Lipid biosynthetic genes and a ribosomal protein gene are cotranscribed

Podkovyrov, S M; Larson, Timothy J.

doi:10.1016/0014-5793(95)00702-b

Cited by 23 publications

(7 citation statements)

References 9 publications

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“…This further highlighted the reliability of translation-related essential proteins as ‘proteomic signatures’ that dictate the cell’s physiology and even the energy status, especially since it was shown earlier that translation proteins consume more than 70 % of the cellular ATP pool [ 50 ]. In addition to their major role in protein synthesis, ribosomes have been implicated in pleiotropic functions, ranging from antibiotic adaptation [ 71 ] to fatty acid biosynthesis [ 72 ], in which we postulate these exceptionally up-regulated ribosomal proteins may be involved. Whether the pattern of differentially expressed S. sanguinis proteins during the stress response is conserved across other bacterial species is currently unclear.…”

Section: Discussionmentioning

confidence: 99%

Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis

et al. 2018

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The paradoxical response of Streptococcus sanguinis to drugs prescribed for dental and clinical practices has complicated treatment guidelines and raised the need for further investigation. We conducted a high throughput study on concomitant transcriptome and proteome dynamics in a time course to assess S. sanguinis behaviour under a sub-inhibitory concentration of ampicillin. Temporal changes at the transcriptome and proteome level were monitored to cover essential genes and proteins over a physiological map of intricate pathways. Our findings revealed that translation was the functional category in S. sanguinis that was most enriched in essential proteins. Moreover, essential proteins in this category demonstrated the greatest conservation across 2774 bacterial proteomes, in comparison to other essential functional categories like cell wall biosynthesis and energy production. In comparison to non-essential proteins, essential proteins were less likely to contain ‘degradation-prone’ amino acids at their N-terminal position, suggesting a longer half-life. Despite the ampicillin-induced stress, the transcriptional up-regulation of amino acid-tRNA synthetases and proteomic elevation of amino acid biosynthesis enzymes favoured the enriched components of essential proteins revealing ‘proteomic signatures’ that can be used to bridge the genotype–phenotype gap of S. sanguinis under ampicillin stress. Furthermore, we identified a significant correlation between the levels of mRNA and protein for essential genes and detected essential protein-enriched pathways differentially regulated through a persistent stress response pattern at late time points. We propose that the current findings will help characterize a bacterial model to study the dynamics of essential genes and proteins under clinically relevant stress conditions.

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Section: Discussionmentioning

confidence: 99%

Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis

et al. 2018

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“…PlsX is the first gene of this cluster; however, its own promoter is rather weak so that about 60% of all transcripts containing plsX -mRNA result from promoters located further upstream [64,158]. This longer mRNA contains transcripts of yceD (coding for an uncharacterized protein) and rpmF (coding for the 50S ribosomal subunit protein L32) so that coordinated regulation of these proteins and fatty acid biosynthesis seems possible [159]. …”

Section: Regulation In E Colimentioning

confidence: 99%

Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels

Janßen

Steinbüchel

2014

Biotechnol Biofuels

238

220

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The idea of renewable and regenerative resources has inspired research for more than a hundred years. Ideally, the only spent energy will replenish itself, like plant material, sunlight, thermal energy or wind. Biodiesel or ethanol are examples, since their production relies mainly on plant material. However, it has become apparent that crop derived biofuels will not be sufficient to satisfy future energy demands. Thus, especially in the last decade a lot of research has focused on the production of next generation biofuels. A major subject of these investigations has been the microbial fatty acid biosynthesis with the aim to produce fatty acids or derivatives for substitution of diesel. As an industrially important organism and with the best studied microbial fatty acid biosynthesis, Escherichia coli has been chosen as producer in many of these studies and several reviews have been published in the fields of E. coli fatty acid biosynthesis or biofuels. However, most reviews discuss only one of these topics in detail, despite the fact, that a profound understanding of the involved enzymes and their regulation is necessary for efficient genetic engineering of the entire pathway. The first part of this review aims at summarizing the knowledge about fatty acid biosynthesis of E. coli and its regulation, and it provides the connection towards the production of fatty acids and related biofuels. The second part gives an overview about the achievements by genetic engineering of the fatty acid biosynthesis towards the production of next generation biofuels. Finally, the actual importance and potential of fatty acid-based biofuels will be discussed.

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“…In the case of ribosomal activity, a cluster is clearly recognized in the whole network and the subnetwork of hub genes, where the rpmF gene is the up-regulated hub element. The rpmF gene encodes for the 50S ribosomal subunit protein L32, which is responsible for protein synthesis and membrane lipid synthesis 101 . It is also involved in multidrug tolerance by modulating biofilm formation and persister cell induction 102 .…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach

Molina-Mora

Chinchilla-Montero

Chavarría-Azofeifa

et al. 2020

Sci Rep

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Pseudomonas aeruginosa is an opportunistic pathogen that thrives in diverse environments and causes a variety of human infections. Pseudomonas aeruginosa AG1 (PaeAG1) is a high-risk sequence type 111 (ST-111) strain isolated from a Costa Rican hospital in 2010. PaeAG1 has both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases, and it is resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. Ciprofloxacin (CIP) is an antibiotic commonly used to treat P. aeruginosa infections, and it is known to produce DNA damage, triggering a complex molecular response. In order to evaluate the effects of a sub-inhibitory CIP concentration on PaeAG1, growth curves using increasing CIP concentrations were compared. We then measured gene expression using RNA-Seq at three time points (0, 2.5 and 5 h) after CIP exposure to identify the transcriptomic determinants of the response (i.e. hub genes, gene clusters and enriched pathways). Changes in expression were determined using differential expression analysis and network analysis using a topdown systems biology approach. A hybrid model using database-based and co-expression analysis approaches was implemented to predict gene-gene interactions. We observed a reduction of the growth curve rate as the sub-inhibitory cip concentrations were increased. in the transcriptomic analysis, we detected that over time CIP treatment resulted in the differential expression of 518 genes, showing a complex impact at the molecular level. The transcriptomic determinants were 14 hub genes, multiple gene clusters at different levels (associated to hub genes or as co-expression modules) and 15 enriched pathways. Down-regulation of genes implicated in several metabolism pathways, virulence elements and ribosomal activity was observed. in contrast, amino acid catabolism, RpoS factor, proteases, and phenazines genes were up-regulated. Remarkably, > 80 resident-phage genes were up-regulated after CIP treatment, which was validated at phenomic level using a phage plaque assay. thus, reduction of the growth curve rate and increasing phage induction was evidenced as the CIP concentrations were increased. In summary, transcriptomic and network analyses, as well as the growth curves and phage plaque assays provide evidence that PaeAG1 presents a complex, concentration-dependent response to sub-inhibitory CIP exposure, showing pleiotropic effects at the systems level. Manipulation of these determinants, such as phage genes, could be used to gain

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Lipid biosynthetic genes and a ribosomal protein gene are cotranscribed

Cited by 23 publications

References 9 publications

Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis

Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis

Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels

Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach

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