Journal of Bacteriology最新文献

Methanol, a renewable non-food C1 substrate, holds great promise as a feedstock for sustainable biomanufacturing and carbon neutral production. However, its industrial application is hindered by low methanol assimilation efficiency in most microbes. Recent advances in synthetic biology and metabolic engineering have enabled the development of methylotrophic microbial cell factories through strategies including building efficient methanol-utilizing pathways, engineering methanol dehydrogenase for enhanced oxidation efficiency, and optimizing redox balance via cofactor utilization. Additionally, approaches such as mitigating the accumulation of toxic metabolites and adaptive laboratory evolution have been adopted to improve the robustness of synthetic methylotrophs. This review summarizes these innovations and provides a blueprint for rationally designing high-performance microbial platforms to facilitate industrial methanol utilization and advance sustainable development.

Caulobacter species are common residents of soil and aquatic ecosystems, where bioavailable iron is often extremely limited. Like other diderm bacteria, Caulobacter crescentus can acquire Fe(III) via outer-membrane TonB-dependent transporters (TBDTs) that recognize and import ferric siderophore complexes. Although C. crescentus is not known to synthesize siderophores, it encodes multiple TBDTs that are transcriptionally regulated by the ferric uptake repressor (Fur), suggesting it acquires iron by scavenging xenosiderophores produced by neighboring microbes. To identify C. crescentus genes required for xenosiderophore utilization, we developed a barcoded transposon screen using ferrioxamine B (FXB), a hydroxamate-family siderophore produced by soil actinomycetes, as a model substrate. This screen identified hiuABC, a conserved, Fur-regulated operon that supports FXB-dependent iron acquisition. We provide evidence that hiuA encodes the primary TBDT responsible for uptake of ferrioxamines and ferrichrome (FC), structurally distinct members of the hydroxamate siderophore family. hiuB encodes a PepSY-domain protein with structural similarity to Pseudomonas aeruginosa FoxB, a known periplasmic ferri-siderophore reductase. hiuC encodes a small, hypothetical membrane protein predicted to form a functional complex with HiuB in the inner membrane. Both hiuB and hiuC are required for utilization of FXB and ferrioxamine E, indicating a shared role in iron acquisition from ferrioxamines. Surprisingly, utilization of FC as an iron source required hiuB but not hiuC, suggesting a substrate-specific role for HiuC in ferri-siderophore processing. We conclude that the conserved hiuABC operon encodes a set of proteins that enable bacteria to acquire iron from structurally diverse hydroxamate-family siderophores.IMPORTANCEIron is often a limiting nutrient due to its poor solubility in the presence of oxygen. To overcome this, some microbes produce specialized molecules known as siderophores, which tightly bind and solubilize iron, facilitating its uptake into the cell. Caulobacter species are common in freshwater, marine, and soil environments, and there is emerging evidence that they play important roles in plant-associated microbial communities. Here, we report the discovery of a three-gene system that allows Caulobacter crescentus to acquire iron from a set of siderophores produced by select soil bacteria and fungi. We define functional roles for each protein component of this system, which informs a mechanism by which Caulobacter can pirate iron-scavenging molecules produced by its neighbors.

The Bacillus strain GB03, the first representative of a group of plant growth-promoting rhizobacteria, now designated Bacillus velezensis, was isolated as Bacillus subtilis A13 around 50 years ago from a wheat field in Australia. With the advent of genome sequencing, FZB42, another example of the same taxonomic group of plant-associated gram-positive bacteria, was sequenced in 2007. FZB42 and other B. velezensis strains devote a much higher proportion of their whole genomic capacity than the model B. subtilis to the synthesis of secondary metabolites with antimicrobial action. This review summarizes the history of discovery and agricultural use, as well as the impressive accumulation of our knowledge base about the mutualistic interactions of B. velezensis with plants obtained during the last two decades.

IncA/C and IncH plasmids commonly carry antimicrobial resistance genes, notably bla_NDM-1. Although these plasmids disseminate among Gram-negative pathogens via conjugation, the mechanisms underlying mating pair stabilization (MPS) and conjugation species specificity remain poorly understood. In IncF plasmids, MPS is mediated by interactions between outer membrane proteins (OMP) encoded by the plasmids in the donor (TraN) and by the chromosome in the recipient. Using the Plascad database, we extracted 1,436 TraN sequences from 1,517 plasmids: 62.5% (898/1,436), mainly in IncF plasmids, are 550-660 amino acids (aa) (we renamed TraN short, TraN_S); 15% (216/1,436), in IncA/C plasmids, are 880-950 aa (TraN medium, TraN_M); and 11% (160/1,436), in IncH plasmids, are 1,050-1,070 aa (TraN long, TraN_L). One TraN, found in six plasmids from Acinetobacter baumannii (891 aa), was designated TraN V-shaped (TraN_V). Like TraN_S, TraN_M and TraN_L contain a base and one distal tip domain essential for conjugation, whereas TraN_V has a base and two distinct tip domains forming a V-shaped structure. TraN_M, TraN_L, and TraN_V determine conjugation species specificity, with TraN_L cooperating with OmpA. Tip swapping reverses conjugation specificity, revealing how TraN_M and TraN_L diversity influence plasmid host range and AMR dissemination. Our new data reveal the molecular basis of plasmid host specificity and broaden our understanding of how conjugation drives the dissemination of antimicrobial resistance genes among clinically relevant bacteria.

Importance: Plasmid conjugation drives the spread of antimicrobial resistance genes between different bacterial species. In IncF plasmids, this process relies on tight interactions between an outer-membrane protein in the recipient and the plasmid-encoded TraN, which consists of conserved base and variable tip domains. So far, TraN was only studied in IncF plasmids. We show that IncA/C and IncH plasmids encode a larger TraN with distinct isoforms that shape host range and species specificity. We also identify a novel TraN variant in Acinetobacter baumannii plasmids containing a base and two tips. These findings broaden our understanding of conjugation specificity and the mechanisms that influence the dissemination of resistance genes across diverse bacterial communities and highlight the evolutionary flexibility of plasmid transfer systems.

Bacteria localize proteins to distinct subcellular locations, including chemoreceptors, which frequently localize to the bacterial pole. Although some polarity-promoting mechanisms have been described, many chemoreceptors lack clear routes to becoming polar. TlpD of the bacterial pathogen Helicobacter pylori is one such protein. This cytoplasmic chemoreceptor localizes to the pole in a manner that is independent of the other chemoreceptors. In this work, we evaluated the role of TlpD domains in its function. Truncated proteins were created that lacked different amounts of the N- or C-termini and expressed in H. pylori in place of native tlpD or as the sole chemoreceptor. These TlpD variants were examined for their presence and abundance, protein localization, association with chemotaxis signaling proteins, and effect on motility. TlpD that lacked any portion of the N-terminal 104 amino acids produced low to no amounts of detectable protein. In contrast, TlpD was detectable with loss of the C-terminal 45 amino acids. TlpD lacking the last 45 amino acids (TlpD∆C4) preserved the ability to interact with CheW and CheV proteins based on bacterial two-hybrid analysis, but was unable to localize to the pole either on their own or in the presence of other chemoreceptors. TlpD∆C4 was found to be diffuse in the cytoplasm and interacted with CheV1, CheV2, and CheV3 at this location but not with CheW. TlpD∆C4 did not confer chemotactic abilities in soft agar chemotaxis assays. These findings suggest the C-terminal end of TlpD plays a previously unappreciated role in promoting TlpD polar localization and function.IMPORTANCEBacteria place their proteins in specific locations that are required for the proteins to function, including the bacterial pole. How the bacterial cell identifies which proteins go to the pole is not fully understood. In this work, we dissect parts of a protein called TlpD that naturally goes to the pole. We find that mutants lacking one end of TlpD lose their polar placement, but retain other abilities. TlpD allows directed motility known as chemotaxis. This ability is critical for infection in Helicobacter pylori and numerous other pathogens. When TlpD loses its polar placement, the protein no longer functions for chemotaxis, laying the foundation for future studies that can dissect how this segment promotes function and eventually translate into therapies for H. pylori infection.

Mycobacterium abscessus (Mab), a rapidly growing mycobacterial species with intrinsic and acquired resistance to multiple antibiotics, is an emerging public health concern. The rise in clinical cases of treatment-refractory infections of M. abscessus has propelled its research toward novel therapeutic approaches. The number of publications entitled "Mycobacterium abscessus" has increased by ~300% over the last decade, of which the majority of studies exploring the fundamental biology and pathogenesis of Mab have used the reference strain ATCC19977. However, whole-genome sequence analyses, combined with transposon-seq based functional genomics, reveal an open pan-genome with significant variations in the essential genes across ATCC19977 and clinical isolates. These new discoveries demand a careful selection of strains and growth conditions in experimental design. In this minireview, we discuss these challenges and propose a framework for future M. abscessus studies in silico, including a new web-based resource for pangenome analysis, in vitro, and in animal models.

Isoprenoids play vital roles in all domains of life, from beta-carotene in bacteria to heme in humans. Two distinct metabolic pathways have evolved to synthesize the critical precursor of all mature isoprenoids: the mevalonate (MEV) and the methylerythritol phosphate (MEP) pathways. Here, we quantify the extensive inter- and intra-genus heterogeneity in the usage of these two pathways with particular emphasis on rare bacteria that encode both, or neither, pathways. Furthermore, MEP intermediates themselves have non-isoprenogenic roles that may underlie evolutionary pressures driving pathway diversification. Understanding isoprenoid biosynthesis in bacteria offers new avenues toward more sustainable engineering of economically relevant molecules in microbes.

In phototrophic cyanobacteria, the signaling molecule bis-(3'-5')-cyclic dimeric-guanosine monophosphate (c-di-GMP) plays important roles in a wide variety of functions associated with environmental conditions, including biofilm formation, motility, heterocyst development, cell size control, phototaxis, and flocculation. However, its role in circadian rhythms, which contribute to fitness under diel light conditions, remains unexplored. In this study, we investigated the impact of changes in intracellular c-di-GMP levels on the circadian clock of the model cyanobacterium Synechococcus elongatus PCC 7942. Using inducible expression systems for the Escherichia coli genes yhjH (encoding a c-di-GMP phosphodiesterase) and ydeH (encoding a diguanylate cyclase), we modulated intracellular c-di-GMP concentrations. The effects were analyzed by monitoring bioluminescence rhythms from a luciferase reporter under the control of the clock. Induction of yhjH lengthened the circadian period by 0.6 h, while ydeH induction caused a phase delay of 5.8 h and reduced peak amplitude on the third circadian day. Additionally, exogenous c-di-GMP administration at the onset of darkness in a 12-h light/12-h dark cycle delayed the peak of the rhythm by 1 h, whereas administration at light onset had no effect. These results demonstrate that c-di-GMP levels in S. elongatus influenced multiple properties of the cyanobacterial circadian clock, including period, phase, and amplitude during light-dark cycles, suggesting that c-di-GMP signaling networks likely integrate environmental cues into circadian regulation through as yet unidentified factors.IMPORTANCEbis-(3'-5')-Cyclic dimeric-guanosine monophosphate (c-di-GMP) is a widely conserved bacterial signaling molecule that controls diverse physiological processes such as biofilm formation and motility, yet its influence on the circadian clock in cyanobacteria has not been described. Using inducible expression of E. coli enzymes and exogenous administration to alter intracellular c-di-GMP in a model cyanobacterium Synechococcus elongatus PCC 7942, we demonstrate that c-di-GMP modulates key properties of the circadian clock, including period, phase, and amplitude. These findings uncover a novel regulatory layer linking bacterial signaling networks to circadian clock regulation in cyanobacteria and suggest that c-di-GMP signaling enhances cyanobacterial fitness in natural light-dark cycles by fine-tuning circadian dynamics.