Only Acyl Carrier Protein 1 (AcpP1) Functions in Pseudomonas aeruginosa Fatty Acid Synthesis

A Nonessential Sfp-Type Phosphopantetheinyl Transferase Contributes Significantly to the Pathogenicity of Ralstonia solanacearum

4'-Phosphopantetheinyl transferases (PPTases) play important roles in the posttranslational modifications of bacterial carrier proteins, which are involved in various metabolic pathways. Here, we found that RsacpS and RspcpS encoded a functional AcpS-type and Sfp-type PPTase, respectively, in Ralstonia solanacearum GMI1000, and both are capable of modifying R. solanacearum AcpP1, AcpP2, AcpP3, and AcpP5 proteins. RspcpS is located on the megaplasmid, which does not affect strain growth and fatty acid synthesis but significantly contributes to the virulence of R. solanacearum and preferentially participates in secondary metabolism. We found that deletion of RspcpS did not affect the abilities of cellulose degradation, biofilm formation, and resistance to NaCl, sodium dodecyl sulfate, and H2O2 and attenuated R. solanacearum pathogenicity only in the assay of soil-drenching infection but not stem injection of tomato. It is hypothesized that RsPcpS plays a role in cell viability in complex environments and in the process during which the strain recognizes and approaches plants. These results suggest that both RsAcpS and RsPcpS may be potential targets for controlling diseases caused by R. solanacearum.

Integrated Transcriptomic and Proteomic Analysis of Nutritional Quality-Related Molecular Mechanisms in "Longjia", "Yangpao", and "Niangqing" Walnuts (Juglans sigillata)

In this study, "Longjia (LJ)" and "Yangpao (YP)"exhibited higher contents of major nutrients compared to "Niangqing (NQ)" walnuts. The combination of transcriptome and proteome by RNA sequencing and isotope labeling for relative and absolute quantification techniques provides new insights into the molecular mechanisms underlying the nutritional quality of the three walnut species. A total of 4146 genes and 139 proteins showed differential expression levels in the three comparison groups. Combined transcriptome and proteome analyses revealed that these genes and proteins were mainly enriched in signaling pathways such as fatty acid biosynthesis, protein processing in endoplasmic reticulum, and amino acid metabolism, revealing their relationship with the nutritional quality of walnut kernels. This study identified key genes and proteins associated with nutrient metabolism and accumulation in walnut kernels, provided transcriptomic and proteomic information on the molecular mechanisms of nutrient differences in walnut kernels, and contributed to the elucidation of the mechanisms of nutrient differences and the selection and breeding of high-quality walnut seedlings.

Protein Interaction Networks of Catalytically Active and Catalytically Inactive PqsE in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a human pathogen that relies on quorum sensing to establish infections. The PqsE quorum-sensing protein is required for P. aeruginosa virulence factor production and infection. PqsE has a reported enzymatic function in the biosynthesis of the quorum-sensing autoinducer called PQS. However, this activity is redundant because, in the absence of PqsE, this role is fulfilled by alternative thioesterases. Rather, PqsE drives P. aeruginosa pathogenic traits via a protein-protein interaction with the quorum-sensing receptor/transcription factor RhlR, an interaction that enhances the affinity of RhlR for target DNA sequences. PqsE catalytic activity is dispensable for interaction with RhlR. Thus, the virulence function of PqsE can be decoupled from its catalytic function. Here, we present an immunoprecipitation-mass spectrometry method employing enhanced green fluorescent protein-PqsE fusions to define the protein interactomes of wild-type PqsE and the catalytically inactive PqsE(D73A) variant in P. aeruginosa and their dependence on RhlR. Several proteins were identified to have specific interactions with wild-type PqsE while not forming associations with PqsE(D73A). In the ΔrhlR strain, an increased number of specific PqsE interactors were identified, including the partner autoinducer synthase for RhlR, called RhlI. Collectively, these results suggest that specific protein-protein interactions depend on PqsE catalytic activity and that RhlR may prevent proteins from interacting with PqsE, possibly due to competition between RhlR and other proteins for PqsE binding. Our results provide a foundation for the identification of the in vivo PqsE catalytic function and, potentially, new proteins involved in P. aeruginosa quorum sensing. IMPORTANCE Pseudomonas aeruginosa causes hospital-borne infections in vulnerable patients, including immunocompromised individuals, burn victims, and cancer patients undergoing chemotherapy. There are no effective treatments for P. aeruginosa infections, which are usually broadly resistant to antibiotics. Animal models show that, to establish infection and to cause illness, P. aeruginosa relies on an interaction between two proteins, namely, PqsE and RhlR. There could be additional protein-protein interactions involving PqsE, which, if defined, could be exploited for the design of new therapeutic strategies to combat P. aeruginosa. Here, we reveal previously unknown protein interactions in which PqsE participates, which will be investigated for potential roles in pathogenesis.

Of its five acyl carrier proteins, only AcpP1 functions in Ralstonia solanacearum fatty acid synthesis

The fatty acid synthesis (FAS) pathway is essential for bacterial survival. Acyl carrier proteins (ACPs), donors of acyl moieties, play a central role in FAS and are considered potential targets for the development of antibacterial agents. Ralstonia solanacearum, a primary phytopathogenic bacterium, causes bacterial wilt in more than 200 plant species. The genome of R. solanacearum contains five annotated acp genes, acpP1, acpP2, acpP3, acpP4, and acpP5. In this study, we characterized the five putative ACPs and confirmed that only AcpP1 is involved in FAS and is necessary for the growth of R. solanacearum. We also found that AcpP2 and AcpP4 participate in the polyketide synthesis pathway. Unexpectedly, the disruption of four acp genes (acpP2, acpP3, acpP4, and acpP5) allowed the mutant strain to grow as well as the wild-type strain, but attenuated the bacterium’s pathogenicity in the host plant tomato, suggesting that these four ACPs contribute to the virulence of R. solanacearum through mechanisms other than the FAS pathway.

Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity

Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.

Proteomics of Streptococcus mutans to Reveal the Antibiofilm Formation Mechanism of Ag/ZnO Nanocomposites with Light-Emitting Diode Radiation

Introduction

As a biofilm-associated disease, dental caries benefits from nanoparticle (NP)-based therapies. Streptococcus mutans (S. mutans) is a primary aetiologic agent for dental caries development. We successfully applied a synergistic therapy of Ag/ZnO nanocomposites combined with light-emitting diode (LED) radiation to inhibit S. mutans biofilms. However, the antibiofilm mechanism has not been fully elucidated, and little is known about the biofilm formation ability of bacteria that survive NP-based therapies.

Methods

This study explored the antibiofilm formation mechanism of this synergistic therapy by an integrated approach based upon proteomics.

Results

Synergistic therapy killed 99.8% of bacteria, while the biofilm formation ability of 0.2% surviving bacteria was inhibited. The proteomic responses of S. mutans to synergistic therapy were comprehensively characterized to unveil the mechanism of bacterial death and biofilm formation inhibition of the surviving bacteria. In total, 55 differentially expressed proteins (12 upregulated and 43 downregulated) were recorded. The bioinformatic analysis demonstrated that cellular integrity damage and regulated expression of structure-associated proteins were the main reasons for bacterial death. In addition, the proteomic study indicated the potential inhibition of metabolism in surviving bacteria and provided a biofilm-related network consisting of 17 differentially expressed proteins, explaining the multiantibiofilm formation actions. Finally, we reported and verified the inhibitory effects of synergistic therapy on sucrose metabolism and D-alanine metabolism, which disturbed the biofilm formation of surviving bacteria.

Conclusion

Our findings demonstrated that synergistic therapy killed most bacteria and inhibited the surviving bacteria from forming biofilms. Furthermore, the antibiofilm formation mechanism was revealed by proteomics analysis of S. mutans after synergistic therapy and subsequent metabolic studies. Our success may provide a showcase to explore the antibiofilm formation mechanism of NP-based therapies using proteomic studies.

Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus

Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.

Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis

The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.

Two Functional Fatty Acyl Coenzyme A Ligases Affect Free Fatty Acid Metabolism To Block Biosynthesis of an Antifungal Antibiotic in Lysobacter enzymogenes

In Lysobacter enzymogenes OH11, RpfB1 and RpfB2 were predicted to encode acyl coenzyme A (CoA) ligases. RpfB1 is located in the Rpf gene cluster. Interestingly, we found an RpfB1 homolog (RpfB2) outside this canonical gene cluster, and nothing is known about its functionality or mechanism. Here, we report that rpfB1 and rpfB2 can functionally replace EcFadD in the Escherichia coli fadD mutant JW1794. RpfB activates long-chain fatty acids (n-C_16:0 and n-C_18:0) for the corresponding fatty acyl-CoA ligase (FCL) activity in vitro, and Glu-361 plays critical roles in the catalytic mechanism of RpfB1 and RpfB2. Deletion of rpfB1 and rpfB2 resulted in significantly increased heat-stable antifungal factor (HSAF) production, and overexpression of rpfB1 or rpfB2 completely suppressed HSAF production. Deletion of rpfB1 and rpfB2 resulted in increased L. enzymogenes diffusible signaling factor 3 (LeDSF3) synthesis in L. enzymogenes Overall, our results showed that changes in intracellular free fatty acid levels significantly altered HSAF production. Our report shows that intracellular free fatty acids are required for HSAF production and that RpfB affects HSAF production via FCL activity. The global transcriptional regulator Clp directly regulated the expression of rpfB1 and rpfB2 In conclusion, these findings reveal new roles of RpfB in antibiotic biosynthesis in L. enzymogenes IMPORTANCE Understanding the biosynthetic and regulatory mechanisms of heat-stable antifungal factor (HSAF) could improve the yield in Lysobacter enzymogenes Here, we report that RpfB1 and RpfB2 encode acyl coenzyme A (CoA) ligases. Our research shows that RpfB1 and RpfB2 affect free fatty acid metabolism via fatty acyl-CoA ligase (FCL) activity to reduce the substrate for HSAF synthesis and, thereby, block HSAF production in L. enzymogenes Furthermore, these findings reveal new roles for the fatty acyl-CoA ligases RpfB1 and RpfB2 in antibiotic biosynthesis in L. enzymogenes Importantly, the novelty of this work is the finding that RpfB2 lies outside the Rpf gene cluster and plays a key role in HSAF production, which has not been reported in other diffusible signaling factor (DSF)/Rpf-producing bacteria.

Biological functions of nirS in Pseudomonas aeruginosa ATCC 9027 under aerobic conditions

Through our previous study, we found an up-regulation in the expression of nitrite reductase (nirS) in the isothiazolone-resistant strain of Pseudomonas aeruginosa. However, the definitive molecular role of nirS in ascribing the resistance remained elusive. In the present study, the nirS gene was deleted from the chromosome of P. aeruginosa ATCC 9027 and the resulting phenotypic changes of ΔnirS were studied alongside the wild-type (WT) strain under aerobic conditions. The results demonstrated a decline in the formations of biofilms but not planktonic growth by ΔnirS as compared to WT, especially in the presence of benzisothiazolinone (BIT). Meanwhile, the deletion of nirS impaired swimming motility of P. aeruginosa under the stress of BIT. To assess the influence of nirS on the transcriptome of P. aeruginosa, RNA-seq experiments comparing the ΔnirS with WT were also performed. A total of 694 genes were found to be differentially expressed in ΔnirS, of which 192 were up-regulated, while 502 were down-regulated. In addition, these differently expressed genes were noted to significantly enrich the carbon metabolism along with glyoxylate and dicarboxylate metabolisms. Meanwhile, results from RT-PCR suggested the contribution of mexEF-oprN to the development of BIT resistance by ΔnirS. Further, c-di-GMP was less in ΔnirS than in WT, as revealed by HPLC. Taken together, our results confirm that nirS of P. aeruginosa ATCC 9027 plays a role in BIT resistance along with biofilm formation and further affects several metabolic patterns under aerobic conditions.

Cardiolipin-Based Lipopolyplex Platform for the Delivery of Diverse Nucleic Acids into Gram-Negative Bacteria

Antibiotic resistance is a growing public health concern. Because only a few novel classes of antibiotics have been developed in the last 40 years, such as the class of oxazolidinones, new antibacterial strategies are urgently needed [1]. Nucleic acid-based antibiotics are a new type of antimicrobials. However, free nucleic acids cannot spontaneously cross the bacterial cell wall and membrane;consequently, their intracellular delivery into bacteria needs to be assisted. Here, we introduce an original lipopolyplex system named liposome polymer nucleic acid (LPN), capable of versatile nucleic acid delivery into bacteria. We characterized LPN formed with significant therapeutic nucleic acids: 11 nt antisense single-stranded (ss) DNA and double-stranded (ds) DNA of 15 and 95 base pairs (bp), 9 kbp plasmid DNA (pDNA), and 1,000 nt ssRNA. All these complexes were efficiently internalized by two different bacterial species, i.e., Escherichia coli and Pseudomonas aeruginosa, as shown by flow cytometry. Consistent with intracellular delivery, LPN prepared with an antisense oligonucleotide and directed against an essential gene, induced specific and important bacterial growth inhibition likely leading to a bactericidal effect. Our findings indicate that LPN is a versatile platform for efficient delivery of diverse nucleic acids into Gram-negative bacteria.

Characterization of 3-Oxacyl-Acyl Carrier Protein Reductase Homolog Genes in Pseudomonas aeruginosa PAO1

Bacterial 3-oxoacyl-ACP reductase (OAR) catalyzes the 3-oxoacyl-ACP reduction step in the fatty acid synthesis pathway. At least 12 genes in the Pseudomonas aeruginosa genome are annotated as OAR-encoding genes. In this study, we characterized the functions of these genes with biochemical and genetic techniques. With the exception of PA2967, which encodes FabG, an essential protein in fatty acid synthesis, only the PA4389 and PA4786 gene products had OAR activity, and the single deletion of these two genes reduced the ability of P. aeruginosa to produce several specific quorum-sensing (QS) signals. However, PA4389 and PA4786 do not have key roles in fatty acid synthesis. Moreover, although most OAR homologs had no OAR activity, some may function in carbon utilization. The PA3128 product may play a role in the TCA cycle, and PA0182 and PA1470 seem to be required for the utilization of several amino acids. The rest of the OAR homologs have no roles in carbon utilization, but the deletion of one of these genes might affect the production of virulence factors by P. aeruginosa. We conclude that most OAR homolog genes do not encode OAR enzymes, and that these proteins do not function in fatty acid synthesis.

Acyl Carrier Protein 3 Is Involved in Oxidative Stress Response in Pseudomonas aeruginosa

The human opportunistic pathogen Pseudomonas aeruginosa expresses three acyl carrier proteins (ACPs): AcpP, Acp1, and Acp3. The function of AcpP in membrane fatty acid synthesis (FAS) was confirmed recently, but the physiological roles of Acp1 and Acp3 remain unclear. To address this, we investigated the physiological role of Acp3 in P. aeruginosa. We found that expression of Acp3 dramatically increases in the log phase of cell growth and that its transcription is under the control of the QS regulators LasR and RhlR. Deletion of acp3 from P. aeruginosa strain PAO1 results in thicker biofilm formation, increased resistance of the strain to hydrogen peroxide, and higher persistence in a mouse infection model. Tandem affinity purification (TAP) experiments revealed several novel protein-binding partners of Acp3, including KatA, the major catalase in P. aeruginosa. Acp3 was found to repress the catalase activity of KatA and, consistent with inhibition by Acp3, less reactive oxygen species are present in the acp3 deletion strain. Overall, our study reveals that Acp3 has a distinct function from that of the canonical AcpP and may be involved in the oxidative stress response.

Acylated-acyl carrier protein stabilizes the Pseudomonas aeruginosa WaaP lipopolysaccharide heptose kinase

Phosphorylation of Pseudomonas aeruginosa lipopolysaccharide (LPS) is important for maintaining outer membrane integrity and intrinsic antibiotic resistance. We solved the crystal structure of the LPS heptose kinase WaaP, which is essential for growth of P. aeruginosa. WaaP was structurally similar to eukaryotic protein kinases and, intriguingly, was complexed with acylated-acyl carrier protein (acyl-ACP). WaaP produced by in vitro transcription-translation was insoluble unless acyl-ACP was present. WaaP variants designed to perturb the acyl-ACP interaction were less stable in cells and exhibited reduced kinase function. Mass spectrometry identified myristyl-ACP as the likely physiological binding partner for WaaP in P. aeruginosa. Together, these results demonstrate that acyl-ACP is required for WaaP protein solubility and kinase function. To the best of our knowledge, this is the first report describing acyl-ACP in the role of a cofactor necessary for the production and stability of a protein partner.

Role of Ttca of Citrobacter Werkmanii in Bacterial Growth, Biocides Resistance, Biofilm Formation and Swimming Motility

To screen, identify and study the genes involved in isothiazolone resistance and biofilm formation in Citrobacter werkmanii strain BF-6. A Tn5 transposon library of approximately 900 mutants of C. werkmanii strain BF-6 was generated and screened to isolate 1,2-benzisothiazolin-3-one (BIT) resistant strains. In addition, the tRNA 2-thiocytidine (32) synthetase gene (ttcA) was deleted through homologous recombination and the resulting phenotypic changes of the ΔttcA mutant were studied. A total of 3 genes were successfully identified, among which ΔttcA mutant exhibited a reduction in growth rate and swimming motility. On the other hand, an increase in biofilms formation in ΔttcA were observed but not with a significant resistance enhancement to BIT. This work, for the first time, highlights the role of ttcA gene of C. werkmanii strain BF-6 in BIT resistance and biofilm formation.

The Involvement of the Cas9 Gene in Virulence of Campylobacter jejuni

Campylobacter jejuni is considered as the leading cause of gastroenteritis all over the world. This bacterium has the CRISPR–cas9 system, which is used as a gene editing technique in different organisms. However, its role in bacterial virulence has just been discovered; that discovery, however, is just the tip of the iceberg. The purpose of this study is to find out the relationship between cas9 and virulence both phenotypically and genotypically in C. jejuni NCTC11168. Understanding both aspects of this relationship allows for a much deeper understanding of the mechanism of bacterial pathogenesis. The present study determined virulence in wild and mutant strains by observing biofilm formation, motility, adhesion and invasion, intracellular survivability, and cytotoxin production, followed by the transcriptomic analysis of both strains. The comparative gene expression profile of wild and mutant strains was determined on the basis of De-Seq transcriptomic analysis, which showed that the cas9 gene is involved in enhancing virulence. Differential gene expression analysis revealed that multiple pathways were involved in virulence, regulated by the CRISPR-cas9 system. Our findings help in understanding the potential role of cas9 in regulating the other virulence associated genes in C. jejuni NCTC11168. The findings of this study provide critical information about cas9's potential involvement in enhancing the virulence of C. jejuni, which is a major public health threat.