Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis

Mechanisms of bacterial pathogenicity

Pathogenic bacteria utilise a number of mechanisms to cause disease in human hosts. Bacterial pathogens express a wide range of molecules that bind host cell targets to facilitate a variety of different host responses. The molecular strategies used by bacteria to interact with the host can be unique to specific pathogens or conserved across several different species. A key to fighting bacterial disease is the identification and characterisation of all these different strategies. The availability of complete genome sequences for several bacterial pathogens coupled with bioinformatics will lead to significant advances toward this goal.

An experimental validation of orphan genes of Buchnera, a symbiont of aphids

Although Buchnera sp. APS, an intracellular symbiont of pea aphids, is a close relative of Escherichia coli, its genome has been extensively modified because of its prolonged intracellular life. In our previous studies on the Buchnera genome, computer analysis predicted three "orphan" genes, yba2, yba3, and yba4, which are open reading frames (ORFs) with no homologs in the database. In this paper, we successfully validated all these orphan genes by RT-PCR and Northern hybridization. The present study also revealed that yba3 and yba4 formed an operon, suggesting that they function in concert. Sequences around transcriptional start sites suggests that these genes are under the control of sigma 70. In view of codon usage and AT bias observed in these genes, it is likely that Buchnera have maintained them for an evolutionarily long time.

Characterization of effector proteins translocated via the SPI1 type III secretion system of Salmonella typhimurium

Salmonella spp. employ a conserved type III secretion system encoded within the pathogenicity island 1 (SPI1; centisome 63) to translocate effector proteins into the host cytosol. The translocated effector proteins trigger diverse responses including bacterial internalization. In a mutation analysis we have defined the set of effector proteins mediating tissue culture cell invasion. This set includes sopE2 (centisome 40-42), sopB (SPI5, centisome 20) and in the case of S. typhimurium SL1344 also the phage-encoded effector sopE (SopEphi, centisome 59-60). A triple mutant SL1344 derivative deficient of SopE, SopE2 and SopB was more than 100-fold attenuated in tissue culture cell invasion. Phylogenetic analyses indicate that the last common ancestor of all contemporary Salmonella lineages already harbored all genes necessary for host cell invasion, namely the SPI1 type III secretion system, sopE2 and sopB. SopE, which is 70% identical to sopE2 is only present in some Salmonella strains and emerged later well after the divergence of the contemporary Salmonella lineages. Interestingly, S. typhimurium strains that harbor sopE are associated with epidemics, arguing that sopE is one of the factors determining the "fitness" of a strain. We found that SopE can specifically activate a different set of host cellular RhoGTPases than SopE2. This allows the bacteria to fine tune host cellular responses very precisely and may offer an explanation for the improved epidemic fitness of sopE-positive S. typhimurium strains.

Unseen forces: the influence of bacteria on animal development

The diversity of developmental programs present in animal phyla first evolved within the world's oceans, an aquatic environment teeming with an abundance of microbial life. All stages in the life histories of these early animals became adapted to microorganisms bathing their tissues, and countless examples of animal-bacterial associations have arisen as a result. Thus far, it has been difficult for biologists to design ways of determining the extent to which these associations have influenced the biology of animals, including their developmental patterns. The following review focuses on an emerging field, the goal of which is to understand the influence of bacteria on animal developmental programs. This integrative area of research is undergoing a revolution that has resulted from advances in technology and the development of suitable animal-bacterial systems for the study of these complex associations. In this contribution, the current status of the field is reviewed and the emerging research horizons are examined.

Eukaryotic genes in Mycobacterium tuberculosis could have a role in pathogenesis and immunomodulation

Acquisition of new genetic material through horizontal gene transfer has been an important feature in the evolution of many pathogenic bacteria. Here, we report the presence of 19 genes of eukaryotic origin in the genome of Mycobacterium tuberculosis, some of which are unique to the M. tuberculosis complex. These genes, having been retained in the genome through selective advantage, most probably have key functions in the organism and in mammalian tuberculosis. We explore the role these genes might have in manipulation of the host immune system by altering the balance of steroid hormones.

Microarrays in ecology and evolution: a preview

Microarray technology provides a new tool with which molecular ecologists and evolutionary biologists can survey genome-wide patterns of gene expression within and among species. New analytical approaches based on analysis of variance will allow quantification of the contributions of among individual variation, genotype, sex, microenvironment, population structure, and geography to variation in gene expression. Applications of this methodology are reviewed in relation to studies of mechanisms of adaptation and divergence; delineation of developmental and physiological pathways and networks; characterization of quantitative genetic parameters at the level of transcription ('quantitative genomics'); molecular dissection of parasitism and symbiosis; and studies of the diversification of gene content. Establishment of microarray resources is neither prohibitively expensive nor technologically demanding, and a commitment to development of gene expression profiling methods for nonmodel organisms could have a tremendous impact on molecular and genetic research at the interface of organismal and population biology.

The genome of the natural genetic engineer Agrobacterium tumefaciens C58

The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids. Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence. Their similarities include metabolic, transport, and regulatory systems that promote survival in the highly competitive rhizosphere; differences are apparent in their genome structure and virulence gene complement. Availability of the A. tumefaciens sequence will facilitate investigations into the molecular basis of pathogenesis and the evolutionary divergence of pathogenic and symbiotic lifestyles.

Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp

Pathoadaptive mutations improve the fitness of pathogenic species by modification of traits that interfere with factors (virulence and ancestral) required for survival in host tissues. A demonstrated pathoadaptive mutation is the loss of lysine decarboxylase (LDC) expression in Shigella species that have evolved from LDC-expressing Escherichia coli. Previous studies demonstrated that the product of LDC activity, cadaverine, blocks the action of Shigella enterotoxins and that the gene encoding LDC, cadA, was abolished by large chromosomal deletions in each Shigella species. To better understand the nature and evolution of these pathoadaptive mutations, remnants of the cad region were sequenced from the four Shigella species. These analyses reveal novel gene arrangements in this region of the pathogens' chromosomes. Insertion sequences, a phage genome, and/or loci from different positions on the ancestral E. coli chromosome displaced the cadA locus to form distinct genetic linkages that are unique to each Shigella species. Hybridization studies, using an E. coli K-12 microarray, indicated that the genes displaced to form the novel linkages still remain in the Shigella genomes. None of these novel gene arrangements were observed in representatives of all E. coli phylogenies. Collectively, these observations indicate that inactivation of the cadA antivirulence gene occurred independently in each Shigella species. The convergent evolution of these pathoadaptive mutations demonstrates that, following evolution from commensal E. coli, strong pressures in host tissues selected Shigella clones with increased fitness and virulence through the loss of an ancestral trait (LDC). These observations strongly support the role of pathoadaptive mutation as an important pathway in the evolution of pathogenic organisms.

Genome size reduction through multiple events of gene disintegration in Buchnera APS

The evolution of the endosymbiont Buchnera during its adaptation to intracellular life involved a massive reduction in its genome. By comparing the orthologous genes of Buchnera, Escherichia coli and Vibrio cholerae, we show that the minimal genome size of Buchnera arose from multiple events of gene disintegration dispersed over the whole genome. The elimination of the genes was a continuous process that began with gene inactivation and progressed until the DNA corresponding to the pseudogenes were completely deleted.

Comparative genomics and bioenergetics

Bacterial and archaeal complete genome sequences have been obtained from a wide range of evolutionary lines, which allows some general conclusions about the phylogenetic distribution and evolution of bioenergetic pathways to be drawn. In particular, I searched in the complete genomes for key enzymes involved in aerobic and anaerobic respiratory pathways and in photosynthesis, and mapped them into an rRNA tree of sequenced species. The phylogenetic distribution of these enzymes is very irregular, and clearly shows the diverse strategies of energy conservation used by prokaryotes. In addition, a thorough phylogenetic analysis of other bioenergetic protein families of wide distribution reveals a complex evolutionary history for the respective genes. A parsimonious explanation for these complex phylogenetic patterns and for the irregular distribution of metabolic pathways is that the last common ancestor of Bacteria and Archaea contained several members of every gene family as a consequence of previous gene or genome duplications, while different patterns of gene loss occurred during the evolution of every gene family. This would imply that the last universal ancestor was a bioenergetically sophisticated organism. Finally, important steps that occurred during the evolution of energetic machineries, such as the early evolution of aerobic respiration and the acquisition of eukaryotic mitochondria from a proteobacterium ancestor, are supported by the analysis of the complete genome sequences.

Deletional bias and the evolution of bacterial genomes

Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality. Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes.

Exploration of sequence space for protein engineering

The process of protein engineering is currently evolving towards a heuristic understanding of the sequence-function relationship. Improved DNA sequencing capacity, efficient protein function characterization and improved quality of data points in conjunction with well-established statistical tools from other industries are changing the protein engineering field. Algorithms capturing the heuristic sequence-function relationships will have a drastic impact on the field of protein engineering. In this review, several alternative approaches to quantitatively assess sequence space are discussed and the relatively few examples of wet-lab validation of statistical sequence-function characterization/correlation are described.

Why we don't get sick: the within-host population dynamics of bacterial infections

To pathogenic microparasites (viruses, bacteria, protozoa, or fungi), we and other mammals (living organisms at large) are little more than soft, thin-walled flasks of culture media. Almost every time we eat, brush our teeth, scrape our skin, have sex, get bitten by insects, and inhale, we are confronted with populations of microbes that are capable of colonizing the mucosa lining our orifices and alimentary tract and proliferating in fluids and cells within us. Nevertheless, we rarely get sick, much less succumb to these infections. The massive numbers of bacteria and other micro- and not-so-micro organisms that abound and replicate in our alimentary tract and cover our skin and the mucosa lining our orifices normally maintain their communities in seemingly peaceful coexistence with the somatic cells that define us. Why don't these microbes invade and proliferate in the culture media within the soft, thin-walled flask that envelops us? Why don't they cause disease and lead to our rapid demise?