Global warming and the significance of fossil fuels

Energy for industrial, commercial and residential purposes, electricity generation and transportation is primarily supplied by fossil fuels (coal, gas and oil) and nuclear power. It is now widely believed that climate change is strongly linked to the increased level of greenhouse gases in the atmosphere, and that human activity especially through the combustion of fossil fuels is a major contributing factor.

One of the main greenhouse gases, accounting for 65% of global warming, is carbon dioxide. Fossil fuels are the stored energy or ‘ancient sunlight’ of aeons and millennia ago that mankind has been burning extensively over a few centuries and more prolifically in recent decades. When such fossil fuels are burned for energy, carbon dioxide that has been locked away for all those years is released into the atmosphere greatly adding to global greenhouse gases. In contrast, when present-day plant material is burned the carbon locked into the biomass for a relatively short period of time is released back into the atmosphere thus recycling the carbon dioxide. Consequently, the system is relatively carbon neutral unlike the burning of fossil fuels.

Global emissions of carbon dioxide from fossil fuels over the first five years of this third millennium were four times greater than for the preceding ten years, despite the decisions of the Kyoto Agreement to reduce carbon dioxide emissions.

The nature of stem cells

Within the mammalian body there is a ranking system of cells from the undifferentiated to the highly specialised cell types and tissues, e.g. liver, brain, lung, blood, skin, etc., which have arisen by the process of cellular differentiation. Cellular differentiation occurs by a variety of biological processes that involve the switching on and off of specific genes, of cell signalling and, especially, where the cell is situated in the body. When a cell achieves terminal differentiation it cannot reproduce itself. Yet, it has long been recognised that systems and tissues of the adult body must have some ability to replace cells such as cells of the blood system (haematopoietic cells) and skin cells (epidermal tissue). The body does, however, retain certain undifferentiated cells within tissues and such cells are termed tissue or adult stem cells (TS).

What are stem cells? Stem cells are undifferentiated cells that have the capacity to self-renew and to achieve multilineage differentiation. Within a particular cell population they can remain in an undifferentiated state and, as such, do not have any specialised function. However, when required they can be induced to differentiate into specific cell types. Stem cells have specific enzymes and cell-specific antigens and have the ability to express developmentally regulated genes. Stem cells have been characterised as totipotent, pluripotent and multipotent.

INTRODUCTION

Virulent phages such as Escherichia coli phage T4 are professional predators of bacteria. It is believed that this predator-prey relationship resulted in an evolutionary arms race in which bacteria developed anti-predation strategies against phages such as loss of receptor structures, restriction-modification systems, and abortive infection mechanisms. Temperate phages can lyse the bacterial host or alternatively integrate their DNA into the bacterial chromosome. As judged from the analysis of bacterial genomes, about a third of the bacteria might contain a prophage sequence. Temperate phages had thus a great impact on bacterial chromosome structure in general and the evolution of bacterial pathogenicity in special.

THEORETICAL FRAMEWORK FOR PHAGE-BACTERIUM INTERACTION

The peculiar life style of temperate phages makes them model systems to address a number of fundamental questions in evolutionary biology. The viral DNA undergoes different selective pressures when replicated during lytic infection cycles as compared to prophage DNA maintained in the bacterial genome during lysogeny. Darwinian considerations along with the selfish gene concept lead to interesting conjectures (Boyd and Brüssow, 2002; Brüssow and Hendrix, 2002; Brüssow et al., 2004; Canchaya et al., 2003, 2004; Lawrence et al., 2001). One could anticipate that the prophage decreases the fitness of its lysogenic host by at least two processes: first by the metabolic burden to replicate extra DNA and second by the lysis of the host after prophage induction. To compensate for these disadvantages one has to invoke the explanation that temperate phages encode functions that increase the fitness of the lysogen.

INTRODUCTION

The current view of eukaryote phylogeny indicates that microbial eukaryotes (protists) represent the vast majority of the biological diversity within the eukaryotic domain of life, and that multicellular eukaryotes have evolved from protist lineages several times independently (Adl et al., 2005). Accordingly, most eukaryote genome evolution has occurred in microbial lineages, and multicellular eukaryotes with sequestered germlines, such as animals and plants, should be seen as recent evolutionary exceptions, rather than the norm, within the eukaryotic domain (Figure 12.1). Yet, most knowledge about eukaryotic genome evolution comes from multicellular organisms and a few representatives of unicellular lineages, such as yeast. Fortunately, this narrow view of eukaryote genome evolution is now expanding with the advance of genomic sequences from diverse protist lineages.

Several aspects of the lifestyles of protists are more similar to prokaryotic organisms, than to multicellular eukaryotes; differentiation into germ and soma cells are rare, and protists often live in close contacts with cells of distantly related species in the environment. Furthermore, many protists have asexual life cycles, although meiosis appears to be ancestral to eukaryotes (Ramesh et al., 2005). These similarities suggest that protists may share some aspects of genome evolution with prokaryotes. As is obvious from this book, the transfer of genetic material between unrelated lineages, lateral (or horizontal) gene transfer (LGT), is a fundamental mechanism in prokaryotic genome evolution, resulting in genomic plasticity which, for example, provides the basis for adaptation processes (Boucher et al., 2003; Gogarten and Townsend, 2005; Pál et al., 2005).

During the past 25 years, a nearly exponential increase has occurred in nucleotide sequences available from databases. The first microbial genomes were published in 1995 (Fleischmann et al., 1995; Fraser et al., 1995; Himmelreich et al., 1996); the NCBI database currently contains 534 complete bacterial chromosome sequences. The genomes have been determined not only from different species, but also from different strains of the same species. This has paved the way for comparative genomics and has allowed detailed analysis of genetic differences between strains (Wren, 2000; Dobrindt and Hacker, 2001; Edwards, Olsen, and Maloy, 2002; Raskin, Seshadri, Pukatzki, and Mekalanos, 2006). Since infectious diseases are a major health threat worldwide and range among the most frequent causes of death worldwide (WHO Health Statistics 2006), it is not surprising that the first two organisms to be sequenced were pathogenic bacteria.

During the past decade many attempts have been made to understand the molecular basis of microbial pathogenicity, and our knowledge has advanced quickly, in particular through the use of methods of cellular biology, genomics, and proteomics. Various events in the pathogenesis of microbial infections, such as adherence to and entry into human and animal host, invasion of host cells, toxin production, establishment and dissemination of bacterial populations in the host, and the role of the host immune system, have been studied in detail for many host-pathogen interactions.

INTRODUCTION

Despite our interest and motivation, bacteria are not particularly easy organisms to study; their niches are complex and poorly understood and the vast majority of these species are difficult to culture or to manipulate in the laboratory. Of all bacteria, it is pathogens whose physical, social, and economic impact on our day-to-day lives garners the most attention, from both scientists and non-scientists alike. As a result, pathogens are among the best-studied bacteria, and lessons we learn from them are often generalized to other, non-pathogenic bacteria. Not surprisingly, the first lessons learned in the so-called genomic era came from pathogens, which were the first organisms with fully sequenced genomes. The promise of genomics was that the limitations of conventional microbiology could be overcome by studies of genome sequences and careful analysis of the genes contained therein. Here we examine how genomics has shaped our understanding of microbial genome evolution and ask how extensible these lessons may be. Among the notions that attracted widespread attention was the finding that certain clusters of genes are specifically responsible for virulence and that these loci are often obviously of foreign origin, having been introduced by the then under-appreciated process of lateral gene transfer or LGT. Coming more than a decade after these findings, this volume is focused on the hugely influential role of LGT in the evolution of genomes, particularly those of pathogenic bacteria.

INTRODUCTION

The bacterial genome, that is, the entirety of all genes of a bacterium, was once viewed as a rather stable entity. However, the observation of spreading resistance to antibiotics led to the discovery of extra-chromosomal elements encoding this property. Obviously, plasmids are able to transfer genes from one bacterium to another not only among one species but also from one species to another. Such transfer of genes is not restricted to antibiotic resistance genes. Examples of further traits often encoded by plasmids include resistance to heavy metals and production of toxins.

Another example of mobile genetic elements is phages, the viruses of bacteria. Phages are not just able to infect and finally lyse the bacterial host cell. Certain phages infect and then integrate their whole genome into the bacterial chromosome and thereby become a prophage. This may add another important factor to the property of the infected bacteria. In the case of pathogenic bacteria the production of toxins is frequently encoded by a prophage. A few medically important examples are bacteriophage β of Corynebacterium diphtheriae encoding diphtheria toxin, phage C1 of Clostridium botulinum coding for the C1 neurotoxin, and phage H-19B of Escherichia coli, which harbors the gene for Shiga toxin Stx1 (for a recent review, see Brüssow et al., 2004).

Smaller but still important mobile genetic units are insertion sequence (IS) elements. IS elements mediate DNA rearrangements by transposition, resulting in off/on switching of gene expression by insertion into, and excision from, open reading frames (ORFs), respectively.

INTRODUCTION

In eukaryotes, the great majority of genetic recombination takes place during the complex and highly organized process of meiotic division, a part of sexual reproduction. As a consequence there are a number of constraints on patterns of variability in the recombination process. Recombination takes place only between organisms that are similar enough for their offspring to be viable, and therefore it is generally limited in the novelty it can introduce. Within species, the most common cause of reproductive isolation is geographical separation. In most higher animals and plants, the number of crossovers per chromosome is predictably a number between 1 and 5 in both sexes. Even where individuals differ in the amount of recombination that they initiate, for example because of the absence of crossing over in male Drosophila, the existence of a common mating pool will tend to homogenize the population with respect to the amount of genetic exchange that has occurred in the ancestry of each individual. In summary, while the mating process is elegant, eukaryotic recombination is typically quite predictable with minimal differences in genetic patterns between individuals in the same species.

In bacteria, there are no such rules. Recombination is never obligate and occurs by three distinct mechanisms; transformation, transduction, and conjugation, each of which in their nature can vary enormously between lineages.

INTRODUCTION

During the past 20,000 years the most striking change in the lifestyle of humans was the transition from the hunter-gatherer culture to the introduction of agriculture and animal husbandry associated with stable settlement in the Neolithic. With sufficient food resources, the human population, which had been scattered, started to grow. Larger urban communities were formed, which was the starting point of culture and technology.

Humans have evolved with bacterial communities (microecological systems) as colonizers (skin, mucosa, gastrointestinal tract) and as conditional pathogens. For true pathogens the more dense human communities became of particular interest, especially for specialization in the human hosts (McKeown, 1988).

The so-called technical revolution that began at the end of the 19th century created a need for energy as a permanent concern. Because of continuing urbanization and the growing human population in the Third World, sustainability of food supply remains an important issue.

When, 200 years ago, a more productive agriculture began that was based on the then-young agricultural sciences, the principle of enduring means of production long endured, especially with regard to recycling of energy. These principles began to fade with the invention of mineral fertilizers, followed by mechanization and energy-consuming (wasting) means of production that were more independent of seasons. By the middle of the last century this had led to a high degree of mechanization of agriculture, where animals and plants were regarded more as “work pieces” than as living beings.

INTRODUCTION

Like most eubacteria, S. aureus possesses a variety of mobile genetic elements (MGEs) that contribute in major ways to pathogenesis and its evolution. In addition to the typical MGEs carried by most bacteria, that is, prophages, transposons, and plasmids, S. aureus possesses two types of novel elements that have not been described for other bacteria, namely the superantigen-encoding pathogenicity islands and the resistance-encoding SCCmec elements. In this chapter, the general properties of these various MGEs are summarized, with special emphasis on the two novel types and on their contributions to pathogenesis and its evolution.

MOLECULAR GENETICS OF THE STAPHYLOCOCCAL MGEs

Plasmids

For a comprehensive review of plasmid origins and interactions, see Firth and Skurray (2006). Staphylococcal plasmids range in size from 1.2 to more than 100 kb; all known staphylococcal plasmids are circular duplex DNA, using either of the two standard modes of replication, theta and rolling circle (RC), with the latter being used principally by those of less than 10 kb, and the former by those larger, though this is only an approximate dividing line. As with all other plasmids, replication of staphylococcal plasmids is negatively autoregulated. For the known small RC plasmids, this is accomplished by cis-encoded antisense RNAs, sometimes with the assistance of small proteins. Theta plasmids of the pSK41/pGO1 family also appear to use an antisense mechanism.

INTRODUCTION

Intracellular bacteria (symbionts and parasites) are characterized by a genome reduction syndrome that, when compared to their free-living relatives, leads us to the conclusion that they are evolving anomalously. Is this right? The notion of anomaly has an anthropocentric connotation, and from such a viewpoint we cannot state that genome reduction is an evolutionary anomaly; likewise we cannot state that parasitic organisms represent a degenerate stage of evolution as compared to their non-parasitic ancestors. By contrast, we can affirm that they represent an anomaly if we are unable to explain their origin and evolution, given there is no suitable theory to explain both the increase in genome size and evolutionary complexity as well as the genome reduction process in endosymbionts. The question is: Do we have such a theory? In the past few years Michel Lynch and collaborators have published a series of papers on this particular issue, trying to integrate the evolution of genome size and concomitantly genome complexity of prokaryotes and eukaryotes into a single theoretical framework following the basic principles of population genetics.

In this chapter, we would like to deal with how basic principles, such as mutation, selection, and effective population size, can give us an acceptable explanation, empirically founded, of the genome reduction process in endosymbiotic bacteria. We propose a model that both explains the huge transformation of endosymbiotic genomes at nucleotide level and accounts for genome reduction.

INTRODUCTION

It appears that one of the first things that occurred to Felix d'Herelle when he discovered bacteriophages in 1917 was that these mysterious objects might provide a means of killing bacteria that are pathogenic to humans (Summers, 1999). The still ongoing story of phage therapy, as this approach was called, has been told elsewhere and will not be retold here, but it serves to point out that scientists have been interested in the effects of phages on their hosts since their discovery. d'Herelle believed, and eventually established, that phages are viruses that infect bacteria. However, it was not until the experimental investigations of phages at the dawn of molecular biology in the 1940s and 1950s that it became clear that phages - and for that matter their bacterial hosts - are genetic organisms (Luria and Delbrück, 1943; Hershey and Rotman, 1949; Hershey and Chase, 1952; Stent, 1963), just like fruit flies, corn, and humans, and so could be expected to mutate and evolve.

Although some work was done on the evolution of phages in the 1960s, 1970s, and 1980s, a more detailed understanding of the genetic mechanisms of phage evolution had to wait until the advent of high-throughput DNA sequencing in the 1990s. This is because the genetic history of a phage, while it is to a significant extent encoded in the phage's genome sequence, is largely invisible to our analysis until we can compare that sequence to the genome sequences of other phages.