Early Stages Of Symbiosis Research Articles

A module centered on the transcription factor Msn2 from arbuscular mycorrhizal fungus Rhizophagus irregularis regulates drought stress tolerance in the host plant.

Arbuscular mycorrhizal (AM) fungi can form mutualistic endosymbiosis with > 70% of land plants for obtaining fatty acids and sugars, in return, AM fungi promote plant nutrients and water acquisition to enhance plant fitness. However, how AM fungi orchestrate its own signaling components in response to drought stress remains elusive. Here, we identify a transcription factor containing C2H2 zinc finger domains, RiMsn2 from Rhizophagus irregularis. To characterize the RiMsn2, we combined heterologous expression, subcellular localization in yeasts, and biochemical and molecular studies with reverse genetics approaches during the in planta phase. The results indicate that RiMsn2 is highly conserved across AM fungal species and induced during the early stages of symbiosis. It is significantly upregulated in mycorrhizal roots under severe drought conditions. The nucleus-localized RiMsn2 regulates osmotic homeostasis and trehalose contents of yeasts. Importantly, gene silencing analyses indicate that RiMsn2 is essential for arbuscule formation and enhances plant tolerance to drought stress. Results from yeasts and biochemical experiments suggest that the RiHog1-RiMsn2-STREs module controls the drought stress-responsive genes in AM fungal symbiont. In conclusion, our findings reveal that a module centered on the transcriptional activator RiMsn2 from AM fungus regulates drought stress tolerance in host plant.

Influence of Methyl Jasmonate and Salicylic Acid as Components of the Cultivation Medium for Rhizobium on Formation of Different-Efficiency Symbiotic Systems Glycine max — Bradyrhizobium japonicum

Phytohormones are important in the main pathways of transduction of symbiotic signals between macro- and microsymbionts, and understanding of their participation in integration with other metabolic pathways, including prooxidant-antioxidant systems, is crucial in the formation of different-efficiency symbiotic systems. Aim. To investigate the effect of salicylic acid (SA, 50 μM) and methyl jasmonate (MJ, 0.75 μM) as components of the cultivation media of different in the activity and virulence rhizobia 604k and B1-20 on the peculiarities of the formation of symbiotic systems in terms of intensity and activity of catalase, as well as on the course of nodulation and nitrogen fixation. Methods. Microbiological (cultivation of nitrogen-fixing microorganisms, seed inoculation), physiological (vegetation experiment), biochemical (spectrophotometry, gas chromatography), and statistical. Results. It was found that the use of SA (50 μM) as an additional component of the culture medium of active rhizobia Tn5-mutant B1-20 for seed inoculation induces increased levels of peroxide production and catalase activity in soybean roots in the early stages of symbiosis, which contributes to the effectiveness of its symbiotic apparatus. Addition of MJ (0.75 μM) to the culture medium of rhizobia B1-20 does not affect changes in peroxide content and catalase activity in the roots, however, stimulates the processes of nodulation and reduces nitrogen fixation. It has been shown that modification of the cultivation medium of inactive rhizobia of the highly virulent strain 604k using SA (50 μM) or MJ (0.75 μM) does not change the peroxide content and leads to an increase in catalase activity in soybean roots during the formation of an ineffective symbiotic system with activation of nodulation processes. Conclusions. When using SA (50 μM) or MJ (0.75 μM) as components of the culture medium for rhizobia of different activity and virulence (604k and B1-20), differences were recorded in the levels of functioning of pro-antioxidant systems, in particular, in the production of peroxides and active catalase complexes, at the early stages of the formation of symbiotic systems of Glycine max — Bradyrhizobium japonicum, which affects the intensity of the processes of nodulation and nitrogen fixation.

Nod factor perception: an integrative view of molecular communication during legume symbiosis.

Compatible interaction between rhizobial Nod factors and host receptors enables initial recognition and signaling events during legume-rhizobia symbiosis. Molecular communication is a new paradigm of information relay, which uses chemical signals or molecules as dialogues for communication and has been witnessed in prokaryotes, plants as well as in animal kingdom. Understanding this fascinating relay of signals between plants and rhizobia during the establishment of a synergistic relationship for biological nitrogen fixation represents one of the hotspots in plant biology research. Predominantly, their interaction is initiated by flavonoids exuding from plant roots, which provokes changes in the expression profile of rhizobial genes. Compatible interactions promote the secretion of Nod factors (NFs) from rhizobia, which are recognised by cognate host receptors. Perception of NFs by host receptors initiates the symbiosis and ultimately leads to the accommodation of rhizobia within root nodules via a series of mutual exchange of signals. This review elucidates the bacterial and plant perspectives during the early stages of symbiosis, explicitly emphasizing the significance of NFs and their cognate NF receptors.

Involvement of Arachis hypogaea Jasmonate ZIM domain/TIFY proteins in root nodule symbiosis.

Jasmonate ZIM domain (JAZ) proteins are the key negative regulators of jasmonate signaling, an important integrator of plant-microbe relationships. Versatility of jasmonate signaling outcomes are maintained through the multiplicity of JAZ proteins and their definitive functionalities. How jasmonate signaling influences the legume-Rhizobium symbiotic relationship is still unclear. In Arachis hypogaea (peanut), a legume plant, one JAZ sub-family (JAZ1) gene and one TIFY sequence containing protein family member (TIFY8) gene show enhanced expression in the early stage and late stage of root nodule symbiosis (RNS) respectively. In plants, JAZ sub-family proteins belong to a larger TIFY family. Here, this study denotes the first attempt to reveal in planta interactions of downstream jasmonate signaling regulators through proteomics and mass spectrometry to find out the mode of jasmonate signaling participation in the RNS process of A. hypogaea. From 4-day old Bradyrhizobium-infected peanut roots, the JAZ1-protein complex shows its contribution towards the rhizobial entry, nodule development, autoregulation of nodulation and photo-morphogenesis during the early stage of symbiosis. From 30-day old Bradyrhizobium infected roots, the TIFY8-protein complex reveals repressor functionality of TIFY8, suppression of root jasmonate signaling, modulation of root circadian rhythm and nodule development. Cellular localization and expression level of the interaction partners during the nodulation process further substantiate the in planta interaction pairs. This study provides a comprehensive insight into the jasmonate functionality in RNS through modulation of nodule number and development, during the early stage and root circadian rhythm during the late stage of nodulation, through the protein complexes of JAZ1 and TIFY8 respectively in A. hypogaea.

Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes.

BackgroundOur aim was to explore how the ectomycorrhizae of an indigenous tree,Quercus acutissima, with a commercial truffle, Chinese black truffle (Tuber indicum), affects the host plant physiology and shapes the associated microbial communities in the surrounding environment during the early stage of symbiosis.MethodsTo achieve this, changes in root morphology and microscopic characteristics, plant physiology indices, and the rhizosphere soil properties were investigated when six-month-old ectomycorrhizae were synthesized. Meanwhile, next-generation sequencing technology was used to analyze the bacterial and fungal communities in the root endosphere and rhizosphere soil inoculated with T. indicum or not.ResultsThe results showed that colonization by T. indicum significantly improved the activity of superoxide dismutase in roots but significantly decreased the root activity. The biomass, leaf chlorophyll content and root peroxidase activity did not obviously differ. Ectomycorrhization of Q. acutissima with T. indicum affected the characteristics of the rhizosphere soil, improving the content of organic matter, total nitrogen, total phosphorus and available nitrogen. The bacterial and fungal community composition in the root endosphere and rhizosphere soil was altered by T. indicum colonization, as was the community richness and diversity. The dominant bacteria in all the samples were Proteobacteria and Actinobacteria, and the dominant fungi were Eukaryota_norank, Ascomycota, and Mucoromycota. Some bacterial communities, such as Streptomyces, SM1A02, and Rhizomicrobium were more abundant in the ectomycorrhizae or ectomycorrhizosphere soil. Tuber was the second-most abundant fungal genus, and Fusarium was present at lower amounts in the inoculated samples.DiscussionOverall, the symbiotic relationship between Q. acutissima and T. indicum had an obvious effect on host plant physiology, soil properties, and microbial community composition in the root endosphere and rhizosphere soil, which could improve our understanding of the symbiotic relationship between Q. acutissima and T. indicum, and may contribute to the cultivation of truffle.

Proteome studies in Legume (Phaseolus vulgaris L.)

Proteomics techniques were used to identify the underlying mechanism of the early stage of symbiosis between the common bean (Phaseolus vulgaris L.) and bacteria. Proteins from roots of common beans inoculated with bacteria were separated using two-dimensional polyacrylamide gel electrophoresis and identified using mass spectrometry. From 483 protein spots, 29 plant and 3 bacterial proteins involved in the early stage of symbiosis were identified. Of the 29 plant proteins, the expression of 19 was up regulated and the expression of 10 was down regulated. Up regulated proteins included those involved in protein destination/storage, energy production, and protein synthesis; whereas the down regulated proteins included those involved in metabolism. Many up regulated proteins involved in protein destination/storage were chaperonins and proteasome subunits. These results suggest that defense mechanisms associated with induction of chaperonins and protein degradation regulated by proteasomes occur during the early stage of symbiosis between the common bean and bacteria.

Interplay of Pathogen-Induced Defense Responses and Symbiotic Establishment in Medicago truncatula

Suppression of host innate immunity appears to be required for the establishment of symbiosis between rhizobia and host plants. In this study, we established a system that included a host plant, a bacterial pathogen and a symbiotic rhizobium to study the role of innate immunity during symbiotic interactions. A pathogenic bacterium, Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000), was shown to cause chlorosis in Medicago truncatula A17. Sinorhizobium meliloti strain Sm2011 (Sm2011) and Pst DC3000 strain alone induced similar defense responses in M. truncatula. However, when co-inoculated, Sm2011 specifically suppressed the defense responses induced by Pst DC3000, such as MAPK activation and ROS production. Inoculation with Sm2011 suppressed the transcription of defense-related genes triggered by Pst DC3000 infection, including the receptor of bacterial flagellin (FLS2), pathogenesis-related protein 10 (PR10), and the transcription factor WRKY33. Interestingly, inoculation with Pst DC3000 specifically inhibited the expression of the symbiosis marker genes nodule inception and nodulation pectate lyase and reduced the numbers of infection threads and nodules on M. truncatula A17 roots, indicating that Pst DC3000 inhibits the establishment of symbiosis in M. truncatula. In addition, defense-related genes, such as MAPK3/6, RbohC, and WRKY33, exhibited a transient increase in their expression in the early stage of symbiosis with Sm2011, but the expression dropped down to normal levels at later symbiotic stages. Our results suggest that plant innate immunity plays an antagonistic role in symbiosis by directly reducing the numbers of infection threads and nodules.

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes.

The marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes, and the establishment of this association involves a number of signaling pathways and transcriptional responses between both partners. We report here the first full RNA-Seq dataset representing host-associated V. fischeri cells from colonized juvenile E. scolopes, as well as comparative transcriptomes under both laboratory and simulated marine planktonic conditions. These data elucidate the broad transcriptional changes that these bacteria undergo during the early stages of symbiotic colonization. We report several previously undescribed and unexpected transcriptional responses within the early stages of this symbiosis, including gene expression patterns consistent with biochemical stresses inside the host, and metabolic patterns distinct from those reported in associations with adult animals. Integration of these transcriptional data with a recently developed metabolic model of V. fischeri provides us with a clearer picture of the metabolic state of symbionts within the juvenile host, including their possible carbon sources. Taken together, these results expand our understanding of the early stages of the squid-vibrio symbiosis, and more generally inform the transcriptional responses underlying the activities of marine microbes during host colonization.

Changes in the Common Bean Transcriptome in Response to Secreted and Surface Signal Molecules of Rhizobium etli.

Establishment of nitrogen-fixing symbiosis requires the recognition of rhizobial molecules to initiate the development of nodules. Using transcriptional profiling of roots inoculated with mutant strains defective in the synthesis of Nod Factor (NF), exopolysaccharide (EPS), or lipopolysaccharide (LPS), we identified 2,606 genes from common bean (Phaseolus vulgaris) that are differentially regulated at early stages of its interaction with Rhizobium etli. Many transcription factors from different families are modulated by NF, EPS, and LPS in different combinations, suggesting that the plant response depends on the integration of multiple signals. Some receptors identified as differentially expressed constitute excellent candidates to participate in signal perception of molecules derived from the bacteria. Several components of the ethylene signal response, a hormone that plays a negative role during early stages of the process, were down-regulated by NF and LPS. In addition, genes encoding proteins involved in small RNA-mediated gene regulation were regulated by these signal molecules, such as Argonaute7, a specific component of the trans-acting short interfering RNA3 pathway, an RNA-dependent RNA polymerase, and an XH/XP domain-containing protein, which is part of the RNA-directed DNA methylation. Interestingly, a number of genes encoding components of the circadian central oscillator were down-regulated by NF and LPS, suggesting that a root circadian clock is adjusted at early stages of symbiosis. Our results reveal a complex interaction of the responses triggered by NF, LPS, and EPS that integrates information of the signals present in the surface or secreted by rhizobia.

NagC represses N-acetyl-glucosamine utilization genes in Vibrio fischeri within the light organ of Euprymna scolopes.

Bacteria often use transcription factors to regulate the expression of metabolic genes in accordance to available nutrients. NagC is a repressor conserved among γ-proteobacteria that regulates expression of enzymes involved in the metabolism of N-acetyl-glucosamine (GlcNAc). The polymeric form of GlcNAc, known as chitin, has been shown to play roles in chemotactic signaling and nutrition within the light organ symbiosis established between the marine bacterium Vibrio fischeri and the Hawaiian squid Euprymna scolopes. Here, we investigate the impact of NagC regulation on the physiology of V. fischeri. We find that NagC repression contributes to the fitness of V. fischeri in the absence of GlcNAc. In addition, the inability to de-repress expression of NagC-regulated genes reduces the fitness of V. fischeri in the presence of GlcNAc. We find that chemotaxis toward GlcNAc or chitobiose, a dimeric form of GlcNAc, is independent of NagC regulation. Finally, we show that NagC represses gene expression during the early stages of symbiosis. Our data suggest that the ability to regulate gene expression with NagC contributes to the overall fitness of V. fischeri in environments that vary in levels of GlcNAc. Furthermore, our finding that NagC represses gene expression within the squid light organ during an early stage of symbiosis supports the notion that the ability of the squid to provide a source of GlcNAc emerges later in host development.

Exopolysaccharides from Sinorhizobium meliloti Can Protect against H2O2-Dependent Damage

Sinorhizobium meliloti requires exopolysaccharides in order to form a successful nitrogen-fixing symbiosis with Medicago species. Additionally, during early stages of symbiosis, S. meliloti is presented with an oxidative burst that must be overcome. Levels of production of the exopolysaccharides succinoglycan (EPS-I) and galactoglucan (EPS-II) were found to correlate positively with survival in hydrogen peroxide (H2O2). H2O2 damage is dependent on the presence of iron and is mitigated when EPS-I and EPS-II mutants are cocultured with cells expressing either exopolysaccharide. Purified EPS-I is able to decrease in vitro levels of H2O2, and this activity is specific to the symbiotically active low-molecular-weight form of EPS-I. This suggests a potential protective function of exopolysaccharides against H2O2 during early symbiosis.

Involvement of a Novel Genistein-Inducible Multidrug Efflux Pump of <i>Bradyrhizobium japonicum</i> Early in the Interaction with <i>Glycine max</i> (L.) Merr

The early molecular dialogue between soybean and the bacterium Bradyrhizobium japonicum is crucial for triggering their symbiotic interaction. Here we found a single large genomic locus that is widely separated from the symbiosis island and was conspicuously induced within minutes after the addition of genistein. This locus (named BjG30) contains genes for the multidrug efflux pump, TetR family transcriptional regulator, and polyhydroxybutyrate (PHB) metabolism. The induction of BjG30 by genistein was competitively inhibited by daidzein, although both genistein and daidzein are soybean-derived inducers of nodulation (nod) genes. Such a differential expression pattern is also observed in some legume-derived flavonoids, which structurally differ in the hydroxy/deoxy group at the 5-position. In addition, not only did the induction start far in advance of nodW and nodD1 after the addition of genistein, but the levels showed distinct concentration dependence, indicating that the induction pattern of BjG30 is completely different from that of nod genes. The deletion of genes encoding either the multidrug efflux pump or PHB metabolism, especially the former, resulted in defective nodulation performance and nitrogen-fixing capability. Taken together, these results indicate that BjG30, and especially its multidrug efflux pump, may play a key role in the early stage of symbiosis by balancing the dual functions of genistein as both a nod gene inducer and toxicant.

Metabolomic profiling reveals suppression of oxylipin biosynthesis during the early stages of legume–rhizobia symbiosis

The establishment of symbiosis between leguminous plants and rhizobial bacteria requires rapid metabolic changes in both partners. We utilized untargeted quantitative mass spectrometry to perform metabolomic profiling of small molecules in extracts of the model legume Medicago truncatula treated with rhizobial Nod factors. One metabolite closely resembling the 9(R)-HODE class of oxylipins reproducibly showed a decrease in concentration within the first hour of in planta nod factor treatment. Oxylipins are precursors of the jasmonic acid biosynthetic pathway and we showed that both this metabolite and jasmonic acid inhibit Nod factor signaling. Since, oxylipins have been implicated as antimicrobial compounds produced by plants, these observations suggest that the oxylipin pathway may play multiple roles in facilitating Nod factor signaling during the early stages of symbiosis.

Analysis of the Proteome of Common Bean (Phaseolus vulgaris L.) Roots after Inoculation with Rhizobium etli

Proteomics techniques were used to identify the underlying mechanism of the early stage of symbiosis between the common bean (Phaseolus vulgaris L.) and bacteria. Proteins from roots of common beans inoculated with bacteria were separated using two-dimensional polyacrylamide gel electrophoresis and identified using mass spectrometry. From 483 protein spots, 29 plant and 3 bacterial proteins involved in the early stage of symbiosis were identified. Of the 29 plant proteins, the expression of 19 was upregulated and the expression of 10 was downregulated. Upregulated proteins included those involved in protein destination/storage, energy production, and protein synthesis; whereas the downregulated proteins included those involved in metabolism. Many upregulated proteins involved in protein destination/storage were chaperonins and proteasome subunits. These results suggest that defense mechanisms associated with induction of chaperonins and protein degradation regulated by proteasomes occur during the early stage of symbiosis between the common bean and bacteria.

A comparative proteomic analysis of the early response to compatible symbiotic bacteria in the roots of a supernodulating soybean variety

To reveal the processes involved in the early stages of symbiosis between soybean plants and root nodule bacteria, we conducted a proteomic analysis of the response to bacterial inoculation in the roots of supernodulating (En-b0-1) and non-nodulating (En1282) varieties, and their parental normal-nodulating variety (Enrei). A total of 56 proteins were identified from 48 differentially expressed protein spots in normal-nodulating variety after bacterial inoculation. Among 56 proteins, metabolism- and energy production-related proteins were upregulated in supernodulating and downregulated in non-nodulating varieties compared to normal-nodulating variety. The supernodulating and non-nodulating varieties responded oppositely to bacterial inoculation with respect to the expression of 11 proteins. Seven proteins of these proteins was downregulated in supernodulating varieties compared to non-nodulating variety, but expression of proteasome subunit alpha type 6, gamma glutamyl hydrolase, glucan endo-1,3-beta glucosidase, and nodulin 35 was upregulated. The expression of seven proteins mirrored the degree of nodule formation. At the transcript level, expression of stem 31kDa glycoprotein, leucine aminopeptidase, phosphoglucomutase, and peroxidase was downregulated in the supernodulating variety compared to the non-nodulating variety, and their expression in the normal-nodulating variety was intermediate. These results suggest that suppression of the autoregulatory mechanism in the supernodulating variety might be due to negative regulation of defense and signal transduction-related processes.

Characterization and Expression Analysis of Medicago truncatula ROP GTPase Family during the Early Stage of Symbiosis

ROPs (Rho-related GTPases of plants) are small GTPases that are plant-specific signaling proteins. They act as molecular switches in a variety of developmental processes. In this study, seven cDNA clones coding for ROP GTPases have been isolated in Medicago truncatula, and conserved and divergent domains are identified in these predicted MtROP proteins. Phylogenetic analysis has indicated that MtROPs are distributed into groups II, III, IV but group I. MtROP genes are expressed in various tissues at different levels. A quantitative reverse transcription PCR analysis indicated that these MtROP genes have different expression profiles in the roots in response to infection with rhizobia. The expression of MtROP3, MtROP5 and MtROP6 are increased, as the expression of Nod factor or rhizobial-induced marker genes--NFP, Rip1 and Enod11; MtROP10 has showed enhanced expression at a certain post-inoculation time point. No significant changes in MtROP7 and MtROP9 expression have been detected and MtROP8 expression is dramatically decreased by about 80%-90%. Additionally, ROP promoter-GUS analysis has showed that MtROP3, MtROP5 and MtROP6 have elevated expression in transgenic root hairs after rhizobial inoculation. These results might suggest a role for some ROP GTPases in the regulation of early stages during rhizobial infection in symbiosis.

A possible role of class 1 plant hemoglobin at the early stage of legume-rhizobium symbiosis

Leguminous plants form root nodules, in which symbiotic rhizobia fix atmospheric nitrogen and supply the fixation products to their host plants as a nitrogen source. On the process of establishing the symbiosis, rhizobia induce genes involved in the defense system of their host plants. However, the host defense responses will be cancelled by unknown mechanism. We focused on nitric oxide (NO) as a key molecule of plant defense system and class 1 plant hemoglobin (Hb) as a scavenger of NO. The inoculation of a symbiotic rhizobium, Mesorhizobium loti MAFF303099, induced transiently NO production and expression of a class 1 Hb gene LjHb1 in the roots of a model legume Lotus japonicus. In this addendum, we show that the lipopolysaccharide of M. loti induces NO production and expression of LjHb1 in L. japonicus, and we propose the role of NO and Hb at the early stage of symbiosis.

STABILIZING MECHANISMS IN A LEGUME-RHIZOBIUM MUTUALISM

Preferential rewarding of more beneficial partners may stabilize mutualisms against the invasion of less beneficial, that is cheater, genotypes. Recent evidence suggests that both partner choice and sanctioning may play roles in preventing the invasion of less-beneficial rhizobia in legume-rhizobium mutualisms. The importance of these mechanisms in natural communities, however, remains unclear. We grew 12 Medicago truncatula maternal families with a mixture of three rhizobium strains from their native range for three plant generations and estimated the symbiotic benefits (nodule number and size) conferred to each rhizobium strain. In this experiment, the majority of M. truncatula genotypes formed more nodules with more beneficial rhizobium strains, providing evidence for adaptive partner choice. We also found that three generations of symbiosis resulted in an increase in the relative frequency of rhizobium strains that were most beneficial to plants--suggesting that partner choice affects rhizobium fitness. By contrast, we found no evidence that plants differentially rewarded rhizobia postnodulation via sanctioning leading to differences in nodule size. Taken together, our data suggest that plants have evolved to recognize beneficial rhizobial signals during the early stages of symbiosis, and that signaling between plants and rhizobia may be subject to coevolutionary pressures.

An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri

BackgroundBiologists are becoming increasingly aware that the interaction of animals, including humans, with their coevolved bacterial partners is essential for health. This growing awareness has been a driving force for the development of models for the study of beneficial animal-bacterial interactions. In the squid-vibrio model, symbiotic Vibrio fischeri induce dramatic developmental changes in the light organ of host Euprymna scolopes over the first hours to days of their partnership. We report here the creation of a juvenile light-organ specific EST database.ResultsWe generated eleven cDNA libraries from the light organ of E. scolopes at developmentally significant time points with and without colonization by V. fischeri. Single pass 3' sequencing efforts generated 42,564 expressed sequence tags (ESTs) of which 35,421 passed our quality criteria and were then clustered via the UIcluster program into 13,962 nonredundant sequences. The cDNA clones representing these nonredundant sequences were sequenced from the 5' end of the vector and 58% of these resulting sequences overlapped significantly with the associated 3' sequence to generate 8,067 contigs with an average sequence length of 1,065 bp. All sequences were annotated with BLASTX (E-value < -03) and Gene Ontology (GO).ConclusionBoth the number of ESTs generated from each library and GO categorizations are reflective of the activity state of the light organ during these early stages of symbiosis. Future analyses of the sequences identified in these libraries promise to provide valuable information not only about pathways involved in colonization and early development of the squid light organ, but also about pathways conserved in response to bacterial colonization across the animal kingdom.

Tempo and mode of early gene loss in endosymbiotic bacteria from insects

BackgroundUnderstanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts.ResultsOur results demonstrate that genes lost in the early stages of symbiosis were on average less selectively constrained than genes conserved in any of the extant symbiotic strains studied. These results also extend to more recent events of gene losses (i.e. among Buchnera strains) that still tend to concentrate on genes with low adaptive bias in E. coli and high evolutionary rates both in free-living and in symbiotic lineages. In addition, we analyzed the physical organization of gene losses for early steps of symbiosis acquisition under the hypothesis of a common origin of different symbioses. In contrast with previous findings we show that gene losses mostly occurred through loss of rather small blocks and mostly in syntenic regions between at least one of the symbionts and present-day E. coli.ConclusionAt both ancient and recent stages of symbiosis evolution, gene loss was at least partially influenced by selection, highly conserved genes being retained more readily than lowly conserved genes: although losses might result from drift due to the bottlenecking of endosymbiontic populations, we demonstrated that purifying selection also acted by retaining genes of greater selective importance.