Host specificity determinants as a genetic continuum

Kirzinger, Morgan W. B.; Stavrinides, John

doi:10.1016/j.tim.2011.11.006

Cited by 41 publications

(39 citation statements)

References 52 publications

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“…Host specificity, an important trait underlying the interaction of rhizobia with their hosts, is still poorly understood [28]. Host switching or host jumping can often be traced to the modification of key microbial genes that facilitate the formation of particular host associations [29]. Because the determinants of host specificity of a bacterium mainly depend on three groups of signaling molecules—nodulation factors (NFs), surface polysaccharides, and secreted proteins [30], we explored genes that affect the biological synthesis of these signaling molecules in the genomes of these two strains and compared them with those of native M. loti strain R7A.…”

Section: Resultsmentioning

confidence: 99%

“…Changes in host specificity determinants—for example, by acquisition of new genetic elements that grant a selective advantage in a particular host environment—can have a great impact on host range and may lead to host jumps [29]. Both intrageneric and intergeneric HGT have been reported as important mechanisms for the spread of symbiotic capacity in the Salado River Basin [16].…”

Section: Resultsmentioning

confidence: 99%

“…The introduction of novel genetic variation by HGT is typically accompanied by the acquisition and incorporation of genetic fragments or intact transcriptional units into the genome [37]. Although NFs and secreted effectors of T3SS in MAFF303099 are associated with genetic fragments and intact transcriptional units, we still cannot confirm the underlying causes of the host specificity changes: there may be a continuum that ranges from changes in single residues to gene domains, whole genes, and eventually entire genomic islands (GEIs) [29]. Consequently, much remains to be learned about whether many or only a few gene loci are involved in the determination of nodulation specificity.…”

Section: Resultsmentioning

confidence: 99%

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Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics

Wang

Hao

et al. 2014

BMC Genomics

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BackgroundEvidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general.ResultsIn this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species.ConclusionsOur ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-15-440) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics

Wang

Hao

et al. 2014

BMC Genomics

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“…Aphid physical and biochemical mechanisms, as well as the composition of honeydew, could be effective filters, allowing only a few bacterial taxa to develop and colonize the gut; similar to what occurs for yeasts in flower nectar (Herrera et al 2010). This kind of partner selection is based on the microbes' abilities to survive in this rather hostile environment (high osmotic pressure, low oxygen, antimicrobial compounds produced by the host) and on the affinity of the microorganism for its host (Á lvarez-Pérez et al 2012;González-Teuber and Heil 2010;Herrera et al 2010;Kirzinger and Stavrinides 2012).…”

Section: Discussionmentioning

confidence: 99%

Bacteria may enhance species association in an ant–aphid mutualistic relationship

et al. 2015

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The mutualistic relationships between certain ant and aphid species are well known, the primary benefits being protection for the aphids and carbohydrate-rich honeydew for the ants. Questions remain, however, as to the exact semiochemical factors that establish and maintain such relationships. In this study, we used a series of treatments and associated controls placed at the end of a two-way olfactometer to determine the degree of attractiveness of a complete plant-aphid-honeydew system as well as individual components of that system. Both the olfactometer branch selected by the black garden ant (Lasius niger) and the linear speed with which ants moved through the device were measured. Study results showed that ants were attracted not just to the complete plant system and the honeydew itself, but also to the microbial flora in the absence of plant or honeydew, and specifically to a bacterium from the black bean aphid (Aphis fabae) honeydew, Staphylococcus xylosus. This bacterium produces a blend of semiochemicals that attract the ant scouts. This information suggests the presence of a naturally occurring, reliable biotic cue for detection of potential aphid partners. This would have to be confirmed in natural conditions by further field experiments. Rather than being opportunistic species that coincidentally colonize a sugarrich environment, microorganisms living in aphid honeydew may be able to alter emissions of volatile organic compounds (VOCs), thus significantly mediating partner attraction. A bacterial involvement in this mutualistic relationship could alter the manner in which these and similar relationships are viewed and evaluated. Future studies into mutualism stability and function among macroscopic partners will likely need for transition from a two-partner perspective to a multiple-partner perspective, and consider the microbial component, with the potential for one or more taxa making significant contributions to the relationship.

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“…Recently, it has become increasingly apparent that defined genetic changes in bacteria at individual loci, single genes, or even nucleotide changes have led to dramatic effects in the evolution of colonizing bacteria. As some examples, the acquisition of the nil locus in Xenorhabdus nematophila contributed to the species-specific association with the worm host Steinernema carpocapsae, inactivation of the RscA biofilm regulator was critical in the evolution of Yersinia pestis from Yersinia pseudotuberculosis, and acquisition of the biofilm regulation of RscS facilitated colonization of north Pacific squid by Vibrio fischeri (3)(4)(5)(6)(7)(8).…”

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confidence: 99%

TfoX-Based Genetic Mapping Identifies Vibrio fischeri Strain-Level Differences and Reveals a Common Lineage of Laboratory Strains

et al. 2015

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Bacterial strain variation exists in natural populations of bacteria and can be generated experimentally through directed or random mutation. The advent of rapid and cost-efficient whole-genome sequencing has facilitated strain-level genotyping. Even with modern tools, however, it often remains a challenge to map specific traits to individual genetic loci, especially for traits that cannot be selected under culture conditions (e.g., colonization level or pathogenicity). Using a combination of classical and modern approaches, we analyzed strain-level variation in Vibrio fischeri and identified the basis by which some strains lack the ability to utilize glycerol as a carbon source. We proceeded to reconstruct the lineage of the commonly used V. fischeri laboratory strains. Compared to the wild-type ES114 strain, we identify in ES114-L a 9.9-kb deletion with endpoints in tadB2 and glpF; restoration of the missing portion of glpF restores the wild-type phenotype. The widely used strains ESR1, JRM100, and JRM200 contain the same deletion, and ES114-L is likely a previously unrecognized intermediate strain in the construction of many ES114 derivatives. ES114-L does not exhibit a defect in competitive squid colonization but ESR1 does, demonstrating that glycerol utilization is not required for early squid colonization. Our genetic mapping approach capitalizes on the recently discovered chitin-based transformation pathway, which is conserved in the Vibrionaceae; therefore, the specific approach used is likely to be useful for mapping genetic traits in other Vibrio species.I dentifying relevant differences in bacterial strains is fundamental to determining the genetic basis of microbial phenotypes. In many cases, the number of polymorphisms between strains is so high that elucidating which locus or loci contribute to specific phenotypes cannot be achieved simply by determining the genome sequence of the isolates. This challenge is especially pronounced in identifying loci that contribute to colonization and/or pathogenicity phenotypes. The study of genomic islands has made it clear that the acquisition of large regions of DNA can profoundly influence a bacterium's ability to engage with a eukaryotic host (1, 2). Recently, it has become increasingly apparent that defined genetic changes in bacteria at individual loci, single genes, or even nucleotide changes have led to dramatic effects in the evolution of colonizing bacteria. As some examples, the acquisition of the nil locus in Xenorhabdus nematophila contributed to the species-specific association with the worm host Steinernema carpocapsae, inactivation of the RscA biofilm regulator was critical in the evolution of Yersinia pestis from Yersinia pseudotuberculosis, and acquisition of the biofilm regulation of RscS facilitated colonization of north Pacific squid by Vibrio fischeri (3-8).In most cases, identification of factors that contribute to host colonization specificity has relied first on identifying the factor as being necessary for host colonization by standard g...

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Host specificity determinants as a genetic continuum

Cited by 41 publications

References 52 publications

Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics

Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics

Bacteria may enhance species association in an ant–aphid mutualistic relationship

TfoX-Based Genetic Mapping Identifies Vibrio fischeri Strain-Level Differences and Reveals a Common Lineage of Laboratory Strains

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