Environment‐driven changes of mRNA and protein levels in <i>Pseudomonas aeruginosa</i>

Erdmann, Jelena; Preuße, Matthias; Khaledi, Ariane; Pich, Andreas; Häußler, Susanne

doi:10.1111/1462-2920.14419

Cited by 12 publications

(17 citation statements)

References 71 publications

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“…Among those pairs, proteins were quantified for all replicates. In mid-log phase, the correlation between LFQ protein abundance and mRNA expression levels was relatively high ( r = 0.557 and 0.578 for CCBAU45436 and CCBAU25509, respectively), which is in the same range as the protein−mRNA correlation coefficient previously published for another Gram-negative bacterium (Kwon et al, 2014; Erdmann et al, 2018). A positive but weak correlation ( r = 0.161 and 0.167) between LFQ protein and mRNA expression was observed during stationary phase.…”

Section: Resultssupporting

confidence: 78%

High-Throughput Mass Spectrometric Analysis of the Whole Proteome and Secretome From Sinorhizobium fredii Strains CCBAU25509 and CCBAU45436

et al. 2019

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Sinorhizobium fredii is a dominant rhizobium on alkaline-saline land that can induce nitrogen-fixing symbiotic root nodules in soybean. Two S. fredii strains, CCBAU25509 and CCBAU45436, were used in this study to facilitate in-depth analyses of this species and its interactions with soybean. We have previously completed the full assembly of the genomes and detailed transcriptomic analyses for these two S. fredii strains, CCBAU25509 and CCBAU45436, that exhibit differential compatibility toward some soybean hosts. In this work, we performed high-throughput Orbitrap analyses of the whole proteomes and secretomes of CCBAU25509 and CCBAU45436 at different growth stages. Our proteomic data cover coding sequences in the chromosome, chromid, symbiotic plasmid, and other accessory plasmids. In general, we found higher levels of protein expression by genes in the chromosomal genome, whereas proteins encoded by the symbiotic plasmid were differentially accumulated in bacteroids. We identified secreted proteins from the extracellular medium, including seven and eight Nodulation Outer Proteins (Nops) encoded by the symbiotic plasmid of CCBAU25509 and CCBAU45436, respectively. Differential host restriction of CCBAU25509 and CCBAU45436 is regulated by the allelic type of the soybean Rj2(Rfg1) protein. Using sequencing data from this work and available in public databases, our analysis confirmed that the soybean Rj2(Rfg1) protein has three major allelic types (Rj2/rfg1, rj2/Rfg1, rj2/rfg1) that determine the host restriction of some Bradyrhizobium diazoefficiens and S. fredii strains. A mutant defective in the type 3 protein secretion system (T3SS) in CCBAU25509 allowed this strain to nodulate otherwise-incompatible soybeans carrying the rj2/Rfg1 allelic type, probably by disrupting Nops secretion. The allelic forms of NopP and NopI in S. fredii might be associated with the restriction imposed by Rfg1. By swapping the NopP between CCBAU25509 and CCBAU45436, we found that only the strains carrying NopP from CCBAU45436 could nodulate soybeans carrying the rj2/Rfg1 allelic type. However, no direct interaction between either forms of NopP and Rfg1 could be observed.

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Section: Resultssupporting

confidence: 78%

High-Throughput Mass Spectrometric Analysis of the Whole Proteome and Secretome From Sinorhizobium fredii Strains CCBAU25509 and CCBAU45436

et al. 2019

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“…Supporting our proposal that P. aeruginosa surface-association/biofilm formation and CRISPR-Cas expression are inversely correlated are two independent observations: i) our analysis of a previously published PA14 RNAseq data set 65 and proteomic data set 66 revealed activation of CRISPR-Cas expression in exponential phase, and strong transcriptional repression during stationary phase and biofilm growth (Supplementary Fig. 4a).…”

Section: Discussionsupporting

confidence: 78%

CRISPR-Cas immunity repressed by a biofilm-activating pathway inPseudomonas aeruginosa

Borges

Castro

Govindarajan

et al. 2019

Preprint

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10 11 CRISPR-Cas systems are adaptive immune systems that protect bacteria from 12 bacteriophage (phage) infection. To provide immunity, RNA-guided protein 13 surveillance complexes recognize foreign nucleic acids, triggering their 14 destruction by Cas nucleases. While the essential requirements for immune 15 activity are well understood, the physiological cues that regulate CRISPR-Cas 16 expression are not. Here, a forward genetic screen identifies a two-component 17 system (KinB/AlgB), previously characterized in regulating Pseudomonas 18 aeruginosa virulence and biofilm establishment, as a regulator of the biogenesis 19 and activity of the Type I-F CRISPR-Cas system. Downstream of the KinB/AlgB 20 system, activators of biofilm production AlgU (a σ E orthologue) and AlgR, act as 21 repressors of CRISPR-Cas activity during planktonic and surface-associated 22 growth. AmrZ, another biofilm activator, functions as a surface-specific repressor 23 of CRISPR-Cas immunity. Pseudomonas phages and plasmids have taken 24 advantage of this regulatory scheme, and carry hijacked homologs of AmrZ, 25 which are functional CRISPR-Cas repressors. This suggests that while CRISPR-26 Cas regulation may be important to limit self-toxicity, endogenous repressive 27 pathways represent a vulnerability for parasite manipulation. 29Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-30 associated (cas) genes are RNA-guided nucleases found in nearly half of all bacteria 1 . 31CRISPR-Cas systems are mechanistically diverse, with six distinct types (I-VI) identified, 32 based on signature genes, mechanisms of action, and the type of nucleic acid target 1 . 33Our strong understanding of the basic components to enable sequence specific DNA 34 and RNA cleavage have enabled functional transplantation into heterologous bacterial 2,3 35 and eukaryotic 4,5 hosts. Given that many Cas proteins encode nucleases 6 the fine-tuned 36 regulation of these systems to avoid toxicity is likely a key factor to enable safe retention 37 of a CRISPR-Cas immune system 7 . Multiple signals have been shown to activate 38 CRISPR-Cas function in diverse organisms, such as quorum sensing 8,9 , temperature 10 , 39 membrane stress 11,12 , altered host metabolite levels 13,14 , and phage infection [15][16][17][18] . 40However, relatively little is known regarding the factors and/or signals that serve to 41 temper CRISPR-Cas activity and mitigate the risk of acquiring and expressing a 42 nucleolytic immune system. 44Type I CRISPR-Cas systems are comprised of a multi-subunit RNA-guided surveillance 45 complex, a trans-acting nuclease (Cas3) [19][20][21] , and proteins dedicated to spacer 46 acquisition, Cas1 and Cas2 22,23 . Pseudomonas aeruginosa has become a powerful 47 model organism for studying Type I CRISPR-Cas mechanisms 24-29 , functions 3,23,30,31 , 48 evolution 32-34 , and interactions with phages utilizing anti-CRISPR proteins [35][36][37][38] . The P. 49aeruginosa strain PA14 possesses an active Type I-F CRISPR-Cas immune system ...

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“…How does the organism translate this information into proteins from mRNAs? Discrepancies between mRNA and protein levels have been frequently noted in various organisms (Erdmann et al ., ; Bathke et al ., ). Bathke et al .…”

Section: Resultsmentioning

confidence: 98%

Section: Correlation Between Transcript Changes and Changes Of The Prmentioning

confidence: 99%

Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

McIntosh

Eisenhardt

Remes

et al. 2019

Environmental Microbiology

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Summary Exhaustion of nutritional resources stimulates bacterial populations to adapt their growth behaviour. General mechanisms are known to facilitate this adaptation by sensing the environmental change and coordinating gene expression. However, the existence of such mechanisms among the Alphaproteobacteria remains unclear. This study focusses on global changes in transcript levels during growth under carbon‐limiting conditions in a model Alphaproteobacterium, Rhodobacter sphaeroides, a metabolically diverse organism capable of multiple modes of growth including aerobic and anaerobic respiration, anaerobic anoxygenic photosynthesis and fermentation. We identified genes that showed changed transcript levels independently of oxygen levels during the adaptation to stationary phase. We selected a subset of these genes and subjected them to mutational analysis, including genes predicted to be involved in manganese uptake, polyhydroxybutyrate production and quorum sensing and an alternative sigma factor. Although these genes have not been previously associated with the adaptation to stationary phase, we found that all were important to varying degrees. We conclude that while R. sphaeroides appears to lack a rpoS‐like master regulator of stationary phase adaptation, this adaptation is nonetheless enabled through the impact of multiple genes, each responding to environmental conditions and contributing to the adaptation to stationary phase.

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Environment‐driven changes of mRNA and protein levels in Pseudomonas aeruginosa

Cited by 12 publications

References 71 publications

High-Throughput Mass Spectrometric Analysis of the Whole Proteome and Secretome From Sinorhizobium fredii Strains CCBAU25509 and CCBAU45436

High-Throughput Mass Spectrometric Analysis of the Whole Proteome and Secretome From Sinorhizobium fredii Strains CCBAU25509 and CCBAU45436

CRISPR-Cas immunity repressed by a biofilm-activating pathway inPseudomonas aeruginosa

Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase

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