Sariaslani Advances in Applied Microbiology

1. Auflage 2009
ISBN: 978-0-08-095114-0
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 69, 300 Seiten

Reihe: Advances in Applied Microbiology

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 sick building syndrome. Impact factor for 2007: 1.821. - Contributions from leading authorities and industry experts - Informs and updates on all the latest developments in the field - Reference and guide for scientists and specialists involved in advancements in applied microbiology

Autoren/Hrsg.

Sariaslani, Sima

Inhaltsverzeichnis

1;Front Cover
;1
2;Advances in Applied Microbiology
;4
3;Copyright Page
;5
4;Contents
;6
5;Contributors
;10
6;Chapter 1: Variation in Form and Function: The Helix-Turn-Helix Regulators of the GntR Superfamily
;12
6.1;I. Introduction ;13
6.2;II. Helix-Turn-Helix DNA-Binding Proteins
;13
6.3;III. GntR Regulators
;14
6.4;IV. Distribution of GntR Regulators
;15
6.5;V. Structure and Classification of GntR Regulators
;17
6.6;VI. DNA Binding, Operator Sequences and Regulation
;22
6.7;VII. Evolution of GntR Regulators
;24
6.8;VIII. GntR Regulators in Primary Metabolism
;26
6.9;IX. GntR Regulators in Virulence
;26
6.10;X. GntR Regulators in Streptomyces Development and Antibiotic Production
;27
6.11;XI. Biotechnology Implications ;28
6.12;XII. Concluding Remarks
;29
6.13;Acknowledgments;29
6.14;References;29
7;Chapter 2: Biogenesis of the Cell Wall and Other Glycoconjugates of Mycobacterium tuberculosis
;34
7.1;I. Introduction
;35
7.2;II. The Mycobacterial Cell Envelope
;37
7.3;III. The Capsular Polysaccharides
;39
7.4;IV. The Non-Covalently Bound Glycoconjugates of the Outer Membrane
;45
7.4.1;A. Phosphatidylinositol mannosides, lipomannan and lipoarabinomannan
;45
7.4.1.1;1. Localization in the cell envelope and biological activities
;45
7.4.1.2;2. Structure of PIM, LM and LAM
;46
7.4.1.3;3. Biosynthesis of PIMs
;49
7.4.1.3.1;a. The early steps of PIM synthesis
;49
7.4.1.3.2;b. The biosynthesis of polar PIMs
;50
7.4.1.3.3;c. Topology of PIM synthesis
;51
7.4.1.4;4. Biosynthesis of LM and LAM
;52
7.4.2;B. Acyltrehaloses
;55
7.4.3;C. p-Hydroxybenzoic acid derivatives and phenolic glycolipids
;58
7.4.4;D. Mannosyl-beta-1-phosphomycoketides
;59
7.4.5;E. Glycoproteins
;60
7.5;V. The Glycoconjugate Polymers of the Cell Wall Core
;61
7.5.1;A. Arabinogalactan
;61
7.5.1.1;1. Structure of AG
;61
7.5.1.2;2. AG biosynthesis
;61
7.5.1.3;3. AG biosynthesis and drug discovery
;65
7.5.2;B. Peptidoglycan
;65
7.6;VI. Cytosolic Glycoconjugates
;69
7.6.1;A. Polymethylated polysaccharides
;69
7.6.2;B. Glycogen
;71
7.6.3;C. Mycothiol
;72
7.7;VII. Conclusions and Future Prospects
;74
7.8;Acknowledgements;75
7.9;References;75
8;Chapter 3: Antimicrobial Properties of Hydroxyxanthenes
;90
8.1;I. Definitions and Chemical Structures
;91
8.2;II. Synthesis
;92
8.3;III. Applications
;94
8.3.1;A. Dyestuffs
;94
8.3.2;B. Pesticides
;94
8.3.3;C. Medical applications
;95
8.3.4;D. Antimicrobials
;95
8.4;IV. Antimicrobial Mechanism
;96
8.4.1;A. Photooxidation and antimicrobial properties
;96
8.4.2;B. Localization of hydroxyxanthenes in microbial cell
;99
8.4.2.1;1. Localization in membranes
;100
8.4.2.2;2. Protein targets
;101
8.4.2.3;3. Nucleic acids
;101
8.4.2.4;4. Other targets
;102
8.4.3;C. Relative resistance of microorganisms to hydroxyxanthenes
;102
8.4.3.1;1. Chelation
;103
8.4.3.2;2. Ultrahigh pressure
;104
8.5;V. Conclusions
;105
8.6;References;105
9;Chapter 4: In Vitro Biofilm Models: An Overview
;110
9.1;I. Introduction
;111
9.2;II. Choosing the Experimental System
;113
9.2.1;A. Pure culture, defined consortium or microcosm?
;113
9.2.2;B. Continuous, semi-continuous or batch culture?
;114
9.3;III. Closed System Biofilm Models
;114
9.3.1;A. The agar plate: A simple biofilm model?

;114
9.3.2;B. Biofilm models based on multi-well plates: Potential for high-throughput analyses
;116
9.4;IV. Open System Biofilm Models
;117
9.4.1;A. Suspended substratum reactors
;117
9.4.1.1;1. SSRs in dental microbiology
;118
9.4.1.2;2. SSRs in colonic microbiology
;118
9.4.1.3;3. SSRs and gene expression in biofilms
;119
9.4.1.4;4. The CDC biofilm reactor
;120
9.4.2;B. Rotating reactors for control of shear stress
;121
9.4.3;C. The Robbins device and flow cells
;121
9.4.3.1;1. Flow cells
;121
9.4.3.2;2. The (modified) Robbins device
;122
9.4.4;D. Drip-fed biofilms
;123
9.4.4.1;1. The constant depth film fermenter (CDFF)
;123
9.4.4.2;2. The drip flow biofilm reactor
;126
9.4.5;E. Perfused biofilm fermenters
;127
9.4.5.1;1. Perfused membrane fermenters
;128
9.4.5.2;2. Sorbarod biofilm fermenters
;131
9.5;V. Overview and Conclusions
;137
9.6;References
;137
10;Chapter 5: Zones of Inhibition? The Transfer of Information Relating to Penicillin in Europe during World War II

;144
10.1;I. Introduction
;145
10.2;II. Early Penicillin Research in Great Britain
;145
10.3;III. Germany
;148
10.4;IV. Holland
;155
10.5;V. France
;159
10.6;VI. Conclusions
;166
10.7;Acknowledgements;167
10.8;References;167
11;Chapter 6: The Genomes of Lager Yeasts
;170
11.1;I. Introduction
;171
11.2;II. Classification
;171
11.3;III. The Lager Yeasts: Saccharomyces pastorianus
;173
11.4;IV. Lager Yeast Chromosomes: Types
;173
11.5;V. Genome Sequence Analysis of a Lager Yeast Strain
;178
11.6;VI. Chromosome Copy Number
;179
11.7;VII. Consequences of Genome Rearrangements
;180
11.8;VIII. The Dynamic Genome of Lager Yeasts
;181
11.9;IX. Gene Expression Patterns of Lager Yeasts
;186
11.10;X. Expression Compared to Haploid S. cerevisiae
;189
11.11;XI. Conclusions
;189
11.12;References;190
12;Index
;194
13;Contents of Previous Volumes
;200
14;Color Plates
;212

Leseproben

Chapter 1 Variation in Form and Function

The Helix-Turn-Helix Regulators of the GntR Superfamily

Paul A. Hoskisson* and Sébastien Rigali†

*Strathclyde Institute of Pharmacy and Biological Science, University of Strathclyde, Royal College Building, George Street, Glasgow, United Kingdom

†Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, Sart-Tilman, B-4000 Liège, Belgium

Abstract

One of the most abundant and widely distributed groups of Helix-turn-helix (HTH) transcription factors is the metabolite-responsive GntR family of regulators (>8500 members in the Pfam database; Jan 2009). These proteins contain a DNA-binding HTH domain at the N terminus of the protein and an effector-binding and/or oligomerisation domain at the C terminus, where upon on binding an effector molecule, a conformational change occurs in the protein which influences the DNA-binding properties of the regulator resulting in repression or activation of transcription. This review summarises what we know about the distribution, structure, function and classification of these regulators and suggests that they may have a future role in biotechnology.

Keywords: GntR; Helix-turn-helix; Repressor protein; DNA binding; Autoregulation; Streptomyces

…endless forms most beautiful and most wonderful have been and are being, evolved.

Charles Darwin, 1859

I. Introduction

As bacteria sense different micro-environments, they modify their gene expression appropriately to enable them to respond to the prevailing conditions. Often the signal sensed within the cell is a metabolic intermediate, and these are sensed by many classes of helix-turn-helix (HTH) transcription factor, through which they modulate gene expression. The effector molecules bound by these proteins are often related catabolic substrates, substrates and/or intermediates of the pathway controlled by the transcription factor.

One of the most abundant groups of HTH bacterial metabolite-responsive transcription factors is the GntR family of regulators (>8500 members in the Pfam database; Jan 2009). These multi-domain transcription factors are widely distributed throughout the bacterial world where they play a fundamental role in modulation of gene expression to respond appropriately to the environment context.

This review aims to bring together and summarise our current thinking on GntR regulators, their structure, function, evolution, and how they may be exploited in biotechnology.

II. Helix-Turn-Helix DNA-Binding Proteins

The identification of a tri-helical domain and its critical role in DNA binding within the bacteriophage Lambda proteins, cI and cro and the lac operon repressor, LacI, were early advances in the pioneering work of Matthews and co-workers (Ohlendorf et al., 1982 and Ohlendorf et al., 1983) and Sauer et al. (1982). The importance of helix two and helix three of the domain led to the identification of what became known as the HTH motif. The third ?-helix is often referred to as the ‘recognition’ helix, which fits within the major groove of the DNA mediating the protein–DNA interaction (Aravind et al., 2005). Ohlendorf et al., 1983 and Sauer et al., 1982 suggested, through extensive sequence analysis and secondary structure analysis, that this domain was present in several DNA-binding bacterial activators and repressors, and they hypothesised that these domains descended from a common ancestor.

Throughout the 1980s and 1990s, extensive sequencing, the emergence of whole genome sequencing and experimental work confirmed the ubiquity and central role this domain played in gene regulation in both prokaryotes and eukaryotes and led to the identification of the HTH motif in all domains of life, suggesting that the HTH domain is one of the most ancient protein folds, although it appears to be most prevalent in prokaryotes (Aravind and Koonin, 1999). The development of specific algorithms for recognition of the HTH motif has become indispensible in genome annotation such as that of Dodd and Egan (1990), enabling rapid identification of HTH-containing proteins.

III. GntR Regulators

The HTH-containing GntR family is widely distributed throughout the bacteria where they regulate many diverse biological processes. It was named GntR after the first member identified, the Bacillus subtilis repressor of the gluconate operon (Haydon and Guest, 1991; Prosite Family PS50949; Pfam family: PF00392). GntR regulators are often located on the chromosome adjacent to the genes that they control, which in many cases allows insight into the metabolites that they may bind. There are however many examples where this is not the case, and identifying their cognate ligands remains a significant barrier to understanding their function.

In general, these proteins contain a DNA-binding HTH domain at the N terminus of the protein and an effector-binding and/or oligomerisation domain at the C terminus (Fig. 1.1). Upon binding an effector molecule at the C-terminal domain, a conformational change occurs in the protein which influences the DNA-binding properties of the regulator resulting in repression or activation of transcription. The DNA-binding domain is conserved throughout the GntR family yet the regions outside the DNA-binding domain are more variable; however, this is not surprising given the diversity of molecules that they bind, and this feature is used to define the GntR-like sub-families (Rigali et al., 2002). Despite the large number of GntR-like regulators identified there are few examples where their effector molecules are known and the complete regulatory circuitry elucidated. Knowledge of this is of particular importance where GntR-like regulators control genes of unknown biochemical function and can provide information of their cellular function and will enable these processes to be built into modelling frameworks in terms of using systems biology approaches. GntR-like regulators are known to control many fundamental cellular processes such as motility (Jaques and McCarter, 2006), development (Hoskisson et al., 2006), antibiotic production (Hillerich and Westpheling, 2006), antibiotic resistance (Truong-Bolduc and Hooper, 2007), Plasmid transfer (Reuther et al., 2006) and virulence (Casali et al., 2006 and Haine et al., 2005). In all these cases the exact ligand regulating gene expression through these proteins is unknown.

Figure 1.1 Schematic representation of a GntR protein. Indicates the N-terminal helix-turn-helix DNA-binding domain and the longer C-terminal effector-binding/oligomerisation domain (E-b/O).

There are many cases where GntR-like regulators are not located next to genes that they control (orphan regulators), or without their effectors they are activators of gene expression elsewhere in the genome. One well-studied example is FadR, the fatty acid metabolism regulator in Escherichia coli, where it is known to negatively control 12 genes or operons and activate transcription of at least three genes when a fatty acid precursor is bound (DiRusso et al., 1993; See section VIII).

The identification of the small molecules that bind to these regulators has traditionally been difficult and has mainly relied on gene context and bioinformatics to identify possible effector molecules. This area remains a significant challenge to researchers in this field and urgently requires novel methods to aid identification of effector molecules.

IV. Distribution of GntR Regulators

Examination and analysis of GntR regulator distribution throughout completely sequenced genomes demonstrate some interesting trends in terms of their abundance and may give clues to how an organism is distributed in a particular ecological niche or the kind of plasticity it experiences within its natural environment.

There are 8561 GntR regulators in the Pfam database (PfAM family GntR: PF00392: Finn et al., 2008). The bulk of these (8561 sequences) are found in 764 bacterial taxa indicating that this protein fold has been widely adopted as a regulatory mechanism. Examination of taxonomic distribution of these regulators throughout the bacteria demonstrates a wide distribution; however, the predominant phyla (from current sequences available in Pfam) are the Proteobacteria, Firmicutes and the Actinobacteria (Fig. 1.2). Detailed examination of the distribution within well-characterised species (Fig. 1.3) shows an interesting trend, not only with increasing genome size, but also with ecological niche. The trend suggests that organisms that live in complex, highly variable environments such as soil (e.g. Streptomyces, Burkholderia, Rhizobium) have a larger complement of the metabolite-responsive GntR regulators than obligate intracellular parasites and endosymbionts (e.g. Chlamydia and Buchnera). This trend is reinforced even within genera with Mycobacterium smegmatis having a complement of about 60 GntR regulators (Vindal et al., 2007), where all these have been lost in the obligate intracellular pathogen Mycobacterium leprae during the...