Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis

Facultative symbionts are potential agents of symbiont-mediated RNAi in aphids

Aphids are major crop pests, and they can be controlled through the application of the promising RNA interference (RNAi) techniques. However, chemical synthesis yield of dsRNA for RNAi is low and costly. Another sustainable aphid pest control strategy takes advantage of symbiont-mediated RNAi (SMR), which can generate dsRNA by engineered microbes. Aphid host the obligate endosymbiont Buchnera aphidicola and various facultative symbionts that not only have a wide host range but are also vertically and horizontally transmitted. Thus, we described the potential of facultative symbionts in aphid pest control by SMR. We summarized the community and host range of these facultative symbionts, and then reviewed their probable horizontal transmitted routes and ecological functions. Moreover, recent advances in the cultivation and genetic engineering of aphid facultative symbionts were discussed. In addition, current legislation of dsRNA-based pest control strategies and their safety assessments were reviewed.

Evolutionary pattern of rDNA following polyploidy in Leymus (Triticeae: Poaceae)

Ribosomal ITS polymorphism and its ancestral genome origin of polyploid Leymus were examined to infer the evolutionary outcome of rDNA gene following allopolyploid speciation and to elucidate the geographic pattern of ITS variation. The results demonstrated that different polyploids have experienced varying fates, including maintenance or homogenization of divergent arrays, occurrence of chimeric repeats and potential pseudogenes. Our data suggested that (1) the Ns, P/F, and St genomic types in Leymus were originated from Psathyrostachys, Agropyron/Eremopyrum, and Pseudoroegneria, respectively; (2) the occurrence of a higher proportion of Leymus species with predominant uniparental rDNA type might associate with the segmental allopolyploid origin, nucleolar dominance of alloploids, and rapid radiation of Leymus; (3) maintenance of multiple parental ITS types in allopolyploid might result from long generation times associated to vegetative multiplication, number and chromosomal location of ribosomal loci and/or recurrent hybridization; (4) the rDNA genealogical structure of Leymus species might associate with the geographic origins; and (5) ITS sequence clade shared by Leymus species from Central Asia, North America, and Nordic might be an outcome of ancestral ITS homogenization. Our results shed new light on understanding evolutionary outcomes of rDNA following allopolyploid speciation and geographic isolation.

Nutrient provisioning facilitates homeostasis between tsetse fly (Diptera: Glossinidae) symbionts

Host-associated microbial interactions may involve genome complementation, driving-enhanced communal efficiency and stability. The tsetse fly (Diptera: Glossinidae), the obligate vector of African trypanosomes (Trypanosoma brucei subspp.), harbours two enteric Gammaproteobacteria symbionts: Wigglesworthia glossinidia and Sodalis glossinidius. Host coevolution has streamlined the Wigglesworthia genome to complement the exclusively sanguivorous tsetse lifestyle. Comparative genomics reveal that the Sodalis genome contains the majority of Wigglesworthia genes. This significant genomic overlap calls into question why tsetse maintains the coresidence of both symbionts and, furthermore, how symbiont homeostasis is maintained. One of the few distinctions between the Wigglesworthia and Sodalis genomes lies in thiamine biosynthesis. While Wigglesworthia can synthesize thiamine, Sodalis lacks this capability but retains a thiamine ABC transporter (tbpAthiPQ) believed to salvage thiamine. This genetic complementation may represent the early convergence of metabolic pathways that may act to retain Wigglesworthia and evade species antagonism. We show that thiamine monophosphate, the specific thiamine derivative putatively synthesized by Wigglesworthia, impacts Sodalis thiamine transporter expression, proliferation and intracellular localization. A greater understanding of tsetse symbiont interactions may generate alternative control strategies for this significant medical and agricultural pest, while also providing insight into the evolution of microbial associations within hosts.

Insect endosymbionts: manipulators of insect herbivore trophic interactions?

Throughout their evolutionary history, insects have formed multiple relationships with bacteria. Although many of these bacteria are pathogenic, with deleterious effects on the fitness of infected insects, there are also numerous examples of symbiotic bacteria that are harmless or even beneficial to their insect host. Symbiotic bacteria that form obligate or facultative associations with insects and that are located intracellularly in the host insect are known as endosymbionts. Endosymbiosis can be a strong driving force for evolution when the acquisition and maintenance of a microorganism by the insect host results in the formation of novel structures or changes in physiology and metabolism. The complex evolutionary dynamics of vertically transmitted symbiotic bacteria have led to distinctive symbiont genome characteristics that have profound effects on the phenotype of the host insect. Symbiotic bacteria are key players in insect-plant interactions influencing many aspects of insect ecology and playing a key role in shaping the diversification of many insect groups. In this review, we discuss the role of endosymbionts in manipulating insect herbivore trophic interactions focussing on their impact on plant utilisation patterns and parasitoid biology.

Endobacteria affect the metabolic profile of their host Gigaspora margarita, an arbuscular mycorrhizal fungus

The aim of this paper was to understand whether the endobacterium identified as Candidatus Glomeribacter gigasporarum has an effect on the biology of its host, the arbuscular mycorrhizal fungus Gigaspora margarita, through the study of the modifications induced on the fungal proteome and lipid profile. The availability of G. margarita cured spores (i.e. spores that do not contain bacteria), represented a crucial tool to enable the comparison between two fungal homogeneous populations in the presence and the absence of the bacterial components. Our results demonstrate that the endobacterial presence leads to a modulation of fungal protein expression in all the different conditions we tested (quiescent, germinating and strigolactone-elicited germinating spores), and in particular after treatment with a strigolactone analogue. The fungal fatty acid profile resulted to be modified both quantitatively and qualitatively in the absence of endobacteria, being fatty acids less abundant in the cured spores. The results offer one of the first comparative metabolic studies of an AM fungus investigated under different physiological conditions, reveal that endobacteria have an important impact on the host fungal activity, influencing both protein expression and lipid profile, and suggest that the bacterial absence is perceived by G. margarita as a stimulus which activates stress-responsive proteins.

Limited endosymbiont variation in Diuraphis noxia (Hemiptera: Aphididae) biotypes from the United States and South Africa

Symbiosis allows an insect access to imbalanced food sources on which other organisms cannot survive. A bacterial endosymbiont, Buchnera aphidicola, gives aphids the ability to feed on phloem depleted of certain essential amino acids by producing those required. Pseudogenes and lower plasmid copy numbers of essential amino acid genes in B. aphidicola, endosymbiont of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae), suggest that this symbiotic relationship is degenerating. The complete endosymbiont assemblages, copy numbers of plasmids (important in essential amino acid production), and sequence variation in B. aphidicola, from 10 Russian wheat aphid biotypes, were investigated. B. aphidicola was found to be monosymbiotic in the Russian wheat aphid biotypes and other Diuraphis species examined. An insert, occurring in an inverted repeat region on the leucine plasmid, was the only variation found in the approximately 10-kb B. aphidicola sequence analyzed from each Russian wheat aphid biotype. This inverted repeat was shown previously to be conserved within the family Aphididae. The insert occurred in B. aphidicola sequences isolated from four Russian wheat aphid biotypes. Copy numbers of the leucine plasmid differ between the South African and U.S. biotypes and were similar to previously reported values for biotypes from the same geographic regions. These results suggest that B. aphidicola may still contribute to Russian wheat aphid fitness when the aphid feeds on a variety of hosts.

Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach

Symbiosis has been among the most important evolutionary steps to generate biological complexity. The establishment of symbiosis required an intimate metabolic link between biological systems with different complexity levels. The strict endo-cellular symbiotic bacteria of insects are beautiful examples of the metabolic coupling between organisms belonging to different kingdoms, a eukaryote and a prokaryote. The host (eukaryote) provides the endosymbiont (prokaryote) with a stable cellular environment while the endosymbiont supplements the host's diet with essential metabolites. For such communication to take place, endosymbionts' genomes have suffered dramatic modifications and reconfigurations of proteins' functions. Two of the main modifications, loss of genes redundant for endosymbiotic bacteria or the host and bacterial genome streamlining, have been extensively studied. However, no studies have accounted for possible functional shifts in the endosymbiotic proteomes. Here, we develop a simple method to screen genomes for evidence of functional divergence between two species clusters, and we apply it to identify functional shifts in the endosymbiotic proteomes. Despite the strong effects of genetic drift in the endosymbiotic systems, we unexpectedly identified genes to be under stronger selective constraints in endosymbionts of aphids and ants than in their free-living bacterial relatives. These genes are directly involved in supplementing the host's diet with essential metabolites. A test of functional divergence supports a strong relationship between the endosymbiosis and the functional shifts of proteins involved in the metabolic communication with the insect host. The correlation between functional divergence in the endosymbiotic bacterium and the ecological requirements of the host uncovers their intimate biochemical and metabolic communication and provides insights on the role of symbiosis in generating species diversity.

Biological complexity has emerged on earth by the combination of living forms. This combination, called symbiosis, had to overcome the problems caused by the uncoupled metabolisms of the organisms involved. One way to do so was through the loss of genes that were no longer needed for the endosymbiont in the protected cellular environment provided by the host. Another step necessary to adjust both metabolisms was through the change in the function of bacterial proteins to perform new roles in the symbiotic system. In this article, we test such events in symbiotic systems involving an insect and a bacterium by developing a new and simple method to identify proteome-wide functional shifts. Our results show that most of the functional changes occurred at genes involved in metabolic communication with the host and are correlated with the host's ecological traits.

Interactions of chaperonin with a weakly active anthranilate synthase from the aphid endosymbiont Buchnera aphidicola

The endosymbiotic bacterium Buchnera provides its aphid host with essential amino acids. Buchnera is typical of intracellular symbiotic and parasitic microorganisms in having a small effective population size, which is believed to accelerate genetic drift and reduce the stability of gene products. It is hypothesized that Buchnera mitigates protein instability with an increased production of the chaperonins GroESL. In this paper, we report the expression and functional analysis of trpE, a plasmid-borne fast-evolving gene encoding the tryptophan biosynthesis enzyme anthranilate synthase. We overcame the problem of low enzyme stability by using an anthranilate synthase-deficient mutant of E. coli as the expression host and the method of genetic complementation for detection of the enzyme activity. We showed that the Buchnera anthranilate synthase was only weakly active at the temperature of 26 degrees C but became inactive at the higher temperatures of 32 degrees C and 37 degrees C and that the coexpression with chaperonin genes groESL of E. coli enhanced the function of the Buchnera enzyme. These findings are consistent with the proposed role of groESL in the Buchnera-aphid symbiosis.

Population structure, levels of selection, and the evolution of intracellular symbionts

Many obligately intracellular symbionts exhibit a characteristic set of genetic changes that include an increase in substitution rates, loss of many genes, and apparent destabilization of many proteins and structural RNAs. Authors have suggested that these changes are due to increased mutation rates, or, more commonly, decreased effective population size due to population bottlenecks at the symbiont or, perhaps, host level. I propose that the increase in substitution rates and accumulation of deleterious mutations is a consequence of the population structure imposed on the endosymbionts by strict host association, loss of horizontal transmission and potentially conflicting levels of selection. I analyze a population genetic model of endosymbiont evolution, and demonstrate that substitution rates will increase, and the effect of those substitutions on endosymbiont fitness will become more deleterious as horizontal transmission among hosts decreases. Additionally, I find that there is a critical level of horizontal transmission below which natural selection cannot effectively purge deleterious mutations, leading to an expected loss of fitness over time. This critical level varies across loci with the degree of correlation between host and endosymbiont fitness, and may help explain differential retention and loss of certain genes.

Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story

Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains already sequenced. We present the analysis of three B. aphidicola strains (BTg, BCt and BCc) belonging to aphids from different tribes of the subfamily Lachninae, that was estimated to harbour the bacteria with the smallest genomes. The presence of both leucine and tryptophan plasmids in BTg, a chimerical leucine-tryptophan plasmid in BCt, and only a leucine plasmid in BCc, indicates the existence of many recombination events in a recA minus bacterium. In addition, these B. aphidicola plasmids are the simplest described in this species, indicating that plasmids are also involved in the genome shrinkage process.

Biology bacteriocyte-associated endosymbionts of plant sap-sucking insects

Psyllids, whiteflies, aphids, and mealybugs are members of the suborder Sternorrhyncha and share a common property, namely the utilization of plant sap as their food source. Each of these insect groups has an obligatory association with a different prokaryotic endosymbiont, and the association is the result of a single infection followed by maternal, vertical transmission of the endosymbionts. The result of this association is the domestication of the free-living bacterium to serve the purposes of the host, namely the synthesis of essential amino acids. This domestication is probably in all cases accompanied by a major reduction in genome size. The different properties of the genomes and fragments of the genomes of these endosymbionts suggest that there are different constraints on the permissible evolutionary changes that are probably a function of the gene repertoire of the endosymbiont ancestor and the gene losses that occurred during the reduction of genome size.

Functional genomics of Buchnera and the ecology of aphid hosts

In many animal groups, mutualistic bacterial symbionts play a central role in host ecology, by provisioning rare nutrients and thus enabling specialization on restricted diets. Among such symbionts, genomic studies are most advanced for Buchnera, the obligate symbiont of aphids, which feed on phloem sap. The contents of the highly reduced Buchnera genomes have verified its role in aphid nutrition. Comparisons of Buchnera gene sets indicate ongoing, irreversible gene losses that are expected to affect aphid nutritional needs. Furthermore, almost all regulatory genes have been eliminated, raising the question of whether and how gene expression responds to environmental change. Microarray studies on genome-wide expression indicate that Buchnera has evolved some constitutive changes in gene expression: homologues of heat stress genes have elevated transcript levels in Buchnera (relative to other bacteria) even in the absence of stress. Additionally, the microarray results indicate that responses to heat stress and to amino acid availability are both few and modest. Observed responses are consistent with control by the few ancestral regulators retained in the genome. Initial studies on the role of host genes in mediating the symbiosis reveal distinctive expression patterns in host cells harbouring Buchnera. In the near future, a complete genome of pea aphid will accelerate progress in understanding the functional integration of aphid and Buchnera genomes. Although information for other insect symbioses is relatively limited, studies on symbionts of carpenter ants and tsetse flies indicate many similarities to Buchnera.

Metabolic interdependence of obligate intracellular bacteria and their insect hosts

Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. However, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism--that of the host cell. This review attempts to provide insights into the complex physiological interactions and the evolution of metabolic pathways of several mutualistic bacteria of aphids, ants, and tsetse flies and their insect hosts.

A genomic perspective on nutrient provisioning by bacterial symbionts of insects

Many animals show intimate interactions with bacterial symbionts that provision hosts with limiting nutrients. The best studied such association is that between aphids and Buchnera aphidicola, which produces essential amino acids that are rare in the phloem sap diet. Genomic studies of Buchnera have provided a new means for inferring metabolic capabilities of the symbionts and their likely contributions to hosts. Despite evolutionary reduction of genome size, involving loss of most ancestral genes, Buchnera retains capabilities for biosynthesis of all essential amino acids. In contrast, most genes duplicating amino acid biosynthetic capabilities of hosts have been eliminated. In Buchnera of many aphids, genes for biosynthesis of leucine and tryptophan have been transferred from the chromosome to distinctive plasmids, a feature interpreted as a mechanism for overproducing these amino acids through gene amplification. However, the extent of plasmid-associated amplification varies between and within species, and plasmid-borne genes are sometimes fewer in number than single copy genes on the (polyploid) main chromosome. This supports the broader interpretation of the plasmid location as a means of achieving regulatory control of gene copy number and/or transcription. Buchnera genomes have eliminated most regulatory sequences, raising the question of the extent to which gene expression is moderated in response to changing demands imposed by host nutrition or other factors. Microarray analyses of the Buchnera transcriptome reveal only slight changes in expression of nutrition-related genes in response to shifts in host diet, with responses less dramatic than those observed for the related nonsymbiotic species, Escherichia coli.

Genome evolution in an insect cell: distinct features of an ant-bacterial partnership

Bacteria that live exclusively within eukaryotic host cells include not only well-known pathogens, but also obligate mutualists, many of which occur in diverse insect groups such as aphids, psyllids, tsetse flies, and the ant genus Camponotus (Buchner, 1965; Douglas, 1998; Moran and Telang, 1998; Baumann et al., 2000; Moran and Baumann, 2000). In contrast to intracellular pathogens, these primary (P) endosymbionts of insects are required for the survival and reproduction of the host, exist within specialized host cells called bacteriocytes, and undergo stable maternal transmission through host lineages (Buchner, 1965; McLean and Houk, 1973). Due to their long-term host associations and close phylogenetic relationship with well-characterized enterobacteria (Fig. 1), P-endosymbionts of insects are ideal model systems to examine changes in genome content and architecture that occur in the context of beneficial, intracellular associations. Since these bacteria have not been cultured outside of the host cell, they are difficult to study with traditional genetic or physiological approaches. However, in recent years, molecular and computational approaches have provided important insights into their genetic diversity and ecological significance. This review describes some recent insights into the evolutionary genetics of obligate insect-bacteria symbioses, with a particular focus on an intriguing association between the bacterial endosymbiont Blochmannia and its ant hosts.

The process of genome shrinkage in the obligate symbiont Buchnera aphidicola

BACKGROUND

Very small genomes have evolved repeatedly in eubacterial lineages that have adopted obligate associations with eukaryotic hosts. Complete genome sequences have revealed that small genomes retain very different gene sets, raising the question of how final genome content is determined. To examine the process of genome reduction, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome, reconstructed on the basis of the phylogenetic distribution of gene orthologs among fully sequenced relatives of Escherichia coli and Buchnera.

RESULTS

The reconstructed ancestral genome contained 2,425 open reading frames (ORFs). The Buchnera genome, containing 564 ORFs, consists of 153 fragments of 1-34 genes that are syntenic with reconstructed ancestral regions. On the basis of this reconstruction, 503 genes were eliminated within syntenic fragments, and 1,403 genes were lost from the gaps between syntenic fragments, probably in connection with genome rearrangements. Lost regions are sometimes large, and often span functionally unrelated genes. In addition, individual genes and regulatory regions have been lost or eroded. For the categories of DNA repair genes and rRNA genes, most lost loci fall in regions between syntenic fragments. This history of gene loss is reflected in the sequences of intergenic spacers at positions where genes were once present.

CONCLUSIONS

The most plausible interpretation of this reconstruction is that Buchnera lost many genes through the fixation of large deletions soon after the acquisition of an obligate endosymbiotic lifestyle. An implication is that final genome composition may be partly the chance outcome of initial deletions and that neighboring genes influence the likelihood of loss of particular genes and pathways.

Where are the pseudogenes in bacterial genomes?

Most bacterial genomes have very few pseudogenes; notable exceptions include the genomes of the intracellular parasites Rickettsia prowazekii and Mycobacterium leprae. As DNA can be introduced into microbial genomes in many ways, the compact nature of these genomes suggests that the rate of DNA influx is balanced by the rate of DNA deletion. We propose that the influx of dangerous genetic elements such as transposons and bacteriophages selects for the maintenance of relatively high deletion rates in most bacteria; the sheltered lifestyle of intracellular parasites removes this threat, leading to reduced deletion rates and larger pseudogene loads.

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.

Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition

The overproduction of essential amino acids by Buchnera aphidicola, the primary bacterial mutualist of aphids, is considered an adaptation for increased production of nutrients that are lacking in aphids' diet of plant sap. Given their shared role in host nutrition, amino acid biosynthetic genes of Buchnera are expected to experience parallel changes in selection that depend on host diet quality, growth rate, and population structure. This study evaluates the hypothesis of parallel selection across biosynthetic pathways by testing for correlated changes in evolutionary rates at biosynthetic genes of Buchnera. Previous studies show fast evolutionary rates at tryptophan biosynthetic genes among Buchnera associated with the aphid genus Uroleucon and suggest reduced purifying selection on symbiont nutritional functions in this aphid group. Here, we test for parallel rate acceleration at other amino acid biosynthetic genes of Buchnera-Uroleucon, including those for leucine (leuABC) and isoleucine/valine biosynthesis (ilvC). Ratios of nonsynonymous to synonymous substitutions (d(N)/d(S)) were estimated using codon-based maximum-likelihood methods that account for the extreme AT compositional bias of Buchnera sequences. A significant elevation in d(N)/d(S) at biosynthetic loci but not at two housekeeping genes sampled (dnaN and tuf) suggests reduced host-level selection on biosynthetic capabilities of Buchnera-Uroleucon. In addition, the discovery of trpEG pseudogenes in Buchnera-U. obscurum further supports reduced selection on amino acid biosynthesis.

Bacterial endosymbionts in animals

Molecular phylogenetic studies reveal that many endosymbioses between bacteria and invertebrate hosts result from ancient infections followed by strict vertical transmission within host lineages. Endosymbionts display a distinctive constellation of genetic properties including AT-biased base composition, accelerated sequence evolution, and, at least sometimes, small genome size; these features suggest increased genetic drift. Molecular genetic characterization also has revealed adaptive, host-beneficial traits such as amplification of genes underlying nutrient provision.