Bacterial Secretion Systems: An Overview

Engineering non-pathogenic bacteria for auto-transporter-driven secretion of functional interferon

In recent years, various strategies have been developed to enable the oral administration of protein-based drugs (biologics) with the aim of overcoming the degradation and inactivation of these drugs that can occur as they traverse the gastrointestinal tract (GIT). In this study, we investigated bacteria as a delivery vehicle for biologics, harnessing their ability to withstand the harsh gastric environment and deliver therapeutic drugs directly to the intestine. Specifically, we explored using the type 5 secretion system (T5SS) to secrete therapeutic cargoes under simulated gut conditions. Our research focused on EspC, a T5SS protein from enteropathogenic Escherichia coli, and its potential to secrete interferon-α (IFNα), a cytokine with immunomodulatory and antiviral properties widely used in the clinic. We demonstrated that EspC can facilitate the secretion of IFNα variant when expressed in nonpathogenic bacteria. Moreover, this EspC-secreted IFN was able to activate the JAK-STAT pathway, upregulate IFN-stimulated genes, and induce a robust antiviral response in cells. Collectively, these findings provide proof of concept supporting the utilization of the EspC protein as a novel delivery platform for protein-based therapeutics.

Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars

BACKGROUND

During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.

RESULTS

We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).

CONCLUSIONS

Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.

Designing live bacterial therapeutics for cancer

Humans are home to a diverse community of bacteria, many of which form symbiotic relationships with their host. Notably, tumors can also harbor their own unique bacterial populations that can influence tumor growth and progression. These bacteria, which selectively colonize hypoxic and acidic tumor microenvironments, present a novel therapeutic strategy to combat cancer. Advancements in synthetic biology enable us to safely and efficiently program therapeutic drug production in bacteria, further enhancing their potential. This review provides a comprehensive guide to utilizing bacteria for cancer treatment. We discuss key considerations for selecting bacterial strains, emphasizing their colonization efficiency, the delicate balance between safety and anti-tumor efficacy, and the availability of tools for genetic engineering. We also delve into strategies for precise spatiotemporal control of drug delivery to minimize adverse effects and maximize therapeutic impact, exploring recent examples of engineered bacteria designed to combat tumors. Finally, we address the underlying challenges and future prospects of bacterial cancer therapy. This review underscores the versatility of bacterial therapies and outlines strategies to fully harness their potential in the fight against cancer.

The Sec secretion system enhances GtfB secretion and exopolysaccharide production to promote the formation of Streptococcus mutans persisters induced by cationic antimicrobials

Bacterial persistence-caused antibacterial tolerance and recurrent infections are critical for clinical treatments. Streptococcus mutans persisters have been reported to enhance bacterial cariogenicity and tolerance to multi-antimicrobial agents, yet their formation mechanisms remain unclear. Here, we investigated the crucial role of the Sec secretion system in persister formation induced by dimethylamino dodecyl methacrylate (DMADDM) and chlorhexidine. DMADDM treated biofilms significantly increased exopolysaccharide (EPS) production and formed a large amount of persisters, while fewer persisters were formed in less EPS produced medium, indicating the important role of EPS in persistence. Persisters significantly upregulated the expressions of gtfB and the Sec secretion system. The Sec secretion system has been previously proposed to secret GtfB. Therefore, nine key gene-knockout mutants of the Sec secretion system and their complementary strains were constructed, including yidC1, yidC2, secY, secA, secE, secG, yajC, ftsY and ffH, respectively; ΔgtfB was also constructed for EPS defect control. ΔyidC2, ΔsecY, ΔsecA and ΔffH significantly decreased the expression and secretion of GtfB, then reduced the amounts of EPS, indicating that these four components from the Sec secretion system were the key proteins responsible for GtfB secretion. Moreover, all Sec secretion system mutants and ΔgtfB reduced persister formation in DMADDM and chlorhexidine induced biofilms, indicating that the Sec secretion system regulates gtfB expression and EPS production, thereby influencing persister formation. Our findings indicated the key roles of the Sec secretion system in S. mutans persistence and suggested that the Sec secretion system and EPS production were key targets to removing biofilms and overcome bacterial persistence.

Identification of the Cytotoxic Transglutaminase from Mycobacterium spp. That Is Involved in RIPK1 Activation

Although the global incidence of tuberculosis has declined in recent years, tuberculosis remains a major global public health challenge. The Mycobacterium tuberculosis complex (MTBC) including M. tuberculosis, M. bovis, M. microti, etc., is the deadliest Mycobacterium spp. that needs more attention. Research on M. microti is significant as it is a zoonotic pathogen that can spread between animals and humans. By exploring the function of a transglutaminase in M. microti (MmTG), which is widely distributed in Mycobacterium and other species, a potential cytotoxic effector has been characterized. MmTG inhibits cell proliferation by inducing the phosphorylation of RIPK1 (receptor-interacting serine/threonine-protein kinase 1) and the Cys159 of MmTG is the highly conserved residue related to its cytotoxicity. Understanding MmTG and its homologs can provide more insights into the pathogenic mechanisms of mycobacteria and contribute to the development of more effective therapeutic strategies against mycobacterial infections.

The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms

Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.

IMPORTANCE

In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.

Protein targeting to the ER membrane: multiple pathways and shared machinery

The endoplasmic reticulum (ER) serves as a central hub for protein production and sorting in eukaryotic cells, processing approximately one-third of the cellular proteome. Protein targeting to the ER occurs through multiple pathways that operate both during and independent of translation. The classical translation-dependent pathway, mediated by cytosolic factors like signal recognition particle, recognizes signal peptides or transmembrane helices in nascent proteins, while translation-independent mechanisms utilize RNA-based targeting through specific sequence elements and RNA-binding proteins. At the core of these processes lies the Sec61 complex, which undergoes dynamic conformational changes and coordinates with numerous accessory factors to facilitate protein translocation and membrane insertion across and into the endoplasmic reticulum membrane. This review focuses on the molecular mechanisms of protein targeting to the ER, from the initial recognition of targeting signals to the dynamics of the translocation machinery, highlighting recent discoveries that have revealed unprecedented complexity in these cellular trafficking pathways.

Pathogenomic Characterization of Multidrug-Resistant Escherichia coli Strains Carrying Wide Efflux-Associated and Virulence Genes from the Dairy Farm Environment in Xinjiang, China

Background/Objectives: Livestock species, particularly dairy animals, can serve as important reservoirs of E. coli, carrying antibiotic resistance and virulence genes under constant selective pressure and their spread in the environment. In this study, we performed the pathogenomic analysis of seven multidrug resistant (MDR) E. coli strains carrying efflux-associated and virulence genes from the dairy farm environment in Xinjiang Province, China. Methods: First, we processed the samples using standard microbiological techniques followed by species identification with MALDI-TOF MS. Then, we performed whole genome sequencing (WGS) on the Illumina NovaSeq PE150 platform and conducted pathogenomic analysis using multiple bioinformatics tools. Results: WGS analysis revealed that the E. coli strains harbored diverse antibiotic efflux-associated genes, including conferring resistance to fluoroquinolones, aminoglycosides, aminocoumarins, macrolides, peptides, phosphonic acid, nitroimidazole, tetracyclines, disinfectants/antiseptics, and multidrug resistance. The phylogenetic analysis classified seven E. coli strains into B1 (n = 4), C (n = 2), and F (n = 1) phylogroups. PathogenFinder predicted all E. coli strains as potential human pathogens belonging to distinct serotypes and carrying broad virulence genes (ranging from 12 to 27), including the Shiga toxin-producing gene (stx1, n = 1). However, we found that a few of the virulence genes were associated with prophages and genomic islands in the E. coli strains. Moreover, all E. coli strains carried a diverse bacterial secretion systems and biofilm-associated genes. Conclusions: The present study highlights the need for large-scale genomic surveillance of antibiotic-resistant bacteria in dairy farm environments to identify AMR reservoir spillover and pathogenic risks to humans and design targeted interventions to further stop their spread under a One Health framework.

Characterization of proteins present in the biofilm matrix and outer membrane vesicles of Histophilus somni during iron-sufficient and iron-restricted growth: identification of potential protective antigens through in silico analyses

There is limited efficacy in vaccines currently available to prevent some animal diseases of bacterial origin, such as bovine respiratory disease caused by Histophilus somni. Protective efficacy can potentially be improved if bacterial antigens that are expressed in the host are included in vaccines. During H. somni infection in the bovine host, biofilms become established, and the availability of essential iron is restricted. To investigate further, the protein composition of spontaneously released outer membrane vesicles (OMVs) during iron-sufficient and iron-restricted growth and the proteins expressed in the biofilm matrix were analyzed and compared. Proteomic analysis revealed a dramatic physiological change in H. somni as it transitioned from the planktonic form to the biofilm mode of growth. All transferrin-binding proteins (Tbps) previously identified in H. somni were detected in the OMVs, suggesting that OMVs could induce antibodies to these proteins. Two TbpA-like proteins and seven total proteins were present in the OMVs only when iron was restricted, indicating the expression of these Tbps was differentially regulated. More proteins associated with quorum-sensing (QS) signaling were detected in the biofilm matrix compared with proteins in the OMVs, supporting a link between QS and biofilm formation. Proteins ACA31267.1 (OmpA) and ACA32419.1 (TonB-dependent receptor) were present in the OMV and biofilm matrix and predicted to be potential protective antigens using an immuno-bioinformatic approach. Overall, the results support the development of novel vaccines that contain OMVs obtained from bacteria grown to simulate the in vivo environment, and possibly biofilm matrix, to prevent diseases caused by bacterial pathogens.IMPORTANCEBovine respiratory disease (BRD) is the most economically important disease affecting the cattle industry. Available BRD vaccines consist of killed bacteria but are not very effective. Poor vaccine efficacy may be because the phenotype of bacteria in the host differs from the phenotype of cultured bacteria. Following host infection, virulent bacteria can express transferrin-binding proteins (Tbps) not expressed in culture medium but are required to sequester iron from host proteins. During chronic infections, such as BRD, bacteria can form a biofilm consisting of novel protein and polysaccharide antigens. The unique proteins expressed on outer membrane vesicles (OMVs) of Histophilus somni (a BRD pathogen) in the absence of iron and as a biofilm were identified and characterized. At least two TbpA-like proteins were expressed in OMVs only under iron-limiting conditions. Quorum-sensing-associated proteins were identified in the H. somni biofilm matrix. In silico analysis identified potential protein targets for vaccine development.

Impact of vancomycin and Clostridioides difficile on the secretome and pathogenicity of Clostridium innocuum

Clostridium innocuum, a member of the human gut microbiome with intrinsic resistance to vancomycin, has been increasingly associated with inflammatory bowel diseases (IBD). Clinical observations indicate that co-infection with Clostridioides difficile and C. innocuum could lead to poorer clinical remission in ulcerative colitis; however, the pathogenic mechanism of C. innocuum remains unclear. Here, we investigated the effects of vancomycin and C. difficile on C. innocuum secretomes and the functions of the modified secretomes on C. innocuum pathogenicity. The results indicated that, compared to co-culturing with C. difficile, vancomycin was more effective in stimulating the secretion of proteins without a signal peptide, whereas C. difficile was better at promoting the secretion of classical secretory proteins. Based on these results, we further analyzed the effects of three abundant classical secretory proteins on C. innocuum virulence utilizing recombinant proteins. The results demonstrated that the NlpC/P60-containing protein (NlpC/P60) can enhance C. innocuum biofilm formation and adherence to HT-29 cells. Additionally, NlpC/P60, D-Ala-D-Ala carboxypeptidase, and a polysaccharide deacetylase were able to stimulate IL-8 production of HT-29 cells and TNF-α production of Raw264.7 macrophages. Additionally, recombinant NlpC/P60 and polysaccharide deacetylase exhibited cytotoxicity on Raw264.7 cells at 48 h. As the production of IL-8 and TNF-α is closely associated with IBD development, it is suggested that C. innocuum secretomes, under the influence of vancomycin or C. difficile, could contribute to IBD progression by enhancing inflammation and host-pathogen interactions.

Chiral pesticide permethrin promotes the antibiotic resistance genes dissemination by transformation: Different chiral isomers engage in distinct regulatory pathways

The global dissemination of antibiotic resistance genes (ARGs) poses an increasingly urgent threat to both environmental and human health. The extensive use of chiral permethrin (PM), the most popular synthetic type I pyrethroid insecticide worldwide, has led to its increased detection in aquatic environments. However, our understanding of PM's role in spreading ARGs is still limited. Here, we systematically assessed the effects of two chiral isomers of 1R-cis-PM (CPM) and 1R-trans-PM (TPM) on the dissemination of ARGs in the aquatic environments by using a natural transformation (NT) model comprising plasmid pWH1274 and Acinetobacter baylyi ADP1. It was found that reactive oxygen species (ROS) was the main factor facilitating the NT of ARGs mediated by CPM and TPM, although their respective production mechanisms exhibited distinct pathways: CPM generates ROS primarily through the primary electron transport chain (ETC), whereas TPM does so via a secondary ETC. Furthermore, CPM enhanced NT by improving the bacterial competent state, while TPM promotes it by enhancing recombination. It was confirmed that both CPM and TPM have the potential to accelerate the spread of ARGs through distinct mechanisms. These findings will help us understand that different chiral isomers may pose risks through distinct mechanisms.

Identification and characterization of Vibrio anguillarum (GA strain) isolated from Obscure Pufferfish Takifugu obscurus

OBJECTIVE

Aquaculture has faced significant challenges due to the emergence of various pathogens affecting fish species. One such species, the Obscure Pufferfish Takifugu obscurus, has experienced high mortality rates due to an outbreak of disease on a fishery farm in Shanghai.

METHODS

The pathogen responsible for this outbreak was isolated and identified as Vibrio anguillarum (GA strain) using a combination of morphological, biochemical, and whole-genome single-nucleotide polymorphism-based phylogenetic analyses. Pathogenicity tests confirmed that the GA strain could cause disease in healthy Obscure Pufferfish, inducing overt hemorrhagic symptoms. Histopathological analysis was performed to assess whether tissue damage had occurred. Whole-genome sequencing revealed that the GA strain possessed 235 virulence genes and two drug resistance-related genes: cyclic AMP receptor protein (CRP) and regulator of secondary metabolites A (rsmA). Testing via PCR further confirmed the presence of 10 common virulence genes.

RESULTS

Antibiotic susceptibility testing showed that the GA strain was highly sensitive to antibiotics such as tetracycline, doxycycline, minocycline, and compound sulfamethoxazole and was resistant to cefradine, cefazolin, penicillin, and vancomycin.

CONCLUSIONS

To the best of our knowledge, this is the first study to report V. anguillarum as the pathogen responsible for this disease in Obscure Pufferfish. The isolate exhibited strong virulence and multidrug resistance. The findings lay the foundation for further disease control in Obscure Pufferfish and the investigation of the epidemiological mechanisms of V. anguillarum.

Providencia pseudovermicola sp. nov.: redefining Providencia vermicola and unveiling multidrug-resistant strains from diabetic foot ulcers in Egypt

BACKGROUND

Providencia species are concerning due to their intrinsic resistance to colistin and tigecycline, complicating the treatment of multidrug-resistant (MDR) infections.

METHODS

In the current study, two MDR isolates, DFU6 and DFU52T, were recovered from infected diabetic foot ulcers in Egypt in 2024. Following their initial identification as Providencia stuartii using VITEK® 2 and MALDI-TOF-MS, the isolates were subjected to whole-genome sequencing via DNBseq.

RESULTS

While the 16S rRNA gene showed 100% similarity to that of Providencia vermicola, phylogenomic analysis against the type strains in the TYGS database, including P. vermicola DSM 17385T confirmed that these isolates represent a distinct species within the genus, further supported by overall genome-relatedness indices (ORGIs). This discrepancy prompted us to revise the taxonomy of all published genomes of P. vermicola strains (n = 59) which revealed misidentification of at least 56 strains that are unrelated to the type strain of this species. DFU6 and DFU52T carried novel sequence types (ST29 and ST41, submitted to PubMLST) and harbored multiple resistance genes. Both strains contained the qnrD1 gene on a small, non-mobilizable plasmid. DFU52T possessed a conjugative plasmid encoding blaCMY-6, blaNDM-1, rmtC, aac(6')-Ib10, sul1, aph(3')-Ia, and qacEΔ1. DFU6 carried an ISEcp1-associated blaCTX-M-14, along with aadA, dfrA1, lnuF in a class 2 integron, and armA, msrE, and mphE on a resistance plasmid. Both isolates also featured a pathogenicity island (PAI) integrated into the pheV gene with fimbriae-encoding genes.

CONCLUSION

Following our reassessment of the taxonomic classification of all P. vermicola strains with published genomes, we propose reclassifying certain strains, including DFU6 and DFU52T, into distinct species for which we propose the name Providencia pseudovermicola sp. nov. We recommend DFU52T (= CCASU-2024-72) as the type strain for the novel species. We also shed light on the public health threat of this novel species as a human pathogen that harbours carbapenem and aminoglycoside resistance genes on mobile genetic elements.

Ehrlichia chaffeensis proteomic profiling reveals distinct expression patterns of infectious and replicating forms

Ehrlichia chaffeensis is a tick-transmitted rickettsial pathogen responsible for causing human monocytic ehrlichiosis (HME). The pathogen's developmental cycle includes infectious dense-core cells (DCs) and non-infectious replicating cells (RCs). Defining the proteins crucial for the two growth forms is of fundamental importance in understanding the infection and replication process, which also aids in identifying novel therapeutic targets against HME and other related rickettsial diseases. E. chaffeensis organisms cultivated in a macrophage cell line were purified as DC and RC fractions and subjected to comprehensive quantitative proteome analysis. From triplicate sample analysis, we identified 195 proteins as commonly expressed in both the DC and RC forms, while an additional 189 proteins were recognized as exclusively expressed in the RC form. Equal numbers of commonly expressed proteins in the RC and DC forms and having substantially more proteins exclusively expressed in the metabolically active RC form may reflect specific functional priorities of E. chaffeensis supporting its replication within a phagosome. The high abundance of metabolic processes and transport proteins in the RC compared to the DC form may reflect its higher metabolic requirements and interactions with a host cell supporting its intraphagosomal replication. This study provides comprehensive proteome data for E. chaffeensis which will be valuable for a better understanding of protein expression dynamics during its infectious and replicating stages.

Characterizing host-microbe interactions with bacterial effector proteins using proximity-dependent biotin identification (BioID)

Bacterial pathogens have evolved diverse strategies to manipulate host cells to establish infection. At a molecular level, this is often mediated by virulence factors that are secreted into host cells (herein referred to as effectors), which target host cellular pathways by initiating host-pathogen protein-protein interactions that alter cellular function in the host. By establishing this network of host-pathogen protein-protein interactions, pathogenic bacteria modulate and hijack host cell processes for the benefit of the pathogen, ultimately promoting survival, replication, and cell-to-cell spread within the host. Effector proteins also mediate diverse host-microbe interactions in nature, contributing to symbiotic relationships spanning from mutualism to commensalism to parasitism. While effector proteins play crucial roles in nature, molecular properties such as the transient nature of the underlying protein-protein interactions and their affinity for targeting host biological membranes often presents challenges to elucidating host targets and mechanism of action. Proximity-dependent biotin identification (termed BioID) has proven to be a valuable tool in the field of cell biology to identify candidate protein-protein interactions in eukaryotic cells, yet has remained relatively underexploited by bacterial pathogenesis researchers. Here, we discuss bacterial effector function at a molecular level, and challenges presented by traditional approaches to host target identification. We highlight the BioID approach and its potential strengths in the context of identifying host-pathogen protein-protein interactions, and explore BioID's implementation to study host-microbe interactions mediated by bacteria. Collectively, BioID represents a powerful tool for the study of bacterial effector proteins, providing new insight into our understanding of pathogenesis and other symbiotic relationships, and opportunities to identify new factors that contribute to host response to infection.

Comparative pan-genomic analysis reveals pathogenic mechanisms and genomic plasticity in Vibrio parahaemolyticus clinical and environmental isolates

Introduction

Vibrio parahaemolyticus is a human pathogen capable of inducing bacterial gastroenteritis. Clinical strains of V. parahaemolyticus are considered pathogenic due to their possession of hemolysin and a type III secretion system (T3SS). Some environmental isolates are also acquiring corresponding virulence genes.

Methods

This study initially examines the infection characteristics of V. parahaemolyticus, and subsequently employs pan-genomic analysis to identify genes that exhibit significant differences in distribution between environmental and clinical isolates, thereby revealing their potential impact on virulence.

Results and discussion

The epidemiological analysis of clinical isolates suggests that infections of V. parahaemolyticus are more prevalent in warm seasons, with O4:KUT serotype presenting more severe symptoms. OrthoFinder analysis revealed that environmental isolates possess a higher number of core genes. PEPPAN and KEGG analysis revealed that the 10 genes exclusively found in clinical isolates were predominantly associated with virulence. Additionally, the functions of genes differentially distributed in the environment were significantly more diverse compared to those in clinical settings. Analysis of mobile genetic elements suggested that environmental isolates harbor more mobile genetic elements, implying a potential for an increased number of resistance genes. The pathogenic characteristics of the strains examined in this study, genomic diversity and variation in mobile genetic elements are highly significant for deepening our understanding of the pathogenic mechanisms of V. parahaemolyticus and for the development of strategies to prevent its infections.

Characterization of enteric pathogens in Harare, Zimbabwe using environmental surveillance and metagenomics

High diarrheal disease burden remains an urgent concern in low- and middle-income countries, greatly affecting children under the age of 5 years and those living with HIV and AIDS. Treatment of infectious diseases has also become increasingly difficult with the rapid rise of antimicrobial resistance (AMR). Environmental surveillance of wastewater can supplement gaps in clinical surveillance as residents on a sewage system contribute to the wastewater, providing simple, composite samples that can improve understanding about both pathogens and AMR in the community. This study evaluated the effectiveness of environmental surveillance with shotgun metagenomics as a tool to characterize a broad range of enteric pathogens, antibiotic resistance genes, and virulence factor genes (VFGs) in wastewater from six neighborhoods in Harare, Zimbabwe. Alpha and beta diversity of the microbial community were similar between high-income and low-income suburbs. Enteric pathogens of high AMR and clinical concern, including Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica, were detected in all samples. The top VFGs were encoded for delivery, adherence, and motility, functions important in toxin secretion, colonization, and immune modulation. The findings provide a foundation for future studies to explore environmental surveillance and shotgun metagenomics as a public health monitoring tool for enteric diseases.

Proteomic Analysis Reveals the Phenotypic Heterogeneity and Tolerance Mechanisms of Halophilic Vibrio parahaemolyticus Under Dual Stress of Low Salinity and Bile Salts in the Human Intestine

Vibrio parahaemolyticus, a halophilic Gram-negative bacterium commonly found in aquatic products, can colonize the human small intestine, causing gastroenteritis and potentially leukemia. As a major intestinal pathogen, it poses a significant threat to public health. This study aims to investigate the phenotypic heterogeneity of V. parahaemolyticus in the low-salinity and bile salt environments of the human intestinal tract and to elucidate its mechanisms of tolerance and pathogenicity using proteomics. The experimental results indicated that under the low salinity and bile salts conditions of the human intestinal environment, the growth, motility, and biofilm formation of the strains were significantly inhibited. Proteomics analysis revealed that, under these conditions, the energy metabolism, chemotaxis system, flagellar motor, and ribosome-related proteins of V. parahaemolyticus were significantly affected, thereby influencing its growth, motility, and biofilm formation. Furthermore, the activation of the secretion system, particularly the T2SS, enhanced the virulence of secreted factors on host cells. Additionally, the activation of the β-lactam resistance pathway increased resistance to the intestinal environment, thereby enhancing the pathogenicity of V. parahaemolyticus.

Mammalian TatD DNase domain containing 1 (TATDN1) is a proteostasis-responsive gene with roles in ventricular structure and neuromuscular function

The characterization of highly conserved but poorly understood genes often reveals unexpected biological roles, advancing our understanding of disease mechanisms. One such gene is Mammalian TatD DNase domain containing 1 (Tatdn1), the mammalian homolog of bacterial Twin-arginine translocation D (TatD), a protein proposed to have roles either in DNA degradation or protein quality control in unicellular organisms. Despite its association with different pathologies, including several cancer types and cardiovascular diseases, the role of TATDN1 in mammals remains unexplored. Here, we demonstrate that Tatdn1 encodes a cytoplasmic protein that does not participate in DNA degradation but is upregulated in cells under proteostasis stress. Tatdn1-deficient mice exhibit dysregulated expression of genes involved in membrane and extracellular protein biology, along with mild dilated cardiomyopathy and impaired motor coordination. These findings identify TATDN1 as a key player in cytosolic processes linked to protein homeostasis, with significant physiological implications for cardiac and neurological function.

A case of septic shock caused by drug-resistant Edwardsiella tarda and literature review

BACKGROUND

Edwardsiella tarda (E. tarda) causes highly mortality, which is rare in septic patients. We herein reported a case of septic shock caused by drug-resistant E. tarda.

CASE PRESENTATION

We herein describe a 32-year-old female with septic shock who had the medical history of abortion 1 month ago and "systemic lupus erythematosus and rheumatoid arthritis" presented abdominal pain, diarrhea, and dyspnea as the primary symptoms and rapidly deteriorated to MODS following breakfast (undercooked fish porridge) in the ICU. Sepsis surviving bundle was initiated by collecting pathogen culture (sputum, urine and blood samples), empirically broad-spectrum antibiotics administration (Meropenem), along with fluid resuscitation, vasopressor use. E. tarda was confirmed both in blood culture and mNGS (metagenomics next generation sequencing). Thus, the antibiotics were switched to piperacillin-tazobactam according to the susceptibility test that was susceptible to piperacillin-tazobactam and resistant to ampicillin, quinolones and gentamicin. The patient finally recovered and discharged after 18 days of ICU treatment.

CONCLUSIONS

Empiric antibiotics should be selected with piperacillin-tazobactam and amikacin, and avoid ampicillin, quinolones and gentamicin for suspecting E. tarda infection in southern China. Bacteremia complicated with septic shock caused by E. tarda requires intensive care to improve survival rates.

Ayu: a machine intelligence tool for identification of extracellular proteins in the marine secretome

Microbes are the engines driving the elemental cycles. In order to interact with their environment and the community, microbes secrete proteins into the environment (known collectively as the secretome), where they remain active for prolonged periods of time. Despite the environmental relevance of microbes, our knowledge of the marine secretome remains limited due to a lack of effective in silico methods for the study of secreted proteins. An alternative approach to characterise the secretome is to combine modern machine learning tools with the evolutionary adaptation changes of the proteome to the marine environment. In this study, we identify and describe adaptations of marine extracellular proteins, which vary between phyla, resulting in differences in ATP costs, amino acid composition and nitrogen and sulphur content. We develop 'Ayu', a machine prediction tool that does not employ homology-based predictors and achieves better and quicker performance than current state-of-the-art software. When applied to oceanic samples (Tara Oceans dataset), our method was able to recover more than double the proteins compared to the most widely used method to identify secreted proteins. The application of this tool to open ocean samples allows better characterisation of the composition of the marine secretome.

Master control of protein secretion by Mycobacterium tuberculosis

Tuberculosis is the leading cause of death from a single infectious disease. Mycobacterium tuberculosis secretes proteins using five ESX systems with distinctive functions essential for its growth and virulence. Here we show that a non-canonical supercomplex of the EsxU-EsxT proteins, encoded in the esx-4 locus, with the orphan EsxE-EsxF proteins, encoded in the cpnT operon, is required for toxin secretion by M. tuberculosis . Surprisingly, the outer membrane localization of all Esx proteins and their secretion into the cytosol of infected macrophages also depend on the EsxEF-EsxUT supercomplex and ESX-4. These results not only demonstrate that the Esx proteins have dual functions as the long-sought outer membrane components of ESX systems and as secreted effector proteins, but also reveal a novel master control mechanism of protein secretion in M. tuberculosis . The mutual dependency of EsxEF and EsxUT on each other synchronizes ESX effector protein secretion, enabling M. tuberculosis to block phagosomal maturation and to permeabilize the phagosomal membrane only when it is capable of killing host cells by toxin secretion. The requirement of the ESX-4 system for general protein secretion is a critical vulnerability which could be targeted by drugs and/or vaccines to simultaneously block many virulence factors of M. tuberculosis .

Pseudomonas aeruginosa assembles H1-T6SS in response to physical and chemical damage of the outer membrane

Bacteria respond to environmental stimuli and attacks from competing organisms. Pseudomonas aeruginosa assembles the type VI secretion system (H1-T6SS) to precisely retaliate against aggressive competing bacteria. However, we lack an understanding of how the H1-T6SS assembly dynamically responds to nanomechanical forces. To address this, we analyzed live cells using correlative atomic force microscopy (AFM) and fluorescence microscopy. We show that indentation forces above 7 nanonewtons trigger local, repeated and targeted H1-T6SS assemblies within seconds of impact by the AFM tip. Analysis of the corresponding AFM force curves shows that a breach of a single layer of the cell envelope is necessary and sufficient for triggering H1-T6SS assembly. Accordingly, polymyxin B nonapeptide, which damages the outer membrane, also triggers H1-T6SS assembly. This suggests that P. aeruginosa has evolved a danger-sensing mechanism that enables rapid and precise deployment of its antibacterial H1-T6SS in response to breaches in the outer membrane.

Herbal formula alleviates heat stress by improving physiological and biochemical attributes and modulating the rumen microbiome in dairy cows

Heat stress significantly impacts dairy cow productivity, health, and welfare. This study evaluated a self-developed herbal formula as a dietary intervention to mitigate heat stress. A total of 198 lactating cows were divided into two groups: a Control group receiving standard total mixed rations and a Herbs group supplemented with herbal formula for 60 days. Various parameters were assessed, including milk yield and composition, antioxidant capacity, immune responses, stress-related gene expression, and rumen microbial composition. Compared to the Control group, cows in the Herbs group showed improved feed intake, milk yield and quality, rumination frequency, and enhanced antioxidant activity and immune response. Rumen microbiome analysis revealed a reduced relative abundance of Proteobacteria and Ochrobactrum in the Herbs group, along with an enrichment of beneficial genera such as Lachnospira. Functional predictions indicated that the Herbs group exhibited enhanced glycolysis/gluconeogenesis, pyruvate metabolism, and starch and sucrose metabolism, reflecting improved fermentation efficiency and energy utilization. In conclusion, the herbal formula improved physiological and biochemical attributes, boosted antioxidant and immune responses, and modulated the rumen microbiome, contributing to the alleviation of heat stress in dairy cows. These findings highlight its potential as a natural dietary strategy to support dairy cow health and productivity under heat stress conditions.

Architecture of an embracing lipase-foldase complex of the type II secretion system of Acinetobacter baumannii

Acinetobacter baumannii is a major human pathogen responsible for a growing number of multi-antibiotic-resistant infections, and of critical priority for the World Health Organization (WHO). A. baumannii employs a type II secretion system (T2SS) to secrete toxins extracellularly to enable cytotoxicity and colonization. Lipase LipA, secreted by the A. baumannii T2SS, is required for virulence and fitness, and in the periplasm is maintained in an active state by its essential foldase, LipB. Here we report that LipA is able to recognize lipids of different chain lengths at extremes of pH and temperature, thanks to its stabilization by LipB through an extended, highly helical "embrace." A vast bioinformatic analysis indicates that LipB-like foldases are widespread over numerous proteobacteria, and thus the extended foldase architecture shown here could be widespread. These results provide new insight into A. baumannii's adaptability as a pathogen in different environments and could facilitate the development of novel antibacterials.

Advancements in Escherichia coli secretion systems for enhanced recombinant protein production

Escherichia coli is inarguably one of the most studied microorganisms across the spectrum of microbiology. It is very widely used in recombinant protein production owing to its rapid growth, ease of genetic manipulation, and relatively high protein yields. Despite all of its advantages, its inability to efficiently secrete proteins naturally remains a drawback leading to protein aggregation as inclusion bodies in the cytoplasm and consequent low overall protein yield. Therefore, many approaches to mitigate this weakness and enhance extracellular secretion to increase protein yield have been devised. This review explores the natural and engineered secretion systems in E. coli, highlighting their potential for enhanced protein secretion for non-glycosylated proteins. Natural one-step (e.g., Type I and III Secretion Systems) and two-step systems (e.g., Sec and Tat pathways) are detailed alongside recent advancements in genetic engineering, mutagenesis, and synthetic biology approaches aimed at improving protein yield, folding, and secretion efficiency. Emerging technologies, such as the ESETEC® and BacSec® platforms, promise scalable and cost-effective solutions for higher protein production. Challenges, including limited cellular capabilities and protein aggregation, are addressed through innovative strategies like cell wall modification, co-expression of chaperones, and medium optimization. This review emphasizes E. coli's adaptability to industrial applications, and the promising future of recombinant protein technologies.

Fighting Antimicrobial Resistance: Innovative Drugs in Antibacterial Research

In the fight against bacterial infections, particularly those caused by multi-resistant pathogens known as "superbugs", the need for new antibacterials is undoubted in scientific communities and is by now also widely perceived by the general population. However, the antibacterial research landscape has changed considerably over the past years. With few exceptions, the majority of big pharma companies has left the field and thus, the decline in R&D on antibacterials severely impacts the drug pipeline. In recent years, antibacterial research has increasingly relied on smaller companies or academic research institutions, which mostly have only limited financial resources, to carry a drug discovery and development process from the beginning and through to the beginning of clinical phases. This review formulates the requirements for an antibacterial in regard of targeted pathogens, resistance mechanisms and drug discovery. Strategies are shown for the discovery of new antibacterial structures originating from natural sources, by chemical synthesis and more recently from artificial intelligence approaches. This is complemented by principles for the computer-aided design of antibacterials and the refinement of a lead structure. The second part of the article comprises a compilation of antibacterial molecules classified according to bacterial target structures, e.g. cell wall synthesis, protein synthesis, as well as more recently emerging target classes, e.g. fatty acid synthesis, proteases and membrane proteins. Aspects of the origin, the antibacterial spectrum, resistance and the current development status of the presented drug molecules are highlighted.

Alisol A 24-Acetate combats Methicillin-Resistant Staphylococcus aureus infection by targeting the mevalonate biosynthesis

Infections caused by Methicillin-resistant Staphylococcus aureus (MRSA) have emerged as one of the most pressing global public health challenges. In concert with global rise of antimicrobial resistance at alarming rate, there is an urgent need for alternative strategies to combat MRSA. Here, the high throughput screening indicated that the Alisol A 24-acetate (AA) effectively inhibits the mevalonate (MVA) synthesis in MRSA. The mechanistic analysis revealed that AA competitively inhibits the 3-hydroxy-3-methyl glutaryl coenzyme A reductase (HMGR) protein to blockade the MVA pathway, thereby disrupting the bacterial membrane integrity and functions. Further investigations showed that this disruption consequently restores the β-lactam susceptibility in MRSA by retarding the expression of PBP2a protein and dampens the virulence of MRSA by reducing the exotoxins secretion. In addition to the effect on MRSA, AA has been found to exert host-acting activity to reduce the MRSA-induced inflammation. The promising anti-MRSA activity of AA was further confirmed in vivo. Collectively, the current study highlighted the potential of AA as a proposing drug for combating MRSA and emphasize the MVA pathway as an ideal therapeutic target for MRSA treatment.

The accessory secretion system in Streptococcus agalactiae regulates protein secretion, stress resistance, adhesion, immune evasion, and virulence

Streptococcus agalactiae is a significant co-pathogenic bacterium in humans and animals, including fish. Bacteria secrete a variety of proteins through an accessory secretion system to modulate their interactions with the host. To investigate the role of the accessory secretion system in S. agalactiae, a deletion mutant strain (ΔaccSec) was constructed via homologous recombination. The accessory secretion system was found to be essential for the viability of S. agalactiae, and its absence led to increased cell death and lysis. In the extracellular fraction of the ΔaccSec mutant, a reduction in the secretion of 33 proteins was observed. Analyses of biological properties indicated that ΔaccSec exhibited significantly reduced stress tolerance and envelope stability. Pathogenicity experiments demonstrated that the ΔaccSec mutant had significantly lower adhesion to cells and fish tissues, as well as decreased resistance to whole blood killing and phagocytosis by macrophages. The cumulative mortality of ΔaccSec in tilapia after intraperitoneal injection was reduced by 55.3-74.2 %. The ΔaccSec mutant exhibited a markedly diminished capacity for colonization in tilapia. Furthermore, we found that ΔaccSec mutant induced higher macrophage reactive oxygen species (ROS) levels and significantly upregulated MHC-II, TLR-2 transcript levels in tilapia spleens compared to the wild-type. Overall, these findings underscore the importance of the accessory secretion system in S. agalactiae pathogenicity, particularly in stabilizing the bacterial envelope, facilitating adhesion, and evading host immunity. The results of this study provide new insights into the mechanisms of virulence regulation in S. agalactiae and lay a foundation for developing live attenuated vaccines.

A lysis less ordinary: The bacterial Type 10 Secretion System

Bacteria have evolved several different biochemical pathways to either export proteins of all shapes and sizes out of the cell cytoplasm, or to secrete those proteins into the extracellular environment. Many bacterial protein secretion systems have evolutionary links to systems used by bacteriophage to move macromolecules across membranes. The Type 10 Secretion System (T10SS) was identified in gram-negative bacteria and comprises genes that bear striking sequence similarities to those found within phage lysis cassettes. The minimum components of a T10SS are an integral membrane holin-like protein together with a peptidoglycan hydrolase. Here, we review recent research in Serratia spp., Salmonella spp, Yersinia spp, and gram-positive Clostridioides spp., and consider the evidence for different T10SS mechanisms ranging from a controlled release of proteins into the environment, to stochastic altruistic lysis of specialised populations of cells.

Oral delivery of therapeutic proteins by engineered bacterial type zero secretion system

Genetically engineered commensal bacteria are promising living drugs, however, their therapeutic molecules are frequently confined to their colonization sites. Herein, we report an oral protein delivery technology utilizing an engineered bacterial type zero secretion system (T0SS) via outer membrane vesicles (OMVs). We find that OMVs produced in situ by Escherichia coli Nissle 1917 (EcN) can penetrate the intact gut epithelial barrier to enter the circulation and that epithelial transcytosis involves pinocytosis and dynamin-dependent pathways. EcN is engineered to endogenously load various enzymes into OMVs, and the secreted enzyme-loaded OMVs are able to stably catalyze diverse detoxification reactions against digestive fluid and even enter the circulation. Using hyperuricemic mice and uricase delivery as a demonstration, we demonstrate that the therapeutic efficacy of our engineered EcN with a modified T0SS outperforms that with a direct protein secretion apparatus. The enzyme-loaded OMVs also effectively detoxify human serum samples, highlighting the potential for the clinical treatment of metabolic disorders.

It's a Small World After All: The Remarkable but Overlooked Diversity of Venomous Organisms, with Candidates Among Plants, Fungi, Protists, Bacteria, and Viruses

Numerous organisms, including animals, plants, fungi, protists, and bacteria, rely on toxins to meet their needs. Biological toxins have been classified into three groups: poisons transferred passively without a delivery mechanism; toxungens delivered to the body surface without an accompanying wound; and venoms conveyed to internal tissues via the creation of a wound. The distinctions highlight the evolutionary pathways by which toxins acquire specialized functions. Heretofore, the term venom has been largely restricted to animals. However, careful consideration reveals a surprising diversity of organisms that deploy toxic secretions via strategies remarkably analogous to those of venomous animals. Numerous plants inject toxins and pathogenic microorganisms into animals through stinging trichomes, thorns, spines, prickles, raphides, and silica needles. Some plants protect themselves via ants as venomous symbionts. Certain fungi deliver toxins via hyphae into infected hosts for nutritional and/or defensive purposes. Fungi can possess penetration structures, sometimes independent of the hyphae, that create a wound to facilitate toxin delivery. Some protists discharge harpoon-like extrusomes (toxicysts and nematocysts) that penetrate their prey and deliver toxins. Many bacteria possess secretion systems or contractile injection systems that can introduce toxins into targets via wounds. Viruses, though not "true" organisms according to many, include a group (the bacteriophages) which can inject nucleic acids and virion proteins into host cells that inflict damage rivaling that of conventional venoms. Collectively, these examples suggest that venom delivery systems-and even toxungen delivery systems, which we briefly address-are much more widespread than previously recognized. Thus, our understanding of venom as an evolutionary novelty has focused on only a small proportion of venomous organisms. With regard to this widespread form of toxin deployment, the words of the Sherman Brothers in Disney's iconic tune, It's a Small World, could hardly be more apt: "There's so much that we share, that it's time we're aware, it's a small world after all".

The ArcB kinase sensor participates in the phagocyte-mediated stress response in Salmonella Typhimurium

The ArcAB two-component system includes a histidine kinase sensor (ArcB) and a regulator (ArcA) that respond to changes in cell oxygen availability. The ArcA transcription factor activates genes related to metabolism, membrane permeability, and virulence, and its presence is required for pathogenicity in Salmonella Typhimurium, which can be phosphorylated independently of its cognate sensor, ArcB. In this study, we aimed to characterize the transcriptional response to hypochlorous acid (HOCl) mediated by the presence of the ArcB sensor. HOCl is a powerful microbicide widely used for sanitization in industrial settings. We used wild-type S. Typhimurium and the mutant lacking the arcB gene exposed to NaOCl to describe the global transcriptional response. We also infected murine neutrophils to evaluate the expression levels of relevant genes related to the resistance and infection process while facing ROS-related stress. Our results indicate that the absence of the arcB gene significantly affects the ability of S. Typhimurium to grow under HOCl stress. Overall, 6.6% of Salmonella genes varied their expression in the mutant strains, while 8.6% changed in response to NaOCl. The transcriptional response associated with the presence of ArcB is associated with metabolism and virulence, suggesting a critical role in pathogenicity and fitness, especially under ROS-related stress. Our results show that ArcB influences the expression of genes associated with fatty acid degradation, protein secretion, cysteine and H2S biosynthesis, and translation, both in vitro and under conditions found within neutrophils. We found that protein carbonylation is significantly higher in the mutant strain than in the wild type, suggesting a critical function for ArcB in the response and repair processes. This study contributes to the understanding of the pathogenicity and adaptation mechanisms that Salmonella employs to establish a successful infection in its host.

A strategy for controlling Hypervirulent Klebsiella pneumoniae: inhibition of ClpV expression

The emergence and prevalence of hypervirulent Klebsiella pneumoniae (hvKP) have proposed a great challenge to control this infection. Therefore, exploring some new drugs or strategies for treating hvKP infection is an urgent issue for scientific researchers. In the present study, the clpV gene deletion strain of hvKP (ΔclpV-hvKP) was constructed using CRISPR-Cas9 technology, and the biological characteristics of ΔclpV-hvKP were investigated to explore the new targets for controlling this pathogen. The results showed that clpV gene deletion did not affect the growth ability of hvKP. However, knocking out the clpV gene markedly decreased the mucoid phenotype and the biofilm formation ability of hvKP. It reduced the interspecific competition of hvKP with Escherichia coli, Salmonella, Pseudomonas aeruginosa, and Staphylococcus aureus. The clpV deletion significantly changed the transcriptome profile of hvKP, inhibited the expression of virulence factors, and decreased the lethality of hvKP against Galleria mellonella larvae. In vitro experiments showed that lithocholic acid could inhibit the expression of the clpV gene and reduce the virulence of hvKP. Our data suggested that the clpV gene may be a potential target for decreasing hvKP infection risk.

Pathogen-pathogen interactions during co-infections

For over a century, bacterial infections have been studied through the lens of the one-microbe, one-disease paradigm. However, it is now clear that multi-pathogen infections are common, and many infectious diseases are inherently polymicrobial. These complex infections can involve a variety of pathogens, including viruses, bacteria, fungi, and parasites, with polyviral and viral-bacterial interactions being the most extensively studied. In this review, we focus on polybacterial infections, providing an in-depth analysis of the diverse strategies bacteria employ to thrive in co-infection scenarios. We examine the mechanisms of bacterial competition, competition avoidance through spatial or temporal separation, and cooperation. Given the association of polymicrobial infections with more severe clinical outcomes and heightened antibiotic tolerance, we also explore novel therapeutic targets to treat these increasingly common and complex infections. Although our review summarizes current knowledge, the vast scope of this phenomenon suggests that many more mechanisms remain undiscovered and warrant further investigation.

Production of α-amylase from gluconate and carbon dioxide by protein synthesis and secretion optimization in Cupriavidus necator H16

Chemoautotrophic Cupriavidus necator H16 has a strong protein synthesis ability and has been used to produce intracellular protein products. However, studies optimizing its secretion system and the producing extracellular enzyme products (EEPs) are lacking. Here, we focused on investigating the feasibility of synthesizing and secreting EEPs in C. necator H16, using α-amylase as a prototype. α-Amylase expression optimization, genome modification, and secretion system engineering were performed to construct and optimize the α-amylase-producing engineering C. necator H16. Finally, the optimized engineering strain could produce α-amylase, with the α-amylase activity per unit cells reaching up to 5.54 U/OD600 using gluconate as substrate, which was 29.2-fold compared with that of initial engineering strain. Additionally, when using carbon dioxide as substrate, the α-amylase activity per unit cells of engineered strain reached 4.26 U/OD600. Overall, this study demonstrates the feasibility of developing C. necator H16 as a host for autotrophic production of α-amylase.

Inhibition of Xanthomonas growth by bioactive volatiles from Pseudomonas sp. triggers remarkable changes in the phytopathogen transcriptome

Volatile organic compounds (VOCs) produced by microorganisms may have a noteworthy role in the control of plant pathogens. Xanthomonas are a well-studied group of phytobacteria that cause diverse diseases in economically important crops worldwide. Key species that infect sugarcane are X. albilineans (Xab) and X. axonopodis pv. vasculorum (Xav). Here, we investigated VOC-producing bacteria with antagonistic effects against Xab and Xav. We demonstrated that VOCs produced by Pseudomonas sp. V5-S-D11 was able to abolish the growth of these pathogens. A set of 32 VOCs was identified in the volatilome of V5-S-D11, with 10 showing a concentration-dependent inhibitory effect on both phytobacteria. Among them, dimethyl disulfide (DMDS), a volatile sulfur compound, has the potential to be biotechnologically explored in agriculture since it can improve plant growth and induce systemic resistance against plant pathogens. Interestingly, transcriptomic analysis of Xab treated with DMDS revealed several up-regulated metabolic pathways such as a two-component system, flagellar assembly, chemotaxis, and a bacterial secretion system. Although the ethanol (ETOH) used as DMDS solvent did not inhibit Xab growth, it triggered a similar up-regulation of some genes, indicating that this phytopathogen can deal with ETOH better than DMDS. Overall, this study explores the wide role of VOCs in the interactions with bacteria. Moreover, our results indicate that VOCs from Pseudomonas sp. may represent a novel biotechnological strategy to counteract diseases caused by Xanthomonas species and can be further exploited for sustainable approaches in agriculture.

Guards and decoys: RIPoptosome and inflammasome pathway regulators of bacterial effector-triggered immunity

Virulent microbes produce proteins that interact with host cell targets to promote pathogenesis. For example, virulent bacterial pathogens have proteins called effectors that are typically enzymes and are secreted into host cells. To detect and respond to the activities of effectors, diverse phyla of host organisms evolved effector-triggered immunity (ETI). In ETI, effectors are often sensed indirectly by detection of their virulence activities in host cells. ETI mechanisms can be complex and involve several classes of host proteins. Guards monitor the functional or physical integrity of another host protein, the guardee or decoy, and become activated to initiate an immune response when the guardee or decoy is modified or disrupted by an effector. A guardee typically has an intrinsic anti-pathogen function and is the intended target of an effector. A decoy structurally mimics a host protein that has intrinsic anti-pathogen activity and is unintentionally targeted by an effector. A decoy can be an individual protein, or a protein domain integrated into a guard. Here, we review the origins of ETI and focus on 5 mechanisms, in which the key steps of a pathway can include activation of a caspase by a RIPoptosome or inflammasome, formation of pores in the plasma membrane, release of cytokines and ending in cell death by pyroptosis. Survey of the 5 mechanisms, which have been shown to be host protective in mouse models of bacterial infection, reveal how distinct regulators of RIPoptosome or inflammasome pathways can act as guards or integrated decoys to trigger ETI. Common themes are highlighted and the limited mechanistic understanding of ETI bactericidal activity is discussed.

Symbiotic T6SS affects horizontal transmission of Paraburkholderia bonniea among Dictyostelium discoideum amoeba hosts

Three species of Paraburkholderia are able to form facultative symbiotic relationships with the amoeba, Dictyostelium discoideum. These symbiotic Paraburkholderia share a type VI secretion system (T6SS) that is absent in other close relatives. We tested the phenotypic and transcriptional effect of tssH ATPase gene disruption in P. bonniea on its symbiosis with D. discoideum. We hypothesized that the ∆tssH mutant would have a significantly reduced ability to affect host fitness or transmit itself from host to host. We found that the T6SS does not directly affect host fitness. Instead, wildtype P. bonniea had significantly higher rates of horizontal transmission compared to ∆tssH. In addition, we observed significant differences in the range of infection prevalence achieved by wildtype vs. ∆tssH symbionts over multiple host social stages in the absence of opportunities for environmental symbiont acquisition. Successful symbiont transmission significantly contributes to sustained symbiotic association. Therefore, the shared T6SS appears necessary for a long-term evolutionary relationship between D. discoideum and its Paraburkholderia symbionts. The lack of difference in host fitness outcomes was confirmed by indistinguishable host gene expression patterns between hosts infected by wildtype or ∆tssH P. bonniea in an RNA-seq time series. These data also provided insight into how Paraburkholderia symbionts may evade phagocytosis by its amoeba host. Most significantly, cellular oxidant detoxification and lysosomal hydrolase delivery appear to be subject to the push and pull of host-symbiont crosstalk.

Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation

Bacteria genetically engineered to execute defined therapeutic and diagnostic functions in physiological settings can be applied to colonize the human microbiome, providing in situ surveillance and conditional disease modulation. However, many engineered microbes can only respond to single-input environmental factors, limiting their tunability, precision, and effectiveness as living diagnostic and therapeutic systems. For engineering microbes to improve complex chronic disorders such as inflammatory bowel disease, the bacteria must respond to combinations of stimuli in the proper context and time. This work implements a previously characterized split activator AND logic gate in the probiotic Escherichia coli strain Nissle 1917 (EcN). Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, anhydrotetracycline (aTc), for manual control. We report 4-6 fold induction with a minimal leak when the two chemical signals are present. We model the AND gate dynamics using chemical reaction networks and tune parameters in silico to identify critical perturbations that affect our circuit's selectivity. Finally, we engineer the optimized AND gate to secrete a therapeutic anti-inflammatory cytokine IL-22 using the hemolysin secretion pathway in the probiotic E. coli strain. We used a germ-free transwell model of the human gut epithelium to show that our engineering bacteria produce similar host cytokine responses compared to recombinant cytokine. Our study presents a scalable workflow to engineer cytokine-secreting microbes driven by logical signal processing. It demonstrates the feasibility of IL-22 derived from probiotic EcN with minimal off-target effects in a gut epithelial context.

Structural and functional analysis of the Helicobacter pylori lipoprotein chaperone LolA

Lipoproteins are crucial for maintaining the structural integrity of bacterial membranes. In Gram-negative bacteria, the localization of lipoprotein (Lol) system facilitates the transport of these proteins from the inner membrane to the outer membrane. In Helicobacter pylori, an ε-proteobacterium, lipoprotein transport differs significantly from the canonical and well-studied system in Escherichia coli, particularly due to the absence of LolB and the use of a LolF homodimer instead of the LolCE heterodimer. This study presents the crystal structure of the H. pylori lipoprotein chaperone LolA (LolA-HP) and its interaction with lipopeptide antibiotics such as polymyxin B and colistin. Isothermal titration calorimetry revealed that, unlike LolA from Vibrio cholerae and Porphyromonas gingivalis, LolA-HP does not bind to these antibiotics. Structural comparisons showed that LolA-HP has a deeper hydrophobic cleft but lacks the negative electrostatic potential critical for binding polymyxins. These findings offer insights into the structural diversity of LolA across bacterial species and its potential as a target for antibacterial agents.

Protein import into bacterial endosymbionts and evolving organelles

Bacterial endosymbionts are common throughout the eukaryotic tree of life and provide a range of essential functions. The intricate integration of bacterial endosymbionts into a host led to the formation of the energy-converting organelles, mitochondria and plastids, that have shaped eukaryotic evolution. Protein import from the host has been regarded as one of the distinguishing features of organelles as compared to endosymbionts. In recent years, research has delved deeper into a diverse range of endosymbioses and discovered evidence for 'exceptional' instances of protein import outside of the canonical organelles. Here we review the current evidence for protein import into bacterial endosymbionts. We cover both 'recently evolved' organelles, where there is evidence for hundreds of imported proteins, and endosymbiotic systems where currently only single protein import candidates are described. We discuss the challenges of establishing protein import machineries and the diversity of mechanisms that have independently evolved to solve them. Understanding these systems and the different independent mechanisms, they have evolved is critical to elucidate how cellular integration arises and deepens at the endosymbiont to organelle interface. We finish by suggesting approaches that could be used in the future to address the open questions. Overall, we believe that the evidence now suggests that protein import into bacterial endosymbionts is more common than generally realized, and thus that there is an increasing number of partnerships that blur the distinction between endosymbiont and organelle.

T6SS-associated Rhs toxin-encapsulating shells: Structural and bioinformatical insights into bacterial weaponry and self-protection

Bacteria use the type VI secretion system (T6SS) to secrete toxins into pro- and eukaryotic cells via machinery consisting of a contractile sheath and a rigid tube. Rearrangement hotspot (Rhs) proteins represent one of the most common T6SS effectors. The Rhs C-terminal toxin domain displays great functional diversity, while the Rhs core is characterized by YD repeats. We elucidate the Rhs core structures of PAAR- and VgrG-linked Rhs proteins from Salmonella bongori and Advenella mimigardefordensis, respectively. The Rhs core forms a large shell of β-sheets with a negatively charged interior and encloses a large volume. The S. bongori Rhs toxin does not lead to ordered density in the Rhs shell, suggesting the toxin is unfolded. Together with bioinformatics analysis showing that Rhs toxins predominantly act intracellularly, this suggests that the Rhs core functions two-fold, as a safety feature for the producer cell and as delivery mechanism for the toxin.

Controlling tumor progression and recurrence in mice through combined treatment with a PD-L1 inhibitor and a designer Salmonella strain that delivers GM-CSF

Combination therapy with checkpoint inhibitors blocks inhibitory immune cell signaling and improves clinical responses to anticancer treatments. However, continued development of innovative and controllable delivery systems for immune-stimulating agents is necessary to optimize clinical responses. Herein, we engineered Salmonella to deliver recombinant granulocyte macrophage colony stimulating factor (GM-CSF) in a controllable manner for combination treatment with a programmed death-ligand 1 (PD-L1) inhibitor. The engineered Salmonella enabled delivery of recombinant GM-CSF into mouse tumors, activating recruitment of immune cells, such as M1-polarized macrophages, dendritic cells, and CD8+ T cells. Combination treatment with the PD-L1 inhibitor and engineered Salmonella increased the survival rate of tumor-bearing mice by 25%. New tumor growth was strongly suppressed, and visible tumors disappeared at 120 days post-infection (dpi) in mice rechallenged with additional tumor implantation at 100 dpi. The number of memory T cells increased >2-fold in tumor-rechallenged mice. Our findings demonstrate superiority of the engineered Salmonella as a cancer therapeutic agent with precise targeting ability, immune-boosting activity, and ease of combination with other therapeutics.

The twin-arginine translocation system is vital for cell adhesion and uptake of iron in the cystic fibrosis pathogen Achromobacter xylosoxidans

Achromobacter xylosoxidans is an emerging pathogen that causes airway infections in patients with cystic fibrosis. Knowledge of virulence factors and protein secretion systems in this bacterium is limited. Twin arginine translocation (Tat) is a protein secretion system that transports folded proteins across the inner cell membranes of gram-negative bacteria. Tat has been shown to be important for virulence and cellular processes in many different bacterial species. This study aimed to investigate the role of Tat in iron metabolism and host cell adhesion in A. xylosoxidans. Putative Tat substrates in A. xylosoxidans were identified using the TatFind, TatP, and PRED-Tat prediction tools. An isogenic tatC deletion mutant (ΔtatC) was generated and phenotypically characterized. The wild-type and ΔtatC A. xylosoxidans were fractionated into cytosolic, membrane, and periplasmic fractions, and the expressed proteome of the different fractions was analysed using liquid chromatography-mass spectrometry (LC-MS/MS). A total of 128 putative Tat substrates were identified in the A. xylosoxidans proteome. The ΔtatC mutant showed attenuated host cell adhesion, growth rate, and iron acquisition. Twenty predicted Tat substrates were identified as expressed proteins in the periplasmic compartment, nine of which were associated with the wild type. The data indicate that Tat secretion is important for iron acquisition and host cell adhesion in A. xylosoxidans.

Synthetic translational coupling element for multiplexed signal processing and cellular control

Repurposing natural systems to develop customized functions in biological systems is one of the main thrusts of synthetic biology. Translational coupling is a common phenomenon in diverse polycistronic operons for efficient allocation of limited genetic space and cellular resources. These beneficial features of translation coupling can provide exciting opportunities for creating novel synthetic biological devices. Here, we introduce a modular synthetic translational coupling element (synTCE) and integrate this design with de novo designed riboregulators, toehold switches. A systematic exploration of sequence domain variants for synTCEs led to the identification of critical design considerations for improving the system performance. Next, this design approach was seamlessly integrated into logic computations and applied to construct multi-output transcripts with well-defined stoichiometric control. This module was further applied to signaling cascades for combined signal transduction and multi-input/multi-output synthetic devices. Further, the synTCEs can precisely manipulate the N-terminal ends of output proteins, facilitating effective protein localization and cellular population control. Therefore, the synTCEs could enhance computational capability and applicability of riboregulators for reprogramming biological systems, leading to future applications in synthetic biology, metabolic engineering and biotechnology.

Perforation of the host cell plasma membrane during Toxoplasma gondii invasion requires rhoptry exocytosis

Toxoplasma gondii is an obligate intracellular parasite, and the delivery of effector proteins from the parasite into the host cell during invasion is critical for invasion itself and for parasite virulence. The effector proteins are released from specialized apical secretory organelles known as rhoptries. While much has been learned recently about the structure and composition of the rhoptry exocytic machinery and the function of individual rhoptry effector proteins that are exocytosed, virtually nothing is known about how the released proteins are translocated across the host cell plasma membrane. Previous electrophysiology experiments reported an unanticipated observation that invasion by T. gondii is preceded by a transient increase in host cell plasma membrane conductance. Here, we confirm this electrophysiological observation and propose that the conductance transient represents a parasite-induced perforation in the host cell plasma membrane through which rhoptry proteins are delivered. As a first step towards testing this hypothesis, and to provide higher throughput than patch clamp electrophysiology, we developed an alternative assay to detect the perforation. This assay utilizes high-speed, multi-wavelength fluorescence imaging to enable simultaneous visualization of host cell perforation and parasite invasion. Using this assay, we interrogated a panel of mutant parasites conditionally depleted of key invasion-related proteins. Parasites lacking signaling proteins involved in triggering rhoptry secretion (e.g., CLAMP) or components of the rhoptry exocytic machinery (e.g., Nd9, RASP2) are defective in their ability to induce the perforation. These data are consistent with a model in which the perforating agents that disrupt host cell membrane integrity during invasion - and may thereby provide the conduit for delivery of rhoptry effector proteins - are stored within the rhoptries themselves and released upon contact with the host cell.

Beta-hemolytic Streptococci in respiratory illness

Beta-hemolytic Streptococci are associated with various respiratory illnesses, such as pharyngitis, scarlet fever and pneumonia, highlighting the need for enhanced diagnostic, therapeutic and preventive strategies. Advances in immunology and molecular biology have provided insights into the etiology and host immune responses to these infections, but many questions remain unanswered. Further research is needed to develop advanced diagnostics, explore vaccine candidates, understand immune responses and address antibiotic resistance. Epidemiological studies are crucial to improving our understanding of these infections and their public health impact. A multidisciplinary approach integrating epidemiology, microbiology, immunology and clinical medicine is essential to reduce the burden of beta-hemolytic streptococcal infections and improve overall treatment and prevention efforts.

Enhanced anti-cancer efficacy of arginine deaminase expressed by tumor-seeking Salmonella Gallinarum

Amino acid deprivation, particularly of nonessential amino acids that can be synthesized by normal cells but not by cancer cells with specific defects in the biosynthesis pathway, has emerged as a potential strategy in cancer therapeutics. In normal cells, arginine is synthesized from citrulline in two steps via two enzymes: argininosuccinate synthetase (ASS1) and argininosuccinate lyase. Several cancer cells exhibit arginine auxotrophy due to the loss or down-regulation of ASS1. These cells undergo starvation-induced cell death in the presence of arginine-degrading enzymes such as arginine deaminase (ADI). Thus, ADI has emerged as a potential therapeutic in cancer therapy. However, the use of ADI has two major disadvantages: ADI of bacterial origin is strongly antigenic in mammals, and ADI has a short circulation half-life (∼5 h). In this study, we engineered tumor-targeting Salmonella Gallinarum to express and secrete ADI and deployed this strain into mice implanted with ASS1-defective mouse colorectal cancer (CT26) through an intravenous route. A notable antitumor effect was observed, suggesting that the disadvantages were overcome as ADI was expressed constitutively by tumor-targeting bacteria. A combination with chloroquine, which inhibits the induction of autophagy, further enhanced the effect. Anti-cancer effect of Salmonella Gallinarum expressing an arginine deiminase (ADI) on arginine-dependent tumors in situ.

Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle

BACKGROUND

Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.

RESULTS

We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.

CONCLUSIONS

We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-µm filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract.