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Volume 7, Issue 6, December Issue - 2019, Pages:521-528

Authors: Bassam Oudh Al johny
Abstract: Post-translational changes including acetylation are universal phenomena in protein and occur in both prokaryotes and eukaryotes. The process of post-translation modifications is initiated by phosphorylation of the acetyl group through an enzymatic pathway using the acetyltransferase enzyme. It is believed that several processes such as cellular process, DNA replication, bacterial chemotaxis and metabolism depend on protein acetylation. It is worth to say that protein acetylation is extremely important in bacterial virulence, as diverse factors have been involved in bacterial virulence. Therefore, current review article summarizes the role of protein acetylation, its mechanism, techniques of acetylome study and its regulation, which may help in the in-depth understanding of bacterial virulence. 
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Full Text: 1 Introduction There are enzymatic and non-enzymatic mechanisms for the regulation of acetylation as manifested in Figure 1. It is believed that during the enzymatic pathway of eN-acetylation the e-amino group of a deprotonated lysine received acetyl group from acetyl COA that is catalyzed by lysine acetyltransferase (KAT) enzyme (Jie Ren et al., 2017). There are three major categories of KATs which are (i) the Gcn5 which belongs to the family N-acetyltransferase (GNAT) (so-called after the Gcn5 protein of yeast), (ii) the family MYST (called after human MOZ, yeast Ybf2/Sas3, yeast Sas2, and human Tip60), and (iii) the p300/CBP family (named after human hp300 and hCBP). The family of GNAT is available in all sectors of life and MYST and p300/CBP are recognized merely in eukaryotic cells (Starai & Escalante-Semerena, 2004; Garrity et al., 2007; Wang et al., 2010). It is reported that different kind of KATs belonging to the same GNAT family have been known from several microorganisms (Thao & Escalante-Semerena., 2011). 2 Protein Acetylation Mechanism in Bacteria Among different KATs, acetyltransferase Pat of the Salmonella enterica protein was the most studied and first recognized protein (Garrity et al., 2007; Sang et al., 2016). In E.coli it has been reported that during a nonenzymatic mechanistic pathway the deprotonated lysine e-amino group received an acetyl group from acetyl phosphate (AcP) (Weinert et al., 2013; Kuhn et al., 2014). AcP is considered as the high energy intermediate where a phosphoryl moiety is best owing in a two component signal transduction process to particular response regulators (Lukat et al., 1992). The yfiQ deletion mutant has less effects on acetylation levels, while increasing AcP concentration will further increase the global acetylation (Weinert et al., 2013; Kuhn et al., 2014). In regulating the bacterial physiological progression, acetylation due to enzyme is more significant as compared to acetylation due to AcP, because there is a direct relation between AcP and global acetylation concentration, while the negligible effect on global acetylation due to the deletion of vfiQ mutant. Enzymatically the lysine deacetylases (KDACs) can remove the acetyl group. KDACs have been classified into two groups and four classes, which are as (i) Class III based on NAD+ dependent sirtuin family (Blander & Guarente, 2014) and (ii) Classes I, II, and IV based on zinc-dependent Rpd3/Hda1 family (Yang & Seto., 2008). NAD+-dependent Cob B, was initially reported in S. enterica and was largely studied in various bacterial strains (Starai et al.,2002), however, its homologs were also identified in other species of bacteria such as Bacillus subtilis (Gardner & Escalante-Semerena.,2009), Streptomyces coelicolor (Mikulik et al., 2012), E. coli (Zhao et al., 2004), and Rhodopseudomonas palustris (Crosby et al.,2010). Usually, CobB substrates take part in various cellular processes and giving no importance for AcP-dependent or acetylated lysines depends on Pat (AbouElfetouh et al., 2015). For instance, the CobB possibly deacetylate the AcP and Pat dependent acetylated DNA (Zhang  et al.,2016) and was believed that in E. coli the CobB was merelythe histone deacetylase (HDAC). The research group of Tu et al. (2015) recognized the discovery of deacetylase YcgCin in E. coli which was related to the hydrolase family of serine. However, it had  non-significant homology with KDACs which were not dependent on Zn2+ or NAD+ known KDACs. In E. coli the YcgC have different catalyzed pathway for substrates deacetylases as well as different substrate as compared to CobB-regulated acetylated proteins. The auto ADP-ribosyltransferase and deacetylase potential of MSMEG_4620 was established in Mycobacterium smegmatis with the identification of MSMEG_4620 and SIRT4 homologue (Tan et al., 2015). Therefore, this study will open new ideas and explore the relationship between deacetylases and acetylation factors as well as novel bacterial deacetylases knowledge. 3 Protein Acetylome in Bacteria The use of antibodies in the acetylated peptides with great specificity involved in immunoprecipitation which largely increases the ability to identify more acetylated lysine residues (Wang et al.,2010; Chen et al., 2012). In this method the quality and amount of acetylated proteins largely depend on various factors including immunoprecipitation efficacy, anti-acetyllysine antibodies quality, strategies established for the fractionation of various sample, mass spectrometry (MS) techniques, software packages used for data acquisition (Mischerikow &Heck.,2011). Acetylome was the first published protein discovered in bacteria. After that, Yu et al. (2008) applied a hyphenated technique comprising of affinity immune-separation technique coupled with nano HPLC/MS/MS by using an anti-acetyllysine antibody for the identification of 125 acetylated sites among 85 different proteins in E. coli. Furthermore, E. coli comprises of 79 proteins where 81 phosphorylation sites and number of acetylated proteins was found to analogous (Macek et al., 2008). A vast detail on the Protein acetylome are available for different bacterial species (Hentchel & Escalante-Semerena, 2015). Most noticeable literature on the acetylome of pathogens are available on Spiroplasma eriocheiris (Liu et al., 2014; Xie et al., 2015; Meng et al., 2016), Porphyromonas gingivalis (Butler et al.,2015), Vibrio parahemolyticus (Pan et al.,2014), and Pseudomonas aeruginosa (Ouidir et al.,2015) and this help in the in-depth understanding of acetylated regulation bacterial virulence. The V. parahemolyticus, 517 succinyllysine sites (26.7%) on 288 proteins (44.9%) was also reported to acetylate (Pan et al., 2015), proposing the general intersection between acetylation and other PTMs enrich levels of regulation and are operating in different cellular practices. There are approximately 2000–5000 proteins in a typical bacterial proteome and among all of them 5% acetylated (Kim &Yang. 2011), but the acetylated proteins percentage is variable ranging from 2-45% depends on the bacterial species. It is also reported that the acetylated proteins is diverse in the same bacterium under different environments and laboratory conditions displayed no satisfactory replicability (Yu et al., 2008; Zhang et al., 2009). This phenomenon required high-throughput analyses to authenticate the experimental data, by avoiding any fabricated outcomes, and to validate the physiological significance in vivo of the acetylated proteins. 4 Mass spectrometry opens avenues for acetylation research Mass spectrometry studies in proteomic are one of the most emerging analysis techniques to determined acetylation. This practice have been applied either for global studies related to target protein analysis for cellular acetylomes determination under diverse conditions in diverse microbial species. In target analyses for instance, protein purification involved the purification of sample through immune affinity methods, and then digested by protease and fragmentation analysis was carried out by Mass spectrometry of the resultant peptides leads to the identification of acetylated sites (Barak & Eisenbach, 2001; Starai et al., 2002; Zhou et al., 2015; Zhang et al., 2016). Under particular conditions protein extraction is the initial step for the acetylome studies, in this the entire proteome digested by enzymatic action and then mass spectrometry was used for the analysis of acetylated peptides enriched with anti-acetyl-lysine antibodies. The degree of peptides acetylation depends on the specificity and affinity of antibodies and sensitivity of mass spectrometer. Many methods have been developed in order to increase the isolation efficiency of peptides, reduction in certain acetylation motifs applied several antibodies to captured acetyl-peptide (Macek et al., 2008; Crosby et al., 2010; Lee et al., 2013; Pan et al., 2014; AbouElfetouh et al ., 2015; Tu et al., 2015; Meng et al., 2016). Many procedure and protocols have been developed for isolation but still only between 25 to 40% isolation has been reported. Therefore, it is utmost to enhanced and improve the isolation efficacy and determination of acetylation sites in various protein (Mouslim et al., 2004; Meng et al., 2016). Lower abundance proteins identification might be improved by fractionations of peptides before capturing the acetyl-peptide, which in turn help to reduce the complexities originated in peptide identifications (AbouElfetouh et al., 2015; Xie et al., 2015; Pan et al., 2015; Zhang et al., 2016; Meng et al., 2016). Improvement in the proteome sectors might be improved with the improvement, development, and sensitivity of mass spectrometer. 4.1 Use of mass spectrometry for in-vivo studies for functional authentications Substitutions of amino acid such as Gln, Arg, and Ala and removal of protein i.e., KATs or sirtuins relied during the investigation of in-vivo studies. The impact of KATs or KDACs/sirtuins to a specific process of acetylation is usually evaluated through deletions, and the function of a specific site can be assessing through point mutants and side chain contribution through Ala substitutions. The side chain contribution is assessed by Ala substation Arg substitutions domain the positive charge without acetylation, so they copy the unacetylated state. The acetylated forms can be mimic from Gln substitutions, because of neutral charge and inability to acetylate (Kamieniarz & Schneider., 2009). These mutations might play an important role in acetylation at specific sites, for instance, during in vivo studies the influence of mutations on the function of protein can be assessed by reporter assays, such as transcriptional fusions to a transcription factors target genes. It is worth to say that data analysis can be performed with extreme cautions because the side chains are chemically different in acetyllysine, Lys, Gln, Ala, and Arg, and with the induction of other amino acid to the protein chain the whole properties such as secondary structure and stability of the protein chain might be greatly affect (Zhang et al., 2013). Furthermore, mutation that leads in a loss-of function phenotype will possibly measure the incorrect contribution of acetylation. Most of the sites is 1% acetylated so will not reproduced in vivo stoichiometry because the stoichiometry of a mutation is 100% (Barak & Eisenbach., 2001; Meyer et al.,2016; Weinert et al., 2017). The physiological effect of a specific acetylation is necessary to investigate in order to exactly determine the stoichiometry of acetylation for the loss-of-function mutations in brief the substation is very important in determining the role of acetylation in vivo studies, but still it is worthwhile that efficacy of such substation is variable in different proteins. For instance, Gln substitutions were found to recapitulate the impact of acetylation in vitro (Simonsson et al., 2006; Wang & Hayes, 2008) and in vivo studies in eukaryotic (Hecht  et al.,1995; Li et al.,2002; Yang et al.,2008), but it is different for different proteins (Sun et al.,2007; Kawai et al.,2011;). Any in vivo results can be supported by integration with in vitro studies. 4.2 Observing in vivo studies through in vitro verifications In vitro studies are helpful in order to examine the in-depth mechanism of acetylation (Barak & Eisenbach., 2001; Thao et al., 2010;Okanishi et al., 2013; Kuhn et al., 2014; Liao et al., 2014; Vergnolle et al., 2016; Song et al., 2016). Acetyl phosphate or acetyl-CoA leads to acetylation in substrates that go through nonenzymatic acetylation. In the in vitro studies, a specific target is acetylated by the purified KATs and deacetylate by deacetylases. Mass spectrometer and radioactive acetyl derivatives addition or deletion can be used to determine the specific sites for acetylation. During in vitro studies the promiscuous in acetylases are often created problem in analysis interpretation (Barak & Eisenbach., 2001), However, this problem could be resolved during in vitro studies by using the Gln substitution mutants isolated from E. coli (Sun et al., 2016; Qin et al., 2016), Interestingly a proteins acetylation can also be achieved through coevolved tRNA-tRNA synthetase pair present in E. coli strain which inserts acetyllysine after amber codon is read (Neumann et al., 2009), as a result, 100% site-specific acetylated protein used in biochemical analyses of in vitro function, till-date no explanatory data are available for the in vivo acetylation. The use of mass spectrometry in vitro and in vivo studies may potentially helped in understating the site-specific acetylation in various proteins. 5 Bacterial virulence regulation through acetylation of protein Various acetylomes of bacterial pathogens has been determined various virulence, but whether the virulence factor is acetylated or not is an area of curiosity. For a curiosity several studies have been put forward, which result that virulence is regulated by the acetylation of protein. 5.1 Bacterial Chemotaxis is regulated by Acetylation In 2004 CheY was identified and explored that it has an important functions in the excitatory response of bacterial chemotaxis (Barak et al., 2004; Kuhn et al., 2014). The lysine acetylated residues has adverse impacts such as aspartyl residue phosphorylation, rotational direction of flagellar, flagellar switch complex formation with kinase CheA, phosphatase CheZ, and the switch protein Film (Barak & Eisenbach, 2001; Barak & Eisenbach., 2004; Yan et al., 2008; Li et al.,2010; Liarzi et al., 2010). It is believed that acetylation is very important for the proper performance of CheY, therefore, acetylation is responsible for the regulation of bacterial virulence. The CheY acetylation has been studied in nonpathogenic strains of E. coli, therefore, it can be suggest that cheY acetylation might have a positive role in bacterial virulence. The involvement of CheY acetylation in bacterial virulence has been also reported in Campylobacter jejuni and Listeria monocytogenes (Yao et al., 1997; Dons et al., 2004). Similarly, involvement of RcsB in Salmonella and Erwinia amylovora virulence has been also reported by various researchers (Bereswill & Geider, 1997; Domínguez et al., 2004; Liao et al., 2014). Furthermore, acetylation is extremely important in the regulation of RcsB potential in E. coli (Thao et al., 2010), bacterial motility, lysine acetylation, impact on the biosynthesis of flagella and diminishing acid stress survival (Castaño et al., 2014). 5.2 Homeostasis of Acetylation process and its Influences on Bacterial Acid Resistance Typhimurium and S. enterica serovar are enteric pathogens that have strong resistance to pH and survive in stomach in the strong acidic medium of pH 2. These bacteria may also attack on other organs of the body such as liver, spleen and epithelium layer of intestine (Drecktrah et al., 2006). The transcriptional levels of pat and the genes Crp and CyaA encoded cyclic AMP receptor protein and adenylate cyclase and are down regulated due to the acidic environment as suggested from the transcriptome patterns. Higher survival rate and higher intracellular pH has been reported under acid stress conditions for the pat deletion mutant than the wild-type strain (Ren et al., 2015). The above discussion inferred that bacterial and other pathogenic virulence response to acidic environment is regulated by acetylation. It is concluded from the above discussion that acetylation is the key for regulating and contributing the bacterial, enteric and pathogenic virulence to acid stress and resistance.   Conflict of Interest The authors declare that there is no conflict of interest.

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