Discover the World of Microbes E-Book

Gerhard Gottschalk

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch
• Veröffentlichungsjahr: 2012

Seitenzahl: 619

Beschreibung

This title is an essential primer for all students who need some background in microbiology and want to become familiar with the universal importance of bacteria for all forms of life.

Written by Gerhard Gottschalk, Fellow of the American Academy of Microbiology and one of the most prominent microbiologists in our time, this text covers the topic in its whole breadth and does not only focus on bacteria as pathogens.

The book is written in an easy-to-read, entertaining style but each chapter also contains a `facts' section with compact text and diagrams for easy learning. In addition, more than 40 famous scientists, including several Nobel Prize winners, contributed sections, written specifically for this title. The book comes with color figures and a companion website with questions and answers.

Key features:

• Unique, introductory text offering a comprehensive overview of the astonishing variety and abilities of Bacteria
• Easy-to-read, fascinating and educational
• Written by one of the best known microbiologists of our time
• Color images throughout
• Each chapter has a compact tutorial part with schemes on the biochemistry and metabolic pathways of Bacteria
• Comes with a companion website with questions and answers 

Leseprobe

Table of Contents

Cover

Related Titles

Title page

Copyright page

Preface

Prolog

Part One: Reading Section

Chapter 1 Extremely small but incredibly active

Chapter 2 Bacteria are organisms like you and me

Chapter 3 My name is LUCA

Chapter 4 From the Big Bang to LUCA

Chapter 5 O2

Chapter 6 Life in boiling water

Chapter 7 Life in the Dead Sea

Chapter 8 Bacteria and archaea are everywhere

Chapter 9 The power of photosynthesis, even in almost complete darkness

Chapter 10 Man and his microbes

Chapter 11 Without bacteria there is no protein

Chapter 12 Napoleon’s victory gardens

Chapter 13 Alessandro Volta’s and George Washington’s combustible air

Chapter 14 Microbes as climate makers

Chapter 15 How a state was founded with the aid of Clostridium acetobutylicum

Chapter 16 Pulque, wine, and biofuel

Chapter 17 Energy conservation from renewable resources

Chapter 18 Cheese and vinegar

Chapter 19 The periodic table of bioelements

Chapter 20 Bacterial sex life

Chapter 21 Bacteria can also catch viruses

Chapter 22 Antibiotics: from microorganisms against microorganisms

Chapter 23 Plasmids and resistances

Chapter 24 Agrobacterium tumefaciens, a genetic engineer par excellence

Chapter 25 Eco R1 and PCR – molecular biology at its finest

Chapter 26 Interbacterial relationships

Chapter 27 From life as a nomad to life as an endosymbiont

Chapter 28 Bacteria as production factories

Chapter 29 Plants, animals, and humans as food resources for bacteria

Chapter 30 Viruses, chemicals causing epidemics?

Chapter 31 The “omics” era

Chapter 32 Incredible microbes

Epilog

Part Two: Study Guide

Overview to the Study Guide

Section 1 Microbial growth

1.1 Batch and continuous culture

1.2 Growth conditions

1.3 Microbial shapes and sizes

Section 2 Molecules that make up microbes

2.1 Informational macromolecules

2.2 The cell membrane and cell wall

2.3 The role of ATP

Section 3 Evolution, from the RNA world to the tree of life

3.1 The RNA world

3.2 Possible properties of LUCA

3.3 Prokaryotes represent two of the three domains of the tree of life

Section 4 Archaea

4.1 The archaeal species

4.2 Habitats

4.3 Archaeal metabolism

4.4 Methanogenesis

4.5 Anabolic metabolism

Section 5 Bacterial diversity

5.1 The phylogenetic tree of bacteria

5.2 Cycles and food chains

5.3 Survival strategies

Section 6 Membranes and energy

6.1 Transport

6.2 Principles of ATP synthesis in microbes

6.3 MCPs and motility

6.4 Two-component systems

6.5 Quorum sensing

Section 7 Carbon metabolism

7.1 Aerobic heterotrophic growth

7.2 Incomplete oxidations

7.3 Autotrophic growth

7.4 Bacterial fermentations

Section 8 Regulation of microbial metabolism

8.1 Regulation at the DNA level

8.2 Transcription and provision of messenger RNA for the translationary machinery

8.3 Translational regulation

8.4 The regulation of enzyme activity

Section 9 Genomes, genes, and gene transfer

9.1 Genomes

9.2 Gene transfer

Section 10 In-depth study of four special topics

10.1 Antibiotics

10.2 Biotechnology

10.3 Pathogenic microorganisms

10.4 Viruses

Appendix A Selected literature

Appendix B Glossary

Appendix C Subject index of figures and tables

Credits

Index

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The Author

Prof. Dr. Gerhard Gottschalk

Institut für Mikrobiologie und Genetik

Georg-August-Universität

Grisebachstr. 8

37077 Göttingen

Germany

Cover

The cover was designed by Anne Kemmling, Göttingen. Source of the micrographs (left to right: row 1, Anne Kemmling; row 2, Manfred Rohde, Braunschweig, fig. 8a (this book), Michael Hoppert, Göttingen; row 3, Michael Hoppert, Manfred Rohde, figures 74b and 75 (this book); row 4, Jim Hogle, Boston, Anne Kemmling.

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Bibliographic information published by the Deutsche Nationalbibliothek

The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.

© 2012 Wiley-VCH Verlag & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany

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Print ISBN: 978-3-527-32845-1

Preface

Numerous discussions have repeatedly made it clear to me that microbes are a mystery to most people. After all, they are invisible. Microbes cause disease; they are involved in all kinds of novel production processes; they can easily be manipulated genetically – so it’s best to keep your distance! Besides, it requires some effort to fathom the secrets of these organisms. However, it is well worth the time. Microbes are fascinating in their diversity, activities, and achievements. Considering their abundance and their involvement in the global cycles of carbon, nitrogen, and sulfur, it is no exaggeration to say that microbes rule our planet. The object of this book is to spark interest in these multifaceted organisms. It consists of two parts, a reading section and a study guide which has been added to the thirty-two essays to allow this book to serve as an introductory text. Formulas and equations have been kept to a minimum whenever possible.

This book was written to include a fictitious conversation with someone who has an interest in the subject without being an expert and who asks questions every now and then. This form has been chosen to keep the text down-to-earth. Statements of highly respected colleagues have lent authenticity and brilliance to many of the chapters, for which I am truly grateful. I am also honored that they have read the respective chapters and complemented them in such a persuasive and competent manner. They are: for Chapter 1: Frank Mayer, Stade (DE); Chapter 3: Ralph Wolfe, Urbana, IL (US); Chapter 4: Manfred Eigen, Goettingen (DE), Gerald Joyce, La Jolla, CA (US); Chapter 5: Joachim Reitner, Goettingen (DE); Chapter 6: Karl Stetter, Regensburg (DE), Gregory Zeikus, East Lansing, MI (US); Chapter 7: Aharon Oren, Jerusalem (IL), Colleen Cavanaugh, Cambridge, MA (US), Antje Boetius, Bremen (DE); Chapter 8: William Whitman, Athens, GA (US), Karl-Heinz Schleifer and Wolfgang Ludwig, Munich (DE), Dieter Oesterhelt, Martinsried (DE), Volker Mueller, Frankfurt/Main (DE), Andrew Benson, Santa Barbara, CA (US); Chapter 9: Joerg Overmann, Munich (DE), Jack C. Meeks, Davis, CA (US); Chapter 10: Holger Brueggemann, Berlin (DE), Michael Blaut, Potsdam-Rehbruecke (DE); Chapter 11: Oliver Einsle, Freiburg (DE), Alfred Puehler, Bielefeld (DE); Chapter 12: Gijs Kuenen, Delft (NL); Chapter 13: Douglas Eveleigh, New Brunswick, NJ (US), Rolf Thauer, Marburg (DE); Chapter 15: Peter Duerre, Ulm and Hubert Bahl, Rostock (DE), Michael Young, Aberystwyth (UK); Chapter 16: Douglas Clark, Berkeley, CA (US); Chapter 18: Hermann Sahm, Juelich (DE), Karl Sanford, Palo Alto, CA (US); Chapter 19: Jan Andreesen, Goettingen (DE), Hans Guenter Schlegel, Goettingen (DE); Chapter 20: Timothy Palzkill, Houston, TX (US), Beate Averhoff, Frankfurt/Main (DE); Chapter 22: David Hopwood, Norwich (UK); Chapter 23: Julian Davies, Vancouver (CA); Chapter 25: Werner Arber, Basel (CH), Chapter 26: Peter Greenberg, Seattle, WA (US), Anne Kemmling, Goettingen (DE); Chapter 27: Eugene Rosenberg, Tel Aviv (IL); Chapter 28: Michael Rey, Davis, CA (US), Gregory Whited, Palo Alto, CA (US), Alexander Steinbuechel, Muenster (DE), Garabed Antranikian Hamburg (DE); Chapter 29: Stefan Kaufmann, Berlin (DE), Joerg Hacker, Berlin (DE), Werner Goebel, Munich (DE), Michael Gilmore, Cambridge, MA (US), Julia Vorholt, Zuerich (CH), Ulla Bonas, Halle (DE); Chapter 30: Eckard Wimmer, Stony Brook, NY (US), Karin Moelling, Zurich (CH), Stephen Gottschalk, Houston, TX (US), Patrick Forterre, Paris (France); Chapter 31: Claire Fraser-Liggett, Baltimore, MD (US), Michael Hecker, Greifswald (DE), Edward DeLong, Cambridge, MA (US), Rolf Daniel, Goettingen (DE); Chapter 32: Kenneth Nealson, San Francisco, CA (US), Friedrich Widdel, Bremen (DE), Douglas Nelson, Davis, CA (US), Michael McInerney, Norman, OK (US), and Koki Horikoshi, Tokyo (JP).

This book tells the story of microbes and the discoveries revolving around these organisms. Some of the scientists involved in these discoveries have been mentioned, whereby the list of names makes no claim to be complete. If in connection with such discoveries the work of some colleagues has not been acknowledged, I would explicitly like to request their understanding.

The compilation of this manuscript was supported by Daniela Dreykluft, for which I am truly grateful. I would especially like to point out the contribution of Dr. Anne Kemmling, who designed a great number of the drawings and illustrations. Dr. Petra Ehrenreich also deserves credit for some of the figures. I am indebted to Theodor Wolpers, Emeritus Professor of English Literature, for his contribution of Shakespeare quotes, Colleen Cavanaugh for discussions on the title of this book, Martin Keller for his advice on Chapter 14, and Eckard Wimmer for his advice on Chapter 30.

Special thanks go to Wiley-VCH, notably Anne du Guerny, Dr. Gregor Cicchetti, and Dr. Andreas Sendtko, for the constructive cooperation in a pleasant atmosphere.

This book would not be what it is without Dr. Lynne Rogers-Blaut. She grew up in Ohio (US), came to Germany, and obtained her PhD in my department, so she is qualified to convert my English into readable English and to discover any inaccuracies and inadequate explanations. Thank you, Lynne – it was a wonderful cooperation.

Last but not least, I thank my wife Ellen for her patience and her support.

Gerhard GottschalkGoettingen, 2011

Prolog

Bacteria: they are a real threat to mankind. They cause plague and cholera, and in previous centuries more people were killed by them than in wars. Still today we may suffer from tuberculosis, intestinal infections, bronchitis, and many other diseases.

Bacteria contaminate water and food. No, I don’t want to know more about these creatures. There is already a lot of information in the press and in package inserts of drugs.

This is not fair towards the bacteria. I admit, they do cause diseases, but only a very small percentage of bacteria is responsible for this. Most microbial species on our planet are peaceful and extremely useful. Without them, life on earth, would not be possible. They also affect our climate and are irreplaceable in the manufacture of biotechnological products.

Aren’t you exaggerating? I have read that bacteria help clean beaches and waters after tanker accidents. They are also used in waste water treatment. But I can’t believe that life on earth, depends on them, and I am sure viruses are not useful at all. By the way, what are archaea?

The discovery of archaea is an exciting story. It will be reported in Chapter 3. These microorganisms look more or less like bacteria, but they are fundamentally different. They represent a separate domain of life, and were already different from the bacterial domain three billion years ago.

Let’s start with bacteria, with their smallness and their enormous activity.

Part One

Reading Section

Chapter 1

Extremely Small But Incredibly Active

It is the greatest dream of a bacterial cellto become two bacterial cells

François Jacob

A visit to our Department of Microbiology was on the agenda of a high-ranking politician. How to impress him? We started with the smallness of bacteria but not in the usual way by stating that bacteria are approximately 1 µm long, so 1000 bacterial cells lined up end-to-end would measure just 1 mm. We tried a different way:

“Sir, this test tube contains nearly 6.5 billion bacterial cells in a spoonful of water. Thus, the number of bacteria nearly equals the number of human beings on our planet.” He took the test tube, looked at it, and could hardly recognize the slight turbidity. One billion bacterial cells in one ml or 1000 billion cells in a liter are barely visible. Then we pulled out a photograph the size of a letter pad and said, “Here are two of these 6.5 billion cells (Figure 1).” The Minister was impressed with the smallness of bacteria, which makes them barely visible even in large numbers, and with the enormous power of the methods used to examine them, for example, electron microscopy.

Figure 1 Test tube with a suspension of 6.5 billion bacteria, of which two are shown in an electron micrograph. The cell on the right has nearly completed cell division. The flagellae (long thread-like structures) provide motility to the cells.

(Source: Frank Mayer and Anne Kemmling, Goettingen, Germany.)

Electron Microscopy? I Used a Light Microscope When I Was at School, But What Is the Principle Behind the Electron Microscope?

Let’s have the expert Frank Mayer (Goettingen, Germany) tell us about this:

“Well, the “light” required for electron microscopy is a beam of electrons. This one is invisible to our eyes, but the pictures produced can be made visible. Because of the shorter wavelength of electron beams, much smaller details of biological objects can be seen than by light microscopy. Even enzyme molecules can be made visible, for example, on photographic paper. The disadvantage of using electrons is that a vacuum is required. Therefore, water has to be removed from samples before they can be examined, and this may cause damage to the objects. But recent improvements in electron microscopy make it possible to avoid damage to the objects by removing water from the objects in the frozen state.”

Isn’t it fascinating that electron microscopy makes it possible to magnify objects 100 000 times? Even light microscopy is capable of enlarging objects 1000-fold. This already impressed the plant physiologist Ferdinand Cohn (1828–1898), who wrote,

“If one could inspect a man under a similar lens system, he would appear as big as Mont Blanc [in the Alps] or even Mount Chimborazo [in Ecuador]. But even under these colossal magnifications, the smallest bacteria look no larger than the periods and commas of a good print; little or nothing can be distinguished of the inner parts and of most of them their very existence would have remained unsuspected if it had not been for their countless numbers.”

Ferdinand Cohn obviously exaggerated somewhat: a man two meters tall magnified 1000 times would be two thousand meters (6600 feet) tall, nearly half the elevation of Mont Blanc and one third that of Mount Chimborazo.

It is difficult to imagine that clear water can actually be highly contaminated, or that one cubic meter of air can contain one thousand microbial cells. Air, of course, is only slightly inhabited by microorganisms, but it is different when we look at our skin, which is densely populated by bacterial cells (see Chapter 10) with amazing biological activities. There are many sites in nature where they are able to multiply rapidly. Escherichia coli (E. coli, for short) resides in our intestine and is able to divide every 20 minutes! To put it casually, if one trillion bacterial cells in my intestine go with me to the movies, and if they manage to grow and divide optimally, then 16 trillion cells will leave the cinema with me 80 minutes later.

Good Example, But Why Do Bacteria Multiply So Astonishingly Fast?

It’s because bacteria have a high metabolic activity due to their high surface-to-volume ratio. Let me give you an example: If we put a cube of sugar into a glass of tea and, at the same time, the same amount of table sugar into a second glass, the table sugar will dissolve faster than the cube of sugar. Its surface-to-volume ratio is larger. A cube with an edge length of 1 cm has a surface-to-volume ratio of 6 : 1, between the total surface area of the sides, 6 cm2, and the total volume, 1 cm3. If we cut the cube into “bacteria-size” cubes with an edge length of 1 µm, we would end up with 100 million cubes with an overall surface area of 60 000 cm2. The total volume would be the same but the surface-to-volume ratio would increase by a factor of 10 000.

That has its consequences. Compared to cells of higher organisms, bacteria have a much larger surface area at their disposal, allowing the faster import of nutrients and export of waste products. Therefore, cell constituents can be synthesized more rapidly, a prerequisite for the rapid multiplication of cells. That’s why bacteria have the highest multiplication rates: some species have a record of around 12 minutes, so every 12 minutes two cells emerge from one. This, of course, cannot be generalized. There are also slow-growing bacteria that divide every 6 hours or even once every few days. Bacteria living in the “land of milk and honey” grow and divide rapidly, whereas the organisms in nutrient-deficient habitats such as oceans are much slower when it comes to cell division.

The Ability of Bacterial Cells to Divide Every 20 Minutes, or Even Every 12 Minutes, Is Quite Impressive. What Does that Mean for a Bacterial Population?

Let’s look at a single bacterial cell multiplying every 20 minutes under optimal conditions. How many cells and how much cell mass would be produced after 48 hours? We have to do some simple calculations. One cell (20) would give rise to two cells (21) after 20 minutes; four cells (22) after 40 minutes; and eight cells (23) after 60 minutes. Three divisions per hour would make a total of 144 divisions in 48 hours, resulting in a total of 2144 cells. This number probably doesn’t impress you. Let’s do a few more calculations: Conversion into a common logarithm (144 × 0.3010), with 10 as a base, yields 1043 cells. The weight of one bacterial cell is around 10−12 g, so 1043 cells weigh 1031 g or 1025 tons. Our planet weighs 6 × 1021 tons, so after 48 hours the total bacterial mass would be nearly 1000 times that of our planet.

Very Impressive, But Certainly Not Realistic.

Of course not, but the calculation is correct. However, the assumption that cells would divide every 20 minutes for a period of 48 hours is incorrect. Nutrients would have become limited after a few hours, so growth would have slowed down and stopped eventually. Perhaps the situation can be compared to that of a large pumpkin, which after reaching a critical size will also stop growing because of shortage of nutrients and accumulation of metabolic byproducts.

I Have Learned Something New. I Would Like to Know How Bacteria Compare with Higher Organisms.

Chapter 2

Bacteria Are Organisms Like You and Me

Nature would not invest herself in suchshadowing passion without some instruction

William Shakespeare, Othello

But What About Archaea and Viruses?

Archaea, to be introduced in Chapter 3, are living organisms like bacteria, but viruses aren’t like them at all because several characteristic features are missing. Viruses look and often act like little golf balls, just lying around or flying through the air. They aren’t able to do much by themselves. But as soon as they have entered a host cell, they start their devilish work. Viruses are able to cause epidemics, so they must somehow have life in them (see Chapter 30).

Bacterial and archaeal cells actually have much in common with plant and animal cells. Of course, you can’t compare a single-celled organism such as our intestinal bacterium Escherichia coli with an oak tree or an elephant. Comparisons have to be made at eye level, for example, comparing an E. coli cell with a cell from an oak leaf or with a muscle cell from an elephant. Then, the features common to all cells will become apparent. Let’s first look at the cell constituents.

All cells contain DNA (DeoxyriboNucleic Acid), but there is one qualitative difference. The DNA in plant and animal cells is localized in the nucleus, a compartment surrounded by a membrane. Plants and animals are therefore called eukaryotic organisms. A simple eukaryotic cell, the yeast cell, is depicted schematically in Figure 2a. Bacteria, on the other hand, are prokaryotic organisms whose DNA more or less floats in the cytoplasm (Figure 2b), which is a sort of gel. This intracellular space contains many proteins, nucleic acids, amino acids, vitamins, and salts.

Figure 2 The eukaryotic and the prokaryotic cell. (a) The eukaryotic cell contains a nucleus (center) surrounded by a membrane (with pores), a vacuole (light blue), the endoplasmatic reticulum (green), the Golgi-apparatus (purple), mitochondria (yellow/orange), ribosomes (black dots) and cytoplasm. The cell is surrounded by a cytoplasmic membrane and a cell wall. Diameter of the yeast cell depicted: 10 µm. (b) The prokaryotic cell contains a circular, coiled-up chromosome; ribosomes; and cytoplasm. The cell is also surrounded by a cytoplasmic membrane and a cell wall. A flagellum is depicted on the left (not present in all bacteria). Bacterial cells have an average length of 1 µm. (c) The cytoplasmic membrane consists of a phospholipid bilayer. In living organisms the membrane is charged, negative inside and positive outside. Proteins (red) are inserted into the membrane.

(Watercolor and gouache: Anne Kemmling, Goettingen, Germany.)

All cells contain three types of RNA (RiboNucleic Acid). The ribosomal RNA, together with the ribosomal proteins, makes up the ribosomes, the protein synthesis factories of the cells. The second type is messenger RNA which transmits DNA-imprinted messages to the protein synthesis factory. Messenger RNA passes the instructions from the DNA to the ribosomes, where proteins are synthesized on the basis of these instructions. There are mechanisms to ensure that only those proteins are synthesized that are required under certain physiological conditions. Not all proteins encoded on the DNA are continuously needed. The third type of RNA, transfer RNA, is required for the alignment of amino acids to form proteins. Each cell contains at least 20 of these transfer RNAs, which are specific for the 20 amino acids present in proteins. According to the synthesis protocol of the messenger RNA, the transfer RNAs, each linked to a respective amino acid, are lined up in the prescribed order then the amino acids are connected.

In all cells the entire machinery discussed above is surrounded by the cytoplasmic membrane, which is negatively charged on the inside and positively charged on the outside (Figure 2c). The membrane contains checkpoints for the transport of materials into the cells. These transport processes are highly specific; for example, there are checkpoints that allow potassium ions to pass but not sodium ions. The interior of most bacteria is high in potassium ions but low in sodium ions. If we were somehow able to taste the interior of a bacterium from the ocean (intracellular volume around 1 µm3, 1 cubic micrometer), it wouldn’t taste salty. Without its charge, the cytoplasmic membrane would be unable to fulfill its functions to ensure that the composition of the cell’s interior differs dramatically from the surrounding fluid. Inside the cell there are favorable conditions for cell division, irregardless of the conditions outside. The cytoplasmic membrane and its functions is one of the greatest miracles of evolution. How the membrane is charged will be described in Chapter 8.

Those Are the Cell Constituents, But How Does One Cell Become Two Cells?

To answer this question we have to look at the processes of life at a cellular level. Which processes are involved when two cells are formed from one? As already discussed, DNA is the carrier of genetic information needed to generate two E. coli-cells from one E. coli-cell. First of all, energy is required for the generation of a new cell. Here, the magic word is ATP, the abbreviation for adenosine-5′-triphosphate. ATP is the energy currency of all organisms on our planet. It powers processes such as thinking or muscle work, also growth, motility, and reproduction in bacteria. When ATP fulfills its role as an energy source, it is at the same time devaluated; it loses one phosphate residue, and adenosine-5′-diphosphate (ADP) is formed. This conversion is coupled with a release of chemical energy that can be invested in the energy-requiring reactions mentioned above.

Before a cell can divide into two cells, the chemical constituents of the cell have to be synthesized. It is as if a completely furnished house is to be converted into a completely furnished duplex. The “furniture” has to be assembled and set up or installed, so that two viable cells will have been formed from one. If we disregard the membrane, the cell wall, and any reserve material such as starch, the cell essentially has to deal with the synthesis of DNA, RNAs, and proteins, the three types of constituents already introduced. Before we go into protein synthesis, let’s look at the role of proteins.

Most of the proteins of a cell are enzymes, except for proteins such as collagen in higher organisms (part of the supporting tissues) or capsular proteins in certain bacteria. Enzymes are also called biocatalysts, and their names usually end in “-ase,” as in lipase or protease. The enzymes consist of 20 different building blocks, called the 20 natural amino acids (Study Guide). These amino acids are found in proteins, not only once but in multiple copies. The chain length of proteins is variable; proteins may consist of 100–300 building blocks. The amino acids have different chemical properties, so their chains fold to yield complicated structures to which metal ions, such as magnesium or ferrous (iron) ions are often bound. Every enzyme contains a catalytic center. This is the place of action, where the enzyme-catalyzed reactions take place. The diversity of enzymes is fantastic. Even our commensal E. coli is able to synthesize approximately four thousand different enzymes. They all have a specific function at defined sites of metabolism. For example, enzymes make the synthesis of DNA and RNA possible. Enzymes exhibit specificity, which means that the catalytic center of a particular enzyme has been designed to fit certain reaction partners. A DNA polymerase is capable of elongating DNA strands but it cannot cleave fat – that’s the job of the lipases. It is important to note that enzymes dramatically increase reaction rates because they bring the reaction partners into optimal spatial positions. Without enzymes, even enzymes themselves would not exist. The interdependence of DNA, RNA, and protein (enzyme) synthesis will become clear when we look at these processes (Figure 3).

Figure 3 The three principal processes for the transmission and utilization of genetic information. (a) Replication: The enzyme helicase separates the double strand into its two single strands. The exposed bases (letters) are then subject to base pairing, and the second, complementary strands are formed by the action of DNA polymerase. (b) Transcription: RNA polymerase widens the double helix and transcribes the base sequence of one DNA strand into the complementary sequence of an RNA strand, messenger RNA (mRNA). The DNA strand subject to transcription is called the codogenic strand. (c) Translation: As soon as mRNA becomes available, it binds to ribosomes (blue) and protein synthesis is initiated. The ribosomes closer to the RNA polymerase in Figure 3c have been “working” for a longer period of time, so “their” amino acid chains are longer. Each of the tRNAs is linked to a specific amino acid. They recognize their “turn” in protein synthesis with the help of an anticodon, which is complementary to the codon on the mRNA.

(Diagrams: Anne Kemmling, Goettingen, Germany.)

The genetic information of a bacterial cell is present in the form of a circular chromosome. It consists of double-stranded DNA, and the double strands are stabilized, as we say, by base pairing. This principle can be considered, without exaggerating, the secret of the conservation and transfer of genetic information in nature. The DNA consists of deoxyribose (a sugar), of phosphate to connect the deoxyribose molecules; and of four chemical compounds linked to deoxyribose. These are adenine, guanine, cytosine, and thymine, or A, G, C, and T, for short. The chemistry of these four compounds, commonly called the four bases, is such that two bases with a high affinity to each other tend to form pairs, referred to as base pairing (Study Guide). The two most-favored base pairs are AT and GC. With this information it is relatively easy to understand how two double-stranded chromosomes are formed from one double-stranded chromosome. In turn, this is a prerequisite for formation of two cells from one. The underlying process is called replication or identical reduplication. Obviously, the circular chromosome has to be replicated precisely, otherwise the genetic information in the two resulting bacterial cells will not be the same as in the original cell. The apparatus by which this is accomplished is commonly called the replication factory. Several enzymes are at work in this factory, DNA polymerase and helicase, to mention two. In the case of E. coli, the task is to exactly replicate the DNA ring, which is 4 938 975 base pairs long, and this in about 20 minutes. This length corresponds to the chromosome size of E. coli strain 536, a strain that causes urinary infections.

We will now attempt to grasp the principle of replication. The helicase man­ages to separate the double strand into single strands, initiating the replication at a distinct point. The single strands then enter the replication factory through different gates. If you understand the principle of base pairing, the next steps are easy to follow. The precursors of the four bases, dATP, dGTP, dCTP, and dTTP, are floating around in the cytoplasm and, of course, are also present in the factory. If a single strand with the sequence ATTCGGA becomes available, the precursors of the DNA to be synthesized are arranged in the sequence dTTP dATP dATP dGTP dCTP dCPT dTTP, so the DNA polymerase only needs to travel along the sequence and connect these precursors. As a result, the fragment TAAGCCT is formed, which is complementary to ATTCGGA. What has been described here for seven building blocks has to proceed 4.9 million times during replication of strain 536, mentioned above, then the second chromosome is completed. There is a slight problem with what is called the polarity of DNA strands; this will be discussed in the Study Guide.

Obviously, two cells require more RNA molecules than one. RNA has several special features: it contains ribose instead of deoxyribose, and the base thymine (T) is replaced by uracil (U). Since T and U hardly differ in their tendency to form a base pair with A, AU instead of AT is therefore the base pair at the RNA level. The process of RNA synthesis is called transcription. As in replication, the principle is base pairing. There are regions on the DNA that contain the information for synthesis of ribosomal RNAs and of transfer RNAs. They are transcribed, thus yielding additional ribosomal RNAs and transfer RNAs. Furthermore, messenger RNA is synthesized. These molecules travel to the ribosomes and transmit the information for protein synthesis. The information for protein synthesis is organized on the DNA and, after transcription, on messenger RNA in the form of genes. A gene is a segment of the nucleic acids that contains the information for the synthesis of a particular protein. It is defined by a start and a stop signal, which are recognized by the machinery. Thus, at the ribosome, a gene of an exactly defined size gives rise to a given protein. The dynamics of these processes are depicted in Figure 3. Ribosomes like start signals. As soon as start signals are available on the messenger RNA, the ribosomes bind to the messenger RNA. The synthesis of an amino acid chain can then begin. When the stop signal is reached, the ribosomes detach from the messenger RNA and release the amino acid chain. Upon folding, the amino acid chain becomes a protein with enzyme activity.

The conversion of a base sequence into an amino acid sequence is called translation. This process is not as simple as transcription because the sequence of the four bases UAGC at the messenger RNA level has to be translated into a sequence of 20 amino acids. To achieve this, the genetic code evolved. The information is not provided by a single base but by a base triplet, a sequence of three bases that gives the code word for a particular amino acid. Therefore, when a gene on the messenger RNA has a length of 990 bases, this represents the information for the synthesis of a protein consisting of 330 amino acids. The number of possible base triplets is large enough to provide organisms with a sufficient number of code words. Four bases allow 43 or 64 possible combinations for triplets. These combinations are used in all of nature (Study Guide).

How Does Cell Division Proceed?

In the cell there is a special protein called the FtsZ protein. In the center of the mother cell, this protein forms a ring structure that contracts until the membranes touch each other and fuse. This results in the formation of two compartments, in other words, two cells (see Figure 1, left cell). It’s fascinating how proteins and structures, not yet known in detail, manage processes essential for life: the distribution of cell constituents such as chromosomes, RNAs, ribosomes, and proteins. In this process, the proper distribution is a prerequisite for formation of two viable cells.

Eukaryotic Cells Are Certainly More Complex Than Prokaryotic Ones

Yes, they are. In addition to the nucleus, there are other compartments in eukaryotic cells, including the mitochondria or the Golgi apparatus (Figure 2a). However, the role of ATP and the processes leading to the synthesis of cell constituents – the 20 amino acids and the substances making up the DNA and RNAs – are quite comparable. Processes in the cell nucleus are much more complex than those occurring in the vicinity of the microbial chromosome. The number of bases making up the human chromosomes is about one thousand times larger than that of the E. coli chromosome. In humans, this information is sufficient for the synthesis of approximately 100 000 proteins. However, in both cases the underlying genetic code is identical. There are significant differences when we examine the localization of genes on human chromosomes in comparison to the E. coli chromosome. The latter – also true for other microbes – is packed with genes. The genes are strung together and there is very little “wasted space” in terms of sequences. By contrast, the intergenic space between the genes on human chromosomes is extremely large. Often there are millions of bases between two genes, and the function of these bases is not yet clear. Maybe this is yet another secret of life that must be brought to light. In addition, a eukaryotic gene differs in one important aspect from a prokaryotic gene. We recall that 990 bases on a prokaryotic genome correspond to 330 amino acids. In higher organisms, the messenger RNAs are much larger. They contain introns that are inserted into the messenger RNA, giving it a mosaic-like structure. In a process called splicing, these inserts have to be removed before the messenger RNA can actually function as a matrix for protein synthesis. When taken together with the cell differentiation processes, the most remarkable features of higher organisms, it becomes clear that there are tremendous differences between prokaryotes and eukaryotes.

Nevertheless, I stick to my statement: Bacteria are organisms like you and me.

Chapter 3

My Name Is LUCA

We need to knowWe will know

Inscription on the tombstone of David Hilbert, mathematician

I Beg Your Pardon, But Isn’t that the Beginning of a Song About “the Girl Who Lives Upstairs?”

I don’t mean that Luca. Here LUCA stands for the Last Universal Common Ancestor, the living organism that was the mother of all organisms on Earth.

Who Was LUCA?

Before this question can be discussed, we need to know if the definition of a species as we know it for animals and plants can also be applied to bacteria.

It was Mrs. Fanny Angelina Hesse whose recommendation made it possible to solidify growth media for bacteria. She suggested using the gelatinizing substance agar (also called agar agar), which was introduced in Robert Koch’s laboratory in 1884. The use of agar allowed bacteria to grow on the surface of growth medium, like on the surface of pudding or a slice of bread. On such a surface, clusters of bacteria originating from one cell are formed. These are called colonies. When a tiny portion of a colony of Escherichia coli is transferred to fresh agar, new colonies of cells of E. coli are recovered (Figure 4). It could then be concluded that the definition of a species could also apply to bacteria. Therefore, elephants arise from elephants, oaks from oaks; E. coli yields E. coli, and Staphylococcus aureus yields Staphylococcus aureus and not a bacterium with completely different properties.

Figure 4 Colonies of a bacterium on agar growth medium in a Petri dish. When a minute amount of cells is streaked out (starting at 9 o’clock on the dish), cells are so separated that round colonies can develop from single cells. Such a cell community then represents a clone because it originates from one cell. Depending on its size, a colony may contain between 50 and 500 million cells.

(Photograph: Anne Kemmling, Goettingen, Germany.)

In the past 120 years, thousands of bacterial species have been isolated and their properties have been described. However, for many years their evolutionary (phylogenetic) relatedness remained unknown. Of course, efforts were made in numerous laboratories to learn something about this relationship. It was necessary to identify bacterial species on the basis of their properties and to develop strategies to control those causing disease. The actual breakthrough, however, occurred just a quarter of a century ago.

I Have a Question Regarding Mrs. Hesse. What Is Agar Agar and How Did She Get the Idea to Use It to Solidify Growth Media for Bacteria?

Fanny Eilshemius was born in 1850 in Laurel Hill, New Jersey (USA), the daughter of German immigrants. While traveling through Europe, she met a medical doctor, Walter Hesse, whom she married. Walter Hesse had a strong interest in bacteriology. He grew bacteria on gelatin surfaces and was very disappointed that the gelatin melted so easily. Fanny remembered a recipe she had from Dutch friends who had lived on the island of Java. They used agar agar, a polymer extracted from algae to solidify deserts. Agar is ideal because hot solutions containing 2 percent agar solidify at about 50 °C and they only melt again upon boiling. In addition, most bacteria do not degrade agar, so the introduction of agar provoked a revolution in microbiological laboratories. Bacteria could then conveniently be grown on agar surfaces in Petri dishes and the properties of pure cultures, those containing only one species, could be studied.

What About the Breakthrough You Mentioned?

In the 1960s a procedure for sequencing DNA fragments was worked out by the British molecular biologist Frederick Sanger. He developed an elegant method to shorten DNA fragments base by base and to determine whether the last base in the fragment is T, C, G, or A (see Chapter 31 for details). This method was so ingenious that Frederick Sanger was awarded the Nobel Prize (together with Walter Gilbert and Paul Berg), his second one – see Chapter 28 for the first one. Progress was enormous, and it is no exaggeration to say that now more than a billion base sequences are determined every day using this and more advanced methods. At the University of Illinois in Urbana, the microbiologist Carl Woese adopted Sanger’s method to learn something about the phylogenetic relationship of bacterial species. He chose the 16S-rRNA to be sequenced. This RNA is present in all bacteria because it is essential for the formation of the ribosomal protein synthesis factories. A milestone in this research was reached in 1977: Carl Woese and his coworkers published their research paper on the “molecular approach to prokaryotic systematics.” The relatedness between bacterial species was determined on the basis of differences in the sequence of 16S-rRNA. At this point, a sensational experiment appeared on the horizon. Ralph S. Wolfe, another eminent microbiologist, was working next to the laboratory of Carl R. Woese. He did pioneering research on methane-producing microorganisms, especially on the biochemistry of the pathways leading to the production of methane. Of course, Ralph Wolfe and Carl Woese talked about their work. They decided to collaborate, but let’s have Ralph Wolfe (Champaign-Urbana, Illinois, USA) tell us about the results of their experiments:

“Early in his career, Woese had studied the ribosome and was convinced that this organelle was of very ancient origin, that it had the same function in all cells, and that variations in the nucleotide sequence in an RNA of the ribosome could reveal evidence of very ancient events in evolution. He chose the 16S-rRNA and developed a similarity coefficient that could be used to compare the relatedness of two different organisms. By 1976 he had documented the 16S-rRNAs of 60 bacteria.

The research program of Ralph Wolfe concerned the biochemistry of methane formation by methanogenic bacteria, an area poorly studied because of the difficulties of cultivating the organisms. Techniques were developed for culture of cells in a pressurized atmosphere of hydrogen and carbon dioxide. By 1976 the structure of two unusual coenzymes, coenzyme M and Factor 420 (a unique deazaflavin), and their enzymology had been elucidated.

The conjunction occurred with an experiment designed to examine the 16S-rRNA of methanogens. The pressurized atmosphere technique proved ideal for containing the high level of injected radioactive phosphorus to label the rRNA of growing cells. The two-dimensional chromatograms of the labelled 16S-rRNA oligonucleotides from the first experiment were so different from anything previously seen, that Woese could only conclude that somehow the wrong RNA had been isolated. The experiment was carefully repeated, and this time with the same results: Woese declared, “Wolfe, these organisms are not bacteria!” “Of course they are, Carl; they look like bacteria.” “They are not related to anything I’ve seen.” This experiment marked the birth of the archaea!”

This is an important contemporary testimonial. It led to the conclusion that a third form of life exists on our planet, the archaea, in addition to the eukaryotes (animals, plants, fungi) and the bacteria. Ralph Wolfe describes why his colleague Carl Woese chose 16S-rRNA, then he describes his own research during which the techniques for growing large amounts of methane-producing microorganisms were developed. These microorganisms were used for biochemical investigations that led to the discovery of novel “methano-vitamins” such as coenzyme M or factor 420.

The studies in Woese’s lab involved growing the methanogenic organisms in the presence of radioactive phosphate. The 16S-rRNA then contained radioactivity because of the phosphate bridges present in the molecule. Fragments were isolated, sequenced, and compared with the 16S-rRNAs of E. coli and other organisms. When they compared the sequences obtained, differences were encountered that could not be explained. Both Carl Woese and Ralph Wolfe were speechless. The sequences of all the bacterial species studied before were written in essentially the same language and contained a number of deviations, which gave insight into the distance between two bacterial species in the phylogenetic tree. But what the researchers now discovered was that parts of the text were deleted and parts were written in another language, say in Hebrew. This was something unique, and this also proved to be the case when the 16S-rRNA of other methanogenic organisms was sequenced.

Could You Please Explain a Bit More About these Differences in the 16S-rRNAs?

Let us imagine a large mosaic, for instance, the triumphal march of Dionysos in one of the Roman houses in Paphos (Cyprus) discovered in 1962. Like 16S-rRNA, mosaics also consist of thousands of building blocks. If we change something in the border surrounding the scene, this will have little effect on the general impression of the mosaic. It is the same with the sequence of the 16S-rRNA of bacteria. Trends as well as a few variations in the sequences can be recognized, making it possible to determine the relatedness of the organisms from which the 16S-rRNAs were isolated. However, if Dionysos were to be replaced in the mosaic by a mythological priest, then the number and color of the mosaic tiles would be quite different. It is impossible to derive one figure from the other, so a common ancestor must be postulated that gave rise to Dionysos, on the one hand, and to the priest, on the other – an ancestor such as LUCA.

Let’s now look at the sequences of the 16S-rRNAs of Escherichia coli (1542 bases long) and Bacillus licheniformis (1548 bases) as representatives of the bacteria and of Methanosarcina mazei (1474 bases), Archaeoglobus fulgidus (1492 bases), and Methanosphaera stadtmanae (1480 bases), representing the archaea. The alignment of these sequences results in a beautiful picture (Figure 5), which was done with the aid of a computer program that searches for maximum correspondence of the sequences. In order to attain this sequence homology, the computer takes sequences apart and introduces gaps. Several archaeal “gaps” are apparent, including some large ones, but there are also a few bacterial gaps. Identical sequences can be seen around 810, 1440, and 1540. Looking at Figure 5 as a whole, the impression is that the upper three sequences are related as well as the lower two. These differences made history.

Figure 5 Base sequence of the 16S rRNAs of three archaea (Methanosarcina mazei, Archaeoglobus fulgidus, and Methanosphaera stadtmanae) and two bacteria (Escherichia coli and Bacillus licheniformis). The depiction is based on a ClustalW-alignment under standard conditions (W.A. Larkin et al., Bioinformatics 23, 2947, 2007). Visualization was done with Jaliew using the standard color code for nucleotides. (C. Clamp et al., Bioinformatics 20, 416, 2004). Gaps were inserted into the sequences to achieve maximal agreement.

(Adaptation: Antje Wollherr, Goettingen, Germany.)

Carl Woese recognized the tremendous importance of his discovery. In the case of the methanogenic organisms, he had sequenced the 16S-rRNA of an organism that phylogenetically does not have much in common with the bacteria. This new domain of organisms was originally called archaebacteria; later the word “bacteria” was omitted, so now we speak of archaea. The terms methanobacteria or methane-forming archaebacteria are no longer used; instead, they are called methanoarchaea.

When these results were published, many microbiologists opposed such views. But there was also a lot of support, for instance by the German microbiologists and molecular biologists Otto Kandler, Wolfram Zillig, and Karl Otto Stetter, who later made important contributions supporting the archaeal concept. In the US, acceptance was slow but became enthusiastic when major textbooks adopted the concept of three domains of life.

Now we will jump from the situation in 1977 to the present and look at an actual phylogenetic tree. It is apparent in Figure 6 that, beginning with LUCA, evolution proceeded to the domains of Archaea and Eukarya, from which the domain of Bacteria branched off early in evolution. Not only methane-forming bacteria belong to the archaea but also the so-called extremophilic microorganisms, which will be discussed in Chapter 6.

Figure 6 Phylogenetic tree of the three domains of all living organisms, depicted clockwise from left to right: Bacteria: Aquifex, Bacteroides, cyanobacteria, proteobacteria, Spirochaeta, Bacilli, green filamentous bacteria. Archaea: Nanoarchaeum equitans (small dots) attached to Ignicoccus hospitalis, Thermoproteus, Pyrodictium, Methanococcus, Methanosarcina, halophilic archaea. Eukarya: Entamoeba, mucilaginous fungi, humans, fungi, plants, ciliates, trichomonads, diplomonads. LUCA (at the bottom) stands for the Last Universal Common Ancestor.

(Diagram: Anne Kemmling, Goettingen, Germany.)

Readers not so familiar with this concept of evolution will find it difficult to accept the idea that two of the three domains of life on our planet are devoted to microorganisms. The third one is reserved for plants, fungi, animals, and us. We may not forget that bacteria and archaea, on the evolutionary time scale, were by themselves during most of the biological evolution on Earth. One might even ask the question why microorganisms allowed the evolution of higher organisms – an interesting but difficult question. But still, what were the properties of LUCA? It can be assumed that it was a bacterial- or archaeal-like organism that lived in the absence of oxygen. LUCA was a fermenting organism or an organism that converted sulfur and molecular hydrogen to hydrogen sulfide. Archaea performing this kind of fermentation are still present on our planet. How LUCA evolved and how our current atmosphere developed with oxygen as the indispensable element will be outlined in the next two chapters.

Chapter 4

From the Big Bang to LUCA

The question “what is life”is precisely the question“what is evolution”

Carl R. Woese

The Big Bang occurred 13.7 billion years ago. Guenther Hasinger (Garching, Germany) compressed this incredibly long time scale into one calendar year. During the first eight months the universe was like Hell. On January 5 the first stars appeared as well as the chemical elements, including carbon, oxygen, and nitrogen. In March, quasars reached their maximum and planets began to appear. At the beginning of September, approximately 9.1 billion years after the Big Bang, our solar system evolved. One month (1.1 billion years) later, life developed on our planet. This was 3.5 billion years ago. Plants and vertebrates appeared after December 19, 500 million years ago. showed up on Earth on December 31 at 8 p.m., and Jesus Christ was born just 5 seconds ago. By the way, by January 12 of the second Big Bang year, our planet will become so hot that life no longer will be possible. This of course has nothing to do with man-made global warming, but has a different reason: By then, the sun will be in the process of becoming a red giant. January 12, by the way, will be 447 million years from now.