Genome-wide identification of
            <i>Pseudomonas syringae</i>
            genes required for fitness during colonization of the leaf surface and apoplast

Helmann, Tyler C.; Deutschbauer, Adam M.; Lindow, Steven E.

doi:10.1073/pnas.1908858116

Cited by 91 publications

(117 citation statements)

References 81 publications

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“…In mice, a meta-analysis found a relationship similar to the one we observed, with aberrant phenotypes more likely to be associated with genes highly transcribed in the tissue exhibiting the phenotype [47]. In contrast to these results, genome scale measurement of the fitness costs of gene knockouts via competitive assays in yeast [51,52] and bacteria [53,54] found that, for particular environmental conditions, there was little to no correlation between the expression level of a gene and its impact on fitness in that condition. This could be indicative of differences between the mechanisms underlying single-celled organisms' response to the environment versus those underlying developmental complexity in multicellular organisms.…”

Section: Maize Pollen Provides a Powerful Model For Quantifying Gene-mentioning

confidence: 50%

High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

et al. 2020

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In flowering plants, gene expression in the haploid male gametophyte (pollen) is essential for sperm delivery and double fertilization. Pollen also undergoes dynamic epigenetic regulation of expression from transposable elements (TEs), but how this process interacts with gene expression is not clearly understood. To explore relationships among these processes, we quantified transcript levels in four male reproductive stages of maize (tassel primordia, microspores, mature pollen, and sperm cells) via RNA-seq. We found that, in contrast with vegetative cell-limited TE expression in Arabidopsis pollen, TE transcripts in maize accumulate as early as the microspore stage and are also present in sperm cells. Intriguingly, coordinate expression was observed between highly expressed protein-coding genes and their neighboring TEs, specifically in mature pollen and sperm cells. To investigate a potential relationship between elevated gene transcript level and pollen function, we measured the fitness cost (male-specific transmission defect) of GFP-tagged coding sequence insertion mutations in over 50 genes identified as highly expressed in the pollen vegetative cell, sperm cell, or seedling (as a sporophytic control). Insertions in seedling genes or sperm cell genes (with one exception) exhibited no difference from the expected 1:1 transmission ratio. In contrast, insertions in over 20% of vegetative cell genes were associated with significant reductions in fitness, showing a positive correlation of transcript level with non-Mendelian segregation when mutant. Insertions in maize gamete expressed2 (Zm gex2), the sole sperm cell gene with measured contributions to fitness, also triggered seed defects when crossed as a male, indicating a conserved role in double fertilization, given the similar phenotype previously demonstrated for the Arabidopsis ortholog GEX2.

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Section: Maize Pollen Provides a Powerful Model For Quantifying Gene-mentioning

confidence: 50%

High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

et al. 2020

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“…For example, in a study comparing the expression and mutant fitness of biosynthetic genes in several bacteria including the metal-reducing bacterium Shewanella oneidensis, E. coli, the ethanol-producing bacterium Zymomonas mobilis, and the sulfate-reducing bacterium Desulfovibrio alaskensis it was reported that there is little correlation between the importance of genes for optimal growth or fitness and their upregulation [100]. Also, a recent study of the plant pathogen Pseudomonas syringae reported the absence of correlation between mutant fitness in planta and either the magnitude of expression or the degree of induction for most genes in planta compared to in vitro conditions [101]. However, fitness is measured cumulatively over several growth cycles, whereas expression is measured during a single growth/infection cycle, making direct comparisons difficult.…”

Section: Testing the Dynamical Behavior Of Codos By Reporter Constructsmentioning

confidence: 99%

Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation

et al. 2019

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Recent studies strongly suggest that in bacteria, both the genomic pattern of DNA thermodynamic stability and the order of genes along the chromosomal origin-to-terminus axis are highly conserved and that this spatial organization plays a crucial role in coordinating genomic transcription. In this article, we explore the relationship between genomic sequence organization and transcription in the commensal bacterium Escherichia coli and the plant pathogen Dickeya. We argue that, while in E. coli the gradient of DNA thermodynamic stability and gene order along the origin-to-terminus axis represent major organizational features orchestrating temporal gene expression, the genomic sequence organization of Dickeya is more complex, demonstrating extended chromosomal domains of thermodynamically distinct DNA sequences eliciting specific transcriptional responses to various kinds of stress encountered during pathogenic growth. This feature of the Dickeya genome is likely an adaptation to the pathogenic lifestyle utilizing differences in genomic sequence organization for the selective expression of virulence traits. We propose that the coupling of DNA thermodynamic stability and genetic function provides a common organizational principle for the coordinated expression of genes during both normal and pathogenic bacterial growth.

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“…Construction of bar-coded transposon libraries. Construction of the B728a WT barcoded transposon insertion library was described previously (32). The ΔmexB library was constructed in a similar fashion.…”

Section: Methodsmentioning

confidence: 99%

“…However, it has remained a challenge to associate particular transporters with their substrates, especially for hostproduced compounds. With few exceptions (17,39), genes encoding efflux transporters in addition to AcrAB-TolC and MexAB-OprM have not been observed to contribute to fitness during plant colonization (32,40,41), likely due to their high level of redundancy. Here, we used a transposon library constructed in a ΔmexB strain to reveal the role of several partially redundant RND efflux pumps.…”

Section: Figmentioning

confidence: 99%

Genome-Wide Transposon Screen of a Pseudomonas syringae mexB Mutant Reveals the Substrates of Efflux Transporters

Helmann

Ongsarte

Lam

et al. 2019

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Bacteria express numerous efflux transporters that confer resistance to diverse toxicants present in their environment. Due to a high level of functional redundancy of these transporters, it is difficult to identify those that are of most importance in conferring resistance to specific compounds. The resistance-nodulation-division (RND) protein family is one such example of redundant transporters that are widespread among Gram-negative bacteria. Within this family, the MexAB-OprM protein complex is highly expressed and conserved among Pseudomonas species. We exposed barcoded transposon mutant libraries in isogenic wild-type and ΔmexB backgrounds in P. syringae B728a to diverse toxic compounds in vitro to identify mutants with increased susceptibility to these compounds. Mutants with mutations in genes encoding both known and novel redundant transporters but with partially overlapping substrate specificities were observed in a ΔmexB background. Psyr_0228, an uncharacterized member of the major facilitator superfamily of transporters, preferentially contributes to tolerance of acridine orange and acriflavine. Another transporter located in the inner membrane, Psyr_0541, contributes to tolerance of acriflavine and berberine. The presence of multiple redundant, genomically encoded efflux transporters appears to enable bacterial strains to tolerate a diversity of environmental toxins. This genome-wide screen performed in a hypersusceptible mutant strain revealed numerous transporters that would otherwise be dispensable under these conditions. Bacterial strains such as P. syringae that likely encounter diverse toxins in their environment, such as in association with many different plant species, probably benefit from possessing multiple redundant transporters that enable versatility with respect to toleration of novel toxicants. IMPORTANCE Bacteria use protein pumps to remove toxic compounds from the cell interior, enabling survival in diverse environments. These protein pumps can be highly redundant, making their targeted examination difficult. In this study, we exposed mutant populations of Pseudomonas syringae to diverse toxicants to identify pumps that contributed to survival in those conditions. In parallel, we examined pump redundancy by testing mutants of a population lacking the primary efflux transporter responsible for toxin tolerance. We identified partial substrate overlap for redundant transporters, as well as several pumps that appeared more substrate specific. For bacteria that are found in diverse environments, having multiple, partially redundant efflux pumps likely allows flexibility in habitat colonization.

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Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast

Cited by 91 publications

References 81 publications

High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements

Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation

Genome-Wide Transposon Screen of a Pseudomonas syringae mexB Mutant Reveals the Substrates of Efflux Transporters

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