Post-translational modification of RNase R is regulated by stress-dependent reduction in the acetylating enzyme Pka (YfiQ)

Differential Abundance of Protein Acylation in Mycobacterium tuberculosis Under Exposure to Nitrosative Stress

BACKGROUND

Human macrophages generate antimicrobial reactive nitrogen species in response to infection by Mycobacterium tuberculosis (Mtb). Exposure to these redox-reactive compounds induces stress response in Mtb, which can affect posttranslational modifications (PTM).

METHODS

Here, we present the global analysis of the PTM acylation of Mtb proteins in response to a sublethal dose of nitrosative stress in the form of nitric oxide (NO) using label free quantification.

RESULTS

A total of 6437 acylation events were identified on 1496 Mtb proteins, and O-acylation accounted for 92.2% of the events identified, while 7.8% were N-acylation events. About 22% of the sites identified were found to be acylated by more than one acyl-group. Furthermore, the abundance of each acyl-group decreased as their molecular weight increased. Quantitative PTM analysis revealed differential abundance of acylation in proteins involved in stress response, iron ion homeostasis, growth, energy metabolism, and antimicrobial resistance (AMR) induced by nitrosative stress over time.

CONCLUSIONS

The results reveal a potential role of Mtb protein acylation in the bacterial stress responses and AMR. To our knowledge, this is the first report on global O-acylation profile of Mtb in response to NO. This will significantly improve our understanding of the changes in Mtb acylation under nitrosative stress, highly relevant for global health.

Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa

Bacteria employ a myriad of regulatory mechanisms to adapt to the continuously changing environments that they face. They can, for example, use post-translational modifications, such as Nε-lysine acetylation, to alter enzyme activity. Although a lot of progress has been made, the extent and role of lysine acetylation in many bacterial strains remains uncharted. Here, we applied stable isotope labeling by amino acids in cell culture (SILAC) in combination with the immunoprecipitation of acetylated peptides and LC-MS/MS to measure the first Pseudomonas aeruginosa PAO1 acetylome, revealing 1076 unique acetylation sites in 508 proteins. Next, we assessed interstrain acetylome differences within P. aeruginosa by comparing our PAO1 acetylome with two publicly available PA14 acetylomes, and postulate that the overall acetylation patterns are not driven by strain-specific factors. In addition, the comparison of the P. aeruginosa acetylome to 30 other bacterial acetylomes revealed that a high percentage of transcription related proteins are acetylated in the majority of bacterial species. This conservation could help prioritize the characterization of functional consequences of individual acetylation sites.

Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism

The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.

An emerging field: Post-translational modification in microbiome

Post-translational modifications (PTMs) play an essential role in most biological processes. PTMs on human proteins have been extensively studied. Studies on bacterial PTMs are emerging, which demonstrate that bacterial PTMs are different from human PTMs in their types, mechanisms and functions. Few PTM studies have been done on the microbiome. Here, we reviewed several studied PTMs in bacteria including phosphorylation, acetylation, succinylation, glycosylation, and proteases. We discussed the enzymes responsible for each PTM and their functions. We also summarized the current methods used to study microbiome PTMs and the observations demonstrating the roles of PTM in the microbe-microbe interactions within the microbiome and their interactions with the environment or host. Although new methods and tools for PTM studies are still needed, the existing technologies have made great progress enabling a deeper understanding of the functional regulation of the microbiome. Large-scale application of these microbiome-wide PTM studies will provide a better understanding of the microbiome and its roles in the development of human diseases.

How hydrolytic exoribonucleases impact human disease: Two sides of the same story

RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.

Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions

Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5 UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.

The essential role of mRNA degradation in understanding and engineering E. coli metabolism

Metabolic engineering strategies are crucial for the development of bacterial cell factories with improved performance. Until now, optimal metabolic networks have been designed based on systems biology approaches integrating large-scale data on the steady-state concentrations of mRNA, protein and metabolites, sometimes with dynamic data on fluxes, but rarely with any information on mRNA degradation. In this review, we compile growing evidence that mRNA degradation is a key regulatory level in E. coli that metabolic engineering strategies should take into account. We first discuss how mRNA degradation interacts with transcription and translation, two other gene expression processes, to balance transcription regulation and remove poorly translated mRNAs. The many reciprocal interactions between mRNA degradation and metabolism are also highlighted: metabolic activity can be controlled by changes in mRNA degradation and in return, the activity of the mRNA degradation machinery is controlled by metabolic factors. The mathematical models of the crosstalk between mRNA degradation dynamics and other cellular processes are presented and discussed with a view towards novel mRNA degradation-based metabolic engineering strategies. We show finally that mRNA degradation-based strategies have already successfully been applied to improve heterologous protein synthesis. Overall, this review underlines how important mRNA degradation is in regulating E. coli metabolism and identifies mRNA degradation as a key target for innovative metabolic engineering strategies in biotechnology.

Regulation of Bacterial Ribonucleases

Ribonucleases (RNases) are essential for almost every aspect of RNA metabolism. However, despite their important metabolic roles, RNases can also be destructive enzymes. As a consequence, cells must carefully regulate the amount, the activity, and the localization of RNases to avoid the inappropriate degradation of essential RNA molecules. In addition, bacterial cells often must adjust RNase levels as environmental situations demand, also requiring careful regulation of these critical enzymes. As the need for strict control of RNases has become more evident, multiple mechanisms for this regulation have been identified and studied, and these are described in this review. The major conclusion that emerges is that no common regulatory mechanism applies to all RNases, or even to a family of RNases; rather, a wide variety of processes have evolved that act on these enzymes, and in some cases, multiple regulatory mechanisms can even act on a single RNase. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Trans-acting regulators of ribonuclease activity

RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.

Trans-acting regulators of ribonuclease activity

RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.

Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions

Post-translational modifications (PTM) decorate proteins to provide functional heterogeneity to an existing proteome. The large number of known PTMs highlights the many ways that cells can modify their proteins to respond to diverse stimuli. Recently, PTMs have begun to receive increased interest because new sensitive proteomics workflows and structural methodologies now allow researchers to obtain large-scale, in-depth and unbiased information concerning PTM type and site localization. However, few PTMs have been extensively assessed for functional consequences, leaving a large knowledge gap concerning the inner workings of the cell. Here, we review understanding of N-𝜀-lysine acetylation in bacteria, a PTM that was largely ignored in bacteria until a decade ago. Acetylation is a modification that can dramatically change the function of a protein through alteration of its properties, including hydrophobicity, solubility, and surface properties, all of which may influence protein conformation and interactions with substrates, cofactors and other macromolecules. Most bacteria carry genes predicted to encode the lysine acetyltransferases and lysine deacetylases that add and remove acetylations, respectively. Many bacteria also exhibit acetylation activities that do not depend on an enzyme, but instead on direct transfer of acetyl groups from the central metabolites acetyl coenzyme A or acetyl phosphate. Regardless of mechanism, most central metabolic enzymes possess lysines that are acetylated in a regulated fashion and many of these regulated sites are conserved across the spectrum of bacterial phylogeny. The interconnectedness of acetylation and central metabolism suggests that acetylation may be a response to nutrient availability or the energy status of the cell. However, this and other hypotheses related to acetylation remain untested.

Bacterial ribonucleases and their roles in RNA metabolism

Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.

Post-Transcriptional Regulation of tRNA Pools To Govern the Central Dogma: A Perspective

Since their initial discovery, tRNAs have risen from sole adapter molecules during protein synthesis to pivotal modulators of gene expression. Through their many interactions with tRNA-associated protein factors, they play a central role in maintaining cell homeostasis, especially regarding the fine-tuning in response to a rapidly changing cellular environment. Here, we provide a perspective on current tRNA topics with a spotlight on the regulation of post-transcriptional shaping of tRNA molecules. First, we give an update on aberrant structural features that a yet functional fraction of mitochondrial tRNAs can exhibit. Then, we outline several aspects of the regulatory contribution of ribonucleases with a focus on tRNA processing versus tRNA elimination. We close with a comment on the possible consequences for the intracellular examination of nascent tRNA precursors regarding respective processing factors that have been shown to associate with the tRNA transcription machinery in alternative moonlighting functions.

Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli

Posttranslational modifications, such as Nε-lysine acetylation, regulate protein function. Nε-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an Nε-lysine residue of a protein. The enzymatic mechanism uses Nε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to Nε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Escherichia coli Here, we demonstrate the existence of 4 additional E. coli KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria.IMPORTANCENε-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, Nε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an E. coli strain that lacked both known acetylation mechanisms to identify four new Nε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.

Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA

3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.

[Role of SMU.2055 gene in regulating acid resistance of Streptococcus mutans UA159]

OBJECTIVE

To evaluate the effect of SMU.2055 gene on acid resistance of Streptococcus mutans.

METHODS

A SMU.2055-dificient mutant strain of S. mutans was constructed using homologous recombination technique. The growth of the wild-type and mutant strains was monitored in both normal and acidic conditions. The lethal pH level, glycolysis, proton permeability, cell permeability and biofilm formation of the two strains were compared.

RESULTS

PCR and sequence analyses verified the successful construction of the SMU.2055-dificient mutant strain. The growth and biofilm formation capacity of the mutant strain were obviously lowered in both normal and acidic conditions. The mutant strain also showed increased lethal pH level, proton permeability, and cell permeability with impaired H⁺-ATPase activity in acidic conditions, but its minimum glycolytic pH remained unaffected.

CONCLUSION

The SMU.2055-deficient S. mutans mutant exhibits a lowered acid resistance, which affects the growth, lethal pH, proton permeability, H⁺-ATPase activity, cell permeability and biofilm formation but not the minimum glycolytic pH of the mutant strain.

[Role of SMU.2055 gene in regulating acid resistance of Streptococcus mutans UA159]

OBJECTIVE

To evaluate the effect of SMU.2055 gene on acid resistance of Streptococcus mutans.

METHODS

A SMU.2055-dificient mutant strain of S. mutans was constructed using homologous recombination technique. The growth of the wild-type and mutant strains was monitored in both normal and acidic conditions. The lethal pH level, glycolysis, proton permeability, cell permeability and biofilm formation of the two strains were compared.

RESULTS

PCR and sequence analyses verified the successful construction of the SMU.2055-dificient mutant strain. The growth and biofilm formation capacity of the mutant strain were obviously lowered in both normal and acidic conditions. The mutant strain also showed increased lethal pH level, proton permeability, and cell permeability with impaired H+-ATPase activity in acidic conditions, but its minimum glycolytic pH remained unaffected.

CONCLUSION

The SMU.2055-deficient S. mutans mutant exhibits a lowered acid resistance, which affects the growth, lethal pH, proton permeability, H+-ATPase activity, cell permeability and biofilm formation but not the minimum glycolytic pH of the mutant strain.

Identification and characterization of two types of amino acid-regulated acetyltransferases in actinobacteria

One hundred and fifty GCN5-like acetyltransferases with amino acid-binding (ACT)-GCN5-related N-acetyltransferase (GNAT) domain organization have been identified in actinobacteria. The ACT domain is fused to the GNAT domain, conferring amino acid-induced allosteric regulation to these protein acetyltransferases (Pat) (amino acid sensing acetyltransferase, (AAPatA)). Members of the AAPatA family share similar secondary structure and are divided into two groups based on the allosteric ligands of the ACT domain: the asparagine (Asn)-activated PatA and the cysteine (Cys)-activated PatA. The former are mainly found in Streptomyces; the latter are distributed in other actinobacteria. We investigated the effect of Asn and Cys on the acetylation activity of Sven_0867 (SvePatA, from Streptomyces venezuelae DSM 40230) and Amir_5672 (AmiPatA, from Actinosynnema mirum strain DSM 43827), respectively, as well as the relationship between the structure and function of these enzymes. These findings indicate that the activity of PatA and acetylation level of proteins may be closely correlated with intracellular concentrations of Asn and Cys in actinobacteria. Amino acid-sensing signal transduction in acetyltransferases may be a mechanism that regulates protein acetylation in response to nutrient availability. Future work examining the relationship between protein acetylation and amino acid metabolism will broaden our understanding of post-translational modifications (PTMs) in feedback regulation.

Studying the Lysine Acetylation of Malate Dehydrogenase

Protein acetylation plays important roles in many biological processes. Malate dehydrogenase (MDH), a key enzyme in the tricarboxylic acid cycle, has been identified to be acetylated in bacteria by proteomic studies, but no further characterization has been reported. One challenge for studying protein acetylation is to get purely acetylated proteins at specific positions. Here, we applied the genetic code expansion strategy to site-specifically incorporate Nε-acetyllysine into MDH. The acetylation of lysine residues in MDH could enhance its enzyme activity. The Escherichia coli deacetylase CobB could deacetylate acetylated MDH, while the E. coli acetyltransferase YfiQ cannot acetylate MDH efficiently. Our results also demonstrated that acetyl-CoA or acetyl-phosphate could acetylate MDH chemically in vitro. Furthermore, the acetylation level of MDH was shown to be affected by carbon sources in the growth medium.

Protein Acetylation and Its Role in Bacterial Virulence

Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the protein acetyltransferase Pat, and nonenzymatically by metabolic intermediates (e.g., acetyl phosphate) in bacteria. Protein acetylation plays a role in bacterial chemotaxis, metabolism, DNA replication, and other cellular processes. Recently, accumulating evidence has suggested that protein acetylation might be involved in bacterial virulence because a number of bacterial virulence factors are acetylated. In this review, we summarize the progress in understanding bacterial protein acetylation and discuss how it mediates bacterial virulence.

Acetylation of Lysine 243 Inhibits the oriC Binding Ability of DnaA in Escherichia coli

DNA replication initiation is a central event in the cell cycle, and it is strictly controlled by multiple regulatory mechanisms. Our previous work showed that acetylation of residue lysine (K) 178 prevents DnaA from binding to ATP, which leads to the inhibition of DNA replication initiation. Here, we show that another residue, K243, is critical for DnaA full activity in vivo. K243 can be acetylated, and its acetylation level varies with cell growth. A homogeneous, recombinant DnaA that contains N^𝜀-acetyllysine at K243 (K243Ac) retained its ATP/ADP binding ability, but showed decreased binding activity to the oriC region. A DNase I footprinting assay showed that DnaA K243Ac failed to recognize DnaA boxes I3, C1, and C3, and, thus, it formed an incomplete initiation complex with oriC. Finally, we found that acetyl phosphate and the deacetylase CobB can regulate the acetylation level of K243 in vivo. These findings suggest that DnaA K243 acetylation disturbs its binding to low-affinity DnaA boxes, and they provide new insights into the regulatory mechanisms of DNA replication initiation.

Lysine acetylation regulates the activity of Escherichia coli pyridoxine 5'-phosphate oxidase

Nɛ-lysine acetylation is one of the most abundant post-translational modifications in eukaryote and prokaryote. Protein acetylome of Escherichia coli has been screened using mass spectrometry (MS) technology, and many acetylated proteins have been identified, including the pyridoxine 5'-phosphate oxidase (EcPNPOx), but the biological roles played by lysine acetylation in EcPNPOx still remain unknown. In this study, EcPNPOx was firstly overexpressed and purified, and two acetylated lysine residues were identified by the subsequent liquid chromatography-tandem mass spectrometry analysis. Site-directed mutagenesis analysis demonstrated that acetylated lysine residues play important roles in the enzymatic activity and enzymatic properties of the protein. EcPNPOx could be non-enzymatically acetylated by acetyl-phosphate and deacetylated by CobB in vitro. Furthermore, enzymatic activities of acetylated and deacetylated EcPNPOx were compared in vitro, and results showed that acetylation led to a decrease of its enzymatic activity, which could be rescued by CobB deacetylation. Taken together, our data suggest that CobB modulates the enzymatic activity of EcPNPOx in vitro.

A glimpse into the modulation of post-translational modifications of human-colonizing bacteria

Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.

The protein acyltransferase Pat post-transcriptionally controls HilD to repress Salmonella invasion

N-Lysine acylation is a post-translational modification important for both prokaryotic and eukaryotic cells to control a wide array of cellular functions. Here we demonstrate that the protein acyltransferase Pat regulates genes on Salmonella Pathogenicity Island 1 (SPI1) that are required for the invasion of the intestinal epithelium. Mutation of pat slightly increased spleen colonization by Salmonella in streptomycin-treated mice, with more of the pat mutant reaching the spleen than the wild type strain. Growth of Salmonella under specific conditions selectively induced expression of Pat, and deletion of pat increased SPI1 gene expression under the same growth conditions. In addition, over-expression of Pat repressed SPI1 expression and bacterial entry into epithelial cells. These results demonstrate that Salmonella invasion is negatively controlled by Pat. Regulation of the SPI1 central regulator HilD was essential for Pat to exert its effects. The control of HilD by Pat was through post-transcriptional mechanisms, moderately repressing hilD translation while significantly reducing HilD stability. Additionally, growth of Salmonella in the presence of histone deacetylases inhibitors reduced expression of SPI1 by affecting HilD stability, supporting the concept that altering the stability of this regulator is required for Pat to control Salmonella invasion.

Reversible acetylation on Lys501 regulates the activity of RNase II

RNase II, a 3' to 5' processive exoribonuclease, is the major hydrolytic enzyme in Escherichia coli accounting for ∼90% of the total activity. Despite its importance, little is actually known about regulation of this enzyme. We show here that one residue, Lys501, is acetylated in RNase II. This modification, reversibly controlled by the acetyltransferase Pka, and the deacetylase CobB, affects binding of the substrate and thus decreases the catalytic activity of RNase II. As a consequence, the steady-state level of target RNAs of RNase II may be altered in the cells. We also find that under conditions of slowed growth, the acetylation level of RNase II is elevated and the activity of RNase II decreases, emphasizing the importance of this regulatory process. These findings indicate that acetylation can regulate the activity of a bacterial ribonuclease.

Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress

Acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. Although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic acids (e.g., short-, medium-, and long-chain mono- and dicarboxylic aliphatics and aromatics) to modify a large suite of targets. Acetylation of biomolecules has been studied for decades within the context of histone-dependent regulation of gene expression and antibiotic resistance. It was not until the early 2000s that the connection between metabolism, physiology, and protein acetylation was reported. This was the first instance of a metabolic enzyme (acetyl coenzyme A [acetyl-CoA] synthetase) whose activity was controlled by acetylation via a regulatory system responsive to physiological cues. The above-mentioned system was comprised of an acyltransferase and a partner deacylase. Given the reversibility of the acylation process, this system is also referred to as reversible lysine acylation (RLA). A wealth of information has been obtained since the discovery of RLA in prokaryotes, and we are just beginning to visualize the extent of the impact that this regulatory system has on cell function.

Turnover of mRNAs is one of the essential functions of RNase E

RNase E is an essential bacterial endoribonuclease with a central role in processing tRNAs and rRNA, and turning over mRNAs. Previous studies in strains carrying mutations in the rne structural gene have shown that tRNA processing is likely to be an essential function of RNase E but have not determined whether mRNA turnover is also an essential function. To address this we selected extragenic suppressors of temperature-sensitive mutations in rne that cause a large increase in mRNA half-life at the non-permissive temperature. Fifteen suppressors were mapped to three different loci: relBE (toxin-antitoxin system); vacB (RNase R); and rpsA (ribosomal protein S1). Each suppressor class has the potential to interact with mRNA and each restores wild-type levels of mRNA turnover but does not reverse the minor defects in tRNA and rRNA processing. RelE toxin is especially interesting because its only known activity is to cleave mRNAs in the ribosomal A-site. The relBE suppressor mutations increase transcription of relE, and controlled overexpression of RelE alone was sufficient to suppress the rne ts phenotype. Suppression increased turnover of some major mRNAs (tufA, ompA) but not all mRNAs. We propose that turnover of some mRNAs is one of the essential functions of RNase E.

sRNA and mRNA turnover in Gram-positive bacteria

It is widely recognized that RNA degradation plays a critical role in gene regulation when fast adaptation of cell growth is required to respond to stress and changing environmental conditions. Bacterial ribonucleases acting alone or in concert with various trans-acting regulatory factors are important mediators of RNA degradation. Here, we will give an overview of what is known about ribonucleases in several Gram-positive bacteria, their specificities and mechanisms of action. In addition, we will illustrate how sRNAs act in a coordinated manner with ribonucleases to regulate the turnover of particular mRNA targets, and the complex interplay existing between the ribosome, the ribonucleases and RNAs.

A role for REP sequences in regulating translation

Repetitive extragenic palindromic (REP) sequences are highly structured elements found downstream of ∼500 genes in Escherichia coli that result in extensive stem-loop structures in their mRNAs. However, their physiological role has remained elusive. Here, we show that REP sequences can downregulate translation, but only if they are within 15 nt of a termination codon; a spacing of 16 nt has no effect, suggesting that the REP element acts to stall ribosome movement. Ribosome stalling leads to cleavage of the mRNA and induction of the trans-translation process. Using nrdAB as a model, we find that its regulation can be partially reversed by overexpression of RNA helicases and can be fully overcome upon UV stress, emphasizing the importance of this regulatory process. Since 50% of REP-associated genes have these elements within the critical 15 nt, these findings identify a regulatory mechanism with the potential to affect translation from a large number of genes.

How bacterial cells keep ribonucleases under control

Ribonucleases (RNases) play an essential role in essentially every aspect of RNA metabolism, but they also can be destructive enzymes that need to be regulated to avoid unwanted degradation of RNA molecules. As a consequence, cells have evolved multiple strategies to protect RNAs against RNase action. They also utilize a variety of mechanisms to regulate the RNases themselves. These include post-transcriptional regulation, post-translational modification, trans-acting inhibitors, cellular localization, as well as others that are less well studied. In this review, I will briefly discuss how RNA molecules are protected and then examine in detail our current understanding of the mechanisms known to regulate individual RNases.

Competition between Decapping Complex Formation and Ubiquitin-Mediated Proteasomal Degradation Controls Human Dcp2 Decapping Activity

mRNA decapping is a central step in eukaryotic mRNA decay that simultaneously shuts down translation initiation and activates mRNA degradation. A major complex responsible for decapping consists of the decapping enzyme Dcp2 in association with decapping enhancers. An important question is how the activity and accumulation of Dcp2 are regulated at the cellular level to ensure the specificity and fidelity of the Dcp2 decapping complex. Here, we show that human Dcp2 levels and activity are controlled by a competition between decapping complex assembly and Dcp2 degradation. This is mediated by a regulatory domain in the Dcp2 C terminus, which, on the one hand, promotes Dcp2 activation via decapping complex formation mediated by the decapping enhancer Hedls and, on the other hand, targets Dcp2 for ubiquitin-mediated proteasomal degradation in the absence of Hedls association. This competition between Dcp2 activation and degradation restricts the accumulation and activity of uncomplexed Dcp2, which may be important for preventing uncontrolled decapping or for regulating Dcp2 levels and activity according to cellular needs.

The role of RNase R in trans-translation and ribosomal quality control

Gene expression not only depends on the rate of transcription but is also largely controlled at the post-transcriptional level. Translation rate and mRNA decay greatly influence the final protein levels. Surveillance mechanisms are essential to ensure the quality of the RNA and proteins produced. Trans-translation is one of the most important systems in the quality control of bacterial translation. This process guarantees the destruction of abnormal proteins and also leads to degradation of the respective defective RNAs through the action of Ribonuclease R (RNase R). This exoribonuclease hydrolyzes RNAs starting from their 3' end. Besides its involvement in trans-translation, RNase R also participates in the quality control of rRNA molecules involved in ribosomal biogenesis. RNase R is thus emerging as a key factor in ensuring translation accuracy. This review focuses on issues related to the quality control of translation, with special emphasis on the role of RNase R.

The E. coli sirtuin CobB shows no preference for enzymatic and nonenzymatic lysine acetylation substrate sites

N^ε-lysine acetylation is an abundant posttranslational modification of thousands of proteins involved in diverse cellular processes. In the model bacterium Escherichia coli, the ε-amino group of a lysine residue can be acetylated either catalytically by acetyl-coenzyme A (acCoA) and lysine acetyltransferases, or nonenzymatically by acetyl phosphate (acP). It is well known that catalytic acCoA-dependent N^ε-lysine acetylation can be reversed by deacetylases. Here, we provide genetic, mass spectrometric, structural and immunological evidence that CobB, a deacetylase of the sirtuin family of NAD⁺-dependent deacetylases, can reverse acetylation regardless of acetyl donor or acetylation mechanism. We analyzed 69 lysines on 51 proteins that we had previously detected as robustly, reproducibly, and significantly more acetylated in a cobB mutant than in its wild-type parent. Functional and pathway enrichment analyses supported the hypothesis that CobB regulates protein function in diverse and often essential cellular processes, most notably translation. Combined mass spectrometry, bioinformatics, and protein structural data provided evidence that the accessibility and three-dimensional microenvironment of the target acetyllysine help determine CobB specificity. Finally, we provide evidence that CobB is the predominate deacetylase in E. coli.

Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation

The emerging view of N^ε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (PTM) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. This PTM is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme A (acCoA) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. Here, we provide genetic, mass spectrometric, biochemical and structural evidence that N^ε-lysine acetylation is an equally abundant and important PTM in bacteria. Applying a recently developed, label-free and global mass spectrometric approach to an isogenic set of mutants, we detected acetylation of thousands of lysine residues on hundreds of Escherichia coli proteins that participate in diverse and often essential cellular processes, including translation, transcription and central metabolism. Many of these acetylations were regulated in an acetyl phosphate (acP)-dependent manner, providing compelling evidence for a recently reported mechanism of bacterial N^ε-lysine acetylation. These mass spectrometric data, coupled with observations made by crystallography, biochemistry, and additional mass spectrometry showed that this acP-dependent acetylation is both non-enzymatic and specific, with specificity determined by the accessibility, reactivity and three-dimensional microenvironment of the target lysine. Crystallographic evidence shows acP can bind to proteins in active sites and cofactor binding sites, but also potentially anywhere molecules with a phosphate moiety could bind. Finally, we provide evidence that acP-dependent acetylation can impact the function of critical enzymes, including glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, and RNA polymerase.

The acetylation motif in AMP-forming Acyl coenzyme A synthetases contains residues critical for acetylation and recognition by the protein acetyltransferase pat of Rhodopseudomonas palustris

The AMP-forming acyl coenzyme A (acyl-CoA) synthetases are a large class of enzymes found in both anabolic and catabolic pathways that activate fatty acids to acyl-CoA molecules. The protein acetyltransferase (Pat) from Rhodopseudomonas palustris (RpPat) inactivates AMP-forming acyl-CoA synthetases by acetylating the ε-amino group of a conserved, catalytic lysine residue. In all of the previously described RpPat substrates, this lysine residue is located within a PX4GK motif that has been proposed to be a recognition motif for RpPat. Here, we report five new substrates for RpPat, all of which are also AMP-forming acyl-CoA synthetases. This finding supports the idea that Pat enzymes may have evolved to control the activity of this family of enzymes. Notably, RpPat did not acetylate the wild-type long-chain acyl-CoA synthetase B (RpLcsB; formerly Rpa2714) enzyme of this bacterium. However, a single amino acid change two residues upstream of the acetylation site was sufficient to convert RpLcsB into an RpPat substrate. The results of mutational and functional analyses of RpLcsB and RpPimA variants led us to propose PK/RTXS/T/V/NGKX2K/R as a substrate recognition motif. The underlined positions within this motif are particularly important for acetylation by RpPat. The first residue, threonine, is located 4 amino acids upstream of the acetylation site. The second residue can be S/T/V/N and is located two positions upstream of the acetylation site. Analysis of published crystal structures suggests that the side chains of these two residues are very close to the acetylated lysine residue, indicating that they may directly interact with RpPat.

Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase III modulator

Background

Ribonuclease III (RNase III) activity modulates hundreds of genes in Escherichia coli (E. coli). YmdB, a member of the macrodomain protein family, is one of known trans-acting regulators of RNase III activity; however, the significance of its regulatory role in specific bacterial cellular processes and related genes has not been determined. YmdB overexpression was used to model YmdB-induced RNase III inhibition in vivo, and microarray analysis identified gene targets and cellular processes related to RNase III inhibition.

Results

The expression of >2,000 E. coli genes was modulated by YmdB induction; 129 genes were strongly regulated, of which 80 have not been reported as RNase III targets. Of these, ten are involved in biofilm formation. Significantly, YmdB overexpression also inhibited biofilm formation via a process that is not uniquely dependent upon RNase III inhibition. Moreover, biofilm formation is interdependently regulated by RpoS, a known stress response regulator and biofilm inhibitor, and by YmdB.

Conclusions

This is the first global profile of target genes modulated by YmdB-induced RNase III inhibition in E. coli, and the data reveal a novel, hitherto unrecognized regulatory role for YmdB in biofilm modulation.

Ribosomes regulate the stability and action of the exoribonuclease RNase R

Ribonucleases play an important role in RNA metabolism. Yet, they are also potentially destructive enzymes whose activity must be controlled. Here we describe a novel regulatory mechanism affecting RNase R, a 3' to 5' exoribonuclease able to act on essentially all RNAs including those with extensive secondary structure. Most RNase R is sequestered on ribosomes in growing cells where it is stable and participates in trans-translation. In contrast, the free form of the enzyme, which is deleterious to cells, is extremely unstable, turning over with a half-life of 2 min. RNase R binding to ribosomes is dependent on transfer-messenger RNA (tmRNA)-SmpB, nonstop mRNA, and the modified form of ribosomal protein S12. Degradation of the free form of RNase R also requires tmRNA-SmpB, but this process is independent of ribosomes, indicating two distinct roles for tmRNA-SmpB. Inhibition of RNase R binding to ribosomes leads to slower growth and a massive increase in RNA degradation. These studies indicate a previously unknown role for ribosomes in cellular homeostasis.

Acetylome with structural mapping reveals the significance of lysine acetylation in Thermus thermophilus

Lysine acetylation in proteins has recently been globally identified in bacteria and eukaryotes. Even though acetylproteins are known to be involved in various cellular processes, its physiological significance has not yet been resolved. Using a proteomics approach in combination with immunoprecipitation, we identified 197 lysine acetylation sites and 4 N-terminal acetylation sites from 128 proteins in Thermus thermophilus HB8, an extremely thermophilic eubacterium. Our analyses revealed that identified acetylproteins are well conserved across all three domains of life and are mainly involved in central metabolism and translation. To characterize the functional significance further, we successfully mapped 172 acetylation sites on their 59 authentic and 54 homologous protein structures. Although the percentage of acetylation on ordered structures was higher than that of the disordered structure, no tendency of acetylation in T. thermophilus was detected in secondary structures. However, the acetylated lysine was situated near the negatively charged glutamic acid residues. In tertiary structure analyses, 58 sites of 103 acetylations mapped on 59 authentic structures of T. thermophilus were located within a considerable distance that can disrupt electrostatic interactions and hydrogen bonding networks on protein surfaces, demonstrating the physiological significance of the acetylation that can directly alter the protein structure. In addition, we found 16 acetylation sites related to Schiff base formation, ligand binding, and protein-RNA and protein-protein interactions that involve the potential function of the proteins. The structural mapping of acetylation sites provides new molecular insight into the role of lysine acetylation in the proteins.

Acetylation of the response regulator RcsB controls transcription from a small RNA promoter

Nε-lysine acetylation was recently discovered on many bacterial proteins that function in diverse cellular processes. Thus, many questions remain unanswered. For example, what mechanisms regulate lysine acetylation? Does acetylation affect physiology? To help answer these questions, we studied the Escherichia coli response regulator and transcription factor RcsB, which is reported to be acetylated in vitro. To characterize RcsB acetylation, we monitored transcription from the rprA promoter, which requires RcsB. The conventional view is that RcsB is activated by phosphorylation through either the Rcs phosphorelay or acetyl phosphate. We affirmed that rprA transcription requires phosphorylated RcsB and showed that acetyl-phosphate (AcP) is a phosphoryl group donor to RcsB. However, a mutant that accumulates AcP (ackA) exhibited a reduction in rprA transcription instead of the predicted increase. rprA transcription also diminished in the cobB mutant, which lacks the only known E. coli protein deacetylase. This suggests the existence of an inhibitory mechanism that involves lysine acetylation, a supposition supported by the observation that RcsB isolated from the ackA or cobB mutant was hyperacetylated. Finally, we used a genetic approach to identify an AckA- and CobB-sensitive lysine (Lys-154) that controls RcsB activity. We propose that acetylation inhibits RcsB activity and that some of this inhibition acts through the acetylation of Lys-154.

Licensing and due process in the turnover of bacterial RNA

RNA enables the material interpretation of genetic information through time and in space. The creation, destruction and activity of RNA must be well controlled and tightly synchronized with numerous cellular processes. We discuss here the pathways and mechanism of bacterial RNA turnover, and describe how RNA itself modulates these processes as part of decision-making networks. The central roles of RNA decay and other aspects of RNA metabolism in cellular control are also suggested by their vulnerability to sabotage by phages; nonetheless, RNA can be used in defense against phage infection, and these processes are described here. Salient aspects of RNA turnover are drawn together to suggest how it could affect complex effects such as phenotypic diversity in populations and responses that persist for multiple generations.

Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation

Quality control of ribosomes is critical for cellular function since protein mistranslation leads to severe physiological consequences. We report evidence of a previously unrecognized ribosome quality control system in bacteria that operates at the level of 70S to remove defective ribosomes. YbeY, a previously unidentified endoribonuclease, and the exonuclease RNase R act together by a process mediated specifically by the 30S ribosomal subunit, to degrade defective 70S ribosomes but not properly matured 70S ribosomes or individual subunits. Furthermore, there is essentially no fully matured 16S rRNA in a ΔybeY mutant at 45°C, making YbeY the only endoribonuclease to be implicated in the critically important processing of the 16S rRNA 3' terminus. These key roles in ribosome quality control and maturation indicate why YbeY is a member of the minimal bacterial gene set and suggest that it could be a potential target for antibacterial drugs.

Structural insights into the substrate specificity of the Rhodopseudomonas palustris protein acetyltransferase RpPat: identification of a loop critical for recognition by RpPat

Lysine acetylation is a post-translational modification that is important for the regulation of metabolism in both prokaryotes and eukaryotes. In bacteria, the best studied protein acetyltransferase is Pat. In the purple photosynthetic bacterium Rhodopseudomonas palustris, at least 10 AMP-forming acyl-CoA synthetase enzymes are acetylated by the Pat homologue RpPat. All bona fide RpPat substrates contain the conserved motif PX(4)GK. Here, we show that the presence of such a motif is necessary but not sufficient for recognition by RpPat. RpPat failed to acetylate the methylmalonyl-CoA synthetase of this bacterium (hereafter RpMatB) in vivo and in vitro, despite the homology of RpMatB to known RpPat substrates. We used RpMatB to identify structural determinants that are recognized by RpPat. To do this, we constructed a series of RpMatB chimeras that became substrates of RpPat. In such chimeras, a short region (11-25 residues) of RpMatB located >20 residues N-terminal to the acetylation site was replaced with the corresponding sequences from other AMP-forming acyl-CoA synthetases that were known RpPat substrates. Strikingly, the enzymatic activity of RpMatB chimeras was regulated by acetylation both in vitro and in vivo. Crystal structures of two of these chimeras showed that the major difference between them and wild-type RpMatB was within a loop region ∼23 Å from the acetylation site. On the basis of these results, we suggest that RpPat likely interacts with a relatively large surface of its substrates, in addition to the PX(4)GK motif, and that RpPat probably has relatively narrow substrate specificity.

Transfer-messenger RNA-SmpB protein regulates ribonuclease R turnover by promoting binding of HslUV and Lon proteases

RNase R, an important exoribonuclease involved in degradation of structured RNA, is subject to a novel mechanism of regulation. The enzyme is extremely unstable in rapidly growing cells but becomes stabilized under conditions of stress, such as stationary phase or cold shock. RNase R instability results from acetylation which promotes binding of tmRNA-SmpB, two trans-translation factors, to its C-terminal region. Here, we examine how binding of tmRNA-SmpB leads to proteolysis of RNase R. We show that RNase R degradation is due to two proteases, HslUV and Lon. In their absence, RNase R is stable. We also show, using an in vitro system that accurately replicates the in vivo process, that tmRNA-SmpB is not essential, but it stimulates binding of the protease to the N-terminal region of RNase R and that it does so by a direct interaction between the protease and SmpB which stabilizes protease binding. Thus, a sequence of events, initiated by acetylation of a single Lys residue, results in proteolysis of RNase R in exponential phase cells. RNase R in stationary phase or in cold-shocked cells is not acetylated, and thereby remains stable. Such a regulatory mechanism, dependent on protein acetylation, has not been observed previously in bacterial cells.

System-wide studies of N-lysine acetylation in Rhodopseudomonas palustris reveal substrate specificity of protein acetyltransferases

N-lysine acetylation is a posttranslational modification that has been well studied in eukaryotes and is likely widespread in prokaryotes as well. The central metabolic enzyme acetyl-CoA synthetase is regulated in both bacteria and eukaryotes by acetylation of a conserved lysine residue in the active site. In the purple photosynthetic α-proteobacterium Rhodopseudomonas palustris, two protein acetyltransferases (RpPat and the newly identified RpKatA) and two deacetylases (RpLdaA and RpSrtN) regulate the activities of AMP-forming acyl-CoA synthetases. In this work, we used LC/MS/MS to identify other proteins regulated by the N-lysine acetylation/deacetylation system of this bacterium. Of the 24 putative acetylated proteins identified, 14 were identified more often in a strain lacking both deacetylases. Nine of these proteins were members of the AMP-forming acyl-CoA synthetase family. RpPat acetylated all nine of the acyl-CoA synthetases identified by this work, and RpLdaA deacetylated eight of them. In all cases, acetylation occurred at the conserved lysine residue in the active site, and acetylation decreased activity of the enzymes by >70%. Our results show that many different AMP-forming acyl-CoA synthetases are regulated by N-lysine acetylation. Five non-acyl-CoA synthetases were identified as possibly acetylated, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Rpa1177, a putative 4-oxalocrotonate tautomerase. Neither RpPat nor RpKatA acetylated either of these proteins in vitro. It has been reported that Salmonella enterica Pat (SePat) can acetylate a number of metabolic enzymes, including GAPDH, but we were unable to confirm this claim, suggesting that the substrate range of SePat is not as broad as suggested previously.