Chapter 8 : Genomic Signatures of Intracellularity: Evolutionary Patterns and Paces in Bacterial Mutualists and Parasites

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This chapter highlights some intriguing patterns of genome change identified from genome-sequencing projects and molecular evolution studies. Trends include striking similarities between intracellular mutualists and parasites that may reflect common pressures of an intracellular lifestyle, as well as key differences that highlight distinct genomic consequences of their host associations. Bacteria form a variety of associations with host cells. At one end of the spectrum, the replication and spread of intracellular parasites impose a fitness cost to hosts. At the other end of the symbiotic spectrum, certain intracellular bacterial groups form exclusively mutualistic associations with hosts. Analysis of partial genome regions indicates that, compared with its relatives, the exceptionally small genome of associated with the aphid shows more extensive loss of metabolic than informational functions. Consistent with their infectious lifestyles, obligately intracellular parasites typically encode numerous mechanisms to invade host tissue and cells and to escape the host immune system. To date, genome-wide rate comparisons strongly suggest a consistent, genome-wide rate increase in intracellular species, as expected under the influences of increased mutation and/or genetic drift. The availability of two or more genomes for a particular group offers a window into the evolution of genome architecture, or changes in the order and strand orientation of shared loci. The rapid growth of genomics has elucidated processes that shape wide variation in genome size, gene content, patterns of DNA sequence evolution, and levels of genome fluidity in the bacterial world.

Citation: Jennifer J. 2007. Genomic Signatures of Intracellularity: Evolutionary Patterns and Paces in Bacterial Mutualists and Parasites, p 196-212. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch8
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Image of FIGURE 1

Schematic representation of associates that bacteria form with hosts, nested by increasing intimacy of the association. Symbiotic bacteria, the broadest category, associate with hosts for some or all of the bacterium’s life cycle. Of these symbionts, some are endosymbiotic and can live within the tissues or cells. Endosymbionts that replicate within host cells are termed intracellular. Of these intracellular associates, certain highly specialized lineages have lost the ability to replicate outside of host cells and are obligately intracellular. The final category is the focus of this chapter.

Citation: Jennifer J. 2007. Genomic Signatures of Intracellularity: Evolutionary Patterns and Paces in Bacterial Mutualists and Parasites, p 196-212. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch8
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Image of FIGURE 2

Genome size and %GC content of bacterial chromosome sequences, illustrating the small size and AT richness of obligate intracellular associates (labeled triangles). Chart is similar to published figures (e.g., reference ) and includes genomes that were publicly available as of July 2005, with the exception of multiple, closely related strains. Gray x, species possessed two or more chromosomes (mark reflects values for single chromosome). Reprinted with permission from reference . © (2005) Elsevier Science.

Citation: Jennifer J. 2007. Genomic Signatures of Intracellularity: Evolutionary Patterns and Paces in Bacterial Mutualists and Parasites, p 196-212. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch8
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Image of FIGURE 3

Percentage of genes encoding particular biosynthetic functions. axis indicates proportion of ORFs involved in biosynthesis of (i) amino acids, (ii) cofactors, prosthetic groups, and carriers, and (iii) purines, pyrimidines, nucleotides and nucleosides. Boldface, obligately intracellular mutualists; underline, obligately intra-cellular pathogen. , and retain a free-living phase and were included for comparisons. Values for and the gamma- nutritional mutualists were based on reanalysis of genome sequences ( ). Data for other species were downloaded from the Comprehensive Microbial Resource at TIGR for a more consistent comparison across genomes ( ). However, as a result of differences in annotation and functional categorization, these counts may differ from original genome papers. Readers interested in particular taxa are encouraged to refer to original genome publications. In the rare cases where TIGR counted two largely overlapping, putative ORFs as two separate genes, these were counted as a single ORF for the purposes of this figure. Reprinted with permission from ( ). © (2005) Elsevier Science.

Citation: Jennifer J. 2007. Genomic Signatures of Intracellularity: Evolutionary Patterns and Paces in Bacterial Mutualists and Parasites, p 196-212. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch8
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Obligately intracellular bacteria for which full genome sequence data were published as of July 2005

Citation: Jennifer J. 2007. Genomic Signatures of Intracellularity: Evolutionary Patterns and Paces in Bacterial Mutualists and Parasites, p 196-212. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch8
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Signatures of distinct mechanisms that may contribute to rapid protein evolution in intracellular bacteria

Citation: Jennifer J. 2007. Genomic Signatures of Intracellularity: Evolutionary Patterns and Paces in Bacterial Mutualists and Parasites, p 196-212. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch8

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