The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays.
Eclectic volumes are supplemented by thematic volumes on various topics including Archaea and Sick Building Syndrome. Impact factor for 2003: 1.893
Published since 1959, Advances in Applied Microbiology continues to be one of the most widely read and authoritative review sources in Microbiology. The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays. Eclectic volumes are supplemented by thematic volumes on various topics including Archaea and "e;Sick Building Syndrome?. Impact factor for 2003: 1.893
Cover 1
Contents 5
Chapter 1: Unusual Two-Component Signal Transduction Pathways in the Actinobacteria 8
I. Introduction 8
II. Unusual Two-Component Systems in Actinobacteria 13
A. VanRS and Vancomycin Resistance 13
B. AbsA1/2 14
C. SenRS and Haemin Resistance 16
D. The sigmaE-CseABC Signal Transduction Pathway 16
E. MtrAB 19
F. Intramembrane-Sensing Histidine Kinases 21
G. Leaderless Transcripts 21
III. Orphan Two-Component Proteins 23
A. DosRST: A Branched Pathway 23
B. Predictions Based on Homology and Ontology 24
C. Typical Response Regulators 25
D. Atypical Response Regulators 26
IV. Conclusions and Perspectives 27
Acknowledgments 28
References 28
Chapter 2: Acyl-HSL Signal Decay: Intrinsic to Bacterial Cell-Cell Communications 34
I. Introduction 34
II. Acyl-HSL-Degrading Organisms, Enzymes, and Homologues 35
III. Mechanisms of Acyl-HSL Degradation 43
A. Chemical Hydrolysis 44
B. Biochemical Hydrolysis by Acyl-HSL Lactonases 46
C. Biochemical Degradation by Acyl-HSL Acylases 47
D. Biochemical Degradation by Acyl-HSL Oxidoreductase 49
E. Inactivation Reactions Involving Oxidized Halogen Antimicrobials 50
F. Inactivation by Eukaryotes 51
IV. Specificity of Acyl-HSL-Degrading Enzymes 53
V. Acyl-HSL Stability in Natural Environments 54
VI. Coevolution of Quorum-Sensing Bacteria with Hosts and Acyl-HSL-Degrading Bacteria 57
VII. Conclusions 58
References 59
Chapter 3: Microbial Exoenzyme Production in Food 66
I. Introduction 66
II. Structure and Function of Exoenzymes 69
III. Classification of Enzymes 71
A. Lipases 71
B. Proteases 71
C. Carbohydrases 72
D. Oxidoreductases 72
IV. Enzyme Synthesis 73
A. Regulation Mechanisms 73
B. Important Inducers and Inhibitors 74
C. Enzyme and Substrate Concentration 75
D. Bacterial Growth 75
E. Influence by Physical Environment 75
V. Enzyme Activity 82
VI. Conclusion and Future Prospects 86
Acknowledgments 88
References 88
Chapter 4: Biogenetic Diversity of Cyanobacterial Metabolites 96
I. Introduction 96
II. Major Biosynthetic Routes in Cyanobacteria 99
A. Polyketide Synthases 99
B. Nonribosomal Peptide Synthetases 102
C. Connecting Product Structures to Gene Sequences 106
III. Polyketides 108
A. Linear Polyketides 109
B. Cyclic Polyketides 114
IV. Cyanopeptides 120
A. Introduction 120
B. Classification and Nomenclature 121
C. Linear Peptides 122
D. Cyclic Peptides 133
E. Cyclic Depsipeptides 141
V. Alkaloids 150
A. Linear Alkaloids 151
B. Ring-Containing Alkaloids 154
VI. Isoprenoids 179
A. Carotenoids 181
B. Terpenoids 181
VII. Other Cyanobacterial Metabolites 185
A. Proteins 185
B. Aromatic Compounds 186
C. Nonaromatic Compounds 188
References 189
Chapter 5: Pathways to Discovering New Microbial Metabolism for Functional Genomics and Biotechnology 226
I. Introduction 226
II. Defining the Hypothesis That Most Metabolic Reactions Are Yet to be Discovered 227
III. Organization of Existing Metabolic Information 228
IV. Approaches for New Discovery 231
V. Newly Discovered Microbial Metabolism 232
A. Azetidine Ring-Opening Metabolism 232
B. Arylboronic Acid Metabolism 233
C. Thioamide Metabolism 234
D. Organobismuth Metabolism 235
VI. Significance of New Discoveries in Novel Functional Group Metabolism 236
VII. Use of Recently Discovered Biocatalysis Industrially 236
References 237
Chapter 6: Biocatalysis by Dehalogenating Enzymes 240
I. Introduction 240
II. Halocarboxylic Acid Dehalogenases 241
III. Haloalkane Dehalogenases 245
A. Properties, Occurrence, and Mechanisms 245
B. Enantioselectivity 246
C. Trichloropropane Conversion 246
IV. Halohydrin Dehalogenases 247
A. Isolation, Properties, and Mechanism 247
B. Biocatalytic Processes 248
C. The use of Alternative Nucleophiles 250
D. Engineering of Halohydrin Dehalogenases 252
E. Halohydrin Dehalogenases in Tandem Reactions 252
F. Statin Side-Chain Synthesis 253
V. Conclusions 254
References 256
Chapter 7: Lipases from Extremophiles and Potential for Industrial Applications 260
I. Introduction 260
II. Lipases from Extreme Microorganisms 262
A. Lipases from Psychrophiles (Cold Active Enzymes) 264
B. Lipases from Thermophiles (Thermoactive Lipases) 266
C. Lipases from Halotolerant/Halophilic Microorganisms (Salt-Tolerant Enzymes) 271
III. Improving Lipases for Efficient Applications 273
IV. Regio- and Stereospecificity of Lipases 275
V. Applications of Lipases 276
A. Medical Biotechnology 277
B. Detergent Industry 277
C. Organic Synthesis 278
D. Biodiesel Production 279
E. Agrochemical Industry 280
F. Flavor and Aroma Industry 280
G. Food Industry 280
VI. Conclusions 281
References 282
Chapter 8: In Situ Bioremediation 292
I. Introduction 292
II. Unsaturated Zone Treatment Methods 294
A. Natural Attenuation 294
B. Enhanced Natural Attenuation 297
III. Saturated Zone Treatment Methods 299
A. Natural Attenuation 299
B. Enhanced Aerobic Natural Attenuation 302
C. Enhanced Anaerobic Natural Attenuation 304
IV. Use of Inocula 305
V. Monitoring Methods 305
VI. Conclusions and Future Prospects 307
Acknowledgment 307
References 308
Chapter 9: Bacterial Cycling of Methyl Halides 314
I. Introduction 315
A. Role of Methyl Halides in Atmospheric Chemistry and as Ozone-Depleting Compounds 315
B. Biogeochemical Cycle of Monohalomethanes 317
C. Anthropogenic Sources 317
D. Natural Chemical Sources and Sinks 318
E. Natural Biological Sources 319
F. Natural Biological Sinks 319
G. Stable Isotope Mass Balances and Fractionation 320
II. Methyl Halide-Degrading Organisms 322
A. Bacterial Degradation of Methyl Halides by Methanotrophs and Nitrifiers 322
B. Diversity and Distribution of Bacteria Capable of Growth on Methyl Halides as a Carbon and Energy Source 322
III. Biochemistry and Genetics of Methyl Halide Degradation 327
A. Metabolism of Methyl Halides by Bacterial Isolates 327
B. The CmuA Pathway of Methyl Halide Degradation in M. chloromethanicum Strain CM4 328
C. Cloning and Sequencing of cmu Gene Clusters 330
D. Mutational and Transcriptional Analysis of cmu Genes of H. chloromethanicum CM2 333
E. Evidence for Operation of the CmuA Pathway in MeCl- and MeBr-Degrading Bacterial Isolates 334
F. Alternative Methyl Halide Degradation Pathways 335
IV. Microbial Ecology of Methyl Halide-Degrading Bacteria 335
A. Development of Functional Gene Markers for CmuA Pathway Methylotrophs 335
B. Stable Isotope Probing of Methyl Halide Degradation in Soils 337
C. Marine Methyl Halide Degradation 341
V. Potential Applications for Bioremediation Using Methyl Halide-Oxidizing Bacteria 341
A. Reducing Fugitive MeBr Emissions 341
B. Previous Efforts to Reduce MeBr Emissions 342
C. Bioremediation Using Methyl Halide-Oxidizing Bacteria 342
VI. Outlook 345
A. Genomics of Methyl Halide-Degrading Bacteria 345
B. Contribution of Alternative Pathways of Methyl Halide Degradation 345
C. Evolutionary Aspects and Role of Methyl Halides as Substrates in the Environment 346
Acknowledgments 347
References 347
Index 354
Contents of Previous Volumes 376
Acyl-HSL Signal Decay: Intrinsic to Bacterial Cell–Cell Communications
Ya-Juan Wang*; Jean Jing Huang†; Jared Renton Leadbetter* * Environmental Science and Engineering, California Institute of Technology, Pasadena, California 91125
† Division of Biology, California Institute of Technology, Pasadena California 91125
I Introduction
Many members of the bacterial phylum Proteobacteria employ low-molecular-weight chemical signaling molecules in the coordination of their group behaviors. This process of cell–cell communication is known as quorum sensing and it was first described as the mechanism that underlies light production by the squid symbiont Vibrio fischeri (Nealson and Hastings, 1979; Nealson et al., 1970). The structure of the signaling molecule of Vibrio fischeri, N-3-(oxohexanoyl) homoserine lactone (3OC6HSL), was determined (Eberhard et al., 1981) and was the first representative of a large family of molecules, the acylhomoserine lactones (acyl-HSLs). These dedicated signaling molecules all have an HSL moiety but can differ in the substituents and length of the acyl chain, which can vary from 4 to 16 carbons (Fuqua et al., 2001). Their function as signaling molecules employed by diverse Gramnegative bacteria has been studied extensively. The canonical way in which acyl-HSLs are utilized in quorum sensing requires the synthesis of acyl-HSL signals by synthases, which are encoded by homologues of the luxI gene and signal response regulator proteins, which are encoded by homologues of the luxR gene (Engebrecht et al., 1983; Gambello and Iglewski, 1991; Piper et al., 1993). The LuxR protein homologues bind to acyl-HSL-signaling molecules and activate the transcription of genes that have proven advantages to express when cell numbers are high. The way these molecules function to coordinate group behaviors at the genetic and biochemical levels has been intensively studied over the last 30 years. The synthesis of acyl-HSLs (Hanzelka et al., 1997; Schaefer et al., 1996), interactions with response regulators (Stevens and Greenberg, 1997), acyl-HSL quorum-sensing controlled regulons (Wagner et al., 2003), and, in recent years, the degradation of acyl-HSL-signaling molecules have been investigated. The latter topic is the subject of this chapter.
Acyl-HSL quorum signal degradation is important given that the presence and concentration of these signaling molecules are key to several microbial group behaviors. Acyl-HSL-mediated quorum sensing has been found to underlie a host of microbial group behaviors from antibiotics and toxins production to swarming motility and biofilm formation (Fuqua et al., 2001; Swift et al., 2001). Quorum sensing would not be effective as a gene regulation mechanism if signaling molecule concentrations did not accurately portray cell numbers. The critical concentration for activation of quorum responses varies for different quorum-sensing microbes from ca. 5 nM to 2 μM in vitro (Fuqua et al., 1995; Kaplan and Greenberg, 1985; Pearson et al., 1995; von Bodman et al., 1998; Whiteley et al., 1999). Since the quorum-sensing process depends on the concentration of signaling molecules accurately reflecting cell population density, signal molecule stability and potential for degradation are key areas of study if we aim to understand how this process functions in nature.
II Acyl-HSL-Degrading Organisms, Enzymes, and Homologues
Since the year 2000 with the first reports of microbially mediated signal degradation (Dong et al., 2000; Leadbetter and Greenberg, 2000), the search and study of microbes and organisms that engage in acyl-HSL signal degradation has been fruitful (Table I). Database searches have identified numerous homologues of known acyl-HSL lactonase and acylase enzymes in a wide range of species suggesting that this activity could be widespread (Table II). Organisms with homologues to known acyl-HSL-degrading enzymes hail from all three domains of life (Bacteria, Eucarya, and Archaea) and dwell in a wide range of environments and conditions, from mesophilic and mesothermic to extreme haloalkaliphilic, thermophilic, and acidophilic environments, suggesting that within a wide range of environments there may be biotic interactions with acyl-HSLs. A variety of these interactions involve acyl-HSLs in host–symbiont relationships (Nealson et al., 1970) and pathogenic infections (de Kievit and Iglewski, 2000; Parsek and Greenberg, 2000). Given such diverse and close interactions, it is perhaps not surprising that eukaryotic hosts have evolved mechanisms to interact with acyl-HSLs (Chun et al., 2004; Telford et al., 1998). Acyl-HSLdegrading activity by paraoxonase (PON) enzymes was discovered from mammalian cells in epithelial and colon cells, which are cells in the front lines of contact with potential pathogens (Chun et al., 2004). Many species containing such homologues reside in environments for which known acyl-HSL producers have been found. The colocalization of acyl-HSL-producing and acyl-HSL-degrading organisms in environments suggests the range of community interactions that could exist. Acyl-HSL production by a haloalkaliphilic archaeon that activates an Agrobacterium biosensor is believed to regulate the production of an extracellular protease (Paggi et al., 2003). Other haloalkaliphilic species are known to have acyl-HSL-degrading lactonase homologues: Natronomonas sp. and Haloarcula sp. (Table II). Also the discovery of nine long-chain acyl-HSLs produced by the acidophilic archaeon Acidithiobacillus ferrooxidans (Farah et al., 2005) provides evidence for the presence of acyl-HSLs in acidic environments. Given the greater stability of long-chain acyl-HSLs under acidic conditions (Yates et al., 2002), these molecules would be stable in this environment and could be subject to degradation by other organisms such as Thermoplasma or Sulfolobus sp., which can exist in such environments and have known acyl-HSL-degrading enzyme homologues. These locations would be interesting environments to study microbial production and degradation of acyl-HSLs.
Table I
Demonstrated Mechanisms and Proteins Involved in Acyl-HSL Degradation by Diverse Bacteria and Eukaryotes
| Bacteria |
| Proteobacteria |
| α-Proteobacteria | Agrobacterium tumefaciens A6 | Lactonase | AttM | Zhang et al., 2002 |
| Agrobacterium tumefaciens C58 | Lactonase | AttM and AiiB | Carlier et al., 2003 |
| β-Proteobacteria | Variovorax paradoxus VAI-C | Acylase | ND* | Leadbetter and Greenberg, 2000 |
| Ralstonia sp. XJ12B | Acylase | AiiD | Lin et al., 2003 |
| γ-Proteobacteria | Pseudomonas aeruginosa PAO1 | Acylase | PvdQ/PA2385 and QuiP/PA1032 | Huang et al., 2003, 2006 |
| Pseudomonas sp. PAI-A | Acylase | ND | Huang et al., 2003 |
| Klebsiella pneumoniae KCTC2241 | Lactonase | AhlK | Park et al., 2003 |
| Acinetobacter sp. C1010 | ND | ND | Kang et al., 2004 |
| Firmicutes Bacilli (Low-G + C Gram-positive) | Bacillus sp. 240B1 | Lactonase | AiiA | Dong et al., 2001, 2000 |
| Bacillus thuringiensis | Lactonase | AiiA homologues | Dong et al., 2002; Lee et al., 2002 |
| Bacillus cereus | Lactonase | AiiA homologues | Dong et al., 2002; Reimmann et al., 2002 |
| Bacillus mycoides | Lactonase | AiiA homologues | Dong et al., 2002 |
| Bacillus stearothermophilus | Lactonase | ND | Park et al., 2003 |
| Bacillus anthracis | Lactonase | AiiA homologues | Ulrich, 2004 |
| Actinobacteria Actinobacteria (High-G + C Gram-positive) | Rhodococcus... |
| Erscheint lt. Verlag | 29.7.2011 |
|---|---|
| Mitarbeit |
Herausgeber (Serie): Geoffrey M. Gadd, Allen I. Laskin, Sima Sariaslani |
| Sprache | englisch |
| Themenwelt | Sachbuch/Ratgeber |
| Medizin / Pharmazie ► Allgemeines / Lexika | |
| Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie | |
| Technik ► Umwelttechnik / Biotechnologie | |
| ISBN-10 | 0-08-048813-7 / 0080488137 |
| ISBN-13 | 978-0-08-048813-4 / 9780080488134 |
| Haben Sie eine Frage zum Produkt? |
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