microLife最新文献

Pyrobaculum arsenaticum and P. aerophilum are two hyperthermophiles that belong to the phylum Thermoproteota (also known as Crenarchaeota), order Thermoproteales. Pyrobaculum arsenaticum is an obligate anaerobe, whereas P. aerophilum is a facultatively aerobic organism. Both species have been described as capable of autotrophic growth with molecular hydrogen. Because their genomes lack genes encoding key enzymes for known autotrophic CO₂ fixation pathways, they have been discussed as organisms that may use unknown pathways. To establish reliable autotrophic cultures, we gradually reduced the supplied concentrations of yeast extract but, in our hands, autotrophy was not attainable for either of the two species. Analysis of the ¹³C-labelling of the biomass of the obtained mixotrophic cultures of P. arsenaticum grown on ¹³CO₂ + H₂ (20:80, v/v), using isotopologue profiling, revealed that their amino acids contained <30% of ¹³C. Amino acids were mainly labelled only in carboxyl groups, demonstrating their purely heterotrophic nature. Our data suggest that the ability to grow autotrophically in currently known Thermoproteales is strictly correlated with the presence of the genes for the dicarboxylate/4-hydroxybutyrate cycle. We discuss the reasons that may lead to misinterpretation of the data on the ability of prokaryotes to grow autotrophically.

Neutrophils are frontline responders against bacterial and fungal pathogens, requiring rapid energy and biosynthetic precursors to mount effective antimicrobial responses. To meet these demands, they primarily rely on aerobic glycolysis, making glucose uptake essential. Murine and human neutrophils express the glucose transporters GLUT1 and GLUT3; however, their specific roles in neutrophil immunobiology have not yet been fully elucidated. Here, we show that neutrophilic immune responses to Candida albicans and Staphylococcus aureus critically depend on GLUT1/3-dependent glucose uptake and glycolysis. Combined deletion of GLUT1 and GLUT3 almost completely abolished glucose uptake and aerobic glycolysis in murine neutrophils, yet did not impair granulopoiesis, indicating that homeostatic neutrophil development is largely independent of extracellular glucose. By contrast, during microbial challenge, loss of GLUT1/3 severely compromised NADPH-dependent ROS production, oxidative burst, and cyclooxygenase-derived lipid mediator (LM) biosynthesis, demonstrating that glucose uptake via GLUT1/3 controls inflammatory effector functions of neutrophils. Moreover, genetic and pharmacologic inhibition of GLUT1/3-mediated glucose utilization reprograms neutrophil metabolism and LM biosynthesis toward an immunomodulatory phenotype. These findings identify a conserved nutrient-sensing metabolic checkpoint that governs neutrophil reprogramming and highlight novel opportunities for therapeutic immunomodulation.

Bacteroidota, a diverse phylum of bacteria, includes classes whose members are increasingly recognized for their significant contributions to host health, particularly through their antimicrobial properties. This study investigates the functional diversity of 42 new Bacteroidia and Sphingobacteriia strains enriched and identified from diverse hosts, including mouse ceca and human stool samples. Using 16S rRNA gene sequencing, we phylogenetically characterized the strains of the genera Bacteroides, Phocaeicola, and Sphingobacterium and assessed their functional properties related to potential beneficial functions. The strains were evaluated concerning their ability to inhibit biofilm formation of the World Health Organization-declared clinically significant pathogens, including Gram-positive Staphylococcus aureus and Staphylococcus epidermidis, Gram-negative Klebsiella oxytoca and Pseudomonas aeruginosa, and the eukaryotic yeast Candida albicans. Additionally, we investigated bile salt hydrolase and quorum-quenching (QQ) activities of the strains, as these functions contribute to microbial community interactions and host-microbe dynamics. Our findings demonstrate that all examined Bacteroidota strains consistently exhibit a capacity to inhibit biofilm formation but to different extents. Furthermore, 14 strains showed QQ activity, and 39 bile salt hydrolase activity, indicating functional diversity among the isolates. High biofilm inhibition as well as QQ activity against both autoinducers, AHL and AI-2, were predominantly observed in Bacteroides caecimuris and Bacteroides muris. These traits suggest that such strains may play important roles in shaping microbial communities and interfering with pathogens and their communication. Overall, this study provides valuable insights into strain-specific functions that could support future microbiome-based strategies for pathogen control and host health modulation.

Brucella spp. are Gram-negative, facultative intracellular bacteria responsible for brucellosis, a globally prevalent zoonosis affecting both humans and animals. The genus includes several pathogenic species which primarily infect mammals but can cause chronic infections in humans through accidental transmission. As for most intracellular pathogens, Brucella pathogenicity relies on its capacity to invade host cells, evade immune defenses, and establish a replicative niche within a specialized organelle, the Brucella-containing vacuole (BCV). Central to this process is the VirB Type IV secretion system (T4SS), a highly conserved molecular apparatus used to translocate effector proteins (EPs) into host cells. These EPs manipulate diverse cellular pathways to promote bacterial survival, replication, and dissemination. This review provides an updated overview of the structure and function of the T4SS, based on a comparison with recent structural information gained on conjugative systems. The current repertoire of known effectors and their roles in host-pathogen interactions are also detailed, highlighting progress made in their identification. Finally, we discuss possible functions of T4SS and speculate on the mechanisms of effector translocation based on insights from other intracellular pathogens or secretion systems.

Small open reading frame (small ORF) encoded proteins fulfil important roles in many cellular processes. In the methanoarchaeon Methanosarcina mazei, numerous small proteins have previously been identified under different nitrogen-availabilities, with only few being subject to functional characterization. Consequently, a detailed expression analysis of small proteins translated under other stress conditions, in conjunction with conservation and sequence-based analyses, may reveal interesting candidates for future downstream analyses. Here, we investigated the small proteome of M. mazei under five growth conditions. By enriching the low molecular weight proteome and combining top-down and bottom-up proteomic analysis, a total of 234 small proteins were validated on protein level, of which 130 were found in top-down proteomics analysis, which were associated with 408 proteoforms. Aiming to unravel functions of the large number of small proteins, we performed sequence-based clustering with emphasis on the presence of characteristic motifs. Thereby, ferredoxin-like small proteins with putative iron-sulphur (Fe-S) cluster binding-sites, as well as possible zinc-binding proteins, both with distinct cysteine motifs, were identified. We further analysed heterologously expressed representatives of the ferredoxin-like and putative zinc-binding small proteins, confirming the zinc-binding capability of two small proteins of the latter group via inductively coupled plasma-mass spectrometry. Overall, the detailed analysis of the M. mazei small proteome under different growth conditions, using various proteomics approaches, as well as sequence-based analyses and biochemical approaches targeting specific protein candidates, represents a key step in systematically uncovering the functions of small proteins in M. mazei.

We investigated the role of cyclic di-adenosine monophosphate (c-di-AMP) in the halophilic archaeon Haloferax volcanii by analysing transcriptomic changes in a strain with lowered c-di-AMP levels and by characterizing the function of key RCK (regulator-of-conductance-of-K⁺) domain proteins. The c-di-AMP-reduced mutant showed elevated expression of cell division genes and metabolic enzymes, whereas a Na⁺/H⁺ antiporter and an aspartate aminotransferase were strongly repressed. These patterns reveal previously unknown links between this messenger and both cell division and osmolyte homeostasis. To probe downstream effectors, we created deletion mutants of four RCK domain proteins and observed distinct phenotypes under potassium or sodium limitation. Deleting the primary RCK protein, linked to a high-affinity potassium importer, abolished growth under potassium limitation and caused extreme cell enlargement under hypoosmotic conditions, underscoring its essential role in potassium uptake and cell volume control. Removing a secondary transporter-associated RCK protein caused only mild defects, mainly under low sodium, indicating an auxiliary potassium acquisition system. Two stand-alone RCK proteins (unlinked to transporters) were dispensable for normal growth yet critical during osmotic stress: one knockout alleviated excessive swelling of c-di-AMP-reduced cells, whereas the other caused hypersensitivity to low-salt conditions. Biochemical assays revealed that only transporter-associated RCK proteins bound c-di-AMP, suggesting direct control of potassium transport, while stand-alone RCK proteins mediate osmotic adaptation through c-di-AMP-independent mechanisms. These findings define a novel osmotic stress regulatory network in H. volcanii integrating second-messenger signalling with ion homeostasis, highlighting the broader importance of cyclic nucleotide signalling in archaeal stress adaptation.

Bacteria constantly adapt to changing environmental conditions through diverse processes that involve numerous regulator and effector proteins. In this regard, small proteins play a significant role in promoting stress adaptation in bacteria. Although they were largely overlooked in early genome annotations, recent technological advances and a growing recognition of their significance have paved the way for the increasing identification and characterization of this intriguing class of proteins. Many small proteins contain a transmembrane domain and are integral to the cytoplasmic membrane. Others interact with and modulate membrane protein complexes. In this review, we focus on the current knowledge of these small membrane proteins, with an emphasis on their interactions, membrane insertion pathways, and toxicity.

Bacteria use small regulatory RNAs (sRNAs) and small proteins to change gene expression and modulate cellular processes in response to changing environmental conditions. In addition, several transcripts have been reported to combine base-pairing sRNA activities and coding capacity. These transcripts are known as dual-function RNAs. In some cases, the sRNA and the protein operate within the same pathway, while in other cases, they modulate separate processes in the cell. Thereby, dual-function RNAs enable bacteria to adjust their gene expression and physiology at multiple levels, which can have synergistic regulatory effects or help to synchronize the output of cellular pathways. In this review, we summarized the regulatory and physiological roles of dual-function RNAs in bacteria, including their roles in intercellular communication, virulence, stress response, and metabolism. In addition, we discuss open challenges and possible future applications for harnessing dual regulators for precise gene expression control in bacteria.