PvrA is a novel regulator that contributes to Pseudomonas aeruginosa pathogenesis by controlling bacterial utilization of long chain fatty acids

Long-chain fatty acids as nutrients for Gram-negative bacteria: stress, proliferation, and virulence

Bacteria use host-derived long-chain fatty acids (LCFAs) as nutrients, signals, and membrane building blocks. Although the impact of LCFAs on the pathogenesis of Gram-negative bacteria via membrane remodeling or signaling is well-documented, their importance as a nutrient source for bacterial proliferation and virulence is an emerging research area with definitive studies reported only for Salmonella Typhimurium, Vibrio cholerae, and Pseudomonas aeruginosa. Moreover, recent studies in Escherichia coli have shown that LCFA degradation confers redox stress. Here, we review the known role of LCFAs as nutrients during infection in Gram-negative human pathogens and the association of LCFA degradation with redox stress and stress response mechanisms. We suggest that for understanding how, as nutrients, LCFAs influence host-bacterial interactions, it is necessary to resolve whether LCFA utilization also causes redox stress in pathogens, with defense mechanisms preconditioning them for challenging host environments, or if pathogens have pre-existing mechanisms that prevent LCFA-induced stress.

The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n-alkane degradation in Pseudomonas aeruginosa SJTD-1

Transmembrane alkane monooxygenase (AlkB)-type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium-to-long-chain n-alkanes in hydrocarbon-utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of Pseudomonas aeruginosa SJTD-1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of alkR enhanced the transcription levels of the alkB2 gene and the utilization efficiency of the medium-to-long-chain n-alkanes by strain SJTD-1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the alkB2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long-chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of alkB2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR-AlkB couples distributed in Pseudomonadaceae with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for n-alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating n-alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution.

Within-host evolution of a transcriptional regulator contributes to the establishment of chronic Pseudomonas aeruginosa infection

As an opportunistic pathogen, Pseudomonas aeruginosa can cause both acute and chronic infections that are notoriously difficult to treat. However, the mechanism underlying acute or chronic P. aeruginosa infection remains unclear. Here, we identify a mutation in a transcriptional regulator PA5438 (named GavR). This mutation causes a 3-amino-acid absence in GavR and is strongly associated with chronic P. aeruginosa infection. Mechanistically, the deletion in GavR directly downregulates the transcription of the aceEF operon and leads to an accumulation of intracellular pyruvate, which can promote bacterial survival in neutrophils. Notably, P. aeruginosa with 9-bp-deleted or full-length gavR composes a mixed population in most patients with chronic or acute infections. Overall, the mutation in gavR attenuates P. aeruginosa virulence and enhances innate immune evasion by reprogramming pyruvate metabolism and the glyoxylate cycle. This work reveals a molecular mechanism of transition control from acute to chronic infection in P. aeruginosa.

Revealing quorum-sensing networks in Pseudomonas aeruginosa infections through internal and external signals to prevent new resistance trends

In the context of growing antibiotic resistance in bacteria, the quorum-sensing (QS) system of Pseudomonas aeruginosa (P. aeruginosa) has become a target for new therapeutic strategies. QS is a crucial communication process and an essential pathogenic mechanism. This comprehensive review explores the critical role of QS in the pathogenesis of P. aeruginosa infections, including lung, burn, bloodstream, gastrointestinal, corneal, and urinary tract infections. In addition, this review delves into the complexity of the bacterial QS communication network and highlights the intricate mechanisms underlying these pathological processes. Notably, in addition to the four main QS systems, bacterial QS can interact with various external and internal signaling networks, such as host environments and nutrients in the external microbiome, as well as internal virulence regulation systems within bacteria. These elements can significantly influence the behavior and virulence of microbial communities. Therefore, this review reveals that inhibitors targeting singular QS pathways may inadvertently promote virulence in other pathways, leading to new trends in drug resistance. In response to evolving resistance challenges, this study proposes more cautious treatment strategies, including multitarget interventions and combination therapies, aimed at combating the escalating issue of resistance.

Comprehensive structural overview of the C-terminal ligand-binding domains of the TetR family regulators

TetR family regulators (TFRs) represent a large group of one-component bacterial signal transduction systems which recognize environmental signals, like the presence of antibiotics or other bactericidal compounds, and trigger the cell response by regulating the expression of genes that secure bacterial survival in harsh environmental conditions. TFRs act as homodimers, each protomer is composed of a conserved DNA-binding N-terminal domain (NTD) and a variable ligand-binding C-terminal domain (CTD). Currently, there are about 500 structures of TFRs available in the Protein Data Bank and one-fourth of them represent the structures of TFR-ligand complexes. In this review, we summarized information on the ligands interacting with TFRs and based on structural data, we compared the CTDs of the TFR family members, as well as their ligand-binding cavities. Additionally, we divided the whole TFR family, including more than half of a million sequences, into subfamilies according to calculated multiple sequence alignment and phylogenetic tree. We also highlighted structural elements characteristic of some of the subfamilies. The presented comprehensive overview of the TFR CTDs provides good bases and future directions for further studies on TFRs that are not only important targets for battling multidrug resistance but also good candidates for many biotechnological approaches, like TFR-based biosensors.

Pseudomonas aeruginosa regulator PvrA binds simultaneously to multiple pseudo-palindromic sites for efficient transcription activation

Tetracycline repressor (TetR) family regulators (TFRs) are the largest group of DNA-binding transcription factors and are widely distributed in bacteria and archaea. TFRs play vital roles in controlling the expression of various genes and regulating diverse physiological processes. Recently, a TFR protein Pseudomonas virulence regulator A (PvrA), was identified from Pseudomonas aeruginosa as the transcriptional activator of genes involved in fatty acid utilization and bacterial virulence. Here, we show that PvrA can simultaneously bind to multiple pseudo-palindromic sites and upregulate the expression levels of target genes. Cryo-electron microscopy (cryo-EM) analysis indicates the simultaneous DNA recognition mechanism of PvrA and suggests that the bound DNA fragments consist of a distorted B-DNA double helix. The crystal structure and functional analysis of PvrA reveal a hinge region that secures the correct domain motion for recognition of the promiscuous promoter. Additionally, our results showed that mutations disrupting the regulatory hinge region have differential effects on biofilm formation and pyocyanin biosynthesis, resulting in attenuated bacterial virulence. Collectively, these findings will improve the understanding of the relationship between the structure and function of the TetR family and provide new insights into the mechanism of regulation of P. aeruginosa virulence.

Filamentous prophage Pf4 promotes genetic exchange in Pseudomonas aeruginosa

Filamentous prophages are widespread among bacteria and play crucial functions in virulence, antibiotic resistance, and biofilm structures. The filamentous Pf4 particles, extruded by an important pathogen Pseudomonas aeruginosa, can protect producing cells from adverse conditions. Contrary to the conventional belief that the Pf4-encoding cells resist reinfection, we herein report that the Pf4 prophage is reciprocally and commonly exchanged within P. aeruginosa colonies, which can repair defective Pf4 within the community. By labeling the Pf4 locus with antibiotic resistance and fluorescence markers, we demonstrate that the Pf4 locus is frequently exchanged within colony biofilms, in artificial sputum media, and in infected mouse lungs. We further show that Pf4 trafficking is a rapid process and capable of rescuing Pf4-defective mutants. The Pf4 phage is highly adaptable and can package additional DNA doubling its genome size. We also report that two clinical P. aeruginosa isolates are susceptible to the Pf4-mediated exchange, and the Pf5 prophage can be exchanged between cells as well. These findings suggest that the genetic exchanging interactions by filamentous prophages may facilitate defect rescue and the sharing of prophage-dependent benefits and costs within the P. aeruginosa community.

Pseudomonas aeruginosa two-component system CprRS regulates HigBA expression and bacterial cytotoxicity in response to LL-37 stress

Pseudomonas aeruginosa is a highly pathogenic bacterium known for its ability to sense and coordinate the production of virulence factors in response to host immune responses. However, the regulatory mechanisms underlying this process have remained largely elusive. In this study, we investigate the two-component system CprRS in P. aeruginosa and unveil the crucial role of the sensor protein CprS in sensing the human host defense peptide LL-37, thereby modulating bacterial virulence. We demonstrate that CprS acts as a phosphatase in the presence of LL-37, leading to the phosphorylation and activation of the response regulator CprR. The results prove that CprR directly recognizes a specific sequence within the promoter region of the HigBA toxin-antitoxin system, resulting in enhanced expression of the toxin HigB. Importantly, LL-37-induced HigB expression promotes the production of type III secretion system effectors, leading to reduced expression of proinflammatory cytokines and increased cytotoxicity towards macrophages. Moreover, mutations in cprS or cprR significantly impair bacterial survival in both macrophage and insect infection models. This study uncovers the regulatory mechanism of the CprRS system, enabling P. aeruginosa to detect and respond to human innate immune responses while maintaining a balanced virulence gene expression profile. Additionally, this study provides new evidence and insights into the complex regulatory system of T3SS in P. aeruginosa within the host environment, contributing to a better understanding of host-microbe communication and the development of novel strategies to combat bacterial infections.

Transcriptional Regulators Controlling Virulence in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a pathogen capable of colonizing virtually every human tissue. The host colonization competence and versatility of this pathogen are powered by a wide array of virulence factors necessary in different steps of the infection process. This includes factors involved in bacterial motility and attachment, biofilm formation, the production and secretion of extracellular invasive enzymes and exotoxins, the production of toxic secondary metabolites, and the acquisition of iron. Expression of these virulence factors during infection is tightly regulated, which allows their production only when they are needed. This process optimizes host colonization and virulence. In this work, we review the intricate network of transcriptional regulators that control the expression of virulence factors in P. aeruginosa, including one- and two-component systems and σ factors. Because inhibition of virulence holds promise as a target for new antimicrobials, blocking the regulators that trigger the production of virulence determinants in P. aeruginosa is a promising strategy to fight this clinically relevant pathogen.

LipR functions as an intracellular pH regulator in Bacillus thuringiensis under glucose conditions

Intracellular pH critically affects various biological processes, and an appropriate cytoplasmic pH is essential for ensuring bacterial growth. Glucose is the preferred carbon source for most heterotrophs; however, excess glucose often causes the accumulation of acidic metabolites, lowering the intracellular pH and inhibiting bacterial growth. Bacillus thuringiensis can effectively cope with glucose-induced stress; unfortunately, little is known about the regulators involved in this process. Here, we document that the target of the dual-function sRNA YhfH, the lipR gene, encodes a LacI-family transcription factor LipR as an intracellular pH regulator when B. thuringiensis BMB171 is suddenly exposed to glucose. Under glucose conditions, lipR deletion leads to early growth arrest by causing a rapid decrease in intracellular pH (~5.4). Then, the direct targets and a binding motif (GAWAWCRWTWTCAT) of LipR were identified based on the electrophoretic mobility shift assay, the DNase-I footprinting assay, and RNA sequencing, and the gapN gene encoding a key enzyme in glycolysis was directly inhibited by LipR. Furthermore, Ni2+ is considered a possible effector for LipR. In addition to YhfH, the lipR expression was coregulated by itself, CcpA, and AbrB. Our study reveals that LipR plays a balancing role between glucose metabolism and intracellular pH in B. thuringiensis subjected to glucose stress.

Characteristics of rare ST463 carbapenem-resistant Pseudomonas aeruginosa clinical isolates from blood

OBJECTIVES

This study aimed to elucidate resistance to carbapenems and fluoroquinolones, the transmission mechanism of bla_KPC-2, and the virulence characteristics of a Pseudomonas aeruginosa strain (TL3773) isolated in East China.

METHODS

The virulence and resistance mechanisms of TL3773 were investigated by whole genome sequencing (WGS), comparative genomic analysis, conjugation experiments, and virulence assays.

RESULTS

This study isolated carbapenem-resistant P. aeruginosa from blood resistant to carbapenems. The patient's clinical data showed poor prognosis compounded by multiple sites of infection. WGS showed that TL3773 carried aph (3')-IIb, bla_PAO, bla_OXA-486, fosA, catB7, and two crpP resistance genes on chromosome, and the carbapenem resistance gene bla_KPC-2 on plasmid. We identified a novel crpP gene named TL3773-crpP2. Cloning experiments proved that TL3773-crpP2 was not the primary cause of fluoroquinolone resistance in TL3773. GyrA and ParC mutations may confer fluoroquinolone resistance. The bla_KPC-2 genetic environment was IS26-TnpR-ISKpn27-bla_KPC-2-ISKpn6-IS26-Tn3-IS26, potentially mediating the transmission of bla_KPC-2 in P. aeruginosa. The overall virulence of TL3773 was lower than that of PAO1. However, the pyocyanin and biofilm formation of TL3773 was higher than that of PAO1. WGS further indicated that TL3773 was less virulent than PAO1. Phylogenetic analysis showed that TL3773 was most similar to the P. aeruginosa isolate ZYPA29 from Hangzhou, China. These observations further indicate that ST463 P. aeruginosa is rapidly spreading.

CONCLUSIONS

The threat of ST463 P. aeruginosa harbouring bla_KPC-2 is emergent and may pose a threat to human health. More extensive surveillance and effective actions are urgently needed to control its further spread.

Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis in Pseudomonas aeruginosa

Pseudomonas aeruginosa is capable of causing acute and chronic infections in various host tissues, which depends on its abilities to effectively utilize host-derived nutrients and produce protein virulence factors and toxic compounds. However, the regulatory mechanisms that direct metabolic intermediates towards production of toxic compounds are poorly understood. We previously identified a regulatory protein PvrA that controls genes involved in fatty acid catabolism by binding to palmitoyl-coenzyme A (CoA). In this study, transcriptomic analyses revealed that PvrA activates the Pseudomonas quinolone signal (PQS) synthesis genes, while suppressing genes for production of polyhydroxyalkanoates (PHAs). When palmitic acid was the sole carbon source, mutation of pvrA reduced production of pyocyanin and rhamnolipids due to defective PQS synthesis, but increased PHA production. We further solved the co-crystal structure of PvrA with palmitoyl-CoA and identified palmitoyl-CoA-binding residues. By using pvrA mutants, we verified the roles of the key palmitoyl-CoA-binding residues in gene regulation in response to palmitic acid. Since the PQS signal molecules, rhamnolipids and PHA synthesis pathways are interconnected by common metabolic intermediates, our results revealed a regulatory mechanism that directs carbon flux from carbon/energy storage to virulence factor production, which might be crucial for the pathogenesis.

MITF Contributes to the Body Color Differentiation of Sea Cucumbers Apostichopus japonicus through Expression Differences and Regulation of Downstream Genes

Melanin, which is a pigment produced in melanocytes, is an important contributor to sea cucumber body color. MITF is one of the most critical genes in melanocyte development and melanin synthesis pathways. However, how MITF regulates body color and differentiation in sea cucumbers is poorly understood. In this study, we analyzed the expression level and location of MITF in white, purple, and green sea cucumbers and identified the genes regulated by MITF using chromatin immunoprecipitation followed by sequencing. The mRNA and protein expression levels of MITF were all highest in purple morphs and lowest in white morphs. In situ hybridization indicated that MITF mRNA were mainly expressed in the epidermis. We also identified 984, 732, and 1191 peaks of MITF binding in green, purple, and white sea cucumbers, which were associated with 727, 557, and 887 genes, respectively. Our findings suggested that MITF contributed to the body color differentiation of green, purple, and white sea cucumbers through expression differences and regulation of downstream genes. These results provided a basis for future studies to determine the mechanisms underlying body color formation and provided insights into gene regulation in sea cucumbers.

High-Level Expression of Cell-Surface Signaling System Hxu Enhances Pseudomonas aeruginosa Bloodstream Infection

Bloodstream infections (BSIs) caused by Pseudomonas aeruginosa are associated with a high mortality rate in the clinic. However, the fitness mechanisms responsible for the evolution of virulence factors that facilitate the dissemination of P. aeruginosa to the bloodstream are poorly understood. In this study, a transcriptomic analysis of the BSI-associated P. aeruginosa clinical isolates showed a high-level expression of cell-surface signaling (CSS) system Hxu. Whole-genome sequencing and comparative genomics of these isolates showed that a mutation in rnfE gene was responsible for the elevated expression of the Hxu-CSS pathway. Most importantly, deletion of the hxuIRA gene cluster in a laboratory strain PAO1 reduced its BSI capability while overexpression of the HxuIRA pathway promoted BSI in a murine sepsis model. We further demonstrated that multiple components in the blood plasma, including heme, hemoglobin, the heme-scavenging proteins haptoglobin, and hemopexin, as well as the iron-delivery protein transferrin, could activate the Hxu system. Together, these studies suggested that the Hxu-CSS system was an important signal transduction pathway contributing to the adaptive pathogenesis of P. aeruginosa in BSI.

Transient Antibiotic Tolerance Triggered by Nutrient Shifts From Gluconeogenic Carbon Sources to Fatty Acid

Nutrient shifts from glycolytic-to-gluconeogenic carbon sources can create large sub-populations of extremely antibiotic tolerant bacteria, called persisters. Positive feedback in Escherichia coli central metabolism was believed to play a key role in the formation of persister cells. To examine whether positive feedback in nutrient transport can also support high persistence to β-lactams, we performed nutrient shifts for E. coli from gluconeogenic carbon sources to fatty acid (FA). We observed tri-phasic antibiotic killing kinetics characterized by a transient period of high antibiotic tolerance, followed by rapid killing then a slower persister-killing phase. The duration of transient tolerance (3-44 h) varies with pre-shift carbon source and correlates strongly with the time needed to accumulate the FA degradation enzyme FadD after the shift. Additionally, FadD accumulation time and thus transient tolerance time can be reduced by induction of the glyoxylate bypass prior to switching, highlighting that two interacting feedback loops simultaneously control the length of transient tolerance. Our results demonstrate that nutrient switches along with positive feedback are not sufficient to trigger persistence in a majority of the population but instead triggers only a temporary tolerance. Additionally, our results demonstrate that the pre-shift metabolic state determines the duration of transient tolerance and that supplying glyoxylate can facilitate antibiotic killing of bacteria.

ECF Sigma Factor HxuI Is Critical for In Vivo Fitness of Pseudomonas aeruginosa during Infection

The opportunistic pathogen Pseudomonas aeruginosa often adapts to its host environment and causes recurrent nosocomial infections. The extracytoplasmic function (ECF) sigma factor enables bacteria to alter their gene expression in response to host environmental stimuli. Here, we report an ECF sigma factor, HxuI, which is rapidly induced once P. aeruginosa encounters the host. Host stresses such as iron limitation, oxidative stress, low oxygen, and nitric oxide induce the expression of hxuI. By combining RNA-seq and promoter-lacZ reporter fusion analysis, we reveal that HxuI can activate the expression of diverse metabolic and virulence pathways which are critical to P. aeruginosa infections, including iron acquisition, denitrification, pyocyanin synthesis, and bacteriocin production. Most importantly, overexpression of the hxuI in the laboratory strain PAO1 promotes its colonization in both murine lung and subcutaneous infections. Together, our findings show that HxuI, a key player in host stress-response, controls the in vivo adaptability and virulence of P. aeruginosa during infection. IMPORTANCE P. aeruginosa has a strong ability to adapt to diverse environments, making it capable of causing recurrent and multisite infections in clinics. Understanding host adaptive mechanisms plays an important guiding role in the development of new anti-infective agents. Here, we demonstrate that an ECFσ factor of P. aeruginosa response to the host-inflicted stresses, which promotes the bacterial in vivo fitness and pathogenicity. Furthermore, our findings may help explain the emergence of highly transmissible strains of P. aeruginosa and the acute exacerbations during chronic infections.

NrtR Mediated Regulation of H1-T6SS in Pseudomonas aeruginosa

NrtR is a Nudix-related transcriptional regulator that is distributed among diverse bacteria and plays an important role in modulating bacterial intracellular NAD homeostasis. Previously, we showed that NrtR influences the T3SS expression and pathogenesis of Pseudomonas aeruginosa and demonstrated that NrtR mediates T3SS regulation through the cAMP/Vfr pathway. In the present study, we found that mutation of the nrtR gene leads to upregulation of the Hcp secretion island-I type VI secretion system (H1-T6SS). Further analysis revealed that mutation of the nrtR gene results in upregulation of regulatory RNAs (RsmY/RsmZ) that are known to control the H1-T6SS by sequestration of RsmA or RsmN. Simultaneous deletion of rsmY/rsmZ reduced the expression of H1-T6SS in the ΔnrtR mutant. In addition, overexpression of either rsmA or rsmN in ΔnrtR decreased H1-T6SS expression. Chromatin immunoprecipitation (ChIP)-Seq and electrophoretic mobility shift assay (EMSA) analyses revealed that NrtR directly binds to the promoters of rsmY, rsmZ and tssA1 (first gene of the H1-T6SS operon). Overall, the results from this study reveal the molecular details of NrtR-mediated regulation of H1-T6SS in P. aeruginosa.

IMPORTANCE NrtR is a Nudix-related transcriptional regulator and controls the NAD cofactor biosynthesis in bacteria. P. aeruginosa NrtR binds to the intergenic region between nadD2 and pcnA to repress the expression of the two operons, therefore controlling the NAD biosynthesis. We have previously reported that NrtR controls T3SS expression via the cAMP/Vfr pathway in P. aeruginosa. However, the global regulatory function and direct binding targets of the NrtR remain elusive in P. aeruginosa. This study reveals novel direct regulatory targets of the NrtR in P. aeruginosa, elucidating the molecular mechanism of NrtR-mediated regulation of H1-T6SS.

The Pseudomonas aeruginosa whole genome sequence: A 20th anniversary celebration

Toward the end of August 2000, the 6.3 Mbp whole genome sequence of Pseudomonas aeruginosa strain PAO1 was published. With 5570 open reading frames (ORFs), PAO1 had the largest microbial genome sequenced up to that point in time-including a large proportion of metabolic, transport and antimicrobial resistance genes supporting its ability to colonize diverse environments. A remarkable 9% of its ORFs were predicted to encode proteins with regulatory functions, providing new insight into bacterial network complexity as a function of network size. In this celebratory article, we fast forward 20 years, and examine how access to this resource has transformed our understanding of P. aeruginosa. What follows is more than a simple review or commentary; we have specifically asked some of the leaders in the field to provide personal reflections on how the PAO1 genome sequence, along with the Pseudomonas Community Annotation Project (PseudoCAP) and Pseudomonas Genome Database (pseudomonas.com), have contributed to the many exciting discoveries in this field. In addition to bringing us all up to date with the latest developments, we also ask our contributors to speculate on how the next 20 years of Pseudomonas research might pan out.

A key antisense sRNA modulates the oxidative stress response and virulence in Xanthomonas oryzae pv. oryzicola

Pathogens integrate multiple environmental signals to navigate the host and control the expression of virulence genes. In this process, small regulatory noncoding RNAs (sRNAs) may function in gene expression as post-transcriptional regulators. In this study, the sRNA Xonc3711 functioned in the response of the rice pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), to oxidative stress. Xonc3711 repressed production of the DNA-binding protein Xoc_3982 by binding to the xoc_3982 mRNA within the coding region. Mutational analysis showed that regulation required an antisense interaction between Xonc3711 and xoc_3982 mRNA, and RNase E was needed for degradation of the xoc_3982 transcript. Deletion of Xonc3711 resulted in a lower tolerance to oxidative stress due to the repression of flagella-associated genes and reduced biofilm formation. Furthermore, ChIP-seq and electrophoretic mobility shift assays showed that Xoc_3982 repressed the transcription of effector xopC2, which contributes to virulence in Xoc BLS256. This study describes how sRNA Xonc3711 modulates multiple traits in Xoc via signals perceived from the external environment.

Small, stable RNA species perform diverse functions in both prokaryotes and eukaryotes. In this study, the sRNA Xonc3711 decreased the production of DNA-binding protein Xoc_3982 in the bacterium Xanthomonas oryzae pv. oryzicola (Xoc) by base pairing with the xoc_3982 transcript. When Xonc3711 was mutated, Xoc was impaired in its ability to form flagella and produce biofilms, which reduced Xoc tolerance to oxidative stress. We also discovered that the DNA-binding protein Xoc_3982 represses the expression of xopC2, which encodes an effector protein, and reduces its expression. Our results show that Xonc3711 modulates and integrates multiple systems in Xoc to protect cells from oxidative damage.

Bacterial adaptation strategies to host-derived fatty acids

Fatty acids (FAs) are potent antimicrobials which hold great promise as viable alternatives or complements to conventional antibiotics. Intriguingly, bacteria are well equipped to use environmental FAs as energy sources and/or building blocks for their membrane lipids. Furthermore, these microbes display a wide array of mechanisms to prevent or mitigate FA toxicity. In this review we discuss strategies that bacteria use to thrive despite extensive exposure to host-derived antimicrobial FAs. We also highlight the altered response of these FA-adapted bacteria to antibiotics. Given the ubiquitous nature of FAs in various host environments, deciphering bacterial adaptation strategies to FAs is of prime importance. This knowledge may pave the way for a rational design of FA-based combination therapies with antibiotics.

Revisiting long-chain fatty acid metabolism in Escherichia coli: integration with stress responses

Long-chain fatty acids (LCFAs) are a tremendous source of metabolic energy, an essential component of membranes, and important effector molecules that regulate a myriad of cellular processes. As an energy-rich nutrient source, the role of LCFAs in promoting bacterial survival and infectivity is well appreciated. LCFA degradation generates a large number of reduced cofactors that may confer redox stress; therefore, it is imperative to understand how bacteria deal with this paradoxical situation. Although the LCFA utilization pathway has been studied in great detail, especially in Escherichia coli, where the earliest studies date back to the 1960s, the interconnection of LCFA degradation with bacterial stress responses remained largely unexplored. Recent work in E. coli shows that LCFA degradation induces oxidative stress and also impedes oxidative protein folding. Importantly, both issues arise due to the insufficiency of ubiquinone, a lipid-soluble electron carrier in the electron transport chain. However, to maintain redox homeostasis, bacteria induce sophisticated cellular responses. Here, we review these findings in light of our current knowledge of the LCFA metabolic pathway, metabolism-induced oxidative stress, the process of oxidative protein folding, and stress combat mechanisms. We discuss probable mechanisms for the activation of defense players during LCFA metabolism and the likely feedback imparted by them. We suggest that besides defending against intrinsic stresses, LCFA-mediated upregulation of stress response pathways primes bacteria to adapt to harsh external environments. Collectively, the interplay between LCFA metabolism and stress responses is likely an important factor that underlies the success of LCFA-utilizing bacteria in the host.