N A Moran

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..Considerable variation also exists, however, in part reflecting unstudied aspects of the population structure and ecology of host-restricted bacterial lineages...

..This pattern appears to be characteristic of symbiont evolution...

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..Although purifying selection eliminates many mutations, some persist, resulting in ongoing loss of genes and DNA from this already tiny genome. Our results provide a general model for the stepwise process leading to genome reduction...

..In addition, insect symbionts provide some of the extremes of cellular genomes, including the smallest and the fastest evolving, raising new questions about the limits of evolution of life...

..These results may reflect the obligate nature of this intimate mutualism and indicate opportunities for adaptive coevolution among linked symbiont genomes...

..Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree...

..pisum and U. ambrosiae containing secondary symbionts. Electron microscopy of R-type and T-type bacteria in A. pisum and in U. ambrosiae revealed rod-shaped organisms that attain extremely high densities within a few bacteriocytes...

..However, our study cannot rule out the possibility that mechanisms other than bottlenecks also contribute to reduced N(e) at aphid and endosymbiont loci...

..Combined, these results suggest a decreased effectiveness of purifying selection in purging endosymbiont populations of slightly deleterious mutations, particularly those affecting codon usage and amino acid identity...

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..Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution...

..This exceptional size conservation may reflect the inability of this obligate mutualist to acquire foreign DNA and reduced selection for genetic novelty within a static intracellular environment...

..Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes...

..This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria...

..These results support the generality of small effective population size in Buchnera and their aphid hosts...

..Patterns of variation in Drosophila mitochondrial haplotypes in Spiroplasma-infected and uninfected flies imply imperfect vertical transmission in host populations and possible horizontal transmission...

..Although our analyses are limited to the gamma-Proteobacteria, these results resolve a long-standing paradox-i.e., the ability to make robust phylogenetic inferences in light of substantial LGT...

..The function of inv/spa genes in maintaining symbiosis is demonstrated by the up-regulation of their expression under both in vivo and in vitro conditions that coincide with host cell invasion...

..The resulting libraries were highly enriched in bacterial sequences. Through the use of alternate enzymes and partial digests, this technique can be adapted to yield virtually pure DNA libraries for individual bacterial species...

..We speculate that distant homologs may replace the functions of some eliminated genes through broadened substrate specificity...

..Molecular genetic characterization also has revealed adaptive, host-beneficial traits such as amplification of genes underlying nutrient provision...

..Synonymous divergences indicate elevated mutation on plasmids relative to chromosomal genes...

..Secondary symbionts were arranged both extracellularly and in clusters of 2000-8000 bacteria inside bacteriocytes. These numbers are consistent with the few previous estimates of symbiont population sizes based on counts of gene copies...

..Analysis of the coding capacities of Sulcia and Baumannia reveals striking complementarity in metabolic capabilities...

..The declining frequencies of Hamiltonella-infected aphids in population cages in the absence of parasitism indicate a probable cost to infection and may explain why Hamiltonella remains at intermediate frequencies in natural populations...

..Multiple symbionts often coexist in the same host, resulting in coadaptation among several phylogenetically distant genomes...

..Other cases in which symbiont microevolution has a major effect on host ecological tolerance are likely to be widespread because of the high mutation rates of symbiotic bacteria and their crucial roles in host metabolism and development...

..Our results indicate that variation among pea aphids in dependence on dietary amino acids can result from Buchnera mutation as well as variation in the host genotype...

..pisum, one subclade of H. defensa appears to be universal within a subclade of the aphid genus Uroleucon, suggesting a transition from facultative, horizontal transmission to strictly vertical inheritance...

..Thus, phage may act as a conduit for ongoing gene exchange among heritable endosymbionts...

..Serratia symbiotica" with Cinara subgenus Cinara species and weigh against an obligate nutritional role. Finally, we show that species belonging to the subfamily Lachninae have a high incidence of facultative symbiont infection...

..This single base polymorphism in Buchnera has the potential to allow aphid populations to adapt quickly to prevailing conditions...

..A mutation causing an amino acid replacement in this desaturase results in loss of torulene and of red body color. Thus, aphids are animals that make their own carotenoids...

..The genome is also littered with mobile DNA, including phage-derived genes, plasmids, and insertion-sequence elements, highlighting its dynamic nature and the continued role horizontal gene transfer plays in shaping it...

..Although it is not clear why this tiny genome lacks the low GC content typical of other small bacterial genomes, these observations support a role of genome reduction rather than base composition as a driver of codon reassignment...

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..Genes for translation and amino acid biosynthesis are relatively well represented, but numerous genes considered essential for life are missing, suggesting that Carsonella may have achieved organelle-like status...

..Our results indicate that in addition to host-symbiont interactions, interactions among the symbionts themselves probably play a critical role in determining the distributions of symbionts in natural populations...

..The irreversible losses of transcriptional regulators constrain ability to alter gene expression in the context of environmental fluctuations affecting the symbiotic partners...

..Because such transfer can generate coinfections, thereby creating opportunities for symbiont competition and recombination, paternal inheritance has major consequences for expectations regarding symbiont evolution...

..Consequently, the plasmid location of trpEG combined with Buchnera's chromosomal polyploidy may functionally limit, rather than increase, tryptophan production within Uroleucon ambrosiae...

..defensa life cycle. We propose that, in these mutualistic symbionts, phage-borne toxin genes provide defense to the aphid host and are a basis for the observed protection against eukaryotic parasites...

..Thus, acquisition of a heritable symbiont appears to be a major mode of adaptation to natural enemy pressure in these insects...

..aphidicola. Our demonstration of a diminished stress response validates reports of temperature sensitivity in B. aphidicola and suggests that this reduced bacterial genome exhibits transcriptional inflexibility...

..The other two symbionts, here designated "Candidatus Hamiltonella defensa" and "Candidatus Regiella insecticola," are sister groups to one another and together show a relationship to species of Photorhabdus...

..Gene phylogenies for the main LuxI/R family in Pseudomonas species imply a complex history of lateral transfer, ancestral duplication, and gene loss within the genus...

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..Although information for other insect symbioses is relatively limited, studies on symbionts of carpenter ants and tsetse flies indicate many similarities to Buchnera...

..quot;Candidatus Sulcia muelleri" is proposed as the name of the new symbiont...

..Development of this dual-genome array represents a first attempt to characterize gene expression in this emerging model system...

..insecticola under these same conditions. These findings reveal a role for heritable symbionts in the adaptation of aphids to their abiotic environments and add to an expanding body of knowledge on the adaptive significance of symbiosis...

..A new genus and species name, 'Candidatus Baumannia cicadellinicola' (sp. nov.) is proposed for this newly characterized clade of symbiotic bacteria...

..Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts...

..Our findings on the prevalence of these symbionts within many aphid taxa, along with published observations concerning their effects on host fitness, imply a significant role of facultative symbiosis in aphid ecology and evolution...

..This conditionality in the social life of P. obesinymphae reveals complex dynamics and a degree of behavioral plasticity not previously known in aphid societies...

..However, there is evidence that bacteria have a constant genome-wide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods...

..This strong interaction between a symbiotic bacterium and a host natural enemy provides a mechanism for the persistence and spread of symbiotic bacteria...

..Although S. symbiotica has a major influence on its host's metabolome and resistance to heat, it induces little change in gene expression in its host...

..Several new strains of Wolbachia and Spiroplasma were discovered, including ones divergent from any reported to date. The phylogenetic distribution of Wolbachia and Spiroplasma in Drosophila is discussed...

..These findings suggest that Spiroplasma has other effects on hosts that allow it to persist, and that environmental or host variation affects transmission or persistence leading to differences among populations in infection frequencies...

..Furthermore, some symbionts use many of the same mechanisms as pathogens to infect hosts and evade immune responses. Here we discuss what is currently known about the interactions between bacterial symbionts and their hosts...

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..The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts...

..Sulcia shows a fivefold lower rate of 16S rDNA sequence divergence than does Baumannia for the same host pairs. The term 'coprimary' symbiont is proposed for such cases...

..One organism, Israeli acute paralysis virus of bees, was strongly correlated with CCD...

..Because multicopy elements can facilitate genomic recombination and deletion, this IS expansion may represent an early stage in the genomic reduction that is common in most ancient endosymbionts...

..coagulata and other sharpshooters serve as vectors of transmission...