Protein Acetylation in Bacteria

VanDrisse, Chelsey M.; Escalante‐Semerena, Jorge C.

doi:10.1146/annurev-micro-020518-115526

Cited by 114 publications

(109 citation statements)

References 109 publications

(157 reference statements)

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“…Although both effects of acetyl-P have been convincingly demonstrated, their impact on cellular physiology is not fully elucidated, so far. Protein acetylation in E. coli has been studied on a global scale and acetylation of central metabolic enzymes is currently discussed as a mechanism to control metabolic fluxes (Weinert et al, 2013;Kuhn et al, 2014;Carabetta and Cristea, 2017;Nakayasu et al, 2017;Brunk et al, 2018;Christensen et al, 2019;VanDrisse and Escalante-Semerena, 2019). Besides such global effects, for a number of proteins an impact of acetylation on activity was shown (Wolfe, 2016;Carabetta and Cristea, 2017).…”

Section: Introductionmentioning

confidence: 99%

The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12

et al. 2020

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Acetate is a characteristic by-product of Escherichia coli K-12 growing in batch cultures with glucose, both under aerobic as well as anaerobic conditions. While the reason underlying aerobic acetate production is still under discussion, during anaerobic growth acetate production is important for ATP generation by substrate level phosphorylation. Under both conditions, acetate is produced by a pathway consisting of the enzyme phosphate acetyltransferase (Pta) producing acetyl-phosphate from acetyl-coenzyme A, and of the enzyme acetate kinase (AckA) producing acetate from acetyl-phosphate, a reaction that is coupled to the production of ATP. Mutants in the AckA-Pta pathway differ from each other in the potential to produce and accumulate acetyl-phosphate. In the publication at hand, we investigated different mutants in the acetate pathway, both under aerobic as well as anaerobic conditions. While under aerobic conditions only small changes in growth rate were observed, all acetate mutants showed severe reduction in growth rate and changes in the by-product pattern during anaerobic growth. The AckA − mutant showed the most severe growth defect. The glucose uptake rate and the ATP concentration were strongly reduced in this strain. This mutant exhibited also changes in gene expression. In this strain, the atoDAEB operon was significantly upregulated under anaerobic conditions hinting to the production of acetoacetate. During anaerobic growth, protein acetylation increased significantly in the ackA mutant. Acetylation of several enzymes of glycolysis and central metabolism, of aspartate carbamoyl transferase, methionine synthase, catalase and of proteins involved in translation was increased. Supplementation of methionine and uracil eliminated the additional growth defect of the ackA mutant. The data show that anaerobic, fermentative growth of mutants in the AckA-Pta pathway is reduced but still possible. Growth reduction can be explained by the lack of an important ATP generating pathway of mixed acid fermentation. An ackA deletion mutant is more severely impaired than pta or ackA-pta deletion mutants. This is most probably due to the production of acetyl-P in the ackA mutant, leading to increased protein acetylation.

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Section: Introductionmentioning

confidence: 99%

The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12

et al. 2020

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“…Nevertheless, if AcbQ is an important enzyme in Actinoplanes sp. SE50/110 preventing its degradation is a possible action to increase production by the cell [67,68]. It is notably, that most of the glutamine to pyroglutamic acid modi cations of the Acb proteins were identi ed during the growth phase (T3 and T4).…”

Section: Identi Cation Of Different Post-translational Modi Cations Bmentioning

confidence: 99%

The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase

Droste

Ortseifen

Schaffert

et al. 2020

Preprint

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Background: Actinoplanes sp. SE50/110 is the natural producer of the diabetes mellitus drug acarbose, which is highly produced during the growth phase and ceases during the stationary phase. In previous works, the growth-dependency of acarbose formation was assumed to be caused by a decreasing transcription of the acarbose biosynthesis genes during transition and stationary growth phase.Results: In this study, transcriptomic data using RNA-seq and state-of-the-art proteomic data from seven time points of controlled bioreactor cultivations were used to analyze expression dynamics during growth of Actinoplanes sp. SE50/110. A hierarchical cluster analysis revealed co-regulated genes, which display similar transcription dynamics over the cultivation time. Aside from the expected metabolic switch from primary to secondary metabolism during transition phase, we observed a significantly decreasing transcript abundance of all acarbose biosynthetic genes, with the strongest decrease for the monocistronically transcribed genes acbA, acbB, acbD and acbE. Our data confirm a similar trend for acb gene transcription and acarbose formation rate.Surprisingly, the proteome dynamics does not follow the respective transcription for all acb genes. This suggests different protein stabilities or post-transcriptional regulation of the Acb proteins, which in turn could indicate bottlenecks in the acarbose biosynthesis. Furthermore, several genes are co-expressed with the acb gene cluster over the course of the cultivation, including eleven transcriptional regulators (e.g. ACSP50_0424), two sigma factors (ACSP50_0644, ACSP50_6006) and further genes, which have not previously been in focus of acarbose research in Actinoplanes sp. SE50/110.Conclusion: In conclusion, we have demonstrated, that a genome wide transcriptome and proteome analysis in a high temporal resolution is well suited to study the acarbose biosynthesis and the transcriptional and post-transcriptional regulation thereof.

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“…One class of modification that has been observed across biological systems is lysine acylation. [6][7][8] Acetylation has been long known as an epigenetic regulator, modulating protein expression by modifying lysine side chains on histone tails. [9][10][11] Later, it was discovered that acetyl and other acyl modifications not only impact histone function, but are also ubiquitous in mammalian metabolic pathways as well as in other eukaryotic and prokaryotic systems.…”

Section: Introductionmentioning

confidence: 99%

“…[9][10][11] Later, it was discovered that acetyl and other acyl modifications not only impact histone function, but are also ubiquitous in mammalian metabolic pathways as well as in other eukaryotic and prokaryotic systems. [6,9] In eukaryotic organisms, these modifications have been shown to correlate with aging as well as an organism's metabolic state. [7,8] In prokaryotes, these modifications have been shown to impact the activity of enzymes in metabolic pathways.…”

Section: Introductionmentioning

confidence: 99%

Leveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets

Muroski

Nguyen

et al. 2020

Preprint

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Acyl modifications vary greatly in terms of elemental composition and site of protein modification.Developing methods to identify these modifications more confidently can help assess the scope of these modifications in large proteomic datasets. Herein we analyze the utility of acyl-lysine immonium ions for identifying the modifications in proteomic datasets. We demonstrate that the cyclized immonium ion is a strong indicator of acyl-lysine presence when its rank or relative abundance compared to other ions within a spectrum is considered. Utilizing a stepped collision energy method in a shotgun experiment highlights the immonium ion strongly. Implementing an analysis that accounted for features within each MS 2 spectra, this method allows peptides with short chain acyl-lysine modifications to be clearly identified in complex lysates. Immonium ions can also be used to validate novel acyl-modifications; in this study we report the first examples of 3-hydroxylpimelyl-lysine modification and validate them using immonium ions. Overall these results solidify the use of the immonium ion as a marker for acyl-lysine modifications in complex proteomic datasets. Statement of SignificanceAcyl-lysine modifications come in a variety of elemental compositions. There is increasing evidence that these modifications can have a functional effect on protein and are present in proteomes across all domains of life. Here we describe a new method that can allow for more confident identification of acyl modifications in proteomes by utilizing the immonium ion of these modifications. Our utilization of these ions allows for more comprehensive insight into the role of acyl modifications at the systems level.

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Protein Acetylation in Bacteria

Cited by 114 publications

References 109 publications

The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12

The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12

The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase

Leveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets

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