Thermophilic Microorganisms | Book
"concise and readable ... an invaluable resource" (Micro. Today)
Caister Academic Press
Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
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Thermophilic microorganisms thrive in a variety of marine and terrestrial habitats. These organisms have evolved several biochemical and molecular strategies to counteract the deleterious effects of the high temperatures in their environments. Given that temperature is considered to be one of the most important physical factors controlling the adaptation and evolution of organisms, the remarkable ability of thermophilic microorganisms to thrive at high temperatures makes them an ideal model to study this phenomenon. Over the decades these organisms and their enzyme systems have found applications in a variety of industrial and biotechnological applications, for example the heat-stable DNA polymerases used in PCR.
In this book leading scientists highlight the current progress in the most topical areas of research providing a timely overview of the field. The book reviews the ecology, enzymology and genetics of thermophiles and includes topics on the diversity and ecological roles of thermophiles, biochemical properties of thermostable biocatalysts and their applications, polyamines and the impact of viruses on thermophiles, DNA replication and metabolic engineering of thermophiles, and much more. An important feature of the book is the extensive focus on the industrial application of thermostable catalysts including alcohol dehydrogenase, glycoside hydrolase, protease and lipases. In addition the authors discuss current technical challenges and future development trends.
The book is of major importance to academic microbiologists as well as those interested in industrial applications and is a recommended guide for scientists in the fields of microbiology, enzymology, molecular biology and ecology.
"by the leading experts in each field ... concise and readable, providing lucid explanations about the current understanding and prospective views of the fields. This book would be an invaluable resource for any researcher interested in these exotic microbes and their applications, from senior undergraduates and postgraduates to scientists and engineers." from Microbiology Today
Table of contents
1. Ecology and Genetics of Deep-sea Thermophiles
LI Xuegong, Zhang Yu and Xiao Xiang
Hydrothermal vent is a typical deep sea ecosystem hosting the largest reservoir of archaea and many bacteria. Through a mixing of hot venting fluid and cold sea water under high hydrostatic pressure, a special environment was created with a steep gradient in terms of temperature, redox potential, pH and substrate concentration. In the past 30 years, the metagenome based analysis has showed at least 20 archaeal orders/lineages and 13 bacterial orders habituating in hydrothermal venting area, among which only a few have cultivatable represents due to the technique difficulties on incubation. Thus, to construct the genetic systems on the model strains become especially necessary. The hydrothermal vent systems and the (hyper) thermophiles are irreplaceable biological materials for a better understanding of life strategy and exploiting for industry use.
2. Diversity of Thermophilic Microorganisms and Their Roles in Carbon Cycle
Shi-Qi Ji, Dong-Dong Meng, Kun-Di Zhang and Fu-Li Li
Thermophiles are a large category of microorganisms that show optimum growth at temperatures of 50°C or higher. These microbes thrive in various environments in both marine and terrestrial habitats. The ability of microorganisms to proliferate under extreme conditions is of widespread importance in microbial physiology, ecological cycle, industry and evolution. Thermophiles play a complex role in ecosystem maintenance, particularly with respect to carbon cycle and biomass deconstruction. These ecological processes are carried out by various thermophilic microorganisms. Temperature is one of the most important factors controlling the activities and evolution of organisms, and limited species diversity found in extreme environments suggests that many organisms lack the capacity for successful adaptation to these environments. High-temperature environments are of special interest, in that they reveal the extremes to which evolution has been pushed. In this chapter, the diversity of thermophiles and their distinct strategies in carbon cycling and biomass degradation are discussed.
3. Biochemical Properties and Applications of Heat-active Biocatalysts
Christian Schäfers, Skander Elleuche and Garabed Antranikian
The discovery of extremophilic microorganisms (extremophiles) and their enzyme systems (extremozymes) has opened new opportunities for various industrial applications over the last decades. Depending on their specific properties such as high thermostability, tolerance at extreme pH values or their performance at high organic solvent concentrations, these microorganisms are suitable tools for wide range of applications. Extremozymes are suitable for a vast number of industrial areas such as waste treatment, food and feed industries, paper industry, pharmaceutical and chemical industries. Thermoactive biocatalysts like proteases, lipases and carbohydrate-degrading enzymes are only a few examples that are of great industrial value and play a crucial role in high-temperature processes. This chapter focuses on different classes of heat-active enzymes that are currently used in various industrial applications. It highlights the value of these biocatalysts and their biochemical properties for the corresponding industry. Moreover some light will be shed on additional enzymes that are less frequently applied, but are of potential use for new applications.
4. Lignocellulosic Biomass Deconstruction by the Extremely Thermophilic Genus Caldicellulosiruptor
Jonathan M. Conway, Jeffrey V. Zurawski, Laura L. Lee, Sara E. Blumer-Schuette and Robert M. Kelly
Extremely thermophilic bacteria from the genus Caldicellulosiruptor produce a variety of large multi-domain proteins for the attachment to and degradation of lignocellulosic biomass. The currently sequenced genomes from the genus Caldicellulosiruptor encode 144 homologous groups of Carbohydrate Active enZymes (CAZymes) containing 128 glycoside hydrolase (GH), 58 carbohydrate binding module (CBM), 9 polysaccharide lyase (PL), and 11 carbohydrate esterase (CE) domains. Extracellular CAZymes from these species have a distinct multi-domain architecture, with multiple catalytic and binding domains in the same protein. This promotes synergy between catalytic domains and enhances the ability of these bacteria to degrade biomass. A number of these extracellular multi-domain proteins are also cell surface associated via surface layer homology (SLH) domains. These SLH domain-containing proteins are thought to help these species attach to the biomass substrate, while catalytic domains in the same proteins degrade it. Because of their highly effective biomass degradation strategy, Caldicellulosiruptor species are of particular interest for development into consolidated bioprocessing microorganisms for the processing of lignocellulosic biomass to biofuels.
5. Cellulases from Thermophilic Fungi
Thermophilic fungi are species that grow at high temperature. Because of their thermostable enzymes, thermophilic fungi have received increasing attention. In this recent decade, cellulases from thermophilic fungi have remarkable progress in many aspects, such as purifying and characterizing the cellulase components, understanding the mechanism of cellulose degradation, cloning and expression of cellulase genes, determining the structures of cellulase components, improving the properties of cellulases by mutation and fusion, understanding structure-function relationships in cellulases and demonstrating the industrial potential of cellulases. Especially, recent genomic sequencing, transcriptome data and secreted proteins showed a number of cellulase genes in thermophilic fungi. The present review will summarizes recent advances in these areas, identify the present gaps and give future perspectives in researches on cellulases from thermophilic fungi.
6. Alcohol Dehydrogenases and their Physiological Functions in Hyperthermophiles
Kesen Ma and Ching Tse
Alcohol dehydrogenases (ADHs) are enzymes that catalyze the inter-conversion of alcohols to corresponding aldehydes/ketones with the concomitant reduction of NAD+ or NADP+. NAD(P)-dependent ADHs from mesophilic and thermophilic bacteria/archaea are orderly clustered as three distinct groups which are zinc-dependent, metal-free short-chain, and iron-containing/activated. ADHs from extreme thermophiles and hyperthermophiles are highly thermostable with optimal temperature of 65°C and above, which is advantageous for industrial applications. To date, ADHs from 10 extreme thermophiles and 15 hyperthermophiles are well characterized with respects to their thermostabilities and catalytic activities. This review aims mainly to provide a review of the most common use of ADHs, physiological functions of ADHs in hyperthermophiles and their potential applications in biotechnology. Relevant aspects including the principal procedures for purification, biophysical, biochemical and catalytic properties of ADHs from extreme thermophiles and hyperthermophiles are also discussed. These information will provide further insight into the importance of the ubiquitously expressed ADHs in microorganisms, particularly hyperthermophiles and their prospective contributions to advancing industrial processes.
7. Roles of Polyamines in Thermophiles
Extreme thermophiles often produce unusual polyamines such as longer polyamines (for instance caldopentamine) and branched polyamines (for instance, tetrakis(3-aminopropyl)ammonium). These polyamines are essential for life at higher temperature and the highest growth temperatures of mutants which lack a gene involved in unusual polyamine synthesis, are lower than those of wild type cells. Unusual polyamines protect DNA and RNA from thermal damages more efficiently than the standard polyamines. Enzymes and metabolic pathways of unusual polyamine biosynthesis are unique and new pathways and new enzymes have been clarified.
8. DNA Replication in Thermophilic Microorganisms
Sonoko Ishino and Yoshizumi Ishino
DNA replication is essential for maintaining genetic information and transferring it from ancestor to descendant. To protect the genetic information from mutations, biological organisms have acquired several types of DNA repair systems. The extreme thermophiles living on the earth are microorganisms from the Bacteria and Archaea domains. The structures of the bacterial and archaeal genomes are circular, and the mechanism of replication initiation, by the binding of the initiator protein to the replication origin (oriC), is conserved in the two domains. The elongation process is also conserved, because similar primase, helicase, polymerase, and ligase functions are observed in the two domains. However, the proteins involved in the DNA replication process are quite different between Bacteria and Archaea, and their replication machineries seem to have evolved independently. The DNA repair system in extreme thermophiles should work efficiently to maintain their genome integrity at high temperatures. However, the DNA repair systems are diverse and still not comprehensively understood yet, although research in this field has been actively pursued in the systems from Escherichia coli to human. In this chapter, we focus on DNA replication in the thermophilic bacteria and archaea, and summarize the current understanding of the molecular mechanisms of replication in thermophilic microorganisms.
9. Metabolic Engineering of Thermophiles for Biofuel Production
Ya-Jun Liu and Qiu Cui
The severe energy crisis and environmental contamination require alternative means of fuel production, and biofuels produced from lignocellulose, a widely available and inexpensive substrate, are ideal substitutes. The major obstacle for the production of lignocellulosic biofuels is the conversion of the recalcitrant lignocellulose into fermentable sugars, although high-temperature conditions are beneficial to the deconstruction progress. Therefore, thermophiles, especially cellulolytic ones such as Clostridium thermocellum, are considered to be promising candidates for lignocellulosic biofuel production. Metabolic engineering is necessary because wild-type thermophilic candidates possess inherent disadvantages and do not meet the standards for industrialization, and several genetic manipulation tools have been developed to promote the targeted engineering and the application of thermophiles in the industrial production of biofuels. This chapter reviews the recent progress in the development of genetic tools for thermophiles and the metabolic engineering focused on the high production of lignocellulosic biofuels.
10. Thermophilic Viruses and Their Association with Thermophiles
Wakao Fukuda and Tadayuki Imanaka
Viruses are small infectious particles containing own genome which consists of either DNA or RNA. Until now, a lot of viruses, which can infect organisms in the three domains, Eukaryote, Bacteria and Archaea, have been found from all over the world. Among them, a few percent of these known viruses can infect thermophilic archaea and bacteria. Viruses of thermophiles are classified into over ten families and virus particles (virions) of them show wide variety of shapes and size. Some viruses are lytic, but the other nonlytic. The wide diversity of virions from thermophiles is interesting to get new insights of the viral world. Viruses are commonly known as the cause of serious disease. In response, adaptive immune systems, named CRISPR (clustered regularly interspaced short palindromic repeat sequences) system, protect most of archaea from infections of extrachromosomal elements (ECEs). On the other hand, viruses can contribute to the evolutions of lives. The ECEs can transfer beneficial genes for adaptation to environment from one organism to another. Intriguingly, the regions formed by integration of viruses (provirus regions) also have been observed in some genomes of extremophiles, but some of these provirus regions lost the ability for virion-formation. The archaeal strains lacking virus-like region have shown growth defects, indicating that virus-like regions help cell growth in the certain conditions. Although virus infected to ancestor in ancient days might include virulence, virus-like regions seem to contribute to adaptation in certain environment at the present day.
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(EAN: 9781910190135 9781910190142 Subjects: [microbiology] [bacteriology] [molecular microbiology] [environmental microbiology] [extremophiles] )