Sariaslani Advances in Applied Microbiology

1. Auflage 2015
ISBN: 978-0-12-802473-7
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 90, 228 Seiten

Reihe: Advances in Applied Microbiology

A compilation of up to date reviews of topics in biotechnology and medical field. - Contributions from leading authorities - Informs and updates on all the latest developments in the field

Autoren/Hrsg.

Sariaslani, Sima

Inhaltsverzeichnis

1;Front Cover;1
2;Advances in Applied Microbiology;2
3;Advances in Applied Microbiology
;4
4;Copyrights
;5
5;Contents;6
6;Contributors
;8
7;Sugar Catabolism in Aspergillus and Other Fungi Related to the Utilization of Plant Biomass;10
7.1;1. Introduction;11
7.2;2. Composition of Plant Biomass;11
7.3;3. Fungal Growth on Plant Biomass;14
7.4;4. Aspergillus as a Plant Biomass Degrader;14
7.4.1;4.1 The Genus Aspergillus;14
7.5;5. Fungal Sugar Catabolism;15
7.5.1;5.1 Catabolism of d-Glucose and d-Fructose through Glycolysis;15
7.5.2;5.2 Pentose Phosphate Pathway;18
7.5.3;5.3 Conversion of d-Xylose and l-Arabinose through the PCP;19
7.5.4;5.4 Catabolism of d-galactose;23
7.5.5;5.5 Catabolism of d-Mannose;26
7.5.6;5.6 Catabolism of l-Rhamnose;27
7.5.7;5.7 Catabolism of d-Galacturonic Acid;28
7.6;6. Conclusions;30
7.7;Acknowledgments;31
7.8;References;31
8;The Evolution of Fungicide Resistance;38
8.1;1. Introduction;39
8.2;2. Fungicide Resistance: The Evolutionary Context;40
8.3;3. Fungicide Use on Cereals in Europe;45
8.4;4. Mechanisms of Resistance to Single-Site Inhibitors;47
8.5;5. Case Histories;48
8.5.1;5.1 Eyespot of Cereals;48
8.5.1.1;5.1.1 Changes in Field Populations of the Cereal Eyespot Pathogens in Response to Fungicide Use;53
8.5.2;5.2 Septoria tritici Blotch of Wheat;56
8.5.2.1;5.2.1 Changes in CYP51;61
8.5.2.2;5.2.2 Additional Resistance Mechanisms to Azoles;63
8.5.2.3;5.2.3 SDHI Fungicides and Z. tritici;64
8.5.3;5.3 Powdery Mildew of Cereals, B. graminis;65
8.5.4;5.4 Fusarium Ear Blight;68
8.6;6. Predictability of Resistance Evolution;70
8.6.1;6.1 Mutagenesis and in vitro Selection;70
8.6.2;6.2 Fitness Costs;72
8.6.3;6.3 Parallel Evolution;73
8.6.4;6.4 Functional Constraints and Epistasis;75
8.7;7. Estimating Resistance Risk;78
8.8;8. Implications for Resistance Management;80
8.8.1;8.1 Resistance Diagnostics;80
8.8.2;8.2 Evaluating Management Strategies;81
8.8.3;8.3 The Impact of Genomics;83
8.9;9. Conclusions;84
8.10;Acknowledgments;85
8.11;References;85
9;Genetic Control of Asexual Development in Aspergillus fumigatus;102
9.1;1. Introduction;103
9.2;2. Central Regulatory Pathway of Conidiation;104
9.3;3. The Roles of the Velvet Regulators in Conidiation;106
9.4;4. FluG and FLBs Govern Upstream Activation of Conidiation;109
9.5;5. Heterotrimeric G-protein Signaling Indirectly Controls Conidiation;110
9.6;6. Light and Conidiation;112
9.7;7. Conclusions and Prospects;113
9.8;Acknowledgments;114
9.9;References;114
10;Escherichia coli ST131: The Quintessential Example of an International Multiresistant High-Risk Clone;118
10.1;1. Introduction;119
10.2;2. Extraintestinal Pathogenic E. coli;120
10.3;3. Expanded-Spectrum ß-Lactamases;122
10.3.1;3.1 CTX-M ß-Lactamases;123
10.3.2;3.2 AmpC ß-Lactamases or Cephalosporinases;125
10.3.3;3.3 NDM ß-Lactamases;126
10.4;4. OXA-48-like ß-Lactamases;128
10.5;5. International Multiresistant High-Risk Clones;129
10.6;6. Escherichia coli ST131;132
10.6.1;6.1 Initial Studies Pertaining to E. coli ST131;132
10.6.2;6.2 Plasmids Associated with E. coli ST131;136
10.6.3;6.3 Recent Developments Pertaining to ST131;138
10.6.3.1;6.3.1 Epidemiology and Clinical Issues;138
10.6.3.2;6.3.2 Population Biology;139
10.6.3.3;6.3.3 O16:H5 H41 Lineage;141
10.6.3.4;6.3.4 Virulence;142
10.6.3.5;6.3.5 ST131 and Carbapenemases;142
10.6.4;6.4 Does ST131 Qualify as an International Multiresistant High-Risk Clone?;143
10.6.4.1;6.4.1 Global Distribution;144
10.6.4.2;6.4.2 Association with Antimicrobial Resistance Mechanisms;144
10.6.4.3;6.4.3 Ability to Colonize Human Hosts;145
10.6.4.4;6.4.4 Effective Transmission among Hosts;145
10.6.4.5;6.4.5 Enhanced Pathogenicity and Fitness;146
10.6.4.6;6.4.6 Causing Severe and/or Recurrent Infections;146
10.7;7. Rapid Methods for the Detection of E. coli ST131;147
10.7.1;7.1 Multilocus Sequence Typing;147
10.7.2;7.2 Pulsed Field Gel Electrophoresis;148
10.7.3;7.3 Repetitive Sequence-Based PCR Typing;148
10.7.4;7.4 Polymerase Chain Reaction;149
10.7.5;7.5 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry;150
10.8;8. Summary;151
10.9;References;152
11;Colonization Factors of Enterotoxigenic Escherichia coli;164
11.1;1. Introduction;165
11.2;2. Pilus and Pilus-Related Colonization Factors;167
11.2.1;2.1 General Characteristics;167
11.2.1.1;2.1.1 Morphology and Composition;167
11.2.1.2;2.1.2 Adherence Function;170
11.2.1.3;2.1.3 Nomenclature;171
11.2.1.4;2.1.4 Genetics;172
11.2.2;2.2 Pili Assembled by the CU Pathway;172
11.2.2.1;2.2.1 CFs of the a-FUP Clade;175
11.2.2.2;2.2.2 CFs of the .2-FUP Clade;178
11.2.2.3;2.2.3 CFs of the .3-FUP Clade;178
11.2.2.4;2.2.4 CFs of the .-FUP Clade;180
11.2.2.5;2.2.5 Structure of CFs Assembled by the CU Pathway;181
11.2.3;2.3 Type IV pili;185
11.2.3.1;2.3.1 CFA/III and Longus;185
11.2.3.2;2.3.2 Structure of Type IV Pili in ETEC;187
11.3;3. Nonpilus Adhesins;189
11.3.1;3.1 Tia;189
11.3.2;3.2 EtpA;190
11.3.3;3.3 TibA;191
11.4;4. Regulation of Pilus Expression;192
11.4.1;4.1 AraC family Transcriptional Regulators;192
11.4.2;4.2 Phase Variation;195
11.5;5. Conclusions;196
11.6;References;197
12;Index;208
13;Contents of Previous Volumes
;216

Leseproben

Chapter One

Sugar Catabolism in Aspergillus and Other Fungi Related to the Utilization of Plant Biomass

Claire Khosravi, Tiziano Benocci, Evy Battaglia, Isabelle Benoit and Ronald P. de Vries1     Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
1 Corresponding author: E-mail: [e-mail] 

Abstract

Fungi are found in all natural and artificial biotopes and can use highly diverse carbon sources. They play a major role in the global carbon cycle by decomposing plant biomass and this biomass is the main carbon source for many fungi. Plant biomass is composed of cell wall polysaccharides (cellulose, hemicellulose, pectin) and lignin. To degrade cell wall polysaccharides to different monosaccharides, fungi produce a broad range of enzymes with a large variety in activities. Through a series of enzymatic reactions, sugar-specific and central metabolic pathways convert these monosaccharides into energy or metabolic precursors needed for the biosynthesis of biomolecules. This chapter describes the carbon catabolic pathways that are required to efficiently use plant biomass as a carbon source. It will give an overview of the known metabolic pathways in fungi, their interconnections, and the differences between fungal species.

Keywords

Aspergillus; Carbon catabolic enzymes; Central carbon metabolism; Plant polysaccharides utilization; Sugar catabolism

1. Introduction

Plant biomass is the main renewable material on earth, and is the major starting material for several industrial areas. A growing industrial sector in which plant-degrading enzymes are used is the production of alternative fuels, such as bio-ethanol, and biochemicals. The substrate for these conversions is plant material, either from crops specially grown for this purpose or agricultural waste. Plant polysaccharides can be converted to fermentable sugars by fungal enzymes. The sugars are then fermented to ethanol and other products by yeast (Saccharomyces cerevisiae). Aspergillus species are organisms of choice for enzyme production for pretreatment of plant material because they have high levels of protein secretion and they produce a wide range of enzymes for plant polysaccharide degradation (de Vries & Visser, 2001). In nature, Aspergillus degrades the polysaccharides to obtain monomeric sugars that can serve as a carbon source. Therefore, Aspergillus uses a variety of catabolic pathways to efficiently convert all the monomeric components of plant biomass.

In this chapter, we present an overview of the main carbon catabolic pathways of Aspergillus and other fungi involved in converting the main monomers (D-glucose, D-xylose, L-arabinose, D-galactose, D-mannose, L-rhamnose, and D-galacturonic acid) present in plant polysaccharides.

2. Composition of Plant Biomass

Plant biomass consists mainly of polysaccharides, lignin, and proteins. The composition of plant polysaccharides depends not only on the plant species, but also on the plant tissue, growth conditions (season), and the age at harvesting. The average composition is 40–45% cellulose, 20–30% hemicellulose, and 15–25% lignin. The different plant cell wall polysaccharides interact with each other and with the aromatic polymer lignin to ensure strength and structural form of the plant cell. The different polysaccharides in the plant cell wall contain a variety of monomers (Table 1).

Table 1

Composition of plant polysaccharides

Type

Monomers

Cellulose

—

D-glucose

Hemicellulose

Xylan

D-xylose

Glucuronoxylan

Arabinoglucuronoxylan

D-xylose, L-arabinose

Arabinoxylan

D-xylose, L-arabinose

Galacto(gluco)mannan

D-glucose, D-mannose, D-galactose

Mannan/galactomannan

D-mannose, D-galactose

Glucuronomannan

D-mannose, D-glucoronic acid, D-galactose, L-arabinose

Xyloglucan

D-glucose, D-xylose, D-fructose, D-galactose

Glucan

D-glucose

Arabinogalactan

D-galactose, L-arabinose, D-glucuronic acid

Pectin

Homogalacturonan

D-galacturonic acid

Xylogalacturonan

D-galacturonic acid, D-xylose

Rhamnogalacturonan I

D-galacturonic acid, L-rhamnose, D-galactose, L-arabinose

Based on Kowalczyk et al. (2014).

Cellulose is a linear polymer of ß-1,4-linked D-glucose residues. The cellulose polymers are present as ordered structures, and their main function is to ensure the rigidity of the plant cell wall (Boyce & Andrianopoulos, 2006). The long glucose chains are tightly bundled together into microfibrils by hydrogen bonds to form an insoluble crystalline fibrous material (de Vries, Nayak, van den Brink, Vivas Duarte, & Stalbrand, 2012). In addition to this crystalline structure, cellulose microfibrils also contain noncrystalline (amorphous) regions. The ratio of crystalline and noncrystalline cellulose depends on its origin (Lin, Tang, & Fellers, 1987).

Hemicelluloses, the second most abundant polysaccharides in nature, have a heterogeneous composition of various sugar units. Hemicelluloses are usually classified according to the main sugar residues in the backbone of the polymer. The major hemicellulose polymer in cereals and hardwood is xylan. Its consists of a backbone of ß-1,4-linked D-xylose residues, which can be acetylated and has mainly a-1,2- or a-1,3-linked L-arabinose (arabinoxylan) and/or a-1,2-linked (4-O-methyl-)D-glucuronic acid (glucuronoxylan) residues attached to the main chain (de Vries & Visser, 2001). In addition, it can also contain D-galactose, feruloyl, and p-coumaroyl residues (van den Brink & de Vries, 2011). The main xylan present in softwood and cereals is arabinoxylan, whereas hardwood contains mainly glucuronoxylan. A second hemicellulose polymer commonly found in soft- and hardwood is galactoglucomannan. This consists of a backbone of ß-1,4-linked D-mannose residues, occasionally interrupted by D-glucose residues with D-galactose side groups (mainly in softwoods). Another hemicellulose, xyloglucan, is present in the cell walls of dicotyledonae and some monocotylodonae (e.g., onion). It consists of ß-1,4-linked D-glucose backbone substituted by D-xylose. There are two major types of xyloglucans in plant cell walls: XXGG and XXXG, representing two and three xylose-substituted glucose residues, separated by two and one unsubstituted glucose residues, respectively (Vincken, York, Beldman, & Voragen, 1997). Different monosaccharides can be attached to the xylose residues (Scheller & Ulvskov, 2010). All hemicelluloses can be acetylated and are cross-linked to cellulose via hydrogen bonds creating a complex and rigid network (Carpita & Gibeaut, 1993; Willats, Orfila, et al., 2001).

Pectin is a complex polysaccharide, which is another major component of primary cell wall. It provides rigidity to the cell and plays an important role in porosity, surface charge, pH, and ion balance of the cell wall (Willats, McCartney, MacKie, & Knox, 2001). Pectin contains two different defined regions (Perez, Mazeau, & Herve du Penhoat, 2000; de Vries & Visser, 2001). The “smooth” regions or homogalacturonan (HGA) consist of a linear chain of a-1,4-linked D-galacturonic acid residues that can be acetylated at O-2 or O-3 or methylated at O-6 (Willats, Orfila, et al., 2001). Pectin methyl and acetyl esterases act on this substrate to de-esterify the backbone after which it can be cross-linked by calcium to form a gel, which plays a role in intracellular adhesion (Braccini & Pérez, 2001; Morris, 1986; Willats et al., 2001b). The “hairy” regions contain two different structures, xylogalacturonan (XGA) and rhamnogalacturonan I (RG-I). XGA, like HGA, contains an a-1,4-linked D-galacturonic acid backbone that contains ß-1,3-linked D-xylose side groups (Schols, Bakx, Schipper, & Voragen, 1995). RG-I contains an alternating backbone of a-1,4-linked D-galacturonic acid and a-1,2-linked L-rhamnose residues. Long side chains of L-arabinose (arabinan), D-galactose (galactan), or a mixture (arabinogalactan) can be attached to the...