References 23
Functional approach for screening 5
Future prospects of extremozymes 5 3 Innovative technologies for
Conclusion 6 enzyme production from
References 6
extremophilic microbes
2 Structure-function relationship of Rachana Singh and Paras Porwal
extremozymes
Introduction 31
Muhammad Fayyaz ur Rehman, Abeera Shaeer, Traditional to modern techniques 31
Aima Iram Batool, and Mehwish Aslam Culture-dependent approach 34
Metagenomics or culture-independent technique 34
Introduction 9
Sequence-based approaches 34
Genome and proteome studies to identify
Function-based approach 35
extremozyme 10
Functional screening of libraries 35
Directed evolution 11
Conclusion 36
Rational/semirational design 12
References 37
Factors affecting extremozyme
functionality and stability 12
4 Cold-active enzymes: Enabling
Changes in amino acid residues 12
Role of ion pairs in hyperthermophilic proteins 13 nonthermal processing in food industry
Cooperative association 15
Vijayanand Adapa, L.N. Ramya, and K.K. Pulicherla
Solvent-exposed surface area 15
Catalytic mechanisms 15 Introduction 39
v
vi Contents
Definition of psychrophilic enzymes 39 Mesophiles 90
Need for psychrophilic enzymes 40 Psychrophiles 91
Nonthermal food processing 40 Acidophiles 91
Ambient temperature biocatalysis 42 Alkaliphiles 91
Utilization of cold-chain 44 Halophiles 92
List of psychrophilic enzymes and their sources 46 Piezophiles 92
Molecular adaptations of cold-active enzymes 46 Metallophiles 92
Conclusion 50 Xerophiles 93
References 50 Geophiles 93
Applications of extremophiles 93
5 Metagenomic approach for the Bioremediation 93
isolation of novel extremophiles Plant growth promotion by extremophiles 96
Potential applications of extremozymes 97
Salma Mukhtar, Naeem Rashid, Muhammad Farhan
Lipases production by extremophiles 97
Ul Haque, and Kauser Abdulla Malik
Proteases production by extremophiles 98
Introduction 55 Amylases production by extremophiles 98
Saline and arid environments 56 l-Glutaminase production by extremophiles 99
Hot and cold environments 60 Beta-galactosidase production by
Acidic and alkaline environments 61 extremophiles 99
High pressure 62 Cellulase production by extremophiles 99
Radiations 62 Xylanases production by extremophiles 100
Conclusions and future perspectives 62 Applications of extremolytes 100
References 62 Acknowledgment 101
References 101
6 Microbial extremozymes: Novel
sources and industrial applications 8 Biomedical application of marine
extremozymes
Hayrunnisa Nadaroglu and Muhammed Seyid Polat
Govindan Nadar Rajivgandhi and Wen-Jun Li
Microorganisms 67
General properties of archaea 67 Introduction 111
Thermophilic proteins 69 Enzyme activity in extreme condition 112
Piezophilic proteins 69 Marine environment 114
Acidophilic proteins 69 Marine bacteria 115
Halophilic proteins 69 Marine actinomycetes 116
Enzyme production in industrial scale 70 Production of extremozymes form marine
Enzymes effective for polysaccharides in microbes 117
industrial scale 70 Psychrophiles 117
Enzymes effective for proteins proteases 77 Thermophiles 118
Proteases enzymes 77 Acidophiles 119
Enzymes effective for lipids esterases and Halophilic 119
lipases 77 Barophilic 119
Industrial applications of enzymes 80 Xerophiles 120
References 82 Biomedical applications of extremozymes 120
Acknowledgments 121
7 Potential of microbial References 121
extremophiles for
9 Pharmaceutical application of
biotechnological applications: An
extremozymes
overview
Govindan Nadar Rajivgandhi, R.T.V. Vimala,
Ashok Bankar, Smita Patil, Manisha Shinde,
S. Sridharan, Govindan Ramachandran, and
Shraddha Shinde, and Bhargavi Kowligi
Natesan Manoharan
Introduction 89
Introduction 125
Ecology and classification of extremophiles 89
Classification of extremophiles 125
Thermophiles 89
Contents vii
Factors affecting the stability of the Food products with thermophilic probiotics 154
extremozymes 127 Future perspectives 156
Ionic interactions 127 Conclusion 157
Cooperative association 128 Acknowledgments 157
Solvent-exposed surface area 128 References 157
Catalytic mechanisms 128
Alteration in amino acid residues 128 12 Current trends in applicability of
Extremophilic enzymes versus mesophilic thermophiles and thermozymes in
enzymes 128 bioremediation of environmental
Pharmaceutical applications of pollutants
extremophilic enzymes 128
Tannases 129 Amrik Bhattacharya and Anshu Gupta
Pullulanases 129
Introduction 161
Chitinases 129
Adaptive or survival strategies of
Esterase 130
thermophiles 162
Nitrile-degrading enzymes 130
Adaptive strategies of thermophiles:
Proteases 132
Whole cell 162
Lipases 132
Adaptive strategies at the level of cellular
Conclusion 132
proteins and enzymes 163
References 132
Environmental applications of thermophiles
and their enzymes 164
10 Extremozymes from extremophilic
Remediation of heavy metals 164
microorganisms as sources of
Bioleaching and electronic waste recycling 166
bioremediation Remediation of polycyclic aromatic
hydrocarbons and petroleum hydrocarbons 167
Tarek A.A. Moussa and Neveen M. Khalil
Remediation of other recalcitrant organic
Introduction 135 pollutants 169
Bioremediation technology 136 Remediation of dyes and textile effluents 169
Extremophiles and extremozymes in Remediation of plastic and related
bioremediation 138 compounds 170
Conclusion 142 Remediation of pharmaceutically active
References 142 compounds 170
Use of thermophiles in treatment of other
11 Functionality of thermophilic industrial wastes/effluents 171
bacteria as probiotics Dairy wastewater 171
Leather and wood pulp processing 171
Claudia Mariana Pérez-Juárez, Adriana Carolina
Agroindustrial wastes/agrobiomass treatment 171
Flores-Gallegos, Marisol Cruz-Requena,
Major issues on application of
Aidé Sáenz-Galindo, Luis Cobos-Puc,
thermophiles/thermozymes in industrial
and Raúl Rodríguez-Herrera
wastes/effluents 173
Introduction 147 Concluding remarks 173
Probiotics 147 References 173
Thermophilic microorganisms 148
Thermophilic probiotic characteristics 148 13 l-Asparaginases from
Mesophilic vs thermophilic hyperthermophilic archaea and
microorganisms 149 their applications
Importance 150
Muhammad Sajed, Sabeel un Naeem,
Industrial 150
and Naeem Rashid
Health 151
Thermophilic strains used in industrial Introduction 177
processes 152 Classification of l-asparaginases 177
Bacillus coagulans 153 l-Asparaginases from hyperthermophilic
Streptococcus (GRAS) 153 archaea 178
Lactobacillus delbrueckii 153 Applications of l-asparaginases 178
viii Contents
In therapeutics 178 16 Extremophilic lipases and
In biosensors 181 esterases: Characteristics and
In food industry 182 industrial applications
Conclusion 182
References 183 Agustín Castilla, Sonia Rodríguez Giordano, and
Gabriela Irazoqui
14 Psychrozymes: A novel and
Introduction 207
promising resource for industrial
Lipases structural features 208
applications Enzyme catalytic mechanism 209
Structural features of extremophilic lipases 209
U.S. Annapure and Nair Pratisha
Biochemical properties of extremophilic
Introduction 185 lipases 210
Historical background of psychrophiles 185 Extremophilic lipases through directed
Biodiversity 186 evolution 213
Habitats 186 Industrial applications of lipases: Current
Cryodefense strategies 186 state and perspectives 215
Regulation of membrane fluidity 187 References 218
Carotenoid pigments 187
Antifreeze, cold-acclimation, and 17 Current applications and future
cold-shock proteins 187 trends of extremozymes in
Cryoprotectants 187 detergent industries
Psychrozymes 187
Industrial applications of psychrozymes 188 Abdullah A. Al-Ghanayem, Babu Joseph,
Pectinase 188 Mohammed S. Alhussaini, and Pramod W. Ramteke
β-Galactosidase 188 Introduction 223
Cellulase 189
Extremozymes and detergents 223
Lipase 189
Lipase 225
Protease 190
Protease 225
Amylase 190
Amylase 225
Phytase 191
Pullulanase 226
Xylanase 191
Cellulase 226
Alkaline phosphatase 191
Mannanase 226
DNA ligase 192
Pectinases 227
Uracil-DNA N-glycosylase and double
Cutinase 227
strand-specific DNase 192
Xylanase 227
Other notable enzymes 192
Protein engineering in extremozymes 227
Manipulation of psychrozymes 192
Future outlook 228
Commercially available psychrozymes 193
References 228
Future prospects 193
References 194 18 Bioenergy production in extremophiles
15 Applications of extremozymes in Mehwish Aslam and Naeem Rashid
the food industry
Introduction 231
Production of biofuels by extremophiles 231
Aysegul Mutlu-Ingok, Derya Kahveci,
Liquid biofuel producing extremophiles 232
Funda Karbancioglu-Guler, and Beraat Ozcelik
Gas biofuel producing extremophiles 238
Introduction 197 Extremophilic enzymes for bioenergy
Pectinases from extremophiles 199 production 238
Amylases from extremophiles 200 Multifunctional chimeras in biofuel
Lipases from extremophiles 201 production 239
Proteases from extremophiles 201 Immobilization and recycling of enzymes
Lactases from extremophiles 202 for biofuel production 240
Conclusion 203 Current and future prospects 240
References 203 References 240
Contents ix
19 Enzyme engineering and Meta-QC chain 264
application of extremozymes: QIIME 264
A vast vision for the future MEGAN and CARMA 264
Thermo-alkalophilic enzymes 264
Sukanchan Palit The need for alkali-thermophilic
enzymes 265
Introduction 247
Applications of alkali-thermophilic
What do you mean by enzymes? 247
enzymes in various industries 265
What do you mean by extremozymes? 248
Enzymes used in the pulp and paper
Scientific doctrine of enzyme engineering
industry 266
and biotechnology 248
Detergent industry 266
Significant advancements in enzyme
Enzymes used in the food industry 266
engineering 248
Conclusion 266
Significant advancements in application of
Acknowledgments 270
extremozymes 251
References 270
Environmental remediation and enzyme
engineering 254
21 Molecular mechanism of
Water and wastewater treatment and
radio-resistance and heavy metal
enzyme engineering 255
Enzyme engineering and science of tolerance adaptation in microbes
sustainability 256
Vikas Kumar, Asha Kumari, Mahima Pandey, and
Future scientific thoughts and
Monica Sharma
recommendations 256
Conclusion 256 Introduction 275
Acknowledgment 257 Radio-resistant bacteria 275
References 257 Mechanism of survival in radio-resistant
organisms 276
20 Metagenomics for mining of Role of PprI-mediated DNA repair in
thermoalkalophilic enzymes Deinococcus radiodurans 276
RecA-dependent radioresistance in
Garima Chauhan, Meghna Arya, Aparna Pathak,
Deinococcus radiodurans 276
Prabhas Singh, and Monica Sharma
RecA-independent radioresistance in
Introduction 259 Deinococcus radiodurans 276
Timeline/history of metagenomics 259 Role of manganese in protection against
Sources of metagenome 261 the oxidative damage 277
Methodologies used in metagenomics 261 Unique morphology of radio-resistant
Selection of sources/niches 261 organisms 278
Isolation or extraction of environmental Heavy metal resistance 278
DNA 261 Effect of heavy metals 279
Construction of the metagenomic library 261 Microbial detoxification strategies 282
Screening of metagenomic libraries 261 Biosorption 282
Approaches used in metagenomics libraries Bioaccumulation 282
screening 262 Siderophore formation 282
Sequence-driven metagenomics Biosurfactants production 283
approach 262 Mechanism of metal resistant 283
Function (phenotypic)-driven Extracellular barrier 283
metagenomics approach 263 Active transport of metal ions (efflux) 283
Softwares used in metagenomics 263 Intracellular sequestration 284
IDBA-UD 263 Extracellular sequestration 285
MEGAHIT 264 Reduction of heavy metal ions by
MetaSPAdes 264 bacteria 285
MetaQUAST 264 Conclusion 287
FastQC 264 Acknowledgment 287
PRINTSEQ 264 References 287