The gut microbiota can be altered by dietary interventions to prevent and treat various diseases. However, the mechanisms by which food products modulate commensals remain largely unknown. We ...demonstrate that plant-derived exosome-like nanoparticles (ELNs) are taken up by the gut microbiota and contain RNAs that alter microbiome composition and host physiology. Ginger ELNs (GELNs) are preferentially taken up by Lactobacillaceae in a GELN lipid-dependent manner and contain microRNAs that target various genes in Lactobacillus rhamnosus (LGG). Among these, GELN mdo-miR7267-3p-mediated targeting of the LGG monooxygenase ycnE yields increased indole-3-carboxaldehyde (I3A). GELN-RNAs or I3A, a ligand for aryl hydrocarbon receptor, are sufficient to induce production of IL-22, which is linked to barrier function improvement. These functions of GELN-RNAs can ameliorate mouse colitis via IL-22-dependent mechanisms. These findings reveal how plant products and their effects on the microbiome may be used to target specific host processes to alleviate disease.
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•Plant exosome-like nanoparticles (ELNs) are taken up by gut bacteria•The lipid composition of ELNs determines uptake by specific bacteria•ELN RNAs affect bacterial genes, notably affecting Lactobacillus production of I3A•ELN-mediated I3A alterations affect IL-22 production, resulting in ameliorated colitis
Teng et al. show that exosome-like nanoparticles (ELNs) from edible plants such as ginger are preferentially taken up by gut bacteria in an ELN lipid-dependent manner. ELN RNAs regulate gut microbiota composition and localization as well as host physiology, notably enhancing gut barrier function to alleviate colitis.
Transglutaminase (EC 2.3.2.13, TGase), an enzyme that catalyzes the formation of covalent cross-links between protein or peptide molecules, plays a critical role in commercial food processing, ...medicine, and textiles. TGase from Streptomyces is the sole commercial enzyme preparation for cross-linking proteins. In this study, we revealed that the SOS response repressor protein LexA in Streptomyces mobaraensis not only triggers morphological development but also enhances TGase synthesis. The absence of lexA significantly diminished TGase production and sporulation. Although LexA does not bind directly to the promoter region of the TGase gene, it indirectly stimulates transcription of the tga gene, which encodes TGase. Furthermore, LexA directly enhances the expression of genes associated with protein synthesis and transcription factors, thus favorably influencing TGase synthesis at both the transcriptional and posttranscriptional levels. Moreover, LexA activates four crucial genes involved in morphological differentiation, promoting spore maturation. Overall, our findings suggest that LexA plays a dual role as a master regulator of the SOS response and a significant contributor to TGase regulation and certain aspects of secondary metabolism, offering insights into the cellular functions of LexA and facilitating the strategic engineering of TGase overproducers.
SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an “SOS-box” motif present in the promoter region of SOS ...genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.
Summary
Specific transcription factors have been identified in various heterotrophic bacterial species that regulate the sets of genes required for fatty acid metabolism. Here, we report that ...expression of the fab genes, encoding fatty acid biosynthetic enzymes, is regulated by the global regulator LexA in the photoautotrophic cyanobacterium Synechocystis sp. PCC 6803. Sll1626, an ortholog of the well‐known LexA repressor involved in the SOS response in heterotrophic bacteria, was isolated from crude extracts of Synechocystis by DNA affinity chromatography, reflecting its binding to the upstream region of the acpP‐fabF and fabI genes. An electrophoresis mobility shift assay revealed that the recombinant LexA protein can bind to the upstream region of each fab gene tested (fabD, fabH, fabF, fabG, fabZ and fabI). Quantitative RT‐PCR analysis of the wild type and a lexA‐disrupted mutant strain suggested that LexA acts as a repressor of the fab genes involved in initiation of fatty acid biosynthesis (fabD, fabH and fabF) and the first reductive step in the subsequent elongation cycle (fabG) under normal growth conditions. Under nitrogen‐depleted conditions, downregulation of fab gene expression is partly achieved through an increase in LexA‐repressing activity. In contrast, under phosphate‐depleted conditions, fab gene expression is upregulated, probably due to the loss of repression by LexA. We further demonstrate that elimination of LexA largely increases the production of fatty acids in strains modified to secrete free fatty acids.
Significance Statement
We found that expression of fatty acid biosynthetic genes in a photoautotrophic cyanobacterium is regulated by the global regulator LexA, unlike in heterotrophic bacteria where specific transcription factors regulate fatty acid metabolism‐related genes. Our finding that elimination of LexA increases the production of fatty acids in strains that secrete free fatty acids will be beneficial for industrial applications.
Bacterial genomes are pervasively transcribed, generating a wide variety of antisense RNAs (asRNAs). Many of them originate from transcriptional read-through events (TREs) during the transcription ...termination process. Previous transcriptome analyses revealed that the
gene from
, which encodes the main SOS response regulator, is affected by the presence of an asRNA. Here, we show that the
antisense RNA (
-asRNA) is generated by a TRE on the intrinsic terminator (TT
) of the
gene, which is located downstream of
, in the opposite strand. Transcriptional read-through occurs by a natural mutation that destabilizes the TT
structure and modifies the efficiency of the intrinsic terminator. Restoring the mispairing mutation in the hairpin of TT
prevented
-asRNA transcription. The level of
-asRNA directly correlated with cellular stress since the expressions of
and
-asRNA depend on the stress transcription factor SigB. Comparative analyses revealed strain-specific nucleotide polymorphisms within TT
, suggesting that this TT could be prone to accumulating natural mutations. A genome-wide analysis of TREs suggested that mispairings in TT hairpins might provide wider transcriptional connections with downstream genes and, ultimately, transcriptomic variability among
strains.
Antimicrobial resistance threatens the eradication of infectious diseases and impairs the efficacy of available therapeutics. The bacterial SOS pathway is a conserved response triggered by genotoxic ...stresses and represents one of the principal mechanisms that lead to resistance. The RecA recombinase acts as a DNA-damage sensor inducing the autoproteolysis of the transcriptional repressor LexA, thereby derepressing SOS genes that mediate DNA repair, survival to chemotherapy, and hypermutation. The inhibition of such pathway represents a promising strategy for delaying the evolution of antimicrobial resistance. We report the identification, via llama immunization and phage display, of nanobodies that bind LexA with sub-micromolar affinity and block autoproteolysis, repressing SOS response in Escherichia coli. Biophysical characterization of nanobody-LexA complexes revealed that they act by trapping LexA in an inactive conformation and interfering with RecA engagement. Our studies pave the way to the development of new-generation antibiotic adjuvants for the treatment of bacterial infections.
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•Nanobodies (NbSOSs) binding Escherichia coli LexA with nanomolar affinity have been discovered•NbSOSs can inhibit LexA autoproteolysis and block the SOS response axis in bacteria•Biophysical characterization of NbSOSs-LexA complexes discloses inhibition mechanism
Maso and colleagues discovered llama-derived nanobodies targeting transcriptional repressor LexA from Escherichia coli. The authors demonstrated that such binders can inhibit RecA stimulated autoproteolysis of LexA, thus blocking the SOS response activation, which is one of the most conserved mechanisms that fuel antimicrobial resistance acquisition in bacterial pathogens.
Summary
We have developed an estrogen receptor‐based chemical‐inducible system for use in transgenic plants. A chimeric transcription activator, XVE, was assembled by fusion of the DNA‐binding domain ...of the bacterial repressor LexA (X), the acidic transactivating domain of VP16 (V) and the regulatory region of the human estrogen receptor (E; ER). The transactivating activity of the chimeric XVE factor, whose expression was controlled by the strong constitutive promoter G10‐90, was strictly regulated by estrogens. In transgenic Arabidopsis and tobacco plants, estradiol‐activated XVE can stimulate expression of a GFP reporter gene controlled by the target promoter, which consists of eight copies of the LexA operator fused upstream of the −46 35S minimal promoter. Upon induction by estradiol, GFP expression levels can be eightfold higher than that transcribed from a 35S promoter, whereas the uninduced controls have no detectable GFP transcripts, as monitored by Northern blot analysis. Neither toxic nor adverse physiological effects of the XVE system have been observed in transgenic Arabidopsis plants under all the conditions tested. The XVE system thus appears to be a reliable and efficient chemical‐inducible system for regulating transgene expression in plants.
The paradigm of involvement of LexA in regulation of only SOS-response in bacteria through the down-regulation of DNA repair genes was challenged in the unicellular cyanobacterium, Synechocystis ...PCC6803, wherein it was originally shown not to be associated with DNA repair and later also involved in management of carbon-starvation through up-regulation of C-metabolism genes. In the filamentous cyanobacterium, Anabaena sp. strain PCC7120, global stress management role for LexA and a consensus LexA-binding box (AnLexA-box) has been established using a LexA-overexpressing recombinant strain, AnlexA+. High levels of LexA rendered Anabaena cells sensitive to different DNA damage and oxidative stress-inducing agents, through the transcriptional down-regulation of the genes involved in DNA repair and alleviation of oxidative stress. LexA overexpression enhanced the ability of Anabaena to tolerate C-depletion, induced by inhibiting photosynthesis, by up-regulating genes involved in C-fixation and down-regulating those involved in C-breakdown, while maintaining the overall photosynthetic efficiency. A consensus LexA-binding box, AnLexA-box AGT-N4–11-ACT was identified upstream of both up- and down-regulated genes using a subset of Anabaena genes identified on the basis of proteomic analysis of AnlexA+ strain along with a few DNA repair genes. A short genome search revealed the presence of AnLexA box in at least 40 more genes, with functional roles in fatty acid biosynthesis, toxin-antitoxin systems in addition to DNA repair, oxidative stress, metal tolerance and C-metabolism. Thus, Anabaena LexA modulates the tolerance to multitude of stresses through transcriptional up/down-regulation of their functional genes directly by binding to the AnLexA Box present in their promoter region.
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•LexA functions both as a transcriptional repressor and an activator protein in Anabaena•LexA modulates the response of Anabaena to varied abiotic stresses in terms of survival and tolerance•AnLexA Box (AGT-N4-11-ACT) present upstream of at least 57 genes of Anabaena belonging to different functional groups
Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter ...systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.
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