| Author: |
Tino Krell
|
| Release at: | 2018 |
| Pages: | 599 |
| Edition: |
First Edition/Handbook of Hydrocarbon and Lipid
Microbiology |
| File Size: | 12 MB |
| File Type: | |
| Language: | English |
Description of Cellular Ecophysiology of Microbe
Hydrocarbons have played a key role in bacterial evolution. Few other compounds cause physiological effects as varied as those elicited by hydrocarbons; many are toxic and cause bacterial cell death, while others serve as important growth substrates. This diversity makes the field of research focused on hydrocarbons and bacteria complex and exciting. Here, we will review different mechanisms by which bacteria sense the presence of hydrocarbons and how these signals translate into bacterial responses. Bacteria rely on two basic evolutionary strategies to cope with the toxic effects of hydrocarbons: fight or flee.
Currently, data suggests that the “fight” strategy is predominant because a multitude of different adaptive mechanisms have been identified that enable bacteria to cope with toxic hydrocarbons, while there are relatively few examples of directed cell movement away from hydrocarbons. Of the different strategies that bacteria use to cope with toxic hydrocarbons, active expulsion of the toxic compound from the cell has been proven to be a particularly successful evolutionary approach. As well, there is a wealth of data available on the different pathways that mediate the degradation of hydrocarbons.
However, there is relatively little information available on how hydrocarbons enter the cell; thus, the exploration of processes related to hydrocarbon uptake represents a major research need. Hydrocarbons also play regulatory roles in the cell by acting as signal molecules. Furthermore, biological molecules are often chemically modified via the attachment of a hydrocarbon – a process that can mediate important effects.
Accordingly, the mechanisms and functional consequences of DNA and protein methylation, which is of central importance to the cell, are also summarized in this book. Other signaling hydrocarbons – many of which contain oxygen and nitrogen in addition to hydrogen and carbon – have been shown to play key roles in quorum sensing processes, and they are also covered here.
Content of Cellular Ecophysiology of Microbe
Part I Problems of Hydrophobicity, Bioavailability 1
1 Problems of Hydrophobicity/Bioavailability: An Introduction 3
Hauke Harms, Kilian E. C. Smith, and Lukas Y. Wick
2 Microorganism-Hydrophobic Compound Interactions 17
Lukas Y. Wick, Hauke Harms, and Kilian E. C. Smith
3 Matrix - Hydrophobic Compound Interactions33
Hauke Harms, Lukas Y. Wick, and Kilian E. C. Smith
4 Assimilation of Hydrocarbons and Lipids by Means of Biofilm
Formation 47
Pierre Sivadon and Régis Grimaud
5 Uptake and Assimilation of Hydrophobic Substrates by
the Oleaginous Yeast Yarrowia lipolytica. 59
France Thevenieau, Athanasios Beopoulos, Thomas Desfougeres,
Julia Sabirova, Koos Albertin, Smita Zinjarde, and Jean-Marc Nicaud
6 Biodiversity of Biosurfactants and Roles in Enhancing
the (Bio)availability of Hydrophobic Substrates75
Amedea Perfumo, Michelle Rudden, Roger Marchant, and
Ibrahim M. Banat
7 Biofilm Stress Responses Associated to Aromatic
Hydrocarbons 105
Laura Barrientos-Moreno and Manuel Espinosa-Urgel
Part II Sensing, Signaling and Uptake 117
8 Sensing, Signaling, and Uptake: An Introduction 119
Tino Krell
9 Bioinformatics, Molecular, and Genetic Tools for Exploring
Genome-Wide Responses to Hydrocarbons 127
O. N. Reva, R. E. Pierneef, and B. Tümmler
10 One-Component Systems that Regulate the Expression
of Degradation Pathways for Aromatic Compounds 137
G. Durante-Rodríguez, H. Gómez-Álvarez, J. Nogales,
M. Carmona, and E. Díaz
11 Transcriptional Regulation of Hydrocarbon Efflux Pump
Expression in Bacteria. 177
Cauã Antunes Westmann, Luana de Fátima Alves, Tiago Cabral
Borelli, Rafael Silva-Rocha, and María-Eugenia Guazzaroni
12 The Family of Two-Component Systems That Regulate
Hydrocarbon Degradation Pathways 201
Andreas Busch, Noel Mesa-Torres, and Tino Krell
13 Chemotaxis to Hydrocarbons 221
Rebecca E. Parales and Jayna L. Ditty
14 The Potential of Hydrocarbon Chemotaxis to Increase
Bioavailability and Biodegradation Efficiency. 241
Jesús Local
15 Amphiphilic Lipids, Signaling Molecules, and
Quorum Sensing 255
M. Dow and L. M. Naughton
16 Fatty Acids as Mediators of Intercellular Signaling 273
Manuel Espinosa-Urgel
17 Substrate Transport 287
Rebecca E. Parales and Jayna L. Ditty
18 Strategies to Increase Bioavailability and Uptake of
Hydrocarbons 303
J. J. Ortega-Calvo
19 The Mycosphere as a Hotspot for the Biotransformation
of Contaminants in Soil. 315
Lukas Y. Wick and Hauke Harms
Part III Problems of Solventogenicity, Solvent Tolerance. 325
20 Problems of Solventogenicity, Solvent Tolerance:
An Introduction 327
Miguel A. Matilla
21 Toxicity of Hydrocarbons to Microorganisms. 335
Hermann J. Heipieper and P. M. Martínez
22 Genetics of Sensing, Accessing, and Exploiting Hydrocarbons 345
Miguel A. Matilla, Craig Daniels, Teresa del Castillo,
Andreas Busch, Jesús Local, Ana Segura, Juan Luis Ramos, and
Tino Krell
23 Extrusion Pumps for Hydrocarbons: An Efficient
Evolutionary Strategy to Confer Resistance to Hydrocarbons 361
Matilde Fernández, Craig Daniels, Vanina García,
Bilge Hilal Cadirci, Ana Segura, Juan Luis Ramos, and Tino Krell
24 Membrane Composition and Modifications in Response to
Aromatic Hydrocarbons in Gram-Negative Bacteria 373
Álvaro Ortega, Ana Segura, Patricia Bernal, Cecilia Pini,
Craig Daniels, Juan Luis Ramos, Tino Krell, and
Miguel A. Matilla
25 Cis–Trans Isomerase of Unsaturated Fatty Acids:
An Immediate Bacterial Adaptive Mechanism to Cope
with Emerging Membrane Perturbation Caused by Toxic
Hydrocarbons 385
Hermann J. Heipieper, J. Fischer, and F. Meinhardt
26 Surface Properties and Cellular Energetics of Bacteria in
Response to the Presence of Hydrocarbons 397
Hermann J. Heipieper, Milva Pepi, Thomas Baumgarten, and
Christian Eberlein
27 Ultrastructural Insights into Microbial Life at the
Hydrocarbon: Aqueous Environment Interface409
Nassim Ataii, Tyne McHugh, Junha Song, Armaity Nasarabadi, and
Manfred Auer
28 Microbiology of Oil Fly Larvae 419
K. W. Nickerson and B. Plantz
Part IV Problems of Feast or Famine429
29 Nitrogen Fixation and Hydrocarbon-Oxidizing Bacteria 431
J. Foght
30 Kinetics and Physiology at Vanishingly Small Substrate
Concentrations 449
D. K. Button
31 Feast: Choking on Acetyl-CoA, the Glyoxylate Shunt, and
Acetyl-CoA-Driven Metabolism 463
M. Peña Mattozzi, Yisheng Kang, and Jay D. Keasling
Part V Hydrophobic Modifications of Biomolecules 475
32 Hydrophobic Modifications of Biomolecules: An Introduction 477
Álvaro Ortega
33 DNA Methylation in Prokaryotes: Regulation and Function 487
Saswat S. Mohapatra and Emanuele G. Biondi
34 DNA Methylation in Eukaryotes: Regulation and Function 509
Hans Helmut Niller, Anett Demcsák, and Janos Minarovits
35 Methylation of Proteins: Biochemistry and Functional
Consequences. 571
Álvaro Ortega
Index. 585
1 Problems of Hydrophobicity/Bioavailability: An Introduction 3
Hauke Harms, Kilian E. C. Smith, and Lukas Y. Wick
2 Microorganism-Hydrophobic Compound Interactions 17
Lukas Y. Wick, Hauke Harms, and Kilian E. C. Smith
3 Matrix - Hydrophobic Compound Interactions33
Hauke Harms, Lukas Y. Wick, and Kilian E. C. Smith
4 Assimilation of Hydrocarbons and Lipids by Means of Biofilm
Formation 47
Pierre Sivadon and Régis Grimaud
5 Uptake and Assimilation of Hydrophobic Substrates by
the Oleaginous Yeast Yarrowia lipolytica. 59
France Thevenieau, Athanasios Beopoulos, Thomas Desfougeres,
Julia Sabirova, Koos Albertin, Smita Zinjarde, and Jean-Marc Nicaud
6 Biodiversity of Biosurfactants and Roles in Enhancing
the (Bio)availability of Hydrophobic Substrates75
Amedea Perfumo, Michelle Rudden, Roger Marchant, and
Ibrahim M. Banat
7 Biofilm Stress Responses Associated to Aromatic
Hydrocarbons 105
Laura Barrientos-Moreno and Manuel Espinosa-Urgel
Part II Sensing, Signaling and Uptake 117
8 Sensing, Signaling, and Uptake: An Introduction 119
Tino Krell
9 Bioinformatics, Molecular, and Genetic Tools for Exploring
Genome-Wide Responses to Hydrocarbons 127
O. N. Reva, R. E. Pierneef, and B. Tümmler
10 One-Component Systems that Regulate the Expression
of Degradation Pathways for Aromatic Compounds 137
G. Durante-Rodríguez, H. Gómez-Álvarez, J. Nogales,
M. Carmona, and E. Díaz
11 Transcriptional Regulation of Hydrocarbon Efflux Pump
Expression in Bacteria. 177
Cauã Antunes Westmann, Luana de Fátima Alves, Tiago Cabral
Borelli, Rafael Silva-Rocha, and María-Eugenia Guazzaroni
12 The Family of Two-Component Systems That Regulate
Hydrocarbon Degradation Pathways 201
Andreas Busch, Noel Mesa-Torres, and Tino Krell
13 Chemotaxis to Hydrocarbons 221
Rebecca E. Parales and Jayna L. Ditty
14 The Potential of Hydrocarbon Chemotaxis to Increase
Bioavailability and Biodegradation Efficiency. 241
Jesús Local
15 Amphiphilic Lipids, Signaling Molecules, and
Quorum Sensing 255
M. Dow and L. M. Naughton
16 Fatty Acids as Mediators of Intercellular Signaling 273
Manuel Espinosa-Urgel
17 Substrate Transport 287
Rebecca E. Parales and Jayna L. Ditty
18 Strategies to Increase Bioavailability and Uptake of
Hydrocarbons 303
J. J. Ortega-Calvo
19 The Mycosphere as a Hotspot for the Biotransformation
of Contaminants in Soil. 315
Lukas Y. Wick and Hauke Harms
Part III Problems of Solventogenicity, Solvent Tolerance. 325
20 Problems of Solventogenicity, Solvent Tolerance:
An Introduction 327
Miguel A. Matilla
21 Toxicity of Hydrocarbons to Microorganisms. 335
Hermann J. Heipieper and P. M. Martínez
22 Genetics of Sensing, Accessing, and Exploiting Hydrocarbons 345
Miguel A. Matilla, Craig Daniels, Teresa del Castillo,
Andreas Busch, Jesús Local, Ana Segura, Juan Luis Ramos, and
Tino Krell
23 Extrusion Pumps for Hydrocarbons: An Efficient
Evolutionary Strategy to Confer Resistance to Hydrocarbons 361
Matilde Fernández, Craig Daniels, Vanina García,
Bilge Hilal Cadirci, Ana Segura, Juan Luis Ramos, and Tino Krell
24 Membrane Composition and Modifications in Response to
Aromatic Hydrocarbons in Gram-Negative Bacteria 373
Álvaro Ortega, Ana Segura, Patricia Bernal, Cecilia Pini,
Craig Daniels, Juan Luis Ramos, Tino Krell, and
Miguel A. Matilla
25 Cis–Trans Isomerase of Unsaturated Fatty Acids:
An Immediate Bacterial Adaptive Mechanism to Cope
with Emerging Membrane Perturbation Caused by Toxic
Hydrocarbons 385
Hermann J. Heipieper, J. Fischer, and F. Meinhardt
26 Surface Properties and Cellular Energetics of Bacteria in
Response to the Presence of Hydrocarbons 397
Hermann J. Heipieper, Milva Pepi, Thomas Baumgarten, and
Christian Eberlein
27 Ultrastructural Insights into Microbial Life at the
Hydrocarbon: Aqueous Environment Interface409
Nassim Ataii, Tyne McHugh, Junha Song, Armaity Nasarabadi, and
Manfred Auer
28 Microbiology of Oil Fly Larvae 419
K. W. Nickerson and B. Plantz
Part IV Problems of Feast or Famine429
29 Nitrogen Fixation and Hydrocarbon-Oxidizing Bacteria 431
J. Foght
30 Kinetics and Physiology at Vanishingly Small Substrate
Concentrations 449
D. K. Button
31 Feast: Choking on Acetyl-CoA, the Glyoxylate Shunt, and
Acetyl-CoA-Driven Metabolism 463
M. Peña Mattozzi, Yisheng Kang, and Jay D. Keasling
Part V Hydrophobic Modifications of Biomolecules 475
32 Hydrophobic Modifications of Biomolecules: An Introduction 477
Álvaro Ortega
33 DNA Methylation in Prokaryotes: Regulation and Function 487
Saswat S. Mohapatra and Emanuele G. Biondi
34 DNA Methylation in Eukaryotes: Regulation and Function 509
Hans Helmut Niller, Anett Demcsák, and Janos Minarovits
35 Methylation of Proteins: Biochemistry and Functional
Consequences. 571
Álvaro Ortega
Index. 585
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