microLife最新文献

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.

Prokaryotic microorganisms coexist with mobile genetic elements (MGEs), which can be both genetic threats and evolutionary catalysts. In Haloferax lucentense, a halophilic archaeon, we have recently identified an unusual genomic arrangement: a complete type I-B CRISPR-Cas system encoded on a megaplasmid and an incomplete type I-B system within an integrated provirus in the main chromosome. The provirus-encoded system lacks the adaptation genes (cas1, cas2, and cas4), suggesting its potential reliance on the megaplasmid-encoded CRISPR-Cas module for the acquisition of new spacers. This arrangement suggests a potential instance of "adaptive outsourcing," where a provirus might leverage a co-resident MGE for a key function. Through comparative genomics, we show that similar proviral CRISPR-Cas systems are found in distantly related haloarchaea (e.g. Natrinema and Halobacterium), indicating probable virus-mediated horizontal transfer and suggesting they may function as mobile defense modules. Phylogenetic analysis highlights distinct evolutionary origins of the two systems: the plasmid system clusters with other Haloferax CRISPR-Cas systems, while the proviral system clusters with those from other genera, consistent with horizontal acquisition. Interestingly, spacer analysis reveals that the proviral systems predominantly target viral sequences, while the plasmid system appears to target both plasmids and viral sequences, a distribution mirroring broader trends observed in other plasmid- and chromosome-encoded CRISPR systems. This observed targeting preference suggests a potential for complementarity that could support a model of cooperative immunity, where each system may protect its genetic "owner" from competition and, indirectly, the host.

[This corrects the article DOI: 10.1093/femsml/uqaf019.].

Scientific publishing faces a credibility crisis driven to a very large extent by predatory journals, paper mills, and exploitative open-access (OA) practices. Structural pressures-publish-or-perish culture, mandatory OA policies, and author publication charges-driven business models-fuel the proliferation of low-quality or fraudulent research, now exacerbated by artificial intelligence-generated content. This opinion, which aligns with a growing clamour from the research community-calls for an international journal accreditation system, guided by a transparent code of conduct and enforced by funding agencies, to restore integrity, prioritize quality over quantity for professional progression, and safeguard trust in scientific communication.

Prokaryotic organisms execute multiple stress response mechanisms in order to cope with rapidly changing environments. Some mechanisms respond to specific cues, such as the OxyR-dependent response to hydrogen peroxide or the SOS-response that is induced upon DNA-damage. These specific responses complement general mechanisms that respond to multiple and diverse stressors. One example is nucleoid condensation, which is a rapid and effective mechanism for genome protection and observed in response to various stresses, including entry into stationary phase. Recently, the upregulation of small membrane proteins (SMPs) in response to stress was observed, but details on how this emerging class of proteins modulate the stress response is largely unknown. Here, we demonstrate that the production of two SMPs, YohP and YncL, cause nucleoid condensation in Escherichia coli. Nucleoid condensation is the result of YohP-/YncL-induced sublethal membrane depolarization, which induces the phage-shock response and leads to a reduction of global protein synthesis. YohP production also prevents the oligomerization of the antimicrobial peptide magainin-2 in the E. coli membrane and reduces the metabolic activity of E. coli cells. Thus, the synthesis of YohP and likely of other SMPs potentially protects bacterial cells against some unfavorable conditions by shifting them into a metabolically silent state.