Hubert Charles

Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola.

The pea aphid genome includes 66 genes contributing to amino acid biosynthesis and 93 genes to amino acid degradation. In several respects, the pea aphid gene inventory complements that of its symbiotic bacterium, Buchnera aphidicola (Buchnera APS). Unlike other insects with completely sequenced genomes, the pea aphid lacks the capacity to synthesize arginine, which is produced by Buchnera APS. However, consistent with other insects, it has genes coding for individual reactions in essential amino acid biosynthesis, including threonine dehydratase and branched‐chain amino acid aminotransferase, which are not coded in the Buchnera APS genome. Overall the genome data suggest that the biosynthesis of certain essential amino acids is shared between the pea aphid and Buchnera APS, providing the opportunity for precise aphid control over Buchnera metabolism.

MOLECULAR CHARACTERIZATION OF THE PRINCIPAL SYMBIOTIC BACTERIA OF THE WEEVIL SITOPHILUS ORYZAE : A PECULIAR G + C CONTENT OF AN ENDOCYTOBIOTIC DNA

Abstract. The principal intracellular symbiotic bacteria of the cereal weevil Sitophilus oryzae were characterized using the sequence of the 16S rDNA gene (rrs gene) and G + C content analysis. Polymerase chain reaction amplification with universal eubacterial primers of the rrs gene showed a single expected sequence of 1,501 bp. Comparison of this sequence with the available database sequences placed the intracellular bacteria of S. oryzae as members of the Enterobacteriaceae family, closely related to the free-living bacteria, Erwinia herbicola and Escherichia coli, and the endocytobiotic bacteria of the tsetse fly and aphids. Moreover, by high-performance liquid chromatography, we measured the genomic G + C content of the S. oryzae principal endocytobiotes (SOPE) as 54%, while the known genomic G + C content of most intracellular bacteria is about 39.5%. Furthermore, based on the third codon position G + C content and the rrs gene G + C content, we demonstrated that most intracellular bacteria except SOPE are A + T biased irrespective of their phylogenetic position. Finally, using the hsp60 gene sequence, the codon usage of SOPE was compared with that of two phylogenetically closely related bacteria: E. coli, a free-living bacterium, and Buchnera aphidicola, the intracellular symbiotic bacteria of aphids. Taken together, these results show a peculiar and distinctly different DNA composition of SOPE with respect to the other obligate intracellular bacteria, and, combined with biological and biochemical data, they elucidate the evolution of symbiosis in S. oryzae.

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to help interpret metabolomics experiments and a wide range of tools have been developed to help place metabolites within metabolic pathways. However, the representation of metabolites within separate disconnected pathways overlooks most of the connectivity of the metabolome. By definition, reference pathways cannot integrate novel pathways nor show relationships between metabolites that may be linked by common neighbours without being considered as joint members of a classical biochemical pathway. MetExplore is a web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis pipeline comprises mapping metabolomics data onto the specific metabolic network of an organism, then applying graph-based methods and advanced visualization tools to enhance data analysis. The MetExplore web server is freely accessible at http://metexplore.toulouse.inra.fr.

Effects of jackbean lectin (ConA) on the feeding behaviour and kinetics of intoxication of the pea aphid, Acyrthosiphon pisum

Mannose‐binding lectins were shown to be useful in creating transgenic plants resistant to insects, including many phloem‐feeding Hemiptera. Before these plants can be used extensively, it is important to understand how these lectins exert their toxic effects on the target organisms. We investigated the feeding alterations induced by presenting the pea aphid, Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae), with a diet containing the lectin from Canavalia ensiformis (ConA). A series of behavioural experiments were carried out to detect potential sensory mediation of lectin activity. Choice tests performed with a 400 µg ml−1 ConA diet (3.7 µm of native tetramer) showed that A. pisum quickly rejected the ConA diet, but that this reaction was not typical of a sensory‐mediated phagodeterrent effect. In addition, the aphids did not develop a conditioned taste aversion to the lectin. Diet uptake was evaluated using a radioactive tracer (14C‐methylated inulin), and showed depression of ingestion only after 16 h at 200 µg ml−1 or after 8 h at 400 µg ml−1 ConA. This effect was reversible under our test conditions. No evidence was obtained for early detection of the lectin, even by intoxicated aphids. An electrical penetration graph technique was adapted to artificial diets and provided short‐term continuous analysis on feeding/probing events. At the 400 µg ml−1 level, adults were affected and had reduced ingestion durations as early as in the first 4 h of contact, but experienced an adaptation to the behavioural alterations induced by lectin feeding. Overall, feeding deterrency following exposure to mannose lectins appeared to be a consequence of intoxication, and not due to a sensory mediated process.

Different Levels of Transcriptional Regulation Due to Trophic Constraints in the Reduced Genome of Buchnera aphidicola APS

ABSTRACT Symbiotic associations involving intracellular microorganisms and animals are widespread, especially for species feeding on poor or unbalanced diets. Buchnera aphidicola, the obligate intracellular bacterium associated with most aphid species, provides its hosts with essential amino acids (EAAs), nutrients in short supply in the plant phloem sap. The Buchnera genome has undergone severe reductions during intracellular evolution. Genes for EAA biosynthesis are conserved, but most of the transcriptional regulatory elements are lost. This work addresses two main questions: is transcription in Buchnera (i) regulated and (ii) scaled to aphid EAA demand? Two microarray experiments were designed for profiling the gene expression in Buchnera. The first one was characterized by a specific depletion of tyrosine and phenylalanine in the aphid diet, and the second experiment combined a global diminution of EAAs in the aphid diet with a sucrose concentration increase to manipulate the aphid growth rate. Aphid biological performance and budget analysis (the balance between EAAs provided by the diet and those synthesized by Buchnera) were performed to quantify the nutritional demand from the aphids toward their symbiotic bacteria. Despite the absence of known regulatory elements, a significant transcriptional regulation was observed at different levels of organization in the Buchnera genome: between genes, within putative transcription units, and within specific metabolic pathways. However, unambiguous evidence for transcriptional changes underpinning the scaling of EAA biosynthesis to aphid demand was not obtained. The phenotypic relevance of the transcriptional response from the reduced genome of Buchnera is addressed.

A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, infered from phylogenetic analysis based on a heterogeneous model of DNA evolution

Insect intracellular symbiotic bacteria (intracellular endosymbionts, or endocytobionts) were positioned within the gamma 3-Proteobacteria using a non-homogeneous model of DNA evolution, allowing for rate variability among sites, for GC content heterogeneity among sequences, and applied to a maximum likelihood framework. Most of them were found to be closely related within the Enterobacteriaceae family, located between Proteus and Yersinia. These results suggest that such a bacterial group might possess several traits allowing for insect infection and the stable establishment of symbiotic relationships and that this could represent a stem clade for numerous insect endocytobionts. Based on the estimations of the equilibrium GC content and branch lengths in the phylogenetic tree, we have made comparisons of the relative ages of these different symbioses.

New insight into the RNA interference response against cathepsin-L gene in the pea aphid, Acyrthosiphon pisum: Molting or gut phenotypes specifically induced by injection or feeding treatments

RNA interference (RNAi) has been widely and successfully used for gene inactivation in insects, including aphids, where dsRNA administration can be performed either by feeding or microinjection. However, several aspects related to the aphid response to RNAi, as well as the influence of the administration method on tissue response, or the mixed success to observe phenotypes specific to the gene targeted, are still unclear in this insect group. In the present study, we made the first direct comparison of two administration methods (injection or feeding) for delivery of dsRNA targeting the cathepsin-L gene in the pea aphid, Acyrthosiphon pisum. In order to maximize the possibility of discovering specific phenotypes, the effect of the treatment was analyzed in single individual aphids at the level of five body compartments: the bacteriocytes, the gut, the embryonic chains, the head and the remaining body carcass. Our analysis revealed that gene expression knockdown effect in each single body compartment was dependent on the administration method used, and allowed us to discover new functions for the cathepsin-L gene in aphids. Injection of cathepsin-L dsRNA was much more effective on carcass and head, inducing body morphology alterations, and suggesting a novel role of this gene in the molting of these insects. Administration by feeding provoked cathepsin-L knockdown in the gut and specific gut epithelial cell alteration, therefore allowing a better characterization of tissue specific role of this gene in aphids.

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum

Buchnera aphidicola is the primary obligate intracellular symbiont of most aphid species. B. aphidicola and aphids have been evolving in parallel since their association started, about 150 Myr ago. Both partners have lost their autonomy, and aphid diversification has been confined to smaller ecological niches by this co-evolution. B. aphidicola has undergone major genomic and biochemical changes as a result of adapting to intracellular life. Several genomes of B. aphidicola from different aphid species have been sequenced in the last decade, making it possible to carry out analyses and comparative studies using system-level in silico methods. This review attempts to provide a systemic description of the symbiotic function of aphid endosymbionts, particularly of B. aphidicola from the pea aphid Acyrthosiphon pisum, by analyzing their structural genomic properties, as well as their genetic and metabolic networks.

Genome size characterization of the principal endocellular symbiotic bacteria of the weevil Sitophilus oryzae, using pulsed field gel electrophoresis

Abstract The chromosome size of the principal intracellular symbiotic bacteria (endocytobiotes) of the weevil Sitophilus oryzae has been determined by pulsed field gel electrophoresis (PFGE). The restriction enzymes SpeI, SwaI and XbaI generated 22, 23 and 24 fragments, respectively. The fragment sizes ranged from 15 to 460 kb and the genome size of the symbiotic bacteria was estimated to be approximately 3.0 Mb. An additional fragment was seen when running total undigested DNA and should correspond to a plasmid of 138 kb. The principal symbiotic bacteria belong to the enterobacteriaceae family and are closely related to Escherichia coli . The difference between the genome size of E. coli (4.7 Mb) and symbiotic bacteria (3.0 Mb) was discussed and might be related to the intracellular evolution of the endocytobiotes within their host. No more than two rDNA (23S) loci were found with I-CeuI digestion, which argues against a serial fragment gene deletion in the course of evolution.

Conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of Buchnera aphidicola

BackgroundGenomic studies on bacteria have clearly shown the existence of chromosomal organization as regards, for example, to gene localization, order and orientation. Moreover, transcriptomic analyses have demonstrated that, in free-living bacteria, gene transcription levels and chromosomal organization are mutually influenced. We have explored the possible conservation of relationships between mRNA abundances and chromosomal organization in the highly reduced genome of Buchnera aphidicola, the primary endosymbiont of the aphids, and a close relative to Escherichia coli.ResultsUsing an oligonucleotide-based microarray, we normalized the transcriptomic data by genomic DNA signals in order to have access to inter-gene comparison data. Our analysis showed that mRNA abundances, gene organization (operon) and gene essentiality are correlated in Buchnera (i.e., the most expressed genes are essential genes organized in operons) whereas no link between mRNA abundances and gene strand bias was found. The effect of Buchnera genome evolution on gene expression levels has also been analysed in order to assess the constraints imposed by the obligate symbiosis with aphids, underlining the importance of some gene sets for the survival of the two partners. Finally, our results show the existence of spatial periodic transcriptional patterns in the genome of Buchnera.ConclusionDespite an important reduction in its genome size and an apparent decay of its capacity for regulating transcription, this work reveals a significant correlation between mRNA abundances and chromosomal organization of the aphid-symbiont Buchnera.