Molecular Microbiology

In most bacteria, peptidoglycan contains mainly 4-3 crosslinks formed by penicillin-binding proteins (PBPs). But in the opportunistic pathogen Clostridioides difficile, 70% of the crosslinks are 3-3 crosslinks formed by L,D-transpeptidases (LDTs), and LDTs are essential for viability. PBPs and LDTs use different acyl donors for crosslinking; PBPs require a pentapeptide, while LDTs require a tetrapeptide. Here, we determined the source of the tetrapeptides in C. difficile and investigated the consequences of reengineering PG crosslinking from predominantly 3-3 to exclusively 4-3. We found that two D-alanyl-D-alanine carboxypeptidases (DD-CPase), DacA and DacC, supply LDTs with tetrapeptides during vegetative growth. Deleting these enzymes was sufficient to bypass the normal requirement for LDTs. The resulting mutant ({Delta}dacAC {Delta}ldt) was remarkably healthy despite the absence of 3-3 crosslinks. Its only major phenotypic defect was a 3- to 4-log decrease in sporulation, which could, however, be overcome by deleting a third DD-CPase, dacB. These findings fill gaps in our understanding of the pathway for LD-transpeptidation in C. difficile and imply that LDTs are not essential components of the elongasome or divisome, both of which function well in the complete absence of LDTs, provided there is sufficient pentapeptide to sustain crosslinking by PBPs. Thus, LDTs are essential for viability because C. difficile has intrinsically high levels of DD-CPase activity. Finally, we propose a model for how PBPs and LDTs work together during PG synthesis. In this model, PBPs construct a sparsely crosslinked PG sacculus that is subsequently strengthened with crosslinks introduced by LDTs.

The horizontally acquired mgtC gene from Salmonella enterica confers this bacterium the abilities to survive episodes of magnesium (Mg2+) starvation, and to replicate in mammalian macrophages. The former property allows bacteria to persist in the environment through periods of Mg2+ depletion, whereas the latter allows S. enterica to overcome self-limiting intestinal colonization and cause an invasive systemic infection in susceptible mammalian hosts. Even though the biochemical function of MgtC is not completely understood, this protein is thought to function primarily by preventing the production of toxic levels of Mg2+-chelating adenosine triphosphate (ATP). In the current work, we investigated the physiological roles of mgtC homologs from an array of bacterial species, by probing the processes controlled by this gene during replication in low Mg2+ medium and in macrophages. We determined that MgtC homologs that do not participate in Pi homeostasis during Mg2+ starvation and do not promote intramacrophage replication in their resident species can partake in these processes when expressed in S. enterica. This indicates that the function of this protein is context dependent. Accordingly, we show that the physiological processes affected by S. enterica MgtC vary, depending on whether the bacteria replicate in low Mg2+ medium or inside macrophages. While these results suggest that MgtC is a regulator, they also demonstrate that horizontally acquired genes can assume different roles, depending on the genome and the biochemical context into which they are inserted. ImportanceThe mgtC gene encodes an inner membrane protein that has been horizontally acquired by multiple bacterial species, including several mammalian pathogens. In Salmonella enterica, MgtC promotes replication in mammalian macrophages and allows this bacterium to survive cytoplasmic magnesium (Mg2+) starvation. These phenotypes are thought to result from MgtCs inhibition of Pi metabolism and ATP production, which prevents the accumulation of toxic levels of Mg2+-chelating ATP and disrupts other physiological processes that are strictly dependent on Mg2+, such as ribosome assembly and translation. In the current study, we show that processes that are controlled by MgtC vary with the genetic and biochemical contexts in which this protein is expressed. While establishing a broader role for MgtC as a regulator, our findings illustrate how horizontally acquired regulatory genes can potentiate regulatory interactions, facilitating the evolution of new traits.

Small RNAs (sRNAs) rarely cause strong growth phenotypes upon overexpression, complicating efforts to link regulatory interactions to physiological outcomes. Here, we report that high levels of the Escherichia coli sRNA OmrA, but not its sibling OmrB, severely inhibit growth in glucose minimal medium. Genetic, biochemical, and physiological analyses indicate that OmrA-dependent toxicity results from reduced flux through the tricarboxylic acid (TCA) cycle. A UV-based suppressor screen identified mutations in the gene encoding Hfq, the RNA-chaperone that aids sRNA-mRNA interactions. Secondly, three independent mutations clustered in the ribosome-binding site of ppc, encoding phosphoenolpyruvate carboxylase, a key anaplerotic enzyme. OmrA directly inhibits Ppc translation via Hfq-dependent base-pairing in the ppc 5' UTR, including the mutated nucleotides obtained in the genetic screen. OmrA is significantly more effective than OmrB in ppc repression in vivo and in vitro, consistent with sequence divergence in their central regions. Supplementation with glutamate, glutamine, or downstream TCA cycle metabolites fully restores growth, linking reduced Ppc levels to metabolic limitation. These results identify ppc as a physiologically relevant OmrA target and suggest how RNA toxicity can uncover central metabolic nodes used by sRNAs to modulate bacterial physiology.

The Escherichia coli protein YbeX/CorC is encoded in the same operon as the ribosome biogenesis factor YbeY, and its deletion leads to accumulation of 17S pre-rRNA and degradation intermediates of 16S rRNA under magnesium limitation. To further investigate the ybeX deletion phenotype, we used rRNA fluorescence in situ hybridization coupled with flow cytometry (rRNA-FISH-flow) to quantify 16S rRNA, 23S rRNA, and 17S pre-rRNA levels at single-cell resolution in{Delta} ybeX and{Delta} ybeY strains.{Delta} ybeX cells grown under limiting Mg2+ develop striking cell-to-cell heterogeneity in 17S pre-rRNA content during the transition to stationary phase, with up to 25-fold differences between individual cells. Upon regrowth from the stationary phase,{Delta} ybeX cultures display a bimodal distribution of 17S pre-rRNA, revealing two distinct subpopulations -- one retaining high levels of unprocessed pre-rRNA and the other with low levels -- whose relative proportions shift over time, until visible growth resumes. The stoichiometry between mature 16S and 23S rRNAs remains tight in both strains, indicating that the heterogeneity is specific to pre-rRNA processing, rather than a general disruption of ribosome homeostasis. The{Delta} ybeY mutant accumulates 17S pre-rRNA more uniformly across cells and primarily during exponential growth in rich medium, consistent with its direct role in 16S rRNA maturation. These single-cell data suggest that YbeX and YbeY affect ribosomal RNA metabolism through distinct mechanisms and that the extended lag phase of{Delta} ybeX is caused by a heterogeneous clearing of pre-ribosomal intermediates in individual cells.

GlnH is an amino acid binding protein that senses aspartate to regulate metabolism via the PknG pathway in diverse Actinobacteria. Information about ligand occupancy of periplasmic GlnH is conveyed to PknG via an uncharacterised transmembrane protein GlnX. This pathway is important in the virulence of Mycobacterium tuberculosis, and in regulating valuable industrial fermentations by Corynebacterium glutamicum. GlnH has a "Venus flytrap"-like structure, comprising two lobes that surround the ligand aspartate. However, the conformational changes that allow GlnH to initiate this signalling pathway are unknown. To address this question, we produced GlnH from pathogens M. tuberculosis and Mycobacterium marinum and non-pathogens Mycobacterium smegmatis and C. glutamicum and used X-ray crystallography and cryo-EM to determine their structures. The results show that amino acid specificity is conserved in all homologues. However, GlnH from Mycobacteria was monomeric and bound aspartate with nanomolar affinity, whereas GlnH from C. glutamicum bound aspartate with micromolar affinity and dimerised upon binding. Whilst GlnH of the non-pathogens was stable at neutral pH, GlnH from the pathogens was most stable at acidic pH, reflecting the environment of host phagosomes. Structures were determined for all homologues, but only M. smegmatis GlnH crystallised in both unbound (Apo) and Asp-bound forms. GlnH has an open structure with a cleft between the lobes to permit access to aspartate. The Asp-bound structure is more compact with the lobes locked together, completely enclosing the ligand. AlphaFold was used to design mutations to disrupt the predicted GlnH-GlnX interface, and these variants failed to complement the metabolic defect of glnX knockout in M. smegmatis, supporting the predicted complex and suggesting how the GlnH conformational change is transmitted GlnX to initiate signalling.

The type VII secretion system (T7SS) is found in many Gram-positive bacteria and secretes toxins with antibacterial activity. Most characterised substrates have an N-terminal LXG domain that interacts with other helical partner proteins to form a composite T7SS targeting signal. Here we describe only the second substrate family to have a reverse domain arrangement. We show that TslM has a C-terminal LXG-like domain and an N-terminal lipase domain that has phospholipase activity. Secretion of TslM requires a single helical partner protein that binds to the TslM C-terminus, and its toxic activity is neutralised by a distinct family of membrane proteins. Genome analysis reveals that Staphylococcus aureus strains have the capacity to encode up to seven paralogous copies of this toxin family. Taken together our findings show that lipases are an important component of the staphylococcal T7SS toxin arsenal, and that toxins with a reverse domain arrangement are more widespread than previously appreciated.

Many protozoan parasites have complex life cycles entailing migration through different organs in their hosts, but the cues guiding them remain poorly understood. Using a semi-solid plate motility assay, we show that early procyclic forms of Trypanosoma brucei, the first stage to develop in the tsetse fly midgut, perceive several metabolites - including glucose, glycerol and proline - as chemoattractants, while the glycolytic end-product succinate acts as a repellent. During adaptation in the fly, T. brucei switches from glucose/glycerol to proline as its primary energy source. We show that the parasite's chemotactic response towards proline requires adenylate cyclase ACP5 and the cyclic AMP response protein CARP3, two components of signalling pathway involved in pH sensing. These results further support a role for T. brucei's expanded repertoire of receptor adenylate cyclases as environmental sensors that guide navigation through the host.

Analysis of RNA-binding proteome data from different bacterial species revealed many cell wall metabolic enzymes cross-linking to RNA in vivo, hinting that these proteins directly bind RNA. Surprisingly, penicillin-binding proteins (PBPs) were also abundantly identified as putative RNA-binding proteins. The cell surface localisation properties of many of these proteins therefore beg the question at what stage of their cellular life cycle these proteins interact with RNA and what the functional significance is. Here, we characterised the RNA-binding activity of PBP2a, the alternative transpeptidase that confers {beta}-lactam resistance in MRSA. Using in vivo RNA-binding assays, we show that PBP2a interacts with hundreds of transcripts without apparent sequence specificity. Computational analyses identified a possible RNA-binding cleft in PBP2a proximal to its active site. Mutation of only two predicted positively charged residues located in this cleft substantially reduced cross-linking in vivo, implying that RNA recognition is largely dictated by RNA backbone interactions. While PBP2a does not regulate RNA steady-state levels, RNA-binding appears important for proper protein function: an RNA-binding deficient mutant exhibits reduced oxacillin resistance. These findings establish PBP2a as an RNA-binding protein in vivo and provide a framework to investigate how this non-canonical interaction may relate to cell wall biogenesis and {beta}-lactam resistance.

Bacteria in natural environments frequently encounter nutrient limitation leading to growth arrest and must balance the potential benefits of continuing to respond to the environment by making new proteins against the costs of depleting limited resources. We previously showed that the RNA polymerase-binding regulator SutA enhances transcription of hundreds of genes during nutrient limitation in Pseudomonas aeruginosa, suggesting that it might be part of a regulatory network facilitating limited new protein synthesis. Here, we sought to expand our understanding of this network by identifying transcriptional regulators influencing sutA expression. Using northern blotting, western blotting, and reporter assays, we found that the sigma factors FliA and RpoS, and the DNA-binding regulator Lrp, impact expression from a proximal sutA promoter during the transition to stationary phase. This constellation of regulators and the dynamics of SutA expression lead us to propose that SutA is part of a regulatory network that facilitates scavenging. Scavenging includes motility toward possible nutrient sources and uptake mechanisms for these nutrients, activities which require an investment of resources but can yield important benefits during starvation. In vitro transcription experiments, proteomic analysis and reporter assays suggest that SutA directly supports new protein synthesis driven by RpoS and indirectly supports flagellar motility, perhaps by helping maintain protein biosynthetic capacity against the metabolic costs of motility. SutA expression is controlled by multiple regulatory inputs, including negative autoregulation, and the protein appears to be short-lived. These properties are consistent with a role in supporting short, controlled bursts of gene expression during nutrient limitation. Author StatementMany bacteria engage in cycles of colonising a nutrient-rich location, using the available nutrients, and then dispersing in search of a new location to colonise. While searching for new nutrients in a low-resource environment, bacteria will be starved and must coordinate resource-intensive processes such as new protein synthesis, motility, and nutrient uptake so that each crucial activity can be accomplished but none use too much of the limited pool of resources. We previously identified a regulator in Pseudomonas aeruginosa called SutA, which facilitates new protein synthesis under starvation conditions. Here, we have identified regulators of SutA expression. We find that the housekeeping sigma factor RpoD drives expression during growth, but at the entry to stationary phase, where SutA has obvious impacts on cellular physiology, the stress sigma factor RpoS, the flagellar sigma factor FliA, and the amino acid sensing transcription factor Lrp are important. Finally, we find that all cells in a nutrient-limited population express some SutA, but appear to do so in infrequent bursts, and that the protein is likely unstable. Together, these findings suggest that SutA contributes to the coordination of resource use while bacteria scavenge for new nutrients, facilitating limited amounts of new protein synthesis.

The Min system disassembles FtsZ-rings after septation in Bacillus subtilis and is localized to the nascent division plane and cell poles by the protein MinJ. The N-terminal region of MinJ contains transmembrane segments while the C-terminal region of MinJ contains a PDZ domain but its topology and functional domains are poorly understood. Here we empirically test MinJ topology based on a variety of transmembrane prediction models and find that the data is most consistent with Alphafold3, which predicts a 9-pass transmembrane protein with an external N-terminus and internal C-terminus. Deletion analysis indicates that all regions of the protein tested are required for function but deletion of the PDZ domain alone preserves polar localization and interaction with both MinD and DivIVA. Moreover, Alphafold predicts that transmembrane segments 6 and 7 comprise staves of an unusual transmembrane {beta}-sheet and deletion of the putative {beta}-sheet in the absence of MinD results in a minicell frequency that exceeds mutation of MinD alone. Bioinformatic analysis indicates that MinJ is highly conserved within Firmicutes and is co-conserved with MinD and DivIVA with which it interacts. Our data clarify the structure of MinJ and support models in which MinJ has functions in addition to restricting the activity of the Min system.

First described pyrroloquinoline quinone-dependent (PQQ) eight-bladed {beta}-propeller proteins are calcium (Ca)-dependent, but many homologous bacterial enzymes are lanthanide (Ln)-dependent. Discovery of Ca-dependent six-bladed {beta}-propeller PQQ-dependent dehydrogenases motivated the search for Ln-dependent six-bladed {beta}-propeller PQQ-dependent enzymes in bacteria. Using in silico structural prediction of sequences from weathered rock, we identified [~]22,000 PQQ six-bladed {beta}-propeller proteins in bacteria from 77 phyla, of which 63% of sequences have the active site residues needed to bind Ln. PQQ and La binding was biochemically confirmed for enzymes from uncultivated Chloroflexi and Acidobacteria. In structural models, Ln-binding periplasmic proteins interact with TonB-dependent transporters that may enable Ln uptake. Most genomes also encode predicted Ln-and PQQ-dependent eight-bladed dehydrogenases that clade with diverse alcohol and sugar dehydrogenases. Thus, Ln-dependent six and eight-bladed PQQ-dependent {beta}-propeller proteins are implicated in diverse carbon substrate metabolisms in weathering rock and soil. We predict that many PQQ-dependent microbial enzymes are lanthanide dependent.

Sulfolobus acidocaldarius is a thermoacidophilic archaeon used as a model system for studying fundamental cellular processes and for emerging biotechnological applications. However, the limited availability of selectable markers restricts advanced genetic manipulation in this organism. Here, we report the development of a tryptophan auxotrophy-based selection system in S. acidocaldarius. A {Delta}trpBA mutant was constructed in the {Delta}pyrE background strain using a classical pop-in/pop-out recombination strategy. The resulting mutant exhibited little growth defects in rich medium, likely due to exogenous tryptophan supplied by complex nutrients, but failed to grow in a newly developed defined Brock-based amino acid dropout medium lacking tryptophan. Exploiting both uracil and tryptophan auxotrophies, we achieved dual-plasmid co-transformation and co-expression of the surface layer proteins and a dominant-negative mutant of the AAA-ATPase Vps4, revealing that the accumulation of surface layer lattice forming protein SlaA at the midzone of division-arrested cells together with its membrane anchor SlaB. Together, these results provide evidence for spatial regulation of S-layer assembly during archaeal cytokinesis while expanding the genetic toolkit available for S. acidocaldarius. ImportanceSulfolobus acidocaldarius is a key archaeal model organism for studying cellular processes shared with more complex life and is increasingly used for biotechnological applications. Here, we establish tryptophan auxotrophy as a new selectable marker in S. acidocaldarius, expanding the range of genetic selection systems available in this organism. By developing a defined Brock-based dropout medium, we enable stringent amino acid auxotrophy selection and precise control over nutrient composition. This system can be combined with existing uracil-based selection to support dual auxotrophy workflows, enabling co-transformation, simultaneous expression of multiple proteins, and more sophisticated genetic manipulation strategies. Using both markers, we show that S-layer proteins are localised to the division bridge in cytokinesis-arrested cells. This exemplifies ways in which the expanding molecular genetic tool kit available for Sulfolobus acidocaldarius is furthering our understanding of archaeal cell biology.

Regulation of class A penicillin-binding proteins (aPBPs) in peptidoglycan biosynthesis is incompletely understood in Gram-positive bacteria. One example is activation of aPBP2a by GpsB and phosphorylated MacP in the ovoid-shaped pathogen, Streptococcus pneumoniae. We set out to examine whether phosphorylation of Thr residues other than Thr32 contributed to MacP activation of aPBP2a. We also wanted to determine whether GpsB and MacP activation of aPBP2a were related. Here we report that MacP was phosphorylated about equally at Thr32 and Thr56 in physiological and biochemical assays. However, based on transformation and growth assays, phosphorylation of MacP was not required for aPBP2a activation. A structure-function analysis confirmed that most of the MacP cytoplasmic domain, which was predicted by AlphaFold3 to be disordered, was not required for aPBP2a activation. These analyses further identified amino acids in the MacP transmembrane domain and the aPBP2a juxtamembrane region, as well as a variant of the GpsB-binding motif in the membrane-proximal cytoplasmic region of MacP, required for aPBP2a activation. Together, these results support a tripartite model in which GpsB acts as an adapter for activation of aPBP2a by MacP. Finally, additional interaction, Tn-seq, and growth assays suggested other modes of direct or indirect regulation of aPBP2a activity.

Mycobacterium tuberculosis (Mtb) must regulate intracellular iron to survive in the host and cause disease. IdeR (Iron-dependent Regulator) is an essential Mtb protein that governs intracellular iron levels by regulating the expression of genes involved in iron metabolism. IdeR expression, however, is iron independent, and the mechanisms that regulate IdeRs function are not fully understood. Here, we report the discovery of a previously unrecognized Mtb peptide (PRI) that regulates IdeR activity. PRI is induced under iron limitation; it binds to IdeR and restricts its activity. In addition, we demonstrate that altering the balance between PRI and IdeR impairs iron homeostasis and intracellular replication of Mtb in macrophages. The findings reveal a new paradigm in mycobacterial iron regulation and open new avenues for targeting iron homeostatic mechanisms in Mtb, which are crucial for virulence and antibiotic resistance.

The insertase Oxa1 is required for protein insertion into the inner mitochondrial membrane and for the biogenesis of oxidative phosphorylation complexes. While most eukaryotes encode one or two Oxa1 proteins, we identified three paralogs in Trypanosoma brucei: TbOxa1-1, TbOxa1-2, and TbOxa1-3. Knock-out of individual paralogs followed by phenotypic analyses and proteomic characterization of submitochondrial fractions revealed distinct functions. Respiratory chain complexes I and IV are primarily affected by loss of TbOxa1-1, whereas complex III and ATP synthase depend on TbOxa1-2; the ablation of TbOxa1-3 results in minor phenotypes in culture. In TbOxa1-2-depleted cells, ATP synthase biogenesis is compromised by the defective import or processing of the nuclear-encoded subunit-c, which also requires a rhomboid peptidase-like protein. Further, the ablation of TbOxa1-2 triggers accumulation of membrane proteins in the matrix, supporting its role in conservative sorting. Together, our results demonstrate that the trypanosomal Oxa1 machinery evolved a paralog-specific division of labor to manage a highly divergent mitochondrial membrane proteome.

Rhodopseudomonas palustris TIE-1 (TIE-1) is a metabolically versatile environmental bacterium that flourishes across gradients of iron, oxygen, and light. This versatility necessitates extensive regulatory control, exemplified by the aerobic-anaerobic metabolic shift controlled by the hierarchy of CRP/FNR-family regulators AadR and FixK. Many anaerobic metabolic pathways demand expression of iron cofactor-intensive proteins, and TIE-1 in particular can generate energy through phototrophic iron oxidation via the PioABC system. However, TIE-1 lacks canonical iron-sensing regulators: IscR, ancestral Fe(II)-sensing Fur, and Fe(II)-sensing RirA of Rhizobiaceae, leaving it unclear how TIE-1 coordinates expression of these iron-requiring metabolisms with bioavailable iron levels. Here, we demonstrate that the AadR-FixK hierarchy plays a previously underappreciated role in iron regulation in TIE-1 by comparing growth and transcription in wild-type and regulatory mutants across wetland-inspired naturomimetic conditions. {Delta}aadR and {Delta}fixK showed defects in iron-dependent growth and Fe(II) oxidation, and the {Delta}aadR{Delta}fixK double mutant was synthetically lethal under anaerobiosis. The regulatory hierarchy of FixK and AadR influences expression of Fur-family regulators: the two irr paralogs were oppositely regulated in the presence of AadR, and absence of AadR perturbed iron-responsive expression of mur. Furthermore, the AadR regulon was significantly enriched for iron-related and iron-containing proteins. Despite initial predictions that AadR directly regulates pioABC, we found no conclusive evidence for direct AadR activity at the pioABC promoter, refining the search for pio regulators. Together, these findings establish AadR as a central integrator of oxygen and iron signals to coordinate iron-requiring anaerobic metabolism in TIE-1.

Bloom-forming cyanobacteria thrive in highly dynamic light environments, yet the mechanisms enabling rapid acclimation to fluctuating irradiance remain poorly understood. Here, we compared light acclimation in the bloom-forming cyanobacterium Microcystis aeruginosa PCC 7806 and the non-bloom-forming model cyanobacterium Synechocystis sp. PCC 6803 and investigated the role of the cyanobacterial toxin microcystin (MC) and its in vivo binding partner RubisCO in this process. Whereas Synechocystis grew faster under sustained high light, Microcystis performed better under low light and responded to transient high-light exposure with a remarkably rapid increase in photosynthetic activity and glycogen accumulation. These responses were markedly attenuated in an MC-deficient mutant. Although RubisCO from Microcystis exhibited pronounced light-dependent changes in activity, MC had only minor effects on RubisCO catalysis, arguing against a direct role in regulating enzyme function. Instead, extracellular MC elicited a transient transcriptional program characterized by induction of inorganic carbon acquisition systems, including the high-affinity bicarbonate transporter BCT1, consistent with activation of the carbon-concentrating mechanism (CCM) and enhanced carbon fixation in vivo. MC further stimulated the expression of photosynthesis-related genes, and altered carboxysome organization, and promoted extracarboxysomal localization of RubisCO. Together, our findings identify MC as a light-responsive signaling molecule that coordinates CCM activity, carbon acquisition, and photosynthetic acclimation, thereby enhancing adaptation of Microcystis to fluctuating irradiance and potentially contributing to its ecological success in cyanobacterial blooms.

During endospore (spore) development in bacteria, polar cell division generates two transcriptionally distinct cellular compartments, the mother cell and future spore (forespore). Signalling between these cells leads to sequential and compartmentalized transcription, along with key morphogenetics events, including the phagocytic-like process of engulfment and the recruitment of coat proteins to the engulfing membrane. The SpoIVA ATPase is an essential sporulation protein that assembles into static filaments at the forespore surface during engulfment, where it functions as the basement layer for coat assembly. Here, using Bacillus subtilis, we reveal an additional role for SpoIVA during engulfment. Cytological analysis of a spoIVA null mutant ({Delta}spoIVA) revealed engulfment defects such as septal membrane bulges and asymmetric membrane migration, similar to those typically associated with impaired peptidoglycan remodelling during engulfment. Engulfment defects were exacerbated when {Delta}spoIVA was combined mutants known to impact engulfment progression and efficiency. Importantly, a spoIVA mutant (K30A) impaired for ATP hydrolysis and filament formation in vitro but partially functional for coat assembly in vivo, closely phenocopies the spoIVA null mutant engulfment defects. Based on these data, we propose a model whereby SpoIVA polymerisation at the spore surface, independently of coat assembly, plays a mechanical and structural role during engulfment, akin to the cytoskeletal proteins that drive phagocytosis in eukaryotic cells.

Toxoplasma gondii relies on tightly regulated protein synthesis to adapt to diverse host environments and to progress through its developmental stages. Here, we investigated the role of the ATP-binding cassette protein ABCE1, a broadly-conserved factor involved in ribosome recycling and translational control. Using a conditional knockdown approach, we demonstrate that depletion of TgABCE1 severely impairs parasite growth and disrupts global protein synthesis, confirming its essential role in maintaining translational capacity. TgABCE1 function depends on the incorporation of iron-sulfur (Fe-S) clusters, likely mediated by the cytosolic iron-sulfur assembly (CIA) pathway component HCF101. Depletion of TgABCE1 phenocopies the defects observed in TgHCF101-depleted parasites, supporting a functional link between these proteins. Notably, loss of TgABCE1 also disrupts lipid homeostasis, resulting in the accumulation of lipid droplets. Together, these findings uncover a critical link between translational regulation, Fe-S cluster biogenesis, and lipid homeostasis, highlighting the central role of proteostasis in parasite survival and development.

Bacteria use post-transcriptional regulatory mechanisms to rapidly adjust gene expression during environmental change. In the gut-associated genus Bacteroides, these mechanisms remain poorly defined as these organisms lack canonical RNA chaperones like Hfq and CsrA that coordinate post-transcriptional stress responses in many well-studied model bacteria. Most Bacteroides possess conserved RNA recognition motif-1 (RRM-1) domain-containing RNA-binding proteins (more common in eukaryotes than bacteria) that have been proposed to act as global RNA chaperones. Here, we show that these RNA binding proteins (RBPs) are central to cold stress adaptation. Simultaneous deletion of all rbp genes produces a cold-sensitive growth defect across multiple Bacteroides species, while single deletions do not, revealing conserved functional redundancy. RBP transcripts and proteins accumulate rapidly after temperature downshift, and loss of RBPs extensively reprograms the transcriptome. Cold sensitivity of Bacteroides rbp mutants is not caused by defects in ribosome assembly or rRNA maturation. Instead, we find that in Bacteroides thetaiotaomicron, RBPs act together with BT1884, the sole canonical cold shock protein possessed by this organism. The combined loss of RBPs and BT1884 produces a synthetic severe cold sensitivity phenotype, defining two functionally redundant cold stress systems belonging to unrelated protein families. Strains lacking RBPs show reduced survival under simultaneous cold and oxygen stress, the conditions Bacteroides cells are expected to encounter during host-to-host transmission. Together, these findings establish RRM-1 RBPs as non-canonical cold shock proteins that enable cold adaptation and environmental survival in Bacteroides and suggest how these organisms withstand the stresses of transmission between hosts. IMPORTANCEBacteroides species are among the most abundant and stable members of the human gut microbiome, and they are also among the most readily transmitted between people. Reaching a new host requires surviving conditions outside the gut, including cold and oxygen exposure, yet how these bacteria withstand such stress is not well understood. Most bacteria manage stress using a well-defined set of RNA-binding proteins, but Bacteroides lack these canonical factors. We show that Bacteroides instead rely on a different family of RNA-binding proteins, more typical of eukaryotes than bacteria, to survive cold stress, and that these proteins promote survival under the conditions encountered during transmission. This work identifies a molecular system that allows an abundant and ecologically successful gut bacterium to endure the environmental challenges of moving between hosts.